From c07f5e83398651cf8d0dccb036705b9eb69d8646 Mon Sep 17 00:00:00 2001
From: Karl Hammond <hammondkd@missouri.edu>
Date: Wed, 19 Oct 2022 10:29:18 -0500
Subject: [PATCH 001/396] Temporary(?) fix for highlighting overflow in
 labelmap.rst

---
 doc/src/labelmap.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/labelmap.rst b/doc/src/labelmap.rst
index 57e4926611..a11ab653f8 100644
--- a/doc/src/labelmap.rst
+++ b/doc/src/labelmap.rst
@@ -25,7 +25,7 @@ Examples
 .. code-block:: LAMMPS
 
    labelmap atom 3 carbon 4 'c3"' 5 "c1'" 6 "c#"
-   labelmap bond 1 carbonyl 2 nitrile 3 """ c1'-c2" """
+   labelmap bond 1 carbonyl 2 nitrile 3 """ c1'-c2" """  #"
    labelmap atom $(label2type(atom,carbon)) C  # change type label from 'carbon' to 'C'
    labelmap clear
    labelmap write mymap.include

From 56ca901cdbd65fe2351b33e93dd90c07eaa5bc34 Mon Sep 17 00:00:00 2001
From: Ian Bogle <Ian.Bogle@amd.com>
Date: Tue, 24 Jan 2023 09:36:18 -0600
Subject: [PATCH 002/396] Implement a "caching in LDS" approach for EAM to
 improve performance on HIP

	- Use a TeamPolicy rather than a RangePolicy to expose scratch
	- Team cooperates to load row-zero of spline into LDS
	- At runtime, decide whether value can be 'cached' in LDS, and conditionally load from LDS based on this

Should be easily extendable / tunable for other architectures if ever required.

Change-Id: Ie4254c8db1a7b14abafffe2b581014c5137bf7ed
---
 src/KOKKOS/pair_eam_kokkos.cpp | 302 +++++++++++++++++++++++++++++++--
 src/KOKKOS/pair_eam_kokkos.h   |  16 ++
 2 files changed, 302 insertions(+), 16 deletions(-)

diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 6e1cd1feea..6837992f8b 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -31,9 +31,25 @@
 #include "pair_kokkos.h"
 
 #include <cmath>
-
 using namespace LAMMPS_NS;
 
+#define MAX_CACHE_ROWS 500
+#define MAX_CACHE_COLS 7
+
+/* ---------------------------------------------------------------------- */
+template<class DeviceType, class tag>
+auto policyInstance(int inum){
+  #ifdef KOKKOS_ENABLE_HIP
+    auto policy = Kokkos::TeamPolicy<DeviceType,tag>((inum+1023)/1024, 1024)
+	                   .set_scratch_size(0,
+			        Kokkos::PerTeam(MAX_CACHE_ROWS*MAX_CACHE_COLS*sizeof(double)));
+    return policy;
+  #else
+    auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
+    return policy;
+  #endif
+}
+
 /* ---------------------------------------------------------------------- */
 
 template<class DeviceType>
@@ -182,9 +198,13 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     // compute kernel AB
 
     if (eflag)
-      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelAB<1> >(0,inum),*this,ev);
+      Kokkos::parallel_reduce(
+		    policyInstance<DeviceType,TagPairEAMKernelAB<1>>(inum),
+		    *this,ev);
     else
-      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelAB<0> >(0,inum),*this);
+      Kokkos::parallel_for(
+		    policyInstance<DeviceType,TagPairEAMKernelAB<0>>(inum),
+		    *this);
   }
 
   if (eflag) {
@@ -203,41 +223,65 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   if (evflag) {
     if (neighflag == HALF) {
       if (newton_pair) {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALF,1,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+	      policyInstance<DeviceType, TagPairEAMKernelC<HALF,1,1>>(inum),
+	      *this,ev);
       } else {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALF,0,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+	      policyInstance<DeviceType, TagPairEAMKernelC<HALF,0,1>>(inum),
+	      *this,ev);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALFTHREAD,1,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+	      policyInstance<DeviceType, TagPairEAMKernelC<HALFTHREAD,1,1>>(inum),
+	      *this,ev);
       } else {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALFTHREAD,0,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              policyInstance<DeviceType, TagPairEAMKernelC<HALFTHREAD,0,1>>(inum),
+	      *this,ev);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<FULL,1,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+	      policyInstance<DeviceType, TagPairEAMKernelC<FULL,1,1>>(inum),
+	      *this,ev);
       } else {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<FULL,0,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+	      policyInstance<DeviceType, TagPairEAMKernelC<FULL,0,1>>(inum),
+	      *this,ev);
       }
     }
   } else {
     if (neighflag == HALF) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALF,1,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+	      policyInstance<DeviceType, TagPairEAMKernelC<HALF,1,0>>(inum),
+	      *this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALF,0,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+	      policyInstance<DeviceType, TagPairEAMKernelC<HALF,0,0>>(inum),
+	      *this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALFTHREAD,1,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+	      policyInstance<DeviceType, TagPairEAMKernelC<HALFTHREAD,1,0>>(inum),
+	      *this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALFTHREAD,0,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+	      policyInstance<DeviceType, TagPairEAMKernelC<HALFTHREAD,0,0>>(inum),
+	      *this);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<FULL,1,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+	      policyInstance<DeviceType, TagPairEAMKernelC<FULL,1,0>>(inum),
+	      *this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<FULL,0,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+	      policyInstance<DeviceType, TagPairEAMKernelC<FULL,0,0>>(inum),
+	      *this);
       }
     }
   }
@@ -614,7 +658,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelB<EFLAG>, const int &
   EV_FLOAT ev;
   this->template operator()<EFLAG>(TagPairEAMKernelB<EFLAG>(), ii, ev);
 }
-
+/* ---------------------------------------------------------------------- */
 /* ---------------------------------------------------------------------- */
 
 ////Specialisation for Neighborlist types Half, HalfThread, Full
@@ -799,6 +843,232 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PA
   EV_FLOAT ev;
   this->template operator()<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(), ii, ev);
 }
+/* ---------------------------------------------------------------------- */
+
+////Specialisation for Neighborlist types Half, HalfThread, Full
+template<class DeviceType>
+template<int EFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
+		                     const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
+				     EV_FLOAT& ev) const {
+  int ii = team_member.league_rank()*team_member.team_size() + team_member.team_rank();
+  // rho = density at each atom
+  // loop over neighbors of my atoms
+  const int m_max = d_rhor_spline.extent_int(1);
+  const int j_max = d_rhor_spline.extent_int(2);
+  const int d_rhor_spline_cached = (m_max > MAX_CACHE_ROWS || j_max > MAX_CACHE_COLS) ? 0 : 1;
+  Kokkos::View<double*[MAX_CACHE_COLS], typename DeviceType::scratch_memory_space,
+	       Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
+
+  if(d_rhor_spline_cached){
+    for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()){
+      int j = i%j_max;
+      int m = i/j_max;
+      A(m,j) = d_rhor_spline(0,m,j);
+    }
+    team_member.team_barrier();
+  }
+
+  const int i = d_ilist[ii];
+  const X_FLOAT xtmp = x(i,0);
+  const X_FLOAT ytmp = x(i,1);
+  const X_FLOAT ztmp = x(i,2);
+  const int itype = type(i);
+
+  const int jnum = d_numneigh[i];
+
+  F_FLOAT rhotmp = 0.0;
+
+  for (int jj = 0; jj < jnum; jj++) {
+    int j = d_neighbors(i,jj);
+    j &= NEIGHMASK;
+
+    const X_FLOAT delx = xtmp - x(j,0);
+    const X_FLOAT dely = ytmp - x(j,1);
+    const X_FLOAT delz = ztmp - x(j,2);
+    const int jtype = type(j);
+    const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
+
+    if (rsq < cutforcesq) {
+      F_FLOAT p = sqrt(rsq)*rdr + 1.0;
+      int m = static_cast<int> (p);
+      m = MIN(m,nr-1);
+      p -= m;
+      p = MIN(p,1.0);
+      const int d_type2rhor_ji = d_type2rhor(jtype,itype);
+      if(d_type2rhor_ji == 0 && d_rhor_spline_cached == 1) {
+        rhotmp += ((A(m,3)*p + A(m,4))*p +
+	           A(m,5))*p + A(m,6);
+      } else
+        rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
+                    d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
+    }
+
+  }
+  d_rho[i] += rhotmp;
+
+  // fp = derivative of embedding energy at each atom
+  // phi = embedding energy at each atom
+  // if rho > rhomax (e.g. due to close approach of two atoms),
+  //   will exceed table, so add linear term to conserve energy
+
+  F_FLOAT p = d_rho[i]*rdrho + 1.0;
+  int m = static_cast<int> (p);
+  m = MAX(1,MIN(m,nrho-1));
+  p -= m;
+  p = MIN(p,1.0);
+  const int d_type2frho_i = d_type2frho[itype];
+  d_fp[i] = (d_frho_spline(d_type2frho_i,m,0)*p + d_frho_spline(d_type2frho_i,m,1))*p + d_frho_spline(d_type2frho_i,m,2);
+  if (EFLAG) {
+    F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
+                    d_frho_spline(d_type2frho_i,m,5))*p + d_frho_spline(d_type2frho_i,m,6);
+    if (d_rho[i] > rhomax) phi += d_fp[i] * (d_rho[i]-rhomax);
+    if (eflag_global) ev.evdwl += phi;
+    if (eflag_atom) d_eatom[i] += phi;
+  }
+
+}
+
+template<class DeviceType>
+template<int EFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
+		                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member) const {
+  EV_FLOAT ev;
+  this->template operator()<EFLAG>(TagPairEAMKernelAB<EFLAG>(), team_member, ev);
+}
+
+/* ---------------------------------------------------------------------- */
+
+////Specialisation for Neighborlist types Half, HalfThread, Full
+template<class DeviceType>
+template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>,
+		                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
+                                           EV_FLOAT& ev) const {
+
+  // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+  int ii = team_member.league_rank()*team_member.team_size() + team_member.team_rank();
+
+  auto v_f = ScatterViewHelper<NeedDup_v<NEIGHFLAG,DeviceType>,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+  auto a_f = v_f.template access<AtomicDup_v<NEIGHFLAG,DeviceType>>();
+
+  const int m_max = d_z2r_spline.extent_int(1);
+  const int j_max = d_z2r_spline.extent_int(2);
+  const int d_z2r_spline_cached = (m_max > MAX_CACHE_ROWS || j_max > MAX_CACHE_COLS) ? 0 : 1;
+  Kokkos::View<double*[MAX_CACHE_COLS], typename DeviceType::scratch_memory_space,
+	       Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
+
+  if(d_z2r_spline_cached){
+    for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()){
+      int j = i%j_max;
+      int m = i/j_max;
+      A(m,j) = d_z2r_spline(0,m,j);
+    }
+    team_member.team_barrier();
+  }
+
+  const int i = d_ilist[ii];
+  const X_FLOAT xtmp = x(i,0);
+  const X_FLOAT ytmp = x(i,1);
+  const X_FLOAT ztmp = x(i,2);
+  const int itype = type(i);
+
+  const int jnum = d_numneigh[i];
+
+  F_FLOAT fxtmp = 0.0;
+  F_FLOAT fytmp = 0.0;
+  F_FLOAT fztmp = 0.0;
+
+  for (int jj = 0; jj < jnum; jj++) {
+    int j = d_neighbors(i,jj);
+    j &= NEIGHMASK;
+    const X_FLOAT delx = xtmp - x(j,0);
+    const X_FLOAT dely = ytmp - x(j,1);
+    const X_FLOAT delz = ztmp - x(j,2);
+    const int jtype = type(j);
+    const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
+
+    if (rsq < cutforcesq) {
+      const F_FLOAT r = sqrt(rsq);
+      F_FLOAT p = r*rdr + 1.0;
+      int m = static_cast<int> (p);
+      m = MIN(m,nr-1);
+      p -= m;
+      p = MIN(p,1.0);
+
+      // rhoip = derivative of (density at atom j due to atom i)
+      // rhojp = derivative of (density at atom i due to atom j)
+      // phi = pair potential energy
+      // phip = phi'
+      // z2 = phi * r
+      // z2p = (phi * r)' = (phi' r) + phi
+      // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+      //   terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+      //   hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+
+      const int d_type2rhor_ij = d_type2rhor(itype,jtype);
+      const F_FLOAT rhoip = (d_rhor_spline(d_type2rhor_ij,m,0)*p + d_rhor_spline(d_type2rhor_ij,m,1))*p +
+                             d_rhor_spline(d_type2rhor_ij,m,2);
+      const int d_type2rhor_ji = d_type2rhor(jtype,itype);
+      const F_FLOAT rhojp = (d_rhor_spline(d_type2rhor_ji,m,0)*p + d_rhor_spline(d_type2rhor_ji,m,1))*p +
+                             d_rhor_spline(d_type2rhor_ji,m,2);
+      const int d_type2z2r_ij = d_type2z2r(itype,jtype);
+
+      const auto have_cache = (d_z2r_spline_cached == 1) && (0 == d_type2z2r_ij);
+      const auto z2r_spline_3 = (have_cache) ? A(m,3) : d_z2r_spline(d_type2z2r_ij,m,3);
+      const auto z2r_spline_4 = (have_cache) ? A(m,4) : d_z2r_spline(d_type2z2r_ij,m,4);
+      const auto z2r_spline_5 = (have_cache) ? A(m,5) : d_z2r_spline(d_type2z2r_ij,m,5);
+      const auto z2r_spline_6 = (have_cache) ? A(m,6) : d_z2r_spline(d_type2z2r_ij,m,6);
+
+      const F_FLOAT z2p = (3.0*rdr*z2r_spline_3*p + 2.0*rdr*z2r_spline_4)*p +
+                           rdr*z2r_spline_5; // the rdr and the factors of 3.0 and 2.0 come out of the interpolate function
+      const F_FLOAT z2 = ((z2r_spline_3*p + z2r_spline_4)*p +
+                           z2r_spline_5)*p + z2r_spline_6;
+
+      const F_FLOAT recip = 1.0/r;
+      const F_FLOAT phi = z2*recip;
+      const F_FLOAT phip = z2p*recip - phi*recip;
+      const F_FLOAT psip = d_fp[i]*rhojp + d_fp[j]*rhoip + phip;
+      const F_FLOAT fpair = -psip*recip;
+
+      fxtmp += delx*fpair;
+      fytmp += dely*fpair;
+      fztmp += delz*fpair;
+
+      if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < nlocal)) {
+        a_f(j,0) -= delx*fpair;
+        a_f(j,1) -= dely*fpair;
+        a_f(j,2) -= delz*fpair;
+      }
+
+      if (EVFLAG) {
+        if (eflag) {
+          ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD)&&(NEWTON_PAIR||(j<nlocal)))?1.0:0.5)*phi;
+        }
+
+        if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG,NEWTON_PAIR>(ev,i,j,phi,fpair,delx,dely,delz);
+      }
+
+    }
+  }
+
+  a_f(i,0) += fxtmp;
+  a_f(i,1) += fytmp;
+  a_f(i,2) += fztmp;
+}
+
+template<class DeviceType>
+template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>,
+		/*const int &ii*/
+		const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member) const {
+  EV_FLOAT ev;
+  this->template operator()<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(), team_member, ev);
+}
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index 006dceb1f2..21cf188cd6 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -89,6 +89,14 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMKernelAB<EFLAG>, const int&) const;
 
+  template<int EFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMKernelAB<EFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&, EV_FLOAT&) const;
+
+  template<int EFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMKernelAB<EFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&) const;
+
   template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int&, EV_FLOAT&) const;
@@ -97,6 +105,14 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int&) const;
 
+  template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&, EV_FLOAT&) const;
+
+  template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&) const;
+
   template<int NEIGHFLAG, int NEWTON_PAIR>
   KOKKOS_INLINE_FUNCTION
   void ev_tally(EV_FLOAT &ev, const int &i, const int &j,

From 55f454db2d2eef62d9551047be26086361f89b7d Mon Sep 17 00:00:00 2001
From: Ian Bogle <Ian.Bogle@amd.com>
Date: Fri, 3 Feb 2023 13:35:38 -0600
Subject: [PATCH 003/396] Addressed feedback from LAMMPS developers:

  - moved policyInstance into the EAM class
  - eliminated MAX_CACHE_COLS define, in favor of the static_extent of the spline view type
  - made inum a protected member var that allows range checking inside TeamPolicy kernels
  - added range checking after initializing the cached table in TeamPolicy kernels
  - correctness and perf checks pass

Change-Id: Iaaf34f7560c37e0a2a34e980761246d3ef42be99
---
 src/KOKKOS/pair_eam_kokkos.cpp | 294 +++++++++++++++++----------------
 src/KOKKOS/pair_eam_kokkos.h   |   7 +-
 2 files changed, 155 insertions(+), 146 deletions(-)

diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 6837992f8b..cc3b606b17 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -34,15 +34,18 @@
 using namespace LAMMPS_NS;
 
 #define MAX_CACHE_ROWS 500
-#define MAX_CACHE_COLS 7
 
 /* ---------------------------------------------------------------------- */
-template<class DeviceType, class tag>
-auto policyInstance(int inum){
+template<class DeviceType>
+template<class tag>
+auto PairEAMKokkos<DeviceType>::policyInstance(int inum){
   #ifdef KOKKOS_ENABLE_HIP
+    static_assert(t_ffloat_2d_n7::static_extent(2) == 7,
+		  "Breaking assumption of spline dim for KernelAB and KernelC scratch caching");
+
     auto policy = Kokkos::TeamPolicy<DeviceType,tag>((inum+1023)/1024, 1024)
 	                   .set_scratch_size(0,
-			        Kokkos::PerTeam(MAX_CACHE_ROWS*MAX_CACHE_COLS*sizeof(double)));
+			        Kokkos::PerTeam(MAX_CACHE_ROWS*t_ffloat_2d_n7::static_extent(2)*sizeof(double)));
     return policy;
   #else
     auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
@@ -129,7 +132,7 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   d_numneigh = k_list->d_numneigh;
   d_neighbors = k_list->d_neighbors;
   d_ilist = k_list->d_ilist;
-  int inum = list->inum;
+  inum = list->inum;
 
   need_dup = lmp->kokkos->need_dup<DeviceType>();
   if (need_dup) {
@@ -199,11 +202,11 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
     if (eflag)
       Kokkos::parallel_reduce(
-		    policyInstance<DeviceType,TagPairEAMKernelAB<1>>(inum),
+		    policyInstance<TagPairEAMKernelAB<1>>(inum),
 		    *this,ev);
     else
       Kokkos::parallel_for(
-		    policyInstance<DeviceType,TagPairEAMKernelAB<0>>(inum),
+		    policyInstance<TagPairEAMKernelAB<0>>(inum),
 		    *this);
   }
 
@@ -224,31 +227,31 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     if (neighflag == HALF) {
       if (newton_pair) {
         Kokkos::parallel_reduce(
-	      policyInstance<DeviceType, TagPairEAMKernelC<HALF,1,1>>(inum),
+	      policyInstance<TagPairEAMKernelC<HALF,1,1>>(inum),
 	      *this,ev);
       } else {
         Kokkos::parallel_reduce(
-	      policyInstance<DeviceType, TagPairEAMKernelC<HALF,0,1>>(inum),
+	      policyInstance<TagPairEAMKernelC<HALF,0,1>>(inum),
 	      *this,ev);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
         Kokkos::parallel_reduce(
-	      policyInstance<DeviceType, TagPairEAMKernelC<HALFTHREAD,1,1>>(inum),
+	      policyInstance<TagPairEAMKernelC<HALFTHREAD,1,1>>(inum),
 	      *this,ev);
       } else {
         Kokkos::parallel_reduce(
-              policyInstance<DeviceType, TagPairEAMKernelC<HALFTHREAD,0,1>>(inum),
+              policyInstance<TagPairEAMKernelC<HALFTHREAD,0,1>>(inum),
 	      *this,ev);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
         Kokkos::parallel_reduce(
-	      policyInstance<DeviceType, TagPairEAMKernelC<FULL,1,1>>(inum),
+	      policyInstance<TagPairEAMKernelC<FULL,1,1>>(inum),
 	      *this,ev);
       } else {
         Kokkos::parallel_reduce(
-	      policyInstance<DeviceType, TagPairEAMKernelC<FULL,0,1>>(inum),
+	      policyInstance<TagPairEAMKernelC<FULL,0,1>>(inum),
 	      *this,ev);
       }
     }
@@ -256,31 +259,31 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     if (neighflag == HALF) {
       if (newton_pair) {
         Kokkos::parallel_for(
-	      policyInstance<DeviceType, TagPairEAMKernelC<HALF,1,0>>(inum),
+	      policyInstance<TagPairEAMKernelC<HALF,1,0>>(inum),
 	      *this);
       } else {
         Kokkos::parallel_for(
-	      policyInstance<DeviceType, TagPairEAMKernelC<HALF,0,0>>(inum),
+	      policyInstance<TagPairEAMKernelC<HALF,0,0>>(inum),
 	      *this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
         Kokkos::parallel_for(
-	      policyInstance<DeviceType, TagPairEAMKernelC<HALFTHREAD,1,0>>(inum),
+	      policyInstance<TagPairEAMKernelC<HALFTHREAD,1,0>>(inum),
 	      *this);
       } else {
         Kokkos::parallel_for(
-	      policyInstance<DeviceType, TagPairEAMKernelC<HALFTHREAD,0,0>>(inum),
+	      policyInstance<TagPairEAMKernelC<HALFTHREAD,0,0>>(inum),
 	      *this);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
         Kokkos::parallel_for(
-	      policyInstance<DeviceType, TagPairEAMKernelC<FULL,1,0>>(inum),
+	      policyInstance<TagPairEAMKernelC<FULL,1,0>>(inum),
 	      *this);
       } else {
         Kokkos::parallel_for(
-	      policyInstance<DeviceType, TagPairEAMKernelC<FULL,0,0>>(inum),
+	      policyInstance<TagPairEAMKernelC<FULL,0,0>>(inum),
 	      *this);
       }
     }
@@ -857,8 +860,8 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
   // loop over neighbors of my atoms
   const int m_max = d_rhor_spline.extent_int(1);
   const int j_max = d_rhor_spline.extent_int(2);
-  const int d_rhor_spline_cached = (m_max > MAX_CACHE_ROWS || j_max > MAX_CACHE_COLS) ? 0 : 1;
-  Kokkos::View<double*[MAX_CACHE_COLS], typename DeviceType::scratch_memory_space,
+  const int d_rhor_spline_cached = (m_max > MAX_CACHE_ROWS || j_max > t_ffloat_2d_n7::static_extent(2)) ? 0 : 1;
+  Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
 	       Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
 
   if(d_rhor_spline_cached){
@@ -869,65 +872,65 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
     }
     team_member.team_barrier();
   }
+  if (ii < inum){
+    const int i = d_ilist[ii];
+    const X_FLOAT xtmp = x(i,0);
+    const X_FLOAT ytmp = x(i,1);
+    const X_FLOAT ztmp = x(i,2);
+    const int itype = type(i);
 
-  const int i = d_ilist[ii];
-  const X_FLOAT xtmp = x(i,0);
-  const X_FLOAT ytmp = x(i,1);
-  const X_FLOAT ztmp = x(i,2);
-  const int itype = type(i);
+    const int jnum = d_numneigh[i];
 
-  const int jnum = d_numneigh[i];
+    F_FLOAT rhotmp = 0.0;
 
-  F_FLOAT rhotmp = 0.0;
+    for (int jj = 0; jj < jnum; jj++) {
+      int j = d_neighbors(i,jj);
+      j &= NEIGHMASK;
 
-  for (int jj = 0; jj < jnum; jj++) {
-    int j = d_neighbors(i,jj);
-    j &= NEIGHMASK;
+      const X_FLOAT delx = xtmp - x(j,0);
+      const X_FLOAT dely = ytmp - x(j,1);
+      const X_FLOAT delz = ztmp - x(j,2);
+      const int jtype = type(j);
+      const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
 
-    const X_FLOAT delx = xtmp - x(j,0);
-    const X_FLOAT dely = ytmp - x(j,1);
-    const X_FLOAT delz = ztmp - x(j,2);
-    const int jtype = type(j);
-    const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
+      if (rsq < cutforcesq) {
+        F_FLOAT p = sqrt(rsq)*rdr + 1.0;
+        int m = static_cast<int> (p);
+        m = MIN(m,nr-1);
+        p -= m;
+        p = MIN(p,1.0);
+        const int d_type2rhor_ji = d_type2rhor(jtype,itype);
+        if(d_type2rhor_ji == 0 && d_rhor_spline_cached == 1) {
+          rhotmp += ((A(m,3)*p + A(m,4))*p +
+  	             A(m,5))*p + A(m,6);
+        } else
+          rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
+                      d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
+      }
 
-    if (rsq < cutforcesq) {
-      F_FLOAT p = sqrt(rsq)*rdr + 1.0;
-      int m = static_cast<int> (p);
-      m = MIN(m,nr-1);
-      p -= m;
-      p = MIN(p,1.0);
-      const int d_type2rhor_ji = d_type2rhor(jtype,itype);
-      if(d_type2rhor_ji == 0 && d_rhor_spline_cached == 1) {
-        rhotmp += ((A(m,3)*p + A(m,4))*p +
-	           A(m,5))*p + A(m,6);
-      } else
-        rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
-                    d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
     }
+    d_rho[i] += rhotmp;
 
+    // fp = derivative of embedding energy at each atom
+    // phi = embedding energy at each atom
+    // if rho > rhomax (e.g. due to close approach of two atoms),
+    //   will exceed table, so add linear term to conserve energy
+
+    F_FLOAT p = d_rho[i]*rdrho + 1.0;
+    int m = static_cast<int> (p);
+    m = MAX(1,MIN(m,nrho-1));
+    p -= m;
+    p = MIN(p,1.0);
+    const int d_type2frho_i = d_type2frho[itype];
+    d_fp[i] = (d_frho_spline(d_type2frho_i,m,0)*p + d_frho_spline(d_type2frho_i,m,1))*p + d_frho_spline(d_type2frho_i,m,2);
+    if (EFLAG) {
+      F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
+                      d_frho_spline(d_type2frho_i,m,5))*p + d_frho_spline(d_type2frho_i,m,6);
+      if (d_rho[i] > rhomax) phi += d_fp[i] * (d_rho[i]-rhomax);
+      if (eflag_global) ev.evdwl += phi;
+      if (eflag_atom) d_eatom[i] += phi;
+    }
   }
-  d_rho[i] += rhotmp;
-
-  // fp = derivative of embedding energy at each atom
-  // phi = embedding energy at each atom
-  // if rho > rhomax (e.g. due to close approach of two atoms),
-  //   will exceed table, so add linear term to conserve energy
-
-  F_FLOAT p = d_rho[i]*rdrho + 1.0;
-  int m = static_cast<int> (p);
-  m = MAX(1,MIN(m,nrho-1));
-  p -= m;
-  p = MIN(p,1.0);
-  const int d_type2frho_i = d_type2frho[itype];
-  d_fp[i] = (d_frho_spline(d_type2frho_i,m,0)*p + d_frho_spline(d_type2frho_i,m,1))*p + d_frho_spline(d_type2frho_i,m,2);
-  if (EFLAG) {
-    F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
-                    d_frho_spline(d_type2frho_i,m,5))*p + d_frho_spline(d_type2frho_i,m,6);
-    if (d_rho[i] > rhomax) phi += d_fp[i] * (d_rho[i]-rhomax);
-    if (eflag_global) ev.evdwl += phi;
-    if (eflag_atom) d_eatom[i] += phi;
-  }
-
 }
 
 template<class DeviceType>
@@ -957,8 +960,8 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PA
 
   const int m_max = d_z2r_spline.extent_int(1);
   const int j_max = d_z2r_spline.extent_int(2);
-  const int d_z2r_spline_cached = (m_max > MAX_CACHE_ROWS || j_max > MAX_CACHE_COLS) ? 0 : 1;
-  Kokkos::View<double*[MAX_CACHE_COLS], typename DeviceType::scratch_memory_space,
+  const int d_z2r_spline_cached = (m_max > MAX_CACHE_ROWS || j_max > t_ffloat_2d_n7::static_extent(2)) ? 0 : 1;
+  Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
 	       Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
 
   if(d_z2r_spline_cached){
@@ -969,95 +972,96 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PA
     }
     team_member.team_barrier();
   }
+  if (ii < inum){
+    const int i = d_ilist[ii];
+    const X_FLOAT xtmp = x(i,0);
+    const X_FLOAT ytmp = x(i,1);
+    const X_FLOAT ztmp = x(i,2);
+    const int itype = type(i);
 
-  const int i = d_ilist[ii];
-  const X_FLOAT xtmp = x(i,0);
-  const X_FLOAT ytmp = x(i,1);
-  const X_FLOAT ztmp = x(i,2);
-  const int itype = type(i);
+    const int jnum = d_numneigh[i];
 
-  const int jnum = d_numneigh[i];
+    F_FLOAT fxtmp = 0.0;
+    F_FLOAT fytmp = 0.0;
+    F_FLOAT fztmp = 0.0;
 
-  F_FLOAT fxtmp = 0.0;
-  F_FLOAT fytmp = 0.0;
-  F_FLOAT fztmp = 0.0;
+    for (int jj = 0; jj < jnum; jj++) {
+      int j = d_neighbors(i,jj);
+      j &= NEIGHMASK;
+      const X_FLOAT delx = xtmp - x(j,0);
+      const X_FLOAT dely = ytmp - x(j,1);
+      const X_FLOAT delz = ztmp - x(j,2);
+      const int jtype = type(j);
+      const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
 
-  for (int jj = 0; jj < jnum; jj++) {
-    int j = d_neighbors(i,jj);
-    j &= NEIGHMASK;
-    const X_FLOAT delx = xtmp - x(j,0);
-    const X_FLOAT dely = ytmp - x(j,1);
-    const X_FLOAT delz = ztmp - x(j,2);
-    const int jtype = type(j);
-    const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
+      if (rsq < cutforcesq) {
+        const F_FLOAT r = sqrt(rsq);
+        F_FLOAT p = r*rdr + 1.0;
+        int m = static_cast<int> (p);
+        m = MIN(m,nr-1);
+        p -= m;
+        p = MIN(p,1.0);
 
-    if (rsq < cutforcesq) {
-      const F_FLOAT r = sqrt(rsq);
-      F_FLOAT p = r*rdr + 1.0;
-      int m = static_cast<int> (p);
-      m = MIN(m,nr-1);
-      p -= m;
-      p = MIN(p,1.0);
+        // rhoip = derivative of (density at atom j due to atom i)
+        // rhojp = derivative of (density at atom i due to atom j)
+        // phi = pair potential energy
+        // phip = phi'
+        // z2 = phi * r
+        // z2p = (phi * r)' = (phi' r) + phi
+        // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+        //   terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+        //   hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
 
-      // rhoip = derivative of (density at atom j due to atom i)
-      // rhojp = derivative of (density at atom i due to atom j)
-      // phi = pair potential energy
-      // phip = phi'
-      // z2 = phi * r
-      // z2p = (phi * r)' = (phi' r) + phi
-      // psip needs both fp[i] and fp[j] terms since r_ij appears in two
-      //   terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
-      //   hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
-
-      const int d_type2rhor_ij = d_type2rhor(itype,jtype);
-      const F_FLOAT rhoip = (d_rhor_spline(d_type2rhor_ij,m,0)*p + d_rhor_spline(d_type2rhor_ij,m,1))*p +
+        const int d_type2rhor_ij = d_type2rhor(itype,jtype);
+        const F_FLOAT rhoip = (d_rhor_spline(d_type2rhor_ij,m,0)*p + d_rhor_spline(d_type2rhor_ij,m,1))*p +
                              d_rhor_spline(d_type2rhor_ij,m,2);
-      const int d_type2rhor_ji = d_type2rhor(jtype,itype);
-      const F_FLOAT rhojp = (d_rhor_spline(d_type2rhor_ji,m,0)*p + d_rhor_spline(d_type2rhor_ji,m,1))*p +
-                             d_rhor_spline(d_type2rhor_ji,m,2);
-      const int d_type2z2r_ij = d_type2z2r(itype,jtype);
+        const int d_type2rhor_ji = d_type2rhor(jtype,itype);
+        const F_FLOAT rhojp = (d_rhor_spline(d_type2rhor_ji,m,0)*p + d_rhor_spline(d_type2rhor_ji,m,1))*p +
+                               d_rhor_spline(d_type2rhor_ji,m,2);
+        const int d_type2z2r_ij = d_type2z2r(itype,jtype);
 
-      const auto have_cache = (d_z2r_spline_cached == 1) && (0 == d_type2z2r_ij);
-      const auto z2r_spline_3 = (have_cache) ? A(m,3) : d_z2r_spline(d_type2z2r_ij,m,3);
-      const auto z2r_spline_4 = (have_cache) ? A(m,4) : d_z2r_spline(d_type2z2r_ij,m,4);
-      const auto z2r_spline_5 = (have_cache) ? A(m,5) : d_z2r_spline(d_type2z2r_ij,m,5);
-      const auto z2r_spline_6 = (have_cache) ? A(m,6) : d_z2r_spline(d_type2z2r_ij,m,6);
+        const auto have_cache = (d_z2r_spline_cached == 1) && (0 == d_type2z2r_ij);
+        const auto z2r_spline_3 = (have_cache) ? A(m,3) : d_z2r_spline(d_type2z2r_ij,m,3);
+        const auto z2r_spline_4 = (have_cache) ? A(m,4) : d_z2r_spline(d_type2z2r_ij,m,4);
+        const auto z2r_spline_5 = (have_cache) ? A(m,5) : d_z2r_spline(d_type2z2r_ij,m,5);
+        const auto z2r_spline_6 = (have_cache) ? A(m,6) : d_z2r_spline(d_type2z2r_ij,m,6);
 
-      const F_FLOAT z2p = (3.0*rdr*z2r_spline_3*p + 2.0*rdr*z2r_spline_4)*p +
-                           rdr*z2r_spline_5; // the rdr and the factors of 3.0 and 2.0 come out of the interpolate function
-      const F_FLOAT z2 = ((z2r_spline_3*p + z2r_spline_4)*p +
-                           z2r_spline_5)*p + z2r_spline_6;
+        const F_FLOAT z2p = (3.0*rdr*z2r_spline_3*p + 2.0*rdr*z2r_spline_4)*p +
+                             rdr*z2r_spline_5; // the rdr and the factors of 3.0 and 2.0 come out of the interpolate function
+        const F_FLOAT z2 = ((z2r_spline_3*p + z2r_spline_4)*p +
+                             z2r_spline_5)*p + z2r_spline_6;
 
-      const F_FLOAT recip = 1.0/r;
-      const F_FLOAT phi = z2*recip;
-      const F_FLOAT phip = z2p*recip - phi*recip;
-      const F_FLOAT psip = d_fp[i]*rhojp + d_fp[j]*rhoip + phip;
-      const F_FLOAT fpair = -psip*recip;
+        const F_FLOAT recip = 1.0/r;
+        const F_FLOAT phi = z2*recip;
+        const F_FLOAT phip = z2p*recip - phi*recip;
+        const F_FLOAT psip = d_fp[i]*rhojp + d_fp[j]*rhoip + phip;
+        const F_FLOAT fpair = -psip*recip;
 
-      fxtmp += delx*fpair;
-      fytmp += dely*fpair;
-      fztmp += delz*fpair;
+        fxtmp += delx*fpair;
+        fytmp += dely*fpair;
+        fztmp += delz*fpair;
 
-      if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < nlocal)) {
-        a_f(j,0) -= delx*fpair;
-        a_f(j,1) -= dely*fpair;
-        a_f(j,2) -= delz*fpair;
-      }
-
-      if (EVFLAG) {
-        if (eflag) {
-          ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD)&&(NEWTON_PAIR||(j<nlocal)))?1.0:0.5)*phi;
+        if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < nlocal)) {
+          a_f(j,0) -= delx*fpair;
+          a_f(j,1) -= dely*fpair;
+          a_f(j,2) -= delz*fpair;
+        }
+
+        if (EVFLAG) {
+          if (eflag) {
+            ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD)&&(NEWTON_PAIR||(j<nlocal)))?1.0:0.5)*phi;
+          }
+
+          if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG,NEWTON_PAIR>(ev,i,j,phi,fpair,delx,dely,delz);
         }
 
-        if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG,NEWTON_PAIR>(ev,i,j,phi,fpair,delx,dely,delz);
       }
-
     }
-  }
 
-  a_f(i,0) += fxtmp;
-  a_f(i,1) += fytmp;
-  a_f(i,2) += fztmp;
+    a_f(i,0) += fxtmp;
+    a_f(i,1) += fytmp;
+    a_f(i,2) += fztmp;
+  }
 }
 
 template<class DeviceType>
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index 21cf188cd6..a42f1efef6 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -55,10 +55,14 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
   typedef ArrayTypes<DeviceType> AT;
   typedef EV_FLOAT value_type;
 
+  template<class tag>
+  auto policyInstance(int inum);
+  
   PairEAMKokkos(class LAMMPS *);
   ~PairEAMKokkos() override;
   void compute(int, int) override;
   void init_style() override;
+  
 
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMPackForwardComm, const int&) const;
@@ -138,7 +142,8 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
   typename AT::t_virial_array d_vatom;
 
   int need_dup;
-
+  int inum;
+  
   using KKDeviceType = typename KKDevice<DeviceType>::value;
 
   template<typename DataType, typename Layout>

From 1c77ffc28894c94007ea5a47e86ea596420424ae Mon Sep 17 00:00:00 2001
From: Nick Curtis <nicholas.curtis@amd.com>
Date: Fri, 3 Feb 2023 14:57:56 -0500
Subject: [PATCH 004/396] catch missing static extents

Change-Id: I456282b172053a3566b1ce9a36bc33d377bd801a
---
 src/KOKKOS/pair_eam_kokkos.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index cc3b606b17..5d441df6a9 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -859,8 +859,8 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
   // rho = density at each atom
   // loop over neighbors of my atoms
   const int m_max = d_rhor_spline.extent_int(1);
-  const int j_max = d_rhor_spline.extent_int(2);
-  const int d_rhor_spline_cached = (m_max > MAX_CACHE_ROWS || j_max > t_ffloat_2d_n7::static_extent(2)) ? 0 : 1;
+  const int j_max = t_ffloat_2d_n7::static_extent(2);
+  const int d_rhor_spline_cached = (m_max > MAX_CACHE_ROWS) ? 0 : 1;
   Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
 	       Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
 
@@ -959,8 +959,8 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PA
   auto a_f = v_f.template access<AtomicDup_v<NEIGHFLAG,DeviceType>>();
 
   const int m_max = d_z2r_spline.extent_int(1);
-  const int j_max = d_z2r_spline.extent_int(2);
-  const int d_z2r_spline_cached = (m_max > MAX_CACHE_ROWS || j_max > t_ffloat_2d_n7::static_extent(2)) ? 0 : 1;
+  const int j_max = t_ffloat_2d_n7::static_extent(2);
+  const int d_z2r_spline_cached = (m_max > MAX_CACHE_ROWS) ? 0 : 1;
   Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
 	       Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
 

From 19bcf6b43cf25062743f2aae15f465c548180de6 Mon Sep 17 00:00:00 2001
From: Nick Curtis <nicholas.curtis@amd.com>
Date: Wed, 8 Feb 2023 13:43:47 -0500
Subject: [PATCH 005/396] revert to simple ParReduce policy for reductions

Change-Id: Ib3018e85f7bc6c97ce9c0320d0ea43c743addacf
---
 src/KOKKOS/pair_eam_kokkos.cpp | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 5d441df6a9..0f5bfdec39 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -202,7 +202,7 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
     if (eflag)
       Kokkos::parallel_reduce(
-		    policyInstance<TagPairEAMKernelAB<1>>(inum),
+		    Kokkos::RangePolicy<DeviceType,TagPairEAMKernelAB<1>>(0,inum),
 		    *this,ev);
     else
       Kokkos::parallel_for(
@@ -227,31 +227,31 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     if (neighflag == HALF) {
       if (newton_pair) {
         Kokkos::parallel_reduce(
-	      policyInstance<TagPairEAMKernelC<HALF,1,1>>(inum),
+	      Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALF,1,1>>(0,inum),
 	      *this,ev);
       } else {
         Kokkos::parallel_reduce(
-	      policyInstance<TagPairEAMKernelC<HALF,0,1>>(inum),
+	      Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALF,0,1>>(0,inum),
 	      *this,ev);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
         Kokkos::parallel_reduce(
-	      policyInstance<TagPairEAMKernelC<HALFTHREAD,1,1>>(inum),
+	      Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALFTHREAD,1,1>>(0,inum),
 	      *this,ev);
       } else {
         Kokkos::parallel_reduce(
-              policyInstance<TagPairEAMKernelC<HALFTHREAD,0,1>>(inum),
+              Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALFTHREAD,0,1>>(0,inum),
 	      *this,ev);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
         Kokkos::parallel_reduce(
-	      policyInstance<TagPairEAMKernelC<FULL,1,1>>(inum),
+	      Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<FULL,1,1>>(0,inum),
 	      *this,ev);
       } else {
         Kokkos::parallel_reduce(
-	      policyInstance<TagPairEAMKernelC<FULL,0,1>>(inum),
+	      Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<FULL,0,1>>(0,inum),
 	      *this,ev);
       }
     }

From 23bfc1666cb48a48b32920662784e1fd7daedc16 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Fri, 10 Feb 2023 09:24:18 -0700
Subject: [PATCH 006/396] Use range_policy if running on host, small cleanup

---
 src/KOKKOS/pair_eam_kokkos.cpp | 61 +++++++++++++++++++---------------
 src/KOKKOS/pair_eam_kokkos.h   |  6 ++--
 2 files changed, 38 insertions(+), 29 deletions(-)

diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 0f5bfdec39..2317f2d367 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -35,24 +35,6 @@ using namespace LAMMPS_NS;
 
 #define MAX_CACHE_ROWS 500
 
-/* ---------------------------------------------------------------------- */
-template<class DeviceType>
-template<class tag>
-auto PairEAMKokkos<DeviceType>::policyInstance(int inum){
-  #ifdef KOKKOS_ENABLE_HIP
-    static_assert(t_ffloat_2d_n7::static_extent(2) == 7,
-		  "Breaking assumption of spline dim for KernelAB and KernelC scratch caching");
-
-    auto policy = Kokkos::TeamPolicy<DeviceType,tag>((inum+1023)/1024, 1024)
-	                   .set_scratch_size(0,
-			        Kokkos::PerTeam(MAX_CACHE_ROWS*t_ffloat_2d_n7::static_extent(2)*sizeof(double)));
-    return policy;
-  #else
-    auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
-    return policy;
-  #endif
-}
-
 /* ---------------------------------------------------------------------- */
 
 template<class DeviceType>
@@ -864,15 +846,15 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
   Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
 	       Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
 
-  if(d_rhor_spline_cached){
-    for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()){
+  if (d_rhor_spline_cached) {
+    for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()) {
       int j = i%j_max;
       int m = i/j_max;
       A(m,j) = d_rhor_spline(0,m,j);
     }
     team_member.team_barrier();
   }
-  if (ii < inum){
+  if (ii < inum) {
     const int i = d_ilist[ii];
     const X_FLOAT xtmp = x(i,0);
     const X_FLOAT ytmp = x(i,1);
@@ -900,7 +882,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
         p -= m;
         p = MIN(p,1.0);
         const int d_type2rhor_ji = d_type2rhor(jtype,itype);
-        if(d_type2rhor_ji == 0 && d_rhor_spline_cached == 1) {
+        if (d_type2rhor_ji == 0 && d_rhor_spline_cached == 1) {
           rhotmp += ((A(m,3)*p + A(m,4))*p +
   	             A(m,5))*p + A(m,6);
         } else
@@ -952,9 +934,10 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PA
 		                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
                                            EV_FLOAT& ev) const {
 
-  // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
   int ii = team_member.league_rank()*team_member.team_size() + team_member.team_rank();
 
+  // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
   auto v_f = ScatterViewHelper<NeedDup_v<NEIGHFLAG,DeviceType>,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
   auto a_f = v_f.template access<AtomicDup_v<NEIGHFLAG,DeviceType>>();
 
@@ -964,15 +947,15 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PA
   Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
 	       Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
 
-  if(d_z2r_spline_cached){
-    for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()){
+  if (d_z2r_spline_cached) {
+    for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()) {
       int j = i%j_max;
       int m = i/j_max;
       A(m,j) = d_z2r_spline(0,m,j);
     }
     team_member.team_barrier();
   }
-  if (ii < inum){
+  if (ii < inum) {
     const int i = d_ilist[ii];
     const X_FLOAT xtmp = x(i,0);
     const X_FLOAT ytmp = x(i,1);
@@ -1172,6 +1155,32 @@ void PairEAMKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &
   }
 }
 
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+template<class tag>
+auto PairEAMKokkos<DeviceType>::policyInstance(int inum) {
+  #ifdef KOKKOS_ENABLE_HIP
+    if (execution_space != Host) {
+    static_assert(t_ffloat_2d_n7::static_extent(2) == 7,
+		  "Breaking assumption of spline dim for KernelAB and KernelC scratch caching");
+
+    auto policy = Kokkos::TeamPolicy<DeviceType,tag>((inum+1023)/1024, 1024)
+	                   .set_scratch_size(0,
+			        Kokkos::PerTeam(MAX_CACHE_ROWS*t_ffloat_2d_n7::static_extent(2)*sizeof(double)));
+    return policy;
+    } else {
+      auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
+      return policy;
+    }
+  #else
+    auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
+    return policy;
+  #endif
+}
+
+/* ---------------------------------------------------------------------- */
+
 namespace LAMMPS_NS {
 template class PairEAMKokkos<LMPDeviceType>;
 #ifdef LMP_KOKKOS_GPU
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index a42f1efef6..7f4ec67f6f 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -55,9 +55,6 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
   typedef ArrayTypes<DeviceType> AT;
   typedef EV_FLOAT value_type;
 
-  template<class tag>
-  auto policyInstance(int inum);
-  
   PairEAMKokkos(class LAMMPS *);
   ~PairEAMKokkos() override;
   void compute(int, int) override;
@@ -183,6 +180,9 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
   void file2array() override;
   void array2spline() override;
 
+  template<class tag>
+  auto policyInstance(int inum);
+
   typename AT::t_neighbors_2d d_neighbors;
   typename AT::t_int_1d d_ilist;
   typename AT::t_int_1d d_numneigh;

From d0c6c310d95af99482f5e41e8cffdc2eaa1d758a Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Fri, 10 Feb 2023 10:50:36 -0700
Subject: [PATCH 007/396] Port changes to other EAM flavors

---
 src/KOKKOS/pair_eam_alloy_kokkos.cpp | 348 +++++++++++++++++++++++---
 src/KOKKOS/pair_eam_alloy_kokkos.h   |  28 ++-
 src/KOKKOS/pair_eam_fs_kokkos.cpp    | 349 ++++++++++++++++++++++++---
 src/KOKKOS/pair_eam_fs_kokkos.h      |  27 ++-
 src/KOKKOS/pair_eam_kokkos.cpp       |  94 ++++----
 src/KOKKOS/pair_eam_kokkos.h         |   5 +-
 6 files changed, 724 insertions(+), 127 deletions(-)

diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index e14b78a36f..477220b65e 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -32,10 +32,10 @@
 #include "potential_file_reader.h"
 
 #include <cmath>
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
+#define MAX_CACHE_ROWS 500
+
 // Cannot use virtual inheritance on the GPU, so must duplicate code
 
 /* ---------------------------------------------------------------------- */
@@ -46,6 +46,7 @@ PairEAMAlloyKokkos<DeviceType>::PairEAMAlloyKokkos(LAMMPS *lmp) : PairEAM(lmp)
   respa_enable = 0;
   single_enable = 0;
   one_coeff = 1;
+  manybody_flag = 1;
 
   kokkosable = 1;
   atomKK = (AtomKokkos *) atom;
@@ -59,10 +60,10 @@ PairEAMAlloyKokkos<DeviceType>::PairEAMAlloyKokkos(LAMMPS *lmp) : PairEAM(lmp)
 template<class DeviceType>
 PairEAMAlloyKokkos<DeviceType>::~PairEAMAlloyKokkos()
 {
-  if (!copymode) {
-    memoryKK->destroy_kokkos(k_eatom,eatom);
-    memoryKK->destroy_kokkos(k_vatom,vatom);
-  }
+  if (copymode) return;
+
+  memoryKK->destroy_kokkos(k_eatom,eatom);
+  memoryKK->destroy_kokkos(k_vatom,vatom);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -118,7 +119,7 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   d_numneigh = k_list->d_numneigh;
   d_neighbors = k_list->d_neighbors;
   d_ilist = k_list->d_ilist;
-  int inum = list->inum;
+  inum = list->inum;
 
   need_dup = lmp->kokkos->need_dup<DeviceType>();
   if (need_dup) {
@@ -138,9 +139,9 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   // zero out density
 
   if (newton_pair)
-    Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyInitialize>(0,nall),*this);
+    Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyInitialize>(0,nall),*this);
   else
-    Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyInitialize>(0,nlocal),*this);
+    Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyInitialize>(0,nlocal),*this);
 
   // loop over neighbors of my atoms
 
@@ -152,15 +153,15 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
     if (neighflag == HALF) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelA<HALF,1> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelA<HALF,1>>(0,inum),*this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelA<HALF,0> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelA<HALF,0>>(0,inum),*this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelA<HALFTHREAD,1> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelA<HALFTHREAD,1>>(0,inum),*this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelA<HALFTHREAD,0> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelA<HALFTHREAD,0>>(0,inum),*this);
       }
     }
 
@@ -178,18 +179,22 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     // compute kernel B
 
     if (eflag)
-      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelB<1> >(0,inum),*this,ev);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelB<1>>(0,inum),*this,ev);
     else
-      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelB<0> >(0,inum),*this);
+      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelB<0>>(0,inum),*this);
 
   } else if (neighflag == FULL) {
 
     // compute kernel AB
 
     if (eflag)
-      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelAB<1> >(0,inum),*this,ev);
+      Kokkos::parallel_reduce(
+             Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelAB<1>>(0,inum),
+             *this,ev);
     else
-      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelAB<0> >(0,inum),*this);
+      Kokkos::parallel_for(
+            policyInstance<TagPairEAMAlloyKernelAB<0>>(inum),
+            *this);
   }
 
   if (eflag) {
@@ -208,41 +213,65 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   if (evflag) {
     if (neighflag == HALF) {
       if (newton_pair) {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<HALF,1,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelC<HALF,1,1>>(0,inum),
+              *this,ev);
       } else {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<HALF,0,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelC<HALF,0,1>>(0,inum),
+              *this,ev);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<HALFTHREAD,1,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelC<HALFTHREAD,1,1>>(0,inum),
+              *this,ev);
       } else {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<HALFTHREAD,0,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelC<HALFTHREAD,0,1>>(0,inum),
+              *this,ev);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<FULL,1,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelC<FULL,1,1>>(0,inum),
+              *this,ev);
       } else {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<FULL,0,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyKernelC<FULL,0,1>>(0,inum),
+              *this,ev);
       }
     }
   } else {
     if (neighflag == HALF) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<HALF,1,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMAlloyKernelC<HALF,1,0>>(inum),
+              *this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<HALF,0,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMAlloyKernelC<HALF,0,0>>(inum),
+              *this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<HALFTHREAD,1,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMAlloyKernelC<HALFTHREAD,1,0>>(inum),
+              *this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<HALFTHREAD,0,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMAlloyKernelC<HALFTHREAD,0,0>>(inum),
+              *this);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<FULL,1,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMAlloyKernelC<FULL,1,0>>(inum),
+              *this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyKernelC<FULL,0,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMAlloyKernelC<FULL,0,0>>(inum),
+              *this);
       }
     }
   }
@@ -427,7 +456,7 @@ int PairEAMAlloyKokkos<DeviceType>::pack_forward_comm_kokkos(int n, DAT::tdual_i
   d_sendlist = k_sendlist.view<DeviceType>();
   iswap = iswap_in;
   v_buf = buf.view<DeviceType>();
-  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyPackForwardComm>(0,n),*this);
+  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyPackForwardComm>(0,n),*this);
   return n;
 }
 
@@ -445,7 +474,7 @@ void PairEAMAlloyKokkos<DeviceType>::unpack_forward_comm_kokkos(int n, int first
 {
   first = first_in;
   v_buf = buf.view<DeviceType>();
-  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMAlloyUnpackForwardComm>(0,n),*this);
+  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMAlloyUnpackForwardComm>(0,n),*this);
 }
 
 template<class DeviceType>
@@ -588,6 +617,7 @@ template<class DeviceType>
 template<int EFLAG>
 KOKKOS_INLINE_FUNCTION
 void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelB<EFLAG>, const int &ii, EV_FLOAT& ev) const {
+
   // fp = derivative of embedding energy at each atom
   // phi = embedding energy at each atom
   // if rho > rhomax (e.g. due to close approach of two atoms),
@@ -625,7 +655,7 @@ void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelB<EFLAG>, c
 ////Specialisation for Neighborlist types Half, HalfThread, Full
 template<class DeviceType>
 template<int EFLAG>
-KOKKOS_INLINE_FUNCTION
+
 void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelAB<EFLAG>, const int &ii, EV_FLOAT& ev) const {
 
   // rho = density at each atom
@@ -644,6 +674,7 @@ void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelAB<EFLAG>,
   for (int jj = 0; jj < jnum; jj++) {
     int j = d_neighbors(i,jj);
     j &= NEIGHMASK;
+
     const X_FLOAT delx = xtmp - x(j,0);
     const X_FLOAT dely = ytmp - x(j,1);
     const X_FLOAT delz = ztmp - x(j,2);
@@ -806,6 +837,235 @@ void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelC<NEIGHFLAG
 
 /* ---------------------------------------------------------------------- */
 
+////Specialisation for Neighborlist types Half, HalfThread, Full
+template<class DeviceType>
+template<int EFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelAB<EFLAG>,
+                                     const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
+                                     EV_FLOAT& ev) const {
+  int ii = team_member.league_rank()*team_member.team_size() + team_member.team_rank();
+  // rho = density at each atom
+  // loop over neighbors of my atoms
+  const int m_max = d_rhor_spline.extent_int(1);
+  const int j_max = t_ffloat_2d_n7::static_extent(2);
+  const int d_rhor_spline_cached = (m_max > MAX_CACHE_ROWS) ? 0 : 1;
+  Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
+               Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
+
+  if (d_rhor_spline_cached) {
+    for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()) {
+      int j = i%j_max;
+      int m = i/j_max;
+      A(m,j) = d_rhor_spline(0,m,j);
+    }
+    team_member.team_barrier();
+  }
+  if (ii < inum) {
+    const int i = d_ilist[ii];
+    const X_FLOAT xtmp = x(i,0);
+    const X_FLOAT ytmp = x(i,1);
+    const X_FLOAT ztmp = x(i,2);
+    const int itype = type(i);
+
+    const int jnum = d_numneigh[i];
+
+    F_FLOAT rhotmp = 0.0;
+
+    for (int jj = 0; jj < jnum; jj++) {
+      int j = d_neighbors(i,jj);
+      j &= NEIGHMASK;
+
+      const X_FLOAT delx = xtmp - x(j,0);
+      const X_FLOAT dely = ytmp - x(j,1);
+      const X_FLOAT delz = ztmp - x(j,2);
+      const int jtype = type(j);
+      const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
+
+      if (rsq < cutforcesq) {
+        F_FLOAT p = sqrt(rsq)*rdr + 1.0;
+        int m = static_cast<int> (p);
+        m = MIN(m,nr-1);
+        p -= m;
+        p = MIN(p,1.0);
+        const int d_type2rhor_ji = d_type2rhor(jtype,itype);
+        if (d_type2rhor_ji == 0 && d_rhor_spline_cached == 1) {
+          rhotmp += ((A(m,3)*p + A(m,4))*p +
+                       A(m,5))*p + A(m,6);
+        } else
+          rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
+                      d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
+      }
+
+    }
+    d_rho[i] += rhotmp;
+
+    // fp = derivative of embedding energy at each atom
+    // phi = embedding energy at each atom
+    // if rho > rhomax (e.g. due to close approach of two atoms),
+    //   will exceed table, so add linear term to conserve energy
+
+    F_FLOAT p = d_rho[i]*rdrho + 1.0;
+    int m = static_cast<int> (p);
+    m = MAX(1,MIN(m,nrho-1));
+    p -= m;
+    p = MIN(p,1.0);
+    const int d_type2frho_i = d_type2frho[itype];
+    d_fp[i] = (d_frho_spline(d_type2frho_i,m,0)*p + d_frho_spline(d_type2frho_i,m,1))*p + d_frho_spline(d_type2frho_i,m,2);
+    if (EFLAG) {
+      F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
+                      d_frho_spline(d_type2frho_i,m,5))*p + d_frho_spline(d_type2frho_i,m,6);
+      if (d_rho[i] > rhomax) phi += d_fp[i] * (d_rho[i]-rhomax);
+      if (eflag_global) ev.evdwl += phi;
+      if (eflag_atom) d_eatom[i] += phi;
+    }
+  }
+}
+
+template<class DeviceType>
+template<int EFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelAB<EFLAG>,
+                                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member) const {
+  EV_FLOAT ev;
+  this->template operator()<EFLAG>(TagPairEAMAlloyKernelAB<EFLAG>(), team_member, ev);
+}
+
+/* ---------------------------------------------------------------------- */
+
+////Specialisation for Neighborlist types Half, HalfThread, Full
+template<class DeviceType>
+template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>,
+                                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
+                                           EV_FLOAT& ev) const {
+
+  int ii = team_member.league_rank()*team_member.team_size() + team_member.team_rank();
+
+  // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+  auto v_f = ScatterViewHelper<NeedDup_v<NEIGHFLAG,DeviceType>,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+  auto a_f = v_f.template access<AtomicDup_v<NEIGHFLAG,DeviceType>>();
+
+  const int m_max = d_z2r_spline.extent_int(1);
+  const int j_max = t_ffloat_2d_n7::static_extent(2);
+  const int d_z2r_spline_cached = (m_max > MAX_CACHE_ROWS) ? 0 : 1;
+  Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
+               Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
+
+  if (d_z2r_spline_cached) {
+    for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()) {
+      int j = i%j_max;
+      int m = i/j_max;
+      A(m,j) = d_z2r_spline(0,m,j);
+    }
+    team_member.team_barrier();
+  }
+  if (ii < inum) {
+    const int i = d_ilist[ii];
+    const X_FLOAT xtmp = x(i,0);
+    const X_FLOAT ytmp = x(i,1);
+    const X_FLOAT ztmp = x(i,2);
+    const int itype = type(i);
+
+    const int jnum = d_numneigh[i];
+
+    F_FLOAT fxtmp = 0.0;
+    F_FLOAT fytmp = 0.0;
+    F_FLOAT fztmp = 0.0;
+
+    for (int jj = 0; jj < jnum; jj++) {
+      int j = d_neighbors(i,jj);
+      j &= NEIGHMASK;
+      const X_FLOAT delx = xtmp - x(j,0);
+      const X_FLOAT dely = ytmp - x(j,1);
+      const X_FLOAT delz = ztmp - x(j,2);
+      const int jtype = type(j);
+      const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
+
+      if (rsq < cutforcesq) {
+        const F_FLOAT r = sqrt(rsq);
+        F_FLOAT p = r*rdr + 1.0;
+        int m = static_cast<int> (p);
+        m = MIN(m,nr-1);
+        p -= m;
+        p = MIN(p,1.0);
+
+        // rhoip = derivative of (density at atom j due to atom i)
+        // rhojp = derivative of (density at atom i due to atom j)
+        // phi = pair potential energy
+        // phip = phi'
+        // z2 = phi * r
+        // z2p = (phi * r)' = (phi' r) + phi
+        // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+        //   terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+        //   hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+
+        const int d_type2rhor_ij = d_type2rhor(itype,jtype);
+        const F_FLOAT rhoip = (d_rhor_spline(d_type2rhor_ij,m,0)*p + d_rhor_spline(d_type2rhor_ij,m,1))*p +
+                             d_rhor_spline(d_type2rhor_ij,m,2);
+        const int d_type2rhor_ji = d_type2rhor(jtype,itype);
+        const F_FLOAT rhojp = (d_rhor_spline(d_type2rhor_ji,m,0)*p + d_rhor_spline(d_type2rhor_ji,m,1))*p +
+                               d_rhor_spline(d_type2rhor_ji,m,2);
+        const int d_type2z2r_ij = d_type2z2r(itype,jtype);
+
+        const auto have_cache = (d_z2r_spline_cached == 1) && (0 == d_type2z2r_ij);
+        const auto z2r_spline_3 = (have_cache) ? A(m,3) : d_z2r_spline(d_type2z2r_ij,m,3);
+        const auto z2r_spline_4 = (have_cache) ? A(m,4) : d_z2r_spline(d_type2z2r_ij,m,4);
+        const auto z2r_spline_5 = (have_cache) ? A(m,5) : d_z2r_spline(d_type2z2r_ij,m,5);
+        const auto z2r_spline_6 = (have_cache) ? A(m,6) : d_z2r_spline(d_type2z2r_ij,m,6);
+
+        const F_FLOAT z2p = (3.0*rdr*z2r_spline_3*p + 2.0*rdr*z2r_spline_4)*p +
+                             rdr*z2r_spline_5; // the rdr and the factors of 3.0 and 2.0 come out of the interpolate function
+        const F_FLOAT z2 = ((z2r_spline_3*p + z2r_spline_4)*p +
+                             z2r_spline_5)*p + z2r_spline_6;
+
+        const F_FLOAT recip = 1.0/r;
+        const F_FLOAT phi = z2*recip;
+        const F_FLOAT phip = z2p*recip - phi*recip;
+        const F_FLOAT psip = d_fp[i]*rhojp + d_fp[j]*rhoip + phip;
+        const F_FLOAT fpair = -psip*recip;
+
+        fxtmp += delx*fpair;
+        fytmp += dely*fpair;
+        fztmp += delz*fpair;
+
+        if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < nlocal)) {
+          a_f(j,0) -= delx*fpair;
+          a_f(j,1) -= dely*fpair;
+          a_f(j,2) -= delz*fpair;
+        }
+
+        if (EVFLAG) {
+          if (eflag) {
+            ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD)&&(NEWTON_PAIR||(j<nlocal)))?1.0:0.5)*phi;
+          }
+
+          if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG,NEWTON_PAIR>(ev,i,j,phi,fpair,delx,dely,delz);
+        }
+
+      }
+    }
+
+    a_f(i,0) += fxtmp;
+    a_f(i,1) += fytmp;
+    a_f(i,2) += fztmp;
+  }
+}
+
+template<class DeviceType>
+template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>,
+                /*const int &ii*/
+                const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member) const {
+  EV_FLOAT ev;
+  this->template operator()<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(TagPairEAMAlloyKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(), team_member, ev);
+}
+
+/* ---------------------------------------------------------------------- */
+
 template<class DeviceType>
 template<int NEIGHFLAG, int NEWTON_PAIR>
 KOKKOS_INLINE_FUNCTION
@@ -1219,6 +1479,30 @@ void PairEAMAlloyKokkos<DeviceType>::file2array_alloy()
 
 /* ---------------------------------------------------------------------- */
 
+template<class DeviceType>
+template<class tag>
+auto PairEAMAlloyKokkos<DeviceType>::policyInstance(int inum) {
+  #ifdef KOKKOS_ENABLE_HIP
+    if (execution_space != Host) {
+    static_assert(t_ffloat_2d_n7::static_extent(2) == 7,
+                  "Breaking assumption of spline dim for KernelAB and KernelC scratch caching");
+
+    auto policy = Kokkos::TeamPolicy<DeviceType,tag>((inum+1023)/1024, 1024)
+                           .set_scratch_size(0,
+                                Kokkos::PerTeam(MAX_CACHE_ROWS*t_ffloat_2d_n7::static_extent(2)*sizeof(double)));
+    return policy;
+    } else {
+      auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
+      return policy;
+    }
+  #else
+    auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
+    return policy;
+  #endif
+}
+
+/* ---------------------------------------------------------------------- */
+
 namespace LAMMPS_NS {
 template class PairEAMAlloyKokkos<LMPDeviceType>;
 #ifdef LMP_KOKKOS_GPU
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h
index c6cb73ca5d..f9703ef473 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.h
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.h
@@ -61,7 +61,6 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
   ~PairEAMAlloyKokkos() override;
   void compute(int, int) override;
   void init_style() override;
-  void *extract(const char *, int &) override { return nullptr; }
   void coeff(int, char **) override;
 
   KOKKOS_INLINE_FUNCTION
@@ -93,6 +92,14 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMAlloyKernelAB<EFLAG>, const int&) const;
 
+  template<int EFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMAlloyKernelAB<EFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&, EV_FLOAT&) const;
+
+  template<int EFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMAlloyKernelAB<EFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&) const;
+
   template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMAlloyKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int&, EV_FLOAT&) const;
@@ -101,6 +108,14 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMAlloyKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int&) const;
 
+  template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMAlloyKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&, EV_FLOAT&) const;
+
+  template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMAlloyKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&) const;
+
   template<int NEIGHFLAG, int NEWTON_PAIR>
   KOKKOS_INLINE_FUNCTION
   void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
@@ -125,7 +140,7 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
   typename AT::t_efloat_1d d_eatom;
   typename AT::t_virial_array d_vatom;
 
-  int need_dup;
+  int need_dup,inum;
 
   using KKDeviceType = typename KKDevice<DeviceType>::value;
 
@@ -139,7 +154,6 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
   DupScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout> dup_f;
   DupScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout> dup_eatom;
   DupScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout> dup_vatom;
-
   NonDupScatterView<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout> ndup_rho;
   NonDupScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout> ndup_f;
   NonDupScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout> ndup_eatom;
@@ -163,17 +177,18 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
   t_ffloat_2d_n7 d_frho_spline;
   t_ffloat_2d_n7 d_rhor_spline;
   t_ffloat_2d_n7 d_z2r_spline;
-
+  void interpolate(int, double, double *, t_host_ffloat_2d_n7, int);
   void file2array() override;
   void file2array_alloy();
   void array2spline() override;
-  void interpolate(int, double, double *, t_host_ffloat_2d_n7, int);
   void read_file(char *) override;
 
+  template<class tag>
+  auto policyInstance(int inum);
+
   typename AT::t_neighbors_2d d_neighbors;
   typename AT::t_int_1d d_ilist;
   typename AT::t_int_1d d_numneigh;
-  //NeighListKokkos<DeviceType> k_list;
 
   int iswap;
   int first;
@@ -187,7 +202,6 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
 };
 
 }
-
 #endif
 #endif
 
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index 811b80e3a0..4a1258f18c 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -32,10 +32,10 @@
 #include "potential_file_reader.h"
 
 #include <cmath>
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
+#define MAX_CACHE_ROWS 500
+
 // Cannot use virtual inheritance on the GPU, so must duplicate code
 
 /* ---------------------------------------------------------------------- */
@@ -46,6 +46,7 @@ PairEAMFSKokkos<DeviceType>::PairEAMFSKokkos(LAMMPS *lmp) : PairEAM(lmp)
   respa_enable = 0;
   single_enable = 0;
   one_coeff = 1;
+  manybody_flag = 1;
 
   kokkosable = 1;
   atomKK = (AtomKokkos *) atom;
@@ -59,10 +60,10 @@ PairEAMFSKokkos<DeviceType>::PairEAMFSKokkos(LAMMPS *lmp) : PairEAM(lmp)
 template<class DeviceType>
 PairEAMFSKokkos<DeviceType>::~PairEAMFSKokkos()
 {
-  if (!copymode) {
-    memoryKK->destroy_kokkos(k_eatom,eatom);
-    memoryKK->destroy_kokkos(k_vatom,vatom);
-  }
+  if (copymode) return;
+
+  memoryKK->destroy_kokkos(k_eatom,eatom);
+  memoryKK->destroy_kokkos(k_vatom,vatom);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -118,7 +119,7 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   d_numneigh = k_list->d_numneigh;
   d_neighbors = k_list->d_neighbors;
   d_ilist = k_list->d_ilist;
-  int inum = list->inum;
+  inum = list->inum;
 
   need_dup = lmp->kokkos->need_dup<DeviceType>();
   if (need_dup) {
@@ -138,9 +139,9 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   // zero out density
 
   if (newton_pair)
-    Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSInitialize>(0,nall),*this);
+    Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMFSInitialize>(0,nall),*this);
   else
-    Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSInitialize>(0,nlocal),*this);
+    Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMFSInitialize>(0,nlocal),*this);
 
   // loop over neighbors of my atoms
 
@@ -152,15 +153,15 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
     if (neighflag == HALF) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelA<HALF,1> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelA<HALF,1>>(0,inum),*this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelA<HALF,0> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelA<HALF,0>>(0,inum),*this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelA<HALFTHREAD,1> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelA<HALFTHREAD,1>>(0,inum),*this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelA<HALFTHREAD,0> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelA<HALFTHREAD,0>>(0,inum),*this);
       }
     }
 
@@ -178,18 +179,22 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     // compute kernel B
 
     if (eflag)
-      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelB<1> >(0,inum),*this,ev);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelB<1>>(0,inum),*this,ev);
     else
-      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelB<0> >(0,inum),*this);
+      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelB<0>>(0,inum),*this);
 
   } else if (neighflag == FULL) {
 
     // compute kernel AB
 
     if (eflag)
-      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelAB<1> >(0,inum),*this,ev);
+      Kokkos::parallel_reduce(
+             Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelAB<1>>(0,inum),
+             *this,ev);
     else
-      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelAB<0> >(0,inum),*this);
+      Kokkos::parallel_for(
+            policyInstance<TagPairEAMFSKernelAB<0>>(inum),
+            *this);
   }
 
   if (eflag) {
@@ -197,7 +202,7 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     ev.evdwl = 0.0;
   }
 
-  // communicate derivative of embedding function (on the device)
+  // communicate derivative of embedding function
 
   k_fp.template modify<DeviceType>();
   comm->forward_comm(this);
@@ -208,41 +213,65 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   if (evflag) {
     if (neighflag == HALF) {
       if (newton_pair) {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALF,1,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelC<HALF,1,1>>(0,inum),
+              *this,ev);
       } else {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALF,0,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelC<HALF,0,1>>(0,inum),
+              *this,ev);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALFTHREAD,1,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelC<HALFTHREAD,1,1>>(0,inum),
+              *this,ev);
       } else {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALFTHREAD,0,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelC<HALFTHREAD,0,1>>(0,inum),
+              *this,ev);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<FULL,1,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelC<FULL,1,1>>(0,inum),
+              *this,ev);
       } else {
-        Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<FULL,0,1> >(0,inum),*this,ev);
+        Kokkos::parallel_reduce(
+              Kokkos::RangePolicy<DeviceType,TagPairEAMFSKernelC<FULL,0,1>>(0,inum),
+              *this,ev);
       }
     }
   } else {
     if (neighflag == HALF) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALF,1,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMFSKernelC<HALF,1,0>>(inum),
+              *this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALF,0,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMFSKernelC<HALF,0,0>>(inum),
+              *this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALFTHREAD,1,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMFSKernelC<HALFTHREAD,1,0>>(inum),
+              *this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALFTHREAD,0,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMFSKernelC<HALFTHREAD,0,0>>(inum),
+              *this);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<FULL,1,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMFSKernelC<FULL,1,0>>(inum),
+              *this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<FULL,0,0> >(0,inum),*this);
+        Kokkos::parallel_for(
+              policyInstance<TagPairEAMFSKernelC<FULL,0,0>>(inum),
+              *this);
       }
     }
   }
@@ -427,7 +456,7 @@ int PairEAMFSKokkos<DeviceType>::pack_forward_comm_kokkos(int n, DAT::tdual_int_
   d_sendlist = k_sendlist.view<DeviceType>();
   iswap = iswap_in;
   v_buf = buf.view<DeviceType>();
-  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSPackForwardComm>(0,n),*this);
+  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMFSPackForwardComm>(0,n),*this);
   return n;
 }
 
@@ -445,7 +474,7 @@ void PairEAMFSKokkos<DeviceType>::unpack_forward_comm_kokkos(int n, int first_in
 {
   first = first_in;
   v_buf = buf.view<DeviceType>();
-  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSUnpackForwardComm>(0,n),*this);
+  Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairEAMFSUnpackForwardComm>(0,n),*this);
 }
 
 template<class DeviceType>
@@ -645,6 +674,7 @@ void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelAB<EFLAG>, const
   for (int jj = 0; jj < jnum; jj++) {
     int j = d_neighbors(i,jj);
     j &= NEIGHMASK;
+
     const X_FLOAT delx = xtmp - x(j,0);
     const X_FLOAT dely = ytmp - x(j,1);
     const X_FLOAT delz = ztmp - x(j,2);
@@ -691,7 +721,7 @@ template<class DeviceType>
 template<int EFLAG>
 KOKKOS_INLINE_FUNCTION
 void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelAB<EFLAG>, const int &ii) const {
-  EV_FLOAT ev;
+  EV_FLOAT ev;  this->template operator()<EFLAG>(TagPairEAMFSKernelAB<EFLAG>(), ii, ev);
   this->template operator()<EFLAG>(TagPairEAMFSKernelAB<EFLAG>(), ii, ev);
 }
 
@@ -807,6 +837,235 @@ void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelC<NEIGHFLAG,NEWTO
 
 /* ---------------------------------------------------------------------- */
 
+////Specialisation for Neighborlist types Half, HalfThread, Full
+template<class DeviceType>
+template<int EFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelAB<EFLAG>,
+                                     const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
+                                     EV_FLOAT& ev) const {
+  int ii = team_member.league_rank()*team_member.team_size() + team_member.team_rank();
+  // rho = density at each atom
+  // loop over neighbors of my atoms
+  const int m_max = d_rhor_spline.extent_int(1);
+  const int j_max = t_ffloat_2d_n7::static_extent(2);
+  const int d_rhor_spline_cached = (m_max > MAX_CACHE_ROWS) ? 0 : 1;
+  Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
+               Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
+
+  if (d_rhor_spline_cached) {
+    for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()) {
+      int j = i%j_max;
+      int m = i/j_max;
+      A(m,j) = d_rhor_spline(0,m,j);
+    }
+    team_member.team_barrier();
+  }
+  if (ii < inum) {
+    const int i = d_ilist[ii];
+    const X_FLOAT xtmp = x(i,0);
+    const X_FLOAT ytmp = x(i,1);
+    const X_FLOAT ztmp = x(i,2);
+    const int itype = type(i);
+
+    const int jnum = d_numneigh[i];
+
+    F_FLOAT rhotmp = 0.0;
+
+    for (int jj = 0; jj < jnum; jj++) {
+      int j = d_neighbors(i,jj);
+      j &= NEIGHMASK;
+
+      const X_FLOAT delx = xtmp - x(j,0);
+      const X_FLOAT dely = ytmp - x(j,1);
+      const X_FLOAT delz = ztmp - x(j,2);
+      const int jtype = type(j);
+      const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
+
+      if (rsq < cutforcesq) {
+        F_FLOAT p = sqrt(rsq)*rdr + 1.0;
+        int m = static_cast<int> (p);
+        m = MIN(m,nr-1);
+        p -= m;
+        p = MIN(p,1.0);
+        const int d_type2rhor_ji = d_type2rhor(jtype,itype);
+        if (d_type2rhor_ji == 0 && d_rhor_spline_cached == 1) {
+          rhotmp += ((A(m,3)*p + A(m,4))*p +
+                       A(m,5))*p + A(m,6);
+        } else
+          rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
+                      d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
+      }
+
+    }
+    d_rho[i] += rhotmp;
+
+    // fp = derivative of embedding energy at each atom
+    // phi = embedding energy at each atom
+    // if rho > rhomax (e.g. due to close approach of two atoms),
+    //   will exceed table, so add linear term to conserve energy
+
+    F_FLOAT p = d_rho[i]*rdrho + 1.0;
+    int m = static_cast<int> (p);
+    m = MAX(1,MIN(m,nrho-1));
+    p -= m;
+    p = MIN(p,1.0);
+    const int d_type2frho_i = d_type2frho[itype];
+    d_fp[i] = (d_frho_spline(d_type2frho_i,m,0)*p + d_frho_spline(d_type2frho_i,m,1))*p + d_frho_spline(d_type2frho_i,m,2);
+    if (EFLAG) {
+      F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
+                      d_frho_spline(d_type2frho_i,m,5))*p + d_frho_spline(d_type2frho_i,m,6);
+      if (d_rho[i] > rhomax) phi += d_fp[i] * (d_rho[i]-rhomax);
+      if (eflag_global) ev.evdwl += phi;
+      if (eflag_atom) d_eatom[i] += phi;
+    }
+  }
+}
+
+template<class DeviceType>
+template<int EFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelAB<EFLAG>,
+                                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member) const {
+  EV_FLOAT ev;
+  this->template operator()<EFLAG>(TagPairEAMFSKernelAB<EFLAG>(), team_member, ev);
+}
+
+/* ---------------------------------------------------------------------- */
+
+////Specialisation for Neighborlist types Half, HalfThread, Full
+template<class DeviceType>
+template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>,
+                                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
+                                           EV_FLOAT& ev) const {
+
+  int ii = team_member.league_rank()*team_member.team_size() + team_member.team_rank();
+
+  // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+  auto v_f = ScatterViewHelper<NeedDup_v<NEIGHFLAG,DeviceType>,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+  auto a_f = v_f.template access<AtomicDup_v<NEIGHFLAG,DeviceType>>();
+
+  const int m_max = d_z2r_spline.extent_int(1);
+  const int j_max = t_ffloat_2d_n7::static_extent(2);
+  const int d_z2r_spline_cached = (m_max > MAX_CACHE_ROWS) ? 0 : 1;
+  Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
+               Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
+
+  if (d_z2r_spline_cached) {
+    for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()) {
+      int j = i%j_max;
+      int m = i/j_max;
+      A(m,j) = d_z2r_spline(0,m,j);
+    }
+    team_member.team_barrier();
+  }
+  if (ii < inum) {
+    const int i = d_ilist[ii];
+    const X_FLOAT xtmp = x(i,0);
+    const X_FLOAT ytmp = x(i,1);
+    const X_FLOAT ztmp = x(i,2);
+    const int itype = type(i);
+
+    const int jnum = d_numneigh[i];
+
+    F_FLOAT fxtmp = 0.0;
+    F_FLOAT fytmp = 0.0;
+    F_FLOAT fztmp = 0.0;
+
+    for (int jj = 0; jj < jnum; jj++) {
+      int j = d_neighbors(i,jj);
+      j &= NEIGHMASK;
+      const X_FLOAT delx = xtmp - x(j,0);
+      const X_FLOAT dely = ytmp - x(j,1);
+      const X_FLOAT delz = ztmp - x(j,2);
+      const int jtype = type(j);
+      const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
+
+      if (rsq < cutforcesq) {
+        const F_FLOAT r = sqrt(rsq);
+        F_FLOAT p = r*rdr + 1.0;
+        int m = static_cast<int> (p);
+        m = MIN(m,nr-1);
+        p -= m;
+        p = MIN(p,1.0);
+
+        // rhoip = derivative of (density at atom j due to atom i)
+        // rhojp = derivative of (density at atom i due to atom j)
+        // phi = pair potential energy
+        // phip = phi'
+        // z2 = phi * r
+        // z2p = (phi * r)' = (phi' r) + phi
+        // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+        //   terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+        //   hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+
+        const int d_type2rhor_ij = d_type2rhor(itype,jtype);
+        const F_FLOAT rhoip = (d_rhor_spline(d_type2rhor_ij,m,0)*p + d_rhor_spline(d_type2rhor_ij,m,1))*p +
+                             d_rhor_spline(d_type2rhor_ij,m,2);
+        const int d_type2rhor_ji = d_type2rhor(jtype,itype);
+        const F_FLOAT rhojp = (d_rhor_spline(d_type2rhor_ji,m,0)*p + d_rhor_spline(d_type2rhor_ji,m,1))*p +
+                               d_rhor_spline(d_type2rhor_ji,m,2);
+        const int d_type2z2r_ij = d_type2z2r(itype,jtype);
+
+        const auto have_cache = (d_z2r_spline_cached == 1) && (0 == d_type2z2r_ij);
+        const auto z2r_spline_3 = (have_cache) ? A(m,3) : d_z2r_spline(d_type2z2r_ij,m,3);
+        const auto z2r_spline_4 = (have_cache) ? A(m,4) : d_z2r_spline(d_type2z2r_ij,m,4);
+        const auto z2r_spline_5 = (have_cache) ? A(m,5) : d_z2r_spline(d_type2z2r_ij,m,5);
+        const auto z2r_spline_6 = (have_cache) ? A(m,6) : d_z2r_spline(d_type2z2r_ij,m,6);
+
+        const F_FLOAT z2p = (3.0*rdr*z2r_spline_3*p + 2.0*rdr*z2r_spline_4)*p +
+                             rdr*z2r_spline_5; // the rdr and the factors of 3.0 and 2.0 come out of the interpolate function
+        const F_FLOAT z2 = ((z2r_spline_3*p + z2r_spline_4)*p +
+                             z2r_spline_5)*p + z2r_spline_6;
+
+        const F_FLOAT recip = 1.0/r;
+        const F_FLOAT phi = z2*recip;
+        const F_FLOAT phip = z2p*recip - phi*recip;
+        const F_FLOAT psip = d_fp[i]*rhojp + d_fp[j]*rhoip + phip;
+        const F_FLOAT fpair = -psip*recip;
+
+        fxtmp += delx*fpair;
+        fytmp += dely*fpair;
+        fztmp += delz*fpair;
+
+        if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < nlocal)) {
+          a_f(j,0) -= delx*fpair;
+          a_f(j,1) -= dely*fpair;
+          a_f(j,2) -= delz*fpair;
+        }
+
+        if (EVFLAG) {
+          if (eflag) {
+            ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD)&&(NEWTON_PAIR||(j<nlocal)))?1.0:0.5)*phi;
+          }
+
+          if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG,NEWTON_PAIR>(ev,i,j,phi,fpair,delx,dely,delz);
+        }
+
+      }
+    }
+
+    a_f(i,0) += fxtmp;
+    a_f(i,1) += fytmp;
+    a_f(i,2) += fztmp;
+  }
+}
+
+template<class DeviceType>
+template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+KOKKOS_INLINE_FUNCTION
+void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>,
+                /*const int &ii*/
+                const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member) const {
+  EV_FLOAT ev;
+  this->template operator()<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(), team_member, ev);
+}
+
+/* ---------------------------------------------------------------------- */
+
 template<class DeviceType>
 template<int NEIGHFLAG, int NEWTON_PAIR>
 KOKKOS_INLINE_FUNCTION
@@ -1230,6 +1489,30 @@ void PairEAMFSKokkos<DeviceType>::file2array_fs()
 
 /* ---------------------------------------------------------------------- */
 
+template<class DeviceType>
+template<class tag>
+auto PairEAMFSKokkos<DeviceType>::policyInstance(int inum) {
+  #ifdef KOKKOS_ENABLE_HIP
+    if (execution_space != Host) {
+    static_assert(t_ffloat_2d_n7::static_extent(2) == 7,
+                  "Breaking assumption of spline dim for KernelAB and KernelC scratch caching");
+
+    auto policy = Kokkos::TeamPolicy<DeviceType,tag>((inum+1023)/1024, 1024)
+                           .set_scratch_size(0,
+                                Kokkos::PerTeam(MAX_CACHE_ROWS*t_ffloat_2d_n7::static_extent(2)*sizeof(double)));
+    return policy;
+    } else {
+      auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
+      return policy;
+    }
+  #else
+    auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
+    return policy;
+  #endif
+}
+
+/* ---------------------------------------------------------------------- */
+
 namespace LAMMPS_NS {
 template class PairEAMFSKokkos<LMPDeviceType>;
 #ifdef LMP_KOKKOS_GPU
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h
index 06a395cba7..f7513b3008 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.h
+++ b/src/KOKKOS/pair_eam_fs_kokkos.h
@@ -61,7 +61,6 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
   ~PairEAMFSKokkos() override;
   void compute(int, int) override;
   void init_style() override;
-  void *extract(const char *, int &) override { return nullptr; }
   void coeff(int, char **) override;
 
   KOKKOS_INLINE_FUNCTION
@@ -93,6 +92,14 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMFSKernelAB<EFLAG>, const int&) const;
 
+  template<int EFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMFSKernelAB<EFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&, EV_FLOAT&) const;
+
+  template<int EFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMFSKernelAB<EFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&) const;
+
   template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int&, EV_FLOAT&) const;
@@ -101,6 +108,14 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int&) const;
 
+  template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&, EV_FLOAT&) const;
+
+  template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const typename Kokkos::TeamPolicy<DeviceType>::member_type&) const;
+
   template<int NEIGHFLAG, int NEWTON_PAIR>
   KOKKOS_INLINE_FUNCTION
   void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
@@ -125,7 +140,7 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
   typename AT::t_efloat_1d d_eatom;
   typename AT::t_virial_array d_vatom;
 
-  int need_dup;
+  int need_dup,inum;
 
   using KKDeviceType = typename KKDevice<DeviceType>::value;
 
@@ -139,7 +154,6 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
   DupScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout> dup_f;
   DupScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout> dup_eatom;
   DupScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout> dup_vatom;
-
   NonDupScatterView<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout> ndup_rho;
   NonDupScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout> ndup_f;
   NonDupScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout> ndup_eatom;
@@ -163,13 +177,15 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
   t_ffloat_2d_n7 d_frho_spline;
   t_ffloat_2d_n7 d_rhor_spline;
   t_ffloat_2d_n7 d_z2r_spline;
-
+  void interpolate(int, double, double *, t_host_ffloat_2d_n7, int);
   void file2array() override;
   void file2array_fs();
   void array2spline() override;
-  void interpolate(int, double, double *, t_host_ffloat_2d_n7, int);
   void read_file(char *) override;
 
+  template<class tag>
+  auto policyInstance(int inum);
+
   typename AT::t_neighbors_2d d_neighbors;
   typename AT::t_int_1d d_ilist;
   typename AT::t_int_1d d_numneigh;
@@ -186,7 +202,6 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
 };
 
 }
-
 #endif
 #endif
 
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 2317f2d367..5e2ea4357f 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -148,15 +148,15 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
     if (neighflag == HALF) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALF,1> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALF,1>>(0,inum),*this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALF,0> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALF,0>>(0,inum),*this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALFTHREAD,1> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALFTHREAD,1>>(0,inum),*this);
       } else {
-        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALFTHREAD,0> >(0,inum),*this);
+        Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALFTHREAD,0>>(0,inum),*this);
       }
     }
 
@@ -174,9 +174,9 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     // compute kernel B
 
     if (eflag)
-      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelB<1> >(0,inum),*this,ev);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelB<1>>(0,inum),*this,ev);
     else
-      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelB<0> >(0,inum),*this);
+      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelB<0>>(0,inum),*this);
 
   } else if (neighflag == FULL) {
 
@@ -184,12 +184,12 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
     if (eflag)
       Kokkos::parallel_reduce(
-		    Kokkos::RangePolicy<DeviceType,TagPairEAMKernelAB<1>>(0,inum),
-		    *this,ev);
+             Kokkos::RangePolicy<DeviceType,TagPairEAMKernelAB<1>>(0,inum),
+             *this,ev);
     else
       Kokkos::parallel_for(
-		    policyInstance<TagPairEAMKernelAB<0>>(inum),
-		    *this);
+            policyInstance<TagPairEAMKernelAB<0>>(inum),
+            *this);
   }
 
   if (eflag) {
@@ -209,64 +209,64 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     if (neighflag == HALF) {
       if (newton_pair) {
         Kokkos::parallel_reduce(
-	      Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALF,1,1>>(0,inum),
-	      *this,ev);
+              Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALF,1,1>>(0,inum),
+              *this,ev);
       } else {
         Kokkos::parallel_reduce(
-	      Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALF,0,1>>(0,inum),
-	      *this,ev);
+              Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALF,0,1>>(0,inum),
+              *this,ev);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
         Kokkos::parallel_reduce(
-	      Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALFTHREAD,1,1>>(0,inum),
-	      *this,ev);
+              Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALFTHREAD,1,1>>(0,inum),
+              *this,ev);
       } else {
         Kokkos::parallel_reduce(
               Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<HALFTHREAD,0,1>>(0,inum),
-	      *this,ev);
+              *this,ev);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
         Kokkos::parallel_reduce(
-	      Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<FULL,1,1>>(0,inum),
-	      *this,ev);
+              Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<FULL,1,1>>(0,inum),
+              *this,ev);
       } else {
         Kokkos::parallel_reduce(
-	      Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<FULL,0,1>>(0,inum),
-	      *this,ev);
+              Kokkos::RangePolicy<DeviceType,TagPairEAMKernelC<FULL,0,1>>(0,inum),
+              *this,ev);
       }
     }
   } else {
     if (neighflag == HALF) {
       if (newton_pair) {
         Kokkos::parallel_for(
-	      policyInstance<TagPairEAMKernelC<HALF,1,0>>(inum),
-	      *this);
+              policyInstance<TagPairEAMKernelC<HALF,1,0>>(inum),
+              *this);
       } else {
         Kokkos::parallel_for(
-	      policyInstance<TagPairEAMKernelC<HALF,0,0>>(inum),
-	      *this);
+              policyInstance<TagPairEAMKernelC<HALF,0,0>>(inum),
+              *this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
         Kokkos::parallel_for(
-	      policyInstance<TagPairEAMKernelC<HALFTHREAD,1,0>>(inum),
-	      *this);
+              policyInstance<TagPairEAMKernelC<HALFTHREAD,1,0>>(inum),
+              *this);
       } else {
         Kokkos::parallel_for(
-	      policyInstance<TagPairEAMKernelC<HALFTHREAD,0,0>>(inum),
-	      *this);
+              policyInstance<TagPairEAMKernelC<HALFTHREAD,0,0>>(inum),
+              *this);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
         Kokkos::parallel_for(
-	      policyInstance<TagPairEAMKernelC<FULL,1,0>>(inum),
-	      *this);
+              policyInstance<TagPairEAMKernelC<FULL,1,0>>(inum),
+              *this);
       } else {
         Kokkos::parallel_for(
-	      policyInstance<TagPairEAMKernelC<FULL,0,0>>(inum),
-	      *this);
+              policyInstance<TagPairEAMKernelC<FULL,0,0>>(inum),
+              *this);
       }
     }
   }
@@ -612,6 +612,7 @@ template<class DeviceType>
 template<int EFLAG>
 KOKKOS_INLINE_FUNCTION
 void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelB<EFLAG>, const int &ii, EV_FLOAT& ev) const {
+
   // fp = derivative of embedding energy at each atom
   // phi = embedding energy at each atom
   // if rho > rhomax (e.g. due to close approach of two atoms),
@@ -643,7 +644,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelB<EFLAG>, const int &
   EV_FLOAT ev;
   this->template operator()<EFLAG>(TagPairEAMKernelB<EFLAG>(), ii, ev);
 }
-/* ---------------------------------------------------------------------- */
+
 /* ---------------------------------------------------------------------- */
 
 ////Specialisation for Neighborlist types Half, HalfThread, Full
@@ -828,6 +829,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PA
   EV_FLOAT ev;
   this->template operator()<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(), ii, ev);
 }
+
 /* ---------------------------------------------------------------------- */
 
 ////Specialisation for Neighborlist types Half, HalfThread, Full
@@ -835,8 +837,8 @@ template<class DeviceType>
 template<int EFLAG>
 KOKKOS_INLINE_FUNCTION
 void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
-		                     const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
-				     EV_FLOAT& ev) const {
+                                     const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
+                                     EV_FLOAT& ev) const {
   int ii = team_member.league_rank()*team_member.team_size() + team_member.team_rank();
   // rho = density at each atom
   // loop over neighbors of my atoms
@@ -844,7 +846,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
   const int j_max = t_ffloat_2d_n7::static_extent(2);
   const int d_rhor_spline_cached = (m_max > MAX_CACHE_ROWS) ? 0 : 1;
   Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
-	       Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
+               Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
 
   if (d_rhor_spline_cached) {
     for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()) {
@@ -884,7 +886,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
         const int d_type2rhor_ji = d_type2rhor(jtype,itype);
         if (d_type2rhor_ji == 0 && d_rhor_spline_cached == 1) {
           rhotmp += ((A(m,3)*p + A(m,4))*p +
-  	             A(m,5))*p + A(m,6);
+                       A(m,5))*p + A(m,6);
         } else
           rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
                       d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
@@ -919,7 +921,7 @@ template<class DeviceType>
 template<int EFLAG>
 KOKKOS_INLINE_FUNCTION
 void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>,
-		                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member) const {
+                                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member) const {
   EV_FLOAT ev;
   this->template operator()<EFLAG>(TagPairEAMKernelAB<EFLAG>(), team_member, ev);
 }
@@ -931,7 +933,7 @@ template<class DeviceType>
 template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
 KOKKOS_INLINE_FUNCTION
 void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>,
-		                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
+                                           const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member,
                                            EV_FLOAT& ev) const {
 
   int ii = team_member.league_rank()*team_member.team_size() + team_member.team_rank();
@@ -945,7 +947,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PA
   const int j_max = t_ffloat_2d_n7::static_extent(2);
   const int d_z2r_spline_cached = (m_max > MAX_CACHE_ROWS) ? 0 : 1;
   Kokkos::View<double*[t_ffloat_2d_n7::static_extent(2)], typename DeviceType::scratch_memory_space,
-	       Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
+               Kokkos::MemoryTraits<Kokkos::Unmanaged>> A(team_member.team_scratch(0), MAX_CACHE_ROWS);
 
   if (d_z2r_spline_cached) {
     for(int i = team_member.team_rank(); i < m_max*j_max; i+= team_member.team_size()) {
@@ -1051,8 +1053,8 @@ template<class DeviceType>
 template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
 KOKKOS_INLINE_FUNCTION
 void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>,
-		/*const int &ii*/
-		const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member) const {
+                /*const int &ii*/
+                const typename Kokkos::TeamPolicy<DeviceType>::member_type& team_member) const {
   EV_FLOAT ev;
   this->template operator()<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(), team_member, ev);
 }
@@ -1163,11 +1165,11 @@ auto PairEAMKokkos<DeviceType>::policyInstance(int inum) {
   #ifdef KOKKOS_ENABLE_HIP
     if (execution_space != Host) {
     static_assert(t_ffloat_2d_n7::static_extent(2) == 7,
-		  "Breaking assumption of spline dim for KernelAB and KernelC scratch caching");
+                  "Breaking assumption of spline dim for KernelAB and KernelC scratch caching");
 
     auto policy = Kokkos::TeamPolicy<DeviceType,tag>((inum+1023)/1024, 1024)
-	                   .set_scratch_size(0,
-			        Kokkos::PerTeam(MAX_CACHE_ROWS*t_ffloat_2d_n7::static_extent(2)*sizeof(double)));
+                           .set_scratch_size(0,
+                                Kokkos::PerTeam(MAX_CACHE_ROWS*t_ffloat_2d_n7::static_extent(2)*sizeof(double)));
     return policy;
     } else {
       auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index 7f4ec67f6f..41e02e68cc 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -138,9 +138,8 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
   typename AT::t_efloat_1d d_eatom;
   typename AT::t_virial_array d_vatom;
 
-  int need_dup;
-  int inum;
-  
+  int need_dup,inum;
+
   using KKDeviceType = typename KKDevice<DeviceType>::value;
 
   template<typename DataType, typename Layout>

From 4d78d987c6d512b6d379b70ce9ef9c386f41b418 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 24 Feb 2023 07:34:58 -0500
Subject: [PATCH 008/396] add unmap_inv function

---
 src/domain.cpp | 23 +++++++++++++++++++++++
 src/domain.h   |  1 +
 2 files changed, 24 insertions(+)

diff --git a/src/domain.cpp b/src/domain.cpp
index e1a508ac51..dcad723b9f 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -1500,6 +1500,29 @@ void Domain::remap_near(double *xnew, double *xold)
   if (triclinic) lamda2x(coordnew,xnew);
 }
 
+/* ----------------------------------------------------------------------
+   remap the point to specific image flags
+   x overwritten with result, reset image flag
+   for triclinic, use h[] to add in tilt factors in other dims as needed
+------------------------------------------------------------------------- */
+
+void Domain::unmap_inv(double *x, imageint image)
+{
+  int xbox = (image & IMGMASK) - IMGMAX;
+  int ybox = (image >> IMGBITS & IMGMASK) - IMGMAX;
+  int zbox = (image >> IMG2BITS) - IMGMAX;
+
+  if (triclinic == 0) {
+    x[0] -= xbox*xprd;
+    x[1] -= ybox*yprd;
+    x[2] -= zbox*zprd;
+  } else {
+    x[0] -= h[0]*xbox + h[5]*ybox + h[4]*zbox;
+    x[1] -= h[1]*ybox + h[3]*zbox;
+    x[2] -= h[2]*zbox;
+  }
+}
+
 /* ----------------------------------------------------------------------
    unmap the point via image flags
    x overwritten with result, don't reset image flag
diff --git a/src/domain.h b/src/domain.h
index 1e9e9caae1..738dc8a2a3 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -126,6 +126,7 @@ class Domain : protected Pointers {
   void remap(double *, imageint &);
   void remap(double *);
   void remap_near(double *, double *);
+  void unmap_inv(double *x, imageint);
   void unmap(double *, imageint);
   void unmap(const double *, imageint, double *);
   void image_flip(int, int, int);

From b0b14bd1d166c78d7357e76a733c56ca8d73970d Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 24 Feb 2023 07:48:34 -0500
Subject: [PATCH 009/396] add fix pimd/langevin

---
 src/REPLICA/fix_pimd_langevin.cpp | 1751 +++++++++++++++++++++++++++++
 src/REPLICA/fix_pimd_langevin.h   |  198 ++++
 2 files changed, 1949 insertions(+)
 create mode 100644 src/REPLICA/fix_pimd_langevin.cpp
 create mode 100644 src/REPLICA/fix_pimd_langevin.h

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
new file mode 100644
index 0000000000..9ac8fc3b17
--- /dev/null
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -0,0 +1,1751 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Package      FixPIMDLangevin
+   Purpose      Quantum Path Integral Algorithm for Quantum Chemistry
+   Copyright    Voth Group @ University of Chicago
+   Authors      Chris Knight & Yuxing Peng (yuxing at uchicago.edu)
+
+   Updated      Oct-01-2011
+   Version      1.0
+
+   Updated      Jun-07-2022
+   Yifan Li @ Princeton University (yifanl0716@gmail.com)
+   Added components:
+   - Multi-processor parallelism for each bead
+   - White-noise Langevin thermostat
+   - Bussi-Zykova-Parrinello barostat (isotropic and anisotropic)
+   - Several quantum estimators
+   Futher plans:
+   - Triclinic barostat
+------------------------------------------------------------------------- */
+
+#include "fix_pimd_langevin.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "compute.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "group.h"
+#include "math_const.h"
+#include "memory.h"
+#include "modify.h"
+#include "random_mars.h"
+#include "universe.h"
+#include "utils.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+using namespace MathConst;
+
+enum { PIMD, NMPIMD, CMD };
+enum { physical, normal };
+enum { baoab, obabo };
+enum { ISO, ANISO, TRICLINIC };
+enum { PILE_L };
+enum { MTTK, BZP };
+// char* Barostats[] = {"MTTK", "BZP"};
+std::map<int, std::string> Barostats {{MTTK, "MTTK"}, {BZP, "BZP"}};
+enum { nve, nvt, nph, npt };
+enum{SINGLE_PROC, MULTI_PROC};
+
+/* ---------------------------------------------------------------------- */
+
+FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr) {
+  time_integrate = 1;
+  tagsend = tagrecv = nullptr;
+  bufsend = bufrecv = nullptr;
+  bufsendall = bufrecvall = nullptr;
+  bufsorted = bufsortedall = nullptr;
+  outsorted = buftransall = nullptr;
+
+  ntotal = 0;
+  maxlocal = maxunwrap = maxxc = 0;
+  bufbeads = nullptr;
+  x_unwrap = xc = nullptr;
+  xcall = nullptr;
+  // x_unwrap = x_unwrapsort = x_unwrapall = nullptr;
+  // tag_init = tag_initall = nullptr;
+  counts = nullptr;
+
+  sizeplan = 0;
+  plansend = planrecv = nullptr;
+
+  M_x2xp = M_xp2x = M_f2fp = M_fp2f = nullptr;
+  lam = nullptr;
+  modeindex = nullptr;
+
+  mass = nullptr;
+
+  method = PIMD;
+  ensemble      = nvt;
+  integrator = obabo;
+  thermostat = PILE_L;
+  barostat = BZP;
+  fmass = 1.0;
+  sp = 1.0;
+  temp          = 298.15;
+  Lan_temp      = 298.15;
+  tau           = 1.0;
+  tau_p         = 1.0;
+  Pext          = 1.0;
+  tstat_flag    = 1;
+  pstat_flag    = 0;
+  mapflag       = 1;
+  removecomflag = 1;
+  fmmode        = physical;
+  pstyle        = ISO;
+  for (int i=0; i<6; i++) p_flag[i] = 0;
+
+  for (int i = 3; i < narg - 1; i += 2) {
+    if (strcmp(arg[i], "method") == 0) {
+      if (strcmp(arg[i + 1], "pimd") == 0)
+        method = PIMD;
+      else if (strcmp(arg[i + 1], "nmpimd") == 0)
+        method = NMPIMD;
+      else if (strcmp(arg[i + 1], "cmd") == 0)
+        method = CMD;
+      else
+        error->universe_all(FLERR, "Unknown method parameter for fix pimd");
+    }
+    else if(strcmp(arg[i], "integrator")==0)
+
+    {
+      if(strcmp(arg[i+1], "obabo")==0) integrator=obabo;
+      else if(strcmp(arg[i+1], "baoab")==0) integrator=baoab;
+      else error->universe_all(FLERR, "Unknown integrator parameter for fix pimd. Only obabo and baoab integrators are supported!");
+    }
+
+    else if(strcmp(arg[i], "ensemble")==0)
+    {
+      if(strcmp(arg[i+1], "nve")==0) { ensemble = nve; tstat_flag = 0; pstat_flag = 0; }
+      else if(strcmp(arg[i+1], "nvt")==0) { ensemble = nvt; tstat_flag = 1; pstat_flag = 0; }
+      else if(strcmp(arg[i+1], "nph")==0) { ensemble = nph; tstat_flag = 0; pstat_flag = 1; }
+      else if(strcmp(arg[i+1], "npt")==0) { ensemble = npt; tstat_flag = 1; pstat_flag = 1; }
+      else error->universe_all(FLERR, "Unknown ensemble parameter for fix pimd. Only nve and nvt ensembles are supported!");
+    }
+
+      else if (strcmp(arg[i], "fmass") == 0) {
+      fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
+      if (fmass < 0.0 || fmass > 1.0)
+        error->universe_all(FLERR, "Invalid fmass value for fix pimd");
+    } 
+
+    else if(strcmp(arg[i], "fmmode")==0)
+    {
+      if(strcmp(arg[i+1], "physical")==0) fmmode=physical;
+      else if(strcmp(arg[i+1], "normal")==0) fmmode=normal;
+      else error->universe_all(FLERR, "Unknown fictitious mass mode for fix pimd. Only physical mass and normal mode mass are supported!");
+    }
+
+    else if(strcmp(arg[i],"scale")==0)
+    {
+      pilescale = atof(arg[i+1]);
+      if(pilescale<0.0) error->universe_all(FLERR,"Invalid pile scale value for fix pimd");
+    }
+
+    else if (strcmp(arg[i], "temp") == 0) {
+      temp = utils::numeric(FLERR, arg[i + 1], false, lmp);
+      if (temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd");
+    } 
+
+    else if (strcmp(arg[i], "lj") == 0) {
+      lj_epsilon = utils::numeric(FLERR, arg[i+1], false, lmp);
+      lj_sigma = utils::numeric(FLERR, arg[i+2], false, lmp);
+      lj_mass = utils::numeric(FLERR, arg[i+3], false, lmp);
+      other_planck = utils::numeric(FLERR, arg[i+4], false, lmp);
+      i++;
+      i++;
+      i++;
+    }
+
+    else if(strcmp(arg[i], "thermostat")==0)
+    {
+      if(strcmp(arg[i+1],"PILE_L")==0) 
+      {
+        thermostat = PILE_L;
+        seed = atoi(arg[i+2]);
+        i++;
+      }
+    }
+
+    else if(strcmp(arg[i], "tau")==0)
+    {
+      tau = atof(arg[i+1]);
+    }
+  
+    else if(strcmp(arg[i], "press")==0)
+    {
+      Pext = atof(arg[i+1]);
+      if(Pext<0.0) error->universe_all(FLERR,"Invalid press value for fix pimd");
+    }
+
+    else if(strcmp(arg[i], "barostat")==0)
+    {
+      if(strcmp(arg[i+1],"MTTK")==0) 
+      {
+        barostat = MTTK;
+      }
+      else if(strcmp(arg[i+1],"BZP")==0)
+      {
+        barostat = BZP;
+      }
+      else error->universe_all(FLERR,"Unknown barostat parameter for fix pimd");
+    }
+
+    else if(strcmp(arg[i], "iso")==0)
+    {
+      pstyle = ISO;
+      i--;
+    }
+
+    else if(strcmp(arg[i], "aniso")==0)
+    {
+      pstyle = ANISO;
+      i--;
+    }
+
+    else if(strcmp(arg[i], "taup")==0)
+    {
+      tau_p = atof(arg[i+1]);
+      if(tau_p<=0.0) error->universe_all(FLERR, "Invalid tau_p value for fix pimd");
+    }
+    else if(strcmp(arg[i], "fixcom")==0)
+    {
+      if(strcmp(arg[i+1], "yes")==0) removecomflag = 1;
+      else if(strcmp(arg[i+1], "no")==0) removecomflag = 0;
+    }
+
+    else if(strcmp(arg[i], "map")==0)
+    {
+      if(strcmp(arg[i+1], "yes")==0) mapflag = 1;
+      else if(strcmp(arg[i+1], "no")==0) mapflag = 0;
+    }
+
+    else  error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd", arg[i]));
+  }
+
+  /* Initiation */
+
+  int nlocal = atom->nlocal;
+  // xc = new double[nlocal*3];
+  // x_unwrap = new double[nlocal*3];
+
+  global_freq = 1;
+  vector_flag = 1;
+  size_vector = 11;
+  // if(pstyle==ISO) {size_vector = 15;}
+  // else if(pstyle==ANISO) {size_vector = 23;}
+  extvector = 1;
+  // comm_forward = 1;
+
+  // some initilizations
+
+  id_pe = new char[8];
+  strcpy(id_pe, "pimd_pe");
+  char **newarg = new char*[3];
+  newarg[0] = id_pe;
+  newarg[1] = (char *) "all";
+  newarg[2] = (char *) "pe";
+  modify->add_compute(3,newarg);
+  delete [] newarg;
+
+
+  id_press = new char[12];
+  strcpy(id_press, "pimd_press");
+  newarg = new char*[5];
+  newarg[0] = id_press;
+  newarg[1] = (char*) "all";
+  newarg[2] = (char*) "pressure";
+  newarg[3] = (char*) "thermo_temp";
+  newarg[4] = (char*) "virial";
+  modify->add_compute(5, newarg);
+  delete [] newarg;
+
+  vol0 = domain->xprd * domain->yprd * domain->zprd;
+
+  fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
+  fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
+  fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]);
+
+  // initialize Marsaglia RNG with processor-unique seed
+
+  if(integrator==baoab || integrator==obabo)
+  {
+    Lan_temp = temp;
+    random = new RanMars(lmp, seed + universe->me);
+  }
+  
+  me = comm->me;
+  nprocs = comm->nprocs;
+  if(nprocs == 1) cmode = SINGLE_PROC;
+  else cmode = MULTI_PROC;
+
+  nprocs_universe = universe->nprocs;
+  nreplica = universe->nworlds;
+  ireplica = universe->iworld;
+
+  int *iroots = new int[nreplica];
+  MPI_Group uworldgroup,rootgroup;
+
+  for (int i=0; i<nreplica; i++) iroots[i] = universe->root_proc[i];
+  MPI_Comm_group(universe->uworld, &uworldgroup);
+  MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup);
+  MPI_Comm_create(universe->uworld, rootgroup, &rootworld);
+  if (rootgroup != MPI_GROUP_NULL) MPI_Group_free(&rootgroup);
+  if (uworldgroup != MPI_GROUP_NULL) MPI_Group_free(&uworldgroup);
+  delete [] iroots;
+
+  ntotal = atom->natoms;
+  if(atom->nmax > maxlocal) reallocate();
+  if(atom->nmax > maxunwrap) reallocate_x_unwrap();
+  if(atom->nmax > maxxc) reallocate_xc();
+  memory->create(xcall, ntotal*3, "FixPIMDLangevin:xcall");
+  // init_x_unwrap();
+
+  if (cmode == SINGLE_PROC)
+  {
+    memory->create(bufsorted, ntotal, 3, "FixPIMDLangevin:bufsorted");
+    memory->create(outsorted, ntotal, 3, "FixPIMDLangevin:outsorted");
+    memory->create(bufsortedall, nreplica*ntotal, 3, "FixPIMDLangevin:bufsortedall");
+    memory->create(buftransall, nreplica*ntotal, 3, "FixPIMDLangevin:buftransall");
+    memory->create(counts, nreplica, "FixPIMDLangevin:counts");
+    memory->create(displacements, nreplica, "FixPIMDLangevin:displacements");
+  }
+
+  if ((cmode == MULTI_PROC) && (counts == nullptr)) {
+    // printf("me = %d, creating bufrecvall\n", universe->me);
+    memory->create(bufsendall,ntotal,3,"FixPIMDLangevin:bufsendall");
+    memory->create(bufrecvall,ntotal,3,"FixPIMDLangevin:bufrecvall");
+    // printf("me = %d, bufrecvall[0][0] = %.4f\n", universe->me, bufrecvall[0][0]);
+    memory->create(tagsendall,ntotal,"FixPIMDLangevin:tagsendall");
+    memory->create(tagrecvall,ntotal,"FixPIMDLangevin:tagrecvall");
+    // printf("me = %d, tagrecvall[0] = %d\n", universe->me, tagrecvall[0]);
+    memory->create(counts,nprocs,"FixPIMDLangevin:counts");
+    memory->create(displacements,nprocs,"FixPIMDLangevin:displacements");
+    // memory->create(x_unwrapall, ntotal, 3, "FixPIMDLangevin:x_unwrapall");
+    // memory->create(tag_initall, ntotal, "FixPIMDLangevin:tag_initall");
+    // printf("me = %d, tag_initall[0] = %d\n", universe->me, tag_initall[0]);
+  }
+
+    // printf("me = %d constructing finished\n", universe->me);
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixPIMDLangevin::~FixPIMDLangevin()
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixPIMDLangevin::setmask()
+{
+  int mask = 0;
+  mask |= POST_FORCE;
+  mask |= INITIAL_INTEGRATE;
+  // mask |= POST_NEIGHBOR;
+  mask |= FINAL_INTEGRATE;
+  mask |= END_OF_STEP;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::init()
+{
+  if (atom->map_style == Atom::MAP_NONE)
+    error->all(FLERR, "Fix pimd requires an atom map, see atom_modify");
+
+  if (universe->me == 0 && universe->uscreen)
+    fprintf(universe->uscreen, "Fix pimd initializing Path-Integral ...\n");
+
+  // prepare the constants
+
+  masstotal = group->mass(igroup);
+  np = universe->nworlds;
+  inverse_np = 1.0 / np;
+
+  const double Boltzmann = force->boltz;
+  if (strcmp(update->unit_style,"lj") == 0) { 
+    double planck_star = sqrt(lj_epsilon)*sqrt(atom->mass[0])*lj_sigma;
+    planck = other_planck / planck_star;
+  }
+  else planck = force->hplanck;
+  const double Planck = planck;
+  printf("planck = %.6e\n", planck);
+
+  // if(force->boltz == 1.0) { hbar = Planck; }
+  // else { hbar = Planck / (2.0 * MY_PI); }
+  hbar = Planck / (2.0 * MY_PI);
+  // hbar = Planck;
+  kBT = force->boltz * temp;
+  double beta = 1.0 / (Boltzmann * temp);
+  double _fbond = 1.0 * np * np / (beta * beta * hbar * hbar);
+
+  omega_np = np / (hbar * beta) * sqrt(force->mvv2e);
+  beta_np = 1.0 / force->boltz / temp / np;
+  fbond = _fbond * force->mvv2e;
+  // printf("_fbond = %.16e\nfbond = %.16e\n", _fbond, fbond);
+
+  if (universe->me == 0)
+    printf("Fix pimd -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
+
+  if(integrator==obabo)
+  {
+    dtf = 0.5 * update->dt * force->ftm2v;
+    dtv = 0.5 * update->dt;
+    dtv2 = dtv * dtv;
+    dtv3 = 1./3 * dtv2 * dtv * force->ftm2v;
+  }
+  else if(integrator==baoab)
+  {
+    dtf = 0.5 * update->dt * force->ftm2v;
+    dtv = 0.5 * update->dt;
+    dtv2 = dtv * dtv;
+    dtv3 = 1./3 * dtv2 * dtv * force->ftm2v;
+  }
+  else
+  {
+    error->universe_all(FLERR,"Unknown integrator parameter for fix pimd");
+  }
+
+  comm_init();
+
+  mass = new double[atom->ntypes + 1];
+
+  nmpimd_init();
+
+  Langevin_init();
+  if (pstat_flag) baro_init();
+
+  int ipe = modify->find_compute(id_pe);
+  c_pe = modify->compute[ipe];
+
+  int ipress = modify->find_compute(id_press);
+  c_press = modify->compute[ipress];
+
+  t_prim = t_vir = t_cv = p_prim = p_vir = p_cv = p_md = 0.0;
+
+  if(universe->me==0) fprintf(screen, "Fix pimd successfully initialized!\n");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::setup(int vflag)
+{
+  if(universe->me==0) printf("Setting up Path-Integral ...\n");
+  int nlocal = atom->nlocal;
+  tagint *tag = atom->tag;
+  double **x = atom->x;
+  double **v = atom->v;
+  imageint *image = atom->image;
+  // nlocal_init = nlocal;
+  if(mapflag){
+    for(int i=0; i<nlocal; i++)
+    {
+      domain->unmap(x[i], image[i]);
+    }
+  }
+  // printf("me = %d after unmapping x_unwrap\n", universe->me);
+
+  // printf("setup already here\n");
+  if(method==NMPIMD)
+  {
+    inter_replica_comm(x);
+    // printf("me = %d after inter\n", universe->me);
+    // printf("%.4f %.4f %.4f\n", bufbeads[0][0], bufbeads[0][1], bufbeads[0][2]);
+    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
+    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
+  }
+  collect_xc();
+  // printf("me = %d setup x2xp done\n", universe->me);
+  compute_spring_energy();
+  if(method==NMPIMD)
+  {
+    inter_replica_comm(x);
+    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_xp2x[universe->iworld]);
+    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
+    // nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
+  }
+  // printf("me = %d setup xp2x done\n", universe->me);
+  if(mapflag){
+    for(int i=0; i<nlocal; i++)
+    {
+      domain->unmap_inv(x[i], image[i]);
+    }
+  }
+
+  if(method==NMPIMD)
+  {
+    inter_replica_comm(v);
+    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, v, M_x2xp[universe->iworld]);
+    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, v, M_x2xp[universe->iworld]);
+    // nmpimd_transform(bufbeads, atom->v, M_x2xp[universe->iworld]);
+  }
+  // printf("me = %d setup v2vp done\n", universe->me);
+  // compute_xc();
+  // update_x_unwrap();
+  // printf("setting up %d\n", vflag);
+  if(universe->me==0 && screen) fprintf(screen,"Setting up Path-Integral ...\n");
+  if(universe->me==0) printf("Setting up Path-Integral ...\n");
+  // printf("setting up, m = %.4e\n", mass[1]);
+  post_force(vflag);
+  // int idx = atom->map(1);
+  // printf("irplica = %d, x[1] = %.6f %.6f %.6f xu[1] = %.6f %.6f %.6f xc[1] = %.6f %.6f %.6f\n", ireplica, x[idx][0], x[idx][1], x[idx][2], x_unwrap[idx][0], x_unwrap[idx][1], x_unwrap[idx][2], xc[idx][0], xc[idx][1], xc[idx][2]);
+  // printf("after post_force, m = %.4e\n", mass[1]);
+  // printf("me = %d after post_force\n", universe->me);
+  compute_totke();
+  // compute_pote();
+  // if(pstyle==ANISO) compute_stress_tensor();
+  end_of_step();
+  c_pe->addstep(update->ntimestep+1); 
+  c_press->addstep(update->ntimestep+1);
+  // printf("setup ending: \ncell = %.16e %.16e %.16e\nvol = %.16e\n", domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
+  // printf("me = %d, setup finished\n", universe->me);   
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::initial_integrate(int /*vflag*/)
+{
+  // printf("step = %d start initial_integrate\ncell = %.16e %.16e %.16e\nvol = %.16e\n", update->ntimestep, domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
+  // printf("me = %d, step %d initial_integrate starts!\n", universe->me, update->ntimestep);
+  // printf("me = %d, step %d if starts!\n", universe->me, update->ntimestep);
+  int nlocal = atom->nlocal;
+  tagint *tag = atom->tag;
+  double **x = atom->x;
+  imageint *image = atom->image;
+  if(mapflag){
+    for(int i=0; i<nlocal; i++)
+    {
+      domain->unmap(x[i], image[i]);
+    }
+  }
+  if(integrator==obabo)
+  {
+  // printf("me = %d, step %d obabo starts!\n", universe->me, update->ntimestep);
+    if(tstat_flag)
+    {
+      o_step();
+      // if(removecomflag) remove_com_motion();
+      if(pstat_flag) press_o_step();
+    }
+    if(pstat_flag)
+    {
+      compute_totke();
+  // printf("me = %d, step %d after totke!\n", universe->me, update->ntimestep);
+      compute_p_cv();
+      press_v_step();
+    }
+      /*
+      if(pstat_flag) 
+      {
+      }
+      */
+  // printf("me = %d, step %d before b_step 1!\n", universe->me, update->ntimestep);
+      b_step();
+  // printf("me = %d, step %d after b_step 1!\n", universe->me, update->ntimestep);
+      // if(removecomflag) remove_com_motion();
+          if(method==NMPIMD)
+    {
+      inter_replica_comm(x);
+    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
+    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
+      // nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
+    }
+      qc_step();
+      a_step();
+      qc_step();
+      a_step();
+  // printf("me = %d, step %d after 2 a_step's!\n", universe->me, update->ntimestep);
+    }
+    else if(integrator==baoab)
+    {
+      if(pstat_flag) 
+      {
+        compute_totke();
+        compute_p_cv();
+        press_v_step();
+      }
+      b_step();
+      // if(removecomflag) remove_com_motion();
+      if(method==NMPIMD)
+      {
+        inter_replica_comm(x);
+    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
+    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
+        // nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
+      }
+      qc_step();
+      a_step();
+      if(tstat_flag)
+      {
+        o_step();
+        // if(removecomflag) remove_com_motion();
+        if(pstat_flag) press_o_step();
+      }
+      qc_step();
+      a_step();      
+    }
+    else
+    {
+      error->universe_all(FLERR,"Unknown integrator parameter for fix pimd");
+    }
+    collect_xc();
+    compute_spring_energy();
+ 
+     if(method==NMPIMD)
+    {
+      inter_replica_comm(x);
+    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_xp2x[universe->iworld]);
+    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
+      // nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
+    }
+
+
+    if(mapflag){
+      for(int i=0; i<nlocal; i++)
+      {
+        domain->unmap_inv(x[i], image[i]);
+      }
+    }
+  // printf("step = %d\ncell = %.16e %.16e %.16e\nvol = %.16e\n", update->ntimestep, domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
+  // printf("me = %d, step %d initial_integrate ends!\n", universe->me, update->ntimestep);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::final_integrate()
+{
+    if(pstat_flag) 
+    {
+      compute_totke();
+      compute_p_cv();
+      press_v_step();
+    }
+   b_step();
+    // if(removecomflag) remove_com_motion();
+    if(integrator==obabo)
+    {
+      if(tstat_flag)
+      {
+        o_step();
+        // if(removecomflag) remove_com_motion();
+        if(pstat_flag) press_o_step();
+      }
+    }
+    else if(integrator==baoab)
+    {
+    
+    }
+    else
+    {
+      error->universe_all(FLERR,"Unknown integrator parameter for fix pimd");
+    }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::post_force(int /*flag*/)
+{
+  // printf("step = %d\ncell = %.16e %.16e %.16e\nvol = %.16e\n", update->ntimestep, domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
+  if(atom->nmax > maxunwrap) reallocate_x_unwrap();
+  if(atom->nmax > maxxc) reallocate_xc();
+  // printf("me = %d, step %d post_force starts!\n", universe->me, update->ntimestep);
+  int nlocal = atom->nlocal;
+  double **x = atom->x;
+  double **f = atom->f;
+  imageint *image = atom->image;
+  tagint *tag = atom->tag;
+  for(int i=0; i<nlocal; i++)
+  {
+    x_unwrap[i][0] = x[i][0];
+    x_unwrap[i][1] = x[i][1];
+    x_unwrap[i][2] = x[i][2];
+  }
+  if(mapflag){
+    for(int i=0; i<nlocal; i++)
+    {
+      domain->unmap(x_unwrap[i], image[i]);
+    }
+  }
+  for(int i=0; i<nlocal; i++)
+  {
+    xc[i][0] = xcall[3*(tag[i]-1)+0];
+    xc[i][1] = xcall[3*(tag[i]-1)+1];
+    xc[i][2] = xcall[3*(tag[i]-1)+2];
+  }
+      int idx = atom->map(1);
+      // printf("in post_force, x_unwrap: %.6f %.6f %.6f xcall: %.6f %.6f %.6f xc: %.6f %.6f %.6f\n", x_unwrap[idx][0], x_unwrap[idx][1], x_unwrap[idx][2], xcall[0], xcall[1], xcall[2], xc[idx][0], xc[idx][1], xc[idx][2]);
+  // MPI_Barrier(universe->uworld);
+  // update_x_unwrap();
+  // MPI_Barrier(universe->uworld);
+  // compute_xc();
+  // MPI_Barrier(universe->uworld);
+  // if(mapflag)
+  // {
+    // for(int i=0; i<nlocal; i++)
+    // {
+      // domain->unmap_inv(x[i], image[i]);
+    // }
+  // }
+  compute_vir();
+  compute_vir_();
+  //  compute_t_prim();
+  //  compute_t_vir();
+  compute_pote();
+   if(method==NMPIMD)
+  {
+    inter_replica_comm(f);
+    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, f, M_x2xp[universe->iworld]);
+    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, f, M_x2xp[universe->iworld]);
+    // nmpimd_transform(bufbeads, f, M_x2xp[universe->iworld]);
+  }
+   c_pe->addstep(update->ntimestep+1); 
+   c_press->addstep(update->ntimestep+1); 
+  // printf("me = %d, step %d post_force ends!\n", universe->me, update->ntimestep);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::end_of_step()
+{
+  compute_totke();
+  // inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
+  // compute_p_prim();
+  compute_p_cv();
+  compute_tote();
+  if(pstat_flag) compute_totenthalpy();
+
+  if(update->ntimestep % 10000 == 0)
+  {
+  if(universe->me==0) printf("This is the end of step %ld.\n", update->ntimestep);
+  }
+  // if(universe->me==0) printf("me = %d This is the end of step %ld.\n", universe->me, update->ntimestep);
+  // printf("me = %d This is the end of step %ld.\n\n", universe->me, update->ntimestep);
+}
+
+void FixPIMDLangevin::collect_xc()
+{
+  int nlocal = atom->nlocal;
+  double **x = atom->x;
+  tagint *tag = atom->tag;
+  if(ireplica == 0)
+  {
+    if(cmode == SINGLE_PROC)
+    {
+      for(int i=0; i<nlocal; i++)
+      {
+        xcall[3*i+0] = xcall[3*i+1] = xcall[3*i+2] = 0.0;
+      }
+    }
+    else if(cmode == MULTI_PROC)
+    {
+      for(int i=0; i<ntotal; i++)
+      {
+        xcall[3*i+0] = xcall[3*i+1] = xcall[3*i+2] = 0.0;
+      }
+    }
+
+    for(int i=0;i<nlocal; i++)
+    {
+      xcall[3*(tag[i]-1)+0] = x[i][0] / sqrt(np);
+      xcall[3*(tag[i]-1)+1] = x[i][1] / sqrt(np);
+      xcall[3*(tag[i]-1)+2] = x[i][2] / sqrt(np);
+    }
+    int idx = atom->map(1);
+    // printf("in init_int, x: %.6f %.6f %.6f xcall: %.6f %.6f %.6f\n", x[idx][0], x[idx][1], x[idx][2], xcall[0], xcall[1], xcall[2]);
+
+    if(cmode == MULTI_PROC)
+    {
+      // printf("trying to add\n");
+      // MPI_Reduce(MPI_IN_PLACE, xcall, ntotal*3, MPI_DOUBLE, MPI_SUM, 0, world);
+      MPI_Allreduce(MPI_IN_PLACE, xcall, ntotal*3, MPI_DOUBLE, MPI_SUM, world);
+      // printf("added\n");
+    }
+  }
+  MPI_Bcast(xcall, ntotal*3, MPI_DOUBLE, 0, universe->uworld);
+}
+
+/* ---------------------------------------------------------------------- */
+/*
+void FixPIMDLangevin::update_x_unwrap()
+{
+  // MPI_Barrier(universe->uworld);
+  // printf("me = %d, starting update_xu\n", universe->me);
+  int nlocal = atom->nlocal;
+  double **x = atom->x;
+  // delete x_unwrap;
+  // memory->sfree(x_unwrap);
+  // printf("me = %d, before deleting xu\n", universe->me);
+  delete [] x_unwrap;
+  x_unwrap = nullptr;
+  x_unwrap = (double*) memory->srealloc(x_unwrap, sizeof(double)*(nlocal+200)*3, "FixDPPimd::x_unwrap");
+  // printf("me = %d, before newing xu\n", universe->me);
+  // x_unwrap = new double[nlocal*3];
+  // printf("me = %d, doing xu\n", universe->me);
+  for(int i=0; i<nlocal; i++)
+  { 
+    for(int j=0; j<3; j++)
+    {
+      x_unwrap[3*i+j] = x[i][j];
+    }
+  }
+  // printf("me = %d, ending update_xu\n", universe->me);
+  // MPI_Barrier(universe->uworld);
+}
+*/
+/* ---------------------------------------------------------------------- */
+/*
+void FixPIMDLangevin::compute_xc()
+{
+  int natoms = atom->natoms;
+  MPI_Barrier(universe->uworld);
+  comm_exec(atom->x);
+  MPI_Barrier(universe->uworld);
+  int nlocal = atom->nlocal;
+  delete [] xc;
+  xc = nullptr;
+  xc = (double*) memory->srealloc(xc, sizeof(double) * nlocal * 3, "FixDPPimd:xc");
+  for(int i=0; i<nlocal; i++)
+  {
+    xc[3*i] = xc[3*i+1] = xc[3*i+2] = 0.0;
+    for(int j=0; j<np; j++)
+    {
+      xc[3*i] += buf_beads[j][3*i+0];
+      xc[3*i+1] += buf_beads[j][3*i+1];
+      xc[3*i+2] += buf_beads[j][3*i+2];
+    }
+    xc[3*i] /= np;
+    xc[3*i+1] /= np;
+    xc[3*i+2] /= np;
+  } 
+}
+*/
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::b_step()
+{
+
+  int n = atom->nlocal;
+  int *type = atom->type;
+  double **v = atom->v;
+  double **f = atom->f;
+
+  for(int i=0; i<n; i++)
+  {
+    double dtfm = dtf / mass[type[i]];
+    v[i][0] += dtfm * f[i][0];
+    v[i][1] += dtfm * f[i][1];
+    v[i][2] += dtfm * f[i][2];
+  }
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::qc_step(){
+  int nlocal = atom->nlocal;
+  double **x = atom->x;
+  double **v = atom->v;
+  tagint *tag = atom->tag;
+  double oldlo, oldhi;
+  if(!pstat_flag) {
+    if(universe->iworld == 0)
+    {
+      for(int i=0; i<nlocal; i++)
+      {
+        x[i][0] += dtv * v[i][0];
+        x[i][1] += dtv * v[i][1];
+        x[i][2] += dtv * v[i][2];
+      }
+    }
+  }
+  else{
+  // printf("step = %d start qc_step\ncell = %.16e %.16e %.16e\nvol = %.16e\n", update->ntimestep, domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
+    if(universe->iworld == 0)
+    {
+      double expp[3], expq[3];
+      // printf("pstyle = %d vw[0] = %.8e\n", pstyle, vw[0]);
+      if(pstyle == ISO) {vw[1] = vw[0]; vw[2] = vw[0];}
+      for(int j=0; j<3; j++)
+      {
+        expq[j] = exp(dtv * vw[j]);
+        expp[j] = exp(-dtv * vw[j]);
+      }
+      if(barostat == BZP)
+      {
+        for(int i=0; i<nlocal; i++)
+        {
+          for(int j=0; j<3; j++)
+          {
+            x[i][j] = expq[j] * x[i][j] + (expq[j] - expp[j]) / 2. / vw[j] * v[i][j];
+            v[i][j] = expp[j] * v[i][j];
+          } 
+        }
+        oldlo = domain->boxlo[0];
+        oldhi = domain->boxhi[0];
+      
+        domain->boxlo[0] = (oldlo-fixedpoint[0])*expq[0] + fixedpoint[0];
+        domain->boxhi[0] = (oldhi-fixedpoint[0])*expq[0] + fixedpoint[0];
+
+        oldlo = domain->boxlo[1];
+        oldhi = domain->boxhi[1];
+        domain->boxlo[1] = (oldlo-fixedpoint[1])*expq[1] + fixedpoint[1];
+        domain->boxhi[1] = (oldhi-fixedpoint[1])*expq[1] + fixedpoint[1];
+  
+        oldlo = domain->boxlo[2];
+        oldhi = domain->boxhi[2];
+        domain->boxlo[2] = (oldlo-fixedpoint[2])*expq[2] + fixedpoint[2];
+        domain->boxhi[2] = (oldhi-fixedpoint[2])*expq[2] + fixedpoint[2];
+      }
+    }    
+    MPI_Barrier(universe->uworld);
+    MPI_Bcast(&domain->boxlo[0], 3, MPI_DOUBLE, 0, universe->uworld);
+    MPI_Bcast(&domain->boxhi[0], 3, MPI_DOUBLE, 0, universe->uworld);
+    domain->set_global_box();
+    domain->set_local_box();
+  }
+  volume = domain->xprd * domain->yprd * domain->zprd;
+  // printf("step = %d end qc_step\ncell = %.16e %.16e %.16e\nvol = %.16e\n", update->ntimestep, domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::a_step(){
+  int n = atom->nlocal;
+  double **x = atom->x;
+  double **v = atom->v;
+  double x0, x1, x2, v0, v1, v2; // three components of x[i] and v[i]
+
+  if(universe->iworld != 0)
+  {
+      // printf("iworld = %d c = %.4e s = %.4e w = %.4e\n", universe->iworld, Lan_c[universe->iworld], Lan_s[universe->iworld], _omega_k[universe->iworld]);
+    for(int i=0; i<n; i++)
+    {
+      x0 = x[i][0]; 
+      x1 = x[i][1]; 
+      x2 = x[i][2];
+      v0 = v[i][0]; v1 = v[i][1]; v2 = v[i][2];
+      x[i][0] = Lan_c[universe->iworld] * x0 + 1./_omega_k[universe->iworld] * Lan_s[universe->iworld] * v0;
+      x[i][1] = Lan_c[universe->iworld] * x1 + 1./_omega_k[universe->iworld] * Lan_s[universe->iworld] * v1;
+      x[i][2] = Lan_c[universe->iworld] * x2 + 1./_omega_k[universe->iworld] * Lan_s[universe->iworld] * v2;
+      v[i][0] = -1.*_omega_k[universe->iworld] * Lan_s[universe->iworld] * x0 + Lan_c[universe->iworld] * v0;
+      v[i][1] = -1.*_omega_k[universe->iworld] * Lan_s[universe->iworld] * x1 + Lan_c[universe->iworld] * v1;
+      v[i][2] = -1.*_omega_k[universe->iworld] * Lan_s[universe->iworld] * x2 + Lan_c[universe->iworld] * v2;
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+/*
+void FixPIMDLangevin::remove_com_motion(){
+  if(universe->iworld == 0)
+  {
+  // double **x = atom->x;
+    double **v = atom->v;
+  int *mask = atom->mask;
+    int nlocal = atom->nlocal;
+    if (dynamic)  masstotal = group->mass(igroup);
+    double vcm[3];
+    group->vcm(igroup,masstotal,vcm);    
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit) {
+        v[i][0] -= vcm[0];
+        v[i][1] -= vcm[1];
+        v[i][2] -= vcm[2];
+      }
+    }
+  }
+}
+*/
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::baro_init()
+{
+  vw[0] = vw[1] = vw[2] = vw[3] = vw[4] = vw[5] = 0.0;
+  if(pstyle == ISO) {W = 3 * (atom->natoms) * tau_p * tau_p * np * kBT;} // consistent with the definition in i-Pi
+  // printf("tau_p = %.6e np = %.6e kBT = %.6e W = %.6e\n", tau_p, np, kBT, W);}
+  else if(pstyle == ANISO) {W = atom->natoms * tau_p * tau_p * np * kBT;}
+  Vcoeff = 1.0;
+  std::string out = fmt::format("\nInitializing PIMD {:s} barostat...\n", Barostats[barostat]);
+  out += fmt::format("The barostat mass is W = {:.16e}\n", W);
+  utils::logmesg(lmp, out);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::press_v_step()
+{
+  int nlocal = atom->nlocal;
+  double **f = atom->f;
+  double **v = atom->v;
+  int *type = atom->type; 
+  volume = domain->xprd * domain->yprd * domain->zprd;
+
+  if(pstyle == ISO)
+  {
+    if(barostat == BZP)
+    {
+      // printf("me = %d step = %d start press_v_step, baro.p = %.30e p_cv = %.30e\n", universe->me, update->ntimestep, W*vw[0], np*p_cv);
+      vw[0] += dtv * 3 * (volume * np * (p_cv - Pext) / force->nktv2p + Vcoeff / beta_np) / W;
+      // printf("me = %d step = %d add p-Pext, baro.p = %.30e\n", universe->me, update->ntimestep, W*vw[0]);
+      if(universe->iworld==0)
+      {
+        double dvw_proc = 0.0, dvw = 0.0;
+        for(int i = 0; i < nlocal; i++)
+        {
+          for(int j = 0; j < 3; j++)
+          {
+            dvw_proc += dtv2 * f[i][j] * v[i][j] / W + dtv3 * f[i][j] * f[i][j] / mass[type[i]] / W;
+          }
+        }
+        MPI_Allreduce(&dvw_proc, &dvw, 1, MPI_DOUBLE, MPI_SUM, world);
+        vw[0] += dvw;
+      }
+      MPI_Barrier(universe->uworld);
+      MPI_Bcast(&vw[0], 1, MPI_DOUBLE, 0, universe->uworld);
+      // printf("me = %d step = %d end press_v_step, baro.p = %.30e\n\n", universe->me, update->ntimestep, W*vw[0]);
+    }
+    else if(barostat == MTTK)
+    {
+        mtk_term1 = 2. / atom->natoms * totke / 3;
+        f_omega = (volume * np * (p_md - Pext) + mtk_term1) / W;
+        vw[0] += 0.5 * dtv * f_omega;
+    }
+  }
+  else if(pstyle == ANISO)
+  {
+    compute_stress_tensor();
+    for(int ii=0; ii<3; ii++)
+    {
+      vw[ii] += dtv * (volume * np * (stress_tensor[ii] - Pext) / force->nktv2p + Vcoeff / beta_np) / W;
+      if(universe->iworld==0)
+      {
+        double dvw_proc = 0.0, dvw = 0.0;
+        for(int i = 0; i < nlocal; i++)
+        {
+          dvw_proc += dtv2 * f[i][ii] * v[i][ii] / W + dtv3 * f[i][ii] * f[i][ii] / mass[type[i]] / W;
+        }
+        MPI_Allreduce(&dvw_proc, &dvw, 1, MPI_DOUBLE, MPI_SUM, world);
+        vw[ii] += dvw;
+      }
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::press_o_step()
+{
+  if(pstyle==ISO)
+  {
+    if(universe->me==0)
+    {
+      r1 = random->gaussian();
+      vw[0] = c1 * vw[0] + c2 * sqrt(1. / W / beta_np) * r1;
+    }
+    MPI_Barrier(universe->uworld);
+    MPI_Bcast(&vw[0], 1, MPI_DOUBLE, 0, universe->uworld);
+  }
+  else if(pstyle==ANISO)
+  {
+    if(universe->me==0)
+    {
+      r1 = random->gaussian();
+      r2 = random->gaussian();
+      r3 = random->gaussian();
+      vw[0] = c1 * vw[0] + c2 * sqrt(1. / W / beta_np) * r1;
+      vw[1] = c1 * vw[1] + c2 * sqrt(1. / W / beta_np) * r2;
+      vw[2] = c1 * vw[2] + c2 * sqrt(1. / W / beta_np) * r3;
+    }
+    MPI_Barrier(universe->uworld);
+    MPI_Bcast(&vw, 3, MPI_DOUBLE, 0, universe->uworld);    
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::Langevin_init()
+{
+  // printf("in Langevin_init\n");
+  double beta = 1.0 / kBT;
+  _omega_np = np / beta / hbar;
+  double _omega_np_dt_half = _omega_np * update->dt * 0.5;
+  // printf("omega_np = %.4e wdt = %.4e\n", _omega_np, _omega_np_dt_half);
+
+  _omega_k = new double[np];
+  Lan_c = new double[np];
+  Lan_s = new double[np];
+  if(fmmode==physical){
+    for (int i=0; i<np; i++)
+    {
+      _omega_k[i] = _omega_np * sqrt(lam[i]); 
+      Lan_c[i] = cos(sqrt(lam[i])*_omega_np_dt_half);
+      Lan_s[i] = sin(sqrt(lam[i])*_omega_np_dt_half);
+      // printf("lam = %.4e s = %.4e c = %.4e w = %.4e\n", lam[i], Lan_s[i], Lan_c[i], _omega_k[i]);
+    }
+  }
+  else if(fmmode==normal){
+    for (int i=0; i<np; i++)
+    {
+      _omega_k[i] = _omega_np; 
+      Lan_c[i] = cos(_omega_np_dt_half);
+      Lan_s[i] = sin(_omega_np_dt_half);
+    }
+  }
+  if(tau > 0) gamma = 1.0 / tau;
+  else gamma = np / beta / hbar;
+  
+  if(integrator==obabo) c1 = exp(-gamma * 0.5 * update->dt); // tau is the damping time of the centroid mode.
+  else if(integrator==baoab) c1 = exp(-gamma * update->dt); 
+  else error->universe_all(FLERR, "Unknown integrator parameter for fix pimd. Only obabo and baoab integrators is supported!");
+
+  c2 = sqrt(1.0 - c1 * c1); // note that c1 and c2 here only works for the centroid mode.
+
+  if( thermostat == PILE_L )
+  {
+    std::string out = "\nInitializing PI Langevin equation thermostat...\n";
+    out += "Bead ID    |    omega    |    tau    |    c1    |    c2\n"; 
+    tau_k = new double[np];
+    c1_k = new double[np];
+    c2_k = new double[np];
+    tau_k[0] = tau; c1_k[0] = c1; c2_k[0] = c2;
+    for(int i=1; i<np; i++)
+    {
+      tau_k[i] = 0.5 / pilescale / _omega_k[i];
+      if(integrator==obabo) c1_k[i] = exp(-0.5 * update->dt / tau_k[i]);
+      else if(integrator==baoab) c1_k[i] = exp(-1.0 * update->dt / tau_k[i]);
+      else error->universe_all(FLERR, "Unknown integrator parameter for fix pimd. Only obabo and baoab integrators is supported!");
+      c2_k[i] = sqrt(1.0 - c1_k[i] * c1_k[i]);
+    }
+    for(int i=0; i<np; i++)
+    {
+      out += fmt::format("    {:d}     {:.8e} {:.8e} {:.8e} {:.8e}\n", i, _omega_k[i], tau_k[i], c1_k[i], c2_k[i]);
+    }
+    if(thermostat == PILE_L) out += "PILE_L thermostat successfully initialized!\n";
+    out += "\n";
+    utils::logmesg(lmp, out);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::o_step()
+{
+  int nlocal = atom->nlocal;
+  int *type = atom->type;
+  double beta_np = 1.0 / force->boltz / Lan_temp / np * force->mvv2e;
+  if(thermostat == PILE_L)
+  {
+    for(int i=0; i<nlocal; i++)
+    {
+      r1 = random->gaussian();
+      r2 = random->gaussian();
+      r3 = random->gaussian();
+      atom->v[i][0] = c1_k[universe->iworld] * atom->v[i][0] + c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r1; 
+      atom->v[i][1] = c1_k[universe->iworld] * atom->v[i][1] + c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r2;
+      atom->v[i][2] = c1_k[universe->iworld] * atom->v[i][2] + c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r3;
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   Normal Mode PIMD
+------------------------------------------------------------------------- */
+
+void FixPIMDLangevin::nmpimd_init()
+{
+    memory->create(M_x2xp, np, np, "fix_feynman:M_x2xp");
+    memory->create(M_xp2x, np, np, "fix_feynman:M_xp2x");
+
+    lam = (double*) memory->smalloc(sizeof(double)*np, "FixPIMDLangevin::lam");
+
+    // Set up  eigenvalues
+    for(int i=0; i<np; i++){
+      double sin_tmp = sin(i * MY_PI / np);
+      lam[i] = 4 * sin_tmp * sin_tmp;
+    }
+
+    // Set up eigenvectors for degenerated modes
+    for(int j=0; j<np; j++){
+      for(int i=1; i<int(np/2) + 1; i++) 
+      {
+        M_x2xp[i][j] =   sqrt(2.0) * cos ( 2.0 * MY_PI * double(i) * double(j) / double(np)) / sqrt(np);
+      }
+      for(int i=int(np/2)+1; i<np; i++)
+      {
+        M_x2xp[i][j] =   sqrt(2.0) * sin ( 2.0 * MY_PI * double(i) * double(j) / double(np)) / sqrt(np);
+      }
+    }
+
+    // Set up eigenvectors for non-degenerated modes
+    for(int i=0; i<np; i++)
+    {
+      M_x2xp[0][i] = 1.0 / sqrt(np);
+      if(np%2==0) M_x2xp[np/2][i] = 1.0 / sqrt(np) * pow(-1.0, i);
+    }
+
+    // Set up Ut
+    for(int i=0; i<np; i++)
+      for(int j=0; j<np; j++)
+      {
+        M_xp2x[i][j] = M_x2xp[j][i];
+      }
+
+    // Set up masses
+    int iworld = universe->iworld;
+    for(int i=1; i<=atom->ntypes; i++)
+    {
+      mass[i] = atom->mass[i];
+      if(iworld)
+      {
+        if(fmmode==physical) { mass[i] *= 1.0; }
+        else if(fmmode==normal) { mass[i] *= lam[iworld]; }
+        mass[i] *= fmass;
+      }
+    }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::nmpimd_transform(double **src, double **des, double *vector)
+{
+  if(cmode == SINGLE_PROC)
+  {
+    for(int i=0; i<ntotal; i++)
+    {
+      for(int d=0; d<3; d++)
+      {
+        bufsorted[i][d] = 0.0;
+        for(int j=0; j<nreplica; j++)
+        {
+          bufsorted[i][d] += src[j*ntotal+i][d] * vector[j];
+        }
+      }
+    }
+    for(int i=0; i<ntotal; i++)
+    {
+      tagint tagtmp = atom->tag[i];
+      for(int d=0; d<3; d++)
+      {
+        des[i][d] = bufsorted[tagtmp-1][d];
+      }
+    }
+  }
+  else if(cmode == MULTI_PROC)
+  {
+  int n = atom->nlocal;
+  int m = 0;
+
+  for (int i = 0; i < n; i++)
+    for (int d = 0; d < 3; d++) {
+      des[i][d] = 0.0;
+      for (int j = 0; j < np; j++) { des[i][d] += (src[j][m] * vector[j]); }
+      m++;
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   Comm operations
+------------------------------------------------------------------------- */
+
+void FixPIMDLangevin::comm_init()
+{
+  // if(me == 0){
+    if (sizeplan) {
+      delete [] plansend;
+      delete [] planrecv;
+    }
+  
+    sizeplan = np - 1;
+    plansend = new int[sizeplan];
+    planrecv = new int[sizeplan];
+    modeindex = new int[sizeplan];
+    for (int i = 0; i < sizeplan; i++) {
+      int isend, irecv;
+      isend = ireplica + i + 1;
+      if (isend >= nreplica) isend -= nreplica;
+      irecv = ireplica - (i + 1);
+      if (irecv < 0) irecv += nreplica;
+      plansend[i] = universe->root_proc[isend];
+      planrecv[i] = universe->root_proc[irecv];
+      modeindex[i] = irecv;
+    }
+  // }
+}
+
+/* ---------------------------------------------------------------------- */
+/*
+void FixPIMDLangevin::init_x_unwrap()
+{
+  maxunwrap = atom->nmax;
+  memory->destroy(x_unwrap);
+  memory->destroy(tag_init);
+  memory->destroy(image_init);
+  memory->destroy(x_unwrapsort);
+  memory->create(x_unwrap, maxunwrap, 3, "FixPIMDLangevin:x_unwrap");  
+  memory->create(tag_init, maxunwrap, "FixPIMDLangevin:tag_init");
+  memory->create(image_init, maxunwrap, "FixPIMDLangevin:image_init");
+  memory->create(x_unwrapsort, ntotal, 3, "FixPIMDLangevin:x_unwrapsort");
+}
+*/
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::reallocate_xc()
+{
+  maxxc = atom->nmax;
+  memory->destroy(xc);
+  memory->create(xc, maxxc, 3, "FixPIMDLangevin:xc");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::reallocate_x_unwrap()
+{
+  maxunwrap = atom->nmax;
+  memory->destroy(x_unwrap);
+  memory->create(x_unwrap, maxunwrap, 3, "FixPIMDLangevin:x_unwrap");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::reallocate()
+{
+  maxlocal = atom->nmax;
+  memory->destroy(bufsend);
+  memory->destroy(bufrecv);
+  memory->destroy(tagsend);
+  memory->destroy(tagrecv);
+  memory->destroy(bufbeads);
+  memory->create(bufsend, maxlocal, 3, "FixPIMDLangevin:bufsend");
+  memory->create(bufrecv, maxlocal, 3, "FixPIMDLangevin:bufrecv");
+  memory->create(tagsend, maxlocal, "FixPIMDLangevin:tagsend");
+  memory->create(tagrecv, maxlocal, "FixPIMDLangevin:tagrecv");
+  memory->create(bufbeads, nreplica, maxlocal*3, "FixPIMDLangevin:bufrecv");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::inter_replica_comm(double **ptr)
+{
+  MPI_Request requests[2];
+  MPI_Status statuses[2];
+  if (atom->nmax > maxlocal) reallocate();
+  int nlocal = atom->nlocal;
+  // printf("me = %d starting inter_comm, nlocal = %d ntotal = %d\n", universe->me, nlocal, ntotal);
+  tagint *tag = atom->tag;
+  int i, m;
+
+  // copy local values
+  for(i=0; i<nlocal; i++)
+  {
+    bufbeads[ireplica][3*i+0] = ptr[i][0];
+    bufbeads[ireplica][3*i+1] = ptr[i][1];
+    bufbeads[ireplica][3*i+2] = ptr[i][2];
+  }
+
+  // communicate values from the other beads
+  if(cmode == SINGLE_PROC)
+  {
+    m = 0;
+    for(i=0; i<nlocal; i++)
+    {
+      tagint tagtmp = atom->tag[i];
+      bufsorted[tagtmp-1][0] = ptr[i][0];
+      bufsorted[tagtmp-1][1] = ptr[i][1];
+      bufsorted[tagtmp-1][2] = ptr[i][2];
+      m++;
+    }
+    MPI_Allgather(&m, 1, MPI_INT, counts, 1, MPI_INT, universe->uworld);
+    for (i = 0; i < nreplica; i++) { counts[i] *= 3; }
+    displacements[0] = 0;
+    for (i = 0; i < nreplica-1; i++) { displacements[i+1] = displacements[i] + counts[i]; }
+    MPI_Allgatherv(bufsorted[0], 3*m, MPI_DOUBLE, bufsortedall[0], counts, displacements, MPI_DOUBLE, universe->uworld);
+    // printf("me = %d bufsortedall[0] = %.8f %.8f %.8f bufsortedall[ntotal] = %.8f %.8f %.8f\n", universe->iworld, bufsortedall[0][0], bufsortedall[0][1], bufsortedall[0][2], bufsortedall[ntotal][0], bufsortedall[ntotal][1], bufsortedall[ntotal][2]);
+    /*
+    m = 0;
+    for(i=0; i<nlocal; i++)
+    {
+      tagsend[m] = tag[i];
+      bufsend[m][0] = ptr[i][0];
+      bufsend[m][1] = ptr[i][1];
+      bufsend[m][2] = ptr[i][2];
+      m++;
+    }
+      // printf("me = %d nlocal = %d ntotal = %d m = %d bufsend finished sizeplan = %d\n", universe->me, nlocal, ntotal, m, sizeplan);
+    for(int iplan=0; iplan<sizeplan; iplan++){
+      MPI_Irecv(bufrecv[0], 3*ntotal, MPI_DOUBLE, planrecv[iplan], 0, universe->uworld, &requests[0]);
+      MPI_Irecv(tagrecv, ntotal, MPI_LMP_TAGINT, planrecv[iplan], 0, universe->uworld, &requests[1]);
+      // printf("me = %d iplan = %d irecv finished, plansend = %d, planrecv = %d, modeindex = %d\n", universe->me, iplan, plansend[iplan], planrecv[iplan], modeindex[iplan]);
+      // printf("bufsend[0]: %.4f %.4f %.4f\ntagsend[0]: %d\n", bufsend[0][0], bufsend[0][1], bufsend[0][2], tagsend[0]);
+      // printf("bufsend[255]: %.4f %.4f %.4f\ntagsend[255]: %d\n", bufsend[255][0], bufsend[255][1], bufsend[255][2], tagsend[255]);
+      MPI_Send(bufsend[0], 3*ntotal, MPI_DOUBLE, plansend[iplan], 0, universe->uworld);
+      MPI_Send(tagsend, ntotal, MPI_LMP_TAGINT, plansend[iplan], 0, universe->uworld);
+      // printf("me = %d MPI_Send done\n", universe->me);
+      MPI_Waitall(2, requests, statuses);
+      // printf("me = %d iplan = %d send recv finished\n", iplan, universe->me);
+      for(i=0; i<nlocal; i++){
+        m = atom->map(tagrecv[i]);
+        bufbeads[modeindex[iplan]][3*m+0] = bufrecv[i][0];
+        bufbeads[modeindex[iplan]][3*m+1] = bufrecv[i][1];
+        bufbeads[modeindex[iplan]][3*m+2] = bufrecv[i][2];
+      }
+    }
+      */
+  // printf("me = %d finishing inter_comm\n", universe->me);
+  }
+  else if(cmode == MULTI_PROC)
+  {
+    m = 0;
+    // printf("me = %d trying to copy bufsend\n", universe->me);
+    for(i=0; i<nlocal; i++)
+    {
+      tagsend[m] = tag[i];
+      bufsend[m][0] = ptr[i][0];
+      bufsend[m][1] = ptr[i][1];
+      bufsend[m][2] = ptr[i][2];
+      m++;
+    }
+    // printf("me = %d copied bufsend, m = %d\n", universe->me, m);
+    // if(me==0) {for(i=0; i<nprocs; i++) {printf("me = %d after copying bufsend counts[%d] = %d\n", universe->me, i, counts[i]);}}
+    // printf("me = %d")
+    MPI_Gather(&m, 1, MPI_INT, counts, 1, MPI_INT, 0, world);
+    // printf("me = %d counts gathered\n", universe->me);
+    // if(me==0) {for(i=0; i<nprocs; i++) {printf("me = %d counts[%d] = %d\n", universe->me, i, counts[i]);}}
+    displacements[0] = 0;
+    // printf("me = %d displacements[0] = %d\n", universe->me, displacements[0]);
+    for (i = 0; i < nprocs-1; i++) { displacements[i+1] = displacements[i] + counts[i]; }
+    // printf("me = %d displacements done\n", universe->me);
+    // if(me==0) {for(i=0; i<nprocs; i++) { printf("me = %d i=%d displacements=%d\n", universe->me, i, displacements[i]);}}
+    MPI_Gatherv(tagsend, m, MPI_LMP_TAGINT, tagsendall, counts, displacements, MPI_LMP_TAGINT, 0, world);
+    // printf("me = %d tags gathered\n", universe->me);
+    for (i = 0; i < nprocs; i++) { counts[i] *= 3; }
+    for (i = 0; i < nprocs-1; i++) { displacements[i+1] = displacements[i] + counts[i]; }
+    MPI_Gatherv(bufsend[0], 3*m, MPI_DOUBLE, bufsendall[0], counts, displacements, MPI_DOUBLE, 0, world);
+    // printf("me = %d bufsend gathered\n", universe->me);
+    // printf("me = %d, tagrecvall[0] = %d bufrecvall[0][0] = %.4f\n", universe->me, tagrecvall[0], bufrecvall[0][0]);
+
+    // printf("universe->me = %d comm->me = %d sizeplan = %d\n", universe->me, comm->me, sizeplan);
+    for(int iplan=0; iplan<sizeplan; iplan++)
+    {
+      if(me == 0){
+        MPI_Irecv(bufrecvall[0], 3*ntotal, MPI_DOUBLE, planrecv[iplan], 0, universe->uworld, &requests[0]);
+        MPI_Irecv(tagrecvall, ntotal, MPI_LMP_TAGINT, planrecv[iplan], 0, universe->uworld, &requests[1]);
+        MPI_Send(bufsendall[0], 3*ntotal, MPI_DOUBLE, plansend[iplan], 0, universe->uworld);
+        MPI_Send(tagsendall, ntotal, MPI_LMP_TAGINT, plansend[iplan], 0, universe->uworld);
+        MPI_Waitall(2,requests,statuses);
+      }
+      // else{
+        // printf("me = %d not sendrecceving\n", universe->me);
+      // }
+
+    // printf("me = %d sendrecv finished\n", universe->me);
+    // printf("me = %d to be bcasted: tag[0] = %d bufrecvall[0][0] = %.4f\n", universe->me, tagrecvall[0], bufrecvall[0][0]);
+      MPI_Bcast(tagrecvall, ntotal, MPI_LMP_TAGINT, 0, world);
+      MPI_Bcast(bufrecvall[0], 3*ntotal, MPI_DOUBLE, 0, world);
+    // printf("me = %d broadcasted\n", universe->me);
+      for(i=0; i<ntotal; i++)
+      {
+        m = atom->map(tagrecvall[i]);
+        if (m < 0 || m >= nlocal) continue;
+        bufbeads[modeindex[iplan]][3*m+0] = bufrecvall[i][0];
+        bufbeads[modeindex[iplan]][3*m+1] = bufrecvall[i][1];
+        bufbeads[modeindex[iplan]][3*m+2] = bufrecvall[i][2];
+      }
+    }
+    // printf("me = %d, tag[0] = %d bufrecvall[0][0] = %.4f bufbeads[0][0] = %.4f bufbeads[1][0] = %.4f bufbeads done\n", universe->me, tag[0], bufrecvall[0][0], bufbeads[0][0], bufbeads[1][0]);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::compute_vir_()
+{
+  int nlocal = atom->nlocal;
+  xf = vir_ = xcf = centroid_vir = 0.0;
+      int idx = atom->map(1);
+      // printf("in post_force, x_unwrap: %.6f %.6f %.6f xcall: %.6f %.6f %.6f\n", x_unwrap[idx][0], x_unwrap[idx][1], x_unwrap[idx][2], xcall[0], xcall[1], xcall[2]);
+  // printf("in compute_vir, xu = %.6f %.6f %.6f xc = %.6f %.6f %.6f\n", x_unwrap[idx][0], x_unwrap[idx][1], x_unwrap[idx][2], xc[idx][0], xc[idx][1], xc[idx][2]);
+  for(int i=0; i<nlocal; i++)
+  {
+    for(int j=0; j<3; j++)
+    {
+      xf += x_unwrap[i][j] * atom->f[i][j];
+      xcf += (x_unwrap[i][j] - xc[i][j]) * atom->f[i][j];
+    }
+    // int idx = atom->map(i+1);
+    // printf("me = %d step = %d tag = %d idx = %d xu = %.6f %.6f %.6f xc = %.6f %.6f %.6f f = %.6f %.6f %.6f\n", universe->me, update->ntimestep, i+1, idx, x_unwrap[idx][0], x_unwrap[idx][1], x_unwrap[idx][2], xc[idx][0], xc[idx][1], xc[idx][2], atom->f[idx][0], atom->f[idx][1], atom->f[idx][2]);
+  }
+  MPI_Allreduce(&xf, &vir_, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
+  MPI_Allreduce(&xcf, &centroid_vir, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
+  if(pstyle == ANISO){
+    for(int i=0; i<6; i++) c_vir_tensor[i] = 0.0;
+    for(int i=0; i<nlocal; i++){
+      c_vir_tensor[0] += (x_unwrap[i][0] - xc[i][0]) * atom->f[i][0];
+      c_vir_tensor[1] += (x_unwrap[i][1] - xc[i][1]) * atom->f[i][1];
+      c_vir_tensor[2] += (x_unwrap[i][2] - xc[i][2]) * atom->f[i][2];
+      c_vir_tensor[3] += (x_unwrap[i][0] - xc[i][0]) * atom->f[i][1];
+      c_vir_tensor[4] += (x_unwrap[i][0] - xc[i][0]) * atom->f[i][2];
+      c_vir_tensor[5] += (x_unwrap[i][1] - xc[i][1]) * atom->f[i][2];
+    }
+    MPI_Allreduce(MPI_IN_PLACE, &c_vir_tensor, 6, MPI_DOUBLE, MPI_SUM, universe->uworld);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::compute_vir()
+{
+  volume = domain->xprd * domain->yprd * domain->zprd;
+  c_press->compute_vector();
+  virial[0] = c_press->vector[0]*volume;
+  virial[1] = c_press->vector[1]*volume;
+  virial[2] = c_press->vector[2]*volume;
+  virial[3] = c_press->vector[3]*volume;
+  virial[4] = c_press->vector[4]*volume;
+  virial[5] = c_press->vector[5]*volume;
+  for(int i=0; i<6; i++) virial[i] /= universe->procs_per_world[universe->iworld];
+  double vir_bead=(virial[0]+virial[1]+virial[2]);
+  MPI_Allreduce(&vir_bead, &vir, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
+  MPI_Allreduce(MPI_IN_PLACE, &virial[0], 6, MPI_DOUBLE, MPI_SUM, universe->uworld);
+  // printf("me = %d step = %d vir = %.30e\n", universe->me, update->ntimestep, vir);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::compute_stress_tensor()
+{
+  int nlocal = atom->nlocal;
+  int *type = atom->type;
+  if(universe->iworld == 0){
+    inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
+    for(int i=0; i<6; i++) ke_tensor[i] = 0.0;
+    for(int i=0; i<nlocal; i++){
+      ke_tensor[0] += 0.5 * mass[type[i]] * atom->v[i][0] * atom->v[i][0] * force->mvv2e;
+      ke_tensor[1] += 0.5 * mass[type[i]] * atom->v[i][1] * atom->v[i][1] * force->mvv2e;
+      ke_tensor[2] += 0.5 * mass[type[i]] * atom->v[i][2] * atom->v[i][2] * force->mvv2e;
+      ke_tensor[3] += 0.5 * mass[type[i]] * atom->v[i][0] * atom->v[i][1] * force->mvv2e;
+      ke_tensor[4] += 0.5 * mass[type[i]] * atom->v[i][0] * atom->v[i][2] * force->mvv2e;
+      ke_tensor[5] += 0.5 * mass[type[i]] * atom->v[i][1] * atom->v[i][2] * force->mvv2e;
+    }
+    // MPI_Allreduce(&ke_tensor, &ke_tensor, 6, MPI_DOUBLE, MPI_SUM, world);
+    MPI_Allreduce(MPI_IN_PLACE, &ke_tensor, 6, MPI_DOUBLE, MPI_SUM, world);
+    for(int i=0; i<6; i++) 
+    {
+      stress_tensor[i] = inv_volume * ((2*ke_tensor[i] - c_vir_tensor[i]) * force->nktv2p + virial[i]) / np;
+      // printf("i = %d, c_vir = %.6f, virial = %.6f stress = %.6f\n", i, c_vir_tensor[i], virial[i], stress_tensor[i]);
+    }
+  }
+  MPI_Bcast(&stress_tensor, 6, MPI_DOUBLE, 0, universe->uworld);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::compute_totke()
+{
+  kine = 0.0;
+  totke = ke_bead = 0.0;
+  int nlocal = atom->nlocal;
+  int *type = atom->type;
+  for(int i=0; i<nlocal; i++)
+  {
+    for(int j=0; j<3; j++)
+    {
+      kine += 0.5 * mass[type[i]] * atom->v[i][j] * atom->v[i][j];
+    }
+  }
+  kine *= force->mvv2e;
+  // printf("me = %d, kine = %.6e\n", universe->me, kine);
+  MPI_Allreduce(&kine, &ke_bead, 1, MPI_DOUBLE, MPI_SUM, world);
+  // MPI_Allreduce(&kine, &totke, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
+  // totke *= force->mvv2e / np;
+
+  // c_press->compute_scalar();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::compute_spring_energy()
+{
+  spring_energy = 0.0;
+  total_spring_energy = se_bead = 0.0;
+
+  double **x = atom->x;
+  double* _mass = atom->mass;
+  int* type = atom->type;
+  int nlocal = atom->nlocal;
+  // printf("iworld = %d, fbond = %.4e lam = %.4e\n", universe->iworld, fbond, lam[universe->iworld]);
+
+  for(int i=0; i<nlocal; i++)
+  {
+    spring_energy += 0.5 * _mass[type[i]] * fbond * lam[universe->iworld] * (x[i][0]*x[i][0] + x[i][1]*x[i][1] + x[i][2]*x[i][2]); 
+  }
+  MPI_Allreduce(&spring_energy, &se_bead, 1, MPI_DOUBLE, MPI_SUM, world);
+  // MPI_Allreduce(&spring_energy, &total_spring_energy, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
+  // total_spring_energy /= np;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::compute_pote()
+{
+  pe_bead = 0.0;
+  pot_energy_partition = 0.0;
+  pote = 0.0;
+  c_pe->compute_scalar();
+  pe_bead = c_pe->scalar;
+  pot_energy_partition = pe_bead / universe->procs_per_world[universe->iworld];
+  // MPI_Allreduce(&pot_energy_partition, &pote, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
+  // pote /= np;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::compute_tote()
+{
+  tote = totke + pote + total_spring_energy;
+}
+
+/* ---------------------------------------------------------------------- */
+/*
+void FixPIMDLangevin::compute_t_prim()
+{
+  t_prim = 1.5 * atom->natoms * np * force->boltz * temp - total_spring_energy;
+}
+*/
+/* ---------------------------------------------------------------------- */
+/*
+void FixPIMDLangevin::compute_t_vir()
+{
+  t_vir = -0.5 / np * vir_;
+  t_cv = 1.5 * atom->natoms * force->boltz * temp - 0.5 / np * centroid_vir;
+}
+*/
+/* ---------------------------------------------------------------------- */
+/*
+void FixPIMDLangevin::compute_p_prim()
+{
+  p_prim = atom->natoms * np * force->boltz * temp * inv_volume - 1.0 / 1.5 * inv_volume * total_spring_energy;
+  p_prim *= force->nktv2p;
+}
+*/
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::compute_p_cv()
+{
+  inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
+  // p_md = 2. / 3 * inv_volume * ((totke - total_spring_energy) * force->nktv2p + 0.5 * vir / np) ;
+  // printf("inv_V = %.30e ke = %.30e cv = %.30e vir = %.30e\n", inv_volume, ke_bead, centroid_vir, vir);
+  if(universe->iworld == 0)
+  {
+    p_cv = 1. / 3.  * inv_volume  * ((2. * ke_bead  - 1. * centroid_vir) * force->nktv2p + 1. * vir) / np; 
+  }
+  MPI_Bcast(&p_cv, 1, MPI_DOUBLE, 0, universe->uworld);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::compute_totenthalpy()
+{
+  volume = domain->xprd * domain->yprd * domain->zprd;
+  if(barostat == BZP)  
+  {
+    if(pstyle == ISO)
+    {
+      totenthalpy = tote + 0.5*W*vw[0]*vw[0]/np + Pext * volume / force->nktv2p - Vcoeff * kBT * log(volume);
+    }
+    else if(pstyle == ANISO)
+    {
+      totenthalpy = tote + 0.5*W*vw[0]*vw[0]/np + 0.5*W*vw[1]*vw[1]/np + 0.5*W*vw[2]*vw[2]/np + Pext * volume / force->nktv2p - Vcoeff * kBT * log(volume);
+    }
+  }
+  else if(barostat == MTTK)  totenthalpy = tote + 1.5*W*vw[0]*vw[0]/np + Pext * (volume - vol0);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double FixPIMDLangevin::compute_vector(int n)
+{
+  if(n==0) { return ke_bead; }
+  if(n==1) { return se_bead; }
+  if(n==2) { return pe_bead; }
+  if(n==3) { return tote; }
+  // if(n==3) { return W*vw[0]; }
+  if(!pstat_flag)
+  {
+    if(n==4) { return t_prim; }
+    if(n==5) { return t_vir; }
+    if(n==6) { return t_cv; }
+  }
+  else if(pstat_flag)
+  {
+    if(pstyle == ISO)
+    {
+      if(barostat == BZP)
+      {
+        if(n==4) { return 0.5*W*vw[0]*vw[0]; }
+      }
+      else if(barostat == MTTK)
+      {
+        if(n==4) { return 1.5*W*vw[0]*vw[0]; }
+      }
+      if(n==5) { volume = domain->xprd * domain->yprd * domain->zprd; return np * Pext * volume / force->nktv2p; }
+      if(n==6) { volume = domain->xprd * domain->yprd * domain->zprd; return - Vcoeff * np * kBT * log(volume); }
+      if(n==7) { return totenthalpy; }
+      if(n==8) { return p_cv; }
+      if(n==9) { return total_spring_energy; }
+    }
+    else if(pstyle == ANISO)
+    {
+      
+    }
+  }
+  /*
+  
+  if(n==7) { return p_prim; }
+  if(n==8) { return p_md; }
+  if(n==9) { return p_cv; }
+  if(n==10) {return totenthalpy;
+  if(pstyle == ISO){
+    if(n==11) { return vw[0]; }
+    if(n==12) { 
+      if(barostat == BZP) {  return 0.5*W*vw[0]*vw[0]; }
+      else if(barostat == MTTK) {  return 1.5*W*vw[0]*vw[0]; }
+    }
+    if(n==13) { volume = domain->xprd * domain->yprd * domain->zprd; return np * Pext * volume / force->nktv2p; }
+    if(n==14) { volume = domain->xprd * domain->yprd * domain->zprd; 
+    // printf("Vcoeff = %.6e np = %d kBT = %.6e logV = %.6e\n", Vcoeff, np, kBT, log(volume));
+    return - Vcoeff * np * kBT * log(volume); }
+  }
+  else if(pstyle==ANISO){
+    if(n>10 && n<=13) return vw[n-11];
+    if(n==14) return 0.5*W*vw[0]*vw[0]+0.5*W*vw[1]*vw[1]+0.5*W*vw[2]*vw[2];
+    if(n>14 && n<21) return stress_tensor[n-15];
+    if(n==21) { volume = domain->xprd * domain->yprd * domain->zprd; return np * Pext * volume / force->nktv2p; }
+    if(n==22) { volume = domain->xprd * domain->yprd * domain->zprd; return - Vcoeff * np * kBT * log(volume); }
+  }
+  return 0.0;
+  */
+}
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
new file mode 100644
index 0000000000..02e78935aa
--- /dev/null
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -0,0 +1,198 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+// clang-format off
+FixStyle(pimd/langevin,FixPIMDLangevin);
+// clang-format on
+#else
+
+#ifndef FIX_PIMD_LANGEVIN_H
+#define FIX_PIMD_LANGEVIN_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixPIMDLangevin : public Fix {
+ public:
+  FixPIMDLangevin(class LAMMPS *, int, char **);
+  ~FixPIMDLangevin() override;
+
+  int setmask() override;
+
+  void init() override;
+  void setup(int) override;
+//   void post_neighbor() override;
+  void post_force(int) override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
+  void end_of_step() override;
+
+  double compute_vector(int) override;
+
+  /* System setting variables */
+  int method; // PIMD or NMPIMD or CMD
+  int fmmode; // physical or normal
+  int np; // number of beads
+  double inverse_np; // 1.0/np
+  double temp; // temperature
+  double planck, hbar; // Planck's constant
+  double lj_epsilon, lj_sigma, lj_mass; // LJ unit energy, length, and mass scales
+  double other_planck;
+  double kBT; // k_B * temp
+  double beta, beta_np; // beta = 1./kBT beta_np = 1./kBT/np
+  int thermostat; // NHC or PILE_L
+  int barostat; // BZP
+  int integrator; // obabo or baoab
+  int ensemble; // nve or nvt or nph or npt
+  int mapflag; // should be 1 if number of beads > 1
+  int removecomflag;
+  double masstotal;
+
+  // void remove_com_motion(); 
+
+  double fixedpoint[3];    // location of dilation fixed-point
+  /* ring-polymer model */
+
+  double omega_np, fbond, spring_energy, sp;
+
+  /* fictitious mass */
+
+  double fmass, *mass;
+
+  /* inter-partition communication */
+
+  MPI_Comm rootworld;
+  int me, nprocs, ireplica, nreplica, nprocs_universe;
+  int ntotal, maxlocal;
+
+  int cmode;
+  int sizeplan;
+  int *plansend, *planrecv;
+
+  tagint *tagsend, *tagrecv; 
+  double **bufsend, **bufrecv, **bufbeads;
+  double **bufsorted, **bufsortedall;
+  double **outsorted, **buftransall;
+
+  tagint *tagsendall, *tagrecvall;
+  double **bufsendall, **bufrecvall;
+
+  int *counts, *displacements;
+
+  void comm_init();
+  void inter_replica_comm(double **ptr);
+
+  /* normal-mode operations */
+
+  double *lam, **M_x2xp, **M_xp2x, **M_f2fp, **M_fp2f;
+  int *modeindex;
+
+  void reallocate();
+  void nmpimd_init();
+  void nmpimd_transform(double **src, double **des, double **mat);
+  void nmpimd_transform(double **, double **, double *);
+
+  /* Langevin integration */
+
+  double dtv, dtf, dtv2, dtv3;
+  double gamma, c1, c2, tau;
+  double *tau_k, *c1_k, *c2_k;
+  double pilescale=1.0;
+  double Lan_temp;
+  double r1, r2, r3;
+  double _omega_np, *_omega_k, *Lan_s, *Lan_c; // sin(omega_k*dt*0.5), cos(omega_k*dt*0.5)
+
+  class RanMars *random;
+  int seed=975481;
+  FILE *frand;
+
+  int tstat_flag; // tstat_flat = 1 if thermostat if used
+  void Langevin_init();
+  void b_step(); // integrate for dt/2 according to B part (v <- v + f * dt/2)
+  void a_step(); // integrate for dt/2 according to A part (non-centroid mode, harmonic force between replicas)
+  void qc_step(); // integrate for dt/2 for the centroid mode (x <- x + v * dt/2)
+  void o_step(); // integrate for dt according to O part (O-U process, for thermostating)
+  
+  /* Bussi-Zykova-Parrinello barostat */
+
+  double f_omega, mtk_term1;
+  int pstat_flag; // pstat_flag = 1 if barostat is used
+  int pstyle; // pstyle = ISO or ANISO (will support TRICLINIC in the future)
+  double W, tau_p, Pext, totenthalpy = 0.0, Vcoeff;
+  int p_flag[6];
+  double vw[6]; // barostat velocity
+  double ke_tensor[6]; // kinetic energy tensor
+  double c_vir_tensor[6]; // centroid-virial tensor
+  double stress_tensor[6]; // path integral centroid-virial stress tensor
+
+  void baro_init();
+  void press_v_step();
+  void press_o_step();
+
+  /* centroid-virial estimator computation */
+  double vol0 = 0.0;
+  double inv_volume = 0.0;
+  // double inv_volume = 0.0, vol_ = 0.0, vol0 = 0.0;
+  double volume = 0.0;
+  double **xc, *xcall;
+  int maxxc;
+  // int n_unwrap;
+  int maxunwrap;
+  // int maxunwrap, nlocal_init;
+//   tagint *tag_init, *tag_initall;
+//   imageint *image_init, *image_initall;
+  double **x_unwrap;
+//   double **x_unwrap, **x_unwrapsort;
+//   double **x_unwrapall;
+//   void init_x_unwrap();
+  void reallocate_x_unwrap();
+  void reallocate_xc();
+  void collect_xc();
+  // void compute_xc();
+  // void compute_fc();
+  double xf, vir, vir_, xcf, centroid_vir;
+  double t_vir, t_cv, p_prim, p_vir, p_cv, p_cv_, p_md;
+  // double vir_, xcf, vir2;
+
+  /* Computes */
+  double kine, pote, tote, totke;
+  double ke_bead, se_bead, pe_bead, pot_energy_partition;
+  double total_spring_energy;
+  double t_prim;
+  // double p_prim;
+  char *id_pe;
+  char *id_press;
+  class Compute *c_pe;
+  class Compute *c_press;
+
+  void compute_totke(); // 1: kinetic energy 
+  void compute_spring_energy(); // 2: spring elastic energy
+  void compute_pote(); // 3: potential energy
+  void compute_tote(); // 4: total energy: 1+2+3 for all the beads
+  // void compute_t_prim();  // 5: primitive kinetic energy estimator
+  // void compute_p_prim();  // primitive pressure estimator
+  void compute_stress_tensor();
+  // void compute_t_vir();  // centroid-virial kinetic energy estimator
+  void compute_p_cv();  // centroid-virial pressure estimator
+  // void compute_p_vir();  // centroid-virial pressure estimator
+  void compute_vir();
+  void compute_vir_();
+  void compute_totenthalpy();
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

From c351b63919f8646cb7943742e6cffed32aa52d79 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 24 Feb 2023 11:48:28 -0500
Subject: [PATCH 010/396] fix pimd/langevin put properties and functions below
 protected

---
 src/REPLICA/fix_pimd_langevin.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 02e78935aa..4f0390c700 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -41,6 +41,7 @@ class FixPIMDLangevin : public Fix {
 
   double compute_vector(int) override;
 
+ protected:
   /* System setting variables */
   int method; // PIMD or NMPIMD or CMD
   int fmmode; // physical or normal

From 3737b5f774b99ed5d8a34b10de6057817afbb875 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 25 Feb 2023 16:22:27 -0500
Subject: [PATCH 011/396] whitespace fixes and clang-format on the header

---
 src/REPLICA/fix_pimd_langevin.cpp | 90 +++++++++++++++----------------
 src/REPLICA/fix_pimd_langevin.h   | 86 ++++++++++++++---------------
 2 files changed, 86 insertions(+), 90 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 9ac8fc3b17..1b2e734922 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -146,7 +146,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
       fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (fmass < 0.0 || fmass > 1.0)
         error->universe_all(FLERR, "Invalid fmass value for fix pimd");
-    } 
+    }
 
     else if(strcmp(arg[i], "fmmode")==0)
     {
@@ -164,7 +164,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
     else if (strcmp(arg[i], "temp") == 0) {
       temp = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd");
-    } 
+    }
 
     else if (strcmp(arg[i], "lj") == 0) {
       lj_epsilon = utils::numeric(FLERR, arg[i+1], false, lmp);
@@ -178,7 +178,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
 
     else if(strcmp(arg[i], "thermostat")==0)
     {
-      if(strcmp(arg[i+1],"PILE_L")==0) 
+      if(strcmp(arg[i+1],"PILE_L")==0)
       {
         thermostat = PILE_L;
         seed = atoi(arg[i+2]);
@@ -190,7 +190,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
     {
       tau = atof(arg[i+1]);
     }
-  
+
     else if(strcmp(arg[i], "press")==0)
     {
       Pext = atof(arg[i+1]);
@@ -199,7 +199,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
 
     else if(strcmp(arg[i], "barostat")==0)
     {
-      if(strcmp(arg[i+1],"MTTK")==0) 
+      if(strcmp(arg[i+1],"MTTK")==0)
       {
         barostat = MTTK;
       }
@@ -292,7 +292,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
     Lan_temp = temp;
     random = new RanMars(lmp, seed + universe->me);
   }
-  
+
   me = comm->me;
   nprocs = comm->nprocs;
   if(nprocs == 1) cmode = SINGLE_PROC;
@@ -385,7 +385,7 @@ void FixPIMDLangevin::init()
   inverse_np = 1.0 / np;
 
   const double Boltzmann = force->boltz;
-  if (strcmp(update->unit_style,"lj") == 0) { 
+  if (strcmp(update->unit_style,"lj") == 0) {
     double planck_star = sqrt(lj_epsilon)*sqrt(atom->mass[0])*lj_sigma;
     planck = other_planck / planck_star;
   }
@@ -517,10 +517,10 @@ void FixPIMDLangevin::setup(int vflag)
   // compute_pote();
   // if(pstyle==ANISO) compute_stress_tensor();
   end_of_step();
-  c_pe->addstep(update->ntimestep+1); 
+  c_pe->addstep(update->ntimestep+1);
   c_press->addstep(update->ntimestep+1);
   // printf("setup ending: \ncell = %.16e %.16e %.16e\nvol = %.16e\n", domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
-  // printf("me = %d, setup finished\n", universe->me);   
+  // printf("me = %d, setup finished\n", universe->me);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -557,7 +557,7 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
       press_v_step();
     }
       /*
-      if(pstat_flag) 
+      if(pstat_flag)
       {
       }
       */
@@ -580,7 +580,7 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
     }
     else if(integrator==baoab)
     {
-      if(pstat_flag) 
+      if(pstat_flag)
       {
         compute_totke();
         compute_p_cv();
@@ -604,7 +604,7 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
         if(pstat_flag) press_o_step();
       }
       qc_step();
-      a_step();      
+      a_step();
     }
     else
     {
@@ -612,7 +612,7 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
     }
     collect_xc();
     compute_spring_energy();
- 
+
      if(method==NMPIMD)
     {
       inter_replica_comm(x);
@@ -636,7 +636,7 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
 
 void FixPIMDLangevin::final_integrate()
 {
-    if(pstat_flag) 
+    if(pstat_flag)
     {
       compute_totke();
       compute_p_cv();
@@ -655,7 +655,7 @@ void FixPIMDLangevin::final_integrate()
     }
     else if(integrator==baoab)
     {
-    
+
     }
     else
     {
@@ -720,8 +720,8 @@ void FixPIMDLangevin::post_force(int /*flag*/)
     else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, f, M_x2xp[universe->iworld]);
     // nmpimd_transform(bufbeads, f, M_x2xp[universe->iworld]);
   }
-   c_pe->addstep(update->ntimestep+1); 
-   c_press->addstep(update->ntimestep+1); 
+   c_pe->addstep(update->ntimestep+1);
+   c_press->addstep(update->ntimestep+1);
   // printf("me = %d, step %d post_force ends!\n", universe->me, update->ntimestep);
 }
 
@@ -804,7 +804,7 @@ void FixPIMDLangevin::update_x_unwrap()
   // x_unwrap = new double[nlocal*3];
   // printf("me = %d, doing xu\n", universe->me);
   for(int i=0; i<nlocal; i++)
-  { 
+  {
     for(int j=0; j<3; j++)
     {
       x_unwrap[3*i+j] = x[i][j];
@@ -838,7 +838,7 @@ void FixPIMDLangevin::compute_xc()
     xc[3*i] /= np;
     xc[3*i+1] /= np;
     xc[3*i+2] /= np;
-  } 
+  }
 }
 */
 /* ---------------------------------------------------------------------- */
@@ -900,11 +900,11 @@ void FixPIMDLangevin::qc_step(){
           {
             x[i][j] = expq[j] * x[i][j] + (expq[j] - expp[j]) / 2. / vw[j] * v[i][j];
             v[i][j] = expp[j] * v[i][j];
-          } 
+          }
         }
         oldlo = domain->boxlo[0];
         oldhi = domain->boxhi[0];
-      
+
         domain->boxlo[0] = (oldlo-fixedpoint[0])*expq[0] + fixedpoint[0];
         domain->boxhi[0] = (oldhi-fixedpoint[0])*expq[0] + fixedpoint[0];
 
@@ -912,13 +912,13 @@ void FixPIMDLangevin::qc_step(){
         oldhi = domain->boxhi[1];
         domain->boxlo[1] = (oldlo-fixedpoint[1])*expq[1] + fixedpoint[1];
         domain->boxhi[1] = (oldhi-fixedpoint[1])*expq[1] + fixedpoint[1];
-  
+
         oldlo = domain->boxlo[2];
         oldhi = domain->boxhi[2];
         domain->boxlo[2] = (oldlo-fixedpoint[2])*expq[2] + fixedpoint[2];
         domain->boxhi[2] = (oldhi-fixedpoint[2])*expq[2] + fixedpoint[2];
       }
-    }    
+    }
     MPI_Barrier(universe->uworld);
     MPI_Bcast(&domain->boxlo[0], 3, MPI_DOUBLE, 0, universe->uworld);
     MPI_Bcast(&domain->boxhi[0], 3, MPI_DOUBLE, 0, universe->uworld);
@@ -942,8 +942,8 @@ void FixPIMDLangevin::a_step(){
       // printf("iworld = %d c = %.4e s = %.4e w = %.4e\n", universe->iworld, Lan_c[universe->iworld], Lan_s[universe->iworld], _omega_k[universe->iworld]);
     for(int i=0; i<n; i++)
     {
-      x0 = x[i][0]; 
-      x1 = x[i][1]; 
+      x0 = x[i][0];
+      x1 = x[i][1];
       x2 = x[i][2];
       v0 = v[i][0]; v1 = v[i][1]; v2 = v[i][2];
       x[i][0] = Lan_c[universe->iworld] * x0 + 1./_omega_k[universe->iworld] * Lan_s[universe->iworld] * v0;
@@ -967,7 +967,7 @@ void FixPIMDLangevin::remove_com_motion(){
     int nlocal = atom->nlocal;
     if (dynamic)  masstotal = group->mass(igroup);
     double vcm[3];
-    group->vcm(igroup,masstotal,vcm);    
+    group->vcm(igroup,masstotal,vcm);
     for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
         v[i][0] -= vcm[0];
@@ -999,7 +999,7 @@ void FixPIMDLangevin::press_v_step()
   int nlocal = atom->nlocal;
   double **f = atom->f;
   double **v = atom->v;
-  int *type = atom->type; 
+  int *type = atom->type;
   volume = domain->xprd * domain->yprd * domain->zprd;
 
   if(pstyle == ISO)
@@ -1079,7 +1079,7 @@ void FixPIMDLangevin::press_o_step()
       vw[2] = c1 * vw[2] + c2 * sqrt(1. / W / beta_np) * r3;
     }
     MPI_Barrier(universe->uworld);
-    MPI_Bcast(&vw, 3, MPI_DOUBLE, 0, universe->uworld);    
+    MPI_Bcast(&vw, 3, MPI_DOUBLE, 0, universe->uworld);
   }
 }
 
@@ -1099,7 +1099,7 @@ void FixPIMDLangevin::Langevin_init()
   if(fmmode==physical){
     for (int i=0; i<np; i++)
     {
-      _omega_k[i] = _omega_np * sqrt(lam[i]); 
+      _omega_k[i] = _omega_np * sqrt(lam[i]);
       Lan_c[i] = cos(sqrt(lam[i])*_omega_np_dt_half);
       Lan_s[i] = sin(sqrt(lam[i])*_omega_np_dt_half);
       // printf("lam = %.4e s = %.4e c = %.4e w = %.4e\n", lam[i], Lan_s[i], Lan_c[i], _omega_k[i]);
@@ -1108,16 +1108,16 @@ void FixPIMDLangevin::Langevin_init()
   else if(fmmode==normal){
     for (int i=0; i<np; i++)
     {
-      _omega_k[i] = _omega_np; 
+      _omega_k[i] = _omega_np;
       Lan_c[i] = cos(_omega_np_dt_half);
       Lan_s[i] = sin(_omega_np_dt_half);
     }
   }
   if(tau > 0) gamma = 1.0 / tau;
   else gamma = np / beta / hbar;
-  
+
   if(integrator==obabo) c1 = exp(-gamma * 0.5 * update->dt); // tau is the damping time of the centroid mode.
-  else if(integrator==baoab) c1 = exp(-gamma * update->dt); 
+  else if(integrator==baoab) c1 = exp(-gamma * update->dt);
   else error->universe_all(FLERR, "Unknown integrator parameter for fix pimd. Only obabo and baoab integrators is supported!");
 
   c2 = sqrt(1.0 - c1 * c1); // note that c1 and c2 here only works for the centroid mode.
@@ -1125,7 +1125,7 @@ void FixPIMDLangevin::Langevin_init()
   if( thermostat == PILE_L )
   {
     std::string out = "\nInitializing PI Langevin equation thermostat...\n";
-    out += "Bead ID    |    omega    |    tau    |    c1    |    c2\n"; 
+    out += "Bead ID    |    omega    |    tau    |    c1    |    c2\n";
     tau_k = new double[np];
     c1_k = new double[np];
     c2_k = new double[np];
@@ -1162,7 +1162,7 @@ void FixPIMDLangevin::o_step()
       r1 = random->gaussian();
       r2 = random->gaussian();
       r3 = random->gaussian();
-      atom->v[i][0] = c1_k[universe->iworld] * atom->v[i][0] + c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r1; 
+      atom->v[i][0] = c1_k[universe->iworld] * atom->v[i][0] + c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r1;
       atom->v[i][1] = c1_k[universe->iworld] * atom->v[i][1] + c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r2;
       atom->v[i][2] = c1_k[universe->iworld] * atom->v[i][2] + c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r3;
     }
@@ -1188,7 +1188,7 @@ void FixPIMDLangevin::nmpimd_init()
 
     // Set up eigenvectors for degenerated modes
     for(int j=0; j<np; j++){
-      for(int i=1; i<int(np/2) + 1; i++) 
+      for(int i=1; i<int(np/2) + 1; i++)
       {
         M_x2xp[i][j] =   sqrt(2.0) * cos ( 2.0 * MY_PI * double(i) * double(j) / double(np)) / sqrt(np);
       }
@@ -1277,7 +1277,7 @@ void FixPIMDLangevin::comm_init()
       delete [] plansend;
       delete [] planrecv;
     }
-  
+
     sizeplan = np - 1;
     plansend = new int[sizeplan];
     planrecv = new int[sizeplan];
@@ -1304,7 +1304,7 @@ void FixPIMDLangevin::init_x_unwrap()
   memory->destroy(tag_init);
   memory->destroy(image_init);
   memory->destroy(x_unwrapsort);
-  memory->create(x_unwrap, maxunwrap, 3, "FixPIMDLangevin:x_unwrap");  
+  memory->create(x_unwrap, maxunwrap, 3, "FixPIMDLangevin:x_unwrap");
   memory->create(tag_init, maxunwrap, "FixPIMDLangevin:tag_init");
   memory->create(image_init, maxunwrap, "FixPIMDLangevin:image_init");
   memory->create(x_unwrapsort, ntotal, 3, "FixPIMDLangevin:x_unwrapsort");
@@ -1552,7 +1552,7 @@ void FixPIMDLangevin::compute_stress_tensor()
     }
     // MPI_Allreduce(&ke_tensor, &ke_tensor, 6, MPI_DOUBLE, MPI_SUM, world);
     MPI_Allreduce(MPI_IN_PLACE, &ke_tensor, 6, MPI_DOUBLE, MPI_SUM, world);
-    for(int i=0; i<6; i++) 
+    for(int i=0; i<6; i++)
     {
       stress_tensor[i] = inv_volume * ((2*ke_tensor[i] - c_vir_tensor[i]) * force->nktv2p + virial[i]) / np;
       // printf("i = %d, c_vir = %.6f, virial = %.6f stress = %.6f\n", i, c_vir_tensor[i], virial[i], stress_tensor[i]);
@@ -1600,7 +1600,7 @@ void FixPIMDLangevin::compute_spring_energy()
 
   for(int i=0; i<nlocal; i++)
   {
-    spring_energy += 0.5 * _mass[type[i]] * fbond * lam[universe->iworld] * (x[i][0]*x[i][0] + x[i][1]*x[i][1] + x[i][2]*x[i][2]); 
+    spring_energy += 0.5 * _mass[type[i]] * fbond * lam[universe->iworld] * (x[i][0]*x[i][0] + x[i][1]*x[i][1] + x[i][2]*x[i][2]);
   }
   MPI_Allreduce(&spring_energy, &se_bead, 1, MPI_DOUBLE, MPI_SUM, world);
   // MPI_Allreduce(&spring_energy, &total_spring_energy, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
@@ -1660,7 +1660,7 @@ void FixPIMDLangevin::compute_p_cv()
   // printf("inv_V = %.30e ke = %.30e cv = %.30e vir = %.30e\n", inv_volume, ke_bead, centroid_vir, vir);
   if(universe->iworld == 0)
   {
-    p_cv = 1. / 3.  * inv_volume  * ((2. * ke_bead  - 1. * centroid_vir) * force->nktv2p + 1. * vir) / np; 
+    p_cv = 1. / 3.  * inv_volume  * ((2. * ke_bead  - 1. * centroid_vir) * force->nktv2p + 1. * vir) / np;
   }
   MPI_Bcast(&p_cv, 1, MPI_DOUBLE, 0, universe->uworld);
 }
@@ -1670,7 +1670,7 @@ void FixPIMDLangevin::compute_p_cv()
 void FixPIMDLangevin::compute_totenthalpy()
 {
   volume = domain->xprd * domain->yprd * domain->zprd;
-  if(barostat == BZP)  
+  if(barostat == BZP)
   {
     if(pstyle == ISO)
     {
@@ -1719,23 +1719,23 @@ double FixPIMDLangevin::compute_vector(int n)
     }
     else if(pstyle == ANISO)
     {
-      
+
     }
   }
   /*
-  
+
   if(n==7) { return p_prim; }
   if(n==8) { return p_md; }
   if(n==9) { return p_cv; }
   if(n==10) {return totenthalpy;
   if(pstyle == ISO){
     if(n==11) { return vw[0]; }
-    if(n==12) { 
+    if(n==12) {
       if(barostat == BZP) {  return 0.5*W*vw[0]*vw[0]; }
       else if(barostat == MTTK) {  return 1.5*W*vw[0]*vw[0]; }
     }
     if(n==13) { volume = domain->xprd * domain->yprd * domain->zprd; return np * Pext * volume / force->nktv2p; }
-    if(n==14) { volume = domain->xprd * domain->yprd * domain->zprd; 
+    if(n==14) { volume = domain->xprd * domain->yprd * domain->zprd;
     // printf("Vcoeff = %.6e np = %d kBT = %.6e logV = %.6e\n", Vcoeff, np, kBT, log(volume));
     return - Vcoeff * np * kBT * log(volume); }
   }
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 4f0390c700..cf2d63b91c 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -33,7 +33,6 @@ class FixPIMDLangevin : public Fix {
 
   void init() override;
   void setup(int) override;
-//   void post_neighbor() override;
   void post_force(int) override;
   void initial_integrate(int) override;
   void final_integrate() override;
@@ -43,26 +42,24 @@ class FixPIMDLangevin : public Fix {
 
  protected:
   /* System setting variables */
-  int method; // PIMD or NMPIMD or CMD
-  int fmmode; // physical or normal
-  int np; // number of beads
-  double inverse_np; // 1.0/np
-  double temp; // temperature
-  double planck, hbar; // Planck's constant
-  double lj_epsilon, lj_sigma, lj_mass; // LJ unit energy, length, and mass scales
+  int method;                              // PIMD or NMPIMD or CMD
+  int fmmode;                              // physical or normal
+  int np;                                  // number of beads
+  double inverse_np;                       // 1.0/np
+  double temp;                             // temperature
+  double planck, hbar;                     // Planck's constant
+  double lj_epsilon, lj_sigma, lj_mass;    // LJ unit energy, length, and mass scales
   double other_planck;
-  double kBT; // k_B * temp
-  double beta, beta_np; // beta = 1./kBT beta_np = 1./kBT/np
-  int thermostat; // NHC or PILE_L
-  int barostat; // BZP
-  int integrator; // obabo or baoab
-  int ensemble; // nve or nvt or nph or npt
-  int mapflag; // should be 1 if number of beads > 1
+  double kBT;              // k_B * temp
+  double beta, beta_np;    // beta = 1./kBT beta_np = 1./kBT/np
+  int thermostat;          // NHC or PILE_L
+  int barostat;            // BZP
+  int integrator;          // obabo or baoab
+  int ensemble;            // nve or nvt or nph or npt
+  int mapflag;             // should be 1 if number of beads > 1
   int removecomflag;
   double masstotal;
 
-  // void remove_com_motion(); 
-
   double fixedpoint[3];    // location of dilation fixed-point
   /* ring-polymer model */
 
@@ -82,7 +79,7 @@ class FixPIMDLangevin : public Fix {
   int sizeplan;
   int *plansend, *planrecv;
 
-  tagint *tagsend, *tagrecv; 
+  tagint *tagsend, *tagrecv;
   double **bufsend, **bufrecv, **bufbeads;
   double **bufsorted, **bufsortedall;
   double **outsorted, **buftransall;
@@ -110,33 +107,34 @@ class FixPIMDLangevin : public Fix {
   double dtv, dtf, dtv2, dtv3;
   double gamma, c1, c2, tau;
   double *tau_k, *c1_k, *c2_k;
-  double pilescale=1.0;
+  double pilescale = 1.0;
   double Lan_temp;
   double r1, r2, r3;
-  double _omega_np, *_omega_k, *Lan_s, *Lan_c; // sin(omega_k*dt*0.5), cos(omega_k*dt*0.5)
+  double _omega_np, *_omega_k, *Lan_s, *Lan_c;    // sin(omega_k*dt*0.5), cos(omega_k*dt*0.5)
 
   class RanMars *random;
-  int seed=975481;
+  int seed = 975481;
   FILE *frand;
 
-  int tstat_flag; // tstat_flat = 1 if thermostat if used
+  int tstat_flag;    // tstat_flat = 1 if thermostat if used
   void Langevin_init();
-  void b_step(); // integrate for dt/2 according to B part (v <- v + f * dt/2)
-  void a_step(); // integrate for dt/2 according to A part (non-centroid mode, harmonic force between replicas)
-  void qc_step(); // integrate for dt/2 for the centroid mode (x <- x + v * dt/2)
-  void o_step(); // integrate for dt according to O part (O-U process, for thermostating)
-  
+  void b_step();    // integrate for dt/2 according to B part (v <- v + f * dt/2)
+  void
+  a_step();    // integrate for dt/2 according to A part (non-centroid mode, harmonic force between replicas)
+  void qc_step();    // integrate for dt/2 for the centroid mode (x <- x + v * dt/2)
+  void o_step();     // integrate for dt according to O part (O-U process, for thermostating)
+
   /* Bussi-Zykova-Parrinello barostat */
 
   double f_omega, mtk_term1;
-  int pstat_flag; // pstat_flag = 1 if barostat is used
-  int pstyle; // pstyle = ISO or ANISO (will support TRICLINIC in the future)
+  int pstat_flag;    // pstat_flag = 1 if barostat is used
+  int pstyle;        // pstyle = ISO or ANISO (will support TRICLINIC in the future)
   double W, tau_p, Pext, totenthalpy = 0.0, Vcoeff;
   int p_flag[6];
-  double vw[6]; // barostat velocity
-  double ke_tensor[6]; // kinetic energy tensor
-  double c_vir_tensor[6]; // centroid-virial tensor
-  double stress_tensor[6]; // path integral centroid-virial stress tensor
+  double vw[6];               // barostat velocity
+  double ke_tensor[6];        // kinetic energy tensor
+  double c_vir_tensor[6];     // centroid-virial tensor
+  double stress_tensor[6];    // path integral centroid-virial stress tensor
 
   void baro_init();
   void press_v_step();
@@ -152,12 +150,12 @@ class FixPIMDLangevin : public Fix {
   // int n_unwrap;
   int maxunwrap;
   // int maxunwrap, nlocal_init;
-//   tagint *tag_init, *tag_initall;
-//   imageint *image_init, *image_initall;
+  //   tagint *tag_init, *tag_initall;
+  //   imageint *image_init, *image_initall;
   double **x_unwrap;
-//   double **x_unwrap, **x_unwrapsort;
-//   double **x_unwrapall;
-//   void init_x_unwrap();
+  //   double **x_unwrap, **x_unwrapsort;
+  //   double **x_unwrapall;
+  //   void init_x_unwrap();
   void reallocate_x_unwrap();
   void reallocate_xc();
   void collect_xc();
@@ -178,22 +176,20 @@ class FixPIMDLangevin : public Fix {
   class Compute *c_pe;
   class Compute *c_press;
 
-  void compute_totke(); // 1: kinetic energy 
-  void compute_spring_energy(); // 2: spring elastic energy
-  void compute_pote(); // 3: potential energy
-  void compute_tote(); // 4: total energy: 1+2+3 for all the beads
+  void compute_totke();            // 1: kinetic energy
+  void compute_spring_energy();    // 2: spring elastic energy
+  void compute_pote();             // 3: potential energy
+  void compute_tote();             // 4: total energy: 1+2+3 for all the beads
   // void compute_t_prim();  // 5: primitive kinetic energy estimator
   // void compute_p_prim();  // primitive pressure estimator
   void compute_stress_tensor();
   // void compute_t_vir();  // centroid-virial kinetic energy estimator
-  void compute_p_cv();  // centroid-virial pressure estimator
+  void compute_p_cv();    // centroid-virial pressure estimator
   // void compute_p_vir();  // centroid-virial pressure estimator
   void compute_vir();
   void compute_vir_();
   void compute_totenthalpy();
 };
-
 }    // namespace LAMMPS_NS
-
 #endif
 #endif

From 0911565660831d554272900e6d140c5a3f46c170 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 25 Feb 2023 16:36:01 -0500
Subject: [PATCH 012/396] prepare for inclusion of fix pimd/langevin

---
 doc/src/Commands_fix.rst |  1 +
 doc/src/fix.rst          |  3 +-
 doc/src/fix_pimd.rst     | 70 ++++++++++++++++++++++------------------
 src/.gitignore           |  2 ++
 4 files changed, 44 insertions(+), 32 deletions(-)

diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst
index d275b33eba..9c5b0d4a0f 100644
--- a/doc/src/Commands_fix.rst
+++ b/doc/src/Commands_fix.rst
@@ -168,6 +168,7 @@ OPT.
    * :doc:`pafi <fix_pafi>`
    * :doc:`pair <fix_pair>`
    * :doc:`phonon <fix_phonon>`
+   * :doc:`pimd/langevin <fix_pimd>`
    * :doc:`pimd/nvt <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
diff --git a/doc/src/fix.rst b/doc/src/fix.rst
index 2dfe97a3ec..6f9f29db25 100644
--- a/doc/src/fix.rst
+++ b/doc/src/fix.rst
@@ -320,7 +320,8 @@ accelerated styles exist.
 * :doc:`pafi <fix_pafi>` - constrained force averages on hyper-planes to compute free energies (PAFI)
 * :doc:`pair <fix_pair>` - access per-atom info from pair styles
 * :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
-* :doc:`pimd/nvt <fix_pimd>` - Feynman path integral molecular dynamics with Nose-Hoover thermostat
+* :doc:`pimd/langevin <fix_pimd>` - Feynman path-integral molecular dynamics with stochastic thermostat
+* :doc:`pimd/nvt <fix_pimd>` - Feynman path-integral molecular dynamics with Nose-Hoover thermostat
 * :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
 * :doc:`plumed <fix_plumed>` - wrapper on PLUMED free energy library
 * :doc:`poems <fix_poems>` - constrain clusters of atoms to move as coupled rigid bodies
diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 0a4f9a38fb..342530e6a9 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -1,17 +1,21 @@
+.. index:: fix pimd/langevin
 .. index:: fix pimd/nvt
 
+fix pimd/langevin command
+=========================
+
 fix pimd/nvt command
-================
+====================
 
 Syntax
 """"""
 
 .. parsed-literal::
 
-   fix ID group-ID pimd/nvt keyword value ...
+   fix ID group-ID style keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* pimd/nvt = style name of this fix command
+* style = *pimd/langevin* or *pimd/nvt* = style name of this fix command
 * zero or more keyword/value pairs may be appended
 * keyword = *method* or *fmass* or *sp* or *temp* or *nhc*
 
@@ -35,14 +39,15 @@ Description
 
 .. versionchanged:: TBD
 
-Fix pimd was renamed to fix pimd/nvt.
+Fix pimd was renamed to fix *pimd/nvt* and fix *pimd/langevin* was added.
 
-This command performs quantum molecular dynamics simulations based on
-the Feynman path integral to include effects of tunneling and
+These fix commands perform quantum molecular dynamics simulations based
+on the Feynman path-integral to include effects of tunneling and
 zero-point motion.  In this formalism, the isomorphism of a quantum
 partition function for the original system to a classical partition
 function for a ring-polymer system is exploited, to efficiently sample
 configurations from the canonical ensemble :ref:`(Feynman) <Feynman>`.
+
 The classical partition function and its components are given
 by the following equations:
 
@@ -53,27 +58,28 @@ by the following equations:
    V_{eff} = & \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
 
 The interested user is referred to any of the numerous references on
-this methodology, but briefly, each quantum particle in a path
-integral simulation is represented by a ring-polymer of P quasi-beads,
-labeled from 1 to P.  During the simulation, each quasi-bead interacts
-with beads on the other ring-polymers with the same imaginary time
-index (the second term in the effective potential above).  The
-quasi-beads also interact with the two neighboring quasi-beads through
-the spring potential in imaginary-time space (first term in effective
-potential).  To sample the canonical ensemble, a Nose-Hoover massive
-chain thermostat is applied :ref:`(Tuckerman) <pimd-Tuckerman>`.  With the
-massive chain algorithm, a chain of NH thermostats is coupled to each
-degree of freedom for each quasi-bead.  The keyword *temp* sets the
-target temperature for the system and the keyword *nhc* sets the
-number *Nc* of thermostats in each chain.  For example, for a
-simulation of N particles with P beads in each ring-polymer, the total
-number of NH thermostats would be 3 x N x P x Nc.
+this methodology, but briefly, each quantum particle in a path integral
+simulation is represented by a ring-polymer of P quasi-beads, labeled
+from 1 to P.  During the simulation, each quasi-bead interacts with
+beads on the other ring-polymers with the same imaginary time index (the
+second term in the effective potential above).  The quasi-beads also
+interact with the two neighboring quasi-beads through the spring
+potential in imaginary-time space (first term in effective potential).
+To sample the canonical ensemble, a Nose-Hoover massive chain thermostat
+is applied :ref:`(Tuckerman) <pimd-Tuckerman>`.  With the massive chain
+algorithm, a chain of NH thermostats is coupled to each degree of
+freedom for each quasi-bead.  The keyword *temp* sets the target
+temperature for the system and the keyword *nhc* sets the number *Nc* of
+thermostats in each chain.  For example, for a simulation of N particles
+with P beads in each ring-polymer, the total number of NH thermostats
+would be 3 x N x P x Nc.
 
 .. note::
 
-   Fix pimd/nvt implements a complete velocity-verlet integrator
+   Fix *pimd/nvt* implements a complete velocity-verlet integrator
    combined with NH massive chain thermostat, so no other time
    integration fix should be used.
+   Similarly fix *pimd/langeving* implements ...
 
 The *method* keyword determines what style of PIMD is performed.  A
 value of *pimd* is standard PIMD.  A value of *nmpimd* is for
@@ -158,16 +164,18 @@ related tasks for each of the partitions, e.g.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-Fix pimd/nvt writes the state of the Nose/Hoover thermostat over all
+Fix *pimd/nvt* writes the state of the Nose/Hoover thermostat over all
 quasi-beads to :doc:`binary restart files <restart>`.  See the
 :doc:`read_restart <read_restart>` command for info on how to re-specify
 a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
 
+Fix *pimd/langevin* ... 
+
 None of the :doc:`fix_modify <fix_modify>` options
 are relevant to fix pimd/nvt.
 
-Fix pimd/nvt computes a global 3-vector, which can be accessed by
+Fix *pimd/nvt* computes a global 3-vector, which can be accessed by
 various :doc:`output commands <Howto_output>`.  The three quantities in
 the global vector are:
 
@@ -176,21 +184,21 @@ the global vector are:
    #. the current value of the scalar virial estimator for the kinetic
       energy of the quantum system :ref:`(Herman) <Herman>`.
 
-The vector values calculated by fix pimd/nvt are "extensive", except for the
+The vector values calculated by fix *pimd/nvt* are "extensive", except for the
 temperature, which is "intensive".
 
-No parameter of fix pimd/nvt can be used with the *start/stop* keywords
-of the :doc:`run <run>` command.  Fix pimd/nvt is not invoked during
+No parameter of fix *pimd/nvt* can be used with the *start/stop* keywords
+of the :doc:`run <run>` command.  Fix *pimd/nvt* is not invoked during
 :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
-This fix is part of the REPLICA package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package
+These fixes are part of the REPLICA package.  They are only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-Fix pimd/nvt cannot be used with :doc:`lj units <units>`.
+Fix *pimd/nvt* cannot be used with :doc:`lj units <units>`.
 
 A PIMD simulation can be initialized with a single data file read via
 the :doc:`read_data <read_data>` command.  However, this means all
@@ -207,7 +215,7 @@ variable, e.g.
 Default
 """""""
 
-The keyword defaults for fix pimd/nvt are method = pimd, fmass = 1.0, sp
+The keyword defaults for fix *pimd/nvt* are method = pimd, fmass = 1.0, sp
 = 1.0, temp = 300.0, and nhc = 2.
 
 ----------
diff --git a/src/.gitignore b/src/.gitignore
index 8f0f577a45..cbe9e76216 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -1533,6 +1533,8 @@
 /fix_mol_swap.h
 /fix_pimd.cpp
 /fix_pimd.h
+/fix_pimd_langevin.cpp
+/fix_pimd_langevin.h
 /fix_pimd_nvt.cpp
 /fix_pimd_nvt.h
 /fix_qbmsst.cpp

From 00a5930d4c93bafe8f2cd8978ab5c5ddfc290ef2 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Sat, 25 Feb 2023 18:58:56 -0500
Subject: [PATCH 013/396] delete default seed

---
 src/REPLICA/fix_pimd_langevin.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index cf2d63b91c..3af036caf9 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -113,7 +113,7 @@ class FixPIMDLangevin : public Fix {
   double _omega_np, *_omega_k, *Lan_s, *Lan_c;    // sin(omega_k*dt*0.5), cos(omega_k*dt*0.5)
 
   class RanMars *random;
-  int seed = 975481;
+  int seed;
   FILE *frand;
 
   int tstat_flag;    // tstat_flat = 1 if thermostat if used

From c950df2ede6bc519ed5f63691bac9579855af715 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Sat, 25 Feb 2023 19:53:19 -0500
Subject: [PATCH 014/396] delete commented-out code

---
 src/REPLICA/fix_pimd_langevin.cpp | 271 ------------------------------
 1 file changed, 271 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 1b2e734922..d4e8648504 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -81,8 +81,6 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
   bufbeads = nullptr;
   x_unwrap = xc = nullptr;
   xcall = nullptr;
-  // x_unwrap = x_unwrapsort = x_unwrapall = nullptr;
-  // tag_init = tag_initall = nullptr;
   counts = nullptr;
 
   sizeplan = 0;
@@ -245,16 +243,11 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
   /* Initiation */
 
   int nlocal = atom->nlocal;
-  // xc = new double[nlocal*3];
-  // x_unwrap = new double[nlocal*3];
 
   global_freq = 1;
   vector_flag = 1;
   size_vector = 11;
-  // if(pstyle==ISO) {size_vector = 15;}
-  // else if(pstyle==ANISO) {size_vector = 23;}
   extvector = 1;
-  // comm_forward = 1;
 
   // some initilizations
 
@@ -318,7 +311,6 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
   if(atom->nmax > maxunwrap) reallocate_x_unwrap();
   if(atom->nmax > maxxc) reallocate_xc();
   memory->create(xcall, ntotal*3, "FixPIMDLangevin:xcall");
-  // init_x_unwrap();
 
   if (cmode == SINGLE_PROC)
   {
@@ -331,21 +323,14 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
   }
 
   if ((cmode == MULTI_PROC) && (counts == nullptr)) {
-    // printf("me = %d, creating bufrecvall\n", universe->me);
     memory->create(bufsendall,ntotal,3,"FixPIMDLangevin:bufsendall");
     memory->create(bufrecvall,ntotal,3,"FixPIMDLangevin:bufrecvall");
-    // printf("me = %d, bufrecvall[0][0] = %.4f\n", universe->me, bufrecvall[0][0]);
     memory->create(tagsendall,ntotal,"FixPIMDLangevin:tagsendall");
     memory->create(tagrecvall,ntotal,"FixPIMDLangevin:tagrecvall");
-    // printf("me = %d, tagrecvall[0] = %d\n", universe->me, tagrecvall[0]);
     memory->create(counts,nprocs,"FixPIMDLangevin:counts");
     memory->create(displacements,nprocs,"FixPIMDLangevin:displacements");
-    // memory->create(x_unwrapall, ntotal, 3, "FixPIMDLangevin:x_unwrapall");
-    // memory->create(tag_initall, ntotal, "FixPIMDLangevin:tag_initall");
-    // printf("me = %d, tag_initall[0] = %d\n", universe->me, tag_initall[0]);
   }
 
-    // printf("me = %d constructing finished\n", universe->me);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -391,12 +376,8 @@ void FixPIMDLangevin::init()
   }
   else planck = force->hplanck;
   const double Planck = planck;
-  printf("planck = %.6e\n", planck);
 
-  // if(force->boltz == 1.0) { hbar = Planck; }
-  // else { hbar = Planck / (2.0 * MY_PI); }
   hbar = Planck / (2.0 * MY_PI);
-  // hbar = Planck;
   kBT = force->boltz * temp;
   double beta = 1.0 / (Boltzmann * temp);
   double _fbond = 1.0 * np * np / (beta * beta * hbar * hbar);
@@ -404,7 +385,6 @@ void FixPIMDLangevin::init()
   omega_np = np / (hbar * beta) * sqrt(force->mvv2e);
   beta_np = 1.0 / force->boltz / temp / np;
   fbond = _fbond * force->mvv2e;
-  // printf("_fbond = %.16e\nfbond = %.16e\n", _fbond, fbond);
 
   if (universe->me == 0)
     printf("Fix pimd -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
@@ -458,35 +438,27 @@ void FixPIMDLangevin::setup(int vflag)
   double **x = atom->x;
   double **v = atom->v;
   imageint *image = atom->image;
-  // nlocal_init = nlocal;
   if(mapflag){
     for(int i=0; i<nlocal; i++)
     {
       domain->unmap(x[i], image[i]);
     }
   }
-  // printf("me = %d after unmapping x_unwrap\n", universe->me);
 
-  // printf("setup already here\n");
   if(method==NMPIMD)
   {
     inter_replica_comm(x);
-    // printf("me = %d after inter\n", universe->me);
-    // printf("%.4f %.4f %.4f\n", bufbeads[0][0], bufbeads[0][1], bufbeads[0][2]);
     if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
     else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
   }
   collect_xc();
-  // printf("me = %d setup x2xp done\n", universe->me);
   compute_spring_energy();
   if(method==NMPIMD)
   {
     inter_replica_comm(x);
     if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_xp2x[universe->iworld]);
     else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
-    // nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
   }
-  // printf("me = %d setup xp2x done\n", universe->me);
   if(mapflag){
     for(int i=0; i<nlocal; i++)
     {
@@ -499,37 +471,20 @@ void FixPIMDLangevin::setup(int vflag)
     inter_replica_comm(v);
     if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, v, M_x2xp[universe->iworld]);
     else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, v, M_x2xp[universe->iworld]);
-    // nmpimd_transform(bufbeads, atom->v, M_x2xp[universe->iworld]);
   }
-  // printf("me = %d setup v2vp done\n", universe->me);
-  // compute_xc();
-  // update_x_unwrap();
-  // printf("setting up %d\n", vflag);
   if(universe->me==0 && screen) fprintf(screen,"Setting up Path-Integral ...\n");
   if(universe->me==0) printf("Setting up Path-Integral ...\n");
-  // printf("setting up, m = %.4e\n", mass[1]);
   post_force(vflag);
-  // int idx = atom->map(1);
-  // printf("irplica = %d, x[1] = %.6f %.6f %.6f xu[1] = %.6f %.6f %.6f xc[1] = %.6f %.6f %.6f\n", ireplica, x[idx][0], x[idx][1], x[idx][2], x_unwrap[idx][0], x_unwrap[idx][1], x_unwrap[idx][2], xc[idx][0], xc[idx][1], xc[idx][2]);
-  // printf("after post_force, m = %.4e\n", mass[1]);
-  // printf("me = %d after post_force\n", universe->me);
   compute_totke();
-  // compute_pote();
-  // if(pstyle==ANISO) compute_stress_tensor();
   end_of_step();
   c_pe->addstep(update->ntimestep+1);
   c_press->addstep(update->ntimestep+1);
-  // printf("setup ending: \ncell = %.16e %.16e %.16e\nvol = %.16e\n", domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
-  // printf("me = %d, setup finished\n", universe->me);
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixPIMDLangevin::initial_integrate(int /*vflag*/)
 {
-  // printf("step = %d start initial_integrate\ncell = %.16e %.16e %.16e\nvol = %.16e\n", update->ntimestep, domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
-  // printf("me = %d, step %d initial_integrate starts!\n", universe->me, update->ntimestep);
-  // printf("me = %d, step %d if starts!\n", universe->me, update->ntimestep);
   int nlocal = atom->nlocal;
   tagint *tag = atom->tag;
   double **x = atom->x;
@@ -542,41 +497,28 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
   }
   if(integrator==obabo)
   {
-  // printf("me = %d, step %d obabo starts!\n", universe->me, update->ntimestep);
     if(tstat_flag)
     {
       o_step();
-      // if(removecomflag) remove_com_motion();
       if(pstat_flag) press_o_step();
     }
     if(pstat_flag)
     {
       compute_totke();
-  // printf("me = %d, step %d after totke!\n", universe->me, update->ntimestep);
       compute_p_cv();
       press_v_step();
     }
-      /*
-      if(pstat_flag)
-      {
-      }
-      */
-  // printf("me = %d, step %d before b_step 1!\n", universe->me, update->ntimestep);
       b_step();
-  // printf("me = %d, step %d after b_step 1!\n", universe->me, update->ntimestep);
-      // if(removecomflag) remove_com_motion();
           if(method==NMPIMD)
     {
       inter_replica_comm(x);
     if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
     else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
-      // nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
     }
       qc_step();
       a_step();
       qc_step();
       a_step();
-  // printf("me = %d, step %d after 2 a_step's!\n", universe->me, update->ntimestep);
     }
     else if(integrator==baoab)
     {
@@ -587,20 +529,17 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
         press_v_step();
       }
       b_step();
-      // if(removecomflag) remove_com_motion();
       if(method==NMPIMD)
       {
         inter_replica_comm(x);
     if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
     else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
-        // nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
       }
       qc_step();
       a_step();
       if(tstat_flag)
       {
         o_step();
-        // if(removecomflag) remove_com_motion();
         if(pstat_flag) press_o_step();
       }
       qc_step();
@@ -618,7 +557,6 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
       inter_replica_comm(x);
     if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_xp2x[universe->iworld]);
     else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
-      // nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
     }
 
 
@@ -628,8 +566,6 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
         domain->unmap_inv(x[i], image[i]);
       }
     }
-  // printf("step = %d\ncell = %.16e %.16e %.16e\nvol = %.16e\n", update->ntimestep, domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
-  // printf("me = %d, step %d initial_integrate ends!\n", universe->me, update->ntimestep);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -643,13 +579,11 @@ void FixPIMDLangevin::final_integrate()
       press_v_step();
     }
    b_step();
-    // if(removecomflag) remove_com_motion();
     if(integrator==obabo)
     {
       if(tstat_flag)
       {
         o_step();
-        // if(removecomflag) remove_com_motion();
         if(pstat_flag) press_o_step();
       }
     }
@@ -667,10 +601,8 @@ void FixPIMDLangevin::final_integrate()
 
 void FixPIMDLangevin::post_force(int /*flag*/)
 {
-  // printf("step = %d\ncell = %.16e %.16e %.16e\nvol = %.16e\n", update->ntimestep, domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
   if(atom->nmax > maxunwrap) reallocate_x_unwrap();
   if(atom->nmax > maxxc) reallocate_xc();
-  // printf("me = %d, step %d post_force starts!\n", universe->me, update->ntimestep);
   int nlocal = atom->nlocal;
   double **x = atom->x;
   double **f = atom->f;
@@ -695,34 +627,17 @@ void FixPIMDLangevin::post_force(int /*flag*/)
     xc[i][2] = xcall[3*(tag[i]-1)+2];
   }
       int idx = atom->map(1);
-      // printf("in post_force, x_unwrap: %.6f %.6f %.6f xcall: %.6f %.6f %.6f xc: %.6f %.6f %.6f\n", x_unwrap[idx][0], x_unwrap[idx][1], x_unwrap[idx][2], xcall[0], xcall[1], xcall[2], xc[idx][0], xc[idx][1], xc[idx][2]);
-  // MPI_Barrier(universe->uworld);
-  // update_x_unwrap();
-  // MPI_Barrier(universe->uworld);
-  // compute_xc();
-  // MPI_Barrier(universe->uworld);
-  // if(mapflag)
-  // {
-    // for(int i=0; i<nlocal; i++)
-    // {
-      // domain->unmap_inv(x[i], image[i]);
-    // }
-  // }
   compute_vir();
   compute_vir_();
-  //  compute_t_prim();
-  //  compute_t_vir();
   compute_pote();
    if(method==NMPIMD)
   {
     inter_replica_comm(f);
     if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, f, M_x2xp[universe->iworld]);
     else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, f, M_x2xp[universe->iworld]);
-    // nmpimd_transform(bufbeads, f, M_x2xp[universe->iworld]);
   }
    c_pe->addstep(update->ntimestep+1);
    c_press->addstep(update->ntimestep+1);
-  // printf("me = %d, step %d post_force ends!\n", universe->me, update->ntimestep);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -730,8 +645,6 @@ void FixPIMDLangevin::post_force(int /*flag*/)
 void FixPIMDLangevin::end_of_step()
 {
   compute_totke();
-  // inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
-  // compute_p_prim();
   compute_p_cv();
   compute_tote();
   if(pstat_flag) compute_totenthalpy();
@@ -740,8 +653,6 @@ void FixPIMDLangevin::end_of_step()
   {
   if(universe->me==0) printf("This is the end of step %ld.\n", update->ntimestep);
   }
-  // if(universe->me==0) printf("me = %d This is the end of step %ld.\n", universe->me, update->ntimestep);
-  // printf("me = %d This is the end of step %ld.\n\n", universe->me, update->ntimestep);
 }
 
 void FixPIMDLangevin::collect_xc()
@@ -773,74 +684,15 @@ void FixPIMDLangevin::collect_xc()
       xcall[3*(tag[i]-1)+2] = x[i][2] / sqrt(np);
     }
     int idx = atom->map(1);
-    // printf("in init_int, x: %.6f %.6f %.6f xcall: %.6f %.6f %.6f\n", x[idx][0], x[idx][1], x[idx][2], xcall[0], xcall[1], xcall[2]);
 
     if(cmode == MULTI_PROC)
     {
-      // printf("trying to add\n");
-      // MPI_Reduce(MPI_IN_PLACE, xcall, ntotal*3, MPI_DOUBLE, MPI_SUM, 0, world);
       MPI_Allreduce(MPI_IN_PLACE, xcall, ntotal*3, MPI_DOUBLE, MPI_SUM, world);
-      // printf("added\n");
     }
   }
   MPI_Bcast(xcall, ntotal*3, MPI_DOUBLE, 0, universe->uworld);
 }
 
-/* ---------------------------------------------------------------------- */
-/*
-void FixPIMDLangevin::update_x_unwrap()
-{
-  // MPI_Barrier(universe->uworld);
-  // printf("me = %d, starting update_xu\n", universe->me);
-  int nlocal = atom->nlocal;
-  double **x = atom->x;
-  // delete x_unwrap;
-  // memory->sfree(x_unwrap);
-  // printf("me = %d, before deleting xu\n", universe->me);
-  delete [] x_unwrap;
-  x_unwrap = nullptr;
-  x_unwrap = (double*) memory->srealloc(x_unwrap, sizeof(double)*(nlocal+200)*3, "FixDPPimd::x_unwrap");
-  // printf("me = %d, before newing xu\n", universe->me);
-  // x_unwrap = new double[nlocal*3];
-  // printf("me = %d, doing xu\n", universe->me);
-  for(int i=0; i<nlocal; i++)
-  {
-    for(int j=0; j<3; j++)
-    {
-      x_unwrap[3*i+j] = x[i][j];
-    }
-  }
-  // printf("me = %d, ending update_xu\n", universe->me);
-  // MPI_Barrier(universe->uworld);
-}
-*/
-/* ---------------------------------------------------------------------- */
-/*
-void FixPIMDLangevin::compute_xc()
-{
-  int natoms = atom->natoms;
-  MPI_Barrier(universe->uworld);
-  comm_exec(atom->x);
-  MPI_Barrier(universe->uworld);
-  int nlocal = atom->nlocal;
-  delete [] xc;
-  xc = nullptr;
-  xc = (double*) memory->srealloc(xc, sizeof(double) * nlocal * 3, "FixDPPimd:xc");
-  for(int i=0; i<nlocal; i++)
-  {
-    xc[3*i] = xc[3*i+1] = xc[3*i+2] = 0.0;
-    for(int j=0; j<np; j++)
-    {
-      xc[3*i] += buf_beads[j][3*i+0];
-      xc[3*i+1] += buf_beads[j][3*i+1];
-      xc[3*i+2] += buf_beads[j][3*i+2];
-    }
-    xc[3*i] /= np;
-    xc[3*i+1] /= np;
-    xc[3*i+2] /= np;
-  }
-}
-*/
 /* ---------------------------------------------------------------------- */
 
 void FixPIMDLangevin::b_step()
@@ -881,11 +733,9 @@ void FixPIMDLangevin::qc_step(){
     }
   }
   else{
-  // printf("step = %d start qc_step\ncell = %.16e %.16e %.16e\nvol = %.16e\n", update->ntimestep, domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
     if(universe->iworld == 0)
     {
       double expp[3], expq[3];
-      // printf("pstyle = %d vw[0] = %.8e\n", pstyle, vw[0]);
       if(pstyle == ISO) {vw[1] = vw[0]; vw[2] = vw[0];}
       for(int j=0; j<3; j++)
       {
@@ -926,7 +776,6 @@ void FixPIMDLangevin::qc_step(){
     domain->set_local_box();
   }
   volume = domain->xprd * domain->yprd * domain->zprd;
-  // printf("step = %d end qc_step\ncell = %.16e %.16e %.16e\nvol = %.16e\n", update->ntimestep, domain->xprd, domain->yprd, domain->zprd, domain->xprd * domain->yprd * domain->zprd);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -939,7 +788,6 @@ void FixPIMDLangevin::a_step(){
 
   if(universe->iworld != 0)
   {
-      // printf("iworld = %d c = %.4e s = %.4e w = %.4e\n", universe->iworld, Lan_c[universe->iworld], Lan_s[universe->iworld], _omega_k[universe->iworld]);
     for(int i=0; i<n; i++)
     {
       x0 = x[i][0];
@@ -956,35 +804,12 @@ void FixPIMDLangevin::a_step(){
   }
 }
 
-/* ---------------------------------------------------------------------- */
-/*
-void FixPIMDLangevin::remove_com_motion(){
-  if(universe->iworld == 0)
-  {
-  // double **x = atom->x;
-    double **v = atom->v;
-  int *mask = atom->mask;
-    int nlocal = atom->nlocal;
-    if (dynamic)  masstotal = group->mass(igroup);
-    double vcm[3];
-    group->vcm(igroup,masstotal,vcm);
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit) {
-        v[i][0] -= vcm[0];
-        v[i][1] -= vcm[1];
-        v[i][2] -= vcm[2];
-      }
-    }
-  }
-}
-*/
 /* ---------------------------------------------------------------------- */
 
 void FixPIMDLangevin::baro_init()
 {
   vw[0] = vw[1] = vw[2] = vw[3] = vw[4] = vw[5] = 0.0;
   if(pstyle == ISO) {W = 3 * (atom->natoms) * tau_p * tau_p * np * kBT;} // consistent with the definition in i-Pi
-  // printf("tau_p = %.6e np = %.6e kBT = %.6e W = %.6e\n", tau_p, np, kBT, W);}
   else if(pstyle == ANISO) {W = atom->natoms * tau_p * tau_p * np * kBT;}
   Vcoeff = 1.0;
   std::string out = fmt::format("\nInitializing PIMD {:s} barostat...\n", Barostats[barostat]);
@@ -1006,9 +831,7 @@ void FixPIMDLangevin::press_v_step()
   {
     if(barostat == BZP)
     {
-      // printf("me = %d step = %d start press_v_step, baro.p = %.30e p_cv = %.30e\n", universe->me, update->ntimestep, W*vw[0], np*p_cv);
       vw[0] += dtv * 3 * (volume * np * (p_cv - Pext) / force->nktv2p + Vcoeff / beta_np) / W;
-      // printf("me = %d step = %d add p-Pext, baro.p = %.30e\n", universe->me, update->ntimestep, W*vw[0]);
       if(universe->iworld==0)
       {
         double dvw_proc = 0.0, dvw = 0.0;
@@ -1024,7 +847,6 @@ void FixPIMDLangevin::press_v_step()
       }
       MPI_Barrier(universe->uworld);
       MPI_Bcast(&vw[0], 1, MPI_DOUBLE, 0, universe->uworld);
-      // printf("me = %d step = %d end press_v_step, baro.p = %.30e\n\n", universe->me, update->ntimestep, W*vw[0]);
     }
     else if(barostat == MTTK)
     {
@@ -1087,11 +909,9 @@ void FixPIMDLangevin::press_o_step()
 
 void FixPIMDLangevin::Langevin_init()
 {
-  // printf("in Langevin_init\n");
   double beta = 1.0 / kBT;
   _omega_np = np / beta / hbar;
   double _omega_np_dt_half = _omega_np * update->dt * 0.5;
-  // printf("omega_np = %.4e wdt = %.4e\n", _omega_np, _omega_np_dt_half);
 
   _omega_k = new double[np];
   Lan_c = new double[np];
@@ -1102,7 +922,6 @@ void FixPIMDLangevin::Langevin_init()
       _omega_k[i] = _omega_np * sqrt(lam[i]);
       Lan_c[i] = cos(sqrt(lam[i])*_omega_np_dt_half);
       Lan_s[i] = sin(sqrt(lam[i])*_omega_np_dt_half);
-      // printf("lam = %.4e s = %.4e c = %.4e w = %.4e\n", lam[i], Lan_s[i], Lan_c[i], _omega_k[i]);
     }
   }
   else if(fmmode==normal){
@@ -1292,24 +1111,8 @@ void FixPIMDLangevin::comm_init()
       planrecv[i] = universe->root_proc[irecv];
       modeindex[i] = irecv;
     }
-  // }
 }
 
-/* ---------------------------------------------------------------------- */
-/*
-void FixPIMDLangevin::init_x_unwrap()
-{
-  maxunwrap = atom->nmax;
-  memory->destroy(x_unwrap);
-  memory->destroy(tag_init);
-  memory->destroy(image_init);
-  memory->destroy(x_unwrapsort);
-  memory->create(x_unwrap, maxunwrap, 3, "FixPIMDLangevin:x_unwrap");
-  memory->create(tag_init, maxunwrap, "FixPIMDLangevin:tag_init");
-  memory->create(image_init, maxunwrap, "FixPIMDLangevin:image_init");
-  memory->create(x_unwrapsort, ntotal, 3, "FixPIMDLangevin:x_unwrapsort");
-}
-*/
 /* ---------------------------------------------------------------------- */
 
 void FixPIMDLangevin::reallocate_xc()
@@ -1353,7 +1156,6 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
   MPI_Status statuses[2];
   if (atom->nmax > maxlocal) reallocate();
   int nlocal = atom->nlocal;
-  // printf("me = %d starting inter_comm, nlocal = %d ntotal = %d\n", universe->me, nlocal, ntotal);
   tagint *tag = atom->tag;
   int i, m;
 
@@ -1382,43 +1184,10 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
     displacements[0] = 0;
     for (i = 0; i < nreplica-1; i++) { displacements[i+1] = displacements[i] + counts[i]; }
     MPI_Allgatherv(bufsorted[0], 3*m, MPI_DOUBLE, bufsortedall[0], counts, displacements, MPI_DOUBLE, universe->uworld);
-    // printf("me = %d bufsortedall[0] = %.8f %.8f %.8f bufsortedall[ntotal] = %.8f %.8f %.8f\n", universe->iworld, bufsortedall[0][0], bufsortedall[0][1], bufsortedall[0][2], bufsortedall[ntotal][0], bufsortedall[ntotal][1], bufsortedall[ntotal][2]);
-    /*
-    m = 0;
-    for(i=0; i<nlocal; i++)
-    {
-      tagsend[m] = tag[i];
-      bufsend[m][0] = ptr[i][0];
-      bufsend[m][1] = ptr[i][1];
-      bufsend[m][2] = ptr[i][2];
-      m++;
-    }
-      // printf("me = %d nlocal = %d ntotal = %d m = %d bufsend finished sizeplan = %d\n", universe->me, nlocal, ntotal, m, sizeplan);
-    for(int iplan=0; iplan<sizeplan; iplan++){
-      MPI_Irecv(bufrecv[0], 3*ntotal, MPI_DOUBLE, planrecv[iplan], 0, universe->uworld, &requests[0]);
-      MPI_Irecv(tagrecv, ntotal, MPI_LMP_TAGINT, planrecv[iplan], 0, universe->uworld, &requests[1]);
-      // printf("me = %d iplan = %d irecv finished, plansend = %d, planrecv = %d, modeindex = %d\n", universe->me, iplan, plansend[iplan], planrecv[iplan], modeindex[iplan]);
-      // printf("bufsend[0]: %.4f %.4f %.4f\ntagsend[0]: %d\n", bufsend[0][0], bufsend[0][1], bufsend[0][2], tagsend[0]);
-      // printf("bufsend[255]: %.4f %.4f %.4f\ntagsend[255]: %d\n", bufsend[255][0], bufsend[255][1], bufsend[255][2], tagsend[255]);
-      MPI_Send(bufsend[0], 3*ntotal, MPI_DOUBLE, plansend[iplan], 0, universe->uworld);
-      MPI_Send(tagsend, ntotal, MPI_LMP_TAGINT, plansend[iplan], 0, universe->uworld);
-      // printf("me = %d MPI_Send done\n", universe->me);
-      MPI_Waitall(2, requests, statuses);
-      // printf("me = %d iplan = %d send recv finished\n", iplan, universe->me);
-      for(i=0; i<nlocal; i++){
-        m = atom->map(tagrecv[i]);
-        bufbeads[modeindex[iplan]][3*m+0] = bufrecv[i][0];
-        bufbeads[modeindex[iplan]][3*m+1] = bufrecv[i][1];
-        bufbeads[modeindex[iplan]][3*m+2] = bufrecv[i][2];
-      }
-    }
-      */
-  // printf("me = %d finishing inter_comm\n", universe->me);
   }
   else if(cmode == MULTI_PROC)
   {
     m = 0;
-    // printf("me = %d trying to copy bufsend\n", universe->me);
     for(i=0; i<nlocal; i++)
     {
       tagsend[m] = tag[i];
@@ -1427,26 +1196,13 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
       bufsend[m][2] = ptr[i][2];
       m++;
     }
-    // printf("me = %d copied bufsend, m = %d\n", universe->me, m);
-    // if(me==0) {for(i=0; i<nprocs; i++) {printf("me = %d after copying bufsend counts[%d] = %d\n", universe->me, i, counts[i]);}}
-    // printf("me = %d")
     MPI_Gather(&m, 1, MPI_INT, counts, 1, MPI_INT, 0, world);
-    // printf("me = %d counts gathered\n", universe->me);
-    // if(me==0) {for(i=0; i<nprocs; i++) {printf("me = %d counts[%d] = %d\n", universe->me, i, counts[i]);}}
     displacements[0] = 0;
-    // printf("me = %d displacements[0] = %d\n", universe->me, displacements[0]);
     for (i = 0; i < nprocs-1; i++) { displacements[i+1] = displacements[i] + counts[i]; }
-    // printf("me = %d displacements done\n", universe->me);
-    // if(me==0) {for(i=0; i<nprocs; i++) { printf("me = %d i=%d displacements=%d\n", universe->me, i, displacements[i]);}}
     MPI_Gatherv(tagsend, m, MPI_LMP_TAGINT, tagsendall, counts, displacements, MPI_LMP_TAGINT, 0, world);
-    // printf("me = %d tags gathered\n", universe->me);
     for (i = 0; i < nprocs; i++) { counts[i] *= 3; }
     for (i = 0; i < nprocs-1; i++) { displacements[i+1] = displacements[i] + counts[i]; }
     MPI_Gatherv(bufsend[0], 3*m, MPI_DOUBLE, bufsendall[0], counts, displacements, MPI_DOUBLE, 0, world);
-    // printf("me = %d bufsend gathered\n", universe->me);
-    // printf("me = %d, tagrecvall[0] = %d bufrecvall[0][0] = %.4f\n", universe->me, tagrecvall[0], bufrecvall[0][0]);
-
-    // printf("universe->me = %d comm->me = %d sizeplan = %d\n", universe->me, comm->me, sizeplan);
     for(int iplan=0; iplan<sizeplan; iplan++)
     {
       if(me == 0){
@@ -1456,15 +1212,8 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
         MPI_Send(tagsendall, ntotal, MPI_LMP_TAGINT, plansend[iplan], 0, universe->uworld);
         MPI_Waitall(2,requests,statuses);
       }
-      // else{
-        // printf("me = %d not sendrecceving\n", universe->me);
-      // }
-
-    // printf("me = %d sendrecv finished\n", universe->me);
-    // printf("me = %d to be bcasted: tag[0] = %d bufrecvall[0][0] = %.4f\n", universe->me, tagrecvall[0], bufrecvall[0][0]);
       MPI_Bcast(tagrecvall, ntotal, MPI_LMP_TAGINT, 0, world);
       MPI_Bcast(bufrecvall[0], 3*ntotal, MPI_DOUBLE, 0, world);
-    // printf("me = %d broadcasted\n", universe->me);
       for(i=0; i<ntotal; i++)
       {
         m = atom->map(tagrecvall[i]);
@@ -1474,7 +1223,6 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
         bufbeads[modeindex[iplan]][3*m+2] = bufrecvall[i][2];
       }
     }
-    // printf("me = %d, tag[0] = %d bufrecvall[0][0] = %.4f bufbeads[0][0] = %.4f bufbeads[1][0] = %.4f bufbeads done\n", universe->me, tag[0], bufrecvall[0][0], bufbeads[0][0], bufbeads[1][0]);
   }
 }
 
@@ -1486,8 +1234,6 @@ void FixPIMDLangevin::compute_vir_()
   int nlocal = atom->nlocal;
   xf = vir_ = xcf = centroid_vir = 0.0;
       int idx = atom->map(1);
-      // printf("in post_force, x_unwrap: %.6f %.6f %.6f xcall: %.6f %.6f %.6f\n", x_unwrap[idx][0], x_unwrap[idx][1], x_unwrap[idx][2], xcall[0], xcall[1], xcall[2]);
-  // printf("in compute_vir, xu = %.6f %.6f %.6f xc = %.6f %.6f %.6f\n", x_unwrap[idx][0], x_unwrap[idx][1], x_unwrap[idx][2], xc[idx][0], xc[idx][1], xc[idx][2]);
   for(int i=0; i<nlocal; i++)
   {
     for(int j=0; j<3; j++)
@@ -1495,8 +1241,6 @@ void FixPIMDLangevin::compute_vir_()
       xf += x_unwrap[i][j] * atom->f[i][j];
       xcf += (x_unwrap[i][j] - xc[i][j]) * atom->f[i][j];
     }
-    // int idx = atom->map(i+1);
-    // printf("me = %d step = %d tag = %d idx = %d xu = %.6f %.6f %.6f xc = %.6f %.6f %.6f f = %.6f %.6f %.6f\n", universe->me, update->ntimestep, i+1, idx, x_unwrap[idx][0], x_unwrap[idx][1], x_unwrap[idx][2], xc[idx][0], xc[idx][1], xc[idx][2], atom->f[idx][0], atom->f[idx][1], atom->f[idx][2]);
   }
   MPI_Allreduce(&xf, &vir_, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
   MPI_Allreduce(&xcf, &centroid_vir, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
@@ -1530,7 +1274,6 @@ void FixPIMDLangevin::compute_vir()
   double vir_bead=(virial[0]+virial[1]+virial[2]);
   MPI_Allreduce(&vir_bead, &vir, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
   MPI_Allreduce(MPI_IN_PLACE, &virial[0], 6, MPI_DOUBLE, MPI_SUM, universe->uworld);
-  // printf("me = %d step = %d vir = %.30e\n", universe->me, update->ntimestep, vir);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1550,12 +1293,10 @@ void FixPIMDLangevin::compute_stress_tensor()
       ke_tensor[4] += 0.5 * mass[type[i]] * atom->v[i][0] * atom->v[i][2] * force->mvv2e;
       ke_tensor[5] += 0.5 * mass[type[i]] * atom->v[i][1] * atom->v[i][2] * force->mvv2e;
     }
-    // MPI_Allreduce(&ke_tensor, &ke_tensor, 6, MPI_DOUBLE, MPI_SUM, world);
     MPI_Allreduce(MPI_IN_PLACE, &ke_tensor, 6, MPI_DOUBLE, MPI_SUM, world);
     for(int i=0; i<6; i++)
     {
       stress_tensor[i] = inv_volume * ((2*ke_tensor[i] - c_vir_tensor[i]) * force->nktv2p + virial[i]) / np;
-      // printf("i = %d, c_vir = %.6f, virial = %.6f stress = %.6f\n", i, c_vir_tensor[i], virial[i], stress_tensor[i]);
     }
   }
   MPI_Bcast(&stress_tensor, 6, MPI_DOUBLE, 0, universe->uworld);
@@ -1577,12 +1318,7 @@ void FixPIMDLangevin::compute_totke()
     }
   }
   kine *= force->mvv2e;
-  // printf("me = %d, kine = %.6e\n", universe->me, kine);
   MPI_Allreduce(&kine, &ke_bead, 1, MPI_DOUBLE, MPI_SUM, world);
-  // MPI_Allreduce(&kine, &totke, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
-  // totke *= force->mvv2e / np;
-
-  // c_press->compute_scalar();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1596,15 +1332,12 @@ void FixPIMDLangevin::compute_spring_energy()
   double* _mass = atom->mass;
   int* type = atom->type;
   int nlocal = atom->nlocal;
-  // printf("iworld = %d, fbond = %.4e lam = %.4e\n", universe->iworld, fbond, lam[universe->iworld]);
 
   for(int i=0; i<nlocal; i++)
   {
     spring_energy += 0.5 * _mass[type[i]] * fbond * lam[universe->iworld] * (x[i][0]*x[i][0] + x[i][1]*x[i][1] + x[i][2]*x[i][2]);
   }
   MPI_Allreduce(&spring_energy, &se_bead, 1, MPI_DOUBLE, MPI_SUM, world);
-  // MPI_Allreduce(&spring_energy, &total_spring_energy, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
-  // total_spring_energy /= np;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1617,8 +1350,6 @@ void FixPIMDLangevin::compute_pote()
   c_pe->compute_scalar();
   pe_bead = c_pe->scalar;
   pot_energy_partition = pe_bead / universe->procs_per_world[universe->iworld];
-  // MPI_Allreduce(&pot_energy_partition, &pote, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
-  // pote /= np;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1656,8 +1387,6 @@ void FixPIMDLangevin::compute_p_prim()
 void FixPIMDLangevin::compute_p_cv()
 {
   inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
-  // p_md = 2. / 3 * inv_volume * ((totke - total_spring_energy) * force->nktv2p + 0.5 * vir / np) ;
-  // printf("inv_V = %.30e ke = %.30e cv = %.30e vir = %.30e\n", inv_volume, ke_bead, centroid_vir, vir);
   if(universe->iworld == 0)
   {
     p_cv = 1. / 3.  * inv_volume  * ((2. * ke_bead  - 1. * centroid_vir) * force->nktv2p + 1. * vir) / np;

From f84765f29e5f3f5236db7b583532fb1a5f4ac916 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Sat, 25 Feb 2023 20:34:10 -0500
Subject: [PATCH 015/396] update document for fix pimd/langevin

---
 doc/src/fix_pimd.rst | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 342530e6a9..4d08497928 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -17,16 +17,29 @@ Syntax
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * style = *pimd/langevin* or *pimd/nvt* = style name of this fix command
 * zero or more keyword/value pairs may be appended
-* keyword = *method* or *fmass* or *sp* or *temp* or *nhc*
+* keywords for style *pimd/nvt* 
 
   .. parsed-literal::
-
+       *keywords* = *method* or *fmass* or *sp* or *temp* or *nhc*
        *method* value = *pimd* or *nmpimd* or *cmd*
        *fmass* value = scaling factor on mass
        *sp* value = scaling factor on Planck constant
        *temp* value = temperature (temperarate units)
        *nhc* value = Nc = number of chains in Nose-Hoover thermostat
 
+* keywords for style *pimd/langevin* 
+
+  .. parsed-literal::
+       *keywords* = *method* or *integrator* or *ensemble* or *fmass* or *fmmode* or *scale* or *lj* or *temp* or *thermostat* or *tau* or *press* or *barostat* or *taup* or *iso* or *aniso*
+       *method* value = *nmpimd*
+       *fmass* value = scaling factor on mass
+       *sp* value = scaling factor on Planck constant
+       *temp* value = target temperature (temperarate units)
+       *thermostat* values = PILE_L *seed*
+          *seed* = random number seed
+       *tau* value = thermostat damping parameter (time unit)
+       *press* value = target pressure (pressure units)
+
 Examples
 """"""""
 

From 25a1996ece081752364cfca146ac0a74d8b9a699 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 25 Feb 2023 22:40:30 -0500
Subject: [PATCH 016/396] some formatting and programming style updates

---
 src/REPLICA/fix_pimd_langevin.cpp | 1209 ++++++++++++++---------------
 src/REPLICA/fix_pimd_langevin.h   |    5 +-
 2 files changed, 569 insertions(+), 645 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index d4e8648504..22bed54c3b 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -14,13 +14,7 @@
 /* ----------------------------------------------------------------------
    Package      FixPIMDLangevin
    Purpose      Quantum Path Integral Algorithm for Quantum Chemistry
-   Copyright    Voth Group @ University of Chicago
-   Authors      Chris Knight & Yuxing Peng (yuxing at uchicago.edu)
 
-   Updated      Oct-01-2011
-   Version      1.0
-
-   Updated      Jun-07-2022
    Yifan Li @ Princeton University (yifanl0716@gmail.com)
    Added components:
    - Multi-processor parallelism for each bead
@@ -45,8 +39,8 @@
 #include "modify.h"
 #include "random_mars.h"
 #include "universe.h"
-#include "utils.h"
 #include "update.h"
+#include "utils.h"
 
 #include <cmath>
 #include <cstring>
@@ -56,19 +50,22 @@ using namespace FixConst;
 using namespace MathConst;
 
 enum { PIMD, NMPIMD, CMD };
-enum { physical, normal };
-enum { baoab, obabo };
+enum { PHYSICAL, NORMAL };
+enum { BAOAB, OBABO };
 enum { ISO, ANISO, TRICLINIC };
 enum { PILE_L };
 enum { MTTK, BZP };
 // char* Barostats[] = {"MTTK", "BZP"};
-std::map<int, std::string> Barostats {{MTTK, "MTTK"}, {BZP, "BZP"}};
-enum { nve, nvt, nph, npt };
-enum{SINGLE_PROC, MULTI_PROC};
+
+static std::map<int, std::string> Barostats{{MTTK, "MTTK"}, {BZP, "BZP"}};
+enum { NVE, NVT, NPH, NPT };
+enum { SINGLE_PROC, MULTI_PROC };
 
 /* ---------------------------------------------------------------------- */
 
-FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr) {
+FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
+    Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr)
+{
   time_integrate = 1;
   tagsend = tagrecv = nullptr;
   bufsend = bufrecv = nullptr;
@@ -93,24 +90,24 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
   mass = nullptr;
 
   method = PIMD;
-  ensemble      = nvt;
-  integrator = obabo;
+  ensemble = NVT;
+  integrator = OBABO;
   thermostat = PILE_L;
   barostat = BZP;
   fmass = 1.0;
   sp = 1.0;
-  temp          = 298.15;
-  Lan_temp      = 298.15;
-  tau           = 1.0;
-  tau_p         = 1.0;
-  Pext          = 1.0;
-  tstat_flag    = 1;
-  pstat_flag    = 0;
-  mapflag       = 1;
+  temp = 298.15;
+  Lan_temp = 298.15;
+  tau = 1.0;
+  tau_p = 1.0;
+  Pext = 1.0;
+  tstat_flag = 1;
+  pstat_flag = 0;
+  mapflag = 1;
   removecomflag = 1;
-  fmmode        = physical;
-  pstyle        = ISO;
-  for (int i=0; i<6; i++) p_flag[i] = 0;
+  fmmode = PHYSICAL;
+  pstyle = ISO;
+  for (int i = 0; i < 6; i++) p_flag[i] = 0;
 
   for (int i = 3; i < narg - 1; i += 2) {
     if (strcmp(arg[i], "method") == 0) {
@@ -121,129 +118,138 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
       else if (strcmp(arg[i + 1], "cmd") == 0)
         method = CMD;
       else
-        error->universe_all(FLERR, "Unknown method parameter for fix pimd");
-    }
-    else if(strcmp(arg[i], "integrator")==0)
+        error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin");
+    } else if (strcmp(arg[i], "integrator") == 0)
 
     {
-      if(strcmp(arg[i+1], "obabo")==0) integrator=obabo;
-      else if(strcmp(arg[i+1], "baoab")==0) integrator=baoab;
-      else error->universe_all(FLERR, "Unknown integrator parameter for fix pimd. Only obabo and baoab integrators are supported!");
+      if (strcmp(arg[i + 1], "obabo") == 0)
+        integrator = OBABO;
+      else if (strcmp(arg[i + 1], "baoab") == 0)
+        integrator = BAOAB;
+      else
+        error->universe_all(FLERR,
+                            "Unknown integrator parameter for fix pimd/langevin. Only obabo and baoab "
+                            "integrators are supported!");
     }
 
-    else if(strcmp(arg[i], "ensemble")==0)
-    {
-      if(strcmp(arg[i+1], "nve")==0) { ensemble = nve; tstat_flag = 0; pstat_flag = 0; }
-      else if(strcmp(arg[i+1], "nvt")==0) { ensemble = nvt; tstat_flag = 1; pstat_flag = 0; }
-      else if(strcmp(arg[i+1], "nph")==0) { ensemble = nph; tstat_flag = 0; pstat_flag = 1; }
-      else if(strcmp(arg[i+1], "npt")==0) { ensemble = npt; tstat_flag = 1; pstat_flag = 1; }
-      else error->universe_all(FLERR, "Unknown ensemble parameter for fix pimd. Only nve and nvt ensembles are supported!");
+    else if (strcmp(arg[i], "ensemble") == 0) {
+      if (strcmp(arg[i + 1], "nve") == 0) {
+        ensemble = NVE;
+        tstat_flag = 0;
+        pstat_flag = 0;
+      } else if (strcmp(arg[i + 1], "nvt") == 0) {
+        ensemble = NVT;
+        tstat_flag = 1;
+        pstat_flag = 0;
+      } else if (strcmp(arg[i + 1], "nph") == 0) {
+        ensemble = NPH;
+        tstat_flag = 0;
+        pstat_flag = 1;
+      } else if (strcmp(arg[i + 1], "npt") == 0) {
+        ensemble = NPT;
+        tstat_flag = 1;
+        pstat_flag = 1;
+      } else
+        error->universe_all(
+            FLERR,
+            "Unknown ensemble parameter for fix pimd/langevin. Only nve and nvt ensembles are supported!");
     }
 
-      else if (strcmp(arg[i], "fmass") == 0) {
+    else if (strcmp(arg[i], "fmass") == 0) {
       fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (fmass < 0.0 || fmass > 1.0)
-        error->universe_all(FLERR, "Invalid fmass value for fix pimd");
+        error->universe_all(FLERR, "Invalid fmass value for fix pimd/langevin");
     }
 
-    else if(strcmp(arg[i], "fmmode")==0)
-    {
-      if(strcmp(arg[i+1], "physical")==0) fmmode=physical;
-      else if(strcmp(arg[i+1], "normal")==0) fmmode=normal;
-      else error->universe_all(FLERR, "Unknown fictitious mass mode for fix pimd. Only physical mass and normal mode mass are supported!");
+    else if (strcmp(arg[i], "fmmode") == 0) {
+      if (strcmp(arg[i + 1], "physical") == 0)
+        fmmode = PHYSICAL;
+      else if (strcmp(arg[i + 1], "normal") == 0)
+        fmmode = NORMAL;
+      else
+        error->universe_all(FLERR,
+                            "Unknown fictitious mass mode for fix pimd/langevin. Only physical mass and "
+                            "normal mode mass are supported!");
     }
 
-    else if(strcmp(arg[i],"scale")==0)
-    {
-      pilescale = atof(arg[i+1]);
-      if(pilescale<0.0) error->universe_all(FLERR,"Invalid pile scale value for fix pimd");
+    else if (strcmp(arg[i], "scale") == 0) {
+      pilescale = atof(arg[i + 1]);
+      if (pilescale < 0.0) error->universe_all(FLERR, "Invalid pile scale value for fix pimd/langevin");
     }
 
     else if (strcmp(arg[i], "temp") == 0) {
       temp = utils::numeric(FLERR, arg[i + 1], false, lmp);
-      if (temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd");
+      if (temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd/langevin");
     }
 
     else if (strcmp(arg[i], "lj") == 0) {
-      lj_epsilon = utils::numeric(FLERR, arg[i+1], false, lmp);
-      lj_sigma = utils::numeric(FLERR, arg[i+2], false, lmp);
-      lj_mass = utils::numeric(FLERR, arg[i+3], false, lmp);
-      other_planck = utils::numeric(FLERR, arg[i+4], false, lmp);
+      lj_epsilon = utils::numeric(FLERR, arg[i + 1], false, lmp);
+      lj_sigma = utils::numeric(FLERR, arg[i + 2], false, lmp);
+      lj_mass = utils::numeric(FLERR, arg[i + 3], false, lmp);
+      other_planck = utils::numeric(FLERR, arg[i + 4], false, lmp);
       i++;
       i++;
       i++;
     }
 
-    else if(strcmp(arg[i], "thermostat")==0)
-    {
-      if(strcmp(arg[i+1],"PILE_L")==0)
-      {
+    else if (strcmp(arg[i], "thermostat") == 0) {
+      if (strcmp(arg[i + 1], "PILE_L") == 0) {
         thermostat = PILE_L;
-        seed = atoi(arg[i+2]);
+        seed = atoi(arg[i + 2]);
         i++;
       }
     }
 
-    else if(strcmp(arg[i], "tau")==0)
-    {
-      tau = atof(arg[i+1]);
+    else if (strcmp(arg[i], "tau") == 0) {
+      tau = atof(arg[i + 1]);
     }
 
-    else if(strcmp(arg[i], "press")==0)
-    {
-      Pext = atof(arg[i+1]);
-      if(Pext<0.0) error->universe_all(FLERR,"Invalid press value for fix pimd");
+    else if (strcmp(arg[i], "press") == 0) {
+      Pext = atof(arg[i + 1]);
+      if (Pext < 0.0) error->universe_all(FLERR, "Invalid press value for fix pimd/langevin");
     }
 
-    else if(strcmp(arg[i], "barostat")==0)
-    {
-      if(strcmp(arg[i+1],"MTTK")==0)
-      {
+    else if (strcmp(arg[i], "barostat") == 0) {
+      if (strcmp(arg[i + 1], "MTTK") == 0) {
         barostat = MTTK;
-      }
-      else if(strcmp(arg[i+1],"BZP")==0)
-      {
+      } else if (strcmp(arg[i + 1], "BZP") == 0) {
         barostat = BZP;
-      }
-      else error->universe_all(FLERR,"Unknown barostat parameter for fix pimd");
+      } else
+        error->universe_all(FLERR, "Unknown barostat parameter for fix pimd/langevin");
     }
 
-    else if(strcmp(arg[i], "iso")==0)
-    {
+    else if (strcmp(arg[i], "iso") == 0) {
       pstyle = ISO;
       i--;
     }
 
-    else if(strcmp(arg[i], "aniso")==0)
-    {
+    else if (strcmp(arg[i], "aniso") == 0) {
       pstyle = ANISO;
       i--;
     }
 
-    else if(strcmp(arg[i], "taup")==0)
-    {
-      tau_p = atof(arg[i+1]);
-      if(tau_p<=0.0) error->universe_all(FLERR, "Invalid tau_p value for fix pimd");
-    }
-    else if(strcmp(arg[i], "fixcom")==0)
-    {
-      if(strcmp(arg[i+1], "yes")==0) removecomflag = 1;
-      else if(strcmp(arg[i+1], "no")==0) removecomflag = 0;
+    else if (strcmp(arg[i], "taup") == 0) {
+      tau_p = atof(arg[i + 1]);
+      if (tau_p <= 0.0) error->universe_all(FLERR, "Invalid tau_p value for fix pimd/langevin");
+    } else if (strcmp(arg[i], "fixcom") == 0) {
+      if (strcmp(arg[i + 1], "yes") == 0)
+        removecomflag = 1;
+      else if (strcmp(arg[i + 1], "no") == 0)
+        removecomflag = 0;
     }
 
-    else if(strcmp(arg[i], "map")==0)
-    {
-      if(strcmp(arg[i+1], "yes")==0) mapflag = 1;
-      else if(strcmp(arg[i+1], "no")==0) mapflag = 0;
+    else if (strcmp(arg[i], "map") == 0) {
+      if (strcmp(arg[i + 1], "yes") == 0)
+        mapflag = 1;
+      else if (strcmp(arg[i + 1], "no") == 0)
+        mapflag = 0;
+    } else {
+      error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix {}", arg[i], style));
     }
-
-    else  error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd", arg[i]));
   }
 
   /* Initiation */
 
-  int nlocal = atom->nlocal;
-
   global_freq = 1;
   vector_flag = 1;
   size_vector = 11;
@@ -253,92 +259,87 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
 
   id_pe = new char[8];
   strcpy(id_pe, "pimd_pe");
-  char **newarg = new char*[3];
+  char **newarg = new char *[3];
   newarg[0] = id_pe;
   newarg[1] = (char *) "all";
   newarg[2] = (char *) "pe";
-  modify->add_compute(3,newarg);
-  delete [] newarg;
-
+  modify->add_compute(3, newarg);
+  delete[] newarg;
 
   id_press = new char[12];
   strcpy(id_press, "pimd_press");
-  newarg = new char*[5];
+  newarg = new char *[5];
   newarg[0] = id_press;
-  newarg[1] = (char*) "all";
-  newarg[2] = (char*) "pressure";
-  newarg[3] = (char*) "thermo_temp";
-  newarg[4] = (char*) "virial";
+  newarg[1] = (char *) "all";
+  newarg[2] = (char *) "pressure";
+  newarg[3] = (char *) "thermo_temp";
+  newarg[4] = (char *) "virial";
   modify->add_compute(5, newarg);
-  delete [] newarg;
+  delete[] newarg;
 
   vol0 = domain->xprd * domain->yprd * domain->zprd;
 
-  fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
-  fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
-  fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]);
+  fixedpoint[0] = 0.5 * (domain->boxlo[0] + domain->boxhi[0]);
+  fixedpoint[1] = 0.5 * (domain->boxlo[1] + domain->boxhi[1]);
+  fixedpoint[2] = 0.5 * (domain->boxlo[2] + domain->boxhi[2]);
 
   // initialize Marsaglia RNG with processor-unique seed
 
-  if(integrator==baoab || integrator==obabo)
-  {
+  if (integrator == BAOAB || integrator == OBABO) {
     Lan_temp = temp;
     random = new RanMars(lmp, seed + universe->me);
   }
 
   me = comm->me;
   nprocs = comm->nprocs;
-  if(nprocs == 1) cmode = SINGLE_PROC;
-  else cmode = MULTI_PROC;
+  if (nprocs == 1)
+    cmode = SINGLE_PROC;
+  else
+    cmode = MULTI_PROC;
 
   nprocs_universe = universe->nprocs;
   nreplica = universe->nworlds;
   ireplica = universe->iworld;
 
   int *iroots = new int[nreplica];
-  MPI_Group uworldgroup,rootgroup;
+  MPI_Group uworldgroup, rootgroup;
 
-  for (int i=0; i<nreplica; i++) iroots[i] = universe->root_proc[i];
+  for (int i = 0; i < nreplica; i++) iroots[i] = universe->root_proc[i];
   MPI_Comm_group(universe->uworld, &uworldgroup);
   MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup);
   MPI_Comm_create(universe->uworld, rootgroup, &rootworld);
   if (rootgroup != MPI_GROUP_NULL) MPI_Group_free(&rootgroup);
   if (uworldgroup != MPI_GROUP_NULL) MPI_Group_free(&uworldgroup);
-  delete [] iroots;
+  delete[] iroots;
 
   ntotal = atom->natoms;
-  if(atom->nmax > maxlocal) reallocate();
-  if(atom->nmax > maxunwrap) reallocate_x_unwrap();
-  if(atom->nmax > maxxc) reallocate_xc();
-  memory->create(xcall, ntotal*3, "FixPIMDLangevin:xcall");
+  if (atom->nmax > maxlocal) reallocate();
+  if (atom->nmax > maxunwrap) reallocate_x_unwrap();
+  if (atom->nmax > maxxc) reallocate_xc();
+  memory->create(xcall, ntotal * 3, "FixPIMDLangevin:xcall");
 
-  if (cmode == SINGLE_PROC)
-  {
+  if (cmode == SINGLE_PROC) {
     memory->create(bufsorted, ntotal, 3, "FixPIMDLangevin:bufsorted");
     memory->create(outsorted, ntotal, 3, "FixPIMDLangevin:outsorted");
-    memory->create(bufsortedall, nreplica*ntotal, 3, "FixPIMDLangevin:bufsortedall");
-    memory->create(buftransall, nreplica*ntotal, 3, "FixPIMDLangevin:buftransall");
+    memory->create(bufsortedall, nreplica * ntotal, 3, "FixPIMDLangevin:bufsortedall");
+    memory->create(buftransall, nreplica * ntotal, 3, "FixPIMDLangevin:buftransall");
     memory->create(counts, nreplica, "FixPIMDLangevin:counts");
     memory->create(displacements, nreplica, "FixPIMDLangevin:displacements");
   }
 
   if ((cmode == MULTI_PROC) && (counts == nullptr)) {
-    memory->create(bufsendall,ntotal,3,"FixPIMDLangevin:bufsendall");
-    memory->create(bufrecvall,ntotal,3,"FixPIMDLangevin:bufrecvall");
-    memory->create(tagsendall,ntotal,"FixPIMDLangevin:tagsendall");
-    memory->create(tagrecvall,ntotal,"FixPIMDLangevin:tagrecvall");
-    memory->create(counts,nprocs,"FixPIMDLangevin:counts");
-    memory->create(displacements,nprocs,"FixPIMDLangevin:displacements");
+    memory->create(bufsendall, ntotal, 3, "FixPIMDLangevin:bufsendall");
+    memory->create(bufrecvall, ntotal, 3, "FixPIMDLangevin:bufrecvall");
+    memory->create(tagsendall, ntotal, "FixPIMDLangevin:tagsendall");
+    memory->create(tagrecvall, ntotal, "FixPIMDLangevin:tagrecvall");
+    memory->create(counts, nprocs, "FixPIMDLangevin:counts");
+    memory->create(displacements, nprocs, "FixPIMDLangevin:displacements");
   }
-
 }
 
 /* ---------------------------------------------------------------------- */
 
-FixPIMDLangevin::~FixPIMDLangevin()
-{
-
-}
+FixPIMDLangevin::~FixPIMDLangevin() {}
 
 /* ---------------------------------------------------------------------- */
 
@@ -358,10 +359,10 @@ int FixPIMDLangevin::setmask()
 void FixPIMDLangevin::init()
 {
   if (atom->map_style == Atom::MAP_NONE)
-    error->all(FLERR, "Fix pimd requires an atom map, see atom_modify");
+    error->all(FLERR, "fix pimd/langevin requires an atom map, see atom_modify");
 
   if (universe->me == 0 && universe->uscreen)
-    fprintf(universe->uscreen, "Fix pimd initializing Path-Integral ...\n");
+    fprintf(universe->uscreen, "fix pimd/langevin initializing Path-Integral ...\n");
 
   // prepare the constants
 
@@ -369,43 +370,38 @@ void FixPIMDLangevin::init()
   np = universe->nworlds;
   inverse_np = 1.0 / np;
 
-  const double Boltzmann = force->boltz;
-  if (strcmp(update->unit_style,"lj") == 0) {
-    double planck_star = sqrt(lj_epsilon)*sqrt(atom->mass[0])*lj_sigma;
+  double planck;
+  if (strcmp(update->unit_style, "lj") == 0) {
+    double planck_star = sqrt(lj_epsilon) * sqrt(atom->mass[0]) * lj_sigma;
     planck = other_planck / planck_star;
+  } else {
+    planck = force->hplanck;
   }
-  else planck = force->hplanck;
-  const double Planck = planck;
 
-  hbar = Planck / (2.0 * MY_PI);
+  hbar = planck / (2.0 * MY_PI);
   kBT = force->boltz * temp;
-  double beta = 1.0 / (Boltzmann * temp);
+  double beta = 1.0 / (force->boltz * temp);
   double _fbond = 1.0 * np * np / (beta * beta * hbar * hbar);
 
   omega_np = np / (hbar * beta) * sqrt(force->mvv2e);
-  beta_np = 1.0 / force->boltz / temp / np;
+  beta_np = 1.0 / force->boltz / temp * inverse_np;
   fbond = _fbond * force->mvv2e;
 
   if (universe->me == 0)
-    printf("Fix pimd -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
+    printf("fix pimd/langevin -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
 
-  if(integrator==obabo)
-  {
+  if (integrator == OBABO) {
     dtf = 0.5 * update->dt * force->ftm2v;
     dtv = 0.5 * update->dt;
     dtv2 = dtv * dtv;
-    dtv3 = 1./3 * dtv2 * dtv * force->ftm2v;
-  }
-  else if(integrator==baoab)
-  {
+    dtv3 = THIRD * dtv2 * dtv * force->ftm2v;
+  } else if (integrator == BAOAB) {
     dtf = 0.5 * update->dt * force->ftm2v;
     dtv = 0.5 * update->dt;
     dtv2 = dtv * dtv;
-    dtv3 = 1./3 * dtv2 * dtv * force->ftm2v;
-  }
-  else
-  {
-    error->universe_all(FLERR,"Unknown integrator parameter for fix pimd");
+    dtv3 = THIRD * dtv2 * dtv * force->ftm2v;
+  } else {
+    error->universe_all(FLERR, "Unknown integrator parameter for fix pimd/langevin");
   }
 
   comm_init();
@@ -425,60 +421,56 @@ void FixPIMDLangevin::init()
 
   t_prim = t_vir = t_cv = p_prim = p_vir = p_cv = p_md = 0.0;
 
-  if(universe->me==0) fprintf(screen, "Fix pimd successfully initialized!\n");
+  if (universe->me == 0) fprintf(screen, "fix pimd/langevin successfully initialized!\n");
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixPIMDLangevin::setup(int vflag)
 {
-  if(universe->me==0) printf("Setting up Path-Integral ...\n");
+  if (universe->me == 0) printf("Setting up Path-Integral ...\n");
   int nlocal = atom->nlocal;
-  tagint *tag = atom->tag;
   double **x = atom->x;
   double **v = atom->v;
   imageint *image = atom->image;
-  if(mapflag){
-    for(int i=0; i<nlocal; i++)
-    {
-      domain->unmap(x[i], image[i]);
-    }
+  if (mapflag) {
+    for (int i = 0; i < nlocal; i++) domain->unmap(x[i], image[i]);
   }
 
-  if(method==NMPIMD)
-  {
+  if (method == NMPIMD) {
     inter_replica_comm(x);
-    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
-    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
+    if (cmode == SINGLE_PROC)
+      nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
+    else if (cmode == MULTI_PROC)
+      nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
   }
   collect_xc();
   compute_spring_energy();
-  if(method==NMPIMD)
-  {
+  if (method == NMPIMD) {
     inter_replica_comm(x);
-    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_xp2x[universe->iworld]);
-    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
+    if (cmode == SINGLE_PROC)
+      nmpimd_transform(bufsortedall, x, M_xp2x[universe->iworld]);
+    else if (cmode == MULTI_PROC)
+      nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
   }
-  if(mapflag){
-    for(int i=0; i<nlocal; i++)
-    {
-      domain->unmap_inv(x[i], image[i]);
-    }
+  if (mapflag) {
+    for (int i = 0; i < nlocal; i++) domain->unmap_inv(x[i], image[i]);
   }
 
-  if(method==NMPIMD)
-  {
+  if (method == NMPIMD) {
     inter_replica_comm(v);
-    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, v, M_x2xp[universe->iworld]);
-    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, v, M_x2xp[universe->iworld]);
+    if (cmode == SINGLE_PROC)
+      nmpimd_transform(bufsortedall, v, M_x2xp[universe->iworld]);
+    else if (cmode == MULTI_PROC)
+      nmpimd_transform(bufbeads, v, M_x2xp[universe->iworld]);
   }
-  if(universe->me==0 && screen) fprintf(screen,"Setting up Path-Integral ...\n");
-  if(universe->me==0) printf("Setting up Path-Integral ...\n");
+  if (universe->me == 0 && screen) fprintf(screen, "Setting up Path-Integral ...\n");
+  if (universe->me == 0) printf("Setting up Path-Integral ...\n");
   post_force(vflag);
   compute_totke();
   end_of_step();
-  c_pe->addstep(update->ntimestep+1);
-  c_press->addstep(update->ntimestep+1);
+  c_pe->addstep(update->ntimestep + 1);
+  c_press->addstep(update->ntimestep + 1);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -486,158 +478,133 @@ void FixPIMDLangevin::setup(int vflag)
 void FixPIMDLangevin::initial_integrate(int /*vflag*/)
 {
   int nlocal = atom->nlocal;
-  tagint *tag = atom->tag;
   double **x = atom->x;
   imageint *image = atom->image;
-  if(mapflag){
-    for(int i=0; i<nlocal; i++)
-    {
-      domain->unmap(x[i], image[i]);
-    }
+  if (mapflag) {
+    for (int i = 0; i < nlocal; i++) domain->unmap(x[i], image[i]);
   }
-  if(integrator==obabo)
-  {
-    if(tstat_flag)
-    {
+  if (integrator == OBABO) {
+    if (tstat_flag) {
       o_step();
-      if(pstat_flag) press_o_step();
+      if (pstat_flag) press_o_step();
     }
-    if(pstat_flag)
-    {
+    if (pstat_flag) {
       compute_totke();
       compute_p_cv();
       press_v_step();
     }
-      b_step();
-          if(method==NMPIMD)
-    {
+    b_step();
+    if (method == NMPIMD) {
       inter_replica_comm(x);
-    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
-    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
+      if (cmode == SINGLE_PROC)
+        nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
+      else if (cmode == MULTI_PROC)
+        nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
     }
-      qc_step();
-      a_step();
-      qc_step();
-      a_step();
+    qc_step();
+    a_step();
+    qc_step();
+    a_step();
+  } else if (integrator == BAOAB) {
+    if (pstat_flag) {
+      compute_totke();
+      compute_p_cv();
+      press_v_step();
     }
-    else if(integrator==baoab)
-    {
-      if(pstat_flag)
-      {
-        compute_totke();
-        compute_p_cv();
-        press_v_step();
-      }
-      b_step();
-      if(method==NMPIMD)
-      {
-        inter_replica_comm(x);
-    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
-    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
-      }
-      qc_step();
-      a_step();
-      if(tstat_flag)
-      {
-        o_step();
-        if(pstat_flag) press_o_step();
-      }
-      qc_step();
-      a_step();
-    }
-    else
-    {
-      error->universe_all(FLERR,"Unknown integrator parameter for fix pimd");
-    }
-    collect_xc();
-    compute_spring_energy();
-
-     if(method==NMPIMD)
-    {
+    b_step();
+    if (method == NMPIMD) {
       inter_replica_comm(x);
-    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, x, M_xp2x[universe->iworld]);
-    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
+      if (cmode == SINGLE_PROC)
+        nmpimd_transform(bufsortedall, x, M_x2xp[universe->iworld]);
+      else if (cmode == MULTI_PROC)
+        nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
     }
-
-
-    if(mapflag){
-      for(int i=0; i<nlocal; i++)
-      {
-        domain->unmap_inv(x[i], image[i]);
-      }
+    qc_step();
+    a_step();
+    if (tstat_flag) {
+      o_step();
+      if (pstat_flag) press_o_step();
     }
+    qc_step();
+    a_step();
+  } else {
+    error->universe_all(FLERR, "Unknown integrator parameter for fix pimd/langevin");
+  }
+  collect_xc();
+  compute_spring_energy();
+
+  if (method == NMPIMD) {
+    inter_replica_comm(x);
+    if (cmode == SINGLE_PROC)
+      nmpimd_transform(bufsortedall, x, M_xp2x[universe->iworld]);
+    else if (cmode == MULTI_PROC)
+      nmpimd_transform(bufbeads, x, M_xp2x[universe->iworld]);
+  }
+
+  if (mapflag) {
+    for (int i = 0; i < nlocal; i++) { domain->unmap_inv(x[i], image[i]); }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixPIMDLangevin::final_integrate()
 {
-    if(pstat_flag)
-    {
-      compute_totke();
-      compute_p_cv();
-      press_v_step();
+  if (pstat_flag) {
+    compute_totke();
+    compute_p_cv();
+    press_v_step();
+  }
+  b_step();
+  if (integrator == OBABO) {
+    if (tstat_flag) {
+      o_step();
+      if (pstat_flag) press_o_step();
     }
-   b_step();
-    if(integrator==obabo)
-    {
-      if(tstat_flag)
-      {
-        o_step();
-        if(pstat_flag) press_o_step();
-      }
-    }
-    else if(integrator==baoab)
-    {
+  } else if (integrator == BAOAB) {
 
-    }
-    else
-    {
-      error->universe_all(FLERR,"Unknown integrator parameter for fix pimd");
-    }
+  } else {
+    error->universe_all(FLERR, "Unknown integrator parameter for fix pimd/langevin");
+  }
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixPIMDLangevin::post_force(int /*flag*/)
 {
-  if(atom->nmax > maxunwrap) reallocate_x_unwrap();
-  if(atom->nmax > maxxc) reallocate_xc();
+  if (atom->nmax > maxunwrap) reallocate_x_unwrap();
+  if (atom->nmax > maxxc) reallocate_xc();
   int nlocal = atom->nlocal;
   double **x = atom->x;
   double **f = atom->f;
   imageint *image = atom->image;
   tagint *tag = atom->tag;
-  for(int i=0; i<nlocal; i++)
-  {
+  for (int i = 0; i < nlocal; i++) {
     x_unwrap[i][0] = x[i][0];
     x_unwrap[i][1] = x[i][1];
     x_unwrap[i][2] = x[i][2];
   }
-  if(mapflag){
-    for(int i=0; i<nlocal; i++)
-    {
-      domain->unmap(x_unwrap[i], image[i]);
-    }
+  if (mapflag) {
+    for (int i = 0; i < nlocal; i++) { domain->unmap(x_unwrap[i], image[i]); }
   }
-  for(int i=0; i<nlocal; i++)
-  {
-    xc[i][0] = xcall[3*(tag[i]-1)+0];
-    xc[i][1] = xcall[3*(tag[i]-1)+1];
-    xc[i][2] = xcall[3*(tag[i]-1)+2];
+  for (int i = 0; i < nlocal; i++) {
+    xc[i][0] = xcall[3 * (tag[i] - 1) + 0];
+    xc[i][1] = xcall[3 * (tag[i] - 1) + 1];
+    xc[i][2] = xcall[3 * (tag[i] - 1) + 2];
   }
-      int idx = atom->map(1);
+
   compute_vir();
   compute_vir_();
   compute_pote();
-   if(method==NMPIMD)
-  {
+  if (method == NMPIMD) {
     inter_replica_comm(f);
-    if(cmode == SINGLE_PROC) nmpimd_transform(bufsortedall, f, M_x2xp[universe->iworld]);
-    else if(cmode == MULTI_PROC) nmpimd_transform(bufbeads, f, M_x2xp[universe->iworld]);
+    if (cmode == SINGLE_PROC)
+      nmpimd_transform(bufsortedall, f, M_x2xp[universe->iworld]);
+    else if (cmode == MULTI_PROC)
+      nmpimd_transform(bufbeads, f, M_x2xp[universe->iworld]);
   }
-   c_pe->addstep(update->ntimestep+1);
-   c_press->addstep(update->ntimestep+1);
+  c_pe->addstep(update->ntimestep + 1);
+  c_press->addstep(update->ntimestep + 1);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -647,11 +614,10 @@ void FixPIMDLangevin::end_of_step()
   compute_totke();
   compute_p_cv();
   compute_tote();
-  if(pstat_flag) compute_totenthalpy();
+  if (pstat_flag) compute_totenthalpy();
 
-  if(update->ntimestep % 10000 == 0)
-  {
-  if(universe->me==0) printf("This is the end of step %ld.\n", update->ntimestep);
+  if (update->ntimestep % 10000 == 0) {
+    if (universe->me == 0) printf("This is the end of step %ld.\n", update->ntimestep);
   }
 }
 
@@ -660,37 +626,28 @@ void FixPIMDLangevin::collect_xc()
   int nlocal = atom->nlocal;
   double **x = atom->x;
   tagint *tag = atom->tag;
-  if(ireplica == 0)
-  {
-    if(cmode == SINGLE_PROC)
-    {
-      for(int i=0; i<nlocal; i++)
-      {
-        xcall[3*i+0] = xcall[3*i+1] = xcall[3*i+2] = 0.0;
+  if (ireplica == 0) {
+    if (cmode == SINGLE_PROC) {
+      for (int i = 0; i < nlocal; i++) {
+        xcall[3 * i + 0] = xcall[3 * i + 1] = xcall[3 * i + 2] = 0.0;
       }
-    }
-    else if(cmode == MULTI_PROC)
-    {
-      for(int i=0; i<ntotal; i++)
-      {
-        xcall[3*i+0] = xcall[3*i+1] = xcall[3*i+2] = 0.0;
+    } else if (cmode == MULTI_PROC) {
+      for (int i = 0; i < ntotal; i++) {
+        xcall[3 * i + 0] = xcall[3 * i + 1] = xcall[3 * i + 2] = 0.0;
       }
     }
 
-    for(int i=0;i<nlocal; i++)
-    {
-      xcall[3*(tag[i]-1)+0] = x[i][0] / sqrt(np);
-      xcall[3*(tag[i]-1)+1] = x[i][1] / sqrt(np);
-      xcall[3*(tag[i]-1)+2] = x[i][2] / sqrt(np);
+    for (int i = 0; i < nlocal; i++) {
+      xcall[3 * (tag[i] - 1) + 0] = x[i][0] / sqrt(np);
+      xcall[3 * (tag[i] - 1) + 1] = x[i][1] / sqrt(np);
+      xcall[3 * (tag[i] - 1) + 2] = x[i][2] / sqrt(np);
     }
-    int idx = atom->map(1);
 
-    if(cmode == MULTI_PROC)
-    {
-      MPI_Allreduce(MPI_IN_PLACE, xcall, ntotal*3, MPI_DOUBLE, MPI_SUM, world);
+    if (cmode == MULTI_PROC) {
+      MPI_Allreduce(MPI_IN_PLACE, xcall, ntotal * 3, MPI_DOUBLE, MPI_SUM, world);
     }
   }
-  MPI_Bcast(xcall, ntotal*3, MPI_DOUBLE, 0, universe->uworld);
+  MPI_Bcast(xcall, ntotal * 3, MPI_DOUBLE, 0, universe->uworld);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -703,51 +660,45 @@ void FixPIMDLangevin::b_step()
   double **v = atom->v;
   double **f = atom->f;
 
-  for(int i=0; i<n; i++)
-  {
+  for (int i = 0; i < n; i++) {
     double dtfm = dtf / mass[type[i]];
     v[i][0] += dtfm * f[i][0];
     v[i][1] += dtfm * f[i][1];
     v[i][2] += dtfm * f[i][2];
   }
-
 }
 
 /* ---------------------------------------------------------------------- */
 
-void FixPIMDLangevin::qc_step(){
+void FixPIMDLangevin::qc_step()
+{
   int nlocal = atom->nlocal;
   double **x = atom->x;
   double **v = atom->v;
-  tagint *tag = atom->tag;
   double oldlo, oldhi;
-  if(!pstat_flag) {
-    if(universe->iworld == 0)
-    {
-      for(int i=0; i<nlocal; i++)
-      {
+
+  if (!pstat_flag) {
+    if (universe->iworld == 0) {
+      for (int i = 0; i < nlocal; i++) {
         x[i][0] += dtv * v[i][0];
         x[i][1] += dtv * v[i][1];
         x[i][2] += dtv * v[i][2];
       }
     }
-  }
-  else{
-    if(universe->iworld == 0)
-    {
+  } else {
+    if (universe->iworld == 0) {
       double expp[3], expq[3];
-      if(pstyle == ISO) {vw[1] = vw[0]; vw[2] = vw[0];}
-      for(int j=0; j<3; j++)
-      {
+      if (pstyle == ISO) {
+        vw[1] = vw[0];
+        vw[2] = vw[0];
+      }
+      for (int j = 0; j < 3; j++) {
         expq[j] = exp(dtv * vw[j]);
         expp[j] = exp(-dtv * vw[j]);
       }
-      if(barostat == BZP)
-      {
-        for(int i=0; i<nlocal; i++)
-        {
-          for(int j=0; j<3; j++)
-          {
+      if (barostat == BZP) {
+        for (int i = 0; i < nlocal; i++) {
+          for (int j = 0; j < 3; j++) {
             x[i][j] = expq[j] * x[i][j] + (expq[j] - expp[j]) / 2. / vw[j] * v[i][j];
             v[i][j] = expp[j] * v[i][j];
           }
@@ -755,18 +706,18 @@ void FixPIMDLangevin::qc_step(){
         oldlo = domain->boxlo[0];
         oldhi = domain->boxhi[0];
 
-        domain->boxlo[0] = (oldlo-fixedpoint[0])*expq[0] + fixedpoint[0];
-        domain->boxhi[0] = (oldhi-fixedpoint[0])*expq[0] + fixedpoint[0];
+        domain->boxlo[0] = (oldlo - fixedpoint[0]) * expq[0] + fixedpoint[0];
+        domain->boxhi[0] = (oldhi - fixedpoint[0]) * expq[0] + fixedpoint[0];
 
         oldlo = domain->boxlo[1];
         oldhi = domain->boxhi[1];
-        domain->boxlo[1] = (oldlo-fixedpoint[1])*expq[1] + fixedpoint[1];
-        domain->boxhi[1] = (oldhi-fixedpoint[1])*expq[1] + fixedpoint[1];
+        domain->boxlo[1] = (oldlo - fixedpoint[1]) * expq[1] + fixedpoint[1];
+        domain->boxhi[1] = (oldhi - fixedpoint[1]) * expq[1] + fixedpoint[1];
 
         oldlo = domain->boxlo[2];
         oldhi = domain->boxhi[2];
-        domain->boxlo[2] = (oldlo-fixedpoint[2])*expq[2] + fixedpoint[2];
-        domain->boxhi[2] = (oldhi-fixedpoint[2])*expq[2] + fixedpoint[2];
+        domain->boxlo[2] = (oldlo - fixedpoint[2]) * expq[2] + fixedpoint[2];
+        domain->boxhi[2] = (oldhi - fixedpoint[2]) * expq[2] + fixedpoint[2];
       }
     }
     MPI_Barrier(universe->uworld);
@@ -780,26 +731,33 @@ void FixPIMDLangevin::qc_step(){
 
 /* ---------------------------------------------------------------------- */
 
-void FixPIMDLangevin::a_step(){
+void FixPIMDLangevin::a_step()
+{
   int n = atom->nlocal;
   double **x = atom->x;
   double **v = atom->v;
-  double x0, x1, x2, v0, v1, v2; // three components of x[i] and v[i]
+  double x0, x1, x2, v0, v1, v2;    // three components of x[i] and v[i]
 
-  if(universe->iworld != 0)
-  {
-    for(int i=0; i<n; i++)
-    {
+  if (universe->iworld != 0) {
+    for (int i = 0; i < n; i++) {
       x0 = x[i][0];
       x1 = x[i][1];
       x2 = x[i][2];
-      v0 = v[i][0]; v1 = v[i][1]; v2 = v[i][2];
-      x[i][0] = Lan_c[universe->iworld] * x0 + 1./_omega_k[universe->iworld] * Lan_s[universe->iworld] * v0;
-      x[i][1] = Lan_c[universe->iworld] * x1 + 1./_omega_k[universe->iworld] * Lan_s[universe->iworld] * v1;
-      x[i][2] = Lan_c[universe->iworld] * x2 + 1./_omega_k[universe->iworld] * Lan_s[universe->iworld] * v2;
-      v[i][0] = -1.*_omega_k[universe->iworld] * Lan_s[universe->iworld] * x0 + Lan_c[universe->iworld] * v0;
-      v[i][1] = -1.*_omega_k[universe->iworld] * Lan_s[universe->iworld] * x1 + Lan_c[universe->iworld] * v1;
-      v[i][2] = -1.*_omega_k[universe->iworld] * Lan_s[universe->iworld] * x2 + Lan_c[universe->iworld] * v2;
+      v0 = v[i][0];
+      v1 = v[i][1];
+      v2 = v[i][2];
+      x[i][0] = Lan_c[universe->iworld] * x0 +
+          1.0 / _omega_k[universe->iworld] * Lan_s[universe->iworld] * v0;
+      x[i][1] = Lan_c[universe->iworld] * x1 +
+          1.0 / _omega_k[universe->iworld] * Lan_s[universe->iworld] * v1;
+      x[i][2] = Lan_c[universe->iworld] * x2 +
+          1.0 / _omega_k[universe->iworld] * Lan_s[universe->iworld] * v2;
+      v[i][0] = -1.0 * _omega_k[universe->iworld] * Lan_s[universe->iworld] * x0 +
+          Lan_c[universe->iworld] * v0;
+      v[i][1] = -1.0 * _omega_k[universe->iworld] * Lan_s[universe->iworld] * x1 +
+          Lan_c[universe->iworld] * v1;
+      v[i][2] = -1.0 * _omega_k[universe->iworld] * Lan_s[universe->iworld] * x2 +
+          Lan_c[universe->iworld] * v2;
     }
   }
 }
@@ -809,8 +767,12 @@ void FixPIMDLangevin::a_step(){
 void FixPIMDLangevin::baro_init()
 {
   vw[0] = vw[1] = vw[2] = vw[3] = vw[4] = vw[5] = 0.0;
-  if(pstyle == ISO) {W = 3 * (atom->natoms) * tau_p * tau_p * np * kBT;} // consistent with the definition in i-Pi
-  else if(pstyle == ANISO) {W = atom->natoms * tau_p * tau_p * np * kBT;}
+  if (pstyle == ISO) {
+    W = 3 * (atom->natoms) * tau_p * tau_p * np * kBT;
+  }    // consistent with the definition in i-Pi
+  else if (pstyle == ANISO) {
+    W = atom->natoms * tau_p * tau_p * np * kBT;
+  }
   Vcoeff = 1.0;
   std::string out = fmt::format("\nInitializing PIMD {:s} barostat...\n", Barostats[barostat]);
   out += fmt::format("The barostat mass is W = {:.16e}\n", W);
@@ -827,18 +789,13 @@ void FixPIMDLangevin::press_v_step()
   int *type = atom->type;
   volume = domain->xprd * domain->yprd * domain->zprd;
 
-  if(pstyle == ISO)
-  {
-    if(barostat == BZP)
-    {
+  if (pstyle == ISO) {
+    if (barostat == BZP) {
       vw[0] += dtv * 3 * (volume * np * (p_cv - Pext) / force->nktv2p + Vcoeff / beta_np) / W;
-      if(universe->iworld==0)
-      {
+      if (universe->iworld == 0) {
         double dvw_proc = 0.0, dvw = 0.0;
-        for(int i = 0; i < nlocal; i++)
-        {
-          for(int j = 0; j < 3; j++)
-          {
+        for (int i = 0; i < nlocal; i++) {
+          for (int j = 0; j < 3; j++) {
             dvw_proc += dtv2 * f[i][j] * v[i][j] / W + dtv3 * f[i][j] * f[i][j] / mass[type[i]] / W;
           }
         }
@@ -847,26 +804,21 @@ void FixPIMDLangevin::press_v_step()
       }
       MPI_Barrier(universe->uworld);
       MPI_Bcast(&vw[0], 1, MPI_DOUBLE, 0, universe->uworld);
+    } else if (barostat == MTTK) {
+      mtk_term1 = 2. / atom->natoms * totke / 3;
+      f_omega = (volume * np * (p_md - Pext) + mtk_term1) / W;
+      vw[0] += 0.5 * dtv * f_omega;
     }
-    else if(barostat == MTTK)
-    {
-        mtk_term1 = 2. / atom->natoms * totke / 3;
-        f_omega = (volume * np * (p_md - Pext) + mtk_term1) / W;
-        vw[0] += 0.5 * dtv * f_omega;
-    }
-  }
-  else if(pstyle == ANISO)
-  {
+  } else if (pstyle == ANISO) {
     compute_stress_tensor();
-    for(int ii=0; ii<3; ii++)
-    {
-      vw[ii] += dtv * (volume * np * (stress_tensor[ii] - Pext) / force->nktv2p + Vcoeff / beta_np) / W;
-      if(universe->iworld==0)
-      {
+    for (int ii = 0; ii < 3; ii++) {
+      vw[ii] +=
+          dtv * (volume * np * (stress_tensor[ii] - Pext) / force->nktv2p + Vcoeff / beta_np) / W;
+      if (universe->iworld == 0) {
         double dvw_proc = 0.0, dvw = 0.0;
-        for(int i = 0; i < nlocal; i++)
-        {
-          dvw_proc += dtv2 * f[i][ii] * v[i][ii] / W + dtv3 * f[i][ii] * f[i][ii] / mass[type[i]] / W;
+        for (int i = 0; i < nlocal; i++) {
+          dvw_proc +=
+              dtv2 * f[i][ii] * v[i][ii] / W + dtv3 * f[i][ii] * f[i][ii] / mass[type[i]] / W;
         }
         MPI_Allreduce(&dvw_proc, &dvw, 1, MPI_DOUBLE, MPI_SUM, world);
         vw[ii] += dvw;
@@ -879,26 +831,21 @@ void FixPIMDLangevin::press_v_step()
 
 void FixPIMDLangevin::press_o_step()
 {
-  if(pstyle==ISO)
-  {
-    if(universe->me==0)
-    {
+  if (pstyle == ISO) {
+    if (universe->me == 0) {
       r1 = random->gaussian();
-      vw[0] = c1 * vw[0] + c2 * sqrt(1. / W / beta_np) * r1;
+      vw[0] = c1 * vw[0] + c2 * sqrt(1.0 / W / beta_np) * r1;
     }
     MPI_Barrier(universe->uworld);
     MPI_Bcast(&vw[0], 1, MPI_DOUBLE, 0, universe->uworld);
-  }
-  else if(pstyle==ANISO)
-  {
-    if(universe->me==0)
-    {
+  } else if (pstyle == ANISO) {
+    if (universe->me == 0) {
       r1 = random->gaussian();
       r2 = random->gaussian();
       r3 = random->gaussian();
-      vw[0] = c1 * vw[0] + c2 * sqrt(1. / W / beta_np) * r1;
-      vw[1] = c1 * vw[1] + c2 * sqrt(1. / W / beta_np) * r2;
-      vw[2] = c1 * vw[2] + c2 * sqrt(1. / W / beta_np) * r3;
+      vw[0] = c1 * vw[0] + c2 * sqrt(1.0 / W / beta_np) * r1;
+      vw[1] = c1 * vw[1] + c2 * sqrt(1.0 / W / beta_np) * r2;
+      vw[2] = c1 * vw[2] + c2 * sqrt(1.0 / W / beta_np) * r3;
     }
     MPI_Barrier(universe->uworld);
     MPI_Bcast(&vw, 3, MPI_DOUBLE, 0, universe->uworld);
@@ -916,52 +863,61 @@ void FixPIMDLangevin::Langevin_init()
   _omega_k = new double[np];
   Lan_c = new double[np];
   Lan_s = new double[np];
-  if(fmmode==physical){
-    for (int i=0; i<np; i++)
-    {
+  if (fmmode == PHYSICAL) {
+    for (int i = 0; i < np; i++) {
       _omega_k[i] = _omega_np * sqrt(lam[i]);
-      Lan_c[i] = cos(sqrt(lam[i])*_omega_np_dt_half);
-      Lan_s[i] = sin(sqrt(lam[i])*_omega_np_dt_half);
+      Lan_c[i] = cos(sqrt(lam[i]) * _omega_np_dt_half);
+      Lan_s[i] = sin(sqrt(lam[i]) * _omega_np_dt_half);
     }
-  }
-  else if(fmmode==normal){
-    for (int i=0; i<np; i++)
-    {
+  } else if (fmmode == NORMAL) {
+    for (int i = 0; i < np; i++) {
       _omega_k[i] = _omega_np;
       Lan_c[i] = cos(_omega_np_dt_half);
       Lan_s[i] = sin(_omega_np_dt_half);
     }
   }
-  if(tau > 0) gamma = 1.0 / tau;
-  else gamma = np / beta / hbar;
+  if (tau > 0)
+    gamma = 1.0 / tau;
+  else
+    gamma = np / beta / hbar;
 
-  if(integrator==obabo) c1 = exp(-gamma * 0.5 * update->dt); // tau is the damping time of the centroid mode.
-  else if(integrator==baoab) c1 = exp(-gamma * update->dt);
-  else error->universe_all(FLERR, "Unknown integrator parameter for fix pimd. Only obabo and baoab integrators is supported!");
+  if (integrator == OBABO)
+    c1 = exp(-gamma * 0.5 * update->dt);    // tau is the damping time of the centroid mode.
+  else if (integrator == BAOAB)
+    c1 = exp(-gamma * update->dt);
+  else
+    error->universe_all(FLERR,
+                        "Unknown integrator parameter for fix pimd/langevin. Only obabo and "
+                        "baoab integrators are supported!");
 
-  c2 = sqrt(1.0 - c1 * c1); // note that c1 and c2 here only works for the centroid mode.
+  c2 = sqrt(1.0 - c1 * c1);    // note that c1 and c2 here only works for the centroid mode.
 
-  if( thermostat == PILE_L )
-  {
+  if (thermostat == PILE_L) {
     std::string out = "\nInitializing PI Langevin equation thermostat...\n";
     out += "Bead ID    |    omega    |    tau    |    c1    |    c2\n";
     tau_k = new double[np];
     c1_k = new double[np];
     c2_k = new double[np];
-    tau_k[0] = tau; c1_k[0] = c1; c2_k[0] = c2;
-    for(int i=1; i<np; i++)
-    {
+    tau_k[0] = tau;
+    c1_k[0] = c1;
+    c2_k[0] = c2;
+    for (int i = 1; i < np; i++) {
       tau_k[i] = 0.5 / pilescale / _omega_k[i];
-      if(integrator==obabo) c1_k[i] = exp(-0.5 * update->dt / tau_k[i]);
-      else if(integrator==baoab) c1_k[i] = exp(-1.0 * update->dt / tau_k[i]);
-      else error->universe_all(FLERR, "Unknown integrator parameter for fix pimd. Only obabo and baoab integrators is supported!");
+      if (integrator == OBABO)
+        c1_k[i] = exp(-0.5 * update->dt / tau_k[i]);
+      else if (integrator == BAOAB)
+        c1_k[i] = exp(-1.0 * update->dt / tau_k[i]);
+      else
+        error->universe_all(FLERR,
+                            "Unknown integrator parameter for fix pimd/langevin. Only obabo and "
+                            "baoab integrators are supported!");
       c2_k[i] = sqrt(1.0 - c1_k[i] * c1_k[i]);
     }
-    for(int i=0; i<np; i++)
-    {
-      out += fmt::format("    {:d}     {:.8e} {:.8e} {:.8e} {:.8e}\n", i, _omega_k[i], tau_k[i], c1_k[i], c2_k[i]);
+    for (int i = 0; i < np; i++) {
+      out += fmt::format("    {:d}     {:.8e} {:.8e} {:.8e} {:.8e}\n", i, _omega_k[i], tau_k[i],
+                         c1_k[i], c2_k[i]);
     }
-    if(thermostat == PILE_L) out += "PILE_L thermostat successfully initialized!\n";
+    if (thermostat == PILE_L) out += "PILE_L thermostat successfully initialized!\n";
     out += "\n";
     utils::logmesg(lmp, out);
   }
@@ -973,17 +929,18 @@ void FixPIMDLangevin::o_step()
 {
   int nlocal = atom->nlocal;
   int *type = atom->type;
-  double beta_np = 1.0 / force->boltz / Lan_temp / np * force->mvv2e;
-  if(thermostat == PILE_L)
-  {
-    for(int i=0; i<nlocal; i++)
-    {
+  double beta_np = 1.0 / force->boltz / Lan_temp * inverse_np * force->mvv2e;
+  if (thermostat == PILE_L) {
+    for (int i = 0; i < nlocal; i++) {
       r1 = random->gaussian();
       r2 = random->gaussian();
       r3 = random->gaussian();
-      atom->v[i][0] = c1_k[universe->iworld] * atom->v[i][0] + c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r1;
-      atom->v[i][1] = c1_k[universe->iworld] * atom->v[i][1] + c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r2;
-      atom->v[i][2] = c1_k[universe->iworld] * atom->v[i][2] + c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r3;
+      atom->v[i][0] = c1_k[universe->iworld] * atom->v[i][0] +
+          c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r1;
+      atom->v[i][1] = c1_k[universe->iworld] * atom->v[i][1] +
+          c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r2;
+      atom->v[i][2] = c1_k[universe->iworld] * atom->v[i][2] +
+          c2_k[universe->iworld] * sqrt(1.0 / mass[type[i]] / beta_np) * r3;
     }
   }
 }
@@ -994,94 +951,79 @@ void FixPIMDLangevin::o_step()
 
 void FixPIMDLangevin::nmpimd_init()
 {
-    memory->create(M_x2xp, np, np, "fix_feynman:M_x2xp");
-    memory->create(M_xp2x, np, np, "fix_feynman:M_xp2x");
+  memory->create(M_x2xp, np, np, "fix_feynman:M_x2xp");
+  memory->create(M_xp2x, np, np, "fix_feynman:M_xp2x");
 
-    lam = (double*) memory->smalloc(sizeof(double)*np, "FixPIMDLangevin::lam");
+  lam = (double *) memory->smalloc(sizeof(double) * np, "FixPIMDLangevin::lam");
 
-    // Set up  eigenvalues
-    for(int i=0; i<np; i++){
-      double sin_tmp = sin(i * MY_PI / np);
-      lam[i] = 4 * sin_tmp * sin_tmp;
+  // Set up  eigenvalues
+  for (int i = 0; i < np; i++) {
+    double sin_tmp = sin(i * MY_PI / np);
+    lam[i] = 4 * sin_tmp * sin_tmp;
+  }
+
+  // Set up eigenvectors for degenerated modes
+  for (int j = 0; j < np; j++) {
+    for (int i = 1; i < int(np / 2) + 1; i++) {
+      M_x2xp[i][j] = sqrt(2.0) * cos(2.0 * MY_PI * double(i) * double(j) / double(np)) / sqrt(np);
     }
-
-    // Set up eigenvectors for degenerated modes
-    for(int j=0; j<np; j++){
-      for(int i=1; i<int(np/2) + 1; i++)
-      {
-        M_x2xp[i][j] =   sqrt(2.0) * cos ( 2.0 * MY_PI * double(i) * double(j) / double(np)) / sqrt(np);
-      }
-      for(int i=int(np/2)+1; i<np; i++)
-      {
-        M_x2xp[i][j] =   sqrt(2.0) * sin ( 2.0 * MY_PI * double(i) * double(j) / double(np)) / sqrt(np);
-      }
+    for (int i = int(np / 2) + 1; i < np; i++) {
+      M_x2xp[i][j] = sqrt(2.0) * sin(2.0 * MY_PI * double(i) * double(j) / double(np)) / sqrt(np);
     }
+  }
 
-    // Set up eigenvectors for non-degenerated modes
-    for(int i=0; i<np; i++)
-    {
-      M_x2xp[0][i] = 1.0 / sqrt(np);
-      if(np%2==0) M_x2xp[np/2][i] = 1.0 / sqrt(np) * pow(-1.0, i);
-    }
+  // Set up eigenvectors for non-degenerated modes
+  for (int i = 0; i < np; i++) {
+    M_x2xp[0][i] = 1.0 / sqrt(np);
+    if (np % 2 == 0) M_x2xp[np / 2][i] = 1.0 / sqrt(np) * pow(-1.0, i);
+  }
 
-    // Set up Ut
-    for(int i=0; i<np; i++)
-      for(int j=0; j<np; j++)
-      {
-        M_xp2x[i][j] = M_x2xp[j][i];
-      }
-
-    // Set up masses
-    int iworld = universe->iworld;
-    for(int i=1; i<=atom->ntypes; i++)
-    {
-      mass[i] = atom->mass[i];
-      if(iworld)
-      {
-        if(fmmode==physical) { mass[i] *= 1.0; }
-        else if(fmmode==normal) { mass[i] *= lam[iworld]; }
-        mass[i] *= fmass;
+  // Set up Ut
+  for (int i = 0; i < np; i++)
+    for (int j = 0; j < np; j++) { M_xp2x[i][j] = M_x2xp[j][i]; }
+
+  // Set up masses
+  int iworld = universe->iworld;
+  for (int i = 1; i <= atom->ntypes; i++) {
+    mass[i] = atom->mass[i];
+    if (iworld) {
+      if (fmmode == PHYSICAL) {
+        mass[i] *= 1.0;
+      } else if (fmmode == NORMAL) {
+        mass[i] *= lam[iworld];
       }
+      mass[i] *= fmass;
     }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixPIMDLangevin::nmpimd_transform(double **src, double **des, double *vector)
 {
-  if(cmode == SINGLE_PROC)
-  {
-    for(int i=0; i<ntotal; i++)
-    {
-      for(int d=0; d<3; d++)
-      {
+  if (cmode == SINGLE_PROC) {
+    for (int i = 0; i < ntotal; i++) {
+      for (int d = 0; d < 3; d++) {
         bufsorted[i][d] = 0.0;
-        for(int j=0; j<nreplica; j++)
-        {
-          bufsorted[i][d] += src[j*ntotal+i][d] * vector[j];
+        for (int j = 0; j < nreplica; j++) {
+          bufsorted[i][d] += src[j * ntotal + i][d] * vector[j];
         }
       }
     }
-    for(int i=0; i<ntotal; i++)
-    {
+    for (int i = 0; i < ntotal; i++) {
       tagint tagtmp = atom->tag[i];
-      for(int d=0; d<3; d++)
-      {
-        des[i][d] = bufsorted[tagtmp-1][d];
-      }
+      for (int d = 0; d < 3; d++) { des[i][d] = bufsorted[tagtmp - 1][d]; }
     }
-  }
-  else if(cmode == MULTI_PROC)
-  {
-  int n = atom->nlocal;
-  int m = 0;
+  } else if (cmode == MULTI_PROC) {
+    int n = atom->nlocal;
+    int m = 0;
 
-  for (int i = 0; i < n; i++)
-    for (int d = 0; d < 3; d++) {
-      des[i][d] = 0.0;
-      for (int j = 0; j < np; j++) { des[i][d] += (src[j][m] * vector[j]); }
-      m++;
-    }
+    for (int i = 0; i < n; i++)
+      for (int d = 0; d < 3; d++) {
+        des[i][d] = 0.0;
+        for (int j = 0; j < np; j++) { des[i][d] += (src[j][m] * vector[j]); }
+        m++;
+      }
   }
 }
 
@@ -1092,25 +1034,25 @@ void FixPIMDLangevin::nmpimd_transform(double **src, double **des, double *vecto
 void FixPIMDLangevin::comm_init()
 {
   // if(me == 0){
-    if (sizeplan) {
-      delete [] plansend;
-      delete [] planrecv;
-    }
+  if (sizeplan) {
+    delete[] plansend;
+    delete[] planrecv;
+  }
 
-    sizeplan = np - 1;
-    plansend = new int[sizeplan];
-    planrecv = new int[sizeplan];
-    modeindex = new int[sizeplan];
-    for (int i = 0; i < sizeplan; i++) {
-      int isend, irecv;
-      isend = ireplica + i + 1;
-      if (isend >= nreplica) isend -= nreplica;
-      irecv = ireplica - (i + 1);
-      if (irecv < 0) irecv += nreplica;
-      plansend[i] = universe->root_proc[isend];
-      planrecv[i] = universe->root_proc[irecv];
-      modeindex[i] = irecv;
-    }
+  sizeplan = np - 1;
+  plansend = new int[sizeplan];
+  planrecv = new int[sizeplan];
+  modeindex = new int[sizeplan];
+  for (int i = 0; i < sizeplan; i++) {
+    int isend, irecv;
+    isend = ireplica + i + 1;
+    if (isend >= nreplica) isend -= nreplica;
+    irecv = ireplica - (i + 1);
+    if (irecv < 0) irecv += nreplica;
+    plansend[i] = universe->root_proc[isend];
+    planrecv[i] = universe->root_proc[irecv];
+    modeindex[i] = irecv;
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1145,7 +1087,7 @@ void FixPIMDLangevin::reallocate()
   memory->create(bufrecv, maxlocal, 3, "FixPIMDLangevin:bufrecv");
   memory->create(tagsend, maxlocal, "FixPIMDLangevin:tagsend");
   memory->create(tagrecv, maxlocal, "FixPIMDLangevin:tagrecv");
-  memory->create(bufbeads, nreplica, maxlocal*3, "FixPIMDLangevin:bufrecv");
+  memory->create(bufbeads, nreplica, maxlocal * 3, "FixPIMDLangevin:bufrecv");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1160,36 +1102,31 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
   int i, m;
 
   // copy local values
-  for(i=0; i<nlocal; i++)
-  {
-    bufbeads[ireplica][3*i+0] = ptr[i][0];
-    bufbeads[ireplica][3*i+1] = ptr[i][1];
-    bufbeads[ireplica][3*i+2] = ptr[i][2];
+  for (i = 0; i < nlocal; i++) {
+    bufbeads[ireplica][3 * i + 0] = ptr[i][0];
+    bufbeads[ireplica][3 * i + 1] = ptr[i][1];
+    bufbeads[ireplica][3 * i + 2] = ptr[i][2];
   }
 
   // communicate values from the other beads
-  if(cmode == SINGLE_PROC)
-  {
+  if (cmode == SINGLE_PROC) {
     m = 0;
-    for(i=0; i<nlocal; i++)
-    {
+    for (i = 0; i < nlocal; i++) {
       tagint tagtmp = atom->tag[i];
-      bufsorted[tagtmp-1][0] = ptr[i][0];
-      bufsorted[tagtmp-1][1] = ptr[i][1];
-      bufsorted[tagtmp-1][2] = ptr[i][2];
+      bufsorted[tagtmp - 1][0] = ptr[i][0];
+      bufsorted[tagtmp - 1][1] = ptr[i][1];
+      bufsorted[tagtmp - 1][2] = ptr[i][2];
       m++;
     }
     MPI_Allgather(&m, 1, MPI_INT, counts, 1, MPI_INT, universe->uworld);
     for (i = 0; i < nreplica; i++) { counts[i] *= 3; }
     displacements[0] = 0;
-    for (i = 0; i < nreplica-1; i++) { displacements[i+1] = displacements[i] + counts[i]; }
-    MPI_Allgatherv(bufsorted[0], 3*m, MPI_DOUBLE, bufsortedall[0], counts, displacements, MPI_DOUBLE, universe->uworld);
-  }
-  else if(cmode == MULTI_PROC)
-  {
+    for (i = 0; i < nreplica - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; }
+    MPI_Allgatherv(bufsorted[0], 3 * m, MPI_DOUBLE, bufsortedall[0], counts, displacements,
+                   MPI_DOUBLE, universe->uworld);
+  } else if (cmode == MULTI_PROC) {
     m = 0;
-    for(i=0; i<nlocal; i++)
-    {
+    for (i = 0; i < nlocal; i++) {
       tagsend[m] = tag[i];
       bufsend[m][0] = ptr[i][0];
       bufsend[m][1] = ptr[i][1];
@@ -1198,29 +1135,31 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
     }
     MPI_Gather(&m, 1, MPI_INT, counts, 1, MPI_INT, 0, world);
     displacements[0] = 0;
-    for (i = 0; i < nprocs-1; i++) { displacements[i+1] = displacements[i] + counts[i]; }
-    MPI_Gatherv(tagsend, m, MPI_LMP_TAGINT, tagsendall, counts, displacements, MPI_LMP_TAGINT, 0, world);
+    for (i = 0; i < nprocs - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; }
+    MPI_Gatherv(tagsend, m, MPI_LMP_TAGINT, tagsendall, counts, displacements, MPI_LMP_TAGINT, 0,
+                world);
     for (i = 0; i < nprocs; i++) { counts[i] *= 3; }
-    for (i = 0; i < nprocs-1; i++) { displacements[i+1] = displacements[i] + counts[i]; }
-    MPI_Gatherv(bufsend[0], 3*m, MPI_DOUBLE, bufsendall[0], counts, displacements, MPI_DOUBLE, 0, world);
-    for(int iplan=0; iplan<sizeplan; iplan++)
-    {
-      if(me == 0){
-        MPI_Irecv(bufrecvall[0], 3*ntotal, MPI_DOUBLE, planrecv[iplan], 0, universe->uworld, &requests[0]);
-        MPI_Irecv(tagrecvall, ntotal, MPI_LMP_TAGINT, planrecv[iplan], 0, universe->uworld, &requests[1]);
-        MPI_Send(bufsendall[0], 3*ntotal, MPI_DOUBLE, plansend[iplan], 0, universe->uworld);
+    for (i = 0; i < nprocs - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; }
+    MPI_Gatherv(bufsend[0], 3 * m, MPI_DOUBLE, bufsendall[0], counts, displacements, MPI_DOUBLE, 0,
+                world);
+    for (int iplan = 0; iplan < sizeplan; iplan++) {
+      if (me == 0) {
+        MPI_Irecv(bufrecvall[0], 3 * ntotal, MPI_DOUBLE, planrecv[iplan], 0, universe->uworld,
+                  &requests[0]);
+        MPI_Irecv(tagrecvall, ntotal, MPI_LMP_TAGINT, planrecv[iplan], 0, universe->uworld,
+                  &requests[1]);
+        MPI_Send(bufsendall[0], 3 * ntotal, MPI_DOUBLE, plansend[iplan], 0, universe->uworld);
         MPI_Send(tagsendall, ntotal, MPI_LMP_TAGINT, plansend[iplan], 0, universe->uworld);
-        MPI_Waitall(2,requests,statuses);
+        MPI_Waitall(2, requests, statuses);
       }
       MPI_Bcast(tagrecvall, ntotal, MPI_LMP_TAGINT, 0, world);
-      MPI_Bcast(bufrecvall[0], 3*ntotal, MPI_DOUBLE, 0, world);
-      for(i=0; i<ntotal; i++)
-      {
+      MPI_Bcast(bufrecvall[0], 3 * ntotal, MPI_DOUBLE, 0, world);
+      for (i = 0; i < ntotal; i++) {
         m = atom->map(tagrecvall[i]);
         if (m < 0 || m >= nlocal) continue;
-        bufbeads[modeindex[iplan]][3*m+0] = bufrecvall[i][0];
-        bufbeads[modeindex[iplan]][3*m+1] = bufrecvall[i][1];
-        bufbeads[modeindex[iplan]][3*m+2] = bufrecvall[i][2];
+        bufbeads[modeindex[iplan]][3 * m + 0] = bufrecvall[i][0];
+        bufbeads[modeindex[iplan]][3 * m + 1] = bufrecvall[i][1];
+        bufbeads[modeindex[iplan]][3 * m + 2] = bufrecvall[i][2];
       }
     }
   }
@@ -1233,20 +1172,17 @@ void FixPIMDLangevin::compute_vir_()
 {
   int nlocal = atom->nlocal;
   xf = vir_ = xcf = centroid_vir = 0.0;
-      int idx = atom->map(1);
-  for(int i=0; i<nlocal; i++)
-  {
-    for(int j=0; j<3; j++)
-    {
+  for (int i = 0; i < nlocal; i++) {
+    for (int j = 0; j < 3; j++) {
       xf += x_unwrap[i][j] * atom->f[i][j];
       xcf += (x_unwrap[i][j] - xc[i][j]) * atom->f[i][j];
     }
   }
   MPI_Allreduce(&xf, &vir_, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
   MPI_Allreduce(&xcf, &centroid_vir, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
-  if(pstyle == ANISO){
-    for(int i=0; i<6; i++) c_vir_tensor[i] = 0.0;
-    for(int i=0; i<nlocal; i++){
+  if (pstyle == ANISO) {
+    for (int i = 0; i < 6; i++) c_vir_tensor[i] = 0.0;
+    for (int i = 0; i < nlocal; i++) {
       c_vir_tensor[0] += (x_unwrap[i][0] - xc[i][0]) * atom->f[i][0];
       c_vir_tensor[1] += (x_unwrap[i][1] - xc[i][1]) * atom->f[i][1];
       c_vir_tensor[2] += (x_unwrap[i][2] - xc[i][2]) * atom->f[i][2];
@@ -1264,14 +1200,14 @@ void FixPIMDLangevin::compute_vir()
 {
   volume = domain->xprd * domain->yprd * domain->zprd;
   c_press->compute_vector();
-  virial[0] = c_press->vector[0]*volume;
-  virial[1] = c_press->vector[1]*volume;
-  virial[2] = c_press->vector[2]*volume;
-  virial[3] = c_press->vector[3]*volume;
-  virial[4] = c_press->vector[4]*volume;
-  virial[5] = c_press->vector[5]*volume;
-  for(int i=0; i<6; i++) virial[i] /= universe->procs_per_world[universe->iworld];
-  double vir_bead=(virial[0]+virial[1]+virial[2]);
+  virial[0] = c_press->vector[0] * volume;
+  virial[1] = c_press->vector[1] * volume;
+  virial[2] = c_press->vector[2] * volume;
+  virial[3] = c_press->vector[3] * volume;
+  virial[4] = c_press->vector[4] * volume;
+  virial[5] = c_press->vector[5] * volume;
+  for (int i = 0; i < 6; i++) virial[i] /= universe->procs_per_world[universe->iworld];
+  double vir_bead = (virial[0] + virial[1] + virial[2]);
   MPI_Allreduce(&vir_bead, &vir, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
   MPI_Allreduce(MPI_IN_PLACE, &virial[0], 6, MPI_DOUBLE, MPI_SUM, universe->uworld);
 }
@@ -1282,10 +1218,10 @@ void FixPIMDLangevin::compute_stress_tensor()
 {
   int nlocal = atom->nlocal;
   int *type = atom->type;
-  if(universe->iworld == 0){
+  if (universe->iworld == 0) {
     inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
-    for(int i=0; i<6; i++) ke_tensor[i] = 0.0;
-    for(int i=0; i<nlocal; i++){
+    for (int i = 0; i < 6; i++) ke_tensor[i] = 0.0;
+    for (int i = 0; i < nlocal; i++) {
       ke_tensor[0] += 0.5 * mass[type[i]] * atom->v[i][0] * atom->v[i][0] * force->mvv2e;
       ke_tensor[1] += 0.5 * mass[type[i]] * atom->v[i][1] * atom->v[i][1] * force->mvv2e;
       ke_tensor[2] += 0.5 * mass[type[i]] * atom->v[i][2] * atom->v[i][2] * force->mvv2e;
@@ -1294,9 +1230,9 @@ void FixPIMDLangevin::compute_stress_tensor()
       ke_tensor[5] += 0.5 * mass[type[i]] * atom->v[i][1] * atom->v[i][2] * force->mvv2e;
     }
     MPI_Allreduce(MPI_IN_PLACE, &ke_tensor, 6, MPI_DOUBLE, MPI_SUM, world);
-    for(int i=0; i<6; i++)
-    {
-      stress_tensor[i] = inv_volume * ((2*ke_tensor[i] - c_vir_tensor[i]) * force->nktv2p + virial[i]) / np;
+    for (int i = 0; i < 6; i++) {
+      stress_tensor[i] =
+          inv_volume * ((2 * ke_tensor[i] - c_vir_tensor[i]) * force->nktv2p + virial[i]) / np;
     }
   }
   MPI_Bcast(&stress_tensor, 6, MPI_DOUBLE, 0, universe->uworld);
@@ -1310,12 +1246,8 @@ void FixPIMDLangevin::compute_totke()
   totke = ke_bead = 0.0;
   int nlocal = atom->nlocal;
   int *type = atom->type;
-  for(int i=0; i<nlocal; i++)
-  {
-    for(int j=0; j<3; j++)
-    {
-      kine += 0.5 * mass[type[i]] * atom->v[i][j] * atom->v[i][j];
-    }
+  for (int i = 0; i < nlocal; i++) {
+    for (int j = 0; j < 3; j++) { kine += 0.5 * mass[type[i]] * atom->v[i][j] * atom->v[i][j]; }
   }
   kine *= force->mvv2e;
   MPI_Allreduce(&kine, &ke_bead, 1, MPI_DOUBLE, MPI_SUM, world);
@@ -1329,13 +1261,13 @@ void FixPIMDLangevin::compute_spring_energy()
   total_spring_energy = se_bead = 0.0;
 
   double **x = atom->x;
-  double* _mass = atom->mass;
-  int* type = atom->type;
+  double *_mass = atom->mass;
+  int *type = atom->type;
   int nlocal = atom->nlocal;
 
-  for(int i=0; i<nlocal; i++)
-  {
-    spring_energy += 0.5 * _mass[type[i]] * fbond * lam[universe->iworld] * (x[i][0]*x[i][0] + x[i][1]*x[i][1] + x[i][2]*x[i][2]);
+  for (int i = 0; i < nlocal; i++) {
+    spring_energy += 0.5 * _mass[type[i]] * fbond * lam[universe->iworld] *
+        (x[i][0] * x[i][0] + x[i][1] * x[i][1] + x[i][2] * x[i][2]);
   }
   MPI_Allreduce(&spring_energy, &se_bead, 1, MPI_DOUBLE, MPI_SUM, world);
 }
@@ -1370,8 +1302,8 @@ void FixPIMDLangevin::compute_t_prim()
 /*
 void FixPIMDLangevin::compute_t_vir()
 {
-  t_vir = -0.5 / np * vir_;
-  t_cv = 1.5 * atom->natoms * force->boltz * temp - 0.5 / np * centroid_vir;
+  t_vir = -0.5 * inverse_np * vir_;
+  t_cv = 1.5 * atom->natoms * force->boltz * temp - 0.5 * inverse_np * centroid_vir;
 }
 */
 /* ---------------------------------------------------------------------- */
@@ -1387,9 +1319,8 @@ void FixPIMDLangevin::compute_p_prim()
 void FixPIMDLangevin::compute_p_cv()
 {
   inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
-  if(universe->iworld == 0)
-  {
-    p_cv = 1. / 3.  * inv_volume  * ((2. * ke_bead  - 1. * centroid_vir) * force->nktv2p + 1. * vir) / np;
+  if (universe->iworld == 0) {
+    p_cv = THIRD * inv_volume * ((2.0 * ke_bead - centroid_vir) * force->nktv2p + vir) / np;
   }
   MPI_Bcast(&p_cv, 1, MPI_DOUBLE, 0, universe->uworld);
 }
@@ -1399,58 +1330,53 @@ void FixPIMDLangevin::compute_p_cv()
 void FixPIMDLangevin::compute_totenthalpy()
 {
   volume = domain->xprd * domain->yprd * domain->zprd;
-  if(barostat == BZP)
-  {
-    if(pstyle == ISO)
-    {
-      totenthalpy = tote + 0.5*W*vw[0]*vw[0]/np + Pext * volume / force->nktv2p - Vcoeff * kBT * log(volume);
+  if (barostat == BZP) {
+    if (pstyle == ISO) {
+      totenthalpy = tote + 0.5 * W * vw[0] * vw[0] * inverse_np + Pext * volume / force->nktv2p -
+          Vcoeff * kBT * log(volume);
+    } else if (pstyle == ANISO) {
+      totenthalpy = tote + 0.5 * W * vw[0] * vw[0] * inverse_np + 0.5 * W * vw[1] * vw[1] * inverse_np +
+          0.5 * W * vw[2] * vw[2] * inverse_np + Pext * volume / force->nktv2p - Vcoeff * kBT * log(volume);
     }
-    else if(pstyle == ANISO)
-    {
-      totenthalpy = tote + 0.5*W*vw[0]*vw[0]/np + 0.5*W*vw[1]*vw[1]/np + 0.5*W*vw[2]*vw[2]/np + Pext * volume / force->nktv2p - Vcoeff * kBT * log(volume);
-    }
-  }
-  else if(barostat == MTTK)  totenthalpy = tote + 1.5*W*vw[0]*vw[0]/np + Pext * (volume - vol0);
+  } else if (barostat == MTTK)
+    totenthalpy = tote + 1.5 * W * vw[0] * vw[0] * inverse_np + Pext * (volume - vol0);
 }
 
 /* ---------------------------------------------------------------------- */
 
 double FixPIMDLangevin::compute_vector(int n)
 {
-  if(n==0) { return ke_bead; }
-  if(n==1) { return se_bead; }
-  if(n==2) { return pe_bead; }
-  if(n==3) { return tote; }
+  if (n == 0) return ke_bead;
+  if (n == 1) return se_bead;
+  if (n == 2) return pe_bead;
+  if (n == 3) return tote;
   // if(n==3) { return W*vw[0]; }
-  if(!pstat_flag)
-  {
-    if(n==4) { return t_prim; }
-    if(n==5) { return t_vir; }
-    if(n==6) { return t_cv; }
-  }
-  else if(pstat_flag)
-  {
-    if(pstyle == ISO)
-    {
-      if(barostat == BZP)
-      {
-        if(n==4) { return 0.5*W*vw[0]*vw[0]; }
+  if (!pstat_flag) {
+    if (n == 4) return t_prim;
+    if (n == 5) return t_vir;
+    if (n == 6) return t_cv;
+  } else if (pstat_flag) {
+    if (pstyle == ISO) {
+      if (barostat == BZP) {
+        if (n == 4) return 0.5 * W * vw[0] * vw[0];
+      } else if (barostat == MTTK) {
+        if (n == 4) return 1.5 * W * vw[0] * vw[0];
       }
-      else if(barostat == MTTK)
-      {
-        if(n==4) { return 1.5*W*vw[0]*vw[0]; }
+      if (n == 5) {
+        volume = domain->xprd * domain->yprd * domain->zprd;
+        return np * Pext * volume / force->nktv2p;
       }
-      if(n==5) { volume = domain->xprd * domain->yprd * domain->zprd; return np * Pext * volume / force->nktv2p; }
-      if(n==6) { volume = domain->xprd * domain->yprd * domain->zprd; return - Vcoeff * np * kBT * log(volume); }
-      if(n==7) { return totenthalpy; }
-      if(n==8) { return p_cv; }
-      if(n==9) { return total_spring_energy; }
-    }
-    else if(pstyle == ANISO)
-    {
-
+      if (n == 6) {
+        volume = domain->xprd * domain->yprd * domain->zprd;
+        return -Vcoeff * np * kBT * log(volume);
+      }
+      if (n == 7) return totenthalpy;
+      if (n == 8) return p_cv;
+      if (n == 9) return total_spring_energy;
+    } else if (pstyle == ANISO) {
     }
   }
+  
   /*
 
   if(n==7) { return p_prim; }
@@ -1474,7 +1400,6 @@ double FixPIMDLangevin::compute_vector(int n)
     if(n>14 && n<21) return stress_tensor[n-15];
     if(n==21) { volume = domain->xprd * domain->yprd * domain->zprd; return np * Pext * volume / force->nktv2p; }
     if(n==22) { volume = domain->xprd * domain->yprd * domain->zprd; return - Vcoeff * np * kBT * log(volume); }
-  }
+  }  */
   return 0.0;
-  */
 }
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 3af036caf9..93f4670808 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -47,7 +47,7 @@ class FixPIMDLangevin : public Fix {
   int np;                                  // number of beads
   double inverse_np;                       // 1.0/np
   double temp;                             // temperature
-  double planck, hbar;                     // Planck's constant
+  double hbar;                             // Planck's constant
   double lj_epsilon, lj_sigma, lj_mass;    // LJ unit energy, length, and mass scales
   double other_planck;
   double kBT;              // k_B * temp
@@ -119,8 +119,7 @@ class FixPIMDLangevin : public Fix {
   int tstat_flag;    // tstat_flat = 1 if thermostat if used
   void Langevin_init();
   void b_step();    // integrate for dt/2 according to B part (v <- v + f * dt/2)
-  void
-  a_step();    // integrate for dt/2 according to A part (non-centroid mode, harmonic force between replicas)
+  void a_step();    // integrate for dt/2 according to A part (non-centroid mode, harmonic force between replicas)
   void qc_step();    // integrate for dt/2 for the centroid mode (x <- x + v * dt/2)
   void o_step();     // integrate for dt according to O part (O-U process, for thermostating)
 

From 6b1cad1e3d1624b947a2798dca3c80bb63161cd0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 25 Feb 2023 23:16:51 -0500
Subject: [PATCH 017/396] programming style updates

---
 src/REPLICA/fix_pimd_langevin.cpp | 155 ++++++++++++------------------
 src/REPLICA/fix_pimd_langevin.h   |   6 +-
 2 files changed, 62 insertions(+), 99 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 22bed54c3b..24b677b141 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -64,7 +64,7 @@ enum { SINGLE_PROC, MULTI_PROC };
 /* ---------------------------------------------------------------------- */
 
 FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
-    Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr)
+  Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr)
 {
   time_integrate = 1;
   tagsend = tagrecv = nullptr;
@@ -101,12 +101,17 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   tau = 1.0;
   tau_p = 1.0;
   Pext = 1.0;
+  pilescale = 1.0;
   tstat_flag = 1;
   pstat_flag = 0;
   mapflag = 1;
   removecomflag = 1;
   fmmode = PHYSICAL;
   pstyle = ISO;
+  totenthalpy = 0.0;
+
+  int seed = -1;
+
   for (int i = 0; i < 6; i++) p_flag[i] = 0;
 
   for (int i = 3; i < narg - 1; i += 2) {
@@ -119,20 +124,17 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         method = CMD;
       else
         error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin");
-    } else if (strcmp(arg[i], "integrator") == 0)
-
-    {
+    } else if (strcmp(arg[i], "integrator") == 0) {
       if (strcmp(arg[i + 1], "obabo") == 0)
         integrator = OBABO;
       else if (strcmp(arg[i + 1], "baoab") == 0)
         integrator = BAOAB;
       else
-        error->universe_all(FLERR,
-                            "Unknown integrator parameter for fix pimd/langevin. Only obabo and baoab "
-                            "integrators are supported!");
-    }
-
-    else if (strcmp(arg[i], "ensemble") == 0) {
+        error->universe_all(
+            FLERR,
+            "Unknown integrator parameter for fix pimd/langevin. Only obabo and baoab "
+            "integrators are supported!");
+    } else if (strcmp(arg[i], "ensemble") == 0) {
       if (strcmp(arg[i + 1], "nve") == 0) {
         ensemble = NVE;
         tstat_flag = 0;
@@ -150,95 +152,69 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         tstat_flag = 1;
         pstat_flag = 1;
       } else
-        error->universe_all(
-            FLERR,
-            "Unknown ensemble parameter for fix pimd/langevin. Only nve and nvt ensembles are supported!");
-    }
-
-    else if (strcmp(arg[i], "fmass") == 0) {
+        error->universe_all(FLERR,
+                            "Unknown ensemble parameter for fix pimd/langevin. Only nve and nvt "
+                            "ensembles are supported!");
+    } else if (strcmp(arg[i], "fmass") == 0) {
       fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (fmass < 0.0 || fmass > 1.0)
         error->universe_all(FLERR, "Invalid fmass value for fix pimd/langevin");
-    }
-
-    else if (strcmp(arg[i], "fmmode") == 0) {
+    } else if (strcmp(arg[i], "fmmode") == 0) {
       if (strcmp(arg[i + 1], "physical") == 0)
         fmmode = PHYSICAL;
       else if (strcmp(arg[i + 1], "normal") == 0)
         fmmode = NORMAL;
       else
-        error->universe_all(FLERR,
-                            "Unknown fictitious mass mode for fix pimd/langevin. Only physical mass and "
-                            "normal mode mass are supported!");
-    }
-
-    else if (strcmp(arg[i], "scale") == 0) {
-      pilescale = atof(arg[i + 1]);
-      if (pilescale < 0.0) error->universe_all(FLERR, "Invalid pile scale value for fix pimd/langevin");
-    }
-
-    else if (strcmp(arg[i], "temp") == 0) {
+        error->universe_all(
+            FLERR,
+            "Unknown fictitious mass mode for fix pimd/langevin. Only physical mass and "
+            "normal mode mass are supported!");
+    } else if (strcmp(arg[i], "scale") == 0) {
+      pilescale = utils::numeric(FLERR, arg[i + 1], false, lmp);
+      if (pilescale < 0.0)
+        error->universe_all(FLERR, "Invalid pile scale value for fix pimd/langevin");
+    } else if (strcmp(arg[i], "temp") == 0) {
       temp = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd/langevin");
-    }
-
-    else if (strcmp(arg[i], "lj") == 0) {
+    } else if (strcmp(arg[i], "lj") == 0) {
       lj_epsilon = utils::numeric(FLERR, arg[i + 1], false, lmp);
       lj_sigma = utils::numeric(FLERR, arg[i + 2], false, lmp);
       lj_mass = utils::numeric(FLERR, arg[i + 3], false, lmp);
       other_planck = utils::numeric(FLERR, arg[i + 4], false, lmp);
-      i++;
-      i++;
-      i++;
-    }
-
-    else if (strcmp(arg[i], "thermostat") == 0) {
+      i += 3;
+    } else if (strcmp(arg[i], "thermostat") == 0) {
       if (strcmp(arg[i + 1], "PILE_L") == 0) {
         thermostat = PILE_L;
-        seed = atoi(arg[i + 2]);
+        seed = utils::inumeric(FLERR, arg[i + 2], false, lmp);
         i++;
       }
-    }
-
-    else if (strcmp(arg[i], "tau") == 0) {
-      tau = atof(arg[i + 1]);
-    }
-
-    else if (strcmp(arg[i], "press") == 0) {
-      Pext = atof(arg[i + 1]);
+    } else if (strcmp(arg[i], "tau") == 0) {
+      tau = utils::numeric(FLERR, arg[i + 1], false, lmp);
+    } else if (strcmp(arg[i], "press") == 0) {
+      Pext = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (Pext < 0.0) error->universe_all(FLERR, "Invalid press value for fix pimd/langevin");
-    }
-
-    else if (strcmp(arg[i], "barostat") == 0) {
+    } else if (strcmp(arg[i], "barostat") == 0) {
       if (strcmp(arg[i + 1], "MTTK") == 0) {
         barostat = MTTK;
       } else if (strcmp(arg[i + 1], "BZP") == 0) {
         barostat = BZP;
       } else
         error->universe_all(FLERR, "Unknown barostat parameter for fix pimd/langevin");
-    }
-
-    else if (strcmp(arg[i], "iso") == 0) {
+    } else if (strcmp(arg[i], "iso") == 0) {
       pstyle = ISO;
       i--;
-    }
-
-    else if (strcmp(arg[i], "aniso") == 0) {
+    } else if (strcmp(arg[i], "aniso") == 0) {
       pstyle = ANISO;
       i--;
-    }
-
-    else if (strcmp(arg[i], "taup") == 0) {
-      tau_p = atof(arg[i + 1]);
+    } else if (strcmp(arg[i], "taup") == 0) {
+      tau_p = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (tau_p <= 0.0) error->universe_all(FLERR, "Invalid tau_p value for fix pimd/langevin");
     } else if (strcmp(arg[i], "fixcom") == 0) {
       if (strcmp(arg[i + 1], "yes") == 0)
         removecomflag = 1;
       else if (strcmp(arg[i + 1], "no") == 0)
         removecomflag = 0;
-    }
-
-    else if (strcmp(arg[i], "map") == 0) {
+    } else if (strcmp(arg[i], "map") == 0) {
       if (strcmp(arg[i + 1], "yes") == 0)
         mapflag = 1;
       else if (strcmp(arg[i + 1], "no") == 0)
@@ -257,25 +233,11 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
 
   // some initilizations
 
-  id_pe = new char[8];
-  strcpy(id_pe, "pimd_pe");
-  char **newarg = new char *[3];
-  newarg[0] = id_pe;
-  newarg[1] = (char *) "all";
-  newarg[2] = (char *) "pe";
-  modify->add_compute(3, newarg);
-  delete[] newarg;
+  id_pe = utils::strdup(std::string(id) + "_pimd_pe");
+  modify->add_compute(std::string(id_pe) + " all pe");
 
-  id_press = new char[12];
-  strcpy(id_press, "pimd_press");
-  newarg = new char *[5];
-  newarg[0] = id_press;
-  newarg[1] = (char *) "all";
-  newarg[2] = (char *) "pressure";
-  newarg[3] = (char *) "thermo_temp";
-  newarg[4] = (char *) "virial";
-  modify->add_compute(5, newarg);
-  delete[] newarg;
+  id_press = utils::strdup(std::string(id) + "_pimd_press");
+  modify->add_compute(std::string(id_press) + " all pressure thermo_temp virial");
 
   vol0 = domain->xprd * domain->yprd * domain->zprd;
 
@@ -339,7 +301,14 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
 
 /* ---------------------------------------------------------------------- */
 
-FixPIMDLangevin::~FixPIMDLangevin() {}
+FixPIMDLangevin::~FixPIMDLangevin()
+{
+  modify->delete_compute(id_pe);
+  modify->delete_compute(id_press);
+  delete[] id_pe;
+  delete[] id_press;
+  delete random;
+}
 
 /* ---------------------------------------------------------------------- */
 
@@ -387,8 +356,8 @@ void FixPIMDLangevin::init()
   beta_np = 1.0 / force->boltz / temp * inverse_np;
   fbond = _fbond * force->mvv2e;
 
-  if (universe->me == 0)
-    printf("fix pimd/langevin -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
+  if ((universe->me == 0) && (universe->uscreen))
+    fprintf(universe->uscreen, "fix pimd/langevin -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
 
   if (integrator == OBABO) {
     dtf = 0.5 * update->dt * force->ftm2v;
@@ -413,15 +382,10 @@ void FixPIMDLangevin::init()
   Langevin_init();
   if (pstat_flag) baro_init();
 
-  int ipe = modify->find_compute(id_pe);
-  c_pe = modify->compute[ipe];
-
-  int ipress = modify->find_compute(id_press);
-  c_press = modify->compute[ipress];
+  c_pe = modify->get_compute_by_id(id_pe);
+  c_press = modify->get_compute_by_id(id_press);
 
   t_prim = t_vir = t_cv = p_prim = p_vir = p_cv = p_md = 0.0;
-
-  if (universe->me == 0) fprintf(screen, "fix pimd/langevin successfully initialized!\n");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1335,8 +1299,9 @@ void FixPIMDLangevin::compute_totenthalpy()
       totenthalpy = tote + 0.5 * W * vw[0] * vw[0] * inverse_np + Pext * volume / force->nktv2p -
           Vcoeff * kBT * log(volume);
     } else if (pstyle == ANISO) {
-      totenthalpy = tote + 0.5 * W * vw[0] * vw[0] * inverse_np + 0.5 * W * vw[1] * vw[1] * inverse_np +
-          0.5 * W * vw[2] * vw[2] * inverse_np + Pext * volume / force->nktv2p - Vcoeff * kBT * log(volume);
+      totenthalpy = tote + 0.5 * W * vw[0] * vw[0] * inverse_np +
+          0.5 * W * vw[1] * vw[1] * inverse_np + 0.5 * W * vw[2] * vw[2] * inverse_np +
+          Pext * volume / force->nktv2p - Vcoeff * kBT * log(volume);
     }
   } else if (barostat == MTTK)
     totenthalpy = tote + 1.5 * W * vw[0] * vw[0] * inverse_np + Pext * (volume - vol0);
@@ -1376,7 +1341,7 @@ double FixPIMDLangevin::compute_vector(int n)
     } else if (pstyle == ANISO) {
     }
   }
-  
+
   /*
 
   if(n==7) { return p_prim; }
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 93f4670808..e68f326ae6 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -107,14 +107,12 @@ class FixPIMDLangevin : public Fix {
   double dtv, dtf, dtv2, dtv3;
   double gamma, c1, c2, tau;
   double *tau_k, *c1_k, *c2_k;
-  double pilescale = 1.0;
+  double pilescale;
   double Lan_temp;
   double r1, r2, r3;
   double _omega_np, *_omega_k, *Lan_s, *Lan_c;    // sin(omega_k*dt*0.5), cos(omega_k*dt*0.5)
 
   class RanMars *random;
-  int seed;
-  FILE *frand;
 
   int tstat_flag;    // tstat_flat = 1 if thermostat if used
   void Langevin_init();
@@ -128,7 +126,7 @@ class FixPIMDLangevin : public Fix {
   double f_omega, mtk_term1;
   int pstat_flag;    // pstat_flag = 1 if barostat is used
   int pstyle;        // pstyle = ISO or ANISO (will support TRICLINIC in the future)
-  double W, tau_p, Pext, totenthalpy = 0.0, Vcoeff;
+  double W, tau_p, Pext, totenthalpy, Vcoeff;
   int p_flag[6];
   double vw[6];               // barostat velocity
   double ke_tensor[6];        // kinetic energy tensor

From 5a593f06f6f48b6bc5220a139fecc704b4193a49 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 10 Mar 2023 02:00:18 -0500
Subject: [PATCH 018/396] apply make fix-whitespace

---
 doc/src/fix_deposit.rst | 6 +++---
 doc/src/fix_pimd.rst    | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst
index 0199ae98ce..7d19e93148 100644
--- a/doc/src/fix_deposit.rst
+++ b/doc/src/fix_deposit.rst
@@ -221,9 +221,9 @@ options choose a z-coordinate for insertion independently.
 
 The vx, vy, and vz components of velocity for the inserted particle
 are set by sampling a uniform distribution between the bounds set by
-the values specified for the *vx*, *vy*, and *vz* keywords. Note that 
-normally, new particles should be a assigned a negative vertical 
-velocity so that they move towards the surface.  For molecules, the 
+the values specified for the *vx*, *vy*, and *vz* keywords. Note that
+normally, new particles should be a assigned a negative vertical
+velocity so that they move towards the surface.  For molecules, the
 same velocity is given to every particle (no rotation or bond vibration).
 
 If the *target* option is used, the velocity vector of the inserted
diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 4d08497928..b774a7c8df 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -17,7 +17,7 @@ Syntax
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * style = *pimd/langevin* or *pimd/nvt* = style name of this fix command
 * zero or more keyword/value pairs may be appended
-* keywords for style *pimd/nvt* 
+* keywords for style *pimd/nvt*
 
   .. parsed-literal::
        *keywords* = *method* or *fmass* or *sp* or *temp* or *nhc*
@@ -27,7 +27,7 @@ Syntax
        *temp* value = temperature (temperarate units)
        *nhc* value = Nc = number of chains in Nose-Hoover thermostat
 
-* keywords for style *pimd/langevin* 
+* keywords for style *pimd/langevin*
 
   .. parsed-literal::
        *keywords* = *method* or *integrator* or *ensemble* or *fmass* or *fmmode* or *scale* or *lj* or *temp* or *thermostat* or *tau* or *press* or *barostat* or *taup* or *iso* or *aniso*
@@ -183,7 +183,7 @@ quasi-beads to :doc:`binary restart files <restart>`.  See the
 a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
 
-Fix *pimd/langevin* ... 
+Fix *pimd/langevin* ...
 
 None of the :doc:`fix_modify <fix_modify>` options
 are relevant to fix pimd/nvt.

From da6d3de48ea6e5b13571339a9a40eec2d1a2574a Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 10 Mar 2023 02:06:40 -0500
Subject: [PATCH 019/396] correct planck's constant for lj units

---
 src/REPLICA/fix_pimd_langevin.cpp | 8 +++-----
 src/REPLICA/fix_pimd_langevin.h   | 1 +
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 24b677b141..879c546326 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -55,7 +55,6 @@ enum { BAOAB, OBABO };
 enum { ISO, ANISO, TRICLINIC };
 enum { PILE_L };
 enum { MTTK, BZP };
-// char* Barostats[] = {"MTTK", "BZP"};
 
 static std::map<int, std::string> Barostats{{MTTK, "MTTK"}, {BZP, "BZP"}};
 enum { NVE, NVT, NPH, NPT };
@@ -181,7 +180,8 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
       lj_sigma = utils::numeric(FLERR, arg[i + 2], false, lmp);
       lj_mass = utils::numeric(FLERR, arg[i + 3], false, lmp);
       other_planck = utils::numeric(FLERR, arg[i + 4], false, lmp);
-      i += 3;
+      other_mvv2e = utils::numeric(FLERR, arg[i + 5], false, lmp);
+      i += 4;
     } else if (strcmp(arg[i], "thermostat") == 0) {
       if (strcmp(arg[i + 1], "PILE_L") == 0) {
         thermostat = PILE_L;
@@ -317,7 +317,6 @@ int FixPIMDLangevin::setmask()
   int mask = 0;
   mask |= POST_FORCE;
   mask |= INITIAL_INTEGRATE;
-  // mask |= POST_NEIGHBOR;
   mask |= FINAL_INTEGRATE;
   mask |= END_OF_STEP;
   return mask;
@@ -341,7 +340,7 @@ void FixPIMDLangevin::init()
 
   double planck;
   if (strcmp(update->unit_style, "lj") == 0) {
-    double planck_star = sqrt(lj_epsilon) * sqrt(atom->mass[0]) * lj_sigma;
+    double planck_star = sqrt(lj_epsilon) * sqrt(lj_mass) * lj_sigma * sqrt(other_mvv2e);
     planck = other_planck / planck_star;
   } else {
     planck = force->hplanck;
@@ -997,7 +996,6 @@ void FixPIMDLangevin::nmpimd_transform(double **src, double **des, double *vecto
 
 void FixPIMDLangevin::comm_init()
 {
-  // if(me == 0){
   if (sizeplan) {
     delete[] plansend;
     delete[] planrecv;
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index e68f326ae6..6c450210e9 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -50,6 +50,7 @@ class FixPIMDLangevin : public Fix {
   double hbar;                             // Planck's constant
   double lj_epsilon, lj_sigma, lj_mass;    // LJ unit energy, length, and mass scales
   double other_planck;
+  double other_mvv2e;
   double kBT;              // k_B * temp
   double beta, beta_np;    // beta = 1./kBT beta_np = 1./kBT/np
   int thermostat;          // NHC or PILE_L

From f301c00406f6699d94f8632dc3ee6e598e89b40d Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 10 Mar 2023 02:37:15 -0500
Subject: [PATCH 020/396] delete unused nmpimd_transform

---
 src/REPLICA/fix_pimd_langevin.h | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 6c450210e9..b491179403 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -100,7 +100,6 @@ class FixPIMDLangevin : public Fix {
 
   void reallocate();
   void nmpimd_init();
-  void nmpimd_transform(double **src, double **des, double **mat);
   void nmpimd_transform(double **, double **, double *);
 
   /* Langevin integration */

From 45da03340ab23ecb62941aad47b5f61bbd0f98d9 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 10 Mar 2023 02:56:44 -0500
Subject: [PATCH 021/396] update package info; delete unused code

---
 src/REPLICA/fix_pimd_langevin.cpp | 9 ++++-----
 src/REPLICA/fix_pimd_langevin.h   | 6 +-----
 2 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 879c546326..1552690a08 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -13,10 +13,10 @@
 
 /* ----------------------------------------------------------------------
    Package      FixPIMDLangevin
-   Purpose      Quantum Path Integral Algorithm for Quantum Chemistry
+   Purpose      Path Integral Molecular Dynamics with Langevin Thermostat
 
    Yifan Li @ Princeton University (yifanl0716@gmail.com)
-   Added components:
+   Current Features:
    - Multi-processor parallelism for each bead
    - White-noise Langevin thermostat
    - Bussi-Zykova-Parrinello barostat (isotropic and anisotropic)
@@ -557,7 +557,7 @@ void FixPIMDLangevin::post_force(int /*flag*/)
   }
 
   compute_vir();
-  compute_vir_();
+  compute_cvir();
   compute_pote();
   if (method == NMPIMD) {
     inter_replica_comm(f);
@@ -1127,10 +1127,9 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
   }
 }
 
-/* ---------------------------------------------------------------------- */
 /* ---------------------------------------------------------------------- */
 
-void FixPIMDLangevin::compute_vir_()
+void FixPIMDLangevin::compute_cvir()
 {
   int nlocal = atom->nlocal;
   xf = vir_ = xcf = centroid_vir = 0.0;
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index b491179403..60eca51907 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -177,14 +177,10 @@ class FixPIMDLangevin : public Fix {
   void compute_spring_energy();    // 2: spring elastic energy
   void compute_pote();             // 3: potential energy
   void compute_tote();             // 4: total energy: 1+2+3 for all the beads
-  // void compute_t_prim();  // 5: primitive kinetic energy estimator
-  // void compute_p_prim();  // primitive pressure estimator
   void compute_stress_tensor();
-  // void compute_t_vir();  // centroid-virial kinetic energy estimator
   void compute_p_cv();    // centroid-virial pressure estimator
-  // void compute_p_vir();  // centroid-virial pressure estimator
   void compute_vir();
-  void compute_vir_();
+  void compute_cvir();
   void compute_totenthalpy();
 };
 }    // namespace LAMMPS_NS

From 266f8fb67e7167d0865a53caf8fe7780f55fa34f Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Mon, 13 Mar 2023 23:42:25 -0400
Subject: [PATCH 022/396] clean up fix pimd/langevin

---
 src/REPLICA/fix_pimd_langevin.cpp | 94 ++++++++++++++++++-------------
 src/REPLICA/fix_pimd_langevin.h   | 19 ++-----
 2 files changed, 60 insertions(+), 53 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 1552690a08..4436878ba4 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -49,7 +49,7 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 using namespace MathConst;
 
-enum { PIMD, NMPIMD, CMD };
+enum { NMPIMD };
 enum { PHYSICAL, NORMAL };
 enum { BAOAB, OBABO };
 enum { ISO, ANISO, TRICLINIC };
@@ -88,7 +88,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
 
   mass = nullptr;
 
-  method = PIMD;
+  method = NMPIMD;
   ensemble = NVT;
   integrator = OBABO;
   thermostat = PILE_L;
@@ -115,15 +115,10 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
 
   for (int i = 3; i < narg - 1; i += 2) {
     if (strcmp(arg[i], "method") == 0) {
-      if (strcmp(arg[i + 1], "pimd") == 0)
-        method = PIMD;
-      else if (strcmp(arg[i + 1], "nmpimd") == 0)
-        method = NMPIMD;
-      else if (strcmp(arg[i + 1], "cmd") == 0)
-        method = CMD;
-      else
-        error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin");
-    } else if (strcmp(arg[i], "integrator") == 0) {
+      if (strcmp(arg[i + 1], "nmpimd") == 0)method = NMPIMD;
+      else error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin");
+    }
+    else if (strcmp(arg[i], "integrator") == 0) {
       if (strcmp(arg[i + 1], "obabo") == 0)
         integrator = OBABO;
       else if (strcmp(arg[i + 1], "baoab") == 0)
@@ -228,7 +223,15 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
 
   global_freq = 1;
   vector_flag = 1;
-  size_vector = 11;
+  if (!pstat_flag)  size_vector = 10;
+  else if (pstat_flag) {
+    if (pstyle == ISO){
+    size_vector = 15;
+    }
+    else if (pstyle == ANISO){
+      size_vector = 17;
+    }
+  }
   extvector = 1;
 
   // some initilizations
@@ -391,7 +394,6 @@ void FixPIMDLangevin::init()
 
 void FixPIMDLangevin::setup(int vflag)
 {
-  if (universe->me == 0) printf("Setting up Path-Integral ...\n");
   int nlocal = atom->nlocal;
   double **x = atom->x;
   double **v = atom->v;
@@ -427,8 +429,6 @@ void FixPIMDLangevin::setup(int vflag)
     else if (cmode == MULTI_PROC)
       nmpimd_transform(bufbeads, v, M_x2xp[universe->iworld]);
   }
-  if (universe->me == 0 && screen) fprintf(screen, "Setting up Path-Integral ...\n");
-  if (universe->me == 0) printf("Setting up Path-Integral ...\n");
   post_force(vflag);
   compute_totke();
   end_of_step();
@@ -558,6 +558,7 @@ void FixPIMDLangevin::post_force(int /*flag*/)
 
   compute_vir();
   compute_cvir();
+  compute_t_vir();
   compute_pote();
   if (method == NMPIMD) {
     inter_replica_comm(f);
@@ -1231,6 +1232,8 @@ void FixPIMDLangevin::compute_spring_energy()
         (x[i][0] * x[i][0] + x[i][1] * x[i][1] + x[i][2] * x[i][2]);
   }
   MPI_Allreduce(&spring_energy, &se_bead, 1, MPI_DOUBLE, MPI_SUM, world);
+  se_bead /= universe->procs_per_world[universe->iworld];
+  MPI_Allreduce(&se_bead, &total_spring_energy, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1243,6 +1246,7 @@ void FixPIMDLangevin::compute_pote()
   c_pe->compute_scalar();
   pe_bead = c_pe->scalar;
   pot_energy_partition = pe_bead / universe->procs_per_world[universe->iworld];
+  MPI_Allreduce(&pot_energy_partition, &pote, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1253,28 +1257,28 @@ void FixPIMDLangevin::compute_tote()
 }
 
 /* ---------------------------------------------------------------------- */
-/*
+
 void FixPIMDLangevin::compute_t_prim()
 {
   t_prim = 1.5 * atom->natoms * np * force->boltz * temp - total_spring_energy;
 }
-*/
+
 /* ---------------------------------------------------------------------- */
-/*
+
 void FixPIMDLangevin::compute_t_vir()
 {
   t_vir = -0.5 * inverse_np * vir_;
   t_cv = 1.5 * atom->natoms * force->boltz * temp - 0.5 * inverse_np * centroid_vir;
 }
-*/
+
 /* ---------------------------------------------------------------------- */
-/*
+
 void FixPIMDLangevin::compute_p_prim()
 {
   p_prim = atom->natoms * np * force->boltz * temp * inv_volume - 1.0 / 1.5 * inv_volume * total_spring_energy;
   p_prim *= force->nktv2p;
 }
-*/
+
 /* ---------------------------------------------------------------------- */
 
 void FixPIMDLangevin::compute_p_cv()
@@ -1312,30 +1316,42 @@ double FixPIMDLangevin::compute_vector(int n)
   if (n == 1) return se_bead;
   if (n == 2) return pe_bead;
   if (n == 3) return tote;
-  // if(n==3) { return W*vw[0]; }
-  if (!pstat_flag) {
-    if (n == 4) return t_prim;
-    if (n == 5) return t_vir;
-    if (n == 6) return t_cv;
-  } else if (pstat_flag) {
-    if (pstyle == ISO) {
-      if (barostat == BZP) {
-        if (n == 4) return 0.5 * W * vw[0] * vw[0];
-      } else if (barostat == MTTK) {
-        if (n == 4) return 1.5 * W * vw[0] * vw[0];
-      }
-      if (n == 5) {
+  if (n == 4) return t_prim;
+  if (n == 5) return t_vir;
+  if (n == 6) return t_cv;
+  if (n == 7) return p_prim;
+  if (n == 8) return p_md;
+  if (n == 9) return p_cv;
+
+  if (pstat_flag) {
         volume = domain->xprd * domain->yprd * domain->zprd;
+    if (pstyle == ISO) {
+      if (n == 10) return vw[0];
+      if (barostat == BZP) {
+        if (n == 11) return 0.5 * W * vw[0] * vw[0];
+      } else if (barostat == MTTK) {
+        if (n == 11) return 1.5 * W * vw[0] * vw[0];
+      }
+      if (n == 12) {
         return np * Pext * volume / force->nktv2p;
       }
-      if (n == 6) {
+      if (n == 13) {
+        return -Vcoeff * np * kBT * log(volume);
+      }
+      if (n == 14) return totenthalpy;
+    } else if (pstyle == ANISO) {
+      if (n == 10) return vw[0];
+      if (n == 11) return vw[1];
+      if (n == 12) return vw[2];
+      if (n == 13) return 0.5 * W * (vw[0] * vw[0] + vw[1] * vw[1] + vw[2] * vw[2]);
+      if (n == 14) {
+        return np * Pext * volume / force->nktv2p;
+      }
+      if (n == 15) {
         volume = domain->xprd * domain->yprd * domain->zprd;
         return -Vcoeff * np * kBT * log(volume);
       }
-      if (n == 7) return totenthalpy;
-      if (n == 8) return p_cv;
-      if (n == 9) return total_spring_energy;
-    } else if (pstyle == ANISO) {
+      if (n == 16) return totenthalpy;
     }
   }
 
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 60eca51907..87481b2770 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -140,34 +140,21 @@ class FixPIMDLangevin : public Fix {
   /* centroid-virial estimator computation */
   double vol0 = 0.0;
   double inv_volume = 0.0;
-  // double inv_volume = 0.0, vol_ = 0.0, vol0 = 0.0;
   double volume = 0.0;
   double **xc, *xcall;
   int maxxc;
-  // int n_unwrap;
   int maxunwrap;
-  // int maxunwrap, nlocal_init;
-  //   tagint *tag_init, *tag_initall;
-  //   imageint *image_init, *image_initall;
   double **x_unwrap;
-  //   double **x_unwrap, **x_unwrapsort;
-  //   double **x_unwrapall;
-  //   void init_x_unwrap();
   void reallocate_x_unwrap();
   void reallocate_xc();
   void collect_xc();
-  // void compute_xc();
-  // void compute_fc();
   double xf, vir, vir_, xcf, centroid_vir;
-  double t_vir, t_cv, p_prim, p_vir, p_cv, p_cv_, p_md;
-  // double vir_, xcf, vir2;
+  double t_prim, t_vir, t_cv, p_prim, p_vir, p_cv, p_md;
 
   /* Computes */
   double kine, pote, tote, totke;
   double ke_bead, se_bead, pe_bead, pot_energy_partition;
   double total_spring_energy;
-  double t_prim;
-  // double p_prim;
   char *id_pe;
   char *id_press;
   class Compute *c_pe;
@@ -178,6 +165,10 @@ class FixPIMDLangevin : public Fix {
   void compute_pote();             // 3: potential energy
   void compute_tote();             // 4: total energy: 1+2+3 for all the beads
   void compute_stress_tensor();
+  void compute_t_prim();
+  void compute_t_vir();
+  void compute_t_cv();
+  void compute_p_prim();
   void compute_p_cv();    // centroid-virial pressure estimator
   void compute_vir();
   void compute_cvir();

From b4dc074638080e8964708c7ac2aaab4381d8e1b6 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Tue, 14 Mar 2023 02:46:31 -0400
Subject: [PATCH 023/396] delete global variable inv_volume

---
 src/REPLICA/fix_pimd_langevin.cpp | 13 ++++++++++---
 src/REPLICA/fix_pimd_langevin.h   |  3 +--
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 4436878ba4..fe1dabd551 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -411,6 +411,8 @@ void FixPIMDLangevin::setup(int vflag)
   }
   collect_xc();
   compute_spring_energy();
+  compute_t_prim();
+  compute_p_prim();
   if (method == NMPIMD) {
     inter_replica_comm(x);
     if (cmode == SINGLE_PROC)
@@ -495,6 +497,8 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
   }
   collect_xc();
   compute_spring_energy();
+  compute_t_prim();
+  compute_p_prim();
 
   if (method == NMPIMD) {
     inter_replica_comm(x);
@@ -1181,7 +1185,7 @@ void FixPIMDLangevin::compute_stress_tensor()
   int nlocal = atom->nlocal;
   int *type = atom->type;
   if (universe->iworld == 0) {
-    inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
+    double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
     for (int i = 0; i < 6; i++) ke_tensor[i] = 0.0;
     for (int i = 0; i < nlocal; i++) {
       ke_tensor[0] += 0.5 * mass[type[i]] * atom->v[i][0] * atom->v[i][0] * force->mvv2e;
@@ -1213,6 +1217,8 @@ void FixPIMDLangevin::compute_totke()
   }
   kine *= force->mvv2e;
   MPI_Allreduce(&kine, &ke_bead, 1, MPI_DOUBLE, MPI_SUM, world);
+  MPI_Allreduce(&ke_bead, &totke, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
+  totke /= universe->procs_per_world[universe->iworld];
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1232,8 +1238,8 @@ void FixPIMDLangevin::compute_spring_energy()
         (x[i][0] * x[i][0] + x[i][1] * x[i][1] + x[i][2] * x[i][2]);
   }
   MPI_Allreduce(&spring_energy, &se_bead, 1, MPI_DOUBLE, MPI_SUM, world);
-  se_bead /= universe->procs_per_world[universe->iworld];
   MPI_Allreduce(&se_bead, &total_spring_energy, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
+  total_spring_energy /= universe->procs_per_world[universe->iworld];
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1275,6 +1281,7 @@ void FixPIMDLangevin::compute_t_vir()
 
 void FixPIMDLangevin::compute_p_prim()
 {
+  double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
   p_prim = atom->natoms * np * force->boltz * temp * inv_volume - 1.0 / 1.5 * inv_volume * total_spring_energy;
   p_prim *= force->nktv2p;
 }
@@ -1283,7 +1290,7 @@ void FixPIMDLangevin::compute_p_prim()
 
 void FixPIMDLangevin::compute_p_cv()
 {
-  inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
+  double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
   if (universe->iworld == 0) {
     p_cv = THIRD * inv_volume * ((2.0 * ke_bead - centroid_vir) * force->nktv2p + vir) / np;
   }
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 87481b2770..43f6df5e84 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -139,8 +139,7 @@ class FixPIMDLangevin : public Fix {
 
   /* centroid-virial estimator computation */
   double vol0 = 0.0;
-  double inv_volume = 0.0;
-  double volume = 0.0;
+  double volume;
   double **xc, *xcall;
   int maxxc;
   int maxunwrap;

From 2c6fe1e8bc337a09df63ebb274b0b8c24362c818 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Wed, 15 Mar 2023 13:57:42 -0400
Subject: [PATCH 024/396] add p_md calculation

---
 src/REPLICA/fix_pimd_langevin.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index fe1dabd551..12233f6ee0 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -585,7 +585,7 @@ void FixPIMDLangevin::end_of_step()
   if (pstat_flag) compute_totenthalpy();
 
   if (update->ntimestep % 10000 == 0) {
-    if (universe->me == 0) printf("This is the end of step %ld.\n", update->ntimestep);
+    if (universe->me == 0) printf("This is the end of step %lld.\n", update->ntimestep);
   }
 }
 
@@ -1294,6 +1294,7 @@ void FixPIMDLangevin::compute_p_cv()
   if (universe->iworld == 0) {
     p_cv = THIRD * inv_volume * ((2.0 * ke_bead - centroid_vir) * force->nktv2p + vir) / np;
   }
+  p_md = THIRD * inv_volume * (totke + vir);
   MPI_Bcast(&p_cv, 1, MPI_DOUBLE, 0, universe->uworld);
 }
 

From 77b9fe37ba8e41b17e15118833ffb2203c162fd5 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Wed, 15 Mar 2023 14:00:56 -0400
Subject: [PATCH 025/396] delete dead code

---
 src/REPLICA/fix_pimd_langevin.cpp | 24 ------------------------
 1 file changed, 24 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 12233f6ee0..2266dc5e6c 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -1363,29 +1363,5 @@ double FixPIMDLangevin::compute_vector(int n)
     }
   }
 
-  /*
-
-  if(n==7) { return p_prim; }
-  if(n==8) { return p_md; }
-  if(n==9) { return p_cv; }
-  if(n==10) {return totenthalpy;
-  if(pstyle == ISO){
-    if(n==11) { return vw[0]; }
-    if(n==12) {
-      if(barostat == BZP) {  return 0.5*W*vw[0]*vw[0]; }
-      else if(barostat == MTTK) {  return 1.5*W*vw[0]*vw[0]; }
-    }
-    if(n==13) { volume = domain->xprd * domain->yprd * domain->zprd; return np * Pext * volume / force->nktv2p; }
-    if(n==14) { volume = domain->xprd * domain->yprd * domain->zprd;
-    // printf("Vcoeff = %.6e np = %d kBT = %.6e logV = %.6e\n", Vcoeff, np, kBT, log(volume));
-    return - Vcoeff * np * kBT * log(volume); }
-  }
-  else if(pstyle==ANISO){
-    if(n>10 && n<=13) return vw[n-11];
-    if(n==14) return 0.5*W*vw[0]*vw[0]+0.5*W*vw[1]*vw[1]+0.5*W*vw[2]*vw[2];
-    if(n>14 && n<21) return stress_tensor[n-15];
-    if(n==21) { volume = domain->xprd * domain->yprd * domain->zprd; return np * Pext * volume / force->nktv2p; }
-    if(n==22) { volume = domain->xprd * domain->yprd * domain->zprd; return - Vcoeff * np * kBT * log(volume); }
-  }  */
   return 0.0;
 }

From f7bc270c00040ae5a2da5cbc9dda990be571f3ab Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Wed, 15 Mar 2023 14:51:04 -0400
Subject: [PATCH 026/396] Do not initialized random number generator when there
 is no thermostat

---
 src/REPLICA/fix_pimd_langevin.cpp | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 2266dc5e6c..bcd94b3beb 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -250,9 +250,11 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
 
   // initialize Marsaglia RNG with processor-unique seed
 
-  if (integrator == BAOAB || integrator == OBABO) {
-    Lan_temp = temp;
-    random = new RanMars(lmp, seed + universe->me);
+  if (tstat_flag) {
+    if (integrator == BAOAB || integrator == OBABO) {
+      Lan_temp = temp;
+      random = new RanMars(lmp, seed + universe->me);
+    }
   }
 
   me = comm->me;

From 3f965a1c337f60262585278753ca2b2e4ae3a197 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Wed, 15 Mar 2023 16:25:56 -0400
Subject: [PATCH 027/396] format the specification of external pressure

---
 src/REPLICA/fix_pimd_langevin.cpp | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index bcd94b3beb..949129873f 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -185,9 +185,6 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
       }
     } else if (strcmp(arg[i], "tau") == 0) {
       tau = utils::numeric(FLERR, arg[i + 1], false, lmp);
-    } else if (strcmp(arg[i], "press") == 0) {
-      Pext = utils::numeric(FLERR, arg[i + 1], false, lmp);
-      if (Pext < 0.0) error->universe_all(FLERR, "Invalid press value for fix pimd/langevin");
     } else if (strcmp(arg[i], "barostat") == 0) {
       if (strcmp(arg[i + 1], "MTTK") == 0) {
         barostat = MTTK;
@@ -197,10 +194,10 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         error->universe_all(FLERR, "Unknown barostat parameter for fix pimd/langevin");
     } else if (strcmp(arg[i], "iso") == 0) {
       pstyle = ISO;
-      i--;
+      Pext = utils::numeric(FLERR, arg[i+1], false, lmp);
     } else if (strcmp(arg[i], "aniso") == 0) {
       pstyle = ANISO;
-      i--;
+      Pext = utils::numeric(FLERR, arg[i+1], false, lmp);
     } else if (strcmp(arg[i], "taup") == 0) {
       tau_p = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (tau_p <= 0.0) error->universe_all(FLERR, "Invalid tau_p value for fix pimd/langevin");

From 0aca0435ef3c852343fa985879623120bb4da199 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Wed, 15 Mar 2023 16:43:44 -0400
Subject: [PATCH 028/396] delete mapflag input script interface

---
 src/REPLICA/fix_pimd_langevin.cpp | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 949129873f..3559fc8efe 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -206,11 +206,6 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         removecomflag = 1;
       else if (strcmp(arg[i + 1], "no") == 0)
         removecomflag = 0;
-    } else if (strcmp(arg[i], "map") == 0) {
-      if (strcmp(arg[i + 1], "yes") == 0)
-        mapflag = 1;
-      else if (strcmp(arg[i + 1], "no") == 0)
-        mapflag = 0;
     } else {
       error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix {}", arg[i], style));
     }

From aa84548002d4ca690f030b6fc3bccbe167f20fbb Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Wed, 15 Mar 2023 16:45:18 -0400
Subject: [PATCH 029/396] set mapflag=0 if there is only 1 bead

---
 src/REPLICA/fix_pimd_langevin.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 3559fc8efe..964cca44c2 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -260,6 +260,9 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   nreplica = universe->nworlds;
   ireplica = universe->iworld;
 
+  if (nreplica == 1) mapflag = 0;
+  else mapflag = 1;
+
   int *iroots = new int[nreplica];
   MPI_Group uworldgroup, rootgroup;
 

From 4e0af69b67d77a247a3495109219697d60e9e7c5 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Wed, 15 Mar 2023 17:06:28 -0400
Subject: [PATCH 030/396] update documentation keyword part

---
 doc/src/fix_pimd.rst | 28 +++++++++++++++++++++-------
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index b774a7c8df..63f57f1fdf 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -30,15 +30,28 @@ Syntax
 * keywords for style *pimd/langevin*
 
   .. parsed-literal::
-       *keywords* = *method* or *integrator* or *ensemble* or *fmass* or *fmmode* or *scale* or *lj* or *temp* or *thermostat* or *tau* or *press* or *barostat* or *taup* or *iso* or *aniso*
+       *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *scale* or *temp* or *thermostat* or *tau* or or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj* 
        *method* value = *nmpimd*
-       *fmass* value = scaling factor on mass
-       *sp* value = scaling factor on Planck constant
-       *temp* value = target temperature (temperarate units)
-       *thermostat* values = PILE_L *seed*
-          *seed* = random number seed
+       *integrator* value = *obabo* or *baoab*
+       *fmmode* value = *physical* or *normal*
+       *temp* value = Temperature (temperarate unit)
+          Temperature = target temperarate of the thermostat
+       *thermostat* values = style seed
+          style value = *PILE_L*
+          seed = random number generator seed
        *tau* value = thermostat damping parameter (time unit)
-       *press* value = target pressure (pressure units)
+       *scale* value = scaling factor of the damping times of non-centroid modes of PILE_L thermostat
+       *iso* or *aniso* values = Pressure (pressure unit)
+         Pressure = scalar external pressure of the barostat 
+       *barostat* value = *BZP* or *MTTK*
+       *taup* value = barostat damping parameter (time unit)
+       *fixcom* value = *yes* or *no*
+       *lj* values = epsilon sigma mass planck mvv2e
+          epsilon = energy scale for reduced units (energy units)
+          sigma = length scale for reduced units (length units)
+          mass = mass scale for reduced units (mass units)
+          planck = Planck's constant for other unit style
+          mvv2e = mass * velocity^2 to energy conversion factor for other unit style
 
 Examples
 """"""""
@@ -46,6 +59,7 @@ Examples
 .. code-block:: LAMMPS
 
    fix 1 all pimd/nvt method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
+   fix 1 all pimd/langevin ensemble npt integrator obabo temp 113.15 thermostat PILE_L 1234 tau 1.0 press 1.0 barostat BZP taup 1.0 iso
 
 Description
 """""""""""

From 5071b2f016e591e9a4c469e9886745fb8d726633 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Wed, 15 Mar 2023 17:25:25 -0400
Subject: [PATCH 031/396] update document notes part

---
 doc/src/fix_pimd.rst | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 63f57f1fdf..5c82e9c55d 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -106,7 +106,9 @@ would be 3 x N x P x Nc.
    Fix *pimd/nvt* implements a complete velocity-verlet integrator
    combined with NH massive chain thermostat, so no other time
    integration fix should be used.
-   Similarly fix *pimd/langeving* implements ...
+   Fix *pimd/langevin* implements a complete velocity-verlet integrator
+   combined with Langevin thermostat in the normal mode representation, and 
+   also provides a barostat to sample the NPH/NPT ensembles.
 
 The *method* keyword determines what style of PIMD is performed.  A
 value of *pimd* is standard PIMD.  A value of *nmpimd* is for

From ad25af56a9bccd8c5da3b1f5ca610af25f0dde08 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 17 Mar 2023 15:29:26 -0400
Subject: [PATCH 032/396] add reference in fix pimd/langevin document

---
 doc/src/fix_pimd.rst | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 5c82e9c55d..1f7d406d5e 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -280,3 +280,10 @@ Path Integrals, McGraw-Hill, New York (1965).
 
 **(Herman)** M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).
 
+.. _Parrinello1:
+
+**(Parrinello1)** G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
+
+.. _Manolopoulos:
+
+**(Manolopoulos)** M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
\ No newline at end of file

From 0e22e36b941d26fd231cd69ce16c090382d91f97 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 17 Mar 2023 15:38:48 -0400
Subject: [PATCH 033/396] add method nmpimd note for fix pimd/langevin document

---
 doc/src/fix_pimd.rst | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 1f7d406d5e..4de504e70c 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -132,6 +132,10 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
    overall translation of the ring-polymer and is assigned the mass of
    the real particle.
 
+.. note::
+   Fix pimd/langevin only supports *method* value *nmpimd*. This should be enough 
+   for most PIMD applications for quantum thermodynamics purpose.
+
    Motion of the centroid can be effectively uncoupled from the other
    normal modes by scaling the fictitious masses to achieve a partial
    adiabatic separation.  This is called a Centroid Molecular Dynamics

From 008147d1f38dd1612d1ebe0e634208e265347dda Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 17 Mar 2023 17:41:29 -0400
Subject: [PATCH 034/396] correct mass preconditioning of fix pimd/langevin

---
 src/REPLICA/fix_pimd_langevin.cpp | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 964cca44c2..671625afc8 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -150,7 +150,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
                             "Unknown ensemble parameter for fix pimd/langevin. Only nve and nvt "
                             "ensembles are supported!");
     } else if (strcmp(arg[i], "fmass") == 0) {
-      fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
+      fmass = utils::numeric(FLERR, arg[i+1], false, lmp);
       if (fmass < 0.0 || fmass > 1.0)
         error->universe_all(FLERR, "Invalid fmass value for fix pimd/langevin");
     } else if (strcmp(arg[i], "fmmode") == 0) {
@@ -830,13 +830,13 @@ void FixPIMDLangevin::Langevin_init()
   Lan_s = new double[np];
   if (fmmode == PHYSICAL) {
     for (int i = 0; i < np; i++) {
-      _omega_k[i] = _omega_np * sqrt(lam[i]);
+      _omega_k[i] = _omega_np * sqrt(lam[i]) / sqrt(fmass);
       Lan_c[i] = cos(sqrt(lam[i]) * _omega_np_dt_half);
       Lan_s[i] = sin(sqrt(lam[i]) * _omega_np_dt_half);
     }
   } else if (fmmode == NORMAL) {
     for (int i = 0; i < np; i++) {
-      _omega_k[i] = _omega_np;
+      _omega_k[i] = _omega_np / sqrt(fmass);
       Lan_c[i] = cos(_omega_np_dt_half);
       Lan_s[i] = sin(_omega_np_dt_half);
     }
@@ -947,17 +947,17 @@ void FixPIMDLangevin::nmpimd_init()
   for (int i = 0; i < np; i++)
     for (int j = 0; j < np; j++) { M_xp2x[i][j] = M_x2xp[j][i]; }
 
-  // Set up masses
+  // Set up fictitious masses
   int iworld = universe->iworld;
   for (int i = 1; i <= atom->ntypes; i++) {
     mass[i] = atom->mass[i];
+    mass[i] *= fmass;
     if (iworld) {
       if (fmmode == PHYSICAL) {
         mass[i] *= 1.0;
       } else if (fmmode == NORMAL) {
         mass[i] *= lam[iworld];
       }
-      mass[i] *= fmass;
     }
   }
 }

From 76c19410c737faaeb2080b7268b31a5aed10b8d5 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 17 Mar 2023 17:44:48 -0400
Subject: [PATCH 035/396] correct fmass input of fix pimd/langevin

---
 src/REPLICA/fix_pimd_langevin.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 671625afc8..88289f7609 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -94,6 +94,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   thermostat = PILE_L;
   barostat = BZP;
   fmass = 1.0;
+  np = universe->nworlds;
   sp = 1.0;
   temp = 298.15;
   Lan_temp = 298.15;
@@ -151,7 +152,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
                             "ensembles are supported!");
     } else if (strcmp(arg[i], "fmass") == 0) {
       fmass = utils::numeric(FLERR, arg[i+1], false, lmp);
-      if (fmass < 0.0 || fmass > 1.0)
+      if (fmass < 0.0 || fmass > np)
         error->universe_all(FLERR, "Invalid fmass value for fix pimd/langevin");
     } else if (strcmp(arg[i], "fmmode") == 0) {
       if (strcmp(arg[i + 1], "physical") == 0)
@@ -335,7 +336,6 @@ void FixPIMDLangevin::init()
   // prepare the constants
 
   masstotal = group->mass(igroup);
-  np = universe->nworlds;
   inverse_np = 1.0 / np;
 
   double planck;

From fd21a584bf01e15639db1823d99524d23748458d Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Sat, 18 Mar 2023 10:17:01 -0400
Subject: [PATCH 036/396] update fmass part of fix pimd/langevin document

---
 doc/src/fix_pimd.rst | 28 ++++++++++++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 4de504e70c..28a5308dd7 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -30,10 +30,11 @@ Syntax
 * keywords for style *pimd/langevin*
 
   .. parsed-literal::
-       *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *scale* or *temp* or *thermostat* or *tau* or or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj* 
+       *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj* 
        *method* value = *nmpimd*
        *integrator* value = *obabo* or *baoab*
        *fmmode* value = *physical* or *normal*
+       *fmass* value = scaling factor on mass
        *temp* value = Temperature (temperarate unit)
           Temperature = target temperarate of the thermostat
        *thermostat* values = style seed
@@ -81,9 +82,11 @@ by the following equations:
 .. math::
 
    Z = & \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\
-   H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2m_i}\bigg) + V_{eff} \\
+   H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2M_i}\bigg) + V_{eff} \\
    V_{eff} = & \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
 
+$M_i$ is the fictitious mass of the $i$-th mode, and m is the actual mass of the atoms.
+
 The interested user is referred to any of the numerous references on
 this methodology, but briefly, each quantum particle in a path integral
 simulation is represented by a ring-polymer of P quasi-beads, labeled
@@ -152,6 +155,27 @@ masses of beads, which can be used for the Partial Adiabatic CMD
 :ref:`(Hone) <Hone>`, or to be set as P, which results in the fictitious
 masses to be equal to the real particle masses.
 
+The keyword *fmmode* of *fix pimd/langevin* determines the mode of fictitious 
+mass preconditioning. There are two options: *physical* and *normal*. If *fmmode* is 
+*physical*, then the physical mass of the particles are used (and then multiplied by
+*fmass*). If *fmmode* is *normal*, then the physical mass is first multiplied by the 
+eigenvalue of each normal mode, and then multiplied by *fmass*. More precisely, the 
+fictitious mass of *fix pimd/langevin* is determined by two factors: *fmmode* and *fmass*.
+If *fmmode* is *physical*, then the fictitious mass is
+.. math::
+   $M_i = \mathrm{fmass} \times m$
+   
+If *fmmode* is *normal*, then the fictitious mass is
+.. math::
+   $M_i = \mathrm{fmass} \times \lambda_i \times m$
+
+where $\lambda_i$ is the eigenvalue of the $i$-th normal mode.
+.. note::
+   Fictitious mass is only used in the momentum of the equation of motion
+   ($\bf{p}_i=M_i\bf{v}_i$), and not used in the spring elastic energy 
+   ($\sum_{i=1}^P \frac{1}{2}m\omega_P^2(q_i - q_{i+1})^2$, $m$ is always the 
+   actual mass of the particles). 
+
 The keyword *sp* is a scaling factor on Planck's constant, which can
 be useful for debugging or other purposes.  The default value of 1.0
 is appropriate for most situations.

From 7beec96dd333601d17088b44efda65a0390cd283 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Sat, 18 Mar 2023 10:23:09 -0400
Subject: [PATCH 037/396] support sp in fix pimd/langevin

---
 src/REPLICA/fix_pimd_langevin.cpp | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 88289f7609..7a901316f3 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -154,6 +154,9 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
       fmass = utils::numeric(FLERR, arg[i+1], false, lmp);
       if (fmass < 0.0 || fmass > np)
         error->universe_all(FLERR, "Invalid fmass value for fix pimd/langevin");
+    } else if (strcmp(arg[i], "sp") == 0) {
+      sp = utils::numeric(FLERR, arg[i+1], false, lmp);
+      if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd/nvt");
     } else if (strcmp(arg[i], "fmmode") == 0) {
       if (strcmp(arg[i + 1], "physical") == 0)
         fmmode = PHYSICAL;
@@ -345,7 +348,7 @@ void FixPIMDLangevin::init()
   } else {
     planck = force->hplanck;
   }
-
+  planck *= sp;
   hbar = planck / (2.0 * MY_PI);
   kBT = force->boltz * temp;
   double beta = 1.0 / (force->boltz * temp);

From d8f41a9032cb6271bb63bd53d8d5231d9051eddf Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Sat, 18 Mar 2023 10:25:05 -0400
Subject: [PATCH 038/396] support sp in fix pimd/nvt

---
 src/REPLICA/fix_pimd_nvt.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/REPLICA/fix_pimd_nvt.cpp b/src/REPLICA/fix_pimd_nvt.cpp
index 1f2f29f35c..e899c75a27 100644
--- a/src/REPLICA/fix_pimd_nvt.cpp
+++ b/src/REPLICA/fix_pimd_nvt.cpp
@@ -219,7 +219,7 @@ void FixPIMDNVT::init()
   const double Boltzmann = force->boltz;
   const double Plank = force->hplanck;
 
-  double hbar = Plank / (2.0 * MY_PI);
+  double hbar = Plank / (2.0 * MY_PI) * sp;
   double beta = 1.0 / (Boltzmann * nhc_temp);
   double _fbond = 1.0 * np / (beta * beta * hbar * hbar);
 

From be8c0b9835d68354e4f5b9925f25eb0bfc9f539b Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Mon, 20 Mar 2023 14:08:42 -0400
Subject: [PATCH 039/396] enable fixcom feature of fix pimd/langevin

---
 src/REPLICA/fix_pimd_langevin.cpp | 24 ++++++++++++++++++++++++
 src/REPLICA/fix_pimd_langevin.h   |  1 +
 2 files changed, 25 insertions(+)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 7a901316f3..e1d3960a50 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -451,6 +451,7 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
   if (integrator == OBABO) {
     if (tstat_flag) {
       o_step();
+      if (removecomflag) remove_com_motion();
       if (pstat_flag) press_o_step();
     }
     if (pstat_flag) {
@@ -488,6 +489,7 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
     a_step();
     if (tstat_flag) {
       o_step();
+      if (removecomflag) remove_com_motion();
       if (pstat_flag) press_o_step();
     }
     qc_step();
@@ -526,6 +528,7 @@ void FixPIMDLangevin::final_integrate()
   if (integrator == OBABO) {
     if (tstat_flag) {
       o_step();
+      if (removecomflag) remove_com_motion();
       if (pstat_flag) press_o_step();
     }
   } else if (integrator == BAOAB) {
@@ -1134,6 +1137,27 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
 
 /* ---------------------------------------------------------------------- */
 
+void FixPIMDLangevin::remove_com_motion(){
+  if(universe->iworld == 0)
+  {
+  double **v = atom->v;
+  int *mask = atom->mask;
+    int nlocal = atom->nlocal;
+    if (dynamic)  masstotal = group->mass(igroup);
+    double vcm[3];
+    group->vcm(igroup,masstotal,vcm);    
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit) {
+        v[i][0] -= vcm[0];
+        v[i][1] -= vcm[1];
+        v[i][2] -= vcm[2];
+      }
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
 void FixPIMDLangevin::compute_cvir()
 {
   int nlocal = atom->nlocal;
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 43f6df5e84..b8bed1a10f 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -147,6 +147,7 @@ class FixPIMDLangevin : public Fix {
   void reallocate_x_unwrap();
   void reallocate_xc();
   void collect_xc();
+  void remove_com_motion();
   double xf, vir, vir_, xcf, centroid_vir;
   double t_prim, t_vir, t_cv, p_prim, p_vir, p_cv, p_md;
 

From 7a38f49a21cacc6f0701e67c715f446f4c835df5 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Mon, 20 Mar 2023 14:10:09 -0400
Subject: [PATCH 040/396] add lj example for fix pimd/langevin

---
 examples/PACKAGES/pimd/lj/data.metalnpt01 | 422 ++++++++++++++++++++++
 examples/PACKAGES/pimd/lj/data.metalnpt02 | 422 ++++++++++++++++++++++
 examples/PACKAGES/pimd/lj/data.metalnpt03 | 422 ++++++++++++++++++++++
 examples/PACKAGES/pimd/lj/data.metalnpt04 | 422 ++++++++++++++++++++++
 examples/PACKAGES/pimd/lj/in.lmp          |  28 ++
 examples/PACKAGES/pimd/lj/run.sh          |   1 +
 6 files changed, 1717 insertions(+)
 create mode 100644 examples/PACKAGES/pimd/lj/data.metalnpt01
 create mode 100644 examples/PACKAGES/pimd/lj/data.metalnpt02
 create mode 100644 examples/PACKAGES/pimd/lj/data.metalnpt03
 create mode 100644 examples/PACKAGES/pimd/lj/data.metalnpt04
 create mode 100755 examples/PACKAGES/pimd/lj/in.lmp
 create mode 100644 examples/PACKAGES/pimd/lj/run.sh

diff --git a/examples/PACKAGES/pimd/lj/data.metalnpt01 b/examples/PACKAGES/pimd/lj/data.metalnpt01
new file mode 100644
index 0000000000..3dc2944ed9
--- /dev/null
+++ b/examples/PACKAGES/pimd/lj/data.metalnpt01
@@ -0,0 +1,422 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
+
+200 atoms
+1 atom types
+
+-11.876696863105703 11.876696863105703 xlo xhi
+-11.876696863105703 11.876696863105703 ylo yhi
+-11.876696863105703 11.876696863105703 zlo zhi
+
+Masses
+
+1 39.948
+
+Pair Coeffs # lj/cut
+
+1 0.00965188 3.4
+
+Atoms # atomic
+
+39 1 -10.338208372875723 -8.724519590498623 -8.445612139491281 0 -1 1
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diff --git a/examples/PACKAGES/pimd/lj/data.metalnpt02 b/examples/PACKAGES/pimd/lj/data.metalnpt02
new file mode 100644
index 0000000000..d48c9e654f
--- /dev/null
+++ b/examples/PACKAGES/pimd/lj/data.metalnpt02
@@ -0,0 +1,422 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
+
+200 atoms
+1 atom types
+
+-11.876696863105703 11.876696863105703 xlo xhi
+-11.876696863105703 11.876696863105703 ylo yhi
+-11.876696863105703 11.876696863105703 zlo zhi
+
+Masses
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diff --git a/examples/PACKAGES/pimd/lj/data.metalnpt03 b/examples/PACKAGES/pimd/lj/data.metalnpt03
new file mode 100644
index 0000000000..ca36561e7a
--- /dev/null
+++ b/examples/PACKAGES/pimd/lj/data.metalnpt03
@@ -0,0 +1,422 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
+
+200 atoms
+1 atom types
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+-11.876696863105703 11.876696863105703 xlo xhi
+-11.876696863105703 11.876696863105703 ylo yhi
+-11.876696863105703 11.876696863105703 zlo zhi
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+Masses
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+1 39.948
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+Pair Coeffs # lj/cut
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+1 0.00965188 3.4
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+Atoms # atomic
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diff --git a/examples/PACKAGES/pimd/lj/data.metalnpt04 b/examples/PACKAGES/pimd/lj/data.metalnpt04
new file mode 100644
index 0000000000..7fcb4a8bac
--- /dev/null
+++ b/examples/PACKAGES/pimd/lj/data.metalnpt04
@@ -0,0 +1,422 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
+
+200 atoms
+1 atom types
+
+-11.876696863105703 11.876696863105703 xlo xhi
+-11.876696863105703 11.876696863105703 ylo yhi
+-11.876696863105703 11.876696863105703 zlo zhi
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+Masses
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+104 -4.901664479006097 1.1052244598202794 3.4465808005881824
+151 -3.983151444075344 -3.2501191110732113 -1.2526584841338049
+60 -1.922006700361108 -0.7785585059363819 -4.390434339117124
+168 -2.788478664171041 3.923738577427861 2.49523972250301
+51 -1.6149322848467969 -3.4296394320723262 4.226459281197094
+97 -1.226730421851149 -2.392775221203476 5.070036120535187
+103 -2.9962982871055357 -2.90339448475708 -1.1348192929647936
+163 0.3128021577268095 -4.112121184421586 2.47129388197539
+175 -4.72131850682648 -1.6008946774115904 -3.6054426092000593
+158 -5.274680729271083 -0.4457302148856164 4.174272671309751
+85 2.9757034033315444 -0.5103121033627565 1.99919210117291
+63 1.600933165736236 1.4604641421860185 5.197681341346513
+133 0.3650834395918216 4.123541846312257 2.1615515366543354
+67 2.0607792864448453 2.3124375339420076 0.21959246817514527
+83 -6.156022387564482 -1.1548915743184078 -0.4948872456362283
+162 -2.1450070724040025 3.9286059442169066 2.007885747151935
+170 1.8166139807691821 -1.95234066921456 -1.8559861240898843
+181 -1.587457433365127 -3.2094890956838205 2.212401241994942
+71 1.7829689662908779 -3.6713609566551657 1.3773962271622693
+31 3.918178411733008 -0.5772484115851036 0.16726508680219976
+139 -4.560722486125075 -0.5471630166750243 5.863010868871481
+3 -3.9686726349917825 3.6173076990026054 2.5273959166862507
+108 0.3042801304200664 4.847444330423647 -0.35518169829313484
+16 -2.4685650045584717 5.98056595230015 0.9384145704518219
+110 -0.6129548866614436 1.8199747299312752 -0.6050782543434758
+50 -1.8884152067915962 -1.4877561250799833 -3.9811275374353494
+191 1.500896458072849 -1.9099553342822155 -5.024921011162899
+187 -2.013243274912701 -0.8604266013822317 -1.038480536601888
+180 1.4966822969502809 2.2104050426784707 3.732721924128324
+30 -2.3551911487538373 -1.0313809690434763 -1.4871503115129143
+2 2.4972367326603697 -1.5125466361921762 1.0762650051734106
+17 0.43112912988867413 -1.9548201848493156 -0.43017998184207773
+7 6.622180146484479 4.7673609572662725 0.19425898871224434
+164 2.301415823751322 0.4827221772498991 4.559127095693677
+69 -3.4364505629674733 -1.1594038113628669 -1.2078137888752072
+61 1.7869953777023173 0.9935547623401149 0.14745693195171444
+34 -0.027807484985171937 -3.1354780466577754 -1.036977576868685
+43 -1.3037743820903311 -5.61028065095172 -4.306710886889687
+177 2.1781720801097206 -1.516912077043328 -2.054689845757315
+179 0.4934049365569875 -4.8639422788504625 -6.225153590664796
+65 2.6970228261721383 0.19294320506195817 6.683323231860031
+27 -1.6731814501881797 0.7519385590564082 3.2183027406212203
+58 -0.7774753429967389 -0.6669437971456971 3.5183225900940927
+32 -5.389835933890947 -0.4954507654154201 0.4594525916972694
+26 0.7382474998065096 -3.102724138188651 -2.185686698723454
+142 -1.944479379421283 -1.2761486898263725 0.72348529709274
+100 -2.739025692998968 -2.6245009262596986 3.182008026346906
+184 1.4210317521782347 3.1395926369797884 5.319543188841913
+105 -1.2308708716614136 -1.2494207925918743 -3.3415190888725443
+75 -1.8835854547991517 -1.3807763884880995 3.052239941977269
+99 2.3501462152911015 -0.09098282020287418 -2.963130739502538
+193 3.2483282921859455 -6.045063326765766 -1.2297831607518321
+33 -1.5552221515820004 2.623852853566988 -0.3953508079233695
+79 2.0518370606822334 1.899510113710928 2.0859744201323727
+92 1.5026700715390955 0.9352029472761221 -5.528904283783295
+165 -2.240438523644089 -0.6103912799862421 0.40653914875448993
+199 -1.2653571662196268 3.710626862073433 1.4730516528440072
+70 1.655492430853343 0.17760859693009826 -1.650919734678463
+146 -1.4225048482747793 2.74232833480091 -3.413198079564811
+106 -1.093901348299414 0.20953760114868714 -0.7298112830112282
+52 6.647000075136453 -0.30141024565553315 1.2035752428962934
+86 0.6741589587443484 4.365068713763016 3.5677961016049315
+197 -0.666824417721529 0.7257967702216201 6.272517109849018
+185 -1.1845876194928404 2.1001111189632264 2.457366035714506
+190 -1.6517508143986053 2.271851696760304 3.7976228734124575
+145 -0.6660913411508007 -2.1887913545610314 1.427073342591097
+131 3.4923356345857024 1.8910870819349503 0.22757964871813297
+156 1.3901143776938099 -0.5912367128957199 -1.945898273856384
+10 -3.3254266550003906 2.363446512042732 -2.8505669909097167
+196 1.9772342503358795 2.9791453967072834 5.0702556945320305
+143 1.3619198656944898 -4.070780999483669 0.554762511858757
+13 -3.6607073229889986 -6.103961980753075 3.3895476442791126
+59 1.3424546798513801 -0.012418821554116527 -1.0607350515292961
+186 -0.19147109350375446 -0.14042042908600805 -5.06183250631794
+136 10.318783006250738 -0.33198398090799297 -3.1695432610471372
+62 -0.9320061937291512 -8.919718141167188 -1.0031472261072583
+192 -6.036717500669019 -0.4626110813075395 -5.283002697165421
+113 -1.9312339562598033 1.2868323831429733 -0.27836767602350954
+74 0.289298974376203 4.639184114550362 -1.3074893268836063
+118 2.3186362762712704 0.014757210175651903 -1.9096714905556824
+117 2.917320124569121 -0.927139463682407 -2.038093079844118
+23 3.445296199640721 -2.484450168397722 6.150025302403371
+171 -1.3488599922862394 -0.40015537573335275 5.541824987776105
+94 2.7016234671889183 -4.500360725821148 -0.3771036206116729
+41 0.040051409073174504 1.3144504850460685 -2.628956804481983
+141 0.8101589418958534 -0.40901282998394567 2.3777914588666906
+159 -2.168905163137191 -3.9077440516609387 3.1238186982134213
diff --git a/examples/PACKAGES/pimd/lj/in.lmp b/examples/PACKAGES/pimd/lj/in.lmp
new file mode 100755
index 0000000000..9670225958
--- /dev/null
+++ b/examples/PACKAGES/pimd/lj/in.lmp
@@ -0,0 +1,28 @@
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+
+fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
+
+dump dcd all custom 100 ${ibead}.xyz id type xu yu zu vx vy vz ix iy iz fx fy fz
+dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
diff --git a/examples/PACKAGES/pimd/lj/run.sh b/examples/PACKAGES/pimd/lj/run.sh
new file mode 100644
index 0000000000..2580ef1a41
--- /dev/null
+++ b/examples/PACKAGES/pimd/lj/run.sh
@@ -0,0 +1 @@
+mpirun -np 4 $LMP -in in.lmp -p 4x1 -log log -screen screen

From 0dd8a6aea2e9183a4b88d13cf36de3307851ae9f Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Mon, 20 Mar 2023 14:27:58 -0400
Subject: [PATCH 041/396] add document for keywords of fix pimd/langevin

---
 doc/src/fix_pimd.rst | 48 ++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 44 insertions(+), 4 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 28a5308dd7..d6808add44 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -24,7 +24,7 @@ Syntax
        *method* value = *pimd* or *nmpimd* or *cmd*
        *fmass* value = scaling factor on mass
        *sp* value = scaling factor on Planck constant
-       *temp* value = temperature (temperarate units)
+       *temp* value = temperature (temperature units)
        *nhc* value = Nc = number of chains in Nose-Hoover thermostat
 
 * keywords for style *pimd/langevin*
@@ -35,8 +35,8 @@ Syntax
        *integrator* value = *obabo* or *baoab*
        *fmmode* value = *physical* or *normal*
        *fmass* value = scaling factor on mass
-       *temp* value = Temperature (temperarate unit)
-          Temperature = target temperarate of the thermostat
+       *temp* value = Temperature (temperature unit)
+          Temperature = target temperature of the thermostat
        *thermostat* values = style seed
           style value = *PILE_L*
           seed = random number generator seed
@@ -180,6 +180,38 @@ The keyword *sp* is a scaling factor on Planck's constant, which can
 be useful for debugging or other purposes.  The default value of 1.0
 is appropriate for most situations.
 
+The keyword *ensemble* for fix style *pimd/langevin* determines which ensemble is it 
+going to sample. The value can be *nve* (microcanonical), *nvt* (canonical), *nph* (isoenthalpic), and *npt* (isothermal-isobaric).
+
+The keyword *temp* specifies temperature parameter for fix styles *pimd/nvt* and *pimd/langevin*. It should read a 
+positive floating-point number.
+.. note::
+   For pimd simulations, a temperature values should be specified even for nve ensemble. Temperature will make a difference
+   for nve pimd, since the spring elastic frequency between the beads will be affected by the temperature.
+
+The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. *style* can only
+be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`(Manolopoulos) <Manolopoulos>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
+
+.. note::
+   The fix style *pimd/langevin* uses the stochastic PILE_L thermostat to control temperature. This thermostat works on the normal modes
+   of the ring polymer. The *tau* parameter controls the centroid mode, and the *scale* parameter controls the non-centroid modes.
+
+The keyword *tau* specifies the thermostat damping time parameter for fix style *pimd/langevin*. It is in time unit. It only works on the centroid mode.
+
+The keyword *scale* specifies a scaling parameter for the damping times of the non-centroid modes for fix style *pimd/langevin*. The default
+damping time of the non-centroid mode $i$ is $\frac{P}{\beta\hbar}\sqrt{\lambda_i\times\mathrm{fmass}}$ (*fmmode* is *physical*) or  $\frac{P}{\beta\hbar}\sqrt{\mathrm{fmass}}$ (*fmmode* is *normal*). The damping times of all non-centroid modes are the default values divided by *scale*.
+
+The barostat parameters for fix style *pimd/langevin* with *npt* or *nph* ensemble is specified using one of *iso* and *aniso* 
+keywords. A *pressure* value should be given with pressure unit. The keyword *iso* means couple all 3 diagonal components together when pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. The keyword *aniso* means x, y, and z dimensions are controlled independently using the Pxx, Pyy, and Pzz components of the stress tensor as the driving forces, and the specified scalar external pressure.
+
+The keyword *barostat* reads *style* of barostat for fix style *pimd/langevin*. *style* can
+be *BZP* (Bussi-Zykova-Parrinello, as described in :ref:`(Parrinello1) <Parrinello1>`) or *MTTK* (Martyna-Tuckerman-Tobias-Klein, as described in :ref:`(Tuckerman2) <Tuckerman2>`).
+
+The keyword *taup* specifies the barostat damping time parameter for fix style *pimd/langevin*. It is in time unit.
+
+The keyword *fixcom* specifies whether the center-of-mass of the extended ring-polymer system is fixed during the pimd simulation. 
+Once *fixcom* is set te be *yes*, the center-of-mass velocity will be distracted from the centroid-mode velocities in each step.
+
 The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
 as described in :ref:`(Calhoun) <Calhoun>`.  In LAMMPS this is done by using
 :doc:`multi-replica feature <Howto_replica>` in LAMMPS, where each
@@ -314,4 +346,12 @@ Path Integrals, McGraw-Hill, New York (1965).
 
 .. _Manolopoulos:
 
-**(Manolopoulos)** M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
\ No newline at end of file
+**(Manolopoulos)** M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
+
+.. _Klein:
+
+**(Klein)** G. Martyna, D. Tobias, M. Klein, J. Chem. Phys. 101, 4177 (1994).
+
+.. _Tuckerman2:
+
+**(Tuckerman2)** G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
\ No newline at end of file

From 3d47c5c6f0fccaf27bf9d81a74df25d29856ab2e Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Tue, 21 Mar 2023 08:38:14 -0400
Subject: [PATCH 042/396] add x/y/z barostating options

---
 src/REPLICA/fix_pimd_langevin.cpp | 86 ++++++++++++++++++++++---------
 src/REPLICA/fix_pimd_langevin.h   |  4 +-
 2 files changed, 65 insertions(+), 25 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index e1d3960a50..d64d948ecf 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -101,6 +101,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   tau = 1.0;
   tau_p = 1.0;
   Pext = 1.0;
+  pdim = 0;
   pilescale = 1.0;
   tstat_flag = 1;
   pstat_flag = 0;
@@ -112,7 +113,11 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
 
   int seed = -1;
 
-  for (int i = 0; i < 6; i++) p_flag[i] = 0;
+  for (int i = 0; i < 6; i++)
+  {
+    p_flag[i] = 0;
+    p_target[i] = 0.0;
+  }
 
   for (int i = 3; i < narg - 1; i += 2) {
     if (strcmp(arg[i], "method") == 0) {
@@ -199,9 +204,29 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
     } else if (strcmp(arg[i], "iso") == 0) {
       pstyle = ISO;
       Pext = utils::numeric(FLERR, arg[i+1], false, lmp);
+      p_target[0] = p_target[1] = p_target[2] = Pext;
+      pdim = 3;
     } else if (strcmp(arg[i], "aniso") == 0) {
       pstyle = ANISO;
+      p_flag[0] = p_flag[1] = p_flag[2] = 1;
       Pext = utils::numeric(FLERR, arg[i+1], false, lmp);
+      p_target[0] = p_target[1] = p_target[2] = Pext;
+      pdim = 3;
+    } else if (strcmp(arg[i], "x") == 0) {
+      pstyle = ANISO;
+      p_flag[0] = 1;
+      p_target[0] = utils::numeric(FLERR, arg[i+1], false, lmp);
+      pdim++;
+    } else if (strcmp(arg[i], "y") == 0) {
+      pstyle = ANISO;
+      p_flag[1] = 1;
+      p_target[1] = utils::numeric(FLERR, arg[i+1], false, lmp);
+      pdim++;
+    } else if (strcmp(arg[i], "z") == 0) {
+      pstyle = ANISO;
+      p_flag[2] = 1;
+      p_target[2] = utils::numeric(FLERR, arg[i+1], false, lmp);
+      pdim++;
     } else if (strcmp(arg[i], "taup") == 0) {
       tau_p = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (tau_p <= 0.0) error->universe_all(FLERR, "Invalid tau_p value for fix pimd/langevin");
@@ -243,6 +268,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   fixedpoint[0] = 0.5 * (domain->boxlo[0] + domain->boxhi[0]);
   fixedpoint[1] = 0.5 * (domain->boxlo[1] + domain->boxhi[1]);
   fixedpoint[2] = 0.5 * (domain->boxlo[2] + domain->boxhi[2]);
+  if (pstat_flag) { p_hydro = (p_target[0]+p_target[1]+p_target[2])/pdim; }
 
   // initialize Marsaglia RNG with processor-unique seed
 
@@ -670,8 +696,15 @@ void FixPIMDLangevin::qc_step()
       if (barostat == BZP) {
         for (int i = 0; i < nlocal; i++) {
           for (int j = 0; j < 3; j++) {
-            x[i][j] = expq[j] * x[i][j] + (expq[j] - expp[j]) / 2. / vw[j] * v[i][j];
-            v[i][j] = expp[j] * v[i][j];
+            if (p_flag[j])
+            {
+              x[i][j] = expq[j] * x[i][j] + (expq[j] - expp[j]) / 2. / vw[j] * v[i][j];
+              v[i][j] = expp[j] * v[i][j];
+            }
+            else
+            {
+              x[i][j] += dtv * v[i][j];
+            }
           }
         }
         oldlo = domain->boxlo[0];
@@ -762,7 +795,7 @@ void FixPIMDLangevin::press_v_step()
 
   if (pstyle == ISO) {
     if (barostat == BZP) {
-      vw[0] += dtv * 3 * (volume * np * (p_cv - Pext) / force->nktv2p + Vcoeff / beta_np) / W;
+      vw[0] += dtv * 3 * (volume * np * (p_cv - p_hydro) / force->nktv2p + Vcoeff / beta_np) / W;
       if (universe->iworld == 0) {
         double dvw_proc = 0.0, dvw = 0.0;
         for (int i = 0; i < nlocal; i++) {
@@ -777,22 +810,25 @@ void FixPIMDLangevin::press_v_step()
       MPI_Bcast(&vw[0], 1, MPI_DOUBLE, 0, universe->uworld);
     } else if (barostat == MTTK) {
       mtk_term1 = 2. / atom->natoms * totke / 3;
-      f_omega = (volume * np * (p_md - Pext) + mtk_term1) / W;
+      f_omega = (volume * np * (p_md - p_hydro) + mtk_term1) / W;
       vw[0] += 0.5 * dtv * f_omega;
     }
   } else if (pstyle == ANISO) {
     compute_stress_tensor();
     for (int ii = 0; ii < 3; ii++) {
-      vw[ii] +=
-          dtv * (volume * np * (stress_tensor[ii] - Pext) / force->nktv2p + Vcoeff / beta_np) / W;
-      if (universe->iworld == 0) {
-        double dvw_proc = 0.0, dvw = 0.0;
-        for (int i = 0; i < nlocal; i++) {
-          dvw_proc +=
-              dtv2 * f[i][ii] * v[i][ii] / W + dtv3 * f[i][ii] * f[i][ii] / mass[type[i]] / W;
+      if (p_flag[ii])
+      {
+        vw[ii] +=
+            dtv * (volume * np * (stress_tensor[ii] - p_hydro) / force->nktv2p + Vcoeff / beta_np) / W;
+        if (universe->iworld == 0) {
+          double dvw_proc = 0.0, dvw = 0.0;
+          for (int i = 0; i < nlocal; i++) {
+            dvw_proc +=
+                dtv2 * f[i][ii] * v[i][ii] / W + dtv3 * f[i][ii] * f[i][ii] / mass[type[i]] / W;
+          }
+          MPI_Allreduce(&dvw_proc, &dvw, 1, MPI_DOUBLE, MPI_SUM, world);
+          vw[ii] += dvw;
         }
-        MPI_Allreduce(&dvw_proc, &dvw, 1, MPI_DOUBLE, MPI_SUM, world);
-        vw[ii] += dvw;
       }
     }
   }
@@ -811,12 +847,14 @@ void FixPIMDLangevin::press_o_step()
     MPI_Bcast(&vw[0], 1, MPI_DOUBLE, 0, universe->uworld);
   } else if (pstyle == ANISO) {
     if (universe->me == 0) {
-      r1 = random->gaussian();
-      r2 = random->gaussian();
-      r3 = random->gaussian();
-      vw[0] = c1 * vw[0] + c2 * sqrt(1.0 / W / beta_np) * r1;
-      vw[1] = c1 * vw[1] + c2 * sqrt(1.0 / W / beta_np) * r2;
-      vw[2] = c1 * vw[2] + c2 * sqrt(1.0 / W / beta_np) * r3;
+      for (int ii=0; ii<3; ii++)
+      {
+        if (p_flag[ii])
+        {
+          r1 = random->gaussian();
+          vw[ii] = c1 * vw[ii] + c2 * sqrt(1.0 / W / beta_np) * r1;
+        }
+      }
     }
     MPI_Barrier(universe->uworld);
     MPI_Bcast(&vw, 3, MPI_DOUBLE, 0, universe->uworld);
@@ -1145,7 +1183,7 @@ void FixPIMDLangevin::remove_com_motion(){
     int nlocal = atom->nlocal;
     if (dynamic)  masstotal = group->mass(igroup);
     double vcm[3];
-    group->vcm(igroup,masstotal,vcm);    
+    group->vcm(igroup,masstotal,vcm);
     for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
         v[i][0] -= vcm[0];
@@ -1329,15 +1367,15 @@ void FixPIMDLangevin::compute_totenthalpy()
   volume = domain->xprd * domain->yprd * domain->zprd;
   if (barostat == BZP) {
     if (pstyle == ISO) {
-      totenthalpy = tote + 0.5 * W * vw[0] * vw[0] * inverse_np + Pext * volume / force->nktv2p -
+      totenthalpy = tote + 0.5 * W * vw[0] * vw[0] * inverse_np + p_hydro * volume / force->nktv2p -
           Vcoeff * kBT * log(volume);
     } else if (pstyle == ANISO) {
       totenthalpy = tote + 0.5 * W * vw[0] * vw[0] * inverse_np +
           0.5 * W * vw[1] * vw[1] * inverse_np + 0.5 * W * vw[2] * vw[2] * inverse_np +
-          Pext * volume / force->nktv2p - Vcoeff * kBT * log(volume);
+          p_hydro * volume / force->nktv2p - Vcoeff * kBT * log(volume);
     }
   } else if (barostat == MTTK)
-    totenthalpy = tote + 1.5 * W * vw[0] * vw[0] * inverse_np + Pext * (volume - vol0);
+    totenthalpy = tote + 1.5 * W * vw[0] * vw[0] * inverse_np + p_hydro * (volume - vol0);
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index b8bed1a10f..6d236718c7 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -126,8 +126,10 @@ class FixPIMDLangevin : public Fix {
   double f_omega, mtk_term1;
   int pstat_flag;    // pstat_flag = 1 if barostat is used
   int pstyle;        // pstyle = ISO or ANISO (will support TRICLINIC in the future)
-  double W, tau_p, Pext, totenthalpy, Vcoeff;
+  double W, tau_p, Pext, p_hydro, totenthalpy, Vcoeff;
+  int pdim;
   int p_flag[6];
+  double p_target[6];
   double vw[6];               // barostat velocity
   double ke_tensor[6];        // kinetic energy tensor
   double c_vir_tensor[6];     // centroid-virial tensor

From f94bea8d972d1f6f7064ebf599283a2d6b89e9d7 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Tue, 21 Mar 2023 09:22:37 -0400
Subject: [PATCH 043/396] correct fix pimd/langevin example file permission

---
 examples/PACKAGES/pimd/lj/in.lmp | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 examples/PACKAGES/pimd/lj/in.lmp

diff --git a/examples/PACKAGES/pimd/lj/in.lmp b/examples/PACKAGES/pimd/lj/in.lmp
old mode 100755
new mode 100644

From 2cb9d2784bd3522911a456029ad3fd7b21f8522a Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Tue, 21 Mar 2023 09:23:04 -0400
Subject: [PATCH 044/396] add false_positive for fix pimd/langevin doc

---
 doc/utils/sphinx-config/false_positives.txt | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 0f18e6822f..e8544a8975 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -2017,6 +2017,7 @@ Marchetti
 Marchi
 Mariella
 Marinica
+Markland
 Marrink
 Marroquin
 Marsaglia
@@ -3577,6 +3578,7 @@ THz
 Tigran
 Tij
 Tildesley
+Timan
 timeI
 timespan
 timestamp
@@ -4071,4 +4073,5 @@ zu
 zx
 zy
 Zybin
+Zykova
 zz

From 32efa1a3af3462c740afd90a1c2fdbbd02ef1e91 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Tue, 21 Mar 2023 09:23:22 -0400
Subject: [PATCH 045/396] update fix pimd/langevin doc

---
 doc/src/fix_pimd.rst | 87 +++++++++++++++++++++++++-------------------
 1 file changed, 49 insertions(+), 38 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index d6808add44..4d72d7232f 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -30,7 +30,8 @@ Syntax
 * keywords for style *pimd/langevin*
 
   .. parsed-literal::
-       *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj* 
+       *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or
+        *tau*or or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj*
        *method* value = *nmpimd*
        *integrator* value = *obabo* or *baoab*
        *fmmode* value = *physical* or *normal*
@@ -43,7 +44,7 @@ Syntax
        *tau* value = thermostat damping parameter (time unit)
        *scale* value = scaling factor of the damping times of non-centroid modes of PILE_L thermostat
        *iso* or *aniso* values = Pressure (pressure unit)
-         Pressure = scalar external pressure of the barostat 
+         Pressure = scalar external pressure of the barostat
        *barostat* value = *BZP* or *MTTK*
        *taup* value = barostat damping parameter (time unit)
        *fixcom* value = *yes* or *no*
@@ -85,7 +86,7 @@ by the following equations:
    H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2M_i}\bigg) + V_{eff} \\
    V_{eff} = & \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
 
-$M_i$ is the fictitious mass of the $i$-th mode, and m is the actual mass of the atoms.
+:math:`M_i` is the fictitious mass of the :math:`i`-th mode, and m is the actual mass of the atoms.
 
 The interested user is referred to any of the numerous references on
 this methodology, but briefly, each quantum particle in a path integral
@@ -109,8 +110,9 @@ would be 3 x N x P x Nc.
    Fix *pimd/nvt* implements a complete velocity-verlet integrator
    combined with NH massive chain thermostat, so no other time
    integration fix should be used.
+
    Fix *pimd/langevin* implements a complete velocity-verlet integrator
-   combined with Langevin thermostat in the normal mode representation, and 
+   combined with Langevin thermostat in the normal mode representation, and
    also provides a barostat to sample the NPH/NPT ensembles.
 
 The *method* keyword determines what style of PIMD is performed.  A
@@ -136,7 +138,7 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
    the real particle.
 
 .. note::
-   Fix pimd/langevin only supports *method* value *nmpimd*. This should be enough 
+   Fix pimd/langevin only supports *method* value *nmpimd*. This should be enough
    for most PIMD applications for quantum thermodynamics purpose.
 
    Motion of the centroid can be effectively uncoupled from the other
@@ -155,42 +157,51 @@ masses of beads, which can be used for the Partial Adiabatic CMD
 :ref:`(Hone) <Hone>`, or to be set as P, which results in the fictitious
 masses to be equal to the real particle masses.
 
-The keyword *fmmode* of *fix pimd/langevin* determines the mode of fictitious 
-mass preconditioning. There are two options: *physical* and *normal*. If *fmmode* is 
+The keyword *fmmode* of *fix pimd/langevin* determines the mode of fictitious
+mass preconditioning. There are two options: *physical* and *normal*. If *fmmode* is
 *physical*, then the physical mass of the particles are used (and then multiplied by
-*fmass*). If *fmmode* is *normal*, then the physical mass is first multiplied by the 
-eigenvalue of each normal mode, and then multiplied by *fmass*. More precisely, the 
+*fmass*). If *fmmode* is *normal*, then the physical mass is first multiplied by the
+eigenvalue of each normal mode, and then multiplied by *fmass*. More precisely, the
 fictitious mass of *fix pimd/langevin* is determined by two factors: *fmmode* and *fmass*.
 If *fmmode* is *physical*, then the fictitious mass is
-.. math::
-   $M_i = \mathrm{fmass} \times m$
-   
-If *fmmode* is *normal*, then the fictitious mass is
-.. math::
-   $M_i = \mathrm{fmass} \times \lambda_i \times m$
 
-where $\lambda_i$ is the eigenvalue of the $i$-th normal mode.
+.. math::
+
+   M_i = \mathrm{fmass} \times m
+
+If *fmmode* is *normal*, then the fictitious mass is
+
+.. math::
+
+   M_i = \mathrm{fmass} \times \lambda_i \times m
+
+where :math:`\lambda_i` is the eigenvalue of the :math:`i`-th normal mode.
+
 .. note::
+
    Fictitious mass is only used in the momentum of the equation of motion
-   ($\bf{p}_i=M_i\bf{v}_i$), and not used in the spring elastic energy 
-   ($\sum_{i=1}^P \frac{1}{2}m\omega_P^2(q_i - q_{i+1})^2$, $m$ is always the 
-   actual mass of the particles). 
+   (:math:`\mathbf{p}_i=M_i\mathbf{v}_i`), and not used in the spring elastic energy
+   (:math:`\sum_{i=1}^P \frac{1}{2}m\omega_P^2(q_i - q_{i+1})^2`, :math:`m` is always the
+   actual mass of the particles).
 
 The keyword *sp* is a scaling factor on Planck's constant, which can
 be useful for debugging or other purposes.  The default value of 1.0
 is appropriate for most situations.
 
-The keyword *ensemble* for fix style *pimd/langevin* determines which ensemble is it 
-going to sample. The value can be *nve* (microcanonical), *nvt* (canonical), *nph* (isoenthalpic), and *npt* (isothermal-isobaric).
+The keyword *ensemble* for fix style *pimd/langevin* determines which ensemble is it
+going to sample. The value can be *nve* (microcanonical), *nvt* (canonical), *nph* (isoenthalpic),
+and *npt* (isothermal-isobaric).
+
+The keyword *temp* specifies temperature parameter for fix styles *pimd/nvt* and *pimd/langevin*. It should read
+a positive floating-point number.
 
-The keyword *temp* specifies temperature parameter for fix styles *pimd/nvt* and *pimd/langevin*. It should read a 
-positive floating-point number.
 .. note::
+
    For pimd simulations, a temperature values should be specified even for nve ensemble. Temperature will make a difference
    for nve pimd, since the spring elastic frequency between the beads will be affected by the temperature.
 
 The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. *style* can only
-be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`(Manolopoulos) <Manolopoulos>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
+be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
 
 .. note::
    The fix style *pimd/langevin* uses the stochastic PILE_L thermostat to control temperature. This thermostat works on the normal modes
@@ -199,21 +210,21 @@ be *PILE_L* (path integral Langevin equation local thermostat, as described in :
 The keyword *tau* specifies the thermostat damping time parameter for fix style *pimd/langevin*. It is in time unit. It only works on the centroid mode.
 
 The keyword *scale* specifies a scaling parameter for the damping times of the non-centroid modes for fix style *pimd/langevin*. The default
-damping time of the non-centroid mode $i$ is $\frac{P}{\beta\hbar}\sqrt{\lambda_i\times\mathrm{fmass}}$ (*fmmode* is *physical*) or  $\frac{P}{\beta\hbar}\sqrt{\mathrm{fmass}}$ (*fmmode* is *normal*). The damping times of all non-centroid modes are the default values divided by *scale*.
+damping time of the non-centroid mode :math:`i` is :math:`\frac{P}{\beta\hbar}\sqrt{\lambda_i\times\mathrm{fmass}}` (*fmmode* is *physical*) or  :math:`\frac{P}{\beta\hbar}\sqrt{\mathrm{fmass}}` (*fmmode* is *normal*). The damping times of all non-centroid modes are the default values divided by *scale*.
 
-The barostat parameters for fix style *pimd/langevin* with *npt* or *nph* ensemble is specified using one of *iso* and *aniso* 
+The barostat parameters for fix style *pimd/langevin* with *npt* or *nph* ensemble is specified using one of *iso* and *aniso*
 keywords. A *pressure* value should be given with pressure unit. The keyword *iso* means couple all 3 diagonal components together when pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. The keyword *aniso* means x, y, and z dimensions are controlled independently using the Pxx, Pyy, and Pzz components of the stress tensor as the driving forces, and the specified scalar external pressure.
 
 The keyword *barostat* reads *style* of barostat for fix style *pimd/langevin*. *style* can
-be *BZP* (Bussi-Zykova-Parrinello, as described in :ref:`(Parrinello1) <Parrinello1>`) or *MTTK* (Martyna-Tuckerman-Tobias-Klein, as described in :ref:`(Tuckerman2) <Tuckerman2>`).
+be *BZP* (Bussi-Zykova-Parrinello, as described in :ref:`Bussi <Bussi>`) or *MTTK* (Martyna-Tuckerman-Tobias-Klein, as described in :ref:`Martyna1 <Martyna1>` and :ref:`Martyna2 <Martyna2>`).
 
 The keyword *taup* specifies the barostat damping time parameter for fix style *pimd/langevin*. It is in time unit.
 
-The keyword *fixcom* specifies whether the center-of-mass of the extended ring-polymer system is fixed during the pimd simulation. 
-Once *fixcom* is set te be *yes*, the center-of-mass velocity will be distracted from the centroid-mode velocities in each step.
+The keyword *fixcom* specifies whether the center-of-mass of the extended ring-polymer system is fixed during the pimd simulation.
+Once *fixcom* is set to be *yes*, the center-of-mass velocity will be distracted from the centroid-mode velocities in each step.
 
 The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
-as described in :ref:`(Calhoun) <Calhoun>`.  In LAMMPS this is done by using
+as described in :ref:`Calhoun <Calhoun>`.  In LAMMPS this is done by using
 :doc:`multi-replica feature <Howto_replica>` in LAMMPS, where each
 quasi-particle system is stored and simulated on a separate partition
 of processors.  The following diagram illustrates this approach.  The
@@ -340,18 +351,18 @@ Path Integrals, McGraw-Hill, New York (1965).
 
 **(Herman)** M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).
 
-.. _Parrinello1:
+.. _Bussi:
 
-**(Parrinello1)** G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
+**(Bussi)** G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
 
-.. _Manolopoulos:
+.. _Ceriotti:
 
-**(Manolopoulos)** M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
+**(Ceriotti)** M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
 
-.. _Klein:
+.. _Martyna1:
 
-**(Klein)** G. Martyna, D. Tobias, M. Klein, J. Chem. Phys. 101, 4177 (1994).
+**(Martyna1)** G. Martyna, D. Tobias, M. Klein, J. Chem. Phys. 101, 4177 (1994).
 
-.. _Tuckerman2:
+.. _Martyna2:
 
-**(Tuckerman2)** G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
\ No newline at end of file
+**(Martyna2)** G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).

From 2c0ac8299640305499f46f48b5641b8734456d9f Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Tue, 21 Mar 2023 09:54:29 -0400
Subject: [PATCH 046/396] update doc press -> iso

---
 doc/src/fix_pimd.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 4d72d7232f..75ba85bc96 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -61,7 +61,7 @@ Examples
 .. code-block:: LAMMPS
 
    fix 1 all pimd/nvt method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
-   fix 1 all pimd/langevin ensemble npt integrator obabo temp 113.15 thermostat PILE_L 1234 tau 1.0 press 1.0 barostat BZP taup 1.0 iso
+   fix 1 all pimd/langevin ensemble npt integrator obabo temp 113.15 thermostat PILE_L 1234 tau 1.0 iso 1.0 barostat BZP taup 1.0
 
 Description
 """""""""""

From af8d4788b8bd4545ef88e098c6dc99a702862866 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Tue, 21 Mar 2023 10:11:37 -0400
Subject: [PATCH 047/396] fix doc errors

---
 doc/src/fix_pimd.rst | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 75ba85bc96..db6700633f 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -30,21 +30,20 @@ Syntax
 * keywords for style *pimd/langevin*
 
   .. parsed-literal::
-       *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or
-        *tau*or or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj*
+       *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj*
        *method* value = *nmpimd*
        *integrator* value = *obabo* or *baoab*
        *fmmode* value = *physical* or *normal*
        *fmass* value = scaling factor on mass
-       *temp* value = Temperature (temperature unit)
-          Temperature = target temperature of the thermostat
+       *temp* value = temperature (temperature unit)
+          temperature = target temperature of the thermostat
        *thermostat* values = style seed
           style value = *PILE_L*
           seed = random number generator seed
        *tau* value = thermostat damping parameter (time unit)
        *scale* value = scaling factor of the damping times of non-centroid modes of PILE_L thermostat
-       *iso* or *aniso* values = Pressure (pressure unit)
-         Pressure = scalar external pressure of the barostat
+       *iso* or *aniso* values = pressure (pressure unit)
+         pressure = scalar external pressure of the barostat
        *barostat* value = *BZP* or *MTTK*
        *taup* value = barostat damping parameter (time unit)
        *fixcom* value = *yes* or *no*

From 5c94806a1d307d5552adeecf634fb9221abb1d71 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Thu, 23 Mar 2023 01:59:38 -0400
Subject: [PATCH 048/396] update doc

---
 doc/src/fix_pimd.rst | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index db6700633f..eca58a409d 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -95,8 +95,10 @@ beads on the other ring-polymers with the same imaginary time index (the
 second term in the effective potential above).  The quasi-beads also
 interact with the two neighboring quasi-beads through the spring
 potential in imaginary-time space (first term in effective potential).
-To sample the canonical ensemble, a Nose-Hoover massive chain thermostat
-is applied :ref:`(Tuckerman) <pimd-Tuckerman>`.  With the massive chain
+To sample the canonical ensemble, any thermostat can be applied.
+
+Fix *pimd/nvt* applies a Nose-Hoover massive chain thermostat
+:ref:`(Tuckerman) <pimd-Tuckerman>`.  With the massive chain
 algorithm, a chain of NH thermostats is coupled to each degree of
 freedom for each quasi-bead.  The keyword *temp* sets the target
 temperature for the system and the keyword *nhc* sets the number *Nc* of
@@ -104,16 +106,15 @@ thermostats in each chain.  For example, for a simulation of N particles
 with P beads in each ring-polymer, the total number of NH thermostats
 would be 3 x N x P x Nc.
 
+Fix *pimd/langevin* implements a Langevin thermostat in the normal mode 
+representation, and also provides a barostat to sample the NPH/NPT ensembles.
+
 .. note::
 
-   Fix *pimd/nvt* implements a complete velocity-verlet integrator
-   combined with NH massive chain thermostat, so no other time
+   Both these *fix* styles implement a complete velocity-verlet integrator
+   combined with a thermostat, so no other time
    integration fix should be used.
 
-   Fix *pimd/langevin* implements a complete velocity-verlet integrator
-   combined with Langevin thermostat in the normal mode representation, and
-   also provides a barostat to sample the NPH/NPT ensembles.
-
 The *method* keyword determines what style of PIMD is performed.  A
 value of *pimd* is standard PIMD.  A value of *nmpimd* is for
 normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics

From 83b4e18704843c86de7cf26e91bae18851b6165a Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Thu, 23 Mar 2023 21:05:07 -0400
Subject: [PATCH 049/396] update doc

---
 doc/src/fix_pimd.rst | 36 ++++++++++++++++++++++++++++--------
 1 file changed, 28 insertions(+), 8 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index eca58a409d..78aa5fa107 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -112,8 +112,7 @@ representation, and also provides a barostat to sample the NPH/NPT ensembles.
 .. note::
 
    Both these *fix* styles implement a complete velocity-verlet integrator
-   combined with a thermostat, so no other time
-   integration fix should be used.
+   combined with a thermostat, so no other time integration fix should be used.
 
 The *method* keyword determines what style of PIMD is performed.  A
 value of *pimd* is standard PIMD.  A value of *nmpimd* is for
@@ -121,7 +120,7 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
 (CMD).  The difference between the styles is as follows.
 
    In standard PIMD, the value used for a bead's fictitious mass is
-   arbitrary.  A common choice is to use Mi = m/P, which results in the
+   arbitrary.  A common choice is to use :math:`M_i = m/P`, which results in the
    mass of the entire ring-polymer being equal to the real quantum
    particle.  But it can be difficult to efficiently integrate the
    equations of motion for the stiff harmonic interactions in the ring
@@ -152,6 +151,10 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
    only the k > 0 modes are thermostatted, not the centroid degrees of
    freedom.
 
+The keyword *integrator* specifies the Trotter splitting method used by *fix pimd/langevin*.
+See :ref:`(Liu) <Liu>` for a discussion on the OBABO and BAOAB splitting schemes. Typically
+either of the two should work fine.
+
 The keyword *fmass* sets a further scaling factor for the fictitious
 masses of beads, which can be used for the Partial Adiabatic CMD
 :ref:`(Hone) <Hone>`, or to be set as P, which results in the fictitious
@@ -201,7 +204,7 @@ a positive floating-point number.
    for nve pimd, since the spring elastic frequency between the beads will be affected by the temperature.
 
 The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. *style* can only
-be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
+be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti2>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
 
 .. note::
    The fix style *pimd/langevin* uses the stochastic PILE_L thermostat to control temperature. This thermostat works on the normal modes
@@ -216,7 +219,7 @@ The barostat parameters for fix style *pimd/langevin* with *npt* or *nph* ensemb
 keywords. A *pressure* value should be given with pressure unit. The keyword *iso* means couple all 3 diagonal components together when pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. The keyword *aniso* means x, y, and z dimensions are controlled independently using the Pxx, Pyy, and Pzz components of the stress tensor as the driving forces, and the specified scalar external pressure.
 
 The keyword *barostat* reads *style* of barostat for fix style *pimd/langevin*. *style* can
-be *BZP* (Bussi-Zykova-Parrinello, as described in :ref:`Bussi <Bussi>`) or *MTTK* (Martyna-Tuckerman-Tobias-Klein, as described in :ref:`Martyna1 <Martyna1>` and :ref:`Martyna2 <Martyna2>`).
+be *BZP* (Bussi-Zykova-Parrinello, as described in :ref:`Bussi <Bussi>`) or *MTTK* (Martyna-Tuckerman-Tobias-Klein, as described in :ref:`Martyna1 <Martyna3>` and :ref:`Martyna2 <Martyna4>`).
 
 The keyword *taup* specifies the barostat damping time parameter for fix style *pimd/langevin*. It is in time unit.
 
@@ -258,9 +261,18 @@ related tasks for each of the partitions, e.g.
 .. code-block:: LAMMPS
 
    dump dcd all dcd 10 system_${ibead}.dcd
+   dump 1 all custom 100 ${ibead}.xyz id type x y z vx vy vz ix iy iz fx fy fz
    restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
    read_restart system_${ibead}.restart2
 
+.. note::
+   Fix *pimd/langevin* dumps the Catersian coordinates, but dumps the velocities and
+   forces in the normal mode representation. If the Catersian velocities and forces are
+   needed, it is easy to perform the transformation when doing post-processing.
+
+   It is recommended to dump the image flags (*ix iy iz*) for fix *pimd/langevin*. It 
+   will be useful if you want to calculate some estimators during post-processing.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
@@ -287,6 +299,10 @@ the global vector are:
 The vector values calculated by fix *pimd/nvt* are "extensive", except for the
 temperature, which is "intensive".
 
+Fix *pimd/langevin* computes a global vector of quantities, which
+can be accessed by various :doc:`output commands <Howto_output>`. If *ensemble*
+is *nve* or *nvt*, the vector has 10 values.
+
 No parameter of fix *pimd/nvt* can be used with the *start/stop* keywords
 of the :doc:`run <run>` command.  Fix *pimd/nvt* is not invoked during
 :doc:`energy minimization <minimize>`.
@@ -355,14 +371,18 @@ Path Integrals, McGraw-Hill, New York (1965).
 
 **(Bussi)** G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
 
-.. _Ceriotti:
+.. _Ceriotti2:
 
 **(Ceriotti)** M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
 
-.. _Martyna1:
+.. _Martyna3:
 
 **(Martyna1)** G. Martyna, D. Tobias, M. Klein, J. Chem. Phys. 101, 4177 (1994).
 
-.. _Martyna2:
+.. _Martyna4:
 
 **(Martyna2)** G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
+
+.. _Liujian:
+
+**(Liu)** J. Liu, D. Li, X. Liu, J. Chem. Phys. 145, 024103 (2016).

From 4e4ae34de601159ffaf8af10eacefeab57781570 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Mon, 27 Mar 2023 22:16:41 -0400
Subject: [PATCH 050/396] update doc with output info and reduced unit
 instructions

---
 doc/src/fix_pimd.rst | 66 +++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 62 insertions(+), 4 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 78aa5fa107..e4a59b0078 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -226,6 +226,9 @@ The keyword *taup* specifies the barostat damping time parameter for fix style *
 The keyword *fixcom* specifies whether the center-of-mass of the extended ring-polymer system is fixed during the pimd simulation.
 Once *fixcom* is set to be *yes*, the center-of-mass velocity will be distracted from the centroid-mode velocities in each step.
 
+The keyword *lj* should be used if :doc:`lj units <units>` is used for *fix pimd/langevin*. Typically one may want to use
+reduced units to run the simulation, and then convert the results into some physical units (for example, :doc:`metal units <units>`). In this case, the 5 quantities in the physical mass units are needed: epsilon (energy scale), sigma (length scale), mass, Planck's constant, mvv2e (mass * velocity^2 to energy conversion factor). Planck's constant and mvv2e can be found in src/update.cpp. If there is no need to convert reduced units to physical units, set all these five value to 1.
+
 The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
 as described in :ref:`Calhoun <Calhoun>`.  In LAMMPS this is done by using
 :doc:`multi-replica feature <Howto_replica>` in LAMMPS, where each
@@ -300,11 +303,65 @@ The vector values calculated by fix *pimd/nvt* are "extensive", except for the
 temperature, which is "intensive".
 
 Fix *pimd/langevin* computes a global vector of quantities, which
-can be accessed by various :doc:`output commands <Howto_output>`. If *ensemble*
-is *nve* or *nvt*, the vector has 10 values.
+can be accessed by various :doc:`output commands <Howto_output>`. Note that
+it outputs multiple log files, and different log files contain information
+about different beads or modes (see detailed explanations below). If *ensemble*
+is *nve* or *nvt*, the vector has 10 values:
 
-No parameter of fix *pimd/nvt* can be used with the *start/stop* keywords
-of the :doc:`run <run>` command.  Fix *pimd/nvt* is not invoked during
+   #. kinetic energy of the normal mode
+   #. spring elastic energy of the normal mode
+   #. potential energy of the bead
+   #. total energy of all beads (conserved if *ensemble* is *nve*)
+   #. primitive kinetic energy estimator
+   #. virial energy estimator
+   #. centroid-virial energy estimator
+   #. primitive pressure estimator
+   #. thermodynamic pressure estimator
+   #. centroid-virial pressure estimator
+
+The first 3 are different for different log files, and the others are the same for different log files.
+
+If *ensemble* is *nph* or *npt*, the vector stores internal variables of the barostat. If *iso* is used,
+the vector has 15 values:
+
+   #. kinetic energy of the normal mode
+   #. spring elastic energy of the normal mode
+   #. potential energy of the bead
+   #. total energy of all beads (conserved if *ensemble* is *nve*)
+   #. primitive kinetic energy estimator
+   #. virial energy estimator
+   #. centroid-virial energy estimator
+   #. primitive pressure estimator
+   #. thermodynamic pressure estimator
+   #. centroid-virial pressure estimator
+   #. barostat velocity
+   #. barostat kinetic energy
+   #. barostat potential energy
+   #. barostat cell Jacobian
+   #. enthalpy of the extended system (sum of 4, 12, 13, and 14; conserved if *ensemble* is *nph*)
+
+If *aniso* or *x* or *y* or *z* is used for the barostat, the vector has 17 values:
+
+   #. kinetic energy of the normal mode
+   #. spring elastic energy of the normal mode
+   #. potential energy of the bead
+   #. total energy of all beads (conserved if *ensemble* is *nve*)
+   #. primitive kinetic energy estimator
+   #. virial energy estimator
+   #. centroid-virial energy estimator
+   #. primitive pressure estimator
+   #. thermodynamic pressure estimator
+   #. centroid-virial pressure estimator
+   #. x component of barostat velocity
+   #. y component of barostat velocity
+   #. z component of barostat velocity
+   #. barostat kinetic energy
+   #. barostat potential energy
+   #. barostat cell Jacobian
+   #. enthalpy of the extended system (sum of 4, 14, 15, and 16; conserved if *ensemble* is *nph*)
+
+No parameter of fix *pimd/nvt* or *pimd/langevin* can be used with the *start/stop* keywords
+of the :doc:`run <run>` command.  Fix *pimd/nvt* or *pimd/langevin* is not invoked during
 :doc:`energy minimization <minimize>`.
 
 Restrictions
@@ -315,6 +372,7 @@ LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
 Fix *pimd/nvt* cannot be used with :doc:`lj units <units>`.
+Fix *pimd/langevin* can be used with :doc:`lj units <units>`. See the above part for how to use it.
 
 A PIMD simulation can be initialized with a single data file read via
 the :doc:`read_data <read_data>` command.  However, this means all

From 561f80ccc731715049fcaa9c9663944089c4353a Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Mon, 27 Mar 2023 22:21:38 -0400
Subject: [PATCH 051/396] add example for fix pimd/langevin with reduced units

---
 .../PACKAGES/pimd/lj_reduced_units/data.lj01  | 219 ++++++++++++++++++
 .../PACKAGES/pimd/lj_reduced_units/data.lj02  | 219 ++++++++++++++++++
 .../PACKAGES/pimd/lj_reduced_units/in.lmp     |  26 +++
 .../PACKAGES/pimd/lj_reduced_units/run.sh     |   1 +
 4 files changed, 465 insertions(+)
 create mode 100644 examples/PACKAGES/pimd/lj_reduced_units/data.lj01
 create mode 100644 examples/PACKAGES/pimd/lj_reduced_units/data.lj02
 create mode 100644 examples/PACKAGES/pimd/lj_reduced_units/in.lmp
 create mode 100644 examples/PACKAGES/pimd/lj_reduced_units/run.sh

diff --git a/examples/PACKAGES/pimd/lj_reduced_units/data.lj01 b/examples/PACKAGES/pimd/lj_reduced_units/data.lj01
new file mode 100644
index 0000000000..e3d6b816a3
--- /dev/null
+++ b/examples/PACKAGES/pimd/lj_reduced_units/data.lj01
@@ -0,0 +1,219 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 2000
+
+200 atoms
+1 atom types
+
+-3.4945130603740377 3.4945130603740377 xlo xhi
+-3.4945130603740377 3.4945130603740377 ylo yhi
+-3.4945130603740377 3.4945130603740377 zlo zhi
+
+Masses
+
+1 1
+
+Pair Coeffs # lj/cut
+
+1 1 1
+
+Atoms # atomic
+
+108 1 -2.7795690566068996 -2.0367677788080942 3.4238258338844894 2 1 -1
+102 1 -2.609481280743025 -1.8912619121268304 -2.399753092988466 1 -1 -1
+141 1 -3.140749645549514 -2.8903241627869427 -2.7071762462261537 2 0 0
+49 1 -2.3658136681990007 -3.088812044820056 3.4760124445890623 0 1 -1
+88 1 -1.6158710173914035 -2.3369020600614756 3.233517474511907 0 1 -1
+192 1 -1.2960228223928079 -3.237522585981233 -3.1506262911155765 1 1 2
+113 1 -0.5058112539671865 -2.175265580488635 -2.895948573481031 -1 0 0
+147 1 -0.22721902013037146 -3.2095321965856187 -2.5444416457809185 0 1 0
+55 1 0.6250447384071113 -2.6446349401275255 -2.959767417439857 -1 0 -1
+63 1 1.6783992808137906 -3.22203513406057 -3.1652676844989256 -1 1 1
+95 1 1.3579478870419064 -2.684729254303277 -2.052496056604152 0 2 -1
+105 1 1.4496281787006915 -1.9673030959679096 -3.332658945278261 0 0 0
+84 1 2.4045875426768606 -1.8297724699275564 -2.7874627893944544 0 0 0
+65 1 -2.68682939849047 -0.8114540186440395 -3.126687818057689 0 -1 0
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+189 1 -0.6249709402997541 -1.252931712435372 -1.9882716349469658 0 0 2
+9 1 -0.23886293275872486 -1.0612344376875333 -3.025432389188406 0 0 1
+146 1 -0.9802936024515303 -0.3953988402073487 -2.8364522494017708 2 1 2
+171 1 0.39730078560778914 -1.7846492070113664 -2.443607407553737 0 2 -1
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+11 1 3.1992117767992068 -1.191883736793153 -3.4723419170834338 -1 2 1
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diff --git a/examples/PACKAGES/pimd/lj_reduced_units/data.lj02 b/examples/PACKAGES/pimd/lj_reduced_units/data.lj02
new file mode 100644
index 0000000000..aab14fd30f
--- /dev/null
+++ b/examples/PACKAGES/pimd/lj_reduced_units/data.lj02
@@ -0,0 +1,219 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 8000
+
+200 atoms
+1 atom types
+
+-3.4945130603740377 3.4945130603740377 xlo xhi
+-3.4945130603740377 3.4945130603740377 ylo yhi
+-3.4945130603740377 3.4945130603740377 zlo zhi
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+121 1 -0.8632847382707834 -2.364486787477818 2.5298242427842235 -1 1 -1
+50 1 -1.3127850841438964 -3.332989957578539 1.7903541140988317 0 1 0
+63 1 1.6040989853168577 -2.8917377487223326 2.9749125296584396 -1 1 0
+27 1 0.22872838010698016 -2.994984028716655 2.6653598205127595 0 0 1
+10 1 0.9362147196804173 -2.581105523755157 1.9878669654444103 0 0 1
+185 1 0.06742724446398485 -1.8726052150227481 3.179787889614259 -2 1 -1
+62 1 0.9381874848569671 3.2183812476038773 2.122950032967029 0 0 0
+108 1 3.2075816395574557 -2.6473251670969744 3.3899630726255054 1 1 -1
+168 1 -3.4886505297786643 -3.024902771510678 1.648075348189236 0 1 -2
+96 1 2.193516168781477 -3.220451114036294 2.031971070369377 -2 2 -1
+57 1 2.897670474066688 -1.7869273194590956 2.7802854592878443 1 0 0
+155 1 2.0203257801003764 -2.093908363815807 2.3651374010253265 0 0 -1
+70 1 -2.289198729241698 -1.0693505000499786 3.3341581014665116 0 1 1
+86 1 3.4317154036170927 -1.33629793948954 1.5868690985104916 -2 0 0
+4 1 -2.642034929204445 -0.5735696636076526 2.24988074624273 0 0 -1
+148 1 -2.7958435550832177 -1.6271830272245196 2.4651167378398258 0 0 0
+197 1 -1.6297637248397103 -1.2496732630952756 2.4653302717640746 0 -1 -1
+23 1 -1.4165843839294037 -0.23332219410733462 -3.3887252652014874 0 0 -1
+78 1 -0.8539129642965406 -1.4368914881460948 3.1097976169270467 1 -1 1
+134 1 -0.7681520363929484 -1.1354013495310054 1.8538106613640677 -1 0 0
+66 1 -0.23373724912576396 -0.5882558302750734 2.5656269999794135 -1 -1 -1
+160 1 -1.1132775718863501 0.16126595419727965 2.3994619853672896 0 0 0
+18 1 0.6168554097448792 -0.8675105647197154 3.3233443940314107 0 -1 -2
+5 1 0.21124689546372627 -1.527936340282886 2.128421015823146 0 -1 -1
+167 1 1.157996163161525 -1.3890474926504965 2.5930120556899743 0 1 -1
+176 1 0.7227757787132028 -0.4265054817409199 2.130677354553178 0 0 0
+77 1 2.0007502274099562 -0.6930768409753575 2.0562080526704536 0 -1 1
+136 1 2.059758900185651 -1.052357318680519 3.1194387358517117 0 -1 -2
+163 1 3.3650479388293877 -0.7812523229666395 2.7231341802578797 -1 -1 0
+53 1 -2.3141819292399695 1.20855609162257 -3.127003289906138 -1 -1 1
+34 1 -2.2520285035649175 0.34377072469492165 3.2433897655354262 1 0 -1
+82 1 -3.1361148993392707 0.2917712829104399 2.508598507937298 0 -1 -1
+47 1 -2.903472142580087 1.2996380231419302 2.6614912616951822 0 1 0
+159 1 -1.8421866316781088 1.3742261871908503 2.7832166426856038 0 0 0
+161 1 -1.2319440636738626 0.9387211724622819 -3.4892930122068617 1 0 2
+33 1 -0.4449542140900899 0.2769280403688486 3.289217283277774 0 -1 -1
+191 1 -0.8687075277531521 1.281273999295463 2.3493691514045447 1 -1 0
+20 1 -0.12835229617409075 0.4001437971686418 2.091186274425671 1 0 -1
+21 1 1.5590447736292827 0.23116165627532026 2.4331182207698356 1 0 -1
+83 1 0.6019872094726322 0.17868421219256525 2.965010196172179 0 -2 0
+107 1 -0.09314344901480053 1.8386195873289717 2.9198165047206524 -1 1 0
+97 1 0.9500008570521725 1.1147256892756756 2.5445482565685626 0 -1 -1
+15 1 2.6866827472081427 0.05611542822496954 2.621280841687164 -1 0 -1
+40 1 2.0535009935702107 1.3482348414084473 2.153119101811638 0 0 0
+110 1 3.037377950690711 1.1454318013031137 2.4602998295324308 0 0 -2
+54 1 2.1368310833242825 0.6989281938007096 3.190545712320829 0 -1 -1
+71 1 -2.6906257490825327 2.3188264822083675 1.851572369390678 0 -1 -1
+45 1 -1.8822606439217724 2.5464355632785174 2.887157746831732 1 0 -1
+2 1 -1.527738763941238 2.1784215473644295 1.8498426738676617 1 -2 -1
+67 1 -1.014923597719753 2.0522310481028465 3.091487536680741 1 0 0
+192 1 -0.8672155474955553 3.087168735274927 2.6165250257240618 1 0 1
+124 1 -0.37769468839105996 2.5506571887551175 1.8053870882842125 1 -1 -1
+46 1 -0.2092884053324724 2.562694157698328 -3.2372195292692605 1 -1 -1
+114 1 -0.2001222858286487 -3.429888000295159 1.8301280696628333 0 0 0
+61 1 0.5140644440329998 2.208326878392573 2.2153556959139413 -1 -2 0
+169 1 1.5629071468921552 2.2983930760888316 2.2366483189031316 0 0 0
+128 1 -3.438885935852406 3.376929578988928 3.002455750479755 1 0 -2
+52 1 -3.4549495641597217 2.178628786705743 2.923210719991474 0 -1 0
+48 1 2.502392696348409 2.9340155922847346 2.5991521468190113 0 0 -1
diff --git a/examples/PACKAGES/pimd/lj_reduced_units/in.lmp b/examples/PACKAGES/pimd/lj_reduced_units/in.lmp
new file mode 100644
index 0000000000..012214c4b2
--- /dev/null
+++ b/examples/PACKAGES/pimd/lj_reduced_units/in.lmp
@@ -0,0 +1,26 @@
+variable ibead uloop 32 pad
+
+units lj
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 2.8015
+read_data data.lj${ibead}
+
+pair_coeff    * * 1.0 1.0
+pair_modify shift yes
+
+mass 1 1.0
+
+timestep 0.00044905847
+
+fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L ${ibead}
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
+
+dump dcd all custom 1 ${ibead}.xyz id type x y z vx vy vz ix iy iz fx fy fz
+dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
diff --git a/examples/PACKAGES/pimd/lj_reduced_units/run.sh b/examples/PACKAGES/pimd/lj_reduced_units/run.sh
new file mode 100644
index 0000000000..adc7f4b955
--- /dev/null
+++ b/examples/PACKAGES/pimd/lj_reduced_units/run.sh
@@ -0,0 +1 @@
+mpirun -np 2 $LMP -in in.lmp -p 2x1 -log log -screen screen

From f6d94a95dddc33e7407e256e79374a69044fc01f Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Mon, 27 Mar 2023 22:45:14 -0400
Subject: [PATCH 052/396] fix whitespace in fix pimd doc

---
 doc/src/fix_pimd.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index e4a59b0078..1767acb134 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -106,7 +106,7 @@ thermostats in each chain.  For example, for a simulation of N particles
 with P beads in each ring-polymer, the total number of NH thermostats
 would be 3 x N x P x Nc.
 
-Fix *pimd/langevin* implements a Langevin thermostat in the normal mode 
+Fix *pimd/langevin* implements a Langevin thermostat in the normal mode
 representation, and also provides a barostat to sample the NPH/NPT ensembles.
 
 .. note::
@@ -273,7 +273,7 @@ related tasks for each of the partitions, e.g.
    forces in the normal mode representation. If the Catersian velocities and forces are
    needed, it is easy to perform the transformation when doing post-processing.
 
-   It is recommended to dump the image flags (*ix iy iz*) for fix *pimd/langevin*. It 
+   It is recommended to dump the image flags (*ix iy iz*) for fix *pimd/langevin*. It
    will be useful if you want to calculate some estimators during post-processing.
 
 Restart, fix_modify, output, run start/stop, minimize info

From 849933a687610642ff26bf3af5ead984f8634e22 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Mon, 27 Mar 2023 23:06:05 -0400
Subject: [PATCH 053/396] add difference part in fix pimd doc

---
 doc/src/fix_pimd.rst | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 1767acb134..fda002484a 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -269,13 +269,25 @@ related tasks for each of the partitions, e.g.
    read_restart system_${ibead}.restart2
 
 .. note::
-   Fix *pimd/langevin* dumps the Catersian coordinates, but dumps the velocities and
-   forces in the normal mode representation. If the Catersian velocities and forces are
+   Fix *pimd/langevin* dumps the Cartesian coordinates, but dumps the velocities and
+   forces in the normal mode representation. If the Cartesian velocities and forces are
    needed, it is easy to perform the transformation when doing post-processing.
 
    It is recommended to dump the image flags (*ix iy iz*) for fix *pimd/langevin*. It
    will be useful if you want to calculate some estimators during post-processing.
 
+Major differences of *fix pimd/nvt* and *fix pimd/langevin* are:
+
+   #. *Fix pimd/nvt* includes Cartesian pimd, normal mode pimd, and centroid md. *Fix pimd/langevin* only intends to support normal mode pimd, as it is commonly enough for thermodynamic sampling.
+   #. *Fix pimd/nvt* uses Nose-Hoover chain thermostat. *Fix pimd/langevin* uses Langevin thermostat.
+   #. *Fix pimd/langevin* provides barostat, so the npt ensemble can be sampled. *Fix pimd/nvt* only support nvt ensemble.
+   #. *Fix pimd/langevin* provides several quantum estimators in output.
+   #. *Fix pimd/langevin* allows multiple processes for each bead. For *fix pimd/nvt*, there is a large chance that multi-process tasks for each bead may fail.
+   #. The dump of *fix pimd/nvt* are all Cartesian. *Fix pimd/langevin* dumps normal-mode velocities and forces, and Cartesian coordinates.
+
+Initially, the inter-replica communication and normal mode transformation parts of *fix pimd/langevin* are written based on
+those of *fix pimd/nvt*, but are significantly revised.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

From 19da998932f4df73954d81bc810d96d9f3df2981 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Mon, 27 Mar 2023 23:11:24 -0400
Subject: [PATCH 054/396] add Jacobian into
 utils/sphinx-config/false_positives.txt

---
 doc/utils/sphinx-config/false_positives.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index fda9fb2b08..6a29c84974 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -1613,6 +1613,7 @@ Izumi
 Izvekov
 izz
 Izz
+Jacobian
 Jacobsen
 Jadhao
 Jadhav

From 18e4ed2e322a51734ca3250ee9aa593a15ef9864 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 31 Mar 2023 00:59:35 -0400
Subject: [PATCH 055/396] do not transform velocity to normal mode in setup

---
 src/REPLICA/fix_pimd_langevin.cpp | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index d64d948ecf..6c5b1a0b09 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -450,13 +450,6 @@ void FixPIMDLangevin::setup(int vflag)
     for (int i = 0; i < nlocal; i++) domain->unmap_inv(x[i], image[i]);
   }
 
-  if (method == NMPIMD) {
-    inter_replica_comm(v);
-    if (cmode == SINGLE_PROC)
-      nmpimd_transform(bufsortedall, v, M_x2xp[universe->iworld]);
-    else if (cmode == MULTI_PROC)
-      nmpimd_transform(bufbeads, v, M_x2xp[universe->iworld]);
-  }
   post_force(vflag);
   compute_totke();
   end_of_step();

From 25c449df8e2b78de7e4c29c8a8ec42ba71fbc8c5 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 31 Mar 2023 03:03:17 -0400
Subject: [PATCH 056/396] enable restart in fix pimd/langevin

---
 src/REPLICA/fix_pimd_langevin.cpp | 53 +++++++++++++++++++++++++++++--
 src/REPLICA/fix_pimd_langevin.h   |  5 +++
 2 files changed, 56 insertions(+), 2 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 6c5b1a0b09..b4ea68d49b 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -65,6 +65,7 @@ enum { SINGLE_PROC, MULTI_PROC };
 FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr)
 {
+  restart_global = 1;
   time_integrate = 1;
   tagsend = tagrecv = nullptr;
   bufsend = bufrecv = nullptr;
@@ -254,6 +255,8 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
     }
   }
   extvector = 1;
+  kBT = force->boltz * temp;
+  if (pstat_flag) baro_init();
 
   // some initilizations
 
@@ -376,7 +379,6 @@ void FixPIMDLangevin::init()
   }
   planck *= sp;
   hbar = planck / (2.0 * MY_PI);
-  kBT = force->boltz * temp;
   double beta = 1.0 / (force->boltz * temp);
   double _fbond = 1.0 * np * np / (beta * beta * hbar * hbar);
 
@@ -408,7 +410,6 @@ void FixPIMDLangevin::init()
   nmpimd_init();
 
   Langevin_init();
-  if (pstat_flag) baro_init();
 
   c_pe = modify->get_compute_by_id(id_pe);
   c_press = modify->get_compute_by_id(id_press);
@@ -1371,6 +1372,54 @@ void FixPIMDLangevin::compute_totenthalpy()
     totenthalpy = tote + 1.5 * W * vw[0] * vw[0] * inverse_np + p_hydro * (volume - vol0);
 }
 
+/* ----------------------------------------------------------------------
+   pack entire state of Fix into one write
+------------------------------------------------------------------------- */
+
+void FixPIMDLangevin::write_restart(FILE *fp)
+{
+  int nsize = size_restart_global();
+
+  double *list;
+  memory->create(list,nsize,"FixPIMDLangevin:list");
+
+  pack_restart_data(list);
+
+  if (comm->me == 0) {
+    int size = nsize * sizeof(double);
+    fwrite(&size,sizeof(int),1,fp);
+    fwrite(list,sizeof(double),nsize,fp);
+  }
+
+  memory->destroy(list);
+}
+/* ---------------------------------------------------------------------- */
+
+int FixPIMDLangevin::size_restart_global()
+{
+  int nsize = 6;
+
+  return nsize;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixPIMDLangevin::pack_restart_data(double *list)
+{
+  int n = 0;
+  for (int i=0; i<6; i++) { list[n++] = vw[i]; }
+  return n;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPIMDLangevin::restart(char *buf)
+{
+  int n = 0;
+  auto list = (double *) buf;
+  for (int i=0; i<6; i++) { vw[i] = list[n++]; }
+}
+
 /* ---------------------------------------------------------------------- */
 
 double FixPIMDLangevin::compute_vector(int n)
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 6d236718c7..79a2ee7477 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -175,6 +175,11 @@ class FixPIMDLangevin : public Fix {
   void compute_vir();
   void compute_cvir();
   void compute_totenthalpy();
+
+  void write_restart(FILE *fp) override;
+  int size_restart_global();
+  int pack_restart_data(double *list);
+  void restart(char *buf) override;
 };
 }    // namespace LAMMPS_NS
 #endif

From c37247eb5a75469493b7a81008c1b2fef9aa30e6 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 31 Mar 2023 03:09:34 -0400
Subject: [PATCH 057/396] add restart info in doc

---
 doc/src/fix_pimd.rst | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index fda002484a..ae325023fd 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -297,7 +297,11 @@ quasi-beads to :doc:`binary restart files <restart>`.  See the
 a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
 
-Fix *pimd/langevin* ...
+Fix *pimd/langevin* writes the state of the barostat overall beads to
+:doc:`binary restart files <restart>`. Since it uses a stochastic thermostat,
+the state of the thermostat is not written. However, the state of the system
+can be restored by reading the restart file, execpt that it will re-initialize
+the random number generator.
 
 None of the :doc:`fix_modify <fix_modify>` options
 are relevant to fix pimd/nvt.

From f444fe8fdf0b139a44f33e4b47120dd45173dea1 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 31 Mar 2023 03:12:38 -0400
Subject: [PATCH 058/396] fix spelling error

---
 doc/src/fix_pimd.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index ae325023fd..7116ce526b 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -300,7 +300,7 @@ operation of the fix continues in an uninterrupted fashion.
 Fix *pimd/langevin* writes the state of the barostat overall beads to
 :doc:`binary restart files <restart>`. Since it uses a stochastic thermostat,
 the state of the thermostat is not written. However, the state of the system
-can be restored by reading the restart file, execpt that it will re-initialize
+can be restored by reading the restart file, except that it will re-initialize
 the random number generator.
 
 None of the :doc:`fix_modify <fix_modify>` options

From 42758d0780835ded30631f8ed1a815f98fff6ec2 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Fri, 31 Mar 2023 03:28:09 -0400
Subject: [PATCH 059/396] delete dynamically allocated arrays in destructor

---
 src/REPLICA/fix_pimd_langevin.cpp | 39 +++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index b4ea68d49b..4d1ca2eb62 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -341,6 +341,45 @@ FixPIMDLangevin::~FixPIMDLangevin()
   delete[] id_pe;
   delete[] id_press;
   delete random;
+  delete c_pe;
+  delete c_press;
+  delete[] mass;
+  delete[] _omega_k;
+  delete[] Lan_c;
+  delete[] Lan_s;
+  delete[] tau_k;
+  delete[] c1_k;
+  delete[] c2_k;
+  delete[] plansend;
+  delete[] planrecv;
+  delete[] modeindex;
+  memory->destroy(xcall);
+  if (cmode == SINGLE_PROC) {
+    memory->destroy(bufsorted);
+    memory->destroy(outsorted);
+    memory->destroy(bufsortedall);
+    memory->destroy(buftransall);
+    memory->destroy(counts);
+    memory->destroy(displacements);
+  }
+
+  if (cmode == MULTI_PROC) {
+    memory->destroy(bufsendall);
+    memory->destroy(bufrecvall);
+    memory->destroy(tagsendall);
+    memory->destroy(tagrecvall);
+    memory->destroy(counts);
+    memory->destroy(displacements);
+  }
+  memory->destroy(M_x2xp);
+  memory->destroy(M_xp2x);
+  memory->destroy(xc);
+  memory->destroy(x_unwrap);
+  memory->destroy(bufsend);
+  memory->destroy(bufrecv);
+  memory->destroy(tagsend);
+  memory->destroy(tagrecv);
+  memory->destroy(bufbeads);
 }
 
 /* ---------------------------------------------------------------------- */

From 7c98d4dba3b56407ff2209e3249c32df9092a36c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 17 May 2023 10:26:33 -0400
Subject: [PATCH 060/396] avoid null pointer dereferences by allocating a
 buffer for at least 1 item

---
 src/library.cpp | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/library.cpp b/src/library.cpp
index cc4e748f57..33f49a4e53 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -3159,7 +3159,8 @@ void lammps_gather_bonds(void *handle, void *data)
     }
 
     tagint **bonds;
-    lmp->memory->create(bonds, localbonds, 3, "library:gather_bonds:localbonds");
+    // add 1 to localbonds, so "bonds" does not become a NULL pointer
+    lmp->memory->create(bonds, localbonds+1, 3, "library:gather_bonds:localbonds");
     lmp->atom->avec->pack_bond(bonds);
     MPI_Allgatherv(&bonds[0][0], 3*localbonds, MPI_LMP_TAGINT, data, bufsizes,
                    bufoffsets, MPI_LMP_TAGINT, lmp->world);
@@ -3269,7 +3270,8 @@ void lammps_gather_angles(void *handle, void *data)
     }
 
     tagint **angles;
-    lmp->memory->create(angles, localangles, 4, "library:gather_angles:localangles");
+    // add 1 to localangles, so "angles" does not become a NULL pointer
+    lmp->memory->create(angles, localangles+1, 4, "library:gather_angles:localangles");
     lmp->atom->avec->pack_angle(angles);
     MPI_Allgatherv(&angles[0][0], 4*localangles, MPI_LMP_TAGINT, data, bufsizes,
                    bufoffsets, MPI_LMP_TAGINT, lmp->world);
@@ -3380,7 +3382,8 @@ void lammps_gather_dihedrals(void *handle, void *data)
     }
 
     tagint **dihedrals;
-    lmp->memory->create(dihedrals, localdihedrals, 5, "library:gather_dihedrals:localdihedrals");
+    // add 1 to localdihedrals, so "dihedrals" does not become a NULL pointer
+    lmp->memory->create(dihedrals, localdihedrals+1, 5, "library:gather_dihedrals:localdihedrals");
     lmp->atom->avec->pack_dihedral(dihedrals);
     MPI_Allgatherv(&dihedrals[0][0], 5*localdihedrals, MPI_LMP_TAGINT, data, bufsizes,
                    bufoffsets, MPI_LMP_TAGINT, lmp->world);
@@ -3491,7 +3494,8 @@ void lammps_gather_impropers(void *handle, void *data)
     }
 
     tagint **impropers;
-    lmp->memory->create(impropers, localimpropers, 5, "library:gather_impropers:localimpropers");
+    // add 1 to localimpropers, so "impropers" does not become a NULL pointer
+    lmp->memory->create(impropers, localimpropers+1, 5, "library:gather_impropers:localimpropers");
     lmp->atom->avec->pack_improper(impropers);
     MPI_Allgatherv(&impropers[0][0], 5*localimpropers, MPI_LMP_TAGINT, data, bufsizes,
                    bufoffsets, MPI_LMP_TAGINT, lmp->world);

From 8736f97792ad951e3430bd678d56de2aa3d8e303 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 17 May 2023 17:35:14 -0400
Subject: [PATCH 061/396] remove dead code

---
 src/REPLICA/fix_pimd_langevin.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 4d1ca2eb62..3760c453ab 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -462,7 +462,6 @@ void FixPIMDLangevin::setup(int vflag)
 {
   int nlocal = atom->nlocal;
   double **x = atom->x;
-  double **v = atom->v;
   imageint *image = atom->image;
   if (mapflag) {
     for (int i = 0; i < nlocal; i++) domain->unmap(x[i], image[i]);

From 79f3eb6a4d2fc2fa3ad596ede196efecda24ee16 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 17 May 2023 17:35:22 -0400
Subject: [PATCH 062/396] remove debug code

---
 src/REPLICA/fix_pimd_langevin.cpp | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 3760c453ab..733d38e038 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -644,10 +644,6 @@ void FixPIMDLangevin::end_of_step()
   compute_p_cv();
   compute_tote();
   if (pstat_flag) compute_totenthalpy();
-
-  if (update->ntimestep % 10000 == 0) {
-    if (universe->me == 0) printf("This is the end of step %lld.\n", update->ntimestep);
-  }
 }
 
 void FixPIMDLangevin::collect_xc()

From 5d66dc6659718d2e16644a7b1c43ae50af134b6d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 17 May 2023 17:38:16 -0400
Subject: [PATCH 063/396] apply clang-format

---
 src/REPLICA/fix_pimd_langevin.cpp | 123 ++++++++++++++----------------
 1 file changed, 58 insertions(+), 65 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 733d38e038..67d7cabe02 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -47,7 +47,8 @@
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
-using namespace MathConst;
+using MathConst::MY_PI;
+using MathConst::THIRD;
 
 enum { NMPIMD };
 enum { PHYSICAL, NORMAL };
@@ -63,7 +64,7 @@ enum { SINGLE_PROC, MULTI_PROC };
 /* ---------------------------------------------------------------------- */
 
 FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
-  Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr)
+    Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr)
 {
   restart_global = 1;
   time_integrate = 1;
@@ -114,18 +115,18 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
 
   int seed = -1;
 
-  for (int i = 0; i < 6; i++)
-  {
+  for (int i = 0; i < 6; i++) {
     p_flag[i] = 0;
     p_target[i] = 0.0;
   }
 
   for (int i = 3; i < narg - 1; i += 2) {
     if (strcmp(arg[i], "method") == 0) {
-      if (strcmp(arg[i + 1], "nmpimd") == 0)method = NMPIMD;
-      else error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin");
-    }
-    else if (strcmp(arg[i], "integrator") == 0) {
+      if (strcmp(arg[i + 1], "nmpimd") == 0)
+        method = NMPIMD;
+      else
+        error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin");
+    } else if (strcmp(arg[i], "integrator") == 0) {
       if (strcmp(arg[i + 1], "obabo") == 0)
         integrator = OBABO;
       else if (strcmp(arg[i + 1], "baoab") == 0)
@@ -157,11 +158,11 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
                             "Unknown ensemble parameter for fix pimd/langevin. Only nve and nvt "
                             "ensembles are supported!");
     } else if (strcmp(arg[i], "fmass") == 0) {
-      fmass = utils::numeric(FLERR, arg[i+1], false, lmp);
+      fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (fmass < 0.0 || fmass > np)
         error->universe_all(FLERR, "Invalid fmass value for fix pimd/langevin");
     } else if (strcmp(arg[i], "sp") == 0) {
-      sp = utils::numeric(FLERR, arg[i+1], false, lmp);
+      sp = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd/nvt");
     } else if (strcmp(arg[i], "fmmode") == 0) {
       if (strcmp(arg[i + 1], "physical") == 0)
@@ -204,29 +205,29 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         error->universe_all(FLERR, "Unknown barostat parameter for fix pimd/langevin");
     } else if (strcmp(arg[i], "iso") == 0) {
       pstyle = ISO;
-      Pext = utils::numeric(FLERR, arg[i+1], false, lmp);
+      Pext = utils::numeric(FLERR, arg[i + 1], false, lmp);
       p_target[0] = p_target[1] = p_target[2] = Pext;
       pdim = 3;
     } else if (strcmp(arg[i], "aniso") == 0) {
       pstyle = ANISO;
       p_flag[0] = p_flag[1] = p_flag[2] = 1;
-      Pext = utils::numeric(FLERR, arg[i+1], false, lmp);
+      Pext = utils::numeric(FLERR, arg[i + 1], false, lmp);
       p_target[0] = p_target[1] = p_target[2] = Pext;
       pdim = 3;
     } else if (strcmp(arg[i], "x") == 0) {
       pstyle = ANISO;
       p_flag[0] = 1;
-      p_target[0] = utils::numeric(FLERR, arg[i+1], false, lmp);
+      p_target[0] = utils::numeric(FLERR, arg[i + 1], false, lmp);
       pdim++;
     } else if (strcmp(arg[i], "y") == 0) {
       pstyle = ANISO;
       p_flag[1] = 1;
-      p_target[1] = utils::numeric(FLERR, arg[i+1], false, lmp);
+      p_target[1] = utils::numeric(FLERR, arg[i + 1], false, lmp);
       pdim++;
     } else if (strcmp(arg[i], "z") == 0) {
       pstyle = ANISO;
       p_flag[2] = 1;
-      p_target[2] = utils::numeric(FLERR, arg[i+1], false, lmp);
+      p_target[2] = utils::numeric(FLERR, arg[i + 1], false, lmp);
       pdim++;
     } else if (strcmp(arg[i], "taup") == 0) {
       tau_p = utils::numeric(FLERR, arg[i + 1], false, lmp);
@@ -245,12 +246,12 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
 
   global_freq = 1;
   vector_flag = 1;
-  if (!pstat_flag)  size_vector = 10;
+  if (!pstat_flag)
+    size_vector = 10;
   else if (pstat_flag) {
-    if (pstyle == ISO){
-    size_vector = 15;
-    }
-    else if (pstyle == ANISO){
+    if (pstyle == ISO) {
+      size_vector = 15;
+    } else if (pstyle == ANISO) {
       size_vector = 17;
     }
   }
@@ -271,7 +272,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   fixedpoint[0] = 0.5 * (domain->boxlo[0] + domain->boxhi[0]);
   fixedpoint[1] = 0.5 * (domain->boxlo[1] + domain->boxhi[1]);
   fixedpoint[2] = 0.5 * (domain->boxlo[2] + domain->boxhi[2]);
-  if (pstat_flag) { p_hydro = (p_target[0]+p_target[1]+p_target[2])/pdim; }
+  if (pstat_flag) { p_hydro = (p_target[0] + p_target[1] + p_target[2]) / pdim; }
 
   // initialize Marsaglia RNG with processor-unique seed
 
@@ -293,8 +294,10 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   nreplica = universe->nworlds;
   ireplica = universe->iworld;
 
-  if (nreplica == 1) mapflag = 0;
-  else mapflag = 1;
+  if (nreplica == 1)
+    mapflag = 0;
+  else
+    mapflag = 1;
 
   int *iroots = new int[nreplica];
   MPI_Group uworldgroup, rootgroup;
@@ -426,7 +429,8 @@ void FixPIMDLangevin::init()
   fbond = _fbond * force->mvv2e;
 
   if ((universe->me == 0) && (universe->uscreen))
-    fprintf(universe->uscreen, "fix pimd/langevin -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
+    fprintf(universe->uscreen,
+            "fix pimd/langevin -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
 
   if (integrator == OBABO) {
     dtf = 0.5 * update->dt * force->ftm2v;
@@ -724,13 +728,10 @@ void FixPIMDLangevin::qc_step()
       if (barostat == BZP) {
         for (int i = 0; i < nlocal; i++) {
           for (int j = 0; j < 3; j++) {
-            if (p_flag[j])
-            {
+            if (p_flag[j]) {
               x[i][j] = expq[j] * x[i][j] + (expq[j] - expp[j]) / 2. / vw[j] * v[i][j];
               v[i][j] = expp[j] * v[i][j];
-            }
-            else
-            {
+            } else {
               x[i][j] += dtv * v[i][j];
             }
           }
@@ -844,10 +845,9 @@ void FixPIMDLangevin::press_v_step()
   } else if (pstyle == ANISO) {
     compute_stress_tensor();
     for (int ii = 0; ii < 3; ii++) {
-      if (p_flag[ii])
-      {
-        vw[ii] +=
-            dtv * (volume * np * (stress_tensor[ii] - p_hydro) / force->nktv2p + Vcoeff / beta_np) / W;
+      if (p_flag[ii]) {
+        vw[ii] += dtv *
+            (volume * np * (stress_tensor[ii] - p_hydro) / force->nktv2p + Vcoeff / beta_np) / W;
         if (universe->iworld == 0) {
           double dvw_proc = 0.0, dvw = 0.0;
           for (int i = 0; i < nlocal; i++) {
@@ -875,10 +875,8 @@ void FixPIMDLangevin::press_o_step()
     MPI_Bcast(&vw[0], 1, MPI_DOUBLE, 0, universe->uworld);
   } else if (pstyle == ANISO) {
     if (universe->me == 0) {
-      for (int ii=0; ii<3; ii++)
-      {
-        if (p_flag[ii])
-        {
+      for (int ii = 0; ii < 3; ii++) {
+        if (p_flag[ii]) {
           r1 = random->gaussian();
           vw[ii] = c1 * vw[ii] + c2 * sqrt(1.0 / W / beta_np) * r1;
         }
@@ -1155,9 +1153,9 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
       m++;
     }
     MPI_Allgather(&m, 1, MPI_INT, counts, 1, MPI_INT, universe->uworld);
-    for (i = 0; i < nreplica; i++) { counts[i] *= 3; }
+    for (i = 0; i < nreplica; i++) counts[i] *= 3;
     displacements[0] = 0;
-    for (i = 0; i < nreplica - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; }
+    for (i = 0; i < nreplica - 1; i++) displacements[i + 1] = displacements[i] + counts[i];
     MPI_Allgatherv(bufsorted[0], 3 * m, MPI_DOUBLE, bufsortedall[0], counts, displacements,
                    MPI_DOUBLE, universe->uworld);
   } else if (cmode == MULTI_PROC) {
@@ -1171,11 +1169,11 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
     }
     MPI_Gather(&m, 1, MPI_INT, counts, 1, MPI_INT, 0, world);
     displacements[0] = 0;
-    for (i = 0; i < nprocs - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; }
+    for (i = 0; i < nprocs - 1; i++) displacements[i + 1] = displacements[i] + counts[i];
     MPI_Gatherv(tagsend, m, MPI_LMP_TAGINT, tagsendall, counts, displacements, MPI_LMP_TAGINT, 0,
                 world);
-    for (i = 0; i < nprocs; i++) { counts[i] *= 3; }
-    for (i = 0; i < nprocs - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; }
+    for (i = 0; i < nprocs; i++) counts[i] *= 3;
+    for (i = 0; i < nprocs - 1; i++) displacements[i + 1] = displacements[i] + counts[i];
     MPI_Gatherv(bufsend[0], 3 * m, MPI_DOUBLE, bufsendall[0], counts, displacements, MPI_DOUBLE, 0,
                 world);
     for (int iplan = 0; iplan < sizeplan; iplan++) {
@@ -1203,15 +1201,15 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr)
 
 /* ---------------------------------------------------------------------- */
 
-void FixPIMDLangevin::remove_com_motion(){
-  if(universe->iworld == 0)
-  {
-  double **v = atom->v;
-  int *mask = atom->mask;
+void FixPIMDLangevin::remove_com_motion()
+{
+  if (universe->iworld == 0) {
+    double **v = atom->v;
+    int *mask = atom->mask;
     int nlocal = atom->nlocal;
-    if (dynamic)  masstotal = group->mass(igroup);
+    if (dynamic) masstotal = group->mass(igroup);
     double vcm[3];
-    group->vcm(igroup,masstotal,vcm);
+    group->vcm(igroup, masstotal, vcm);
     for (int i = 0; i < nlocal; i++) {
       if (mask[i] & groupbit) {
         v[i][0] -= vcm[0];
@@ -1372,7 +1370,8 @@ void FixPIMDLangevin::compute_t_vir()
 void FixPIMDLangevin::compute_p_prim()
 {
   double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
-  p_prim = atom->natoms * np * force->boltz * temp * inv_volume - 1.0 / 1.5 * inv_volume * total_spring_energy;
+  p_prim = atom->natoms * np * force->boltz * temp * inv_volume -
+      1.0 / 1.5 * inv_volume * total_spring_energy;
   p_prim *= force->nktv2p;
 }
 
@@ -1415,14 +1414,14 @@ void FixPIMDLangevin::write_restart(FILE *fp)
   int nsize = size_restart_global();
 
   double *list;
-  memory->create(list,nsize,"FixPIMDLangevin:list");
+  memory->create(list, nsize, "FixPIMDLangevin:list");
 
   pack_restart_data(list);
 
   if (comm->me == 0) {
     int size = nsize * sizeof(double);
-    fwrite(&size,sizeof(int),1,fp);
-    fwrite(list,sizeof(double),nsize,fp);
+    fwrite(&size, sizeof(int), 1, fp);
+    fwrite(list, sizeof(double), nsize, fp);
   }
 
   memory->destroy(list);
@@ -1441,7 +1440,7 @@ int FixPIMDLangevin::size_restart_global()
 int FixPIMDLangevin::pack_restart_data(double *list)
 {
   int n = 0;
-  for (int i=0; i<6; i++) { list[n++] = vw[i]; }
+  for (int i = 0; i < 6; i++) list[n++] = vw[i];
   return n;
 }
 
@@ -1451,7 +1450,7 @@ void FixPIMDLangevin::restart(char *buf)
 {
   int n = 0;
   auto list = (double *) buf;
-  for (int i=0; i<6; i++) { vw[i] = list[n++]; }
+  for (int i = 0; i < 6; i++) vw[i] = list[n++];
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1470,7 +1469,7 @@ double FixPIMDLangevin::compute_vector(int n)
   if (n == 9) return p_cv;
 
   if (pstat_flag) {
-        volume = domain->xprd * domain->yprd * domain->zprd;
+    volume = domain->xprd * domain->yprd * domain->zprd;
     if (pstyle == ISO) {
       if (n == 10) return vw[0];
       if (barostat == BZP) {
@@ -1478,21 +1477,15 @@ double FixPIMDLangevin::compute_vector(int n)
       } else if (barostat == MTTK) {
         if (n == 11) return 1.5 * W * vw[0] * vw[0];
       }
-      if (n == 12) {
-        return np * Pext * volume / force->nktv2p;
-      }
-      if (n == 13) {
-        return -Vcoeff * np * kBT * log(volume);
-      }
+      if (n == 12) { return np * Pext * volume / force->nktv2p; }
+      if (n == 13) { return -Vcoeff * np * kBT * log(volume); }
       if (n == 14) return totenthalpy;
     } else if (pstyle == ANISO) {
       if (n == 10) return vw[0];
       if (n == 11) return vw[1];
       if (n == 12) return vw[2];
       if (n == 13) return 0.5 * W * (vw[0] * vw[0] + vw[1] * vw[1] + vw[2] * vw[2]);
-      if (n == 14) {
-        return np * Pext * volume / force->nktv2p;
-      }
+      if (n == 14) { return np * Pext * volume / force->nktv2p; }
       if (n == 15) {
         volume = domain->xprd * domain->yprd * domain->zprd;
         return -Vcoeff * np * kBT * log(volume);

From 81a497adcd6d1fa52ac3bf0931bec76a7c8caaf4 Mon Sep 17 00:00:00 2001
From: oywg11 <ouyang@Lab-406>
Date: Thu, 18 May 2023 21:51:53 +0800
Subject: [PATCH 064/396] add standard version of ilp_water_2dm

---
 src/INTERLAYER/pair_ilp_graphene_hbn.cpp |  25 +--
 src/INTERLAYER/pair_ilp_graphene_hbn.h   |  38 +++-
 src/INTERLAYER/pair_ilp_tmd.cpp          | 213 +++++++++++++++++++----
 src/INTERLAYER/pair_ilp_tmd.h            |   2 +-
 src/INTERLAYER/pair_ilp_water_2dm.cpp    |  80 +++++++++
 src/INTERLAYER/pair_ilp_water_2dm.h      |  67 +++++++
 6 files changed, 373 insertions(+), 52 deletions(-)
 create mode 100644 src/INTERLAYER/pair_ilp_water_2dm.cpp
 create mode 100644 src/INTERLAYER/pair_ilp_water_2dm.h

diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
index 0ff2811339..956d7ba2be 100644
--- a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
+++ b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   LAMMPS development team: developers@lammps.org
+   Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -47,11 +47,11 @@ using namespace InterLayer;
 static const char cite_ilp[] =
     "ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848\n"
     "@Article{Ouyang2018\n"
-    " author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},\n"
+    " author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},\n"
     " title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},\n"
     " journal = {Nano Letters},\n"
     " volume =  18,\n"
-    " pages =   6009,\n"
+    " pages =   {6009}\n"
     " year =    2018,\n"
     "}\n\n";
 
@@ -59,7 +59,10 @@ static const char cite_ilp[] =
 static std::map<int, std::string> variant_map = {
     {PairILPGrapheneHBN::ILP_GrhBN, "ilp/graphene/hbn"},
     {PairILPGrapheneHBN::ILP_TMD, "ilp/tmd"},
-    {PairILPGrapheneHBN::SAIP_METAL, "saip/metal"}};
+    {PairILPGrapheneHBN::ILP_PHOSPHORUS, "ilp/phosphorus"},
+    {PairILPGrapheneHBN::ILP_WATER_2DM, "ilp/water/2dm"},
+    {PairILPGrapheneHBN::SAIP_METAL, "saip/metal"},
+    {PairILPGrapheneHBN::SAIP_METAL_TMD, "saip/metal/tmd"}};
 
 /* ---------------------------------------------------------------------- */
 
@@ -313,14 +316,14 @@ void PairILPGrapheneHBN::read_file(char *filename)
       for (int m = 0; m < nparams; m++) {
         if (i == params[m].ielement && j == params[m].jelement) {
           if (n >= 0)
-            error->all(FLERR, "{} potential file {} has a duplicate entry for: {} {}",
-                       variant_map[variant], filename, elements[i], elements[j]);
+            error->all(FLERR, "{} potential file {} has a duplicate entry", variant_map[variant],
+                       filename);
           n = m;
         }
       }
       if (n < 0)
-        error->all(FLERR, "{} potential file {} is missing an entry for: {} {}",
-                   variant_map[variant], filename, elements[i], elements[j]);
+        error->all(FLERR, "{} potential file {} is missing an entry", variant_map[variant],
+                   filename);
       elem2param[i][j] = n;
       cutILPsq[i][j] = params[n].rcut * params[n].rcut;
     }
@@ -632,7 +635,7 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */)
 
 void PairILPGrapheneHBN::ILP_neigh()
 {
-  int i, j, ii, jj, n, allnum, jnum, itype, jtype;
+  int i, j, ii, jj, n, inum, jnum, itype, jtype;
   double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
   int *ilist, *jlist, *numneigh, **firstneigh;
   int *neighptr;
@@ -649,7 +652,7 @@ void PairILPGrapheneHBN::ILP_neigh()
         (int **) memory->smalloc(maxlocal * sizeof(int *), "ILPGrapheneHBN:firstneigh");
   }
 
-  allnum = list->inum + list->gnum;
+  inum = list->inum; // + list->gnum;
   ilist = list->ilist;
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
@@ -659,7 +662,7 @@ void PairILPGrapheneHBN::ILP_neigh()
 
   ipage->reset();
 
-  for (ii = 0; ii < allnum; ii++) {
+  for (ii = 0; ii < inum; ii++) {
     i = ilist[ii];
 
     n = 0;
diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.h b/src/INTERLAYER/pair_ilp_graphene_hbn.h
index 9987830b1d..6381fb8f35 100644
--- a/src/INTERLAYER/pair_ilp_graphene_hbn.h
+++ b/src/INTERLAYER/pair_ilp_graphene_hbn.h
@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   LAMMPS development team: developers@lammps.org
+   Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -35,11 +35,19 @@ class PairILPGrapheneHBN : public Pair {
   double init_one(int, int) override;
   void init_style() override;
   void calc_FvdW(int, int);
+  virtual void calc_FRep(int, int);
+  virtual void ILP_neigh();
+  virtual void calc_normal();
+  void read_file(char *);
+  void allocate();
+
   double single(int, int, int, int, double, double, double, double &) override;
 
   static constexpr int NPARAMS_PER_LINE = 13;
 
-  enum { ILP_GrhBN, ILP_TMD, SAIP_METAL };    // for telling class variants apart in shared code
+  // for telling class variants apart in shared code
+  enum { ILP_GrhBN, ILP_TMD, SAIP_METAL, 
+         ILP_WATER_2DM, SAIP_METAL_TMD, ILP_PHOSPHORUS };
 
  protected:
   int me;
@@ -51,6 +59,7 @@ class PairILPGrapheneHBN : public Pair {
   int *ILP_numneigh;       // # of pair neighbors for each atom
   int **ILP_firstneigh;    // ptr to 1st neighbor of each atom
   int tap_flag;            // flag to turn on/off taper function
+  double ncf;                 // for ilp/phosphorus, coefficients for calcualting the normals 
 
   struct Param {
     double z0, alpha, epsilon, C, delta, d, sR, reff, C6, S;
@@ -76,15 +85,28 @@ class PairILPGrapheneHBN : public Pair {
   double ***dpvet1;
   double ***dpvet2;
   double ***dNave;
-
-  virtual void ILP_neigh();
-  virtual void calc_normal();
-  virtual void calc_FRep(int, int);
-  void read_file(char *);
-  void allocate();
 };
 
 }    // namespace LAMMPS_NS
 
 #endif
 #endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+E: All pair coeffs are not set
+
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+*/
diff --git a/src/INTERLAYER/pair_ilp_tmd.cpp b/src/INTERLAYER/pair_ilp_tmd.cpp
index c024e23079..d855b9423d 100644
--- a/src/INTERLAYER/pair_ilp_tmd.cpp
+++ b/src/INTERLAYER/pair_ilp_tmd.cpp
@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   LAMMPS development team: developers@lammps.org
+   Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -22,12 +22,14 @@
 
 #include "atom.h"
 #include "citeme.h"
+#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "interlayer_taper.h"
 #include "memory.h"
 #include "my_page.h"
 #include "neigh_list.h"
+#include "neighbor.h"
 
 #include <cmath>
 #include <cstring>
@@ -35,22 +37,20 @@
 using namespace LAMMPS_NS;
 using namespace InterLayer;
 
-#define MAXLINE 1024
 #define DELTA 4
 #define PGDELTA 1
 
-static const char cite_ilp_tmd[] =
-    "ilp/tmd potential doi:10.1021/acs.jctc.1c00782\n"
-    "@Article{Ouyang2021\n"
-    "  author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and\n"
-    "    A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},\n"
-    "  title = {Anisotropic Interlayer Force Field for Transition\n"
-    "    Metal Dichalcogenides: The Case of Molybdenum Disulfide},\n"
-    "  journal = {J.~Chem.\\ Theory Comput.},\n"
-    " volume   = 17,\n"
-    " pages    = {7237--7245}\n"
-    " year     = 2021,\n"
-    "}\n\n";
+static const char cite_ilp_tmd[] = "ilp/tmd potential doi/10.1021/acs.jctc.1c00782\n"
+                                   "@Article{Ouyang2021\n"
+                                   " author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. "
+                                   "Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},\n"
+                                   " title = {Anisotropic Interlayer Force Field for Transition "
+                                   "Metal Dichalcogenides: The Case of Molybdenum Disulfide},\n"
+                                   " journal = {J. Chem. Theory Comput.},\n"
+                                   " volume =  17,\n"
+                                   " pages =   {7237–7245}\n"
+                                   " year =    2021,\n"
+                                   "}\n\n";
 
 /* ---------------------------------------------------------------------- */
 
@@ -232,7 +232,7 @@ void PairILPTMD::calc_FRep(int eflag, int /* vflag */)
 
 void PairILPTMD::ILP_neigh()
 {
-  int i, j, l, ii, jj, ll, n, allnum, jnum, itype, jtype, ltype, imol, jmol, count;
+  int i, j, l, ii, jj, ll, n, inum, jnum, itype, jtype, ltype, imol, jmol, count;
   double xtmp, ytmp, ztmp, delx, dely, delz, deljx, deljy, deljz, rsq, rsqlj;
   int *ilist, *jlist, *numneigh, **firstneigh;
   int *neighsort;
@@ -249,7 +249,7 @@ void PairILPTMD::ILP_neigh()
     ILP_firstneigh = (int **) memory->smalloc(maxlocal * sizeof(int *), "ILPTMD:firstneigh");
   }
 
-  allnum = list->inum + list->gnum;
+  inum = list->inum; //+ list->gnum;
   ilist = list->ilist;
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
@@ -259,7 +259,7 @@ void PairILPTMD::ILP_neigh()
 
   ipage->reset();
 
-  for (ii = 0; ii < allnum; ii++) {
+  for (ii = 0; ii < inum; ii++) {
     i = ilist[ii];
 
     //initialize varibles
@@ -288,21 +288,21 @@ void PairILPTMD::ILP_neigh()
       delz = ztmp - x[j][2];
       rsq = delx * delx + dely * dely + delz * delz;
 
-      // check if the atom i is TMD, i.e., Mo/S/W/Se
-      if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
-          strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
+      // check if the atom i is a TMD atom, i.e., Mo/S/W/Se
+      if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W")  == 0 ||
+          strcmp(elements[itype], "S")  == 0 || strcmp(elements[itype], "Se") == 0 ||
           strcmp(elements[itype], "Te") == 0) {
         if (rsq != 0 && rsq < cutILPsq[itype][jtype] && imol == jmol && type[i] == type[j]) {
           neighptr[n++] = j;
         }
-      } else {    // atom i is C, B, N or H.
+      } else {    // atom i can be P, C, B, N or H.
         if (rsq != 0 && rsq < cutILPsq[itype][jtype] && imol == jmol) { neighptr[n++] = j; }
       }
     }    // loop over jj
 
     // if atom i is Mo/W/S/Se/Te, then sorting the orders of neighbors
-    if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
-        strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
+    if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W")  == 0 ||
+        strcmp(elements[itype], "S")  == 0 || strcmp(elements[itype], "Se") == 0 ||
         strcmp(elements[itype], "Te") == 0) {
       // initialize neighsort
       for (ll = 0; ll < n; ll++) {
@@ -367,11 +367,11 @@ void PairILPTMD::ILP_neigh()
           ll++;
         }
       }         // end of sorting the order of neighbors
-    } else {    // for B/N/C/H atoms
+    } else {    // for P/B/N/C/H atoms
       if (n > 3)
         error->one(
             FLERR,
-            "There are too many neighbors for B/N/C/H atoms, please check your configuration");
+            "There are too many neighbors for P/B/N/C/H atoms, please check your configuration");
       for (ll = 0; ll < n; ll++) { neighsort[ll] = neighptr[ll]; }
     }
 
@@ -390,12 +390,14 @@ void PairILPTMD::calc_normal()
 {
   int i, j, ii, jj, inum, jnum;
   int cont, id, ip, m, k, itype;
-  double nn, xtp, ytp, ztp, delx, dely, delz, nn2;
   int *ilist, *jlist;
+  int iH1,iH2,jH1,jH2;
   double Nave[3], dni[3], dpvdri[3][3];
+  double nn, xtp, ytp, ztp, delx, dely, delz, nn2;
 
   double **x = atom->x;
   int *type = atom->type;
+  tagint *tag = atom->tag;
 
   memory->destroy(dnn);
   memory->destroy(vect);
@@ -479,9 +481,63 @@ void PairILPTMD::calc_normal()
           for (m = 0; m < Nnei; m++) { dnormal[i][id][m][ip] = 0.0; }
         }
       }
+      // for hydrogen in water molecule
+      if (strcmp(elements[itype], "Hw") == 0) {
+        if(cont == 0) {
+          jH1 = atom->map(tag[i] - 1);
+          jH2 = atom->map(tag[i] - 2);
+          iH1 = map[type[jH1]];
+          iH2 = map[type[jH2]];
+          if (strcmp(elements[iH1], "Ow") == 0 ) { 
+            vect[0][0] = x[jH1][0] - xtp;
+            vect[0][1] = x[jH1][1] - ytp;
+            vect[0][2] = x[jH1][2] - ztp;
+          } else if (strcmp(elements[iH2], "Ow") == 0 ) { 
+            vect[0][0] = x[jH2][0] - xtp;
+            vect[0][1] = x[jH2][1] - ytp;
+            vect[0][2] = x[jH2][2] - ztp;
+          } else {
+            fprintf(screen, "jH1 jH2 = %d %d\n", jH1,jH2);
+            fprintf(screen, "Atom Type = %d %d\n", type[jH1],type[jH2]);
+            fprintf(screen, "For atom i = %d %d\n", tag[i],type[i]);
+            error->one(FLERR, "The order of atoms in water molecule should be O H H !");
+          }
+        }
+        Nave[0] = vect[0][0];
+        Nave[1] = vect[0][1];
+        Nave[2] = vect[0][2];
+        // the magnitude of the normal vector
+        nn2 = Nave[0] * Nave[0] + Nave[1] * Nave[1] + Nave[2] * Nave[2];
+        nn = sqrt(nn2);
+        if (nn == 0) error->one(FLERR, "The magnitude of the normal vector is zero");
+        // the unit normal vector
+        normal[i][0] = Nave[0] / nn;
+        normal[i][1] = Nave[1] / nn;
+        normal[i][2] = Nave[2] / nn;
+
+        // Calculte dNave/dri, defined as dpvdri
+        for (id = 0; id < 3; id++) {
+          for (ip = 0; ip < 3; ip++) {
+            if (ip == id) { dpvdri[id][ip] = -1.0;} 
+            else {dpvdri[id][ip] = 0.0;}
+          }
+        }
+
+        // derivatives of nn, dnn:3x1 vector
+        dni[0] = (Nave[0] * dpvdri[0][0] + Nave[1] * dpvdri[1][0] + Nave[2] * dpvdri[2][0]) / nn;
+        dni[1] = (Nave[0] * dpvdri[0][1] + Nave[1] * dpvdri[1][1] + Nave[2] * dpvdri[2][1]) / nn;
+        dni[2] = (Nave[0] * dpvdri[0][2] + Nave[1] * dpvdri[1][2] + Nave[2] * dpvdri[2][2]) / nn;
+        // derivatives of unit vector ni respect to ri, the result is 3x3 matrix
+        for (id = 0; id < 3; id++) {
+          for (ip = 0; ip < 3; ip++) {
+            dnormdri[i][id][ip] = dpvdri[id][ip] / nn - Nave[id] * dni[ip] / nn2;
+            dnormal[i][id][0][ip] = -dnormdri[i][id][ip];
+          }
+        }
+      }
     }
     //############################ For the edge atoms of TMD ################################
-    else if (cont < Nnei) {
+    else if (cont > 1 && cont < Nnei) {
       if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
           strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0) {
         // derivatives of Ni[l] respect to the cont neighbors
@@ -557,8 +613,7 @@ void PairILPTMD::calc_normal()
         for (m = 0; m < cont; m++) {
           for (id = 0; id < 3; id++) {
             dnn[m][id] = (Nave[0] * dNave[0][m][id] + Nave[1] * dNave[1][m][id] +
-                          Nave[2] * dNave[2][m][id]) /
-                nn;
+                          Nave[2] * dNave[2][m][id]) / nn;
           }
         }
         // dnormal[i][id][m][ip]: the derivative of normal[i][id] respect to r[m][ip], id,ip=0,1,2.
@@ -589,12 +644,107 @@ void PairILPTMD::calc_normal()
           }
         }
       }    // for TMD
+      //############################ For Oxygen in the water molecule #######################
+      else if (strcmp(elements[itype], "Ow") == 0) {
+        if(cont == 0) {
+          jH1 = atom->map(tag[i] + 1);
+          jH2 = atom->map(tag[i] + 2);
+          iH1 = map[type[jH1]];
+          iH2 = map[type[jH2]];
+          if (strcmp(elements[iH1], "Hw") == 0 && strcmp(elements[iH2], "Hw") == 0) {
+            vect[0][0] = x[jH1][0] - xtp;
+            vect[0][1] = x[jH1][1] - ytp;
+            vect[0][2] = x[jH1][2] - ztp;
+
+            vect[1][0] = x[jH2][0] - xtp;
+            vect[1][1] = x[jH2][1] - ytp;
+            vect[1][2] = x[jH2][2] - ztp;
+
+            cont = 2;
+          } else {
+            fprintf(screen, "jH1 jH2 = %d %d\n", jH1,jH2);
+            fprintf(screen, "Atom Type = %d %d\n", type[jH1],type[jH2]);
+            fprintf(screen, "ID and type of atom i = %d %d\n", tag[i],type[i]);
+            error->one(FLERR, "The order of atoms in water molecule should be O H H !");
+          }
+        }
+        if (cont == 2) {
+          Nave[0] = (vect[0][0] + vect[1][0])/cont;
+          Nave[1] = (vect[0][1] + vect[1][1])/cont;
+          Nave[2] = (vect[0][2] + vect[1][2])/cont;
+          // the magnitude of the normal vector
+          nn2 = Nave[0] * Nave[0] + Nave[1] * Nave[1] + Nave[2] * Nave[2];
+          nn = sqrt(nn2);
+          if (nn == 0) error->one(FLERR, "The magnitude of the normal vector is zero");
+          // the unit normal vector
+          normal[i][0] = Nave[0] / nn;
+          normal[i][1] = Nave[1] / nn;
+          normal[i][2] = Nave[2] / nn;
+
+          // derivatives of non-normalized normal vector, dNave:3xcontx3 array
+          // dNave[id][m][ip]: the derivatve of the id component of Nave 
+          // respect to the ip component of atom m
+          for (id = 0; id < 3; id++) {
+            for (ip = 0; ip < 3; ip++) {
+              for (m = 0; m < cont; m++) {
+                if (ip == id) { dNave[id][m][ip] = 0.5;} 
+                else {dNave[id][m][ip] = 0.0;}
+              }
+            }
+          }
+          // derivatives of nn, dnn:contx3 vector
+          // dnn[m][id]: the derivative of nn respect to r[m][id], m=0,...Nnei-1; id=0,1,2
+          // r[m][id]: the id's component of atom m
+          for (m = 0; m < cont; m++) {
+            for (id = 0; id < 3; id++) {
+              dnn[m][id] = (Nave[0] * dNave[0][m][id] + Nave[1] * dNave[1][m][id] +
+                            Nave[2] * dNave[2][m][id]) / nn;
+            }
+          }
+          // dnormal[i][id][m][ip]: the derivative of normal[i][id] respect to r[m][ip], id,ip=0,1,2.
+          // for atom m, which is a neighbor atom of atom i, m = 0,...,Nnei-1
+          for (m = 0; m < cont; m++) {
+            for (id = 0; id < 3; id++) {
+              for (ip = 0; ip < 3; ip++) {
+                dnormal[i][id][m][ip] = dNave[id][m][ip] / nn - Nave[id] * dnn[m][ip] / nn2;
+              }
+            }
+          }
+          // Calculte dNave/dri, defined as dpvdri
+          for (id = 0; id < 3; id++) {
+            for (ip = 0; ip < 3; ip++) {
+              dpvdri[id][ip] = 0.0;
+              for (k = 0; k < cont; k++) { dpvdri[id][ip] -= dNave[id][k][ip]; }
+            }
+          }
+
+          // derivatives of nn, dnn:3x1 vector
+          dni[0] = (Nave[0] * dpvdri[0][0] + Nave[1] * dpvdri[1][0] + Nave[2] * dpvdri[2][0]) / nn;
+          dni[1] = (Nave[0] * dpvdri[0][1] + Nave[1] * dpvdri[1][1] + Nave[2] * dpvdri[2][1]) / nn;
+          dni[2] = (Nave[0] * dpvdri[0][2] + Nave[1] * dpvdri[1][2] + Nave[2] * dpvdri[2][2]) / nn;
+          // derivatives of unit vector ni respect to ri, the result is 3x3 matrix
+          for (id = 0; id < 3; id++) {
+            for (ip = 0; ip < 3; ip++) {
+              dnormdri[i][id][ip] = dpvdri[id][ip] / nn - Nave[id] * dni[ip] / nn2;
+            }
+          }
+          // printf("%4d:\t%e %e %e\n\t%e %e %e\n\t%e %e %e\n",
+          //        i, dnormdri[i][0][0], dnormdri[i][0][1], dnormdri[i][0][2],
+          //        dnormdri[i][1][0],dnormdri[i][1][1],dnormdri[i][1][2],
+          //        dnormdri[i][2][0],dnormdri[i][2][1],dnormdri[i][2][2]);
+          // exit(0);
+        }
+        else if (cont >= 3) {
+          error->one(FLERR,
+                     "There are too many neighbors for calculating normals of water molecules");
+        }
+      }
       //############################ For the edge & bulk atoms of GrhBN ################################
       else {
         if (cont == 2) {
           for (ip = 0; ip < 3; ip++) {
             pvet[0][ip] = vect[0][modulo(ip + 1, 3)] * vect[1][modulo(ip + 2, 3)] -
-                vect[0][modulo(ip + 2, 3)] * vect[1][modulo(ip + 1, 3)];
+                          vect[0][modulo(ip + 2, 3)] * vect[1][modulo(ip + 1, 3)];
           }
           // dpvet1[k][l][ip]: the derivatve of the k (=0,...cont-1)th Nik respect to the ip component of atom l
           // derivatives respect to atom l
@@ -657,8 +807,7 @@ void PairILPTMD::calc_normal()
           for (m = 0; m < cont; m++) {
             for (id = 0; id < 3; id++) {
               dnn[m][id] = (Nave[0] * dNave[0][m][id] + Nave[1] * dNave[1][m][id] +
-                            Nave[2] * dNave[2][m][id]) /
-                  nn;
+                            Nave[2] * dNave[2][m][id]) / nn;
             }
           }
           // dnormal[i][id][m][ip]: the derivative of normal[i][id] respect to r[m][ip], id,ip=0,1,2.
diff --git a/src/INTERLAYER/pair_ilp_tmd.h b/src/INTERLAYER/pair_ilp_tmd.h
index 8381c2e830..8d5446d49c 100644
--- a/src/INTERLAYER/pair_ilp_tmd.h
+++ b/src/INTERLAYER/pair_ilp_tmd.h
@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   LAMMPS development team: developers@lammps.org
+   Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
diff --git a/src/INTERLAYER/pair_ilp_water_2dm.cpp b/src/INTERLAYER/pair_ilp_water_2dm.cpp
new file mode 100644
index 0000000000..58e56894f5
--- /dev/null
+++ b/src/INTERLAYER/pair_ilp_water_2dm.cpp
@@ -0,0 +1,80 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Wengen Ouyang (Wuhan University)
+   e-mail: w.g.ouyang at gmail dot com
+
+   This is a full version of the potential described in
+   [Feng and Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).]
+------------------------------------------------------------------------- */
+
+#include "pair_ilp_water_2dm.h"
+
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "interlayer_taper.h"
+#include "memory.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+
+#include <cmath>
+#include <cstring>
+
+using namespace LAMMPS_NS;
+using namespace InterLayer;
+
+#define MAXLINE 1024
+#define DELTA 4
+#define PGDELTA 1
+
+static const char cite_ilp_water[] = "ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464\n"
+                                   "@Article{Feng2023\n"
+                                   " author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},\n"
+                                   " title = {Registry-Dependent Potential for Interfaces of Water with Graphene},\n"
+                                   " journal = {J. Phys. Chem. C},\n"
+                                   " volume =  127,\n"
+                                   " pages =   {8704-8713}\n"
+                                   " year =    2023,\n"
+                                   "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+PairILPWATER2DM::PairILPWATER2DM(LAMMPS *lmp) : PairILPGrapheneHBN(lmp), PairILPTMD(lmp)
+{
+  variant = ILP_WATER_2DM;
+  single_enable = 0;
+
+  // for TMD, each atom have six neighbors
+  Nnei = 6;
+
+  if (lmp->citeme) lmp->citeme->add(cite_ilp_water);
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairILPWATER2DM::settings(int narg, char **arg)
+{
+  if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command");
+  if (!utils::strmatch(force->pair_style, "^hybrid/overlay"))
+    error->all(FLERR, "Pair style ilp/water/2dm must be used as sub-style with hybrid/overlay");
+
+  cut_global = utils::numeric(FLERR, arg[0], false, lmp);
+  if (narg == 2) tap_flag = utils::numeric(FLERR, arg[1], false, lmp);
+}
diff --git a/src/INTERLAYER/pair_ilp_water_2dm.h b/src/INTERLAYER/pair_ilp_water_2dm.h
new file mode 100644
index 0000000000..c35d757ea0
--- /dev/null
+++ b/src/INTERLAYER/pair_ilp_water_2dm.h
@@ -0,0 +1,67 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+// clang-format off
+PairStyle(ilp/water/2dm,PairILPWATER2DM);
+// clang-format on
+#else
+
+#ifndef LMP_PAIR_ILP_WATER_2DM_H
+#define LMP_PAIR_ILP_WATER_2DM_H
+
+#include "pair_ilp_tmd.h"
+
+namespace LAMMPS_NS {
+
+class PairILPWATER2DM : virtual public PairILPTMD {
+ public:
+  PairILPWATER2DM(class LAMMPS *);
+
+ protected:
+  void settings(int, char **) override;
+
+  /**************************************************************/
+  /*       modulo operation with cycling around range           */
+
+  inline int modulo(int k, int range)
+  {
+    if (k < 0) k += range;
+    return k % range;
+  }
+  /**************************************************************/
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+E: All pair coeffs are not set
+
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+*/

From cc30c4478dcfe6c73d908398437cc58909d1be5c Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Thu, 18 May 2023 21:58:40 +0800
Subject: [PATCH 065/396] add optmized verion of ilp_water_2dm

---
 src/OPT/pair_ilp_graphene_hbn_opt.cpp | 99 +++++++++++++++++++++++----
 src/OPT/pair_ilp_graphene_hbn_opt.h   | 12 +++-
 src/OPT/pair_ilp_water_2dm_opt.cpp    | 73 ++++++++++++++++++++
 src/OPT/pair_ilp_water_2dm_opt.h      | 39 +++++++++++
 4 files changed, 207 insertions(+), 16 deletions(-)
 create mode 100644 src/OPT/pair_ilp_water_2dm_opt.cpp
 create mode 100644 src/OPT/pair_ilp_water_2dm_opt.h

diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.cpp b/src/OPT/pair_ilp_graphene_hbn_opt.cpp
index 586c44be08..63822ad4c6 100644
--- a/src/OPT/pair_ilp_graphene_hbn_opt.cpp
+++ b/src/OPT/pair_ilp_graphene_hbn_opt.cpp
@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   LAMMPS development team: developers@lammps.org
+   Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -23,24 +23,27 @@
 
 #include "atom.h"
 #include "citeme.h"
+#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "interlayer_taper.h"
 #include "memory.h"
 #include "neigh_list.h"
+#include "neigh_request.h"
 #include "neighbor.h"
+#include "pointers.h"
 
 #include <cmath>
-#include <utility>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace InterLayer;
 
 static const char cite_ilp_cur[] =
-    "ilp/graphene/hbn/opt potential: doi:10.1145/3458817.3476137\n"
+    "ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137\n"
     "@inproceedings{gao2021lmff\n"
-    " author = {Gao, Ping and Duan, Xiaohui and others},\n"
-    " title = {{LMFF}: Efficient and Scalable Layered Materials Force Field on Heterogeneous "
+    " author = {Gao, Ping and Duan, Xiaohui and Others},\n"
+    " title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous "
     "Many-Core Processors},\n"
     " year = {2021},\n"
     " isbn = {9781450384421},\n"
@@ -50,14 +53,12 @@ static const char cite_ilp_cur[] =
     " doi = {10.1145/3458817.3476137},\n"
     " booktitle = {Proceedings of the International Conference for High Performance Computing, "
     "Networking, Storage and Analysis},\n"
-    " pages    = {42},\n"
+    " articleno = {42},\n"
     " numpages = {14},\n"
-    " location = {St.~Louis, Missouri},\n"
+    " location = {St. Louis, Missouri},\n"
     " series = {SC'21},\n"
     "}\n\n";
 
-static bool check_vdw(tagint itag, tagint jtag, double *xi, double *xj);
-
 /* ---------------------------------------------------------------------- */
 
 PairILPGrapheneHBNOpt::PairILPGrapheneHBNOpt(LAMMPS *lmp) :
@@ -168,6 +169,36 @@ void PairILPGrapheneHBNOpt::compute(int eflag, int vflag)
         }
       }
     }
+  } else if (variant == ILP_WATER_2DM) {
+    if (eflag_global || eflag_atom) {
+      if (vflag_either) {
+        if (tap_flag) {
+          eval<6, 1, 1, 1, ILP_WATER_2DM>();
+        } else {
+          eval<6, 1, 1, 0, ILP_WATER_2DM>();
+        }
+      } else {
+        if (tap_flag) {
+          eval<6, 1, 0, 1, ILP_WATER_2DM>();
+        } else {
+          eval<6, 1, 0, 0, ILP_WATER_2DM>();
+        }
+      }
+    } else {
+      if (vflag_either) {
+        if (tap_flag) {
+          eval<6, 0, 1, 1, ILP_WATER_2DM>();
+        } else {
+          eval<6, 0, 1, 0, ILP_WATER_2DM>();
+        }
+      } else {
+        if (tap_flag) {
+          eval<6, 0, 0, 1, ILP_WATER_2DM>();
+        } else {
+          eval<6, 0, 0, 0, ILP_WATER_2DM>();
+        }
+      }
+    }
   } else if (variant == SAIP_METAL) {
     if (eflag_global || eflag_atom) {
       if (vflag_either) {
@@ -255,7 +286,7 @@ void PairILPGrapheneHBNOpt::eval()
       rsq = delx * delx + dely * dely + delz * delz;
 
       if (rsq != 0 && rsq < cutILPsq[itype_map][jtype]) {
-        if (VARIANT == ILP_TMD && special_type[itype] && itype != type[j]) continue;
+        if ((VARIANT == ILP_TMD || VARIANT == ILP_WATER_2DM) && special_type[itype] == TMD_METAL && itype != type[j]) continue;
         if (ILP_nneigh >= MAX_NNEIGH) {
           error->one(FLERR, "There are too many neighbors for calculating normals");
         }
@@ -269,7 +300,8 @@ void PairILPGrapheneHBNOpt::eval()
     dproddni[2] = 0.0;
 
     double norm[3], dnormdxi[3][3], dnormdxk[MAX_NNEIGH][3][3];
-    calc_normal<MAX_NNEIGH>(i, ILP_neigh, ILP_nneigh, norm, dnormdxi, dnormdxk);
+
+    calc_normal<MAX_NNEIGH>(i, itype, ILP_neigh, ILP_nneigh, norm, dnormdxi, dnormdxk);
 
     for (jj = 0; jj < jnum_inter; jj++) {
       j = jlist_inter[jj];
@@ -298,7 +330,7 @@ void PairILPGrapheneHBNOpt::eval()
           Tap = 1.0;
           dTap = 0.0;
         }
-        if (VARIANT != SAIP_METAL || !special_type[itype]) {
+        if (VARIANT != SAIP_METAL || special_type[itype] != SAIP_BNCH) {
           // Calculate the transverse distance
           prodnorm1 = norm[0] * delx + norm[1] * dely + norm[2] * delz;
           rhosq1 = rsq - prodnorm1 * prodnorm1;    // rho_ij
@@ -310,7 +342,7 @@ void PairILPGrapheneHBNOpt::eval()
 
           frho1 = exp1 * p.C;
           Erep = 0.5 * p.epsilon + frho1;
-          if (VARIANT == SAIP_METAL && special_type[jtype]) { Erep += 0.5 * p.epsilon + p.C; }
+          if (VARIANT == SAIP_METAL && special_type[jtype] == SAIP_BNCH) { Erep += 0.5 * p.epsilon + p.C; }
           Vilp = exp0 * Erep;
 
           // derivatives
@@ -428,6 +460,19 @@ inline void deriv_normal(double dndr[3][3], double *del, double *n, double rnnor
   dndr[1][2] = (del[1] * n[0] * n[1] + del[0] * (n[0] * n[0] + n[2] * n[2])) * rnnorm;
   dndr[2][2] = (del[1] * n[0] * n[2] - del[0] * n[1] * n[2]) * rnnorm;
 }
+inline void deriv_hat(double dnhatdn[3][3], double *n, double rnnorm, double factor){
+  double cfactor = rnnorm * factor;
+  dnhatdn[0][0] = (n[1]*n[1]+n[2]*n[2])*cfactor;
+  dnhatdn[1][0] = -n[1]*n[0]*cfactor;
+  dnhatdn[2][0] = -n[2]*n[0]*cfactor;
+  dnhatdn[0][1] = -n[0]*n[1]*cfactor;
+  dnhatdn[1][1] = (n[0]*n[0]+n[2]*n[2])*cfactor;
+  dnhatdn[2][1] = -n[2]*n[1]*cfactor;
+  dnhatdn[0][2] = -n[0]*n[2]*cfactor;
+  dnhatdn[1][2] = -n[1]*n[2]*cfactor;
+  dnhatdn[2][2] = (n[0]*n[0]+n[1]*n[1])*cfactor;
+    
+}
 inline double normalize_factor(double *n)
 {
   double nnorm = sqrt(n[0] * n[0] + n[1] * n[1] + n[2] * n[2]);
@@ -441,7 +486,7 @@ inline double normalize_factor(double *n)
   Yet another normal calculation method for simpiler code.
  */
 template <int MAX_NNEIGH>
-void PairILPGrapheneHBNOpt::calc_normal(int i, int *ILP_neigh, int nneigh, double *n,
+void PairILPGrapheneHBNOpt::calc_normal(int i, int itype, int *ILP_neigh, int nneigh, double *n,
                                         double (*dnormdri)[3], double (*dnormdrk)[3][3])
 {
   double **x = atom->x;
@@ -475,6 +520,32 @@ void PairILPGrapheneHBNOpt::calc_normal(int i, int *ILP_neigh, int nneigh, doubl
     vet[jj][2] = x[j][2] - x[i][2];
   }
 
+  //specialize for ILP_WATER_2DM for hydrogen has special normal vector rule
+  if (variant == ILP_WATER_2DM && special_type[itype] == WATER) {
+    if (nneigh == 1){
+      n[0] = vet[0][0];
+      n[1] = vet[0][1];
+      n[2] = vet[0][2];
+
+      double rnnorm = normalize_factor(n);
+
+      deriv_hat(dnormdri, n, rnnorm, -1.0);
+      deriv_hat(dnormdrk[0], n, rnnorm, 1.0);
+
+    } else if (nneigh == 2){
+      n[0] = (vet[0][0] + vet[1][0])*0.5;
+      n[1] = (vet[0][1] + vet[1][1])*0.5;
+      n[2] = (vet[0][2] + vet[1][2])*0.5;
+      double rnnorm = normalize_factor(n);
+
+      deriv_hat(dnormdri, n, rnnorm, -1.0);
+      deriv_hat(dnormdrk[0], n, rnnorm, 0.5);
+      deriv_hat(dnormdrk[1], n, rnnorm, 0.5);
+    } else {
+      error->one(FLERR, "malformed water");
+    }
+    return;
+  }
   if (nneigh <= 1) {
     n[0] = 0.0;
     n[1] = 0.0;
diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.h b/src/OPT/pair_ilp_graphene_hbn_opt.h
index 0721014e00..bc22ab22b0 100644
--- a/src/OPT/pair_ilp_graphene_hbn_opt.h
+++ b/src/OPT/pair_ilp_graphene_hbn_opt.h
@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   LAMMPS development team: developers@lammps.org
+   Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -35,7 +35,7 @@ class PairILPGrapheneHBNOpt : virtual public PairILPGrapheneHBN {
  protected:
   void update_internal_list();
   template <int MAX_NNEIGH>
-  void calc_normal(int i, int *ILP_neigh, int nneigh, double *normal, double (*dnormdri)[3],
+  void calc_normal(int i, int itype, int *ILP_neigh, int nneigh, double *normal, double (*dnormdri)[3],
                    double (*dnormdrk)[3][3]);
   template <int MAX_NNEIGH, int EFLAG, int VFLAG_EITHER, int TAP_FLAG, int VARIANT = ILP_GrhBN>
   void eval();
@@ -44,6 +44,14 @@ class PairILPGrapheneHBNOpt : virtual public PairILPGrapheneHBN {
   int *special_type;
   int *num_intra, *num_inter, *num_vdw;
   int inum_max, jnum_max;
+
+  enum special_type_const {
+    NOT_SPECIAL = 0,
+    TMD_METAL,
+    SAIP_BNCH,
+    WATER,
+  };
+
 };
 
 }    // namespace LAMMPS_NS
diff --git a/src/OPT/pair_ilp_water_2dm_opt.cpp b/src/OPT/pair_ilp_water_2dm_opt.cpp
new file mode 100644
index 0000000000..6cdac00ed9
--- /dev/null
+++ b/src/OPT/pair_ilp_water_2dm_opt.cpp
@@ -0,0 +1,73 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   This is an optimized version of ilp/water/2dm based on the contribution of:
+     author: Wengen Ouyang (Wuhan University)
+     e-mail: w.g.ouyang at gmail dot com
+
+   Optimizations are done by:
+     author1: Xiaohui Duan (National Supercomputing Center in Wuxi, China)
+     e-mail: sunrise_duan at 126 dot com
+
+     author2: Ping Gao (National Supercomputing Center in Wuxi, China)
+     e-mail: qdgaoping at gmail dot com
+
+   Optimizations are described in:
+     Gao, Ping and Duan, Xiaohui, et al:
+       LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
+     DOI: 10.1145/3458817.3476137
+
+   Potential is described by:
+     [Feng and Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).]
+*/
+#include "pair_ilp_water_2dm_opt.h"
+
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "interlayer_taper.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+
+#include <cmath>
+#include <cstring>
+
+using namespace LAMMPS_NS;
+using namespace InterLayer;
+
+PairILPWATER2DMOpt::PairILPWATER2DMOpt(LAMMPS *lmp) :
+  PairILPGrapheneHBN(lmp), PairILPTMD(lmp), PairILPWATER2DM(lmp), PairILPGrapheneHBNOpt(lmp)
+{
+}
+
+void PairILPWATER2DMOpt::coeff(int narg, char **args)
+{
+  PairILPTMD::coeff(narg, args);
+  memory->create(special_type, atom->ntypes + 1, "PairILPWATER2DMOpt:check_sublayer");
+  for (int i = 1; i <= atom->ntypes; i++) {
+    int itype = map[i];
+    if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
+        strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
+        strcmp(elements[itype], "Te") == 0) {
+      special_type[i] = TMD_METAL;
+    } else if (strcmp(elements[itype], "Hw") == 0 || strcmp(elements[itype], "Ow") == 0) {
+      special_type[i] = WATER;
+    } else {
+      special_type[i] = NOT_SPECIAL;
+    }
+  }
+}
diff --git a/src/OPT/pair_ilp_water_2dm_opt.h b/src/OPT/pair_ilp_water_2dm_opt.h
new file mode 100644
index 0000000000..25905643af
--- /dev/null
+++ b/src/OPT/pair_ilp_water_2dm_opt.h
@@ -0,0 +1,39 @@
+  /* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+// clang-format off
+PairStyle(ilp/water/2dm/opt,PairILPWATER2DMOpt);
+// clang-format on
+#else
+
+#ifndef LMP_PAIR_ILP_WATER_2DM_OPT_H
+#define LMP_PAIR_ILP_WATER_2DM_OPT_H
+
+#include "pair_ilp_graphene_hbn_opt.h"
+#include "pair_ilp_water_2dm.h"
+
+namespace LAMMPS_NS {
+
+class PairILPWATER2DMOpt : public PairILPWATER2DM, public PairILPGrapheneHBNOpt {
+ public:
+  PairILPWATER2DMOpt(class LAMMPS *);
+  void coeff(int narg, char **args) override;
+
+ protected:
+};
+
+}    // namespace LAMMPS_NS
+#endif
+#endif
+

From af04ecc53217f52e32bc51f626cfdabc067792ec Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Thu, 18 May 2023 21:59:07 +0800
Subject: [PATCH 066/396] add potential file

---
 potentials/COH.ILP | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100755 potentials/COH.ILP

diff --git a/potentials/COH.ILP b/potentials/COH.ILP
new file mode 100755
index 0000000000..bd815b5c00
--- /dev/null
+++ b/potentials/COH.ILP
@@ -0,0 +1,28 @@
+# DATE: 2023-05-18 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com CITATION: Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C 127, 8704 (2023).
+# Interlayer Potential (ILP) for water/graphene heterojunctions
+# The parameters below are fitted against the PBE + MBD-NL DFT reference data from 2.5 A to 15 A.
+#
+# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
+#    beta(A)    alpha    delta(A)  epsilon(meV)  C(meV)        d         sR      reff(A)   C6(meV*A^6)    S    rcut
+# For graphene and hydrocarbons
+C C  3.205843  7.511126  1.235334  1.528338E-5  37.530428  15.499947  0.7954443  3.681440  25.714535E3   1.0   2.0
+H H  3.974540   6.53799  1.080633  0.6700556    0.8333833  15.022371  0.7490632  2.767223  1.6159581E3   1.0   1.2
+C H  2.642950  12.91410  1.020257  0.9750012    25.340996  15.222927  0.8115998  3.887324  5.6874617E3   1.0   1.5
+H C  2.642950  12.91410  1.020257  0.9750012    25.340996  15.222927  0.8115998  3.887324  5.6874617E3   1.0   1.5
+
+# For water-graphene
+C Ow  5.45369612 6.18172364 1.25025450  3.34909245   0.68780636 9.05706482 1.23249498 2.77577173 100226.55503127   1.0   2.0
+C Hw  2.55380862 9.68664390 1.96489198 41.77617053 -16.30012807 9.01568534 0.74415463 2.41545571   7409.12856378   1.0   2.0
+Ow C  5.45369612 6.18172364 1.25025450  3.34909245   0.68780636 9.05706482 1.23249498 2.77577173 100226.55503127   1.0   1.2
+Hw C  2.55380862 9.68664390 1.96489198 41.77617053 -16.30012807 9.01568534 0.74415463 2.41545571   7409.12856378   1.0   1.2
+
+# # The ILPs for other systems are set to zero
+H Ow  5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+H Hw  5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+Ow H  5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+Hw H  5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+
+Ow Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+Hw Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+Ow Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+Hw Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2

From 3d35d68a4bd9fc432e40239c5d0ad6c8169e75d1 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Thu, 18 May 2023 22:00:03 +0800
Subject: [PATCH 067/396] add doc file

---
 doc/src/pair_ilp_graphene_hbn.rst       |  20 +--
 doc/src/pair_ilp_tmd.rst                |   4 +-
 doc/src/pair_ilp_water_2dm.rst          | 166 ++++++++++++++++++++++++
 doc/src/pair_kolmogorov_crespi_full.rst |   2 +-
 doc/src/pair_saip_metal.rst             |   4 +-
 5 files changed, 181 insertions(+), 15 deletions(-)
 create mode 100644 doc/src/pair_ilp_water_2dm.rst

diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst
index de088f2926..36e971ef62 100644
--- a/doc/src/pair_ilp_graphene_hbn.rst
+++ b/doc/src/pair_ilp_graphene_hbn.rst
@@ -155,8 +155,8 @@ interactions.
 
 The BNCH.ILP potential file provided with LAMMPS (see the potentials
 directory) are parameterized for *metal* units.  You can use this
-potential with any LAMMPS units, but you would need to create your
-BNCH.ILP potential file with coefficients listed in the appropriate
+potential with any LAMMPS units, but you would need to create your own
+custom BNCH.ILP potential file with coefficients listed in the appropriate
 units, if your simulation does not use *metal* units.
 
 Related commands
@@ -181,6 +181,14 @@ tap_flag = 1
 
 ----------
 
+.. _Ouyang1:
+
+**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
+
+.. _Ouyang2:
+
+**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
+
 .. _Leven1:
 
 **(Leven1)** I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
@@ -196,11 +204,3 @@ tap_flag = 1
 .. _Kolmogorov2:
 
 **(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
-
-.. _Ouyang1:
-
-**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
-
-.. _Ouyang2:
-
-**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
diff --git a/doc/src/pair_ilp_tmd.rst b/doc/src/pair_ilp_tmd.rst
index 77fa8bbfd5..482d75a100 100644
--- a/doc/src/pair_ilp_tmd.rst
+++ b/doc/src/pair_ilp_tmd.rst
@@ -135,8 +135,8 @@ interactions.
 
 The TMD.ILP potential file provided with LAMMPS (see the potentials
 directory) are parameterized for *metal* units.  You can use this
-potential with any LAMMPS units, but you would need to create your
-BNCH.ILP potential file with coefficients listed in the appropriate
+potential with any LAMMPS units, but you would need to create your own
+custom TMD.ILP potential file with coefficients listed in the appropriate
 units, if your simulation does not use *metal* units.
 
 Related commands
diff --git a/doc/src/pair_ilp_water_2dm.rst b/doc/src/pair_ilp_water_2dm.rst
new file mode 100644
index 0000000000..5dc287493b
--- /dev/null
+++ b/doc/src/pair_ilp_water_2dm.rst
@@ -0,0 +1,166 @@
+.. index:: pair_style ilp/water/2dm
+.. index:: pair_style ilp/water/2dm/opt
+
+pair_style ilp/tmd command
+===================================
+
+Accelerator Variant: *ilp/water/2dm/opt*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style [hybrid/overlay ...] ilp/tmd cutoff tap_flag
+
+* cutoff = global cutoff (distance units)
+* tap_flag = 0/1 to turn off/on the taper function
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style  hybrid/overlay ilp/water/2dm 16.0 1
+   pair_coeff  * * ilp/water/2dm  COH.ILP C Ow Hw
+
+   pair_style  hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+   pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+   pair_coeff  2 3   lj/cut/tip4p/long    0.0        0.0     # O-H
+   pair_coeff  3 3   lj/cut/tip4p/long    0.0        0.0     # H-H
+   pair_coeff  * *   ilp/water/2dm        COH.ILP    C Ow Hw
+
+Description
+"""""""""""
+
+.. versionadded:: xxxx2023
+
+The *ilp/water/2dm* style computes the registry-dependent interlayer
+potential (ILP) potential for interfaces of water with two-dimensinal (2D)
+materials as described in :ref:`(Feng) <Feng>`.
+
+.. math::
+
+   E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
+   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+                \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
+                 \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
+                 \cdot \frac{C_6}{r^6_{ij}} \right \}\\
+   \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
+   \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
+   f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
+   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+                           70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
+                           84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
+                           35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
+
+Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides
+a continuous cutoff (up to third derivative) for interatomic separations
+larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`.
+
+It is important to include all the pairs to build the neighbor list for
+calculating the normals.
+
+.. note::
+
+   Since each water molecule contains one oxygen atom and two hydrogen atoms,
+   a new definition is proposed (see In :ref:`(Feng) <Feng>`),the atomic
+   normal vectors of hydrogen atoms are assumed to lie along the corresponding
+   oxygen-hydrogen bonds and the normal vector of the central oxygen atom
+   is defined as their average.
+
+The parameter file (e.g. COH.ILP), is intended for use with *metal*
+:doc:`units <units>`, with energies in meV. Two additional parameters,
+*S*, and *rcut* are included in the parameter file. *S* is designed to
+facilitate scaling of energies. *rcut* is designed to build the neighbor
+list for calculating the normals for each atom pair.
+
+.. note::
+
+   The parameters presented in the parameter file (e.g. COH.ILP),
+   are fitted with taper function by setting the cutoff equal to 16.0
+   Angstrom.  Using different cutoff or taper function should be careful.
+   These parameters provide a good description in both short- and long-range
+   interaction regimes. This feature is essential for simulations in high pressure
+   regime (i.e., the interlayer distance is smaller than the equilibrium
+   distance).
+
+This potential must be used in combination with hybrid/overlay.
+Other interactions can be set to zero using pair_style *none*\ .
+
+This pair style tallies a breakdown of the total interlayer potential
+energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 2.
+The 2 values correspond to the following sub-categories:
+
+1. *E_vdW* = vdW (attractive) energy
+2. *E_Rep* = Repulsive energy
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+.. code-block:: LAMMPS
+
+   compute 0 all pair ilp/water/2dm
+   variable Evdw  equal c_0[1]
+   variable Erep  equal c_0[2]
+   thermo_style custom step temp epair v_Erep v_Evdw
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This pair style does not support the pair_modify mix, shift, table, and
+tail options.
+
+This pair style does not write their information to binary restart
+files, since it is stored in potential files. Thus, you need to
+re-specify the pair_style and pair_coeff commands in an input script
+that reads a restart file.
+
+Restrictions
+""""""""""""
+
+This pair style is part of the INTERLAYER package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style requires the newton setting to be *on* for pair
+interactions.
+
+The COH.ILP potential file provided with LAMMPS (see the potentials
+directory) are parameterized for *metal* units.  You can use this
+potential with any LAMMPS units, but you would need to create your
+COH.ILP potential file with coefficients listed in the appropriate
+units, if your simulation does not use *metal* units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_coeff <pair_coeff>`,
+:doc:`pair_none <pair_none>`,
+:doc:`pair_style hybrid/overlay <pair_hybrid>`,
+:doc:`pair_style drip <pair_drip>`,
+:doc:`pair_style ilp_tmd <pair_ilp_tmd>`,
+:doc:`pair_style saip_metal <pair_saip_metal>`,
+:doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`,
+:doc:`pair_style pair_kolmogorov_crespi_z <pair_kolmogorov_crespi_z>`,
+:doc:`pair_style pair_kolmogorov_crespi_full <pair_kolmogorov_crespi_full>`,
+:doc:`pair_style pair_lebedeva_z <pair_lebedeva_z>`,
+:doc:`pair_style pair_coul_shield <pair_coul_shield>`.
+
+Default
+"""""""
+
+tap_flag = 1
+
+
+----------
+
+.. _Feng:
+
+**(Feng)** Z. Feng, W. Ouyang, J. Phys. Chem. C. accepted (2023).
diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst
index 1a33a3f4bb..1a4706dd6f 100644
--- a/doc/src/pair_kolmogorov_crespi_full.rst
+++ b/doc/src/pair_kolmogorov_crespi_full.rst
@@ -129,7 +129,7 @@ interactions.
 The CH.KC potential file provided with LAMMPS (see the potentials
 folder) is parameterized for metal units.  You can use this pair style
 with any LAMMPS units, but you would need to create your own custom
-CC.KC potential file with all coefficients converted to the appropriate
+CH.KC potential file with all coefficients converted to the appropriate
 units.
 
 Related commands
diff --git a/doc/src/pair_saip_metal.rst b/doc/src/pair_saip_metal.rst
index 21bfeb0aa9..ed011894c9 100644
--- a/doc/src/pair_saip_metal.rst
+++ b/doc/src/pair_saip_metal.rst
@@ -134,8 +134,8 @@ interactions.
 
 The CHAu.ILP potential file provided with LAMMPS (see the potentials
 directory) are parameterized for *metal* units.  You can use this
-potential with any LAMMPS units, but you would need to create your
-BNCH.ILP potential file with coefficients listed in the appropriate
+potential with any LAMMPS units, but you would need to create your own
+custom CHAu.ILP potential file with coefficients listed in the appropriate
 units, if your simulation does not use *metal* units.
 
 Related commands

From bbff6c25b33625a1b34ff95e581c78d59eb74e56 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Thu, 18 May 2023 22:01:19 +0800
Subject: [PATCH 068/396] add examples

---
 .../PACKAGES/interlayer/ilp_water_2dm/COH.ILP |    1 +
 .../interlayer/ilp_water_2dm/gra_water.data   | 2040 +++++++++++++++++
 .../interlayer/ilp_water_2dm/in.gr_water      |   51 +
 .../interlayer/ilp_water_2dm/in.gr_water.opt  |   51 +
 .../ilp_water_2dm/log.18May23.water.g++.1     |  234 ++
 .../ilp_water_2dm/log.18May23.water.g++.4     |  234 ++
 .../ilp_water_2dm/log.18May23.water.opt.g++.1 |  251 ++
 .../ilp_water_2dm/log.18May23.water.opt.g++.4 |  251 ++
 8 files changed, 3113 insertions(+)
 create mode 120000 examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP
 create mode 100644 examples/PACKAGES/interlayer/ilp_water_2dm/gra_water.data
 create mode 100644 examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water
 create mode 100644 examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water.opt
 create mode 100644 examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.1
 create mode 100644 examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.4
 create mode 100644 examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.1
 create mode 100644 examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.4

diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP b/examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP
new file mode 120000
index 0000000000..526995dae4
--- /dev/null
+++ b/examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP
@@ -0,0 +1 @@
+../../../../potentials/COH.ILP
\ No newline at end of file
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/gra_water.data b/examples/PACKAGES/interlayer/ilp_water_2dm/gra_water.data
new file mode 100644
index 0000000000..7e6d3925f0
--- /dev/null
+++ b/examples/PACKAGES/interlayer/ilp_water_2dm/gra_water.data
@@ -0,0 +1,2040 @@
+LAMMPS data file via write_data, version 23 Jun 2022, timestep = 100000
+
+936 atoms
+3 atom types
+96 bonds
+1 bond types
+48 angles
+1 angle types
+
+0 46.92336 xlo xhi
+0 44.331078317370086 ylo yhi
+0 200 zlo zhi
+
+Atoms # full
+
+1 1 1 0 0 0 0 0 0 0
+2 1 1 0 0.71096 1.231418842149169 0 0 0 0
+3 1 1 0 2.13288 1.231418842149169 0 0 0 0
+4 1 1 0 2.84384 0 0 0 0 0
+5 1 1 0 0 2.462837684298338 0 0 0 0
+6 1 1 0 0.71096 3.694256526447507 0 0 0 0
+7 1 1 0 2.13288 3.694256526447507 0 0 0 0
+8 1 1 0 2.84384 2.462837684298338 0 0 0 0
+9 1 1 0 0 4.925675368596676 0 0 0 0
+10 1 1 0 0.71096 6.157094210745845 0 0 0 0
+11 1 1 0 2.13288 6.157094210745845 0 0 0 0
+12 1 1 0 2.84384 4.925675368596676 0 0 0 0
+13 1 1 0 0 7.388513052895014 0 0 0 0
+14 1 1 0 0.71096 8.619931895044184 0 0 0 0
+15 1 1 0 2.13288 8.619931895044184 0 0 0 0
+16 1 1 0 2.84384 7.388513052895014 0 0 0 0
+17 1 1 0 0 9.851350737193352 0 0 0 0
+20 1 1 0 2.84384 9.851350737193352 0 0 0 0
+73 1 1 0 4.26576 0 0 0 0 0
+74 1 1 0 4.97672 1.231418842149169 0 0 0 0
+77 1 1 0 4.26576 2.462837684298338 0 0 0 0
+78 1 1 0 4.97672 3.694256526447507 0 0 0 0
+81 1 1 0 4.26576 4.925675368596676 0 0 0 0
+82 1 1 0 4.97672 6.157094210745845 0 0 0 0
+85 1 1 0 4.26576 7.388513052895014 0 0 0 0
+86 1 1 0 4.97672 8.619931895044184 0 0 0 0
+89 1 1 0 4.26576 9.851350737193352 0 0 0 0
+18 1 1 0 0.71096 11.082769579342521 0 0 0 0
+19 1 1 0 2.13288 11.082769579342521 0 0 0 0
+21 1 1 0 0 12.31418842149169 0 0 0 0
+22 1 1 0 0.71096 13.545607263640859 0 0 0 0
+23 1 1 0 2.13288 13.545607263640859 0 0 0 0
+24 1 1 0 2.84384 12.31418842149169 0 0 0 0
+25 1 1 0 0 14.777026105790029 0 0 0 0
+26 1 1 0 0.71096 16.008444947939196 0 0 0 0
+27 1 1 0 2.13288 16.008444947939196 0 0 0 0
+28 1 1 0 2.84384 14.777026105790029 0 0 0 0
+29 1 1 0 0 17.239863790088364 0 0 0 0
+30 1 1 0 0.71096 18.471282632237532 0 0 0 0
+31 1 1 0 2.13288 18.471282632237532 0 0 0 0
+32 1 1 0 2.84384 17.239863790088364 0 0 0 0
+33 1 1 0 0 19.702701474386703 0 0 0 0
+34 1 1 0 0.71096 20.93412031653587 0 0 0 0
+35 1 1 0 2.13288 20.93412031653587 0 0 0 0
+36 1 1 0 2.84384 19.702701474386703 0 0 0 0
+90 1 1 0 4.97672 11.082769579342521 0 0 0 0
+93 1 1 0 4.26576 12.31418842149169 0 0 0 0
+94 1 1 0 4.97672 13.545607263640859 0 0 0 0
+97 1 1 0 4.26576 14.777026105790029 0 0 0 0
+98 1 1 0 4.97672 16.008444947939196 0 0 0 0
+101 1 1 0 4.26576 17.239863790088364 0 0 0 0
+102 1 1 0 4.97672 18.471282632237532 0 0 0 0
+105 1 1 0 4.26576 19.702701474386703 0 0 0 0
+106 1 1 0 4.97672 20.93412031653587 0 0 0 0
+37 1 1 0 0 22.165539158685043 0 0 0 0
+38 1 1 0 0.71096 23.39695800083421 0 0 0 0
+39 1 1 0 2.13288 23.39695800083421 0 0 0 0
+40 1 1 0 2.84384 22.165539158685043 0 0 0 0
+41 1 1 0 0 24.62837684298338 0 0 0 0
+42 1 1 0 0.71096 25.859795685132546 0 0 0 0
+43 1 1 0 2.13288 25.859795685132546 0 0 0 0
+44 1 1 0 2.84384 24.62837684298338 0 0 0 0
+45 1 1 0 0 27.091214527281718 0 0 0 0
+46 1 1 0 0.71096 28.322633369430886 0 0 0 0
+47 1 1 0 2.13288 28.322633369430886 0 0 0 0
+48 1 1 0 2.84384 27.091214527281718 0 0 0 0
+49 1 1 0 0 29.554052211580057 0 0 0 0
+50 1 1 0 0.71096 30.785471053729225 0 0 0 0
+51 1 1 0 2.13288 30.785471053729225 0 0 0 0
+52 1 1 0 2.84384 29.554052211580057 0 0 0 0
+53 1 1 0 0 32.01688989587839 0 0 0 0
+56 1 1 0 2.84384 32.01688989587839 0 0 0 0
+109 1 1 0 4.26576 22.165539158685043 0 0 0 0
+110 1 1 0 4.97672 23.39695800083421 0 0 0 0
+113 1 1 0 4.26576 24.62837684298338 0 0 0 0
+114 1 1 0 4.97672 25.859795685132546 0 0 0 0
+117 1 1 0 4.26576 27.091214527281718 0 0 0 0
+118 1 1 0 4.97672 28.322633369430886 0 0 0 0
+121 1 1 0 4.26576 29.554052211580057 0 0 0 0
+122 1 1 0 4.97672 30.785471053729225 0 0 0 0
+125 1 1 0 4.26576 32.01688989587839 0 0 0 0
+54 1 1 0 0.71096 33.24830873802756 0 0 0 0
+55 1 1 0 2.13288 33.24830873802756 0 0 0 0
+57 1 1 0 0 34.47972758017673 0 0 0 0
+58 1 1 0 0.71096 35.711146422325896 0 0 0 0
+59 1 1 0 2.13288 35.711146422325896 0 0 0 0
+60 1 1 0 2.84384 34.47972758017673 0 0 0 0
+61 1 1 0 0 36.94256526447507 0 0 0 0
+62 1 1 0 0.71096 38.17398410662424 0 0 0 0
+63 1 1 0 2.13288 38.17398410662424 0 0 0 0
+64 1 1 0 2.84384 36.94256526447507 0 0 0 0
+65 1 1 0 0 39.40540294877341 0 0 0 0
+66 1 1 0 0.71096 40.636821790922575 0 0 0 0
+67 1 1 0 2.13288 40.636821790922575 0 0 0 0
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+78 1 850 852
+79 1 799 800
+80 1 799 801
+81 1 853 854
+82 1 853 855
+83 1 796 797
+84 1 796 798
+85 1 898 899
+86 1 898 900
+87 1 922 923
+88 1 922 924
+89 1 901 902
+90 1 901 903
+91 1 871 872
+92 1 871 873
+93 1 910 911
+94 1 910 912
+95 1 868 869
+96 1 868 870
+
+Angles
+
+1 1 881 880 882
+2 1 824 823 825
+3 1 839 838 840
+4 1 896 895 897
+5 1 914 913 915
+6 1 917 916 918
+7 1 818 817 819
+8 1 935 934 936
+9 1 845 844 846
+10 1 866 865 867
+11 1 929 928 930
+12 1 833 832 834
+13 1 794 793 795
+14 1 884 883 885
+15 1 857 856 858
+16 1 893 892 894
+17 1 887 886 888
+18 1 827 826 828
+19 1 926 925 927
+20 1 878 877 879
+21 1 836 835 837
+22 1 812 811 813
+23 1 848 847 849
+24 1 842 841 843
+25 1 806 805 807
+26 1 863 862 864
+27 1 809 808 810
+28 1 821 820 822
+29 1 815 814 816
+30 1 803 802 804
+31 1 932 931 933
+32 1 908 907 909
+33 1 905 904 906
+34 1 830 829 831
+35 1 920 919 921
+36 1 860 859 861
+37 1 890 889 891
+38 1 875 874 876
+39 1 851 850 852
+40 1 800 799 801
+41 1 854 853 855
+42 1 797 796 798
+43 1 899 898 900
+44 1 923 922 924
+45 1 902 901 903
+46 1 872 871 873
+47 1 911 910 912
+48 1 869 868 870
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water b/examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water
new file mode 100644
index 0000000000..9fccbf733b
--- /dev/null
+++ b/examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water
@@ -0,0 +1,51 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+read_data       ./gra_water.data
+mass            1 12.0107   # carbon   	mass (g/mole) 
+mass            2 15.9994   # oxygen    mass (g/mole) 
+mass            3 1.008     # hydrogen 	mass (g/mole) 
+# Separate atom groups
+group 		gr    molecule 1
+group 		water molecule 2
+######################## Potential defition ##############################
+# Interlayer potential
+pair_style  hybrid/overlay  ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+####################################################################
+pair_coeff  1 1   none
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
+pair_coeff  * *   ilp/water/2dm        COH.ILP C Ow Hw    # C-water    
+# bond and angle
+bond_style  	  harmonic
+bond_coeff  	  1 	0.0  0.9572
+angle_style 	  harmonic
+angle_coeff 	  1 	0.0  104.52
+# define kspace calculation
+kspace_style      pppm/tip4p 1E-5
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify every 1 delay 5 check yes page 1000000 one 100000
+####################################################################
+# Calculate pair energy
+compute   	1 all pair lj/cut/tip4p/long
+compute   	2 all pair ilp/water/2dm
+compute		wt water temp
+variable  	TIP4P  equal  c_1
+variable  	EILP   equal  c_2     # total interlayer energy
+variable	temp_wt equal c_wt
+############# Output ##############
+thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
+thermo          100
+thermo_modify   lost error
+
+fix				subf gr setforce 0.0 0.0 0.0
+fix 			1 	water shake 0.0001 20 100 b 1 a 1
+
+timestep  		1e-3  
+velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix				2 water nve
+run			    1000
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water.opt b/examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water.opt
new file mode 100644
index 0000000000..1b38ab6e6e
--- /dev/null
+++ b/examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water.opt
@@ -0,0 +1,51 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+read_data       ./gra_water.data
+mass            1 12.0107   # carbon   	mass (g/mole) 
+mass            2 15.9994   # oxygen    mass (g/mole) 
+mass            3 1.008     # hydrogen 	mass (g/mole) 
+# Separate atom groups
+group 		gr    molecule 1
+group 		water molecule 2
+######################## Potential defition ##############################
+# Interlayer potential
+pair_style  hybrid/overlay  ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+####################################################################
+pair_coeff  1 1   none
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
+pair_coeff  * *   ilp/water/2dm/opt        COH.ILP C Ow Hw    # C-water    
+# bond and angle
+bond_style  	  harmonic
+bond_coeff  	  1 	0.0  0.9572
+angle_style 	  harmonic
+angle_coeff 	  1 	0.0  104.52
+# define kspace calculation
+kspace_style      pppm/tip4p 1E-5
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify every 1 delay 5 check yes page 1000000 one 100000
+####################################################################
+# Calculate pair energy
+compute   	1 all pair lj/cut/tip4p/long
+compute   	2 all pair ilp/water/2dm/opt
+compute		wt water temp
+variable  	TIP4P  equal  c_1
+variable  	EILP   equal  c_2     # total interlayer energy
+variable	temp_wt equal c_wt
+############# Output ##############
+thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
+thermo          100
+thermo_modify   lost error
+
+fix				subf gr setforce 0.0 0.0 0.0
+fix 			1 	water shake 0.0001 20 100 b 1 a 1
+
+timestep  		1e-3  
+velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix				2 water nve
+run			    1000
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.1 b/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.1
new file mode 100644
index 0000000000..6e13280f70
--- /dev/null
+++ b/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.1
@@ -0,0 +1,234 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+read_data       ./gra_water.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (46.92336 44.331078 200)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  936 atoms
+  reading velocities ...
+  936 velocities
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  96 bonds
+  reading angles ...
+  48 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.005 seconds
+  read_data CPU = 0.020 seconds
+mass            1 12.0107   # carbon   	mass (g/mole)
+mass            2 15.9994   # oxygen    mass (g/mole)
+mass            3 1.008     # hydrogen 	mass (g/mole)
+# Separate atom groups
+group 		gr    molecule 1
+792 atoms in group gr
+group 		water molecule 2
+144 atoms in group water
+######################## Potential defition ##############################
+# Interlayer potential
+pair_style  hybrid/overlay  ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+####################################################################
+pair_coeff  1 1   none
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
+pair_coeff  * *   ilp/water/2dm        COH.ILP C Ow Hw    # C-water
+Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
+# bond and angle
+bond_style  	  harmonic
+bond_coeff  	  1 	0.0  0.9572
+angle_style 	  harmonic
+angle_coeff 	  1 	0.0  104.52
+# define kspace calculation
+kspace_style      pppm/tip4p 1E-5
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify every 1 delay 5 check yes page 1000000 one 100000
+####################################################################
+# Calculate pair energy
+compute   	1 all pair lj/cut/tip4p/long
+compute   	2 all pair ilp/water/2dm
+compute		wt water temp
+variable  	TIP4P  equal  c_1
+variable  	EILP   equal  c_2     # total interlayer energy
+variable	temp_wt equal c_wt
+############# Output ##############
+thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
+thermo          100
+thermo_modify   lost error
+
+fix				subf gr setforce 0.0 0.0 0.0
+fix 			1 	water shake 0.0001 20 100 b 1 a 1
+       0 = # of size 2 clusters
+       0 = # of size 3 clusters
+       0 = # of size 4 clusters
+      48 = # of frozen angles
+  find clusters CPU = 0.001 seconds
+
+timestep  		1e-3
+velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix				2 water nve
+run			    1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
+@Article{Ouyang2018
+ author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
+ title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
+ journal = {Nano Letters},
+ volume =  18,
+ pages =   {6009}
+ year =    2018,
+}
+
+- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
+@Article{Ouyang2021
+ author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
+ title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
+ journal = {J. Chem. Theory Comput.},
+ volume =  17,
+ pages =   {7237–7245}
+ year =    2021,
+}
+
+- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
+@Article{Feng2023
+ author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
+ title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
+ journal = {J. Phys. Chem. C},
+ volume =  127,
+ pages =   {8704-8713}
+ year =    2023,
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM initialization ...
+  extracting TIP4P info from pair style
+  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
+  G vector (1/distance) = 0.28684806
+  grid = 25 24 80
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0001640931
+  estimated relative force accuracy = 1.1395635e-05
+  using single precision MKL FFT
+  3d grid and FFT values/proc = 84320 48000
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 100000, page size: 1000000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 6 5 23
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair ilp/water/2dm, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair lj/cut/tip4p/long, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+SHAKE stats (type/ave/delta/count) on step 0
+Bond:   1   0.957201  2.19705e-06       96
+Angle:  1   104.52    0.000203056       48
+Per MPI rank memory allocation (min/avg/max) = 33.53 | 33.53 | 33.53 Mbytes
+   Step         TotEng         PotEng         KinEng        v_TIP4P         v_EILP       v_temp_wt   
+         0  -16.131263     -19.815178      3.6839141      189.37246     -1.903543       300          
+SHAKE stats (type/ave/delta/count) on step 100
+Bond:   1   0.9572    9.54949e-07       96
+Angle:  1   104.52    6.01522e-05       48
+       100  -17.494868     -20.796993      3.3021253      188.4955      -1.8981262      268.90898    
+SHAKE stats (type/ave/delta/count) on step 200
+Bond:   1   0.9572    9.63922e-07       96
+Angle:  1   104.52    7.7021e-05        48
+       200  -17.486271     -21.194892      3.7086213      188.14561     -1.9871708      302.01203    
+SHAKE stats (type/ave/delta/count) on step 300
+Bond:   1   0.9572    1.4264e-06        96
+Angle:  1   104.52    6.48393e-05       48
+       300  -17.502844     -20.993704      3.49086        188.23268     -1.8457229      284.27861    
+SHAKE stats (type/ave/delta/count) on step 400
+Bond:   1   0.9572    1.33728e-06       96
+Angle:  1   104.52    7.6239e-05        48
+       400  -17.495287     -20.828353      3.3330658      188.48002     -1.8429075      271.42862    
+SHAKE stats (type/ave/delta/count) on step 500
+Bond:   1   0.9572    1.14685e-06       96
+Angle:  1   104.52    8.58621e-05       48
+       500  -17.491435     -20.443044      2.9516084      188.7589      -1.8566335      240.36459    
+SHAKE stats (type/ave/delta/count) on step 600
+Bond:   1   0.9572    9.17601e-07       96
+Angle:  1   104.52    8.24516e-05       48
+       600  -17.505684     -20.608457      3.1027731      188.72078     -1.9560796      252.67471    
+SHAKE stats (type/ave/delta/count) on step 700
+Bond:   1   0.9572    9.50422e-07       96
+Angle:  1   104.52    5.62423e-05       48
+       700  -17.496703     -21.072663      3.5759596      188.2777      -1.9833956      291.20871    
+SHAKE stats (type/ave/delta/count) on step 800
+Bond:   1   0.9572    1.15262e-06       96
+Angle:  1   104.52    7.02157e-05       48
+       800  -17.478623     -20.819504      3.3408809      188.37868     -1.9112996      272.06505    
+SHAKE stats (type/ave/delta/count) on step 900
+Bond:   1   0.9572    9.14138e-07       96
+Angle:  1   104.52    6.98742e-05       48
+       900  -17.48086      -20.728495      3.2476349      188.59022     -1.8922102      264.47155    
+SHAKE stats (type/ave/delta/count) on step 1000
+Bond:   1   0.9572    1.00586e-06       96
+Angle:  1   104.52    0.000111712       48
+      1000  -17.498465     -20.331545      2.8330804      188.87473     -1.812177       230.71225    
+Loop time of 20.801 on 1 procs for 1000 steps with 936 atoms
+
+Performance: 4.154 ns/day, 5.778 hours/ns, 48.075 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 16.429     | 16.429     | 16.429     |   0.0 | 78.98
+Bond    | 0.0010991  | 0.0010991  | 0.0010991  |   0.0 |  0.01
+Kspace  | 3.4769     | 3.4769     | 3.4769     |   0.0 | 16.72
+Neigh   | 0.83359    | 0.83359    | 0.83359    |   0.0 |  4.01
+Comm    | 0.028825   | 0.028825   | 0.028825   |   0.0 |  0.14
+Output  | 0.00046349 | 0.00046349 | 0.00046349 |   0.0 |  0.00
+Modify  | 0.01943    | 0.01943    | 0.01943    |   0.0 |  0.09
+Other   |            | 0.01154    |            |       |  0.06
+
+Nlocal:            936 ave         936 max         936 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           5242 ave        5242 max        5242 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       431382 ave      431382 max      431382 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 431382
+Ave neighs/atom = 460.87821
+Ave special neighs/atom = 0.30769231
+Neighbor list builds = 28
+Dangerous builds = 0
+Total wall time: 0:00:21
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.4 b/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.4
new file mode 100644
index 0000000000..078ca76e2e
--- /dev/null
+++ b/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.4
@@ -0,0 +1,234 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+read_data       ./gra_water.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (46.92336 44.331078 200)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  936 atoms
+  reading velocities ...
+  936 velocities
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  96 bonds
+  reading angles ...
+  48 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.003 seconds
+  read_data CPU = 0.018 seconds
+mass            1 12.0107   # carbon   	mass (g/mole)
+mass            2 15.9994   # oxygen    mass (g/mole)
+mass            3 1.008     # hydrogen 	mass (g/mole)
+# Separate atom groups
+group 		gr    molecule 1
+792 atoms in group gr
+group 		water molecule 2
+144 atoms in group water
+######################## Potential defition ##############################
+# Interlayer potential
+pair_style  hybrid/overlay  ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+####################################################################
+pair_coeff  1 1   none
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
+pair_coeff  * *   ilp/water/2dm        COH.ILP C Ow Hw    # C-water
+Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
+# bond and angle
+bond_style  	  harmonic
+bond_coeff  	  1 	0.0  0.9572
+angle_style 	  harmonic
+angle_coeff 	  1 	0.0  104.52
+# define kspace calculation
+kspace_style      pppm/tip4p 1E-5
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify every 1 delay 5 check yes page 1000000 one 100000
+####################################################################
+# Calculate pair energy
+compute   	1 all pair lj/cut/tip4p/long
+compute   	2 all pair ilp/water/2dm
+compute		wt water temp
+variable  	TIP4P  equal  c_1
+variable  	EILP   equal  c_2     # total interlayer energy
+variable	temp_wt equal c_wt
+############# Output ##############
+thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
+thermo          100
+thermo_modify   lost error
+
+fix				subf gr setforce 0.0 0.0 0.0
+fix 			1 	water shake 0.0001 20 100 b 1 a 1
+       0 = # of size 2 clusters
+       0 = # of size 3 clusters
+       0 = # of size 4 clusters
+      48 = # of frozen angles
+  find clusters CPU = 0.001 seconds
+
+timestep  		1e-3
+velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix				2 water nve
+run			    1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
+@Article{Ouyang2018
+ author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
+ title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
+ journal = {Nano Letters},
+ volume =  18,
+ pages =   {6009}
+ year =    2018,
+}
+
+- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
+@Article{Ouyang2021
+ author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
+ title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
+ journal = {J. Chem. Theory Comput.},
+ volume =  17,
+ pages =   {7237–7245}
+ year =    2021,
+}
+
+- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
+@Article{Feng2023
+ author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
+ title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
+ journal = {J. Phys. Chem. C},
+ volume =  127,
+ pages =   {8704-8713}
+ year =    2023,
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM initialization ...
+  extracting TIP4P info from pair style
+  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
+  G vector (1/distance) = 0.28684806
+  grid = 25 24 80
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0001640931
+  estimated relative force accuracy = 1.1395635e-05
+  using single precision MKL FFT
+  3d grid and FFT values/proc = 30685 12480
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 100000, page size: 1000000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 6 5 23
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair ilp/water/2dm, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair lj/cut/tip4p/long, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+SHAKE stats (type/ave/delta/count) on step 0
+Bond:   1   0.957201  2.19705e-06       96
+Angle:  1   104.52    0.000203056       48
+Per MPI rank memory allocation (min/avg/max) = 25.84 | 25.88 | 25.92 Mbytes
+   Step         TotEng         PotEng         KinEng        v_TIP4P         v_EILP       v_temp_wt   
+         0  -16.131263     -19.815178      3.6839141      189.37246     -1.903543       300          
+SHAKE stats (type/ave/delta/count) on step 100
+Bond:   1   0.9572    9.54949e-07       96
+Angle:  1   104.52    6.01522e-05       48
+       100  -17.494869     -20.796995      3.3021253      188.4955      -1.8981262      268.90898    
+SHAKE stats (type/ave/delta/count) on step 200
+Bond:   1   0.9572    9.63922e-07       96
+Angle:  1   104.52    7.7021e-05        48
+       200  -17.48627      -21.194892      3.7086213      188.14561     -1.9871708      302.01203    
+SHAKE stats (type/ave/delta/count) on step 300
+Bond:   1   0.9572    1.4264e-06        96
+Angle:  1   104.52    6.48393e-05       48
+       300  -17.502843     -20.993703      3.4908599      188.23268     -1.8457229      284.27861    
+SHAKE stats (type/ave/delta/count) on step 400
+Bond:   1   0.9572    1.33728e-06       96
+Angle:  1   104.52    7.6239e-05        48
+       400  -17.495285     -20.82835       3.333065       188.48003     -1.8429074      271.42856    
+SHAKE stats (type/ave/delta/count) on step 500
+Bond:   1   0.9572    1.14685e-06       96
+Angle:  1   104.52    8.58621e-05       48
+       500  -17.491436     -20.443043      2.9516075      188.7589      -1.8566335      240.36452    
+SHAKE stats (type/ave/delta/count) on step 600
+Bond:   1   0.9572    9.17601e-07       96
+Angle:  1   104.52    8.24517e-05       48
+       600  -17.505683     -20.608456      3.1027734      188.72078     -1.9560795      252.67474    
+SHAKE stats (type/ave/delta/count) on step 700
+Bond:   1   0.9572    9.50425e-07       96
+Angle:  1   104.52    5.62422e-05       48
+       700  -17.496706     -21.072664      3.575958       188.2777      -1.9833951      291.20858    
+SHAKE stats (type/ave/delta/count) on step 800
+Bond:   1   0.9572    1.15256e-06       96
+Angle:  1   104.52    7.02177e-05       48
+       800  -17.478628     -20.819507      3.340879       188.37868     -1.9113009      272.06489    
+SHAKE stats (type/ave/delta/count) on step 900
+Bond:   1   0.9572    9.14163e-07       96
+Angle:  1   104.52    6.98849e-05       48
+       900  -17.480865     -20.728504      3.2476386      188.5902      -1.8922108      264.47185    
+SHAKE stats (type/ave/delta/count) on step 1000
+Bond:   1   0.9572    1.00568e-06       96
+Angle:  1   104.52    0.000111707       48
+      1000  -17.498474     -20.331607      2.833133       188.87466     -1.8121689      230.71654    
+Loop time of 9.42273 on 4 procs for 1000 steps with 936 atoms
+
+Performance: 9.169 ns/day, 2.617 hours/ns, 106.126 timesteps/s
+97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.2328     | 4.3228     | 7.5931     | 103.1 | 45.88
+Bond    | 0.00084131 | 0.00088983 | 0.00095229 |   0.0 |  0.01
+Kspace  | 1.3979     | 4.6476     | 6.7252     |  98.8 | 49.32
+Neigh   | 0.34367    | 0.34371    | 0.34376    |   0.0 |  3.65
+Comm    | 0.042806   | 0.062908   | 0.075887   |   5.4 |  0.67
+Output  | 0.00037677 | 0.00041431 | 0.0004619  |   0.0 |  0.00
+Modify  | 0.028432   | 0.031138   | 0.034528   |   1.3 |  0.33
+Other   |            | 0.01321    |            |       |  0.14
+
+Nlocal:            234 ave         302 max         198 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost:         2876.5 ave        3122 max        2632 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:       107846 ave      150684 max       82181 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 431382
+Ave neighs/atom = 460.87821
+Ave special neighs/atom = 0.30769231
+Neighbor list builds = 28
+Dangerous builds = 0
+Total wall time: 0:00:09
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.1 b/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.1
new file mode 100644
index 0000000000..c6a11d209d
--- /dev/null
+++ b/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.1
@@ -0,0 +1,251 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+read_data       ./gra_water.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (46.92336 44.331078 200)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  936 atoms
+  reading velocities ...
+  936 velocities
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  96 bonds
+  reading angles ...
+  48 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.005 seconds
+  read_data CPU = 0.020 seconds
+mass            1 12.0107   # carbon   	mass (g/mole)
+mass            2 15.9994   # oxygen    mass (g/mole)
+mass            3 1.008     # hydrogen 	mass (g/mole)
+# Separate atom groups
+group 		gr    molecule 1
+792 atoms in group gr
+group 		water molecule 2
+144 atoms in group water
+######################## Potential defition ##############################
+# Interlayer potential
+pair_style  hybrid/overlay  ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+####################################################################
+pair_coeff  1 1   none
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
+pair_coeff  * *   ilp/water/2dm/opt        COH.ILP C Ow Hw    # C-water
+Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
+# bond and angle
+bond_style  	  harmonic
+bond_coeff  	  1 	0.0  0.9572
+angle_style 	  harmonic
+angle_coeff 	  1 	0.0  104.52
+# define kspace calculation
+kspace_style      pppm/tip4p 1E-5
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify every 1 delay 5 check yes page 1000000 one 100000
+####################################################################
+# Calculate pair energy
+compute   	1 all pair lj/cut/tip4p/long
+compute   	2 all pair ilp/water/2dm/opt
+compute		wt water temp
+variable  	TIP4P  equal  c_1
+variable  	EILP   equal  c_2     # total interlayer energy
+variable	temp_wt equal c_wt
+############# Output ##############
+thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
+thermo          100
+thermo_modify   lost error
+
+fix				subf gr setforce 0.0 0.0 0.0
+fix 			1 	water shake 0.0001 20 100 b 1 a 1
+       0 = # of size 2 clusters
+       0 = # of size 3 clusters
+       0 = # of size 4 clusters
+      48 = # of frozen angles
+  find clusters CPU = 0.001 seconds
+
+timestep  		1e-3
+velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix				2 water nve
+run			    1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
+@Article{Ouyang2018
+ author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
+ title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
+ journal = {Nano Letters},
+ volume =  18,
+ pages =   {6009}
+ year =    2018,
+}
+
+- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
+@Article{Ouyang2021
+ author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
+ title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
+ journal = {J. Chem. Theory Comput.},
+ volume =  17,
+ pages =   {7237–7245}
+ year =    2021,
+}
+
+- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
+@Article{Feng2023
+ author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
+ title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
+ journal = {J. Phys. Chem. C},
+ volume =  127,
+ pages =   {8704-8713}
+ year =    2023,
+}
+
+- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
+@inproceedings{gao2021lmff
+ author = {Gao, Ping and Duan, Xiaohui and Others},
+ title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
+ year = {2021},
+ isbn = {9781450384421},
+ publisher = {Association for Computing Machinery},
+ address = {New York, NY, USA},
+ url = {https://doi.org/10.1145/3458817.3476137},
+ doi = {10.1145/3458817.3476137},
+ booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
+ articleno = {42},
+ numpages = {14},
+ location = {St. Louis, Missouri},
+ series = {SC'21},
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM initialization ...
+  extracting TIP4P info from pair style
+  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
+  G vector (1/distance) = 0.28684806
+  grid = 25 24 80
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0001640931
+  estimated relative force accuracy = 1.1395635e-05
+  using single precision MKL FFT
+  3d grid and FFT values/proc = 84320 48000
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 100000, page size: 1000000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 6 5 23
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair ilp/water/2dm/opt, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair lj/cut/tip4p/long, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+SHAKE stats (type/ave/delta/count) on step 0
+Bond:   1   0.957201  2.19705e-06       96
+Angle:  1   104.52    0.000203056       48
+Per MPI rank memory allocation (min/avg/max) = 25.89 | 25.89 | 25.89 Mbytes
+   Step         TotEng         PotEng         KinEng        v_TIP4P         v_EILP       v_temp_wt   
+         0  -16.131263     -19.815178      3.6839141      189.37246     -1.903543       300          
+SHAKE stats (type/ave/delta/count) on step 100
+Bond:   1   0.9572    9.54949e-07       96
+Angle:  1   104.52    6.01522e-05       48
+       100  -17.494868     -20.796993      3.3021253      188.4955      -1.8981262      268.90898    
+SHAKE stats (type/ave/delta/count) on step 200
+Bond:   1   0.9572    9.63922e-07       96
+Angle:  1   104.52    7.7021e-05        48
+       200  -17.486271     -21.194892      3.7086213      188.14561     -1.9871708      302.01203    
+SHAKE stats (type/ave/delta/count) on step 300
+Bond:   1   0.9572    1.4264e-06        96
+Angle:  1   104.52    6.48393e-05       48
+       300  -17.502844     -20.993704      3.49086        188.23268     -1.8457229      284.27861    
+SHAKE stats (type/ave/delta/count) on step 400
+Bond:   1   0.9572    1.33728e-06       96
+Angle:  1   104.52    7.6239e-05        48
+       400  -17.495287     -20.828353      3.3330658      188.48002     -1.8429075      271.42862    
+SHAKE stats (type/ave/delta/count) on step 500
+Bond:   1   0.9572    1.14685e-06       96
+Angle:  1   104.52    8.58621e-05       48
+       500  -17.491436     -20.443044      2.9516084      188.7589      -1.8566335      240.36459    
+SHAKE stats (type/ave/delta/count) on step 600
+Bond:   1   0.9572    9.17601e-07       96
+Angle:  1   104.52    8.24516e-05       48
+       600  -17.505684     -20.608457      3.1027731      188.72078     -1.9560796      252.67471    
+SHAKE stats (type/ave/delta/count) on step 700
+Bond:   1   0.9572    9.50422e-07       96
+Angle:  1   104.52    5.62423e-05       48
+       700  -17.496701     -21.07266       3.5759595      188.2777      -1.9833956      291.20871    
+SHAKE stats (type/ave/delta/count) on step 800
+Bond:   1   0.9572    1.15262e-06       96
+Angle:  1   104.52    7.02158e-05       48
+       800  -17.478623     -20.819504      3.340881       188.37868     -1.9112996      272.06506    
+SHAKE stats (type/ave/delta/count) on step 900
+Bond:   1   0.9572    9.14138e-07       96
+Angle:  1   104.52    6.98742e-05       48
+       900  -17.480864     -20.728498      3.2476343      188.59022     -1.8922102      264.4715     
+SHAKE stats (type/ave/delta/count) on step 1000
+Bond:   1   0.9572    1.00586e-06       96
+Angle:  1   104.52    0.000111711       48
+      1000  -17.498466     -20.331547      2.8330808      188.87473     -1.8121768      230.71228    
+Loop time of 8.95265 on 1 procs for 1000 steps with 936 atoms
+
+Performance: 9.651 ns/day, 2.487 hours/ns, 111.699 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.2127     | 5.2127     | 5.2127     |   0.0 | 58.23
+Bond    | 0.00083377 | 0.00083377 | 0.00083377 |   0.0 |  0.01
+Kspace  | 3.5005     | 3.5005     | 3.5005     |   0.0 | 39.10
+Neigh   | 0.17946    | 0.17946    | 0.17946    |   0.0 |  2.00
+Comm    | 0.028553   | 0.028553   | 0.028553   |   0.0 |  0.32
+Output  | 0.00035446 | 0.00035446 | 0.00035446 |   0.0 |  0.00
+Modify  | 0.01889    | 0.01889    | 0.01889    |   0.0 |  0.21
+Other   |            | 0.01135    |            |       |  0.13
+
+Nlocal:            936 ave         936 max         936 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           5242 ave        5242 max        5242 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       431382 ave      431382 max      431382 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 431382
+Ave neighs/atom = 460.87821
+Ave special neighs/atom = 0.30769231
+Neighbor list builds = 28
+Dangerous builds = 0
+Total wall time: 0:00:09
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.4 b/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.4
new file mode 100644
index 0000000000..852c429323
--- /dev/null
+++ b/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.4
@@ -0,0 +1,251 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+read_data       ./gra_water.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (46.92336 44.331078 200)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  936 atoms
+  reading velocities ...
+  936 velocities
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  96 bonds
+  reading angles ...
+  48 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.003 seconds
+  read_data CPU = 0.017 seconds
+mass            1 12.0107   # carbon   	mass (g/mole)
+mass            2 15.9994   # oxygen    mass (g/mole)
+mass            3 1.008     # hydrogen 	mass (g/mole)
+# Separate atom groups
+group 		gr    molecule 1
+792 atoms in group gr
+group 		water molecule 2
+144 atoms in group water
+######################## Potential defition ##############################
+# Interlayer potential
+pair_style  hybrid/overlay  ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+####################################################################
+pair_coeff  1 1   none
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
+pair_coeff  * *   ilp/water/2dm/opt        COH.ILP C Ow Hw    # C-water
+Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
+# bond and angle
+bond_style  	  harmonic
+bond_coeff  	  1 	0.0  0.9572
+angle_style 	  harmonic
+angle_coeff 	  1 	0.0  104.52
+# define kspace calculation
+kspace_style      pppm/tip4p 1E-5
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify every 1 delay 5 check yes page 1000000 one 100000
+####################################################################
+# Calculate pair energy
+compute   	1 all pair lj/cut/tip4p/long
+compute   	2 all pair ilp/water/2dm/opt
+compute		wt water temp
+variable  	TIP4P  equal  c_1
+variable  	EILP   equal  c_2     # total interlayer energy
+variable	temp_wt equal c_wt
+############# Output ##############
+thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
+thermo          100
+thermo_modify   lost error
+
+fix				subf gr setforce 0.0 0.0 0.0
+fix 			1 	water shake 0.0001 20 100 b 1 a 1
+       0 = # of size 2 clusters
+       0 = # of size 3 clusters
+       0 = # of size 4 clusters
+      48 = # of frozen angles
+  find clusters CPU = 0.001 seconds
+
+timestep  		1e-3
+velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix				2 water nve
+run			    1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
+@Article{Ouyang2018
+ author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
+ title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
+ journal = {Nano Letters},
+ volume =  18,
+ pages =   {6009}
+ year =    2018,
+}
+
+- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
+@Article{Ouyang2021
+ author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
+ title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
+ journal = {J. Chem. Theory Comput.},
+ volume =  17,
+ pages =   {7237–7245}
+ year =    2021,
+}
+
+- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
+@Article{Feng2023
+ author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
+ title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
+ journal = {J. Phys. Chem. C},
+ volume =  127,
+ pages =   {8704-8713}
+ year =    2023,
+}
+
+- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
+@inproceedings{gao2021lmff
+ author = {Gao, Ping and Duan, Xiaohui and Others},
+ title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
+ year = {2021},
+ isbn = {9781450384421},
+ publisher = {Association for Computing Machinery},
+ address = {New York, NY, USA},
+ url = {https://doi.org/10.1145/3458817.3476137},
+ doi = {10.1145/3458817.3476137},
+ booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
+ articleno = {42},
+ numpages = {14},
+ location = {St. Louis, Missouri},
+ series = {SC'21},
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM initialization ...
+  extracting TIP4P info from pair style
+  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
+  G vector (1/distance) = 0.28684806
+  grid = 25 24 80
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0001640931
+  estimated relative force accuracy = 1.1395635e-05
+  using single precision MKL FFT
+  3d grid and FFT values/proc = 30685 12480
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 100000, page size: 1000000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 6 5 23
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair ilp/water/2dm/opt, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair lj/cut/tip4p/long, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+SHAKE stats (type/ave/delta/count) on step 0
+Bond:   1   0.957201  2.19705e-06       96
+Angle:  1   104.52    0.000203056       48
+Per MPI rank memory allocation (min/avg/max) = 22.03 | 22.06 | 22.1 Mbytes
+   Step         TotEng         PotEng         KinEng        v_TIP4P         v_EILP       v_temp_wt   
+         0  -16.131263     -19.815178      3.6839141      189.37246     -1.903543       300          
+SHAKE stats (type/ave/delta/count) on step 100
+Bond:   1   0.9572    9.54949e-07       96
+Angle:  1   104.52    6.01522e-05       48
+       100  -17.494869     -20.796995      3.3021253      188.4955      -1.8981262      268.90898    
+SHAKE stats (type/ave/delta/count) on step 200
+Bond:   1   0.9572    9.63922e-07       96
+Angle:  1   104.52    7.7021e-05        48
+       200  -17.48627      -21.194892      3.7086213      188.14561     -1.9871708      302.01203    
+SHAKE stats (type/ave/delta/count) on step 300
+Bond:   1   0.9572    1.4264e-06        96
+Angle:  1   104.52    6.48393e-05       48
+       300  -17.502843     -20.993703      3.4908599      188.23268     -1.8457229      284.27861    
+SHAKE stats (type/ave/delta/count) on step 400
+Bond:   1   0.9572    1.33728e-06       96
+Angle:  1   104.52    7.6239e-05        48
+       400  -17.495285     -20.82835       3.333065       188.48003     -1.8429074      271.42856    
+SHAKE stats (type/ave/delta/count) on step 500
+Bond:   1   0.9572    1.14685e-06       96
+Angle:  1   104.52    8.58621e-05       48
+       500  -17.491436     -20.443043      2.9516075      188.7589      -1.8566335      240.36452    
+SHAKE stats (type/ave/delta/count) on step 600
+Bond:   1   0.9572    9.17601e-07       96
+Angle:  1   104.52    8.24517e-05       48
+       600  -17.505682     -20.608456      3.1027734      188.72078     -1.9560795      252.67474    
+SHAKE stats (type/ave/delta/count) on step 700
+Bond:   1   0.9572    9.50425e-07       96
+Angle:  1   104.52    5.62423e-05       48
+       700  -17.496706     -21.072664      3.575958       188.2777      -1.9833951      291.20858    
+SHAKE stats (type/ave/delta/count) on step 800
+Bond:   1   0.9572    1.15256e-06       96
+Angle:  1   104.52    7.02177e-05       48
+       800  -17.478628     -20.819507      3.340879       188.37868     -1.9113009      272.0649     
+SHAKE stats (type/ave/delta/count) on step 900
+Bond:   1   0.9572    9.14163e-07       96
+Angle:  1   104.52    6.98849e-05       48
+       900  -17.480868     -20.728506      3.2476383      188.5902      -1.8922108      264.47182    
+SHAKE stats (type/ave/delta/count) on step 1000
+Bond:   1   0.9572    1.00568e-06       96
+Angle:  1   104.52    0.000111707       48
+      1000  -17.498472     -20.331605      2.8331335      188.87466     -1.8121689      230.71657    
+Loop time of 4.7828 on 4 procs for 1000 steps with 936 atoms
+
+Performance: 18.065 ns/day, 1.329 hours/ns, 209.082 timesteps/s
+96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.26735    | 1.3839     | 3.2059     |  99.7 | 28.93
+Bond    | 0.00079377 | 0.00086039 | 0.00093529 |   0.0 |  0.02
+Kspace  | 1.4248     | 3.2254     | 4.3332     |  64.6 | 67.44
+Neigh   | 0.061885   | 0.061916   | 0.061951   |   0.0 |  1.29
+Comm    | 0.044281   | 0.065185   | 0.078628   |   5.1 |  1.36
+Output  | 0.0003482  | 0.0003787  | 0.00040746 |   0.0 |  0.01
+Modify  | 0.028727   | 0.031529   | 0.034914   |   1.3 |  0.66
+Other   |            | 0.01367    |            |       |  0.29
+
+Nlocal:            234 ave         302 max         198 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost:         2876.5 ave        3122 max        2632 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:       107846 ave      150684 max       82181 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 431382
+Ave neighs/atom = 460.87821
+Ave special neighs/atom = 0.30769231
+Neighbor list builds = 28
+Dangerous builds = 0
+Total wall time: 0:00:04

From 9da310a33e947d9e07a7b3ea4540b9aaeab61274 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 19 May 2023 00:40:45 -0400
Subject: [PATCH 069/396] spelling

---
 doc/src/Build_manual.rst                    | 2 +-
 doc/src/variable.rst                        | 2 +-
 doc/utils/sphinx-config/false_positives.txt | 1 +
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst
index e9a55134da..4b4bfa5a45 100644
--- a/doc/src/Build_manual.rst
+++ b/doc/src/Build_manual.rst
@@ -52,7 +52,7 @@ can be translated to different output format using the `Sphinx
 incorporates programmer documentation extracted from the LAMMPS C++
 sources through the `Doxygen <https://doxygen.nl/>`_ program.  Currently
 the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
-and MOBI (for Amazon Kindle(tm) readers) are supported.  For that to work a
+and MOBI (for Amazon Kindle readers) are supported.  For that to work a
 Python interpreter version 3.8 or later, the ``doxygen`` tools and
 internet access to download additional files and tools are required.
 This download is usually only required once or after the documentation
diff --git a/doc/src/variable.rst b/doc/src/variable.rst
index afa491e96e..1c76a2acf4 100644
--- a/doc/src/variable.rst
+++ b/doc/src/variable.rst
@@ -1474,7 +1474,7 @@ commands
 .. code-block:: LAMMPS
 
    # delete_atoms random fraction 0.5 yes all NULL 49839
-   # run 0
+   # run 0 post no
    variable t equal temp    # this thermo keyword invokes a temperature compute
    print "Temperature of system = $t"
    run 1000
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index d2d15633af..2951f7d12e 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -3736,6 +3736,7 @@ Umin
 un
 unary
 uncomment
+uncommented
 uncompress
 uncompute
 underprediction

From 7c14b750ef5fbf9be610aeaf122c37d6d872537e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 19 May 2023 00:40:54 -0400
Subject: [PATCH 070/396] improve error message

---
 src/DIFFRACTION/compute_xrd.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/DIFFRACTION/compute_xrd.cpp b/src/DIFFRACTION/compute_xrd.cpp
index 010e5bcb7d..426248b31e 100644
--- a/src/DIFFRACTION/compute_xrd.cpp
+++ b/src/DIFFRACTION/compute_xrd.cpp
@@ -90,8 +90,7 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
         ztype[i] = j;
        }
      }
-    if (ztype[i] == XRDmaxType + 1)
-        error->all(FLERR,"Compute XRD: Invalid ASF atom type");
+    if (ztype[i] == XRDmaxType + 1) error->all(FLERR,"Compute XRD: Invalid ASF atom type {}", arg[iarg]);
     iarg++;
   }
 

From 22d9c047f44a9417028831c981889ec8e08f2e05 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Fri, 19 May 2023 22:52:18 +0800
Subject: [PATCH 071/396] update doc file

---
 doc/src/pair_ilp_water_2dm.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/pair_ilp_water_2dm.rst b/doc/src/pair_ilp_water_2dm.rst
index 5dc287493b..c611fb9275 100644
--- a/doc/src/pair_ilp_water_2dm.rst
+++ b/doc/src/pair_ilp_water_2dm.rst
@@ -163,4 +163,4 @@ tap_flag = 1
 
 .. _Feng:
 
-**(Feng)** Z. Feng, W. Ouyang, J. Phys. Chem. C. accepted (2023).
+**(Feng)** Z. Feng and W. Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).

From 0334ddb7c69a36b33757694b905820f56d8b90f2 Mon Sep 17 00:00:00 2001
From: Wengen Ouyang <34092370+oywg11@users.noreply.github.com>
Date: Fri, 19 May 2023 22:57:45 +0800
Subject: [PATCH 072/396] Update pair_ilp_water_2dm.rst

---
 doc/src/pair_ilp_water_2dm.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/pair_ilp_water_2dm.rst b/doc/src/pair_ilp_water_2dm.rst
index 5dc287493b..8ba75fb857 100644
--- a/doc/src/pair_ilp_water_2dm.rst
+++ b/doc/src/pair_ilp_water_2dm.rst
@@ -163,4 +163,4 @@ tap_flag = 1
 
 .. _Feng:
 
-**(Feng)** Z. Feng, W. Ouyang, J. Phys. Chem. C. accepted (2023).
+**(Feng)** Z. Feng and W. Ouyang et al., J. Phys. Chem. C. 127, 8704-8713 (2023).

From 7ec842d9cbcfa1f63496383f66125cdc1a9d47dd Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Fri, 19 May 2023 13:50:11 -0600
Subject: [PATCH 073/396] Adding requested feature to normalize forces

---
 src/BPM/bond_bpm_rotational.cpp | 28 ++++++++++++++++++++--------
 src/BPM/bond_bpm_rotational.h   |  2 +-
 src/BPM/bond_bpm_spring.cpp     | 16 ++++++++++++++--
 src/BPM/bond_bpm_spring.h       |  2 +-
 4 files changed, 36 insertions(+), 12 deletions(-)

diff --git a/src/BPM/bond_bpm_rotational.cpp b/src/BPM/bond_bpm_rotational.cpp
index ac29c0e376..5c5c0218b6 100644
--- a/src/BPM/bond_bpm_rotational.cpp
+++ b/src/BPM/bond_bpm_rotational.cpp
@@ -50,6 +50,7 @@ BondBPMRotational::BondBPMRotational(LAMMPS *_lmp) :
 {
   partial_flag = 1;
   smooth_flag = 1;
+  normalize_flag = 0;
 
   single_extra = 7;
   svector = new double[7];
@@ -203,6 +204,13 @@ double BondBPMRotational::elastic_forces(int i1, int i2, int type, double r_mag,
   double Ts[3], Tb[3], Tt[3], Tbp[3], Ttp[3], Tsp[3], T_rot[3], Ttmp[3];
 
   double **quat = atom->quat;
+  double r0_mag_inv = 1.0 / r0_mag;
+  double Kr_type = Kr[type];
+  double Ks_type = Ks[type];
+  if (normalize_flag) {
+    Kr_type *= r0_mag_inv;
+    Ks_type *= r0_mag_inv;
+  }
 
   q1[0] = quat[i1][0];
   q1[1] = quat[i1][1];
@@ -217,26 +225,26 @@ double BondBPMRotational::elastic_forces(int i1, int i2, int type, double r_mag,
   // Calculate normal forces, rb = bond vector in particle 1's frame
   MathExtra::qconjugate(q2, q2inv);
   MathExtra::quatrotvec(q2inv, r, rb);
-  Fr = Kr[type] * (r_mag - r0_mag);
+  Fr = Kr_type * (r_mag - r0_mag);
 
   MathExtra::scale3(Fr * r_mag_inv, rb, F_rot);
 
   // Calculate forces due to tangential displacements (no rotation)
   r0_dot_rb = MathExtra::dot3(r0, rb);
-  c = r0_dot_rb * r_mag_inv / r0_mag;
+  c = r0_dot_rb * r_mag_inv * r0_mag_inv;
   gamma = acos_limit(c);
 
   MathExtra::cross3(rb, r0, rb_x_r0);
   MathExtra::cross3(rb, rb_x_r0, s);
   MathExtra::norm3(s);
 
-  MathExtra::scale3(Ks[type] * r_mag * gamma, s, Fs);
+  MathExtra::scale3(Ks_type * r_mag * gamma, s, Fs);
 
   // Calculate torque due to tangential displacements
   MathExtra::cross3(r0, rb, t);
   MathExtra::norm3(t);
 
-  MathExtra::scale3(0.5 * r_mag * Ks[type] * r_mag * gamma, t, Ts);
+  MathExtra::scale3(0.5 * r_mag * Ks_type * r_mag * gamma, t, Ts);
 
   // Relative rotation force/torque
   // Use representation of X'Y'Z' rotations from Wang, Mora 2009
@@ -316,12 +324,12 @@ double BondBPMRotational::elastic_forces(int i1, int i2, int type, double r_mag,
   Ttp[1] = 0.0;
   Ttp[2] = Kt[type] * psi;
 
-  Fsp[0] = -0.5 * Ks[type] * r_mag * theta * cos_phi;
-  Fsp[1] = -0.5 * Ks[type] * r_mag * theta * sin_phi;
+  Fsp[0] = -0.5 * Ks_type * r_mag * theta * cos_phi;
+  Fsp[1] = -0.5 * Ks_type * r_mag * theta * sin_phi;
   Fsp[2] = 0.0;
 
-  Tsp[0] = 0.25 * Ks[type] * r_mag * r_mag * theta * sin_phi;
-  Tsp[1] = -0.25 * Ks[type] * r_mag * r_mag * theta * cos_phi;
+  Tsp[0] = 0.25 * Ks_type * r_mag * r_mag * theta * sin_phi;
+  Tsp[1] = -0.25 * Ks_type * r_mag * r_mag * theta * cos_phi;
   Tsp[2] = 0.0;
 
   // Rotate forces/torques back to 1st particle's frame
@@ -667,6 +675,10 @@ void BondBPMRotational::settings(int narg, char **arg)
       if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for smooth");
       smooth_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
       i += 1;
+    } else if (strcmp(arg[iarg], "normalize") == 0) {
+      if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for normalize");
+      normalize_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
+      i += 1;
     } else {
       error->all(FLERR, "Illegal bond bpm command, invalid argument {}", arg[iarg]);
     }
diff --git a/src/BPM/bond_bpm_rotational.h b/src/BPM/bond_bpm_rotational.h
index 0fb38e7343..9fdc418d2d 100644
--- a/src/BPM/bond_bpm_rotational.h
+++ b/src/BPM/bond_bpm_rotational.h
@@ -41,7 +41,7 @@ class BondBPMRotational : public BondBPM {
  protected:
   double *Kr, *Ks, *Kt, *Kb, *gnorm, *gslide, *groll, *gtwist;
   double *Fcr, *Fcs, *Tct, *Tcb;
-  int smooth_flag;
+  int smooth_flag, normalize_flag;
 
   double elastic_forces(int, int, int, double, double, double, double *, double *, double *,
                         double *, double *, double *);
diff --git a/src/BPM/bond_bpm_spring.cpp b/src/BPM/bond_bpm_spring.cpp
index ed4e71daf1..37b79f93fb 100644
--- a/src/BPM/bond_bpm_spring.cpp
+++ b/src/BPM/bond_bpm_spring.cpp
@@ -37,6 +37,7 @@ BondBPMSpring::BondBPMSpring(LAMMPS *_lmp) :
 {
   partial_flag = 1;
   smooth_flag = 1;
+  normalize_flag = 0;
 
   single_extra = 1;
   svector = new double[1];
@@ -190,7 +191,10 @@ void BondBPMSpring::compute(int eflag, int vflag)
     }
 
     rinv = 1.0 / r;
-    fbond = k[type] * (r0 - r);
+    if (normalize_flag)
+      fbond = -k[type] * e;
+    else
+      fbond = k[type] * (r0 - r);
 
     delvx = v[i1][0] - v[i2][0];
     delvy = v[i1][1] - v[i2][1];
@@ -302,6 +306,10 @@ void BondBPMSpring::settings(int narg, char **arg)
       if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for smooth");
       smooth_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
       i += 1;
+    } else if (strcmp(arg[iarg], "normalize") == 0) {
+      if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for normalize");
+      normalize_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
+      i += 1;
     } else {
       error->all(FLERR, "Illegal bond bpm command, invalid argument {}", arg[iarg]);
     }
@@ -376,7 +384,11 @@ double BondBPMSpring::single(int type, double rsq, int i, int j, double &fforce)
 
   double r = sqrt(rsq);
   double rinv = 1.0 / r;
-  fforce = k[type] * (r0 - r);
+
+  if (normalize_flag)
+    fforce = k[type] * (r0 - r) / r0;
+  else
+    fforce = k[type] * (r0 - r);
 
   double **x = atom->x;
   double **v = atom->v;
diff --git a/src/BPM/bond_bpm_spring.h b/src/BPM/bond_bpm_spring.h
index 409469bef3..93f4b49a26 100644
--- a/src/BPM/bond_bpm_spring.h
+++ b/src/BPM/bond_bpm_spring.h
@@ -40,7 +40,7 @@ class BondBPMSpring : public BondBPM {
 
  protected:
   double *k, *ecrit, *gamma;
-  int smooth_flag;
+  int smooth_flag, normalize_flag;
 
   void allocate();
   void store_data();

From cb5934cbcdbf6ea4098451473d45126c79f99ca2 Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Fri, 19 May 2023 13:51:53 -0600
Subject: [PATCH 074/396] Adding option to doc files, clarifying normal forces
 in compute pair/bond local

---
 doc/src/bond_bpm_rotational.rst | 6 ++++++
 doc/src/bond_bpm_spring.rst     | 8 +++++++-
 doc/src/compute_bond_local.rst  | 5 ++++-
 doc/src/compute_pair_local.rst  | 4 +++-
 4 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/doc/src/bond_bpm_rotational.rst b/doc/src/bond_bpm_rotational.rst
index ba93d679ba..0baf7e35b1 100644
--- a/doc/src/bond_bpm_rotational.rst
+++ b/doc/src/bond_bpm_rotational.rst
@@ -30,6 +30,9 @@ Syntax
        *smooth* value = *yes* or *no*
           smooths bond forces near the breaking point
 
+       *normalize* value = *yes* or *no*
+          normalizes normal and shear forces by the reference length
+
        *break/no*
           indicates that bonds should not break during a run
 
@@ -136,6 +139,9 @@ or :doc:`read_restart <read_restart>` commands:
 * :math:`\gamma_r`      (force*distance/velocity units)
 * :math:`\gamma_t`      (force*distance/velocity units)
 
+However, the *normalize* option will normalize the radial and shear forces
+by :math:`r_0` such that :math:`k_r` and :math:`k_s` are unit less.
+
 By default, pair forces are not calculated between bonded particles.
 Pair forces can alternatively be overlaid on top of bond forces using
 the *overlay/pair* keyword. These settings require specific
diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst
index 5762dbe208..6da0d25a4a 100644
--- a/doc/src/bond_bpm_spring.rst
+++ b/doc/src/bond_bpm_spring.rst
@@ -30,6 +30,9 @@ Syntax
        *smooth* value = *yes* or *no*
           smooths bond forces near the breaking point
 
+       *normalize* value = *yes* or *no*
+          normalizes bond forces by their reference length
+
        *break/no*
           indicates that bonds should not break during a run
 
@@ -66,7 +69,7 @@ particles based on a model described by Clemmer and Robbins
 
    F = k (r - r_0) w
 
-where :math:`k_r` is a stiffness, :math:`r` is the current distance
+where :math:`k` is a stiffness, :math:`r` is the current distance
 and :math:`r_0` is the initial distance between the two particles, and
 :math:`w` is an optional smoothing factor discussed below. Bonds will
 break at a strain of :math:`\epsilon_c`.  This is done by setting by
@@ -102,6 +105,9 @@ the data file or restart files read by the :doc:`read_data
 * :math:`\epsilon_c`    (unit less)
 * :math:`\gamma`        (force/velocity units)
 
+However, the *normalize* option will normalize the elastic bond force by
+:math:`r_0` such that :math:`k` is unit less.
+
 By default, pair forces are not calculated between bonded particles.
 Pair forces can alternatively be overlaid on top of bond forces using
 the *overlay/pair* keyword. These settings require specific
diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst
index f3fb752ebe..10e86bbe44 100644
--- a/doc/src/compute_bond_local.rst
+++ b/doc/src/compute_bond_local.rst
@@ -76,7 +76,10 @@ The value *force* is the magnitude of the force acting between the
 pair of atoms in the bond.
 
 The values *fx*, *fy*, and *fz* are the xyz components of
-*force* between the pair of atoms in the bond.
+*force* between the pair of atoms in the bond. For bond styles that apply
+non-central forces, such as :doc:`bond_style bpm/rotational
+<bond_bpm_rotational>`, these values only include the :math:`(x,y,z)`
+components of the normal force component.
 
 The remaining properties are all computed for motion of the two atoms
 relative to the center of mass (COM) velocity of the 2 atoms in the
diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst
index dace280dee..31209f63f4 100644
--- a/doc/src/compute_pair_local.rst
+++ b/doc/src/compute_pair_local.rst
@@ -66,7 +66,9 @@ The value *eng* is the interaction energy for the pair of atoms.
 The value *force* is the force acting between the pair of atoms, which
 is positive for a repulsive force and negative for an attractive
 force.  The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
-*force* on atom I.
+*force* on atom I. For pair styles that apply non-central forces,
+such as :doc:`granular pair styles <pair_gran>`, these values only include
+the :math:`(x,y,z)` components of the normal force component.
 
 A pair style may define additional pairwise quantities which can be
 accessed as *p1* to *pN*, where :math:`N` is defined by the pair style.

From 0dd26189d4e8fb5b5630618687f74cd032d6ad62 Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Fri, 19 May 2023 13:52:35 -0600
Subject: [PATCH 075/396] Adding missing factor in bpm/rotational single method

---
 src/BPM/bond_bpm_rotational.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/BPM/bond_bpm_rotational.cpp b/src/BPM/bond_bpm_rotational.cpp
index 5c5c0218b6..ffb0d9521d 100644
--- a/src/BPM/bond_bpm_rotational.cpp
+++ b/src/BPM/bond_bpm_rotational.cpp
@@ -805,7 +805,7 @@ double BondBPMRotational::single(int type, double rsq, int i, int j, double &ffo
   double breaking = elastic_forces(i, j, type, r_mag, r0_mag, r_mag_inv, rhat, r, r0, force1on2,
                                    torque1on2, torque2on1);
   damping_forces(i, j, type, rhat, r, force1on2, torque1on2, torque2on1);
-  fforce = MathExtra::dot3(force1on2, r);
+  fforce = MathExtra::dot3(force1on2, rhat);
   fforce *= -1;
 
   double smooth = 1.0;

From 8d0eb9b1f71c3454d84f5c289d816deea29c5aed Mon Sep 17 00:00:00 2001
From: srtee <uqstee4@uq.edu.au>
Date: Tue, 9 May 2023 22:07:48 +1000
Subject: [PATCH 076/396] hook up efield variables to qeq/reaxff

---
 src/REAXFF/fix_qeq_reaxff.cpp | 41 +++++++++++++++++++---------
 src/fix_efield.cpp            | 50 +++++++++++++++++++++--------------
 src/fix_efield.h              |  1 +
 3 files changed, 60 insertions(+), 32 deletions(-)

diff --git a/src/REAXFF/fix_qeq_reaxff.cpp b/src/REAXFF/fix_qeq_reaxff.cpp
index 704b43e642..5dc739d5e8 100644
--- a/src/REAXFF/fix_qeq_reaxff.cpp
+++ b/src/REAXFF/fix_qeq_reaxff.cpp
@@ -404,8 +404,6 @@ void FixQEqReaxFF::init()
     efield->init();
     if (strcmp(update->unit_style,"real") != 0)
       error->all(FLERR,"Must use unit_style real with fix {} and external fields", style);
-    if (efield->varflag != FixEfield::CONSTANT)
-      error->all(FLERR,"Cannot (yet) use fix {} with variable efield", style);
 
     if (((fabs(efield->ex) > SMALL) && domain->xperiodic) ||
          ((fabs(efield->ey) > SMALL) && domain->yperiodic) ||
@@ -1101,26 +1099,45 @@ void FixQEqReaxFF::get_chi_field()
 
   // efield energy is in real units of kcal/mol/angstrom, need to convert to eV
 
-  const double factor = -1.0/force->qe2f;
+  const double qe2f = force->qe2f;
+  const double factor = -1.0/qe2f;
+
+
+  if (efield->varflag != FixEfield::CONSTANT) {
+    efield->update_efield_variables();
+  }
 
-  // currently we only support constant efield
   // atom selection is for the group of fix efield
 
-  if (efield->varflag == FixEfield::CONSTANT) {
-    double unwrap[3];
-    const double fx = efield->ex;
-    const double fy = efield->ey;
-    const double fz = efield->ez;
-    const int efgroupbit = efield->groupbit;
+  double unwrap[3];
+  const double ex = efield->ex;
+  const double ey = efield->ey;
+  const double ez = efield->ez;
+  const int efgroupbit = efield->groupbit;
 
     // charge interactions
     // force = qE, potential energy = F dot x in unwrapped coords
-
+  if (efield->varflag != FixEfield::ATOM) {
     for (int i = 0; i < nlocal; i++) {
       if (mask[i] & efgroupbit) {
         if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
         domain->unmap(x[i],image[i],unwrap);
-        chi_field[i] = factor*(fx*unwrap[0] + fy*unwrap[1] + fz*unwrap[2]);
+        chi_field[i] = factor*(ex*unwrap[0] + ey*unwrap[1] + ez*unwrap[2]);
+      }
+    }
+  } else {
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & efgroupbit) {
+        if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
+        domain->unmap(x[i],image[i],unwrap);
+        double edisp = 0; // accumulate E dot displacement
+        edisp += unwrap[0]*(
+            (efield->xstyle == FixEfield::ATOM) ? qe2f*efield->efield[i][0] : ex);
+        edisp += unwrap[1]*(
+            (efield->ystyle == FixEfield::ATOM) ? qe2f*efield->efield[i][1] : ey);
+        edisp += unwrap[2]*(
+            (efield->zstyle == FixEfield::ATOM) ? qe2f*efield->efield[i][2] : ez);
+        chi_field[i] = factor*edisp;
       }
     }
   }
diff --git a/src/fix_efield.cpp b/src/fix_efield.cpp
index 7880655973..f1adc722ae 100644
--- a/src/fix_efield.cpp
+++ b/src/fix_efield.cpp
@@ -346,26 +346,7 @@ void FixEfield::post_force(int vflag)
 
   } else {
 
-    modify->clearstep_compute();
-
-    if (xstyle == EQUAL) {
-      ex = qe2f * input->variable->compute_equal(xvar);
-    } else if (xstyle == ATOM) {
-      input->variable->compute_atom(xvar, igroup, &efield[0][0], 4, 0);
-    }
-    if (ystyle == EQUAL) {
-      ey = qe2f * input->variable->compute_equal(yvar);
-    } else if (ystyle == ATOM) {
-      input->variable->compute_atom(yvar, igroup, &efield[0][1], 4, 0);
-    }
-    if (zstyle == EQUAL) {
-      ez = qe2f * input->variable->compute_equal(zvar);
-    } else if (zstyle == ATOM) {
-      input->variable->compute_atom(zvar, igroup, &efield[0][2], 4, 0);
-    }
-    if (estyle == ATOM) input->variable->compute_atom(evar, igroup, &efield[0][3], 4, 0);
-
-    modify->addstep_compute(update->ntimestep + 1);
+    update_efield_variables();
 
     // charge interactions
     // force = qE
@@ -470,3 +451,32 @@ double FixEfield::compute_vector(int n)
   }
   return fsum_all[n + 1];
 }
+
+/* ----------------------------------------------------------------------
+   update efield variables without doing anything else
+   called by fix_qeq_reaxff
+------------------------------------------------------------------------- */
+
+void FixEfield::update_efield_variables()
+{
+  modify->clearstep_compute();
+
+  if (xstyle == EQUAL) {
+    ex = qe2f * input->variable->compute_equal(xvar);
+  } else if (xstyle == ATOM) {
+    input->variable->compute_atom(xvar, igroup, &efield[0][0], 4, 0);
+  }
+  if (ystyle == EQUAL) {
+    ey = qe2f * input->variable->compute_equal(yvar);
+  } else if (ystyle == ATOM) {
+    input->variable->compute_atom(yvar, igroup, &efield[0][1], 4, 0);
+  }
+  if (zstyle == EQUAL) {
+    ez = qe2f * input->variable->compute_equal(zvar);
+  } else if (zstyle == ATOM) {
+    input->variable->compute_atom(zvar, igroup, &efield[0][2], 4, 0);
+  }
+  if (estyle == ATOM) input->variable->compute_atom(evar, igroup, &efield[0][3], 4, 0);
+
+  modify->addstep_compute(update->ntimestep + 1);
+}
diff --git a/src/fix_efield.h b/src/fix_efield.h
index 52c827bb50..2bab26e140 100644
--- a/src/fix_efield.h
+++ b/src/fix_efield.h
@@ -59,6 +59,7 @@ class FixEfield : public Fix {
 
   int force_flag;
   double fsum[4], fsum_all[4];
+  void update_efield_variables();
 };
 }    // namespace LAMMPS_NS
 #endif

From fe7a6fce296846e278233b2572f808d5da4eeb65 Mon Sep 17 00:00:00 2001
From: srtee <uqstee4@uq.edu.au>
Date: Wed, 17 May 2023 16:13:27 +1000
Subject: [PATCH 077/396] make QEQ work with atom-style potential

---
 src/REAXFF/fix_qeq_reaxff.cpp | 15 ++++--------
 src/fix_efield.cpp            | 45 ++++++++++++++++++++++++++---------
 src/fix_efield.h              |  5 ++--
 3 files changed, 42 insertions(+), 23 deletions(-)

diff --git a/src/REAXFF/fix_qeq_reaxff.cpp b/src/REAXFF/fix_qeq_reaxff.cpp
index 5dc739d5e8..b25ce479cd 100644
--- a/src/REAXFF/fix_qeq_reaxff.cpp
+++ b/src/REAXFF/fix_qeq_reaxff.cpp
@@ -405,6 +405,9 @@ void FixQEqReaxFF::init()
     if (strcmp(update->unit_style,"real") != 0)
       error->all(FLERR,"Must use unit_style real with fix {} and external fields", style);
 
+    if (efield->varflag == FixEfield::ATOM && efield->pstyle != FixEfield::ATOM)
+      error->all(FLERR,"Atom-style external electric field requires atom-style "
+                       "potential variable when used with fix {}", style);
     if (((fabs(efield->ex) > SMALL) && domain->xperiodic) ||
          ((fabs(efield->ey) > SMALL) && domain->yperiodic) ||
          ((fabs(efield->ez) > SMALL) && domain->zperiodic))
@@ -1125,19 +1128,11 @@ void FixQEqReaxFF::get_chi_field()
         chi_field[i] = factor*(ex*unwrap[0] + ey*unwrap[1] + ez*unwrap[2]);
       }
     }
-  } else {
+  } else { // must use atom-style potential from FixEfield
     for (int i = 0; i < nlocal; i++) {
       if (mask[i] & efgroupbit) {
         if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
-        domain->unmap(x[i],image[i],unwrap);
-        double edisp = 0; // accumulate E dot displacement
-        edisp += unwrap[0]*(
-            (efield->xstyle == FixEfield::ATOM) ? qe2f*efield->efield[i][0] : ex);
-        edisp += unwrap[1]*(
-            (efield->ystyle == FixEfield::ATOM) ? qe2f*efield->efield[i][1] : ey);
-        edisp += unwrap[2]*(
-            (efield->zstyle == FixEfield::ATOM) ? qe2f*efield->efield[i][2] : ez);
-        chi_field[i] = factor*edisp;
+        chi_field[i] = -efield->efield[i][3];
       }
     }
   }
diff --git a/src/fix_efield.cpp b/src/fix_efield.cpp
index f1adc722ae..f335d8a765 100644
--- a/src/fix_efield.cpp
+++ b/src/fix_efield.cpp
@@ -41,7 +41,7 @@ using namespace FixConst;
 
 FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
     Fix(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), estr(nullptr),
-    idregion(nullptr), region(nullptr), efield(nullptr)
+    pstr(nullptr), idregion(nullptr), region(nullptr), efield(nullptr)
 {
   if (narg < 6) utils::missing_cmd_args(FLERR, std::string("fix ") + style, error);
 
@@ -100,6 +100,14 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
       } else
         error->all(FLERR, "Unsupported argument for fix {} energy command: {}", style, arg[iarg]);
       iarg += 2;
+    } else if (strcmp(arg[iarg], "potential") == 0) {
+      if (iarg + 2 > narg)
+        utils::missing_cmd_args(FLERR, std::string("fix ") + style + "potential", error);
+      if (utils::strmatch(arg[iarg + 1], "^v_")) {
+        pstr = utils::strdup(arg[iarg + 1] + 2);
+      } else
+        error->all(FLERR, "Unsupported argument for fix {} energy command: {}", style, arg[iarg]);
+      iarg += 2;
     } else {
       error->all(FLERR, "Unknown keyword for fix {} command: {}", style, arg[iarg]);
     }
@@ -122,6 +130,7 @@ FixEfield::~FixEfield()
   delete[] ystr;
   delete[] zstr;
   delete[] estr;
+  delete[] pstr;
   delete[] idregion;
   memory->destroy(efield);
 }
@@ -157,43 +166,55 @@ void FixEfield::init()
 
   if (xstr) {
     xvar = input->variable->find(xstr);
-    if (xvar < 0) error->all(FLERR, "Variable {} for fix {} does not exist", xstr, style);
+    if (xvar < 0) error->all(FLERR, "Variable {} for x-field in fix {} does not exist", xstr, style);
     if (input->variable->equalstyle(xvar))
       xstyle = EQUAL;
     else if (input->variable->atomstyle(xvar))
       xstyle = ATOM;
     else
-      error->all(FLERR, "Variable {} for fix {} is invalid style", xstr, style);
+      error->all(FLERR, "Variable {} for x-field in fix {} is invalid style", xstr, style);
   }
   if (ystr) {
     yvar = input->variable->find(ystr);
-    if (yvar < 0) error->all(FLERR, "Variable {} for fix {} does not exist", ystr, style);
+    if (yvar < 0) error->all(FLERR, "Variable {} for y-field in fix {} does not exist", ystr, style);
     if (input->variable->equalstyle(yvar))
       ystyle = EQUAL;
     else if (input->variable->atomstyle(yvar))
       ystyle = ATOM;
     else
-      error->all(FLERR, "Variable {} for fix {} is invalid style", ystr, style);
+      error->all(FLERR, "Variable {} for y-field in fix {} is invalid style", ystr, style);
   }
   if (zstr) {
     zvar = input->variable->find(zstr);
-    if (zvar < 0) error->all(FLERR, "Variable {} for fix {} does not exist", zstr, style);
+    if (zvar < 0) error->all(FLERR, "Variable {} for z-field in fix {} does not exist", zstr, style);
     if (input->variable->equalstyle(zvar))
       zstyle = EQUAL;
     else if (input->variable->atomstyle(zvar))
       zstyle = ATOM;
     else
-      error->all(FLERR, "Variable {} for fix {} is invalid style", zstr, style);
+      error->all(FLERR, "Variable {} for z-field in fix {} is invalid style", zstr, style);
   }
   if (estr) {
     evar = input->variable->find(estr);
-    if (evar < 0) error->all(FLERR, "Variable {} for fix {} does not exist", estr, style);
+    if (evar < 0) error->all(FLERR, "Variable {} for energy in fix {} does not exist", estr, style);
     if (input->variable->atomstyle(evar))
       estyle = ATOM;
     else
-      error->all(FLERR, "Variable {} for fix {} is invalid style", estr, style);
+      error->all(FLERR, "Variable {} for energy in fix {} must be atom-style", estr, style);
   } else
     estyle = NONE;
+  if (pstr) {
+    pvar = input->variable->find(pstr);
+    if (pvar < 0) error->all(FLERR, "Variable {} for potential in fix {} does not exist", pstr, style);
+    if (input->variable->atomstyle(pvar))
+      pstyle = ATOM;
+    else
+      error->all(FLERR, "Variable {} for potential in fix {} must be atom-style", pstr, style);
+    if (estyle != NONE)
+      error->warning(FLERR, "fix {} will ignore variable {} for energy "
+          "because atom-style potential has been specified", estr, style);
+  } else
+    pstyle = NONE;
 
   // set index and check validity of region
 
@@ -376,7 +397,8 @@ void FixEfield::post_force(int vflag)
           }
           f[i][2] += fz;
           fsum[3] += fz;
-          if (estyle == ATOM) fsum[0] += efield[i][3];
+          if (pstyle == ATOM) fsum[0] += qe2f * q[i] * efield[i][3];
+          else if (estyle == ATOM) fsum[0] += efield[i][3];
         }
     }
 
@@ -476,7 +498,8 @@ void FixEfield::update_efield_variables()
   } else if (zstyle == ATOM) {
     input->variable->compute_atom(zvar, igroup, &efield[0][2], 4, 0);
   }
-  if (estyle == ATOM) input->variable->compute_atom(evar, igroup, &efield[0][3], 4, 0);
+  if (pstyle == ATOM) input->variable->compute_atom(pvar, igroup, &efield[0][3], 4, 0);
+  else if (estyle == ATOM) input->variable->compute_atom(evar, igroup, &efield[0][3], 4, 0);
 
   modify->addstep_compute(update->ntimestep + 1);
 }
diff --git a/src/fix_efield.h b/src/fix_efield.h
index 2bab26e140..72fd204898 100644
--- a/src/fix_efield.h
+++ b/src/fix_efield.h
@@ -46,10 +46,11 @@ class FixEfield : public Fix {
  protected:
   double ex, ey, ez;
   int varflag;
-  char *xstr, *ystr, *zstr, *estr;
+  char *xstr, *ystr, *zstr, *estr, *pstr;
   char *idregion;
   class Region *region;
-  int xvar, yvar, zvar, evar, xstyle, ystyle, zstyle, estyle;
+  int xvar, yvar, zvar, xstyle, ystyle, zstyle;
+  int evar, pvar, estyle, pstyle;
   int ilevel_respa;
   double qe2f;
   int qflag, muflag;

From 36eb11f499d2ebfa896e14bd0caa8792561788ad Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sat, 20 May 2023 12:59:34 +0300
Subject: [PATCH 078/396] Include method for bond contribution & variables to
 compute_stress_mop.h

---
 src/EXTRA-COMPUTE/compute_stress_mop.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.h b/src/EXTRA-COMPUTE/compute_stress_mop.h
index 5357d36371..c9f95c1996 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.h
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.h
@@ -38,11 +38,13 @@ class ComputeStressMop : public Compute {
 
  private:
   void compute_pairs();
+  void compute_bonds();
 
   int me, nvalues, dir;
   int *which;
 
   double *values_local, *values_global;
+  double *bond_local, *bond_global;
   double pos, pos1, dt, nktv2p, ftm2v;
   double area;
   class NeighList *list;

From 5da65bbd0a158e89b06e959a17cde3af02474d71 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sat, 20 May 2023 13:06:19 +0300
Subject: [PATCH 079/396] Code for bond contribution to stress/mop

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 137 ++++++++++++++++++++++-
 1 file changed, 132 insertions(+), 5 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 60f2d76e06..7900a62bef 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -19,10 +19,13 @@
 #include "compute_stress_mop.h"
 
 #include "atom.h"
+#include "atom_vec.h"
+#include "bond.h"
 #include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "memory.h"
+#include "molecule.h"
 #include "neigh_list.h"
 #include "neighbor.h"
 #include "pair.h"
@@ -118,12 +121,16 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
   // Initialize some variables
 
   values_local = values_global = vector = nullptr;
+  bond_local = nullptr;
+  bond_global = nullptr;
 
   // this fix produces a global vector
 
   memory->create(vector,nvalues,"stress/mop:vector");
   memory->create(values_local,nvalues,"stress/mop/spatial:values_local");
   memory->create(values_global,nvalues,"stress/mop/spatial:values_global");
+  memory->create(bond_local,nvalues,"stress/mop/spatial:bond_local");
+  memory->create(bond_global,nvalues,"stress/mop/spatial:bond_global");
   size_vector = nvalues;
 
   vector_flag = 1;
@@ -140,6 +147,8 @@ ComputeStressMop::~ComputeStressMop()
 
   memory->destroy(values_local);
   memory->destroy(values_global);
+  memory->destroy(bond_local);
+  memory->destroy(bond_global);
   memory->destroy(vector);
 }
 
@@ -185,8 +194,8 @@ void ComputeStressMop::init()
     //Compute stress/mop only accounts for pair interactions.
     // issue a warning if any intramolecular potential or Kspace is defined.
 
-    if (force->bond!=nullptr)
-      error->warning(FLERR,"compute stress/mop does not account for bond potentials");
+    //if (force->bond!=nullptr)
+    //  error->warning(FLERR,"compute stress/mop does not account for bond potentials");
     if (force->angle!=nullptr)
       error->warning(FLERR,"compute stress/mop does not account for angle potentials");
     if (force->dihedral!=nullptr)
@@ -224,9 +233,14 @@ void ComputeStressMop::compute_vector()
   MPI_Allreduce(values_local,values_global,nvalues,
                 MPI_DOUBLE,MPI_SUM,world);
 
-  int m;
-  for (m=0; m<nvalues; m++) {
-    vector[m] = values_global[m];
+  //Compute bond contribution on separate procs
+  compute_bonds();
+
+  // sum bond contribution over all procs
+  MPI_Allreduce(bond_local,bond_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
+
+  for (int m=0; m<nvalues; m++) {
+    vector[m] = values_global[m] + bond_global[m];
   }
 
 }
@@ -427,3 +441,116 @@ void ComputeStressMop::compute_pairs()
   }
 }
 
+/*------------------------------------------------------------------------
+ *   compute bond contribution to pressure of local proc
+ *     -------------------------------------------------------------------------*/
+
+void ComputeStressMop::compute_bonds()
+{
+  int i, nb, atom1, atom2, imol, iatom, btype;
+  tagint tagprev;
+  double rsq, fpair;
+
+  double **x = atom->x;
+  tagint *tag = atom->tag;
+  int *num_bond = atom->num_bond;
+  tagint **bond_atom = atom->bond_atom;
+  int **bond_type = atom->bond_type;
+  int *mask = atom->mask;
+
+  int *molindex = atom->molindex;
+  int *molatom = atom->molatom;
+  Molecule **onemols = atom->avec->onemols;
+
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+  int molecular = atom->molecular;
+
+  Bond *bond = force->bond;
+
+  double dx[3] {0};
+  double x_bond_1[3] {0};
+  double x_bond_2[3] {0};
+  double local_contribution[3] {0};
+
+  // initialization
+  for (int i {0}; i < nvalues; i++) bond_local[i] = 0.0;
+
+  // loop over all bonded atoms in the current proc
+  for (atom1 = 0; atom1 < nlocal; atom1++) {
+    if (!(mask[atom1] & groupbit)) continue;
+
+    if (molecular == 1)
+      nb = num_bond[atom1];
+    else {
+      if (molindex[atom1] < 0) continue;
+      imol = molindex[atom1];
+      iatom = molatom[atom1];
+      nb = onemols[imol]->num_bond[iatom];
+    }
+
+    for (i = 0; i < nb; i++) {
+      if (molecular == 1) {
+        btype = bond_type[atom1][i];
+        atom2 = atom->map(bond_atom[atom1][i]);
+      } else {
+        tagprev = tag[atom1] - iatom - 1;
+        btype = onemols[imol]->bond_type[iatom][i];
+        atom2 = atom->map(onemols[imol]->bond_atom[iatom][i] + tagprev);
+      }
+
+      if (atom2 < 0 || !(mask[atom2] & groupbit)) continue;
+      if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
+      if (btype <= 0) continue;
+
+      // minimum image of atom1 with respect to the plane of interest
+      dx[0] = x[atom1][0];
+      dx[1] = x[atom1][1];
+      dx[2] = x[atom1][2];
+      dx[dir] -= pos;
+      domain->minimum_image(dx[0], dx[1], dx[2]);
+      x_bond_1[0] = dx[0];
+      x_bond_1[1] = dx[1];
+      x_bond_1[2] = dx[2];
+      x_bond_1[dir] += pos;
+
+      // minimum image of atom2 with respect to atom1
+      dx[0] = x[atom2][0] - x_bond_1[0];
+      dx[1] = x[atom2][1] - x_bond_1[1];
+      dx[2] = x[atom2][2] - x_bond_1[2];
+      domain->minimum_image(dx[0], dx[1], dx[2]);
+      x_bond_2[0] = x_bond_1[0] + dx[0];
+      x_bond_2[1] = x_bond_1[1] + dx[1];
+      x_bond_2[2] = x_bond_1[2] + dx[2];
+
+      // check if the bond vector crosses the plane of interest
+      double tau = (x_bond_1[dir] - pos) / (x_bond_1[dir] - x_bond_2[dir]);
+      if ((tau <= 1) and (tau >= 0))
+      {
+        //std::cout << "I have found one crossing bond " << tau << std::endl;
+        dx[0] = x_bond_1[0] - x_bond_2[0];
+        dx[1] = x_bond_1[1] - x_bond_2[1];
+        dx[2] = x_bond_1[2] - x_bond_2[2];
+        rsq = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
+        bond->single(btype, rsq, atom1, atom2, fpair);
+
+        // check the correct contribution with the + or - sign
+        local_contribution[0] += fpair*dx[0]/area*nktv2p;
+        local_contribution[1] += fpair*dx[1]/area*nktv2p;
+        local_contribution[2] += fpair*dx[2]/area*nktv2p;
+      }
+    }
+  }
+
+  // loop over the keywords and if necessary add the bond contribution
+  int m {0};
+  while (m<nvalues) {
+    if (which[m] == CONF || which[m] == TOTAL) {
+      bond_local[m] = local_contribution[0];
+      bond_local[m+1] = local_contribution[1];
+      bond_local[m+2] = local_contribution[2];
+    }
+    m += 3;
+  }
+  return;
+}

From 90427c8750cab12a342ef42ee9fe9a5356e2a213 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sat, 20 May 2023 15:12:42 +0300
Subject: [PATCH 080/396] Update compute_stress_mop.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 7900a62bef..89ef4e8b2b 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -525,16 +525,13 @@ void ComputeStressMop::compute_bonds()
 
       // check if the bond vector crosses the plane of interest
       double tau = (x_bond_1[dir] - pos) / (x_bond_1[dir] - x_bond_2[dir]);
-      if ((tau <= 1) and (tau >= 0))
-      {
-        //std::cout << "I have found one crossing bond " << tau << std::endl;
+      if ((tau <= 1) and (tau >= 0)) {
         dx[0] = x_bond_1[0] - x_bond_2[0];
         dx[1] = x_bond_1[1] - x_bond_2[1];
         dx[2] = x_bond_1[2] - x_bond_2[2];
         rsq = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
         bond->single(btype, rsq, atom1, atom2, fpair);
 
-        // check the correct contribution with the + or - sign
         local_contribution[0] += fpair*dx[0]/area*nktv2p;
         local_contribution[1] += fpair*dx[1]/area*nktv2p;
         local_contribution[2] += fpair*dx[2]/area*nktv2p;
@@ -552,5 +549,4 @@ void ComputeStressMop::compute_bonds()
     }
     m += 3;
   }
-  return;
 }

From 1d7a6f813bd623ba1d483da70e13d1c40ef24a43 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sat, 20 May 2023 15:14:47 +0300
Subject: [PATCH 081/396] Update compute_stress_mop.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 89ef4e8b2b..8391622242 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -525,7 +525,7 @@ void ComputeStressMop::compute_bonds()
 
       // check if the bond vector crosses the plane of interest
       double tau = (x_bond_1[dir] - pos) / (x_bond_1[dir] - x_bond_2[dir]);
-      if ((tau <= 1) and (tau >= 0)) {
+      if ((tau <= 1) && (tau >= 0)) {
         dx[0] = x_bond_1[0] - x_bond_2[0];
         dx[1] = x_bond_1[1] - x_bond_2[1];
         dx[2] = x_bond_1[2] - x_bond_2[2];

From 6977f71eb0ad15e370e330739cf6cf937f4ceca0 Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Sat, 20 May 2023 13:53:22 -0600
Subject: [PATCH 082/396] Initial example

---
 examples/mliap/jax/README.md            |  38 +++++++++++
 examples/mliap/jax/deploy_script.py     |  32 +++++++++
 examples/mliap/jax/in.run               |  48 +++++++++++++
 examples/mliap/jax/mliap_jax.pkl        | Bin 0 -> 234 bytes
 examples/mliap/jax/mliap_unified_jax.py |   0
 examples/mliap/jax/write_unified.py     |  86 ++++++++++++++++++++++++
 6 files changed, 204 insertions(+)
 create mode 100644 examples/mliap/jax/README.md
 create mode 100644 examples/mliap/jax/deploy_script.py
 create mode 100644 examples/mliap/jax/in.run
 create mode 100644 examples/mliap/jax/mliap_jax.pkl
 create mode 100644 examples/mliap/jax/mliap_unified_jax.py
 create mode 100644 examples/mliap/jax/write_unified.py

diff --git a/examples/mliap/jax/README.md b/examples/mliap/jax/README.md
new file mode 100644
index 0000000000..14a049221a
--- /dev/null
+++ b/examples/mliap/jax/README.md
@@ -0,0 +1,38 @@
+# Running JAX from LAMMPS
+
+### Getting started
+
+First make a Python environment with dependencies:
+
+    conda create --name jax python=3.10
+    conda activate jax
+    # Upgrade pip
+    python -m pip install --upgrade pip
+    # Install JAX:
+    python -m pip install --upgrade "jax[cpu]"
+    # Install other dependencies:
+    python -m pip install numpy scipy torch scikit-learn virtualenv psutil tabulate mpi4py Cython
+
+Install LAMMPS:
+
+    cd /path/to/lammps
+    mkdir build-jax; cd build-jax
+    cmake ../cmake -DLAMMPS_EXCEPTIONS=yes \
+                   -DBUILD_SHARED_LIBS=yes \
+                   -DMLIAP_ENABLE_PYTHON=yes \
+                   -DPKG_PYTHON=yes \
+                   -DPKG_ML-SNAP=yes \
+                   -DPKG_ML-IAP=yes \
+                   -DPYTHON_EXECUTABLE:FILEPATH=`which python`
+    make -j4
+    make install-python
+
+### Wrapping JAX code
+
+Take inspiration from the `FitSNAP` ML-IAP wrapper: https://github.com/rohskopf/FitSNAP/blob/mliap-unified/fitsnap3lib/tools/write_unified.py
+
+First define JAX model in `deploy_script.py`, which will wrap model with `write_unified`.
+
+    python deploy_script.py
+
+Then load model in LAMMPS and run:
\ No newline at end of file
diff --git a/examples/mliap/jax/deploy_script.py b/examples/mliap/jax/deploy_script.py
new file mode 100644
index 0000000000..58af797766
--- /dev/null
+++ b/examples/mliap/jax/deploy_script.py
@@ -0,0 +1,32 @@
+import numpy as np
+import pickle
+from pathlib import Path
+from write_unified import MLIAPInterface
+
+class MyModel():
+  def __init__(self,blah):
+      """
+      coeffs = np.genfromtxt(file,skip_header=6)
+      self.bias = coeffs[0]
+      self.weights = coeffs[1:]
+      """
+      self.blah = blah
+      self.n_params = 3 #len(coeffs)
+      self.n_descriptors = 1 #len(self.weights)
+      self.n_elements = 1
+
+  def __call__(self,rij):
+      print(rij)
+      #energy[:] = bispectrum @ self.weights + self.bias
+      #beta[:] = self.weights
+      return 5
+
+model = MyModel(1)
+
+#unified = MLIAPInterface(model, ["Ta"], model_device="cpu")
+
+def create_pickle():
+    unified = MLIAPInterface(model, ["Ta"])
+    unified.pickle('mliap_jax.pkl')
+
+create_pickle()
\ No newline at end of file
diff --git a/examples/mliap/jax/in.run b/examples/mliap/jax/in.run
new file mode 100644
index 0000000000..1ffc2d3c0f
--- /dev/null
+++ b/examples/mliap/jax/in.run
@@ -0,0 +1,48 @@
+# Initialize simulation
+
+variable nsteps index 10000
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+#boundary        p p p
+#read_data DATA
+
+variable nrep equal 2 #10
+variable a equal 3.316
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+lattice         bcc $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      1 box
+create_atoms    1 box
+mass 1 180.88
+
+pair_style mliap unified mliap_jax.pkl 0
+pair_coeff * * Ta
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+# is this neigh modify every 1 slow?
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 3200.0 4928459 loop geom
+dump 1 all xyz 10 dump.xyz 
+fix 1 all nve
+run             ${nsteps}
\ No newline at end of file
diff --git a/examples/mliap/jax/mliap_jax.pkl b/examples/mliap/jax/mliap_jax.pkl
new file mode 100644
index 0000000000000000000000000000000000000000..2cbbedb7c1bd8dd8af97d7312471cf2054e163d1
GIT binary patch
literal 234
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zJGXo59rlk#TZD@AUSlFW3Rl5=6Ocu-S24;}CKox$m<Rf|t=Y#EGb9VPF0hoHaA&JT
z@sJWMW1|b3n^Kl-cBxQCWli_kHF0Gds4QlkkG+@W38un*fJ|uu5O%{le2qV|6Q%0#
Yg!Ku&v@ZJue=d*UbL*+DqAHp`06B$LI{*Lx

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HcmV?d00001

diff --git a/examples/mliap/jax/mliap_unified_jax.py b/examples/mliap/jax/mliap_unified_jax.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/examples/mliap/jax/write_unified.py b/examples/mliap/jax/write_unified.py
new file mode 100644
index 0000000000..55f46a0af4
--- /dev/null
+++ b/examples/mliap/jax/write_unified.py
@@ -0,0 +1,86 @@
+"""
+interface for creating LAMMPS MLIAP Unified models.
+"""
+import pickle
+
+import numpy as np
+
+from lammps.mliap.mliap_unified_abc import MLIAPUnified
+
+class MLIAPInterface(MLIAPUnified):
+    """
+    Class for creating ML-IAP Unified model based on hippynn graphs.
+    """
+    def __init__(self, model, element_types, cutoff=4.5, ndescriptors=1):
+        """
+        :param model: class defining the model
+        :param element_types: list of atomic symbols corresponding to element types
+        :param ndescriptors: the number of descriptors to report to LAMMPS
+        :param model_device: the device to send torch data to (cpu or cuda)
+        """
+        super().__init__()
+        self.model = model
+        self.element_types = element_types
+        self.ndescriptors = ndescriptors
+        #self.model_device = model_device
+        
+
+        # Build the calculator
+        # TODO: Make this cutoff depend on model cutoff, ideally from deployed model itself but could 
+        # be part of deploy step.
+        #rc = 4.5
+        self.rcutfac = 0.5*cutoff # Actual cutoff will be 2*rc
+        #print(self.model.nparams)
+        self.nparams = 10
+        #self.rcutfac, self.species_set, self.graph = setup_LAMMPS()
+        #self.nparams = sum(p.nelement() for p in self.graph.parameters())
+        #self.graph.to(torch.float64)
+
+    def compute_descriptors(self, data):
+        pass
+
+    def compute_gradients(self, data):
+        pass
+
+    def compute_forces(self, data):
+        #print(">>>>> hey!")
+        #elems = self.as_tensor(data.elems).type(torch.int64).reshape(1, data.ntotal)
+
+        """
+        elems = self.as_tensor(data.elems).type(torch.int64) + 1
+        #z_vals = self.species_set[elems+1]
+        pair_i = self.as_tensor(data.pair_i).type(torch.int64)
+        pair_j = self.as_tensor(data.pair_j).type(torch.int64)
+        rij = self.as_tensor(data.rij).type(torch.float64).requires_grad_(True)
+        nlocal = self.as_tensor(data.nlistatoms) 
+        """
+
+        rij = data.rij
+
+        #(total_energy, fij) = self.network(rij, None, None, None, nlocal, elems, pair_i, pair_j, "cpu", dtype=torch.float64, mode="lammps")
+
+        test = self.model(rij)
+         
+        #data.update_pair_forces(fij)
+        #data.energy = total_energy.item()
+ 
+        pass
+
+def setup_LAMMPS(energy):
+    """
+
+    :param energy: energy node for lammps interface
+    :return: graph for computing from lammps MLIAP unified inputs.
+    """
+
+    model = TheModelClass(*args, **kwargs)
+
+    save_state_dict = torch.load("Ta_Pytorch.pt")
+    model.load_state_dict(save_state_dict["model_state_dict"])
+
+
+    #model.load_state_dict(torch.load(PATH))
+    model.eval()
+    
+    #model.eval()
+    return model
\ No newline at end of file

From 28c9c274be1fd270a866258dafc09486d3cccf1a Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Sat, 20 May 2023 14:08:20 -0600
Subject: [PATCH 083/396] Copy MLIAPUnified LJ example

---
 examples/mliap/jax/README.md                |   6 +-
 examples/mliap/jax/deploy_script.py         |  33 ++---------
 examples/mliap/jax/in.run                   |  59 ++++++++------------
 examples/mliap/jax/mliap_unified_jax.py     |  41 ++++++++++++++
 examples/mliap/jax/mliap_unified_jax_Ar.pkl | Bin 0 -> 181 bytes
 examples/mliap/jax/write_unified.py         |   1 +
 6 files changed, 76 insertions(+), 64 deletions(-)
 create mode 100644 examples/mliap/jax/mliap_unified_jax_Ar.pkl

diff --git a/examples/mliap/jax/README.md b/examples/mliap/jax/README.md
index 14a049221a..320d87e465 100644
--- a/examples/mliap/jax/README.md
+++ b/examples/mliap/jax/README.md
@@ -35,4 +35,8 @@ First define JAX model in `deploy_script.py`, which will wrap model with `write_
 
     python deploy_script.py
 
-Then load model in LAMMPS and run:
\ No newline at end of file
+This creates `.pkl` file to be loaded by LAMMPS ML-IAP Unified.
+
+Run LAMMPS with the model:
+
+    mpirun -np P lmp -in in.run
\ No newline at end of file
diff --git a/examples/mliap/jax/deploy_script.py b/examples/mliap/jax/deploy_script.py
index 58af797766..5e73995565 100644
--- a/examples/mliap/jax/deploy_script.py
+++ b/examples/mliap/jax/deploy_script.py
@@ -1,32 +1,11 @@
-import numpy as np
-import pickle
-from pathlib import Path
-from write_unified import MLIAPInterface
+import lammps
+import lammps.mliap
 
-class MyModel():
-  def __init__(self,blah):
-      """
-      coeffs = np.genfromtxt(file,skip_header=6)
-      self.bias = coeffs[0]
-      self.weights = coeffs[1:]
-      """
-      self.blah = blah
-      self.n_params = 3 #len(coeffs)
-      self.n_descriptors = 1 #len(self.weights)
-      self.n_elements = 1
-
-  def __call__(self,rij):
-      print(rij)
-      #energy[:] = bispectrum @ self.weights + self.bias
-      #beta[:] = self.weights
-      return 5
-
-model = MyModel(1)
-
-#unified = MLIAPInterface(model, ["Ta"], model_device="cpu")
+#from lammps.mliap.mliap_unified_lj import MLIAPUnifiedLJ
+from mliap_unified_jax import MLIAPUnifiedJAX
 
 def create_pickle():
-    unified = MLIAPInterface(model, ["Ta"])
-    unified.pickle('mliap_jax.pkl')
+    unified = MLIAPUnifiedJAX(["Ar"])
+    unified.pickle('mliap_unified_jax_Ar.pkl')
 
 create_pickle()
\ No newline at end of file
diff --git a/examples/mliap/jax/in.run b/examples/mliap/jax/in.run
index 1ffc2d3c0f..354dfd769f 100644
--- a/examples/mliap/jax/in.run
+++ b/examples/mliap/jax/in.run
@@ -1,48 +1,35 @@
-# Initialize simulation
+# 3d Lennard-Jones melt
 
-variable nsteps index 10000
-units           metal
+units           lj
+atom_style      atomic
 
-# generate the box and atom positions using a BCC lattice
-
-#boundary        p p p
-#read_data DATA
-
-variable nrep equal 2 #10
-variable a equal 3.316
-variable nx equal ${nrep}
-variable ny equal ${nrep}
-variable nz equal ${nrep}
-lattice         bcc $a
-region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+lattice         fcc 0.8442
+region          box block 0 10 0 10 0 10
 create_box      1 box
 create_atoms    1 box
-mass 1 180.88
+mass            1 1.0
 
-pair_style mliap unified mliap_jax.pkl 0
-pair_coeff * * Ta
+velocity        all create 3.0 87287 loop geom
 
-compute  eatom all pe/atom
-compute  energy all reduce sum c_eatom
+pair_style      mliap unified mliap_unified_jax_Ar.pkl 0
+pair_coeff      * * Ar
 
-compute  satom all stress/atom NULL
-compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
-variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+neighbor        0.3 bin
+neigh_modify    every 20 delay 0 check no
 
-thermo_style    custom step temp epair c_energy etotal press v_press
-thermo          10
-thermo_modify norm yes
+fix             1 all nve
 
-# Set up NVE run
+#dump           id all atom 50 dump.melt
 
-timestep 0.5e-3
-neighbor 1.0 bin
-# is this neigh modify every 1 slow?
-neigh_modify once no every 1 delay 0 check yes
+#dump           2 all image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    2 pad 3
 
-# Run MD
+#dump           3 all movie 1 movie.mpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    3 pad 3
 
-velocity all create 3200.0 4928459 loop geom
-dump 1 all xyz 10 dump.xyz 
-fix 1 all nve
-run             ${nsteps}
\ No newline at end of file
+#dump 4 all custom 1 forces.xyz fx fy fz
+
+thermo          50
+run             250
\ No newline at end of file
diff --git a/examples/mliap/jax/mliap_unified_jax.py b/examples/mliap/jax/mliap_unified_jax.py
index e69de29bb2..a2447d1cdb 100644
--- a/examples/mliap/jax/mliap_unified_jax.py
+++ b/examples/mliap/jax/mliap_unified_jax.py
@@ -0,0 +1,41 @@
+from lammps.mliap.mliap_unified_abc import MLIAPUnified
+import numpy as np
+
+
+class MLIAPUnifiedJAX(MLIAPUnified):
+    """Test implementation for MLIAPUnified."""
+
+    def __init__(self, element_types, epsilon=1.0, sigma=1.0, rcutfac=1.25):
+        # ARGS: interface, element_types, ndescriptors, nparams, rcutfac
+        super().__init__(None, element_types, 1, 3, rcutfac)
+        # Mimicking the LJ pair-style:
+        # pair_style lj/cut 2.5
+        # pair_coeff * * 1 1
+        self.epsilon = epsilon
+        self.sigma = sigma
+
+    def compute_gradients(self, data):
+        """Test compute_gradients."""
+
+    def compute_descriptors(self, data):
+        """Test compute_descriptors."""
+
+    def compute_forces(self, data):
+        """Test compute_forces."""
+        eij, fij = self.compute_pair_ef(data)
+        data.update_pair_energy(eij)
+        data.update_pair_forces(fij)
+
+    def compute_pair_ef(self, data):
+        rij = data.rij
+
+        r2inv = 1.0 / np.sum(rij ** 2, axis=1)
+        r6inv = r2inv * r2inv * r2inv
+
+        lj1 = 4.0 * self.epsilon * self.sigma**12
+        lj2 = 4.0 * self.epsilon * self.sigma**6
+
+        eij = r6inv * (lj1 * r6inv - lj2)
+        fij = r6inv * (3.0 * lj2 - 6.0 * lj2 * r6inv) * r2inv
+        fij = fij[:, np.newaxis] * rij
+        return eij, fij
\ No newline at end of file
diff --git a/examples/mliap/jax/mliap_unified_jax_Ar.pkl b/examples/mliap/jax/mliap_unified_jax_Ar.pkl
new file mode 100644
index 0000000000000000000000000000000000000000..04b173031520d82eb1b407293993b6329e52765e
GIT binary patch
literal 181
zcmZo*nYxMr0(t~<b21YP;!E=~(=t<2;<FMfru6Xp`gl49ghGV893!Soo}$?}rFM!&
z4`*gxNorAAVsh#fzaHMyoYdUZyps5m%7WD5DX~*}m>i3yB=+#+rKA=o7iAWd<QElB
z@n-B{&nrkQO3VeanS0oal1oc~2263c{{nRadul;(W=?({Q0N0xh_yH~JvR{{P@1F%
E01c-;o&W#<

literal 0
HcmV?d00001

diff --git a/examples/mliap/jax/write_unified.py b/examples/mliap/jax/write_unified.py
index 55f46a0af4..af2627dfef 100644
--- a/examples/mliap/jax/write_unified.py
+++ b/examples/mliap/jax/write_unified.py
@@ -6,6 +6,7 @@ import pickle
 import numpy as np
 
 from lammps.mliap.mliap_unified_abc import MLIAPUnified
+#from deploy_script import MyModel
 
 class MLIAPInterface(MLIAPUnified):
     """

From 3822e6ff0f6f9eb500ed0a02d74001bb31da309c Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sun, 21 May 2023 10:29:24 +0800
Subject: [PATCH 084/396] add potential file that parameterized against with
 DMC reference data

---
 potentials/COH.DMC.ILP | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100755 potentials/COH.DMC.ILP

diff --git a/potentials/COH.DMC.ILP b/potentials/COH.DMC.ILP
new file mode 100755
index 0000000000..7235afcdab
--- /dev/null
+++ b/potentials/COH.DMC.ILP
@@ -0,0 +1,28 @@
+# DATE: 2023-05-18 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com CITATION: Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C 127, 8704 (2023).
+# Interlayer Potential (ILP) for water/graphene heterojunctions
+# The parameters below are fitted against the DMC reference data that rescaled from PBE+MBD-NL.
+#
+# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
+#    beta(A)    alpha    delta(A)  epsilon(meV)  C(meV)        d         sR      reff(A)   C6(meV*A^6)    S    rcut
+# For graphene and hydrocarbons
+C C  3.205843  7.511126  1.235334  1.528338E-5  37.530428  15.499947  0.7954443  3.681440  25.714535E3   1.0   2.0
+H H  3.974540   6.53799  1.080633  0.6700556    0.8333833  15.022371  0.7490632  2.767223  1.6159581E3   1.0   1.2
+C H  2.642950  12.91410  1.020257  0.9750012    25.340996  15.222927  0.8115998  3.887324  5.6874617E3   1.0   1.5
+H C  2.642950  12.91410  1.020257  0.9750012    25.340996  15.222927  0.8115998  3.887324  5.6874617E3   1.0   1.5
+
+# For water-graphene
+C Ow  4.03686677 15.09817069  1.00000323 1.03838111  0.16372013 9.00010553 1.12057182 2.96484087 21887.14173222   1.0     2.0
+C Hw  3.08246994  6.412090180 1.00000265 2.89390420 -1.85748759 9.00009101 1.04574423 2.21642099  4652.78021666   1.0     2.0
+Ow C  4.03686677 15.09817069  1.00000323 1.03838111  0.16372013 9.00010553 1.12057182 2.96484087 21887.14173222   1.0     1.2
+Hw C  3.08246994  6.412090180 1.00000265 2.89390420 -1.85748759 9.00009101 1.04574423 2.21642099  4652.78021666   1.0     1.2
+
+# # The ILPs for other systems are set to zero
+H Ow  5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+H Hw  5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+Ow H  5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+Hw H  5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+
+Ow Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+Hw Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+Ow Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
+Hw Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
\ No newline at end of file

From 91ac9ef3fc4c88ddcb7b1356a62c3c927535fb2c Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sun, 21 May 2023 11:29:28 +0800
Subject: [PATCH 085/396] update doc file

---
 doc/src/pair_ilp_water_2dm.rst | 170 +++++++++++++++++++++++++++++++++
 1 file changed, 170 insertions(+)
 create mode 100644 doc/src/pair_ilp_water_2dm.rst

diff --git a/doc/src/pair_ilp_water_2dm.rst b/doc/src/pair_ilp_water_2dm.rst
new file mode 100644
index 0000000000..82cf1a6580
--- /dev/null
+++ b/doc/src/pair_ilp_water_2dm.rst
@@ -0,0 +1,170 @@
+.. index:: pair_style ilp/water/2dm
+.. index:: pair_style ilp/water/2dm/opt
+
+pair_style ilp/tmd command
+===================================
+
+Accelerator Variant: *ilp/water/2dm/opt*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style [hybrid/overlay ...] ilp/tmd cutoff tap_flag
+
+* cutoff = global cutoff (distance units)
+* tap_flag = 0/1 to turn off/on the taper function
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style  hybrid/overlay ilp/water/2dm 16.0 1
+   pair_coeff  * * ilp/water/2dm  COH.ILP C Ow Hw
+
+   pair_style  hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+   pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+   pair_coeff  2 3   lj/cut/tip4p/long    0.0        0.0     # O-H
+   pair_coeff  3 3   lj/cut/tip4p/long    0.0        0.0     # H-H
+   pair_coeff  * *   ilp/water/2dm        COH.ILP    C Ow Hw
+
+Description
+"""""""""""
+
+.. versionadded:: xxxx2023
+
+The *ilp/water/2dm* style computes the registry-dependent interlayer
+potential (ILP) potential for interfaces of water with two-dimensinal (2D)
+materials as described in :ref:`(Feng) <Feng>`.
+
+.. math::
+
+   E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
+   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+                \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
+                 \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
+                 \cdot \frac{C_6}{r^6_{ij}} \right \}\\
+   \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
+   \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
+   f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
+   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+                           70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
+                           84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
+                           35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
+
+Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides
+a continuous cutoff (up to third derivative) for interatomic separations
+larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`.
+
+It is important to include all the pairs to build the neighbor list for
+calculating the normals.
+
+.. note::
+
+   Since each water molecule contains one oxygen atom and two hydrogen atoms,
+   a new definition is proposed (see In :ref:`(Feng) <Feng>`),the atomic
+   normal vectors of hydrogen atoms are assumed to lie along the corresponding
+   oxygen-hydrogen bonds and the normal vector of the central oxygen atom
+   is defined as their average.
+
+The parameter file (e.g. COH.ILP), is intended for use with *metal*
+:doc:`units <units>`, with energies in meV. Two additional parameters,
+*S*, and *rcut* are included in the parameter file. *S* is designed to
+facilitate scaling of energies. *rcut* is designed to build the neighbor
+list for calculating the normals for each atom pair.
+
+.. note::
+
+   The parameters presented in the parameter file (e.g. COH.ILP),
+   are fitted with taper function by setting the cutoff equal to 16.0
+   Angstrom.  Using different cutoff or taper function should be careful.
+   These parameters provide a good description in both short- and long-range
+   interaction regimes. This feature is essential for simulations in high pressure
+   regime (i.e., the interlayer distance is smaller than the equilibrium
+   distance).
+
+This potential must be used in combination with hybrid/overlay.
+Other interactions can be set to zero using pair_style *none*\ .
+
+This pair style tallies a breakdown of the total interlayer potential
+energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 2.
+The 2 values correspond to the following sub-categories:
+
+1. *E_vdW* = vdW (attractive) energy
+2. *E_Rep* = Repulsive energy
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+.. code-block:: LAMMPS
+
+   compute 0 all pair ilp/water/2dm
+   variable Evdw  equal c_0[1]
+   variable Erep  equal c_0[2]
+   thermo_style custom step temp epair v_Erep v_Evdw
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This pair style does not support the pair_modify mix, shift, table, and
+tail options.
+
+This pair style does not write their information to binary restart
+files, since it is stored in potential files. Thus, you need to
+re-specify the pair_style and pair_coeff commands in an input script
+that reads a restart file.
+
+Restrictions
+""""""""""""
+
+This pair style is part of the INTERLAYER package.  It is only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style requires the newton setting to be *on* for pair
+interactions.
+
+The COH.ILP potential file provided with LAMMPS (see the potentials
+directory) are parameterized for *metal* units.  You can use this
+potential with any LAMMPS units, but you would need to create your
+COH.ILP potential file with coefficients listed in the appropriate
+units, if your simulation does not use *metal* units.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_coeff <pair_coeff>`,
+:doc:`pair_none <pair_none>`,
+:doc:`pair_style hybrid/overlay <pair_hybrid>`,
+:doc:`pair_style drip <pair_drip>`,
+:doc:`pair_style ilp_tmd <pair_ilp_tmd>`,
+:doc:`pair_style saip_metal <pair_saip_metal>`,
+:doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`,
+:doc:`pair_style pair_kolmogorov_crespi_z <pair_kolmogorov_crespi_z>`,
+:doc:`pair_style pair_kolmogorov_crespi_full <pair_kolmogorov_crespi_full>`,
+:doc:`pair_style pair_lebedeva_z <pair_lebedeva_z>`,
+:doc:`pair_style pair_coul_shield <pair_coul_shield>`.
+
+Default
+"""""""
+
+tap_flag = 1
+
+
+----------
+
+.. _Feng:
+
+<<<<<<< HEAD
+**(Feng)** Z. Feng and W. Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).
+=======
+**(Feng)** Z. Feng and W. Ouyang et al., J. Phys. Chem. C. 127, 8704-8713 (2023).
+>>>>>>> 0334ddb7c69a36b33757694b905820f56d8b90f2

From 685255083efaed1049724351fdfc33193ee493a5 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sun, 21 May 2023 11:43:39 +0800
Subject: [PATCH 086/396] clean the duplicate info

---
 doc/src/pair_ilp_water_2dm.rst | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/doc/src/pair_ilp_water_2dm.rst b/doc/src/pair_ilp_water_2dm.rst
index 82cf1a6580..6a364f38ed 100644
--- a/doc/src/pair_ilp_water_2dm.rst
+++ b/doc/src/pair_ilp_water_2dm.rst
@@ -162,9 +162,4 @@ tap_flag = 1
 ----------
 
 .. _Feng:
-
-<<<<<<< HEAD
-**(Feng)** Z. Feng and W. Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).
-=======
 **(Feng)** Z. Feng and W. Ouyang et al., J. Phys. Chem. C. 127, 8704-8713 (2023).
->>>>>>> 0334ddb7c69a36b33757694b905820f56d8b90f2

From d190249e98b40e17995d6d96dad06533e6ad28ca Mon Sep 17 00:00:00 2001
From: srtee <uqstee4@uq.edu.au>
Date: Mon, 22 May 2023 00:10:01 +1000
Subject: [PATCH 087/396] add documentation and checks

---
 doc/src/fix_efield.rst        | 26 +++++++++++++++++++++++---
 doc/src/fix_qeq_reaxff.rst    | 10 +++++++---
 src/REAXFF/fix_qeq_reaxff.cpp |  5 +++++
 src/fix_efield.cpp            |  6 ++++--
 4 files changed, 39 insertions(+), 8 deletions(-)

diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst
index e72510e4da..271912097f 100644
--- a/doc/src/fix_efield.rst
+++ b/doc/src/fix_efield.rst
@@ -19,7 +19,7 @@ Syntax
 * ex,ey,ez = E-field component values (electric field units)
 * any of ex,ey,ez can be a variable (see below)
 * zero or more keyword/value pairs may be appended to args
-* keyword = *region* or *energy*
+* keyword = *region* or *energy* or *potential*
 
   .. parsed-literal::
 
@@ -27,6 +27,8 @@ Syntax
          region-ID = ID of region atoms must be in to have added force
        *energy* value = v_name
          v_name = variable with name that calculates the potential energy of each atom in the added E-field
+       *potential* value = v_name
+         v_name = variable with name that calculates the electric potential of each atom in the added E-field (overrides *energy*)
 
 Examples
 """"""""
@@ -112,7 +114,8 @@ one or more variables, and if you are performing dynamics via the
 :doc:`run <run>` command.  If the keyword is not used, LAMMPS will set
 the energy to 0.0, which is typically fine for dynamics.
 
-The *energy* keyword is required if the added force is defined with
+The *energy* keyword (or *potential* keyword, described below)
+is required if the added force is defined with
 one or more variables, and you are performing energy minimization via
 the "minimize" command for charged particles.  It is not required for
 point-dipoles, but a warning is issued since the minimizer in LAMMPS
@@ -122,7 +125,7 @@ minimize the orientation of dipoles in an applied electric field.
 The *energy* keyword specifies the name of an atom-style
 :doc:`variable <variable>` which is used to compute the energy of each
 atom as function of its position.  Like variables used for *ex*,
-*ey*, *ez*, the energy variable is specified as v_name, where name
+*ey*, *ez*, the energy variable is specified as "v_name", where "name"
 is the variable name.
 
 Note that when the *energy* keyword is used during an energy
@@ -133,6 +136,23 @@ due to the electric field were a spring-like F = kx, then the energy
 formula should be E = -0.5kx\^2.  If you don't do this correctly, the
 minimization will not converge properly.
 
+The *potential* keyword can be used as an alternative to the *energy*
+keyword to specify the name of an atom-style variable, which is used to compute
+the added electric potential to each atom as a function of its position.
+The variable should have units of electric field times distance (that is,
+in `units real`, the potential should be in volts). As with the *energy*
+keyword, the variable name is specified as "v_name". The energy added by this
+fix is then calculated as the electric potential multiplied by charge.
+
+The *potential* keyword is mainly intended for correct charge equilibration
+in simulations with :doc:`fix qeq/reaxff<fix_qeq_reaxff>`, since with variable
+charges the electric potential can be known beforehand but the energy cannot.
+A small additional benefit is that the *energy* keyword requires an additional
+conversion to energy units which the *potential* keyword avoids. Thus, when the
+*potential* keyword is specified the *energy* keyword is ignored (the simulation
+will proceed but with a warning issued). As with *energy*, the *potential*
+keyword is not allowed if the added field is a constant vector.
+
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
diff --git a/doc/src/fix_qeq_reaxff.rst b/doc/src/fix_qeq_reaxff.rst
index db9015f187..4422ddc89c 100644
--- a/doc/src/fix_qeq_reaxff.rst
+++ b/doc/src/fix_qeq_reaxff.rst
@@ -128,9 +128,13 @@ periodic cell dimensions less than 10 Angstroms.
 
 This fix may be used in combination with :doc:`fix efield <fix_efield>`
 and will apply the external electric field during charge equilibration,
-but there may be only one fix efield instance used, it may only use a
-constant electric field, and the electric field vector may only have
-components in non-periodic directions.
+but there may be only one fix efield instance used and the electric field
+vector may only have components in non-periodic directions. Equal-style
+variables can be used for electric field vector components without any further
+settings. Atom-style variables can be used for spatially-varying electric field
+vector components, but the resulting electric potential must be specified
+as an atom-style variable using the (new) *potential* keyword for 
+`fix efield`.
 
 Related commands
 """"""""""""""""
diff --git a/src/REAXFF/fix_qeq_reaxff.cpp b/src/REAXFF/fix_qeq_reaxff.cpp
index b25ce479cd..4c0864ac27 100644
--- a/src/REAXFF/fix_qeq_reaxff.cpp
+++ b/src/REAXFF/fix_qeq_reaxff.cpp
@@ -408,6 +408,11 @@ void FixQEqReaxFF::init()
     if (efield->varflag == FixEfield::ATOM && efield->pstyle != FixEfield::ATOM)
       error->all(FLERR,"Atom-style external electric field requires atom-style "
                        "potential variable when used with fix {}", style);
+    if (((efield->xstyle != FixEfield::CONSTANT) && domain->xperiodic) ||
+         ((efield->ystyle != FixEfield::CONSTANT) && domain->yperiodic) ||
+         ((efield->zstyle != FixEfield::CONSTANT) && domain->zperiodic))
+      error->all(FLERR,"Must not have electric field component in direction of periodic "
+                       "boundary when using charge equilibration with ReaxFF.");
     if (((fabs(efield->ex) > SMALL) && domain->xperiodic) ||
          ((fabs(efield->ey) > SMALL) && domain->yperiodic) ||
          ((fabs(efield->ez) > SMALL) && domain->zperiodic))
diff --git a/src/fix_efield.cpp b/src/fix_efield.cpp
index f335d8a765..d2c0dc1ef6 100644
--- a/src/fix_efield.cpp
+++ b/src/fix_efield.cpp
@@ -238,8 +238,10 @@ void FixEfield::init()
 
   if (varflag == CONSTANT && estyle != NONE)
     error->all(FLERR, "Cannot use variable energy with constant efield in fix {}", style);
-  if ((varflag == EQUAL || varflag == ATOM) && update->whichflag == 2 && estyle == NONE)
-    error->all(FLERR, "Must use variable energy with fix {}", style);
+  if (varflag == CONSTANT && pstyle != NONE)
+    error->all(FLERR, "Cannot use variable potential with constant efield in fix {}", style);
+  if ((varflag == EQUAL || varflag == ATOM) && update->whichflag == 2 && estyle == NONE && pstyle == NONE)
+    error->all(FLERR, "Must use variable energy or potential with fix {} during minimization", style);
 
   if (utils::strmatch(update->integrate_style, "^respa")) {
     ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels - 1;

From 0692ed3bd72bfbd9f0524baa8ea45dadefb08407 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Wed, 24 May 2023 11:47:15 +0300
Subject: [PATCH 088/396] @evoyiatzis Include method for angle contribution &
 variables to compute_stress_mop.h

---
 src/EXTRA-COMPUTE/compute_stress_mop.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.h b/src/EXTRA-COMPUTE/compute_stress_mop.h
index c9f95c1996..d1074e002a 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.h
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.h
@@ -39,12 +39,14 @@ class ComputeStressMop : public Compute {
  private:
   void compute_pairs();
   void compute_bonds();
+  void compute_angles();
 
   int me, nvalues, dir;
   int *which;
 
   double *values_local, *values_global;
   double *bond_local, *bond_global;
+  double *angle_local, *angle_global;
   double pos, pos1, dt, nktv2p, ftm2v;
   double area;
   class NeighList *list;

From df708a67a5f56f6ac64bd03ac2f6b8f3033f1cb4 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Wed, 24 May 2023 11:55:08 +0300
Subject: [PATCH 089/396]  Code for angle contribution to stress/mop

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 186 ++++++++++++++++++++++-
 1 file changed, 184 insertions(+), 2 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 8391622242..139c5b5903 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -18,6 +18,7 @@
 
 #include "compute_stress_mop.h"
 
+#include "angle.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "bond.h"
@@ -123,6 +124,8 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
   values_local = values_global = vector = nullptr;
   bond_local = nullptr;
   bond_global = nullptr;
+  angle_local = nullptr;
+  angle_global = nullptr;
 
   // this fix produces a global vector
 
@@ -131,6 +134,8 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
   memory->create(values_global,nvalues,"stress/mop/spatial:values_global");
   memory->create(bond_local,nvalues,"stress/mop/spatial:bond_local");
   memory->create(bond_global,nvalues,"stress/mop/spatial:bond_global");
+  memory->create(angle_local,nvalues,"stress/mop/spatial:angle_local");
+  memory->create(angle_global,nvalues,"stress/mop/spatial:angle_global");
   size_vector = nvalues;
 
   vector_flag = 1;
@@ -149,6 +154,8 @@ ComputeStressMop::~ComputeStressMop()
   memory->destroy(values_global);
   memory->destroy(bond_local);
   memory->destroy(bond_global);
+  memory->destroy(angle_local);
+  memory->destroy(angle_global);
   memory->destroy(vector);
 }
 
@@ -197,7 +204,8 @@ void ComputeStressMop::init()
     //if (force->bond!=nullptr)
     //  error->warning(FLERR,"compute stress/mop does not account for bond potentials");
     if (force->angle!=nullptr)
-      error->warning(FLERR,"compute stress/mop does not account for angle potentials");
+      if (force->angle->born_matrix_enable == 0)
+        error->warning(FLERR,"compute stress/mop does not account for angle potentials");
     if (force->dihedral!=nullptr)
       error->warning(FLERR,"compute stress/mop does not account for dihedral potentials");
     if (force->improper!=nullptr)
@@ -239,8 +247,14 @@ void ComputeStressMop::compute_vector()
   // sum bond contribution over all procs
   MPI_Allreduce(bond_local,bond_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
 
+  //Compute angle contribution on separate procs
+  compute_angles();
+
+  // sum angle contribution over all procs
+  MPI_Allreduce(angle_local,angle_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
+   
   for (int m=0; m<nvalues; m++) {
-    vector[m] = values_global[m] + bond_global[m];
+    vector[m] = values_global[m] + bond_global[m] + angle_global[m];
   }
 
 }
@@ -550,3 +564,171 @@ void ComputeStressMop::compute_bonds()
     m += 3;
   }
 }
+
+/*------------------------------------------------------------------------
+  compute angle contribution to pressure of local proc
+  -------------------------------------------------------------------------*/
+
+void ComputeStressMop::compute_angles()
+{
+  int na, atom1, atom2, atom3, imol, iatom, atype;
+  tagint tagprev;
+  double r1, r2, cos_theta;
+
+  double **x = atom->x;
+  tagint *tag = atom->tag;
+  int *num_angle = atom->num_angle;
+  tagint **angle_atom1 = atom->angle_atom1;
+  tagint **angle_atom2 = atom->angle_atom2;
+  tagint **angle_atom3 = atom->angle_atom3;
+  int **angle_type = atom->angle_type;
+  int *mask = atom->mask;
+
+  int *molindex = atom->molindex;
+  int *molatom = atom->molatom;
+  Molecule **onemols = atom->avec->onemols;
+
+  int nlocal = atom->nlocal;
+  int molecular = atom->molecular;
+
+  // loop over all atoms and their angles
+
+  Angle *angle = force->angle;
+
+  double duang, du2ang;
+  double dx[3] {0};
+  double dx_left[3] {0};
+  double dx_right[3] {0};
+  double x_angle_left[3] {0};
+  double x_angle_middle[3] {0};
+  double x_angle_right[3] {0};
+  double dcos_theta[3] {0};
+  double local_contribution[3] {0};
+
+  // initialization
+  for (int i {0}; i < nvalues; i++) angle_local[i] = 0.0;
+
+  for (atom2 = 0; atom2 < nlocal; atom2++) {
+    if (!(mask[atom2] & groupbit)) continue;
+
+    if (molecular == 1)
+      na = num_angle[atom2];
+    else {
+      if (molindex[atom2] < 0) continue;
+      imol = molindex[atom2];
+      iatom = molatom[atom2];
+      na = onemols[imol]->num_angle[iatom];
+    }
+
+    for (int i = 0; i < na; i++) {
+      if (molecular == 1) {
+        if (tag[atom2] != angle_atom2[atom2][i]) continue;
+        atype = angle_type[atom2][i];
+        atom1 = atom->map(angle_atom1[atom2][i]);
+        atom3 = atom->map(angle_atom3[atom2][i]);
+      } else {
+        if (tag[atom2] != onemols[imol]->angle_atom2[atom2][i]) continue;
+        atype = onemols[imol]->angle_type[atom2][i];
+        tagprev = tag[atom2] - iatom - 1;
+        atom1 = atom->map(onemols[imol]->angle_atom1[atom2][i] + tagprev);
+        atom3 = atom->map(onemols[imol]->angle_atom3[atom2][i] + tagprev);
+      }
+
+      if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
+      if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
+      if (atype <= 0) continue;
+
+      // minimum image of atom1 with respect to the plane of interest
+      dx[0] = x[atom1][0];
+      dx[1] = x[atom1][1];
+      dx[2] = x[atom1][2];
+      dx[dir] -= pos;
+      domain->minimum_image(dx[0], dx[1], dx[2]);
+      x_angle_left[0] = dx[0];
+      x_angle_left[1] = dx[1];
+      x_angle_left[2] = dx[2];
+      x_angle_left[dir] += pos;
+      // minimum image of atom2 with respect to atom1
+      dx_left[0] = x[atom2][0] - x_angle_left[0];
+      dx_left[1] = x[atom2][1] - x_angle_left[1];
+      dx_left[2] = x[atom2][2] - x_angle_left[2];
+      domain->minimum_image(dx_left[0], dx_left[1], dx_left[2]);
+      x_angle_middle[0] = x_angle_left[0] + dx_left[0];
+      x_angle_middle[1] = x_angle_left[1] + dx_left[1];
+      x_angle_middle[2] = x_angle_left[2] + dx_left[2];
+
+      // minimum image of atom3 with respect to atom2
+      dx_right[0] = x[atom3][0] - x_angle_middle[0];
+      dx_right[1] = x[atom3][1] - x_angle_middle[1];
+      dx_right[2] = x[atom3][2] - x_angle_middle[2];
+      domain->minimum_image(dx_right[0], dx_right[1], dx_right[2]);
+      x_angle_right[0] = x_angle_middle[0] + dx_right[0];
+      x_angle_right[1] = x_angle_middle[1] + dx_right[1];
+      x_angle_right[2] = x_angle_middle[2] + dx_right[2];
+
+      // check if any bond vector crosses the plane of interest
+      double tau_right = (x_angle_right[dir] - pos) / (x_angle_right[dir] - x_angle_middle[dir]);
+      double tau_left = (x_angle_middle[dir] - pos) / (x_angle_middle[dir] - x_angle_left[dir]);
+      bool right_cross = ((tau_right >=0) && (tau_right  <= 1));
+      bool left_cross = ((tau_left >=0) && (tau_left <= 1));
+
+      // no bonds crossing the plane
+      if (!right_cross && !left_cross) continue;
+
+      // compute the cos(theta) of the angle
+      r1 = sqrt(dx_left[0]*dx_left[0] + dx_left[1]*dx_left[1] + dx_left[2]*dx_left[2]);
+      r2 = sqrt(dx_right[0]*dx_right[0] + dx_right[1]*dx_right[1] + dx_right[2]*dx_right[2]);
+      cos_theta = (dx_right[0]*dx_left[0] + dx_right[1]*dx_left[1] + dx_right[2]*dx_left[2])/(r1*r2);
+
+      if (cos_theta >  1.0) cos_theta = 1.0;
+      if (cos_theta < -1.0) cos_theta = -1.0;
+
+      // The method returns derivative with regards to cos(theta)
+      angle->born_matrix(atype, atom1, atom2, atom3, duang, du2ang);
+      // only right bond crossing the plane
+      if (right_cross && !left_cross)
+      {
+        dcos_theta[0] = (dx_right[0]*cos_theta/r2 - dx_left[0]/r1)/r2;
+        dcos_theta[1] = (dx_right[1]*cos_theta/r2 - dx_left[1]/r1)/r2;
+        dcos_theta[2] = (dx_right[1]*cos_theta/r2 - dx_left[2]/r1)/r2;
+      }
+
+      // only left bond crossing the plane
+      if (!right_cross && left_cross)
+      {
+        dcos_theta[0] = -(dx_left[0]*cos_theta/r1 - dx_right[0]/r2)/r1;
+        dcos_theta[1] = -(dx_left[1]*cos_theta/r1 - dx_right[1]/r2)/r1;
+        dcos_theta[2] = -(dx_left[2]*cos_theta/r1 - dx_right[2]/r2)/r1;
+      }
+
+      // both bonds crossing the plane
+      if (right_cross && left_cross)
+      {
+        // due to right bond
+        dcos_theta[0] = -(dx_right[0]*cos_theta/r2 - dx_left[0]/r1)/r2;
+        dcos_theta[1] = -(dx_right[1]*cos_theta/r2 - dx_left[1]/r1)/r2;
+        dcos_theta[2] = -(dx_right[1]*cos_theta/r2 - dx_left[2]/r1)/r2;
+
+        // due to left bond
+        dcos_theta[0] += (dx_left[0]*cos_theta/r1 - dx_right[0]/r2)/r1;
+        dcos_theta[1] += (dx_left[1]*cos_theta/r1 - dx_right[1]/r2)/r1;
+        dcos_theta[2] += (dx_left[2]*cos_theta/r1 - dx_right[2]/r2)/r1;
+      }
+
+      // final contribution of the given angle term
+      local_contribution[0] += duang*dcos_theta[0]/area*nktv2p;
+      local_contribution[1] += duang*dcos_theta[1]/area*nktv2p;
+      local_contribution[2] += duang*dcos_theta[2]/area*nktv2p;
+    }
+  }
+  // loop over the keywords and if necessary add the angle contribution
+  int m {0};
+  while (m<nvalues) {
+    if (which[m] == CONF || which[m] == TOTAL) {
+      angle_local[m] = local_contribution[0];
+      angle_local[m+1] = local_contribution[1];
+      angle_local[m+2] = local_contribution[2];
+    }
+    m += 3;
+  }
+}

From 25bff3e4ed2cd3a2da70d607dae801bec7dd6ec8 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Wed, 24 May 2023 16:24:33 +0300
Subject: [PATCH 090/396] fixing bug with sign for angle contribution in
 compute_stress_mop.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 139c5b5903..ff7c6d9e1b 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -705,14 +705,14 @@ void ComputeStressMop::compute_angles()
       if (right_cross && left_cross)
       {
         // due to right bond
-        dcos_theta[0] = -(dx_right[0]*cos_theta/r2 - dx_left[0]/r1)/r2;
-        dcos_theta[1] = -(dx_right[1]*cos_theta/r2 - dx_left[1]/r1)/r2;
-        dcos_theta[2] = -(dx_right[1]*cos_theta/r2 - dx_left[2]/r1)/r2;
+        dcos_theta[0] = (dx_right[0]*cos_theta/r2 - dx_left[0]/r1)/r2;
+        dcos_theta[1] = (dx_right[1]*cos_theta/r2 - dx_left[1]/r1)/r2;
+        dcos_theta[2] = (dx_right[1]*cos_theta/r2 - dx_left[2]/r1)/r2;
 
         // due to left bond
-        dcos_theta[0] += (dx_left[0]*cos_theta/r1 - dx_right[0]/r2)/r1;
-        dcos_theta[1] += (dx_left[1]*cos_theta/r1 - dx_right[1]/r2)/r1;
-        dcos_theta[2] += (dx_left[2]*cos_theta/r1 - dx_right[2]/r2)/r1;
+        dcos_theta[0] -= (dx_left[0]*cos_theta/r1 - dx_right[0]/r2)/r1;
+        dcos_theta[1] -= (dx_left[1]*cos_theta/r1 - dx_right[1]/r2)/r1;
+        dcos_theta[2] -= (dx_left[2]*cos_theta/r1 - dx_right[2]/r2)/r1;
       }
 
       // final contribution of the given angle term

From c7c8b065a259979e7fcd3b6ccc777d3068a68d52 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Wed, 24 May 2023 16:49:35 +0300
Subject: [PATCH 091/396] fixing bug with sign issue for bond contribution in
 compute_stress_mop.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index ff7c6d9e1b..2454f93b7a 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -546,9 +546,10 @@ void ComputeStressMop::compute_bonds()
         rsq = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
         bond->single(btype, rsq, atom1, atom2, fpair);
 
-        local_contribution[0] += fpair*dx[0]/area*nktv2p;
-        local_contribution[1] += fpair*dx[1]/area*nktv2p;
-        local_contribution[2] += fpair*dx[2]/area*nktv2p;
+        double sgn = copysign(1.0, x_bond_1[dir] - pos);
+        local_contribution[0] += sgn*fpair*dx[0]/area*nktv2p;
+        local_contribution[1] += sgn*fpair*dx[1]/area*nktv2p;
+        local_contribution[2] += sgn*fpair*dx[2]/area*nktv2p;
       }
     }
   }

From 9ee40cceef79043d8c6c8c41e41093e227f97ff6 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Wed, 24 May 2023 17:01:13 +0300
Subject: [PATCH 092/396] fixing indexing issue and more sign problems for
 angle contributions

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 27 +++++++++++++-----------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 2454f93b7a..63d671eee7 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -689,31 +689,34 @@ void ComputeStressMop::compute_angles()
       // only right bond crossing the plane
       if (right_cross && !left_cross)
       {
-        dcos_theta[0] = (dx_right[0]*cos_theta/r2 - dx_left[0]/r1)/r2;
-        dcos_theta[1] = (dx_right[1]*cos_theta/r2 - dx_left[1]/r1)/r2;
-        dcos_theta[2] = (dx_right[1]*cos_theta/r2 - dx_left[2]/r1)/r2;
+        double sgn = copysign(1.0, x_angle_right[dir] - pos);
+        dcos_theta[0] = sgn*(dx_right[0]*cos_theta/r2 - dx_left[0]/r1)/r2;
+        dcos_theta[1] = sgn*(dx_right[1]*cos_theta/r2 - dx_left[1]/r1)/r2;
+        dcos_theta[2] = sgn*(dx_right[2]*cos_theta/r2 - dx_left[2]/r1)/r2;
       }
 
       // only left bond crossing the plane
       if (!right_cross && left_cross)
       {
-        dcos_theta[0] = -(dx_left[0]*cos_theta/r1 - dx_right[0]/r2)/r1;
-        dcos_theta[1] = -(dx_left[1]*cos_theta/r1 - dx_right[1]/r2)/r1;
-        dcos_theta[2] = -(dx_left[2]*cos_theta/r1 - dx_right[2]/r2)/r1;
+        double sgn = copysign(1.0, x_angle_left[dir] - pos);
+        dcos_theta[0] = -sgn*(dx_left[0]*cos_theta/r1 - dx_right[0]/r2)/r1;
+        dcos_theta[1] = -sgn*(dx_left[1]*cos_theta/r1 - dx_right[1]/r2)/r1;
+        dcos_theta[2] = -sgn*(dx_left[2]*cos_theta/r1 - dx_right[2]/r2)/r1;
       }
 
       // both bonds crossing the plane
       if (right_cross && left_cross)
       {
         // due to right bond
-        dcos_theta[0] = (dx_right[0]*cos_theta/r2 - dx_left[0]/r1)/r2;
-        dcos_theta[1] = (dx_right[1]*cos_theta/r2 - dx_left[1]/r1)/r2;
-        dcos_theta[2] = (dx_right[1]*cos_theta/r2 - dx_left[2]/r1)/r2;
+        double sgn = copysign(1.0, x_angle_middle[dir] - pos);
+        dcos_theta[0] = -sgn*(dx_right[0]*cos_theta/r2 - dx_left[0]/r1)/r2;
+        dcos_theta[1] = -sgn*(dx_right[1]*cos_theta/r2 - dx_left[1]/r1)/r2;
+        dcos_theta[2] = -sgn*(dx_right[2]*cos_theta/r2 - dx_left[2]/r1)/r2;
 
         // due to left bond
-        dcos_theta[0] -= (dx_left[0]*cos_theta/r1 - dx_right[0]/r2)/r1;
-        dcos_theta[1] -= (dx_left[1]*cos_theta/r1 - dx_right[1]/r2)/r1;
-        dcos_theta[2] -= (dx_left[2]*cos_theta/r1 - dx_right[2]/r2)/r1;
+        dcos_theta[0] += sgn*(dx_left[0]*cos_theta/r1 - dx_right[0]/r2)/r1;
+        dcos_theta[1] += sgn*(dx_left[1]*cos_theta/r1 - dx_right[1]/r2)/r1;
+        dcos_theta[2] += sgn*(dx_left[2]*cos_theta/r1 - dx_right[2]/r2)/r1;
       }
 
       // final contribution of the given angle term

From ecca46acf9fd283e2c40e57a3135618c9108a9eb Mon Sep 17 00:00:00 2001
From: Lars Veldscholte <lars@tuxplace.nl>
Date: Tue, 9 May 2023 17:11:06 +0200
Subject: [PATCH 093/396] Include bond interactions in force

---
 .../compute_stress_cartesian.cpp              | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
index 53ff70c561..d2b9fe7bd7 100644
--- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
@@ -14,6 +14,7 @@
 #include "compute_stress_cartesian.h"
 
 #include "atom.h"
+#include "bond.h"
 #include "citeme.h"
 #include "comm.h"
 #include "domain.h"
@@ -365,6 +366,38 @@ void ComputeStressCartesian::compute_array()
     }
   }
 
+  // Loop over all bonds
+  for (int i_bond = 0; i_bond < neighbor->nbondlist; i_bond++) {
+    // i == atom1, j == atom2
+    int i = neighbor->bondlist[i_bond][0];
+    int j = neighbor->bondlist[i_bond][1];
+    int type  = neighbor->bondlist[i_bond][2];
+
+    // Skip if one of both atoms is not in group
+    if (!(atom->mask[i] & groupbit)) continue;
+    if (!(atom->mask[j] & groupbit)) continue;
+
+    // if newton_bond is off and atom2 is a ghost atom, only compute this on one processor
+    if (!force->newton_bond && j >= atom->nlocal) {
+      if (tag[i] > tag[j]) {
+        if ((tag[i] + tag[j]) % 2 == 0) continue;
+      } else if (tag[i] < tag[j]) {
+        if ((tag[i] < tag[j]) % 2 == 1) continue;
+      }
+    }
+
+    double dx = x[j][0] - x[i][0];
+    double dy = x[j][1] - x[i][1];
+    double dz = x[j][2] - x[i][2];
+    double rsq = dx*dx + dy*dy + dz*dz;
+    double xi = x[i][dir1] - boxlo[dir1];
+    double yi = x[i][dir2] - boxlo[dir2];
+
+    double fbond;
+    force->bond->single(type, rsq, i, j, fbond);
+    compute_pressure(fbond, xi, yi, dx, dy, dz);
+  }
+
   // normalize pressure
   for (bin = 0; bin < nbins1 * nbins2; bin++) {
     tdens[bin] *= invV;

From e246864682f00655749a3a251965f82a81dae3d3 Mon Sep 17 00:00:00 2001
From: Lars Veldscholte <lars@tuxplace.nl>
Date: Wed, 24 May 2023 16:17:20 +0200
Subject: [PATCH 094/396] Refactor compute_array() and compute_pressure():

Remove unnecessary copies of variables, declare variables locally so they are properly scoped
---
 .../compute_stress_cartesian.cpp              | 136 +++++++-----------
 1 file changed, 52 insertions(+), 84 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
index d2b9fe7bd7..2f6e75b528 100644
--- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
@@ -230,35 +230,16 @@ void ComputeStressCartesian::init_list(int /* id */, NeighList *ptr)
 
 void ComputeStressCartesian::compute_array()
 {
-  int i, j, ii, jj, inum, jnum, itype, jtype;
-  int bin, bin1, bin2;
-  tagint itag, jtag;
-  double xtmp, ytmp, ztmp, delx, dely, delz;
-  double rsq, fpair, factor_coul, factor_lj;
-  int *ilist, *jlist, *numneigh, **firstneigh;
-
   double **x = atom->x;
   double **v = atom->v;
-  double *mass = atom->mass;
   tagint *tag = atom->tag;
-  int *type = atom->type;
-  int *mask = atom->mask;
-  int nlocal = atom->nlocal;
-  double *special_coul = force->special_coul;
-  double *special_lj = force->special_lj;
-  int newton_pair = force->newton_pair;
   double *boxlo = domain->boxlo;
 
   // invoke half neighbor list (will copy or build if necessary)
   neighbor->build_one(list);
 
-  inum = list->inum;
-  ilist = list->ilist;
-  numneigh = list->numneigh;
-  firstneigh = list->firstneigh;
-
   // Zero arrays
-  for (bin = 0; bin < nbins1 * nbins2; bin++) {
+  for (int bin = 0; bin < nbins1 * nbins2; bin++) {
     tdens[bin] = 0;
     tpkxx[bin] = 0;
     tpkyy[bin] = 0;
@@ -269,9 +250,9 @@ void ComputeStressCartesian::compute_array()
   }
 
   // calculate number density and kinetic contribution to pressure
-  for (i = 0; i < nlocal; i++) {
-    bin1 = (int) ((x[i][dir1] - boxlo[dir1]) / bin_width1) % nbins1;
-    bin2 = 0;
+  for (int i = 0; i < atom->nlocal; i++) {
+    int bin1 = (int) ((x[i][dir1] - boxlo[dir1]) / bin_width1) % nbins1;
+    int bin2 = 0;
     if (dims == 2) bin2 = (int) ((x[i][dir2] - boxlo[dir2]) / bin_width2) % nbins2;
 
     // Apply periodic boundary conditions and avoid out of range access
@@ -295,73 +276,59 @@ void ComputeStressCartesian::compute_array()
     else if (bin2 >= nbins2)
       bin2 = nbins2 - 1;
 
-    j = bin1 + bin2 * nbins1;
+    int j = bin1 + bin2 * nbins1;
     tdens[j] += 1;
-    tpkxx[j] += mass[type[i]] * v[i][0] * v[i][0];
-    tpkyy[j] += mass[type[i]] * v[i][1] * v[i][1];
-    tpkzz[j] += mass[type[i]] * v[i][2] * v[i][2];
+    tpkxx[j] += atom->mass[atom->type[i]] * v[i][0] * v[i][0];
+    tpkyy[j] += atom->mass[atom->type[i]] * v[i][1] * v[i][1];
+    tpkzz[j] += atom->mass[atom->type[i]] * v[i][2] * v[i][2];
   }
 
   // loop over neighbors of my atoms
-  // skip if I or J are not in group
-  // for newton = 0 and J = ghost atom,
-  //   need to ensure I,J pair is only output by one proc
-  //   use same itag,jtag logic as in Neighbor::neigh_half_nsq()
-  // for flag = 0, just count pair interactions within force cutoff
-  // for flag = 1, calculate requested output fields
+  for (int ii = 0; ii < list->inum; ii++) {
+    int i = list->ilist[ii];
 
-  Pair *pair = force->pair;
-  double **cutsq = force->pair->cutsq;
+    // skip if I or J are not in group
+    if (!(atom->mask[i] & groupbit)) continue;
 
-  double xi1, xi2;
+    double xi1 = x[i][dir1] - boxlo[dir1];
+    double xi2 = x[i][dir2] - boxlo[dir2];
 
-  for (ii = 0; ii < inum; ii++) {
-    i = ilist[ii];
-    if (!(mask[i] & groupbit)) continue;
-
-    xtmp = x[i][0];
-    ytmp = x[i][1];
-    ztmp = x[i][2];
-    xi1 = x[i][dir1] - boxlo[dir1];
-    xi2 = x[i][dir2] - boxlo[dir2];
-    itag = tag[i];
-    itype = type[i];
-    jlist = firstneigh[i];
-    jnum = numneigh[i];
-
-    for (jj = 0; jj < jnum; jj++) {
-      j = jlist[jj];
-      factor_lj = special_lj[sbmask(j)];
-      factor_coul = special_coul[sbmask(j)];
+    for (int jj = 0; jj < list->numneigh[i]; jj++) {
+      int j = list->firstneigh[i][jj];
+      double factor_lj = force->special_lj[sbmask(j)];
+      double factor_coul = force->special_coul[sbmask(j)];
       j &= NEIGHMASK;
-      if (!(mask[j] & groupbit)) continue;
+      if (!(atom->mask[j] & groupbit)) continue;
 
-      // itag = jtag is possible for long cutoffs that include images of self
-      // do calculation only on appropriate processor
-      if (newton_pair == 0 && j >= nlocal) {
-        jtag = tag[j];
-        if (itag > jtag) {
-          if ((itag + jtag) % 2 == 0) continue;
-        } else if (itag < jtag) {
-          if ((itag + jtag) % 2 == 1) continue;
+      // for newton = 0 and J = ghost atom, need to ensure I,J pair is only output by one proc
+      // use same tag[i],tag[j] logic as in Neighbor::neigh_half_nsq()
+      if (force->newton_pair == 0 && j >= atom->nlocal) {
+        if (tag[i] > tag[j]) {
+          if ((tag[i] + tag[j]) % 2 == 0) continue;
+        } else if (tag[i] < tag[j]) {
+          if ((tag[i] + tag[j]) % 2 == 1) continue;
         } else {
-          if (x[j][2] < ztmp) continue;
-          if (x[j][2] == ztmp) {
-            if (x[j][1] < ytmp) continue;
-            if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+          // tag[i] = tag[j] is possible for long cutoffs that include images of self
+          if (x[j][2] < x[i][2]) continue;
+          if (x[j][2] == x[i][2]) {
+            if (x[j][1] < x[i][1]) continue;
+            if (x[j][1] == x[i][1] && x[j][0] < x[i][0]) continue;
           }
         }
       }
-      delx = x[j][0] - xtmp;
-      dely = x[j][1] - ytmp;
-      delz = x[j][2] - ztmp;
 
-      rsq = delx * delx + dely * dely + delz * delz;
-      jtype = type[j];
+      double delx = x[j][0] - x[i][0];
+      double dely = x[j][1] - x[i][1];
+      double delz = x[j][2] - x[i][2];
+      double rsq = delx * delx + dely * dely + delz * delz;
 
       // Check if inside cut-off
-      if (rsq >= cutsq[itype][jtype]) continue;
-      pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
+      int itype = atom->type[i];
+      int jtype = atom->type[j];
+      if (rsq >= force->pair->cutsq[itype][jtype]) continue;
+
+      double fpair;
+      force->pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
       compute_pressure(fpair, xi1, xi2, delx, dely, delz);
     }
   }
@@ -399,7 +366,7 @@ void ComputeStressCartesian::compute_array()
   }
 
   // normalize pressure
-  for (bin = 0; bin < nbins1 * nbins2; bin++) {
+  for (int bin = 0; bin < nbins1 * nbins2; bin++) {
     tdens[bin] *= invV;
     tpkxx[bin] *= invV;
     tpkyy[bin] *= invV;
@@ -419,7 +386,7 @@ void ComputeStressCartesian::compute_array()
   MPI_Allreduce(tpczz, pczz, nbins1 * nbins2, MPI_DOUBLE, MPI_SUM, world);
 
   // populate array to output.
-  for (bin = 0; bin < nbins1 * nbins2; bin++) {
+  for (int bin = 0; bin < nbins1 * nbins2; bin++) {
     array[bin][0] = (bin % nbins1 + 0.5) * bin_width1;
     if (dims == 2) array[bin][1] = ((int) (bin / nbins1) + 0.5) * bin_width2;
     array[bin][0 + dims] = dens[bin];
@@ -435,25 +402,26 @@ void ComputeStressCartesian::compute_array()
 void ComputeStressCartesian::compute_pressure(double fpair, double xi, double yi, double delx,
                                               double dely, double delz)
 {
-  int bin1, bin2, next_bin1, next_bin2;
   double la = 0.0, lb = 0.0, l_sum = 0.0;
   double rij[3] = {delx, dely, delz};
-  double l1 = 0.0, l2, rij1, rij2;
-  rij1 = rij[dir1];
-  rij2 = rij[dir2];
+  double rij1 = rij[dir1];
+  double rij2 = rij[dir2];
 
-  next_bin1 = (int) floor(xi / bin_width1);
-  next_bin2 = (int) floor(yi / bin_width2);
+  int next_bin1 = (int) floor(xi / bin_width1);
+  int next_bin2 = (int) floor(yi / bin_width2);
 
   // Integrating along line
   while (lb < 1.0) {
-    bin1 = next_bin1;
-    bin2 = next_bin2;
+    int bin1 = next_bin1;
+    int bin2 = next_bin2;
 
+    double l1;
     if (rij1 > 0)
       l1 = ((bin1 + 1) * bin_width1 - xi) / rij1;
     else
       l1 = (bin1 * bin_width1 - xi) / rij1;
+
+    double l2;
     if (rij2 > 0)
       l2 = ((bin2 + 1) * bin_width2 - yi) / rij2;
     else

From d66504be8159801f8efa1415344a5208d249ae41 Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Wed, 24 May 2023 11:39:05 -0600
Subject: [PATCH 095/396] Properly decorate energy/force compute

---
 examples/mliap/jax/in.run               |  2 +-
 examples/mliap/jax/mliap_unified_jax.py | 29 ++++++++++++++++++++-----
 2 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/examples/mliap/jax/in.run b/examples/mliap/jax/in.run
index 354dfd769f..0685d58f08 100644
--- a/examples/mliap/jax/in.run
+++ b/examples/mliap/jax/in.run
@@ -32,4 +32,4 @@ fix             1 all nve
 #dump 4 all custom 1 forces.xyz fx fy fz
 
 thermo          50
-run             250
\ No newline at end of file
+run             100
\ No newline at end of file
diff --git a/examples/mliap/jax/mliap_unified_jax.py b/examples/mliap/jax/mliap_unified_jax.py
index a2447d1cdb..b986b1247e 100644
--- a/examples/mliap/jax/mliap_unified_jax.py
+++ b/examples/mliap/jax/mliap_unified_jax.py
@@ -1,5 +1,9 @@
 from lammps.mliap.mliap_unified_abc import MLIAPUnified
 import numpy as np
+import jax
+import jax.numpy as jnp
+from jax import jit
+from functools import partial
 
 
 class MLIAPUnifiedJAX(MLIAPUnified):
@@ -13,6 +17,7 @@ class MLIAPUnifiedJAX(MLIAPUnified):
         # pair_coeff * * 1 1
         self.epsilon = epsilon
         self.sigma = sigma
+        self.npair_max = 250000
 
     def compute_gradients(self, data):
         """Test compute_gradients."""
@@ -22,12 +27,26 @@ class MLIAPUnifiedJAX(MLIAPUnified):
 
     def compute_forces(self, data):
         """Test compute_forces."""
-        eij, fij = self.compute_pair_ef(data)
-        data.update_pair_energy(eij)
-        data.update_pair_forces(fij)
+        rij  = data.rij
 
-    def compute_pair_ef(self, data):
-        rij = data.rij
+        # TODO: Take max npairs from the LAMMPS Cython side.
+        if (data.npairs > self.npair_max):
+            self.npair_max = data.npairs
+
+        npad = self.npair_max - data.npairs
+        # TODO: Take pre-padded rij from the LAMMPS Cython side.
+        #       This might account for ~2-3x slowdown compared to original LJ.
+        rij = np.pad(rij, ((0,npad), (0,0)), 'constant')
+
+        eij, fij = self.compute_pair_ef(rij)
+
+        data.update_pair_energy(np.array(np.double(eij)))
+        data.update_pair_forces(np.array(np.double(fij)))
+
+    #@jax.jit # <-- This will error! See https://github.com/google/jax/issues/1251
+    # @partial takes a function (e.g. jax.jit) as an arg.
+    @partial(jax.jit, static_argnums=(0,))
+    def compute_pair_ef(self, rij):
 
         r2inv = 1.0 / np.sum(rij ** 2, axis=1)
         r6inv = r2inv * r2inv * r2inv

From b2e5f93d490652d35dd67da8a1796b4912d7352a Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Wed, 24 May 2023 13:08:10 -0600
Subject: [PATCH 096/396] Use jax functions

---
 examples/mliap/jax/mliap_unified_jax.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/examples/mliap/jax/mliap_unified_jax.py b/examples/mliap/jax/mliap_unified_jax.py
index b986b1247e..4625fbf7f7 100644
--- a/examples/mliap/jax/mliap_unified_jax.py
+++ b/examples/mliap/jax/mliap_unified_jax.py
@@ -17,6 +17,7 @@ class MLIAPUnifiedJAX(MLIAPUnified):
         # pair_coeff * * 1 1
         self.epsilon = epsilon
         self.sigma = sigma
+        # TODO: Take this from the LAMMPS Cython side.
         self.npair_max = 250000
 
     def compute_gradients(self, data):
@@ -48,7 +49,7 @@ class MLIAPUnifiedJAX(MLIAPUnified):
     @partial(jax.jit, static_argnums=(0,))
     def compute_pair_ef(self, rij):
 
-        r2inv = 1.0 / np.sum(rij ** 2, axis=1)
+        r2inv = 1.0 / jnp.sum(rij ** 2, axis=1)
         r6inv = r2inv * r2inv * r2inv
 
         lj1 = 4.0 * self.epsilon * self.sigma**12
@@ -56,5 +57,5 @@ class MLIAPUnifiedJAX(MLIAPUnified):
 
         eij = r6inv * (lj1 * r6inv - lj2)
         fij = r6inv * (3.0 * lj2 - 6.0 * lj2 * r6inv) * r2inv
-        fij = fij[:, np.newaxis] * rij
-        return eij, fij
\ No newline at end of file
+        fij = fij[:, jnp.newaxis] * rij
+        return eij, fij

From 29ba0e3f184337ed74b342d00521ee6835c1fd68 Mon Sep 17 00:00:00 2001
From: Linux-cpp-lisp <1473644+Linux-cpp-lisp@users.noreply.github.com>
Date: Wed, 24 May 2023 18:15:56 -0700
Subject: [PATCH 097/396] Update MLIAP JAX example to use jax.grad

---
 examples/mliap/jax/mliap_unified_jax.py | 42 ++++++++++++++-----------
 1 file changed, 23 insertions(+), 19 deletions(-)

diff --git a/examples/mliap/jax/mliap_unified_jax.py b/examples/mliap/jax/mliap_unified_jax.py
index 4625fbf7f7..d4e75ee5c0 100644
--- a/examples/mliap/jax/mliap_unified_jax.py
+++ b/examples/mliap/jax/mliap_unified_jax.py
@@ -5,10 +5,30 @@ import jax.numpy as jnp
 from jax import jit
 from functools import partial
 
+#               /- ensure epsilon and sigma are treated as compile-time constants
+@partial(jit, static_argnums=(0, 1))
+def lj_potential(epsilon: float, sigma: float, rij):
+    # a pure function we can differentiate:
+    def _tot_e(rij):
+        r2inv = 1.0 / jnp.sum(rij ** 2, axis=1)
+        r6inv = r2inv * r2inv * r2inv
+
+        lj1 = 4.0 * epsilon * sigma**12
+        lj2 = 4.0 * epsilon * sigma**6
+
+        eij = r6inv * (lj1 * r6inv - lj2)
+        return jnp.sum(eij)
+    #                   /-  construct a function computing _tot_e and its derivative
+    tot_e, fij = jax.value_and_grad(_tot_e)(rij)
+    return tot_e, fij
+
 
 class MLIAPUnifiedJAX(MLIAPUnified):
     """Test implementation for MLIAPUnified."""
 
+    epsilon: float
+    sigma: float
+
     def __init__(self, element_types, epsilon=1.0, sigma=1.0, rcutfac=1.25):
         # ARGS: interface, element_types, ndescriptors, nparams, rcutfac
         super().__init__(None, element_types, 1, 3, rcutfac)
@@ -39,23 +59,7 @@ class MLIAPUnifiedJAX(MLIAPUnified):
         #       This might account for ~2-3x slowdown compared to original LJ.
         rij = np.pad(rij, ((0,npad), (0,0)), 'constant')
 
-        eij, fij = self.compute_pair_ef(rij)
+        e_tot, fij = lj_potential(rij)
 
-        data.update_pair_energy(np.array(np.double(eij)))
-        data.update_pair_forces(np.array(np.double(fij)))
-
-    #@jax.jit # <-- This will error! See https://github.com/google/jax/issues/1251
-    # @partial takes a function (e.g. jax.jit) as an arg.
-    @partial(jax.jit, static_argnums=(0,))
-    def compute_pair_ef(self, rij):
-
-        r2inv = 1.0 / jnp.sum(rij ** 2, axis=1)
-        r6inv = r2inv * r2inv * r2inv
-
-        lj1 = 4.0 * self.epsilon * self.sigma**12
-        lj2 = 4.0 * self.epsilon * self.sigma**6
-
-        eij = r6inv * (lj1 * r6inv - lj2)
-        fij = r6inv * (3.0 * lj2 - 6.0 * lj2 * r6inv) * r2inv
-        fij = fij[:, jnp.newaxis] * rij
-        return eij, fij
+        data.energy = e_tot.item()
+        data.update_pair_forces(np.array(fij, dtype=np.float64))

From 35a55068d7d1d2cd9448f36a4130fe4c88301989 Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Thu, 25 May 2023 01:35:08 -0600
Subject: [PATCH 098/396] Add input padded rij from LAMMPS Cython side

---
 examples/mliap/jax/mliap_unified_jax.py | 26 ++++++++-----------------
 src/ML-IAP/mliap_unified_couple.pyx     | 11 +++++++++++
 2 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/examples/mliap/jax/mliap_unified_jax.py b/examples/mliap/jax/mliap_unified_jax.py
index d4e75ee5c0..ee09392ee8 100644
--- a/examples/mliap/jax/mliap_unified_jax.py
+++ b/examples/mliap/jax/mliap_unified_jax.py
@@ -5,10 +5,9 @@ import jax.numpy as jnp
 from jax import jit
 from functools import partial
 
-#               /- ensure epsilon and sigma are treated as compile-time constants
-@partial(jit, static_argnums=(0, 1))
-def lj_potential(epsilon: float, sigma: float, rij):
-    # a pure function we can differentiate:
+@jax.jit
+def lj_potential(epsilon, sigma, rij):
+    # A pure function we can differentiate:
     def _tot_e(rij):
         r2inv = 1.0 / jnp.sum(rij ** 2, axis=1)
         r6inv = r2inv * r2inv * r2inv
@@ -17,8 +16,8 @@ def lj_potential(epsilon: float, sigma: float, rij):
         lj2 = 4.0 * epsilon * sigma**6
 
         eij = r6inv * (lj1 * r6inv - lj2)
-        return jnp.sum(eij)
-    #                   /-  construct a function computing _tot_e and its derivative
+        return 0.5 * jnp.sum(eij)
+    # Construct a function computing _tot_e and its derivative
     tot_e, fij = jax.value_and_grad(_tot_e)(rij)
     return tot_e, fij
 
@@ -37,8 +36,6 @@ class MLIAPUnifiedJAX(MLIAPUnified):
         # pair_coeff * * 1 1
         self.epsilon = epsilon
         self.sigma = sigma
-        # TODO: Take this from the LAMMPS Cython side.
-        self.npair_max = 250000
 
     def compute_gradients(self, data):
         """Test compute_gradients."""
@@ -48,18 +45,11 @@ class MLIAPUnifiedJAX(MLIAPUnified):
 
     def compute_forces(self, data):
         """Test compute_forces."""
-        rij  = data.rij
 
-        # TODO: Take max npairs from the LAMMPS Cython side.
-        if (data.npairs > self.npair_max):
-            self.npair_max = data.npairs
+        # NOTE: Use data.rij_max with JAX.
+        rij = data.rij_max
 
-        npad = self.npair_max - data.npairs
-        # TODO: Take pre-padded rij from the LAMMPS Cython side.
-        #       This might account for ~2-3x slowdown compared to original LJ.
-        rij = np.pad(rij, ((0,npad), (0,0)), 'constant')
-
-        e_tot, fij = lj_potential(rij)
+        e_tot, fij = lj_potential(self.epsilon, self.sigma, rij)
 
         data.energy = e_tot.item()
         data.update_pair_forces(np.array(fij, dtype=np.float64))
diff --git a/src/ML-IAP/mliap_unified_couple.pyx b/src/ML-IAP/mliap_unified_couple.pyx
index 3fde99a25e..25852a1c5f 100644
--- a/src/ML-IAP/mliap_unified_couple.pyx
+++ b/src/ML-IAP/mliap_unified_couple.pyx
@@ -281,6 +281,16 @@ cdef class MLIAPDataPy:
             return None
         return np.asarray(<double[:self.npairs, :3]> &self.data.rij[0][0])
 
+    @property
+    def rij_max(self):
+        if self.data.rij is NULL:
+            return None
+        return np.asarray(<double[:self.nneigh_max, :3]> &self.data.rij[0][0])
+
+    @property
+    def nneigh_max(self):
+        return self.data.nneigh_max
+
     @write_only_property
     def graddesc(self, value):
         if self.data.graddesc is NULL:
@@ -357,6 +367,7 @@ cdef public object mliap_unified_connect(char *fname, MLIAPDummyModel * model,
     unified_int.descriptor = descriptor
 
     unified.interface = unified_int
+    #print(unified_int)
 
     if unified.ndescriptors is None:
         raise ValueError("no descriptors set")

From 8e6615918b0c7414664e17cea86378921d132069 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Thu, 25 May 2023 14:39:03 +0300
Subject: [PATCH 099/396] avoid crashing when no bonds or no angles exist

---
 src/EXTRA-COMPUTE/compute_stress_mop.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.h b/src/EXTRA-COMPUTE/compute_stress_mop.h
index d1074e002a..791e18d624 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.h
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.h
@@ -44,6 +44,8 @@ class ComputeStressMop : public Compute {
   int me, nvalues, dir;
   int *which;
 
+  int bondflag, angleflag;
+
   double *values_local, *values_global;
   double *bond_local, *bond_global;
   double *angle_local, *angle_global;

From f26f397e087c183facd9e1cb108fe7f1b777a221 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Thu, 25 May 2023 14:47:20 +0300
Subject: [PATCH 100/396] avoid crashing when there are no bonds or no angles

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 27 ++++++++++++++++++------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 63d671eee7..e7a602e583 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -51,6 +51,9 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
 
   MPI_Comm_rank(world,&me);
 
+  bondflag = 0;
+  angleflag = 0;
+
   // set compute mode and direction of plane(s) for pressure calculation
 
   if (strcmp(arg[3],"x")==0) {
@@ -201,11 +204,13 @@ void ComputeStressMop::init()
     //Compute stress/mop only accounts for pair interactions.
     // issue a warning if any intramolecular potential or Kspace is defined.
 
-    //if (force->bond!=nullptr)
-    //  error->warning(FLERR,"compute stress/mop does not account for bond potentials");
+    if (force->bond!=nullptr) bondflag = 1;
     if (force->angle!=nullptr)
-      if (force->angle->born_matrix_enable == 0)
+      if (force->angle->born_matrix_enable == 0) {
         error->warning(FLERR,"compute stress/mop does not account for angle potentials");
+      } else {
+         angleflag = 1;
+      }
     if (force->dihedral!=nullptr)
       error->warning(FLERR,"compute stress/mop does not account for dihedral potentials");
     if (force->improper!=nullptr)
@@ -241,14 +246,22 @@ void ComputeStressMop::compute_vector()
   MPI_Allreduce(values_local,values_global,nvalues,
                 MPI_DOUBLE,MPI_SUM,world);
 
-  //Compute bond contribution on separate procs
-  compute_bonds();
+  if (bondflag) {
+    //Compute bond contribution on separate procs
+    compute_bonds();
+  } else {
+    for (int i=0; i<nvalues; i++) bond_local[i] = 0.0;
+  }
 
   // sum bond contribution over all procs
   MPI_Allreduce(bond_local,bond_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
 
-  //Compute angle contribution on separate procs
-  compute_angles();
+  if (angleflag) {
+    //Compute angle contribution on separate procs
+    compute_angles();
+  } else {
+    for (int i=0; i<nvalues; i++) angle_local[i] = 0.0;
+  }
 
   // sum angle contribution over all procs
   MPI_Allreduce(angle_local,angle_global,nvalues,MPI_DOUBLE,MPI_SUM,world);

From ceed30e7c63bd58ed698a2e6deff2052fbb573e3 Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Thu, 25 May 2023 12:58:57 -0600
Subject: [PATCH 101/396] Fixing mistakes in doc pages

---
 doc/src/compute_fabric.rst           | 12 ++++++------
 doc/src/pair_granular.rst            |  2 +-
 src/GRANULAR/gran_sub_mod_normal.cpp |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/doc/src/compute_fabric.rst b/doc/src/compute_fabric.rst
index f1a5d3d7f9..b38ffafa48 100644
--- a/doc/src/compute_fabric.rst
+++ b/doc/src/compute_fabric.rst
@@ -146,13 +146,13 @@ m to :math:`M` (inclusive).  A middle asterisk means all types from m to n
 Output info
 """""""""""
 
-This compute calculates a local vector of doubles and a scalar. The vector
-stores the unique components of the first requested tensor in the order
-:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`
-followed by the same components for all subsequent tensors.
+This compute calculates a global vector of doubles and a global scalar. The
+vector stores the unique components of the first requested tensor in the
+order :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
+:math:`yz` followed by the same components for all subsequent tensors.
 The length of the vector is therefore six times the number of requested
-tensors. The scalar output is the number of pairwise interactions included in
-the calculation of the fabric tensor.
+tensors. The scalar output is the number of pairwise interactions included
+in the calculation of the fabric tensor.
 
 Restrictions
 """"""""""""
diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst
index 0911a3486a..8a4d44fbf7 100644
--- a/doc/src/pair_granular.rst
+++ b/doc/src/pair_granular.rst
@@ -736,7 +736,7 @@ or
 
 .. math::
 
-   E_{eff,ij} = \frac{E_{ij}}{2(1-\nu_{ij})}
+   E_{eff,ij} = \frac{E_{ij}}{2(1-\nu_{ij}^2)}
 
 These pair styles write their information to :doc:`binary restart files <restart>`, so a pair_style command does not need to be
 specified in an input script that reads a restart file.
diff --git a/src/GRANULAR/gran_sub_mod_normal.cpp b/src/GRANULAR/gran_sub_mod_normal.cpp
index 05639feb9d..f08892d6f2 100644
--- a/src/GRANULAR/gran_sub_mod_normal.cpp
+++ b/src/GRANULAR/gran_sub_mod_normal.cpp
@@ -167,7 +167,7 @@ void GranSubModNormalHertzMaterial::coeffs_to_local()
 
 void GranSubModNormalHertzMaterial::mix_coeffs(double* icoeffs, double* jcoeffs)
 {
-  coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0],icoeffs[2], jcoeffs[2]);
+  coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0], icoeffs[2], jcoeffs[2]);
   coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
   coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
   coeffs_to_local();

From edfb8cf10021ec15509a3cb04e306496222eeff4 Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Thu, 25 May 2023 13:54:12 -0600
Subject: [PATCH 102/396] Fixing double mixing of normal coeffs

---
 src/GRANULAR/gran_sub_mod_normal.cpp | 50 ++++++++++++++++++++--------
 src/GRANULAR/gran_sub_mod_normal.h   |  4 +++
 2 files changed, 40 insertions(+), 14 deletions(-)

diff --git a/src/GRANULAR/gran_sub_mod_normal.cpp b/src/GRANULAR/gran_sub_mod_normal.cpp
index f08892d6f2..9e19cab1f4 100644
--- a/src/GRANULAR/gran_sub_mod_normal.cpp
+++ b/src/GRANULAR/gran_sub_mod_normal.cpp
@@ -145,6 +145,7 @@ GranSubModNormalHertzMaterial::GranSubModNormalHertzMaterial(GranularModel *gm,
   material_properties = 1;
   num_coeffs = 3;
   contact_radius_flag = 1;
+  mixed_coefficients = 0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -154,10 +155,12 @@ void GranSubModNormalHertzMaterial::coeffs_to_local()
   Emod = coeffs[0];
   damp = coeffs[1];
   poiss = coeffs[2];
-  if (gm->contact_type == PAIR) {
-    k = FOURTHIRDS * mix_stiffnessE(Emod, Emod, poiss, poiss);
-  } else {
-    k = FOURTHIRDS * mix_stiffnessE_wall(Emod, poiss);
+  if (!mixed_coefficients) {
+    if (gm->contact_type == PAIR) {
+      k = FOURTHIRDS * mix_stiffnessE(Emod, Emod, poiss, poiss);
+    } else {
+      k = FOURTHIRDS * mix_stiffnessE_wall(Emod, poiss);
+    }
   }
 
   if (Emod < 0.0 || damp < 0.0) error->all(FLERR, "Illegal Hertz material normal model");
@@ -170,6 +173,10 @@ void GranSubModNormalHertzMaterial::mix_coeffs(double* icoeffs, double* jcoeffs)
   coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0], icoeffs[2], jcoeffs[2]);
   coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
   coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
+
+  k = FOURTHIRDS * coeffs[0];
+  mixed_coefficients = 1;
+
   coeffs_to_local();
 }
 
@@ -183,6 +190,7 @@ GranSubModNormalDMT::GranSubModNormalDMT(GranularModel *gm, LAMMPS *lmp) : GranS
   cohesive_flag = 1;
   num_coeffs = 4;
   contact_radius_flag = 1;
+  mixed_coefficients = 0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -193,10 +201,13 @@ void GranSubModNormalDMT::coeffs_to_local()
   damp = coeffs[1];
   poiss = coeffs[2];
   cohesion = coeffs[3];
-  if (gm->contact_type == PAIR) {
-    k = FOURTHIRDS * mix_stiffnessE(Emod, Emod, poiss, poiss);
-  } else {
-    k = FOURTHIRDS * mix_stiffnessE_wall(Emod, poiss);
+
+  if (!mixed_coefficients) {
+    if (gm->contact_type == PAIR) {
+      k = FOURTHIRDS * mix_stiffnessE(Emod, Emod, poiss, poiss);
+    } else {
+      k = FOURTHIRDS * mix_stiffnessE_wall(Emod, poiss);
+    }
   }
 
   if (Emod < 0.0 || damp < 0.0) error->all(FLERR, "Illegal DMT normal model");
@@ -206,10 +217,14 @@ void GranSubModNormalDMT::coeffs_to_local()
 
 void GranSubModNormalDMT::mix_coeffs(double* icoeffs, double* jcoeffs)
 {
-  coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0],icoeffs[2], jcoeffs[2]);
+  coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0], icoeffs[2], jcoeffs[2]);
   coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
   coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
   coeffs[3] = mix_geom(icoeffs[3], jcoeffs[3]);
+
+  k = FOURTHIRDS * coeffs[0];
+  mixed_coefficients = 1;
+
   coeffs_to_local();
 }
 
@@ -241,6 +256,7 @@ GranSubModNormalJKR::GranSubModNormalJKR(GranularModel *gm, LAMMPS *lmp) : GranS
   beyond_contact = 1;
   num_coeffs = 4;
   contact_radius_flag = 1;
+  mixed_coefficients = 0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -252,10 +268,12 @@ void GranSubModNormalJKR::coeffs_to_local()
   poiss = coeffs[2];
   cohesion = coeffs[3];
 
-  if (gm->contact_type == PAIR) {
-    Emix = mix_stiffnessE(Emod, Emod, poiss, poiss);
-  } else {
-    Emix = mix_stiffnessE_wall(Emod, poiss);
+  if (!mixed_coefficients) {
+    if (gm->contact_type == PAIR) {
+      Emix = mix_stiffnessE(Emod, Emod, poiss, poiss);
+    } else {
+      Emix = mix_stiffnessE_wall(Emod, poiss);
+    }
   }
 
   k = FOURTHIRDS * Emix;
@@ -267,10 +285,14 @@ void GranSubModNormalJKR::coeffs_to_local()
 
 void GranSubModNormalJKR::mix_coeffs(double* icoeffs, double* jcoeffs)
 {
-  coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0],icoeffs[2], jcoeffs[2]);
+  coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0], icoeffs[2], jcoeffs[2]);
   coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
   coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
   coeffs[3] = mix_geom(icoeffs[3], jcoeffs[3]);
+
+  Emix = coeffs[0];
+  mixed_coefficients = 1;
+
   coeffs_to_local();
 }
 
diff --git a/src/GRANULAR/gran_sub_mod_normal.h b/src/GRANULAR/gran_sub_mod_normal.h
index ef022f864f..15e4c28701 100644
--- a/src/GRANULAR/gran_sub_mod_normal.h
+++ b/src/GRANULAR/gran_sub_mod_normal.h
@@ -99,6 +99,8 @@ class GranSubModNormalHertzMaterial : public GranSubModNormalHertz {
   GranSubModNormalHertzMaterial(class GranularModel *, class LAMMPS *);
   void coeffs_to_local() override;
   void mix_coeffs(double*, double*) override;
+ private:
+  int mixed_coefficients;
 };
 
 /* ---------------------------------------------------------------------- */
@@ -113,6 +115,7 @@ class GranSubModNormalDMT : public GranSubModNormal {
  protected:
   double k, cohesion;
   double F_pulloff, Fne;
+  int mixed_coefficients;
 };
 
 /* ---------------------------------------------------------------------- */
@@ -130,6 +133,7 @@ class GranSubModNormalJKR : public GranSubModNormal {
  protected:
   double k, cohesion;
   double Emix, F_pulloff, Fne;
+  int mixed_coefficients;
 };
 
 }    // namespace Granular_NS

From 1fd34ffac602723d8279cad1274bc15554e5a8dc Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Thu, 25 May 2023 14:49:38 -0600
Subject: [PATCH 103/396] Update

---
 examples/mliap/jax/in.run | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/mliap/jax/in.run b/examples/mliap/jax/in.run
index 0685d58f08..354dfd769f 100644
--- a/examples/mliap/jax/in.run
+++ b/examples/mliap/jax/in.run
@@ -32,4 +32,4 @@ fix             1 all nve
 #dump 4 all custom 1 forces.xyz fx fy fz
 
 thermo          50
-run             100
\ No newline at end of file
+run             250
\ No newline at end of file

From 3012426bd51261f04f5a87188dbb8fa80196ca16 Mon Sep 17 00:00:00 2001
From: Linux-cpp-lisp <1473644+Linux-cpp-lisp@users.noreply.github.com>
Date: Thu, 25 May 2023 17:49:02 -0400
Subject: [PATCH 104/396] send eij to LAMMPS

---
 examples/mliap/jax/mliap_unified_jax.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/examples/mliap/jax/mliap_unified_jax.py b/examples/mliap/jax/mliap_unified_jax.py
index ee09392ee8..96f9a067cc 100644
--- a/examples/mliap/jax/mliap_unified_jax.py
+++ b/examples/mliap/jax/mliap_unified_jax.py
@@ -15,11 +15,11 @@ def lj_potential(epsilon, sigma, rij):
         lj1 = 4.0 * epsilon * sigma**12
         lj2 = 4.0 * epsilon * sigma**6
 
-        eij = r6inv * (lj1 * r6inv - lj2)
-        return 0.5 * jnp.sum(eij)
+        eij = 0.5 * r6inv * (lj1 * r6inv - lj2)
+        return jnp.sum(eij), eij
     # Construct a function computing _tot_e and its derivative
-    tot_e, fij = jax.value_and_grad(_tot_e)(rij)
-    return tot_e, fij
+    (_, eij), fij = jax.value_and_grad(_tot_e, has_aux=True)(rij)
+    return eij, fij
 
 
 class MLIAPUnifiedJAX(MLIAPUnified):
@@ -49,7 +49,7 @@ class MLIAPUnifiedJAX(MLIAPUnified):
         # NOTE: Use data.rij_max with JAX.
         rij = data.rij_max
 
-        e_tot, fij = lj_potential(self.epsilon, self.sigma, rij)
+        eij, fij = lj_potential(self.epsilon, self.sigma, rij)
 
-        data.energy = e_tot.item()
+        data.update_pair_energy(np.array(eij, dtype=np.float64))
         data.update_pair_forces(np.array(fij, dtype=np.float64))

From 4174116014ef72d232511adaf4e9163d5fc94b58 Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Thu, 25 May 2023 16:02:45 -0600
Subject: [PATCH 105/396] Fix 1/2 factor in energy

---
 examples/mliap/jax/mliap_unified_jax.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/mliap/jax/mliap_unified_jax.py b/examples/mliap/jax/mliap_unified_jax.py
index 96f9a067cc..42134c19d2 100644
--- a/examples/mliap/jax/mliap_unified_jax.py
+++ b/examples/mliap/jax/mliap_unified_jax.py
@@ -15,8 +15,8 @@ def lj_potential(epsilon, sigma, rij):
         lj1 = 4.0 * epsilon * sigma**12
         lj2 = 4.0 * epsilon * sigma**6
 
-        eij = 0.5 * r6inv * (lj1 * r6inv - lj2)
-        return jnp.sum(eij), eij
+        eij = r6inv * (lj1 * r6inv - lj2)
+        return 0.5 * jnp.sum(eij), eij
     # Construct a function computing _tot_e and its derivative
     (_, eij), fij = jax.value_and_grad(_tot_e, has_aux=True)(rij)
     return eij, fij

From 3d8df660c350b256bb6759f7c5783a5cf8af77f1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 25 May 2023 18:08:42 -0400
Subject: [PATCH 106/396] make rigid water examples more realistic and
 consistent. avoid warnings.

---
 doc/src/Howto_spc.rst   |  6 ++----
 doc/src/Howto_tip3p.rst |  4 ++--
 doc/src/Howto_tip4p.rst | 13 +++++++------
 doc/src/Howto_tip5p.rst |  5 +++--
 4 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst
index 6414d3b846..6dedfe40c4 100644
--- a/doc/src/Howto_spc.rst
+++ b/doc/src/Howto_spc.rst
@@ -69,15 +69,13 @@ SPC/E with rigid bonds.
    timestep 1.0
    fix rigid     all shake 0.0001 10 10000 b 1 a 1
    minimize 0.0 0.0 1000 10000
-   run 0 post no
-   reset_timestep 0
    velocity all create 300.0 5463576
-   fix integrate all nvt temp 300.0 300.0 1.0
+   fix integrate all nvt temp 300.0 300.0 100.0
 
    thermo_style custom step temp press etotal density pe ke
    thermo 1000
    run 20000 upto
-   write_data tip4p.data nocoeff
+   write_data spce.data nocoeff
 
 .. _spce_molecule:
 .. code-block::
diff --git a/doc/src/Howto_tip3p.rst b/doc/src/Howto_tip3p.rst
index 682c7f2640..5419b9ba1b 100644
--- a/doc/src/Howto_tip3p.rst
+++ b/doc/src/Howto_tip3p.rst
@@ -128,11 +128,11 @@ TIP3P with rigid bonds.
 
     fix rigid all shake 0.001 10 10000 b 1 a 1
     minimize 0.0 0.0 1000 10000
-    run 0 post no
 
     reset_timestep 0
+    timestep 1.0
     velocity all create 300.0 5463576
-    fix integrate all nvt temp 300 300 1.0
+    fix integrate all nvt temp 300 300 100.0
 
     thermo_style custom step temp press etotal pe
 
diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst
index 7775d43e76..4d9b514e0d 100644
--- a/doc/src/Howto_tip4p.rst
+++ b/doc/src/Howto_tip4p.rst
@@ -180,17 +180,17 @@ file changed):
 
     fix rigid all shake 0.001 10 10000 b 1 a 1
     minimize 0.0 0.0 1000 10000
-    run 0 post no
 
     reset_timestep 0
+    timestep 1.0
     velocity all create 300.0 5463576
-    fix integrate all nvt temp 300 300 1.0
+    fix integrate all nvt temp 300 300 100.0
 
     thermo_style custom step temp press etotal pe
 
     thermo 1000
     run 20000
-    write_data tip3p.data nocoeff
+    write_data tip4p-implicit.data nocoeff
 
 Below is the code for a LAMMPS input file using the explicit method and
 a TIP4P molecule file.  Because of using :doc:`fix rigid/nvt/small
@@ -203,6 +203,7 @@ rigid/nvt/small can identify rigid bodies by their molecule ID:
 
     units real
     atom_style charge
+    atom_modify map array
     region box block -5 5 -5 5 -5 5
     create_box 3 box
 
@@ -219,14 +220,14 @@ rigid/nvt/small can identify rigid bodies by their molecule ID:
     molecule water tip4p.mol
     create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
 
-    timestep 0.1
-    fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
+    timestep 0.5
+    fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
     velocity all create 300.0 5463576
 
     thermo_style custom step temp press etotal density pe ke
     thermo 1000
     run 20000
-    write_data tip4p.data nocoeff
+    write_data tip4p-explicit.data nocoeff
 
 .. _tip4p_molecule:
 .. code-block::
diff --git a/doc/src/Howto_tip5p.rst b/doc/src/Howto_tip5p.rst
index 21cc78a684..10674a04b6 100644
--- a/doc/src/Howto_tip5p.rst
+++ b/doc/src/Howto_tip5p.rst
@@ -91,6 +91,7 @@ ID:
 
     units real
     atom_style charge
+    atom_modify map array
     region box block -5 5 -5 5 -5 5
     create_box 3 box
 
@@ -107,8 +108,8 @@ ID:
     molecule water tip5p.mol
     create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
 
-    timestep 0.20
-    fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
+    timestep 0.5
+    fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
     reset_timestep 0
     velocity all create 300.0 5463576
 

From ff7bae17394d8ed47fb533e983d406ff28384d59 Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Thu, 25 May 2023 18:43:18 -0600
Subject: [PATCH 107/396] Add Kokkos getters

---
 src/KOKKOS/mliap_unified_couple_kokkos.pyx | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/KOKKOS/mliap_unified_couple_kokkos.pyx b/src/KOKKOS/mliap_unified_couple_kokkos.pyx
index 5e274d7f36..bd94b79eb4 100644
--- a/src/KOKKOS/mliap_unified_couple_kokkos.pyx
+++ b/src/KOKKOS/mliap_unified_couple_kokkos.pyx
@@ -346,6 +346,16 @@ cdef class MLIAPDataPy:
             return None
         return create_array(self.data.dev, self.data.rij, [self.npairs,3],False)
 
+    @property
+    def rij_max(self):
+        if self.data.rij is NULL:
+            return None
+        return create_array(self.data.dev, self.data.rij, [self.nneigh_max,3], False)
+
+    @property
+    def nneigh_max(self):
+        return self.data.nneigh_max
+
     @write_only_property
     def graddesc(self, value):
         if self.data.graddesc is NULL:

From b7146c900ffd09adfc7513691674a46de82cf83f Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Thu, 25 May 2023 18:58:56 -0600
Subject: [PATCH 108/396] Add instructions

---
 examples/mliap/jax/README.md | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/examples/mliap/jax/README.md b/examples/mliap/jax/README.md
index 320d87e465..c56c9e6d93 100644
--- a/examples/mliap/jax/README.md
+++ b/examples/mliap/jax/README.md
@@ -27,6 +27,33 @@ Install LAMMPS:
     make -j4
     make install-python
 
+### Kokkos install
+
+Make sure you install cupy properly!
+
+    python -m pip cupy
+
+Install LAMMPS. Take care to change `Kokkos_ARCH_*` flag:
+
+    cmake ../cmake -DLAMMPS_EXCEPTIONS=yes \
+                  -DBUILD_SHARED_LIBS=yes \
+                  -DPKG_PYTHON=yes \
+                  -DPKG_ML-SNAP=yes \
+                  -DPKG_ML-IAP=yes \
+                  -DMLIAP_ENABLE_PYTHON=yes \
+                  -DPKG_KOKKOS=yes \
+                  -DKokkos_ARCH_TURING75=yes \
+                  -DKokkos_ENABLE_CUDA=yes \
+                  -DKokkos_ENABLE_OPENMP=yes \
+                  -DCMAKE_CXX_COMPILER=${HOME}/lammps/lib/kokkos/bin/nvcc_wrapper \
+                  -DPYTHON_EXECUTABLE:FILEPATH=`which python`
+    make -j
+    make install-python
+
+Run example:
+
+    mpirun -np 1 lmp -k on g 1 -sf kk -pk kokkos newton on -in in.run
+
 ### Wrapping JAX code
 
 Take inspiration from the `FitSNAP` ML-IAP wrapper: https://github.com/rohskopf/FitSNAP/blob/mliap-unified/fitsnap3lib/tools/write_unified.py

From 6eb586e66fb9811d89083d072a0325aba2416e15 Mon Sep 17 00:00:00 2001
From: Linux-cpp-lisp <1473644+Linux-cpp-lisp@users.noreply.github.com>
Date: Thu, 25 May 2023 21:03:32 -0400
Subject: [PATCH 109/396] update_atom_energy initial

---
 src/KOKKOS/mliap_unified_kokkos.cpp | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/src/KOKKOS/mliap_unified_kokkos.cpp b/src/KOKKOS/mliap_unified_kokkos.cpp
index 1fdf039473..deb9cbc346 100644
--- a/src/KOKKOS/mliap_unified_kokkos.cpp
+++ b/src/KOKKOS/mliap_unified_kokkos.cpp
@@ -371,6 +371,25 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij)
   }
 }
 
+/* ----------------------------------------------------------------------
+   set energy for i indexed atoms
+   ---------------------------------------------------------------------- */
+
+void LAMMPS_NS::update_atom_energy(MLIAPDataKokkosDevice *data, double *ei)
+{
+  auto d_eatoms = data->eatoms;
+  const auto nlistatoms = data->nlistatoms;
+
+  Kokkos::parallel_reduce(nlistatoms, KOKKOS_LAMBDA(int i, double &local_sum){
+    double e = ei[i];
+    // must not count any contribution where i is not a local atom
+    if (i < nlistatoms) {
+      d_eatoms[i] = e;
+      local_sum += e;
+    }
+  },*data->energy);
+}
+
 namespace LAMMPS_NS {
 template class MLIAPDummyModelKokkos<LMPDeviceType>;
 template class MLIAPDummyDescriptorKokkos<LMPDeviceType>;

From 49b2c299a7ba44e95d958e1ed94005041373b811 Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Fri, 26 May 2023 10:48:58 -0600
Subject: [PATCH 110/396] Add Kokkos example

---
 examples/mliap/jax/README.md                  | 20 ++++--
 examples/mliap/jax/in.run                     |  6 +-
 .../mliap/jax/mliap_unified_jax_kokkos.py     | 62 +++++++++++++++++++
 3 files changed, 81 insertions(+), 7 deletions(-)
 create mode 100644 examples/mliap/jax/mliap_unified_jax_kokkos.py

diff --git a/examples/mliap/jax/README.md b/examples/mliap/jax/README.md
index c56c9e6d93..3a5fe0105c 100644
--- a/examples/mliap/jax/README.md
+++ b/examples/mliap/jax/README.md
@@ -54,11 +54,9 @@ Run example:
 
     mpirun -np 1 lmp -k on g 1 -sf kk -pk kokkos newton on -in in.run
 
-### Wrapping JAX code
+### Deploying JAX models on CPU
 
-Take inspiration from the `FitSNAP` ML-IAP wrapper: https://github.com/rohskopf/FitSNAP/blob/mliap-unified/fitsnap3lib/tools/write_unified.py
-
-First define JAX model in `deploy_script.py`, which will wrap model with `write_unified`.
+Use `deploy_script.py`, which will wrap model with `write_unified_jax`.
 
     python deploy_script.py
 
@@ -66,4 +64,16 @@ This creates `.pkl` file to be loaded by LAMMPS ML-IAP Unified.
 
 Run LAMMPS with the model:
 
-    mpirun -np P lmp -in in.run
\ No newline at end of file
+    mpirun -np P lmp -in in.run
+
+### Deploying JAX models in Kokkos
+
+Use `deploy_script_kokkos.py`, which will wrap model with `write_unified_jax_kokkos`.
+
+    python deploy_script_kokkos.py
+
+This creates `.pkl` file to be loaded by LAMMPS ML-IAP Unified.
+
+Run LAMMPS with the model:
+
+    mpirun -np 1 lmp -k on g 1 -sf kk -pk kokkos newton on -in in.run
\ No newline at end of file
diff --git a/examples/mliap/jax/in.run b/examples/mliap/jax/in.run
index 354dfd769f..d0560e6620 100644
--- a/examples/mliap/jax/in.run
+++ b/examples/mliap/jax/in.run
@@ -31,5 +31,7 @@ fix             1 all nve
 
 #dump 4 all custom 1 forces.xyz fx fy fz
 
-thermo          50
-run             250
\ No newline at end of file
+dump 1 all xyz 10 dump.xyz
+
+thermo          1
+run             250
diff --git a/examples/mliap/jax/mliap_unified_jax_kokkos.py b/examples/mliap/jax/mliap_unified_jax_kokkos.py
new file mode 100644
index 0000000000..5006936884
--- /dev/null
+++ b/examples/mliap/jax/mliap_unified_jax_kokkos.py
@@ -0,0 +1,62 @@
+from lammps.mliap.mliap_unified_abc import MLIAPUnified
+import numpy as np
+import jax
+import jax.dlpack
+import jax.numpy as jnp
+from jax import jit
+from functools import partial
+import cupy
+
+@jax.jit
+def lj_potential(epsilon, sigma, rij):
+    # A pure function we can differentiate:
+    def _tot_e(rij):
+        r2inv = 1.0 / jnp.sum(rij ** 2, axis=1)
+        r6inv = r2inv * r2inv * r2inv
+
+        lj1 = 4.0 * epsilon * sigma**12
+        lj2 = 4.0 * epsilon * sigma**6
+
+        eij = r6inv * (lj1 * r6inv - lj2)
+        return 0.5 * jnp.sum(eij), eij
+    # Construct a function computing _tot_e and its derivative
+    (_, eij), fij = jax.value_and_grad(_tot_e, has_aux=True)(rij)
+    return eij, fij
+
+
+class MLIAPUnifiedJAXKokkos(MLIAPUnified):
+    """JAX wrapper for MLIAPUnified."""
+
+    epsilon: float
+    sigma: float
+
+    def __init__(self, element_types, epsilon=1.0, sigma=1.0, rcutfac=1.25):
+        # ARGS: interface, element_types, ndescriptors, nparams, rcutfac
+        super().__init__(None, element_types, 1, 3, rcutfac)
+        # Mimicking the LJ pair-style:
+        # pair_style lj/cut 2.5
+        # pair_coeff * * 1 1
+        self.epsilon = epsilon
+        self.sigma = sigma
+
+    def compute_gradients(self, data):
+        """Test compute_gradients."""
+
+    def compute_descriptors(self, data):
+        """Test compute_descriptors."""
+
+    def compute_forces(self, data):
+        """Test compute_forces."""
+
+        # NOTE: Use data.rij_max with JAX.
+        #       dlpack requires cudnn:
+        rij = jax.dlpack.from_dlpack(data.rij_max.toDlpack())
+        eij, fij = lj_potential(self.epsilon, self.sigma, rij)
+
+        # Convert back to cupy.
+        eij = cupy.from_dlpack(jax.dlpack.to_dlpack(eij)).astype(np.float64)
+        fij = cupy.from_dlpack(jax.dlpack.to_dlpack(fij)).astype(np.float64)
+
+        # Send to LAMMPS.
+        data.update_pair_energy(eij)
+        data.update_pair_forces(fij)

From 87850f31cafb5c991a4a2520ac2c581f37586b97 Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Fri, 26 May 2023 11:18:37 -0600
Subject: [PATCH 111/396] Add Kokkos instructions

---
 examples/mliap/jax/README.md | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/examples/mliap/jax/README.md b/examples/mliap/jax/README.md
index 3a5fe0105c..ccaa234034 100644
--- a/examples/mliap/jax/README.md
+++ b/examples/mliap/jax/README.md
@@ -29,9 +29,17 @@ Install LAMMPS:
 
 ### Kokkos install
 
-Make sure you install cupy properly!
+Use same Python dependencies as above, with some extra changes:
 
-    python -m pip cupy
+1. Make sure you install cupy properly! E.g. 
+
+    python -m pip install cupy-cuda12x
+
+2. Install JAX for GPU/CUDA:
+
+    python -m pip install --trusted-host storage.googleapis.com --upgrade "jax[cuda12_local]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+
+3. Install cudNN: https://developer.nvidia.com/cudnn
 
 Install LAMMPS. Take care to change `Kokkos_ARCH_*` flag:
 

From 2e68930f2a1873826055223db7a6173be0e73b1f Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Fri, 26 May 2023 11:21:13 -0600
Subject: [PATCH 112/396] Format readme

---
 examples/mliap/jax/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/mliap/jax/README.md b/examples/mliap/jax/README.md
index ccaa234034..5cc0c49f16 100644
--- a/examples/mliap/jax/README.md
+++ b/examples/mliap/jax/README.md
@@ -33,11 +33,11 @@ Use same Python dependencies as above, with some extra changes:
 
 1. Make sure you install cupy properly! E.g. 
 
-    python -m pip install cupy-cuda12x
+        python -m pip install cupy-cuda12x
 
 2. Install JAX for GPU/CUDA:
 
-    python -m pip install --trusted-host storage.googleapis.com --upgrade "jax[cuda12_local]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+        python -m pip install --trusted-host storage.googleapis.com --upgrade "jax[cuda12_local]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
 
 3. Install cudNN: https://developer.nvidia.com/cudnn
 

From b5a1c6d47f54ddb6bd2d646a8e51fe4a933fcc2c Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Fri, 26 May 2023 11:25:29 -0600
Subject: [PATCH 113/396] Declare update per atom function

---
 src/KOKKOS/mliap_unified_kokkos.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/KOKKOS/mliap_unified_kokkos.h b/src/KOKKOS/mliap_unified_kokkos.h
index aad25891b0..1af7715dad 100644
--- a/src/KOKKOS/mliap_unified_kokkos.h
+++ b/src/KOKKOS/mliap_unified_kokkos.h
@@ -60,6 +60,7 @@ template <class DeviceType>
 MLIAPBuildUnifiedKokkos_t<DeviceType> build_unified(char *, MLIAPDataKokkos<DeviceType> *, LAMMPS *, char * = NULL);
 void update_pair_energy(MLIAPDataKokkosDevice *, double *);
 void update_pair_forces(MLIAPDataKokkosDevice *, double *);
+void update_atom_energy(MLIAPDataKokkosDevice *, double *);
 
 }    // namespace LAMMPS_NS
 

From 16751b06b3c5c8949e164e709816f410d8d2b798 Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Fri, 26 May 2023 12:52:51 -0600
Subject: [PATCH 114/396] Add os env vars to allow more MPI procs

---
 examples/mliap/jax/mliap_unified_jax.py        | 10 ++++++++--
 examples/mliap/jax/mliap_unified_jax_kokkos.py |  7 +++++++
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/examples/mliap/jax/mliap_unified_jax.py b/examples/mliap/jax/mliap_unified_jax.py
index 42134c19d2..69cbee6221 100644
--- a/examples/mliap/jax/mliap_unified_jax.py
+++ b/examples/mliap/jax/mliap_unified_jax.py
@@ -4,11 +4,17 @@ import jax
 import jax.numpy as jnp
 from jax import jit
 from functools import partial
+import os
+
+# Required else get `jaxlib.xla_extension.XlaRuntimeError: RESOURCE_EXHAUSTED: Out of memory`
+os.environ["XLA_PYTHON_CLIENT_PREALLOCATE"]="false"
+os.environ["XLA_PYTHON_CLIENT_MEM_FRACTION"]=".XX"
+os.environ["XLA_PYTHON_CLIENT_ALLOCATOR"]="platform"
 
 @jax.jit
 def lj_potential(epsilon, sigma, rij):
-    # A pure function we can differentiate:
     def _tot_e(rij):
+        """A differentiable fn for total energy."""
         r2inv = 1.0 / jnp.sum(rij ** 2, axis=1)
         r6inv = r2inv * r2inv * r2inv
 
@@ -17,7 +23,7 @@ def lj_potential(epsilon, sigma, rij):
 
         eij = r6inv * (lj1 * r6inv - lj2)
         return 0.5 * jnp.sum(eij), eij
-    # Construct a function computing _tot_e and its derivative
+    # Compute _tot_e and its derivative.
     (_, eij), fij = jax.value_and_grad(_tot_e, has_aux=True)(rij)
     return eij, fij
 
diff --git a/examples/mliap/jax/mliap_unified_jax_kokkos.py b/examples/mliap/jax/mliap_unified_jax_kokkos.py
index 5006936884..fd7f106f47 100644
--- a/examples/mliap/jax/mliap_unified_jax_kokkos.py
+++ b/examples/mliap/jax/mliap_unified_jax_kokkos.py
@@ -6,6 +6,13 @@ import jax.numpy as jnp
 from jax import jit
 from functools import partial
 import cupy
+import os
+
+# Required else get `jaxlib.xla_extension.XlaRuntimeError: RESOURCE_EXHAUSTED: Out of memory`
+# Does not fix GPU problem with larger num. atoms.
+#os.environ["XLA_PYTHON_CLIENT_PREALLOCATE"]="false"
+#os.environ["XLA_PYTHON_CLIENT_MEM_FRACTION"]=".XX"
+#os.environ["XLA_PYTHON_CLIENT_ALLOCATOR"]="platform"
 
 @jax.jit
 def lj_potential(epsilon, sigma, rij):

From 01b481ec4f708ebeef3e856dcb3b9ab8ab53d289 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 26 May 2023 15:27:15 -0700
Subject: [PATCH 115/396] Small tweaks

---
 doc/src/fix_efield.rst        | 10 +++++-----
 doc/src/fix_qeq_reaxff.rst    |  3 +--
 src/REAXFF/fix_qeq_reaxff.cpp |  3 +--
 3 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst
index 271912097f..0b94f80b8c 100644
--- a/doc/src/fix_efield.rst
+++ b/doc/src/fix_efield.rst
@@ -136,10 +136,10 @@ due to the electric field were a spring-like F = kx, then the energy
 formula should be E = -0.5kx\^2.  If you don't do this correctly, the
 minimization will not converge properly.
 
-The *potential* keyword can be used as an alternative to the *energy*
-keyword to specify the name of an atom-style variable, which is used to compute
-the added electric potential to each atom as a function of its position.
-The variable should have units of electric field times distance (that is,
+The *potential* keyword can be used as an alternative to the *energy* keyword
+to specify the name of an atom-style variable, which is used to compute the
+added electric potential to each atom as a function of its position.  The
+variable should have units of electric field multiplied by distance (that is,
 in `units real`, the potential should be in volts). As with the *energy*
 keyword, the variable name is specified as "v_name". The energy added by this
 fix is then calculated as the electric potential multiplied by charge.
@@ -149,7 +149,7 @@ in simulations with :doc:`fix qeq/reaxff<fix_qeq_reaxff>`, since with variable
 charges the electric potential can be known beforehand but the energy cannot.
 A small additional benefit is that the *energy* keyword requires an additional
 conversion to energy units which the *potential* keyword avoids. Thus, when the
-*potential* keyword is specified the *energy* keyword is ignored (the simulation
+*potential* keyword is specified, the *energy* keyword is ignored (the simulation
 will proceed but with a warning issued). As with *energy*, the *potential*
 keyword is not allowed if the added field is a constant vector.
 
diff --git a/doc/src/fix_qeq_reaxff.rst b/doc/src/fix_qeq_reaxff.rst
index 4422ddc89c..00cfb6d3ce 100644
--- a/doc/src/fix_qeq_reaxff.rst
+++ b/doc/src/fix_qeq_reaxff.rst
@@ -133,8 +133,7 @@ vector may only have components in non-periodic directions. Equal-style
 variables can be used for electric field vector components without any further
 settings. Atom-style variables can be used for spatially-varying electric field
 vector components, but the resulting electric potential must be specified
-as an atom-style variable using the (new) *potential* keyword for 
-`fix efield`.
+as an atom-style variable using the *potential* keyword for `fix efield`.
 
 Related commands
 """"""""""""""""
diff --git a/src/REAXFF/fix_qeq_reaxff.cpp b/src/REAXFF/fix_qeq_reaxff.cpp
index 4c0864ac27..554b911151 100644
--- a/src/REAXFF/fix_qeq_reaxff.cpp
+++ b/src/REAXFF/fix_qeq_reaxff.cpp
@@ -1111,9 +1111,8 @@ void FixQEqReaxFF::get_chi_field()
   const double factor = -1.0/qe2f;
 
 
-  if (efield->varflag != FixEfield::CONSTANT) {
+  if (efield->varflag != FixEfield::CONSTANT)
     efield->update_efield_variables();
-  }
 
   // atom selection is for the group of fix efield
 

From 458cce76999318fa4dd990aa57f5506d782d6b40 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sat, 27 May 2023 14:33:46 +0300
Subject: [PATCH 116/396] Updating unit test for mop to reflect the
 contribution from bonds

---
 unittest/commands/test_compute_global.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/unittest/commands/test_compute_global.cpp b/unittest/commands/test_compute_global.cpp
index 6c365c8c2b..66a24f049f 100644
--- a/unittest/commands/test_compute_global.cpp
+++ b/unittest/commands/test_compute_global.cpp
@@ -225,9 +225,9 @@ TEST_F(ComputeGlobalTest, Geometry)
         EXPECT_DOUBLE_EQ(mom2[0], -0.022332069630161717);
         EXPECT_DOUBLE_EQ(mom2[1], -0.056896553865696115);
         EXPECT_DOUBLE_EQ(mom2[2], 0.069179891052881484);
-        EXPECT_DOUBLE_EQ(mop1[0], 3522311.3572200728);
-        EXPECT_DOUBLE_EQ(mop1[1], 2871104.9055934539);
-        EXPECT_DOUBLE_EQ(mop1[2], -4136077.5224247416);
+        EXPECT_DOUBLE_EQ(mop1[0], 3536584.0880458541);
+        EXPECT_DOUBLE_EQ(mop1[1], 2887485.033995091);
+        EXPECT_DOUBLE_EQ(mop1[2], -4154145.8952306858);
         EXPECT_DOUBLE_EQ(mop2[0][0], -8.0869239999999998);
         EXPECT_DOUBLE_EQ(mop2[0][1], 0.0);
         EXPECT_DOUBLE_EQ(mop2[0][2], 0.0);

From b28ee36f000af8e90a70390b72f6d132312de43c Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sat, 27 May 2023 14:50:31 +0300
Subject: [PATCH 117/396] update documentation for compute stress/mop

---
 doc/src/compute_stress_mop.rst | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst
index 4ad2261bb0..a8a3bc5660 100644
--- a/doc/src/compute_stress_mop.rst
+++ b/doc/src/compute_stress_mop.rst
@@ -117,8 +117,13 @@ size does not change in time, and axis-aligned planes.
 
 The method only works with two-body pair interactions, because it
 requires the class method pair->single() to be implemented. In
-particular, it does not work with more than two-body pair interactions,
-intra-molecular interactions, and long range (kspace) interactions.
+particular, compute *stress/mop/profile* does not work with more than 
+two-body pair interactions, intra-molecular interactions, and long range 
+(kspace) interactions. Similarly, compute *stress/mop* does not work with more than 
+two-body pair interactions, long range (kspace) interactions and dihedral/improper
+intramolecular interactions but works with all bond interactions with the class method
+single() implemented and all angle interactions with the class method born_matrix() 
+implemented.
 
 Related commands
 """"""""""""""""

From 4c4eb6ee1e00fcb0b7efefa8a6e47459e7dc5c33 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 28 May 2023 00:49:52 -0400
Subject: [PATCH 118/396] improve error message

---
 src/EXTRA-FIX/fix_electron_stopping.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/EXTRA-FIX/fix_electron_stopping.cpp b/src/EXTRA-FIX/fix_electron_stopping.cpp
index 4a9421be6c..37f33f4ea0 100644
--- a/src/EXTRA-FIX/fix_electron_stopping.cpp
+++ b/src/EXTRA-FIX/fix_electron_stopping.cpp
@@ -175,7 +175,8 @@ void FixElectronStopping::post_force(int /*vflag*/)
     if (energy < Ecut) continue;
     if (energy < elstop_ranges[0][0]) continue;
     if (energy > elstop_ranges[0][table_entries - 1])
-      error->one(FLERR, "Atom kinetic energy too high for fix electron/stopping");
+      error->one(FLERR, "Fix electron/stopping: kinetic energy too high for atom {}: {} vs {}",
+                 atom->tag[i], energy, elstop_ranges[0][table_entries - 1]);
 
     if (region) {
       // Only apply in the given region

From f69b50408d98bc49ff0a6787e9ae59caea4d1a82 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 28 May 2023 11:47:32 -0400
Subject: [PATCH 119/396] improve error messages

---
 src/output.cpp | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/src/output.cpp b/src/output.cpp
index 6282b85b76..ed8fa48831 100644
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -276,7 +276,8 @@ void Output::setup(int memflag)
         auto  nextrestart = static_cast<bigint>
           (input->variable->compute_equal(ivar_restart_single));
         if (nextrestart <= ntimestep)
-          error->all(FLERR,"Restart variable returned a bad timestep");
+          error->all(FLERR,"Restart variable returned a bad next timestep: {} vs {}",
+                     nextrestart, ntimestep);
         next_restart_single = nextrestart;
       }
     } else next_restart_single = update->laststep + 1;
@@ -289,7 +290,8 @@ void Output::setup(int memflag)
         auto  nextrestart = static_cast<bigint>
           (input->variable->compute_equal(ivar_restart_double));
         if (nextrestart <= ntimestep)
-          error->all(FLERR,"Restart variable returned a bad timestep");
+          error->all(FLERR,"Restart variable returned a bad next timestep: {} vs {}",
+                     nextrestart, ntimestep);
         next_restart_double = nextrestart;
       }
     } else next_restart_double = update->laststep + 1;
@@ -401,7 +403,8 @@ void Output::write(bigint ntimestep)
         auto  nextrestart = static_cast<bigint>
           (input->variable->compute_equal(ivar_restart_single));
         if (nextrestart <= ntimestep)
-          error->all(FLERR,"Restart variable returned a bad timestep");
+          error->all(FLERR,"Restart variable returned a bad next timestep: {} vs {}",
+                     nextrestart, ntimestep);
         next_restart_single = nextrestart;
         modify->addstep_compute(next_restart_single);
       }
@@ -424,7 +427,8 @@ void Output::write(bigint ntimestep)
         auto  nextrestart = static_cast<bigint>
           (input->variable->compute_equal(ivar_restart_double));
         if (nextrestart <= ntimestep)
-          error->all(FLERR,"Restart variable returned a bad timestep");
+          error->all(FLERR,"Restart variable returned a bad next timestep: {} <= {}",
+                     nextrestart, ntimestep);
         next_restart_double = nextrestart;
         modify->addstep_compute(next_restart_double);
       }
@@ -647,7 +651,8 @@ void Output::reset_timestep(bigint ntimestep)
       auto  nextrestart = static_cast<bigint>
         (input->variable->compute_equal(ivar_restart_single));
       if (nextrestart < ntimestep)
-        error->all(FLERR,"Restart variable returned a bad timestep");
+        error->all(FLERR,"Restart variable returned a bad next timestep: {} <= {}",
+                   nextrestart, ntimestep);
       update->ntimestep++;
       next_restart_single = nextrestart;
       modify->addstep_compute(next_restart_single);
@@ -666,7 +671,8 @@ void Output::reset_timestep(bigint ntimestep)
       auto  nextrestart = static_cast<bigint>
         (input->variable->compute_equal(ivar_restart_double));
       if (nextrestart < ntimestep)
-        error->all(FLERR,"Restart variable returned a bad timestep");
+        error->all(FLERR,"Restart variable returned a bad next timestep: {} <= {}",
+                   nextrestart, ntimestep);
       update->ntimestep++;
       next_restart_double = nextrestart;
       modify->addstep_compute(next_restart_double);

From f9ee2ad42b991ed221da79f217e7f71d544427b0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 28 May 2023 11:49:02 -0400
Subject: [PATCH 120/396] reorder thermo and dump output so dump styles include
 correct thermo data

---
 src/output.cpp | 90 +++++++++++++++++++++++++-------------------------
 1 file changed, 45 insertions(+), 45 deletions(-)

diff --git a/src/output.cpp b/src/output.cpp
index ed8fa48831..6e57122ffe 100644
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -190,6 +190,32 @@ void Output::setup(int memflag)
 {
   bigint ntimestep = update->ntimestep;
 
+  // print memory usage unless being called between multiple runs
+
+  if (memflag) memory_usage();
+
+  // set next_thermo to multiple of every or variable eval if var defined
+  // ensure thermo output on last step of run
+  // thermo may invoke computes so wrap with clear/add
+
+  modify->clearstep_compute();
+
+  thermo->header();
+  thermo->compute(0);
+  last_thermo = ntimestep;
+
+  if (var_thermo) {
+    next_thermo = static_cast<bigint>
+      (input->variable->compute_equal(ivar_thermo));
+    if (next_thermo <= ntimestep)
+      error->all(FLERR,"Thermo every variable returned a bad timestep");
+  } else if (thermo_every) {
+    next_thermo = (ntimestep/thermo_every)*thermo_every + thermo_every;
+    next_thermo = MIN(next_thermo,update->laststep);
+  } else next_thermo = update->laststep;
+
+  modify->addstep_compute(next_thermo);
+
   // consider all dumps
   // decide whether to write snapshot and/or calculate next step for dump
 
@@ -257,7 +283,7 @@ void Output::setup(int memflag)
       next_dump_any = MIN(next_dump_any,next_dump[idump]);
     }
 
-  // if no dumps, set next_dump_any to last+1 so will not influence next
+    // if no dumps, set next_dump_any to last+1 so will not influence next
 
   } else next_dump_any = update->laststep + 1;
 
@@ -298,32 +324,6 @@ void Output::setup(int memflag)
     next_restart = MIN(next_restart_single,next_restart_double);
   } else next_restart = update->laststep + 1;
 
-  // print memory usage unless being called between multiple runs
-
-  if (memflag) memory_usage();
-
-   // set next_thermo to multiple of every or variable eval if var defined
-   // ensure thermo output on last step of run
-   // thermo may invoke computes so wrap with clear/add
-
-  modify->clearstep_compute();
-
-  thermo->header();
-  thermo->compute(0);
-  last_thermo = ntimestep;
-
-  if (var_thermo) {
-    next_thermo = static_cast<bigint>
-      (input->variable->compute_equal(ivar_thermo));
-    if (next_thermo <= ntimestep)
-      error->all(FLERR,"Thermo every variable returned a bad timestep");
-  } else if (thermo_every) {
-    next_thermo = (ntimestep/thermo_every)*thermo_every + thermo_every;
-    next_thermo = MIN(next_thermo,update->laststep);
-  } else next_thermo = update->laststep;
-
-  modify->addstep_compute(next_thermo);
-
   // next = next timestep any output will be done
 
   next = MIN(next_dump_any,next_restart);
@@ -338,6 +338,24 @@ void Output::setup(int memflag)
 
 void Output::write(bigint ntimestep)
 {
+  // ensure next_thermo forces output on last step of run
+  // thermo may invoke computes so wrap with clear/add
+
+  if (next_thermo == ntimestep) {
+    modify->clearstep_compute();
+    if (last_thermo != ntimestep) thermo->compute(1);
+    last_thermo = ntimestep;
+    if (var_thermo) {
+      next_thermo = static_cast<bigint>
+        (input->variable->compute_equal(ivar_thermo));
+      if (next_thermo <= ntimestep)
+        error->all(FLERR,"Thermo every variable returned a bad timestep");
+    } else if (thermo_every) next_thermo += thermo_every;
+    else next_thermo = update->laststep;
+    next_thermo = MIN(next_thermo,update->laststep);
+    modify->addstep_compute(next_thermo);
+  }
+
   // perform dump if its next_dump = current ntimestep
   //   but not if it was already written on this step
   // set next_dump and also next_time_dump for mode_dump = 1
@@ -437,24 +455,6 @@ void Output::write(bigint ntimestep)
     next_restart = MIN(next_restart_single,next_restart_double);
   }
 
-  // ensure next_thermo forces output on last step of run
-  // thermo may invoke computes so wrap with clear/add
-
-  if (next_thermo == ntimestep) {
-    modify->clearstep_compute();
-    if (last_thermo != ntimestep) thermo->compute(1);
-    last_thermo = ntimestep;
-    if (var_thermo) {
-      next_thermo = static_cast<bigint>
-        (input->variable->compute_equal(ivar_thermo));
-      if (next_thermo <= ntimestep)
-        error->all(FLERR,"Thermo every variable returned a bad timestep");
-    } else if (thermo_every) next_thermo += thermo_every;
-    else next_thermo = update->laststep;
-    next_thermo = MIN(next_thermo,update->laststep);
-    modify->addstep_compute(next_thermo);
-  }
-
   // next = next timestep any output will be done
 
   next = MIN(next_dump_any,next_restart);

From c934208a4a462ec55c4a25cadd6b6d3adc307edc Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Sun, 28 May 2023 14:07:25 -0400
Subject: [PATCH 121/396] only update ivector if it still exists

---
 src/atom.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/atom.cpp b/src/atom.cpp
index f30ace174e..d5f8b64a52 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -2129,7 +2129,8 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint off
 
   // initialize custom per-atom properties to zero if present
 
-  for (int i = 0; i < nivector; ++i) ivector[i][ilocal] = 0;
+  for (int i = 0; i < nivector; ++i)
+    if (ivname[i] != nullptr) ivector[i][ilocal] = 0;
   for (int i = 0; i < ndvector; ++i) dvector[i][ilocal] = 0.0;
   for (int i = 0; i < niarray; ++i)
     for (int j = 0; j < icols[i]; ++j)

From 86743bc0a6fa09ffd630d4d9220c76f60823d18d Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Mon, 29 May 2023 10:59:18 +0300
Subject: [PATCH 122/396] Update compute_stress_mop.cpp

The angle was computed using the dot product of the vectors x[atom2] - x[atom1] and x[atom3] - x[atom2]. This is not consistent with the lammps convention where the angle is computed using the dot product between x[atom1]-x[atom2] and x[atom3]-x[atom2].
---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index e7a602e583..d512ce4810 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -692,7 +692,7 @@ void ComputeStressMop::compute_angles()
       // compute the cos(theta) of the angle
       r1 = sqrt(dx_left[0]*dx_left[0] + dx_left[1]*dx_left[1] + dx_left[2]*dx_left[2]);
       r2 = sqrt(dx_right[0]*dx_right[0] + dx_right[1]*dx_right[1] + dx_right[2]*dx_right[2]);
-      cos_theta = (dx_right[0]*dx_left[0] + dx_right[1]*dx_left[1] + dx_right[2]*dx_left[2])/(r1*r2);
+      cos_theta = -(dx_right[0]*dx_left[0] + dx_right[1]*dx_left[1] + dx_right[2]*dx_left[2])/(r1*r2);
 
       if (cos_theta >  1.0) cos_theta = 1.0;
       if (cos_theta < -1.0) cos_theta = -1.0;

From 3b38145d91b130b72a6770992efa35b282f0cfee Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Mon, 29 May 2023 16:34:44 +0300
Subject: [PATCH 123/396] Update compute_stress_mop.cpp

Fixing sign issues because I was considering the theta angle to be formed by vectors x[atom2] - x[atom1] & x[atom3] - x[atom2] instead of x[atom1] - x[atom2] & x[atom3] - x[atom2] as done in lammps
---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index d512ce4810..a5f5969317 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -703,18 +703,18 @@ void ComputeStressMop::compute_angles()
       if (right_cross && !left_cross)
       {
         double sgn = copysign(1.0, x_angle_right[dir] - pos);
-        dcos_theta[0] = sgn*(dx_right[0]*cos_theta/r2 - dx_left[0]/r1)/r2;
-        dcos_theta[1] = sgn*(dx_right[1]*cos_theta/r2 - dx_left[1]/r1)/r2;
-        dcos_theta[2] = sgn*(dx_right[2]*cos_theta/r2 - dx_left[2]/r1)/r2;
+        dcos_theta[0] = sgn*(dx_right[0]*cos_theta/r2 + dx_left[0]/r1)/r2;
+        dcos_theta[1] = sgn*(dx_right[1]*cos_theta/r2 + dx_left[1]/r1)/r2;
+        dcos_theta[2] = sgn*(dx_right[2]*cos_theta/r2 + dx_left[2]/r1)/r2;
       }
 
       // only left bond crossing the plane
       if (!right_cross && left_cross)
       {
         double sgn = copysign(1.0, x_angle_left[dir] - pos);
-        dcos_theta[0] = -sgn*(dx_left[0]*cos_theta/r1 - dx_right[0]/r2)/r1;
-        dcos_theta[1] = -sgn*(dx_left[1]*cos_theta/r1 - dx_right[1]/r2)/r1;
-        dcos_theta[2] = -sgn*(dx_left[2]*cos_theta/r1 - dx_right[2]/r2)/r1;
+        dcos_theta[0] = -sgn*(dx_left[0]*cos_theta/r1 + dx_right[0]/r2)/r1;
+        dcos_theta[1] = -sgn*(dx_left[1]*cos_theta/r1 + dx_right[1]/r2)/r1;
+        dcos_theta[2] = -sgn*(dx_left[2]*cos_theta/r1 + dx_right[2]/r2)/r1;
       }
 
       // both bonds crossing the plane
@@ -722,14 +722,14 @@ void ComputeStressMop::compute_angles()
       {
         // due to right bond
         double sgn = copysign(1.0, x_angle_middle[dir] - pos);
-        dcos_theta[0] = -sgn*(dx_right[0]*cos_theta/r2 - dx_left[0]/r1)/r2;
-        dcos_theta[1] = -sgn*(dx_right[1]*cos_theta/r2 - dx_left[1]/r1)/r2;
-        dcos_theta[2] = -sgn*(dx_right[2]*cos_theta/r2 - dx_left[2]/r1)/r2;
+        dcos_theta[0] = -sgn*(dx_right[0]*cos_theta/r2 + dx_left[0]/r1)/r2;
+        dcos_theta[1] = -sgn*(dx_right[1]*cos_theta/r2 + dx_left[1]/r1)/r2;
+        dcos_theta[2] = -sgn*(dx_right[2]*cos_theta/r2 + dx_left[2]/r1)/r2;
 
         // due to left bond
-        dcos_theta[0] += sgn*(dx_left[0]*cos_theta/r1 - dx_right[0]/r2)/r1;
-        dcos_theta[1] += sgn*(dx_left[1]*cos_theta/r1 - dx_right[1]/r2)/r1;
-        dcos_theta[2] += sgn*(dx_left[2]*cos_theta/r1 - dx_right[2]/r2)/r1;
+        dcos_theta[0] += sgn*(dx_left[0]*cos_theta/r1 + dx_right[0]/r2)/r1;
+        dcos_theta[1] += sgn*(dx_left[1]*cos_theta/r1 + dx_right[1]/r2)/r1;
+        dcos_theta[2] += sgn*(dx_left[2]*cos_theta/r1 + dx_right[2]/r2)/r1;
       }
 
       // final contribution of the given angle term

From b3e9efcb50ded57acff46cc52305c59a0adb04a8 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Mon, 29 May 2023 17:55:24 +0300
Subject: [PATCH 124/396] Use system periodicity to find an equivalent position
 of the plane

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index a5f5969317..9249e4ce2d 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -74,6 +74,18 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
     pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]);
   } else pos = utils::numeric(FLERR,arg[4],false,lmp);
 
+  // plane inside the box
+  if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir]) {
+    error->warning(FLERR,"The specified initial plane lies outside of the simulation box");
+    double dx[3] {0};
+    dx[dir] = pos - 0.5*(domain->boxhi[dir] + domain->boxlo[dir]);
+    domain->minimum_image(dx[0], dx[1], dx[2]);
+    pos = 0.5*(domain->boxhi[dir] + domain->boxlo[dir]) + dx[dir];
+
+    if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
+      error->all(FLERR, "Plane for compute stress/mop is out of bounds");
+  }
+     
   if (pos < (domain->boxlo[dir]+domain->prd_half[dir])) {
     pos1 = pos + domain->prd[dir];
   } else {
@@ -117,10 +129,6 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
   // orthogonal simulation box
   if (domain->triclinic != 0)
     error->all(FLERR, "Compute stress/mop incompatible with triclinic simulation box");
-  // plane inside the box
-  if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
-    error->all(FLERR, "Plane for compute stress/mop is out of bounds");
-
 
   // Initialize some variables
 

From 088d870e2062e7613b60f317eaccccd1dfff41cf Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Tue, 30 May 2023 17:17:54 -0400
Subject: [PATCH 125/396] check remaining per-atom initializations

---
 src/atom.cpp | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/atom.cpp b/src/atom.cpp
index d5f8b64a52..3e9e177ae0 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -2131,13 +2131,16 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint off
 
   for (int i = 0; i < nivector; ++i)
     if (ivname[i] != nullptr) ivector[i][ilocal] = 0;
-  for (int i = 0; i < ndvector; ++i) dvector[i][ilocal] = 0.0;
+  for (int i = 0; i < ndvector; ++i)
+    if (dvname[i] != nullptr) dvector[i][ilocal] = 0.0;
   for (int i = 0; i < niarray; ++i)
-    for (int j = 0; j < icols[i]; ++j)
-      iarray[i][ilocal][j] = 0;
+    if (ianame[i] != nullptr)
+      for (int j = 0; j < icols[i]; ++j)
+        iarray[i][ilocal][j] = 0;
   for (int i = 0; i < ndarray; ++i)
-    for (int j = 0; j < dcols[i]; ++j)
-      darray[i][ilocal][j] = 0.0;
+    if (daname[i] != nullptr)
+      for (int j = 0; j < dcols[i]; ++j)
+        darray[i][ilocal][j] = 0.0;
 
   if (molecular != Atom::MOLECULAR) return;
 

From ddc34e03d66452402993ec20203b12a089f2fe21 Mon Sep 17 00:00:00 2001
From: Lars Veldscholte <lars@tuxplace.nl>
Date: Wed, 31 May 2023 09:50:50 +0200
Subject: [PATCH 126/396] Revert removal of copies of pointers

---
 .../compute_stress_cartesian.cpp              | 52 ++++++++++++-------
 1 file changed, 32 insertions(+), 20 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
index 2f6e75b528..106ffef8fb 100644
--- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
@@ -232,12 +232,24 @@ void ComputeStressCartesian::compute_array()
 {
   double **x = atom->x;
   double **v = atom->v;
+  double *mass = atom->mass;
   tagint *tag = atom->tag;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  double *special_coul = force->special_coul;
+  double *special_lj = force->special_lj;
+  int newton_pair = force->newton_pair;
   double *boxlo = domain->boxlo;
 
   // invoke half neighbor list (will copy or build if necessary)
   neighbor->build_one(list);
 
+  int inum = list->inum;
+  int *ilist = list->ilist;
+  int *numneigh = list->numneigh;
+  int **firstneigh = list->firstneigh;
+
   // Zero arrays
   for (int bin = 0; bin < nbins1 * nbins2; bin++) {
     tdens[bin] = 0;
@@ -250,7 +262,7 @@ void ComputeStressCartesian::compute_array()
   }
 
   // calculate number density and kinetic contribution to pressure
-  for (int i = 0; i < atom->nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     int bin1 = (int) ((x[i][dir1] - boxlo[dir1]) / bin_width1) % nbins1;
     int bin2 = 0;
     if (dims == 2) bin2 = (int) ((x[i][dir2] - boxlo[dir2]) / bin_width2) % nbins2;
@@ -278,31 +290,31 @@ void ComputeStressCartesian::compute_array()
 
     int j = bin1 + bin2 * nbins1;
     tdens[j] += 1;
-    tpkxx[j] += atom->mass[atom->type[i]] * v[i][0] * v[i][0];
-    tpkyy[j] += atom->mass[atom->type[i]] * v[i][1] * v[i][1];
-    tpkzz[j] += atom->mass[atom->type[i]] * v[i][2] * v[i][2];
+    tpkxx[j] += mass[type[i]] * v[i][0] * v[i][0];
+    tpkyy[j] += mass[type[i]] * v[i][1] * v[i][1];
+    tpkzz[j] += mass[type[i]] * v[i][2] * v[i][2];
   }
 
   // loop over neighbors of my atoms
-  for (int ii = 0; ii < list->inum; ii++) {
-    int i = list->ilist[ii];
+  for (int ii = 0; ii < inum; ii++) {
+    int i = ilist[ii];
 
     // skip if I or J are not in group
-    if (!(atom->mask[i] & groupbit)) continue;
+    if (!(mask[i] & groupbit)) continue;
 
     double xi1 = x[i][dir1] - boxlo[dir1];
     double xi2 = x[i][dir2] - boxlo[dir2];
 
-    for (int jj = 0; jj < list->numneigh[i]; jj++) {
-      int j = list->firstneigh[i][jj];
-      double factor_lj = force->special_lj[sbmask(j)];
-      double factor_coul = force->special_coul[sbmask(j)];
+    for (int jj = 0; jj < numneigh[i]; jj++) {
+      int j = firstneigh[i][jj];
+      double factor_lj = special_lj[sbmask(j)];
+      double factor_coul = special_coul[sbmask(j)];
       j &= NEIGHMASK;
-      if (!(atom->mask[j] & groupbit)) continue;
+      if (!(mask[j] & groupbit)) continue;
 
       // for newton = 0 and J = ghost atom, need to ensure I,J pair is only output by one proc
       // use same tag[i],tag[j] logic as in Neighbor::neigh_half_nsq()
-      if (force->newton_pair == 0 && j >= atom->nlocal) {
+      if (newton_pair == 0 && j >= nlocal) {
         if (tag[i] > tag[j]) {
           if ((tag[i] + tag[j]) % 2 == 0) continue;
         } else if (tag[i] < tag[j]) {
@@ -323,8 +335,8 @@ void ComputeStressCartesian::compute_array()
       double rsq = delx * delx + dely * dely + delz * delz;
 
       // Check if inside cut-off
-      int itype = atom->type[i];
-      int jtype = atom->type[j];
+      int itype = type[i];
+      int jtype = type[j];
       if (rsq >= force->pair->cutsq[itype][jtype]) continue;
 
       double fpair;
@@ -338,14 +350,14 @@ void ComputeStressCartesian::compute_array()
     // i == atom1, j == atom2
     int i = neighbor->bondlist[i_bond][0];
     int j = neighbor->bondlist[i_bond][1];
-    int type  = neighbor->bondlist[i_bond][2];
+    int btype  = neighbor->bondlist[i_bond][2];
 
     // Skip if one of both atoms is not in group
-    if (!(atom->mask[i] & groupbit)) continue;
-    if (!(atom->mask[j] & groupbit)) continue;
+    if (!(mask[i] & groupbit)) continue;
+    if (!(mask[j] & groupbit)) continue;
 
     // if newton_bond is off and atom2 is a ghost atom, only compute this on one processor
-    if (!force->newton_bond && j >= atom->nlocal) {
+    if (!force->newton_bond && j >= nlocal) {
       if (tag[i] > tag[j]) {
         if ((tag[i] + tag[j]) % 2 == 0) continue;
       } else if (tag[i] < tag[j]) {
@@ -361,7 +373,7 @@ void ComputeStressCartesian::compute_array()
     double yi = x[i][dir2] - boxlo[dir2];
 
     double fbond;
-    force->bond->single(type, rsq, i, j, fbond);
+    force->bond->single(btype, rsq, i, j, fbond);
     compute_pressure(fbond, xi, yi, dx, dy, dz);
   }
 

From 69c549363171fb98524e49b09ac2461ff079f2eb Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 31 May 2023 09:09:35 -0400
Subject: [PATCH 127/396] silence compiler warning

---
 src/variable.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/variable.cpp b/src/variable.cpp
index 783ceab832..81f0bdcfd6 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -1052,7 +1052,7 @@ char *Variable::retrieve(const char *name)
     if (vecs[ivar].dynamic || vecs[ivar].currentstep != update->ntimestep) {
       eval_in_progress[ivar] = 0;
       double *result;
-      int nvec = compute_vector(ivar,&result);
+      compute_vector(ivar,&result);
       delete[] data[ivar][1];
       std::vector <double> vectmp(vecs[ivar].values,vecs[ivar].values + vecs[ivar].n);
       std::string str = fmt::format("[{}]", fmt::join(vectmp,","));

From c0602b65000f654bfa8e19619e63ab899342ad88 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 31 May 2023 13:20:35 -0400
Subject: [PATCH 128/396] make using energy and potential keyword at the same
 time an error

---
 src/fix_efield.cpp | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/src/fix_efield.cpp b/src/fix_efield.cpp
index d2c0dc1ef6..d01a498d39 100644
--- a/src/fix_efield.cpp
+++ b/src/fix_efield.cpp
@@ -58,7 +58,7 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
   virial_global_flag = virial_peratom_flag = 1;
 
   qe2f = force->qe2f;
-  xstr = ystr = zstr = nullptr;
+  xstyle = ystyle = zstyle = estyle = pstyle = NONE;
 
   if (utils::strmatch(arg[3], "^v_")) {
     xstr = utils::strdup(arg[3] + 2);
@@ -113,6 +113,9 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
     }
   }
 
+  if (estr && pstr)
+    error->all(FLERR, "Must not use energy and potential keywords at the same time with fix efield");
+
   force_flag = 0;
   fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
 
@@ -174,6 +177,7 @@ void FixEfield::init()
     else
       error->all(FLERR, "Variable {} for x-field in fix {} is invalid style", xstr, style);
   }
+
   if (ystr) {
     yvar = input->variable->find(ystr);
     if (yvar < 0) error->all(FLERR, "Variable {} for y-field in fix {} does not exist", ystr, style);
@@ -184,6 +188,7 @@ void FixEfield::init()
     else
       error->all(FLERR, "Variable {} for y-field in fix {} is invalid style", ystr, style);
   }
+
   if (zstr) {
     zvar = input->variable->find(zstr);
     if (zvar < 0) error->all(FLERR, "Variable {} for z-field in fix {} does not exist", zstr, style);
@@ -194,6 +199,7 @@ void FixEfield::init()
     else
       error->all(FLERR, "Variable {} for z-field in fix {} is invalid style", zstr, style);
   }
+
   if (estr) {
     evar = input->variable->find(estr);
     if (evar < 0) error->all(FLERR, "Variable {} for energy in fix {} does not exist", estr, style);
@@ -201,8 +207,8 @@ void FixEfield::init()
       estyle = ATOM;
     else
       error->all(FLERR, "Variable {} for energy in fix {} must be atom-style", estr, style);
-  } else
-    estyle = NONE;
+  }
+
   if (pstr) {
     pvar = input->variable->find(pstr);
     if (pvar < 0) error->all(FLERR, "Variable {} for potential in fix {} does not exist", pstr, style);
@@ -210,11 +216,7 @@ void FixEfield::init()
       pstyle = ATOM;
     else
       error->all(FLERR, "Variable {} for potential in fix {} must be atom-style", pstr, style);
-    if (estyle != NONE)
-      error->warning(FLERR, "fix {} will ignore variable {} for energy "
-          "because atom-style potential has been specified", estr, style);
-  } else
-    pstyle = NONE;
+  }
 
   // set index and check validity of region
 

From cb02563d3d749d46a8ee69dc2c64a6bf27f5c226 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 31 May 2023 13:29:41 -0400
Subject: [PATCH 129/396] the potential keyword is not (yet) supported by fix
 efield/tip4p

---
 src/EXTRA-FIX/fix_efield_tip4p.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/EXTRA-FIX/fix_efield_tip4p.cpp b/src/EXTRA-FIX/fix_efield_tip4p.cpp
index 3d6a2f66b7..47b1d9e27a 100644
--- a/src/EXTRA-FIX/fix_efield_tip4p.cpp
+++ b/src/EXTRA-FIX/fix_efield_tip4p.cpp
@@ -47,6 +47,7 @@ void FixEfieldTIP4P::init()
   if (atom->tag_enable == 0) error->all(FLERR, "Fix efield/tip4p requires atom IDs");
   if (!atom->q_flag) error->all(FLERR, "Fix efield/tip4p requires atom attribute q");
   if (!force->pair) error->all(FLERR, "A TIP4P pair style must be defined fix efield/tip4p");
+  if (pstr) error->all(FLERR, "Fix efield/tip4p does not support the potential keyword");
 
   int itmp;
   double *p_qdist = (double *) force->pair->extract("qdist", itmp);

From 90000ca166c14c34e59306c7751b6d77ee71a168 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 31 May 2023 13:29:48 -0400
Subject: [PATCH 130/396] update docs

---
 doc/src/fix_efield.rst | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst
index 0b94f80b8c..4cf92cf946 100644
--- a/doc/src/fix_efield.rst
+++ b/doc/src/fix_efield.rst
@@ -28,7 +28,7 @@ Syntax
        *energy* value = v_name
          v_name = variable with name that calculates the potential energy of each atom in the added E-field
        *potential* value = v_name
-         v_name = variable with name that calculates the electric potential of each atom in the added E-field (overrides *energy*)
+         v_name = variable with name that calculates the electric potential of each atom in the added E-field
 
 Examples
 """"""""
@@ -136,6 +136,8 @@ due to the electric field were a spring-like F = kx, then the energy
 formula should be E = -0.5kx\^2.  If you don't do this correctly, the
 minimization will not converge properly.
 
+.. versionadded:: TBD
+
 The *potential* keyword can be used as an alternative to the *energy* keyword
 to specify the name of an atom-style variable, which is used to compute the
 added electric potential to each atom as a function of its position.  The
@@ -144,14 +146,16 @@ in `units real`, the potential should be in volts). As with the *energy*
 keyword, the variable name is specified as "v_name". The energy added by this
 fix is then calculated as the electric potential multiplied by charge.
 
-The *potential* keyword is mainly intended for correct charge equilibration
-in simulations with :doc:`fix qeq/reaxff<fix_qeq_reaxff>`, since with variable
-charges the electric potential can be known beforehand but the energy cannot.
-A small additional benefit is that the *energy* keyword requires an additional
-conversion to energy units which the *potential* keyword avoids. Thus, when the
-*potential* keyword is specified, the *energy* keyword is ignored (the simulation
-will proceed but with a warning issued). As with *energy*, the *potential*
-keyword is not allowed if the added field is a constant vector.
+The *potential* keyword is mainly intended for correct charge
+equilibration in simulations with :doc:`fix qeq/reaxff<fix_qeq_reaxff>`,
+since with variable charges the electric potential can be known
+beforehand but the energy cannot.  A small additional benefit is that
+the *energy* keyword requires an additional conversion to energy units
+which the *potential* keyword avoids.  Thus, when the *potential*
+keyword is specified, the *energy* keyword must not be used.  As with
+*energy*, the *potential* keyword is not allowed if the added field is a
+constant vector.  The *potential* keyword is not supported by *fix
+efield/tip4p*.
 
 ----------
 

From 6138b2b1f78e223c5e0d00d614d5399c3849a8ed Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 31 May 2023 13:31:45 -0400
Subject: [PATCH 131/396] fix grammar

---
 src/variable.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/variable.cpp b/src/variable.cpp
index 81f0bdcfd6..437e4ac917 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -224,7 +224,7 @@ void Variable::set(int narg, char **arg)
       if (narg == 5 && strcmp(arg[4],"pad") == 0) {
         pad[nvar] = fmt::format("{}",nlast).size();
       } else pad[nvar] = 0;
-    } else error->all(FLERR,"Illegal variable loop command: too much arguments");
+    } else error->all(FLERR,"Illegal variable loop command: too many arguments");
     num[nvar] = nlast;
     which[nvar] = nfirst-1;
     data[nvar] = new char*[1];

From cae2414126faa47448a8d7d4822cc5659b2b3241 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Wed, 31 May 2023 13:09:07 -0600
Subject: [PATCH 132/396] Fix compiler warnings in Kokkos ACKS2

---
 src/KOKKOS/fix_acks2_reaxff_kokkos.h | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/KOKKOS/fix_acks2_reaxff_kokkos.h b/src/KOKKOS/fix_acks2_reaxff_kokkos.h
index 3e89cb4d43..127c8d0402 100644
--- a/src/KOKKOS/fix_acks2_reaxff_kokkos.h
+++ b/src/KOKKOS/fix_acks2_reaxff_kokkos.h
@@ -66,10 +66,10 @@ class FixACKS2ReaxFFKokkos : public FixACKS2ReaxFF, public KokkosBase {
   FixACKS2ReaxFFKokkos(class LAMMPS *, int, char **);
   ~FixACKS2ReaxFFKokkos();
 
+  void init() override;
+  void setup_pre_force(int) override;
+  void pre_force(int) override;
   void cleanup_copy();
-  void init();
-  void setup_pre_force(int);
-  void pre_force(int);
 
   DAT::tdual_ffloat_1d get_s() {return k_s;}
 
@@ -235,11 +235,11 @@ class FixACKS2ReaxFFKokkos : public FixACKS2ReaxFF, public KokkosBase {
 
   void init_shielding_k();
   void init_hist();
-  void allocate_matrix();
+  void allocate_matrix() override;
   void allocate_array();
   void deallocate_array();
   int bicgstab_solve();
-  void calculate_Q();
+  void calculate_Q() override;
 
   int neighflag;
   int nlocal,nall,nmax,newton_pair;
@@ -251,13 +251,13 @@ class FixACKS2ReaxFFKokkos : public FixACKS2ReaxFF, public KokkosBase {
   typename AT::t_int_2d d_sendlist;
   typename AT::t_xfloat_1d_um v_buf;
 
-  void grow_arrays(int);
-  void copy_arrays(int, int, int);
+  void grow_arrays(int) override;
+  void copy_arrays(int, int, int) override;
   void sort_kokkos(Kokkos::BinSort<KeyViewType, BinOp> &Sorter) override;
-  int pack_exchange(int, double *);
-  int unpack_exchange(int, double *);
-  void get_chi_field();
-  double memory_usage();
+  int pack_exchange(int, double *) override;
+  int unpack_exchange(int, double *) override;
+  void get_chi_field() override;
+  double memory_usage() override;
 
   void sparse_matvec_acks2(typename AT::t_ffloat_1d &, typename AT::t_ffloat_1d &);
 };

From a0461d29ddc23485c5995490bdbb126b0e917cfb Mon Sep 17 00:00:00 2001
From: Jacob Gissinger <jrgiss05@gmail.com>
Date: Wed, 31 May 2023 17:04:49 -0400
Subject: [PATCH 133/396] Update atom.cpp

---
 src/atom.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/atom.cpp b/src/atom.cpp
index 3e9e177ae0..08e9639440 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -2130,15 +2130,15 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint off
   // initialize custom per-atom properties to zero if present
 
   for (int i = 0; i < nivector; ++i)
-    if (ivname[i] != nullptr) ivector[i][ilocal] = 0;
+    if (ivname[i]) ivector[i][ilocal] = 0;
   for (int i = 0; i < ndvector; ++i)
-    if (dvname[i] != nullptr) dvector[i][ilocal] = 0.0;
+    if (dvname[i]) dvector[i][ilocal] = 0.0;
   for (int i = 0; i < niarray; ++i)
-    if (ianame[i] != nullptr)
+    if (ianame[i])
       for (int j = 0; j < icols[i]; ++j)
         iarray[i][ilocal][j] = 0;
   for (int i = 0; i < ndarray; ++i)
-    if (daname[i] != nullptr)
+    if (daname[i])
       for (int j = 0; j < dcols[i]; ++j)
         darray[i][ilocal][j] = 0.0;
 

From ea6ece510edc25cc8f381d7d67e546f62bbd8058 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Thu, 1 Jun 2023 10:22:01 +0300
Subject: [PATCH 134/396] turning warning into errors for unsupported styles

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 9249e4ce2d..0199a49c01 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -205,26 +205,25 @@ void ComputeStressMop::init()
   if (force->pair->single_enable == 0)
     error->all(FLERR,"Pair style does not support compute stress/mop");
 
-  // Warnings
+  // Errors
 
   if (me==0) {
 
-    //Compute stress/mop only accounts for pair interactions.
-    // issue a warning if any intramolecular potential or Kspace is defined.
+    // issue an error for unimplemented intramolecular potentials or Kspace.
 
     if (force->bond!=nullptr) bondflag = 1;
     if (force->angle!=nullptr)
       if (force->angle->born_matrix_enable == 0) {
-        error->warning(FLERR,"compute stress/mop does not account for angle potentials");
+        error->all(FLERR,"compute stress/mop does not account for angle potentials");
       } else {
          angleflag = 1;
       }
     if (force->dihedral!=nullptr)
-      error->warning(FLERR,"compute stress/mop does not account for dihedral potentials");
+      error->all(FLERR,"compute stress/mop does not account for dihedral potentials");
     if (force->improper!=nullptr)
-      error->warning(FLERR,"compute stress/mop does not account for improper potentials");
+      error->all(FLERR,"compute stress/mop does not account for improper potentials");
     if (force->kspace!=nullptr)
-      error->warning(FLERR,"compute stress/mop does not account for kspace contributions");
+      error->all(FLERR,"compute stress/mop does not account for kspace contributions");
   }
 
   // need an occasional half neighbor list

From b01db47b2d83a5d4656ef279c318c717cfefe192 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Thu, 1 Jun 2023 10:33:50 +0300
Subject: [PATCH 135/396] consistency in issuing errors between mop and
 mop/profile

---
 src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index 709f109cb1..ffcc712548 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -178,23 +178,23 @@ void ComputeStressMopProfile::init()
   if (force->pair->single_enable == 0)
     error->all(FLERR,"Pair style does not support compute stress/mop/profile");
 
-  // Warnings
+  // Errors
 
   if (me==0) {
 
     //Compute stress/mop/profile only accounts for pair interactions.
-    // issue a warning if any intramolecular potential or Kspace is defined.
+    // issue an error if any intramolecular potential or Kspace is defined.
 
     if (force->bond!=nullptr)
-      error->warning(FLERR,"compute stress/mop/profile does not account for bond potentials");
+      error->all(FLERR,"compute stress/mop/profile does not account for bond potentials");
     if (force->angle!=nullptr)
-      error->warning(FLERR,"compute stress/mop/profile does not account for angle potentials");
+      error->all(FLERR,"compute stress/mop/profile does not account for angle potentials");
     if (force->dihedral!=nullptr)
-      error->warning(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
+      error->all(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
     if (force->improper!=nullptr)
-      error->warning(FLERR,"compute stress/mop/profile does not account for improper potentials");
+      error->all(FLERR,"compute stress/mop/profile does not account for improper potentials");
     if (force->kspace!=nullptr)
-      error->warning(FLERR,"compute stress/mop/profile does not account for kspace contributions");
+      error->all(FLERR,"compute stress/mop/profile does not account for kspace contributions");
   }
 
   // need an occasional half neighbor list

From 6bc27db58c2829dab6f13b8cb5e69702a2cd2b36 Mon Sep 17 00:00:00 2001
From: Yifan Li <yifanl0716@gmail.com>
Date: Thu, 1 Jun 2023 06:17:11 -0400
Subject: [PATCH 136/396] do not delete c_pe and c_press in destructor

---
 src/REPLICA/fix_pimd_langevin.cpp | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 67d7cabe02..f9c7772d63 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -344,8 +344,6 @@ FixPIMDLangevin::~FixPIMDLangevin()
   delete[] id_pe;
   delete[] id_press;
   delete random;
-  delete c_pe;
-  delete c_press;
   delete[] mass;
   delete[] _omega_k;
   delete[] Lan_c;

From f3bf20be8b15a9d82028934f27f33af019ae469e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Yifan=20Li=E6=9D=8E=E4=B8=80=E5=B8=86?=
 <yifanl0716@gmail.com>
Date: Thu, 1 Jun 2023 08:26:02 -0400
Subject: [PATCH 137/396] The first three p_flags for iso should be 1.

---
 src/REPLICA/fix_pimd_langevin.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index f9c7772d63..2e4b1c17b8 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -205,6 +205,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         error->universe_all(FLERR, "Unknown barostat parameter for fix pimd/langevin");
     } else if (strcmp(arg[i], "iso") == 0) {
       pstyle = ISO;
+      p_flag[0] = p_flag[1] = p_flag[2] = 1;
       Pext = utils::numeric(FLERR, arg[i + 1], false, lmp);
       p_target[0] = p_target[1] = p_target[2] = Pext;
       pdim = 3;

From c1cec4565250c5a1b28c850badae0785b140c60d Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Thu, 1 Jun 2023 15:26:43 +0300
Subject: [PATCH 138/396] add keywords to specify contributions to stress/mop

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 0199a49c01..071bdf31ee 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -38,7 +38,7 @@
 using namespace LAMMPS_NS;
 
 enum{X,Y,Z};
-enum{TOTAL,CONF,KIN};
+enum{TOTAL,CONF,KIN,PAIR,BOND,ANGLE};
 
 #define BIG 1000000000
 
@@ -115,6 +115,21 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
         which[nvalues] = TOTAL;
         nvalues++;
       }
+    } else if (strcmp(arg[iarg],"pair") == 0) {
+      for (i=0; i<3; i++) {
+        which[nvalues] = PAIR;
+        nvalues++;
+      }
+    } else if (strcmp(arg[iarg],"bond") == 0) {
+      for (i=0; i<3; i++) {
+        which[nvalues] = BOND;
+        nvalues++;
+      }
+    } else if (strcmp(arg[iarg],"angle") == 0) {
+      for (i=0; i<3; i++) {
+        which[nvalues] = ANGLE;
+        nvalues++;
+      }
     } else error->all(FLERR, "Illegal compute stress/mop command"); //break;
 
     iarg++;
@@ -329,7 +344,7 @@ void ComputeStressMop::compute_pairs()
 
   m = 0;
   while (m<nvalues) {
-    if (which[m] == CONF || which[m] == TOTAL) {
+    if (which[m] == CONF || which[m] == TOTAL || which[m] == PAIR) {
 
       //Compute configurational contribution to pressure
       for (ii = 0; ii < inum; ii++) {
@@ -577,7 +592,7 @@ void ComputeStressMop::compute_bonds()
   // loop over the keywords and if necessary add the bond contribution
   int m {0};
   while (m<nvalues) {
-    if (which[m] == CONF || which[m] == TOTAL) {
+    if (which[m] == CONF || which[m] == TOTAL || which[m] == BOND) {
       bond_local[m] = local_contribution[0];
       bond_local[m+1] = local_contribution[1];
       bond_local[m+2] = local_contribution[2];
@@ -748,7 +763,7 @@ void ComputeStressMop::compute_angles()
   // loop over the keywords and if necessary add the angle contribution
   int m {0};
   while (m<nvalues) {
-    if (which[m] == CONF || which[m] == TOTAL) {
+    if (which[m] == CONF || which[m] == TOTAL || which[m] == ANGLE) {
       angle_local[m] = local_contribution[0];
       angle_local[m+1] = local_contribution[1];
       angle_local[m+2] = local_contribution[2];

From c310616bb76b2e1b15a3c57bd8f747d708445923 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Thu, 1 Jun 2023 15:34:41 +0300
Subject: [PATCH 139/396] Update compute_stress_mop.rst to reflect the added
 keywords

---
 doc/src/compute_stress_mop.rst | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst
index a8a3bc5660..b4c15257af 100644
--- a/doc/src/compute_stress_mop.rst
+++ b/doc/src/compute_stress_mop.rst
@@ -18,7 +18,7 @@ Syntax
 * style = *stress/mop* or *stress/mop/profile*
 * dir = *x* or *y* or *z* is the direction normal to the plane
 * args = argument specific to the compute style
-* keywords = *kin* or *conf* or *total* (one of more can be specified)
+* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* (one or more can be specified)
 
 .. parsed-literal::
 
@@ -64,9 +64,11 @@ atoms have crossed the plane if their positions at times :math:`t-\Delta t`
 and :math:`t` are one on either side of the plane, and uses the velocity at
 time :math:`t-\Delta t/2` given by the velocity Verlet algorithm.
 
-Between one and three keywords can be used to indicate which
-contributions to the stress must be computed: kinetic stress (kin),
-configurational stress (conf), and/or total stress (total).
+Between one and six keywords can be used to indicate which
+contributions to the stress must be computed: total stress (total),  kinetic stress (kin),
+configurational stress (conf), stress due to bond stretching (bond),
+stress due to angle bending (angle) and/or due to pairwise non-bonded interactions (pair).
+The last three keywords are currently available only for the stress/mop command and not the stress/mop/profile. 
 
 NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
 

From 1189661edc3fa2fe0ecfb54c8fc048bdf0d42b3c Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Thu, 1 Jun 2023 21:00:16 +0800
Subject: [PATCH 140/396] revise the code files of standard version based on
 latest version of LAMMPS

---
 src/INTERLAYER/pair_ilp_graphene_hbn.cpp | 21 ++++++-------
 src/INTERLAYER/pair_ilp_graphene_hbn.h   | 38 +++++-------------------
 src/INTERLAYER/pair_ilp_tmd.cpp          | 30 +++++++++----------
 src/INTERLAYER/pair_ilp_tmd.h            |  2 +-
 src/INTERLAYER/pair_ilp_water_2dm.cpp    | 23 +++++++-------
 src/INTERLAYER/pair_ilp_water_2dm.h      | 21 +------------
 6 files changed, 45 insertions(+), 90 deletions(-)

diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
index 956d7ba2be..401d7f7b12 100644
--- a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
+++ b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -47,11 +47,11 @@ using namespace InterLayer;
 static const char cite_ilp[] =
     "ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848\n"
     "@Article{Ouyang2018\n"
-    " author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},\n"
+    " author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},\n"
     " title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},\n"
     " journal = {Nano Letters},\n"
     " volume =  18,\n"
-    " pages =   {6009}\n"
+    " pages =   6009,\n"
     " year =    2018,\n"
     "}\n\n";
 
@@ -59,10 +59,7 @@ static const char cite_ilp[] =
 static std::map<int, std::string> variant_map = {
     {PairILPGrapheneHBN::ILP_GrhBN, "ilp/graphene/hbn"},
     {PairILPGrapheneHBN::ILP_TMD, "ilp/tmd"},
-    {PairILPGrapheneHBN::ILP_PHOSPHORUS, "ilp/phosphorus"},
-    {PairILPGrapheneHBN::ILP_WATER_2DM, "ilp/water/2dm"},
-    {PairILPGrapheneHBN::SAIP_METAL, "saip/metal"},
-    {PairILPGrapheneHBN::SAIP_METAL_TMD, "saip/metal/tmd"}};
+    {PairILPGrapheneHBN::SAIP_METAL, "saip/metal"}};
 
 /* ---------------------------------------------------------------------- */
 
@@ -316,14 +313,14 @@ void PairILPGrapheneHBN::read_file(char *filename)
       for (int m = 0; m < nparams; m++) {
         if (i == params[m].ielement && j == params[m].jelement) {
           if (n >= 0)
-            error->all(FLERR, "{} potential file {} has a duplicate entry", variant_map[variant],
-                       filename);
+            error->all(FLERR, "{} potential file {} has a duplicate entry for: {} {}",
+                       variant_map[variant], filename, elements[i], elements[j]);
           n = m;
         }
       }
       if (n < 0)
-        error->all(FLERR, "{} potential file {} is missing an entry", variant_map[variant],
-                   filename);
+        error->all(FLERR, "{} potential file {} is missing an entry for: {} {}",
+                   variant_map[variant], filename, elements[i], elements[j]);
       elem2param[i][j] = n;
       cutILPsq[i][j] = params[n].rcut * params[n].rcut;
     }
@@ -652,7 +649,7 @@ void PairILPGrapheneHBN::ILP_neigh()
         (int **) memory->smalloc(maxlocal * sizeof(int *), "ILPGrapheneHBN:firstneigh");
   }
 
-  inum = list->inum; // + list->gnum;
+  inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.h b/src/INTERLAYER/pair_ilp_graphene_hbn.h
index 6381fb8f35..9987830b1d 100644
--- a/src/INTERLAYER/pair_ilp_graphene_hbn.h
+++ b/src/INTERLAYER/pair_ilp_graphene_hbn.h
@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -35,19 +35,11 @@ class PairILPGrapheneHBN : public Pair {
   double init_one(int, int) override;
   void init_style() override;
   void calc_FvdW(int, int);
-  virtual void calc_FRep(int, int);
-  virtual void ILP_neigh();
-  virtual void calc_normal();
-  void read_file(char *);
-  void allocate();
-
   double single(int, int, int, int, double, double, double, double &) override;
 
   static constexpr int NPARAMS_PER_LINE = 13;
 
-  // for telling class variants apart in shared code
-  enum { ILP_GrhBN, ILP_TMD, SAIP_METAL, 
-         ILP_WATER_2DM, SAIP_METAL_TMD, ILP_PHOSPHORUS };
+  enum { ILP_GrhBN, ILP_TMD, SAIP_METAL };    // for telling class variants apart in shared code
 
  protected:
   int me;
@@ -59,7 +51,6 @@ class PairILPGrapheneHBN : public Pair {
   int *ILP_numneigh;       // # of pair neighbors for each atom
   int **ILP_firstneigh;    // ptr to 1st neighbor of each atom
   int tap_flag;            // flag to turn on/off taper function
-  double ncf;                 // for ilp/phosphorus, coefficients for calcualting the normals 
 
   struct Param {
     double z0, alpha, epsilon, C, delta, d, sR, reff, C6, S;
@@ -85,28 +76,15 @@ class PairILPGrapheneHBN : public Pair {
   double ***dpvet1;
   double ***dpvet2;
   double ***dNave;
+
+  virtual void ILP_neigh();
+  virtual void calc_normal();
+  virtual void calc_FRep(int, int);
+  void read_file(char *);
+  void allocate();
 };
 
 }    // namespace LAMMPS_NS
 
 #endif
 #endif
-
-/* ERROR/WARNING messages:
-
-E: Illegal ... command
-
-Self-explanatory.  Check the input script syntax and compare to the
-documentation for the command.  You can use -echo screen as a
-command-line option when running LAMMPS to see the offending line.
-
-E: Incorrect args for pair coefficients
-
-Self-explanatory.  Check the input script or data file.
-
-E: All pair coeffs are not set
-
-All pair coefficients must be set in the data file or by the
-pair_coeff command before running a simulation.
-
-*/
diff --git a/src/INTERLAYER/pair_ilp_tmd.cpp b/src/INTERLAYER/pair_ilp_tmd.cpp
index d855b9423d..f5636ce3fa 100644
--- a/src/INTERLAYER/pair_ilp_tmd.cpp
+++ b/src/INTERLAYER/pair_ilp_tmd.cpp
@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -22,14 +22,12 @@
 
 #include "atom.h"
 #include "citeme.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "interlayer_taper.h"
 #include "memory.h"
 #include "my_page.h"
 #include "neigh_list.h"
-#include "neighbor.h"
 
 #include <cmath>
 #include <cstring>
@@ -37,20 +35,22 @@
 using namespace LAMMPS_NS;
 using namespace InterLayer;
 
+#define MAXLINE 1024
 #define DELTA 4
 #define PGDELTA 1
 
-static const char cite_ilp_tmd[] = "ilp/tmd potential doi/10.1021/acs.jctc.1c00782\n"
-                                   "@Article{Ouyang2021\n"
-                                   " author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. "
-                                   "Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},\n"
-                                   " title = {Anisotropic Interlayer Force Field for Transition "
-                                   "Metal Dichalcogenides: The Case of Molybdenum Disulfide},\n"
-                                   " journal = {J. Chem. Theory Comput.},\n"
-                                   " volume =  17,\n"
-                                   " pages =   {7237–7245}\n"
-                                   " year =    2021,\n"
-                                   "}\n\n";
+static const char cite_ilp_tmd[] =
+    "ilp/tmd potential doi:10.1021/acs.jctc.1c00782\n"
+    "@Article{Ouyang2021\n"
+    "  author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and\n"
+    "    A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},\n"
+    "  title = {Anisotropic Interlayer Force Field for Transition\n"
+    "    Metal Dichalcogenides: The Case of Molybdenum Disulfide},\n"
+    "  journal = {J.~Chem.\\ Theory Comput.},\n"
+    " volume   = 17,\n"
+    " pages    = {7237--7245}\n"
+    " year     = 2021,\n"
+    "}\n\n";
 
 /* ---------------------------------------------------------------------- */
 
@@ -249,7 +249,7 @@ void PairILPTMD::ILP_neigh()
     ILP_firstneigh = (int **) memory->smalloc(maxlocal * sizeof(int *), "ILPTMD:firstneigh");
   }
 
-  inum = list->inum; //+ list->gnum;
+  inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;
   firstneigh = list->firstneigh;
diff --git a/src/INTERLAYER/pair_ilp_tmd.h b/src/INTERLAYER/pair_ilp_tmd.h
index 8d5446d49c..8381c2e830 100644
--- a/src/INTERLAYER/pair_ilp_tmd.h
+++ b/src/INTERLAYER/pair_ilp_tmd.h
@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
diff --git a/src/INTERLAYER/pair_ilp_water_2dm.cpp b/src/INTERLAYER/pair_ilp_water_2dm.cpp
index 58e56894f5..2eb50305cc 100644
--- a/src/INTERLAYER/pair_ilp_water_2dm.cpp
+++ b/src/INTERLAYER/pair_ilp_water_2dm.cpp
@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -22,7 +22,6 @@
 
 #include "atom.h"
 #include "citeme.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "interlayer_taper.h"
@@ -30,7 +29,6 @@
 #include "my_page.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "neighbor.h"
 
 #include <cmath>
 #include <cstring>
@@ -42,15 +40,16 @@ using namespace InterLayer;
 #define DELTA 4
 #define PGDELTA 1
 
-static const char cite_ilp_water[] = "ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464\n"
-                                   "@Article{Feng2023\n"
-                                   " author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},\n"
-                                   " title = {Registry-Dependent Potential for Interfaces of Water with Graphene},\n"
-                                   " journal = {J. Phys. Chem. C},\n"
-                                   " volume =  127,\n"
-                                   " pages =   {8704-8713}\n"
-                                   " year =    2023,\n"
-                                   "}\n\n";
+static const char cite_ilp_water[] = 
+    "ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464\n"
+    "@Article{Feng2023\n"
+    " author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},\n"
+    " title = {Registry-Dependent Potential for Interfaces of Water with Graphene},\n"
+    " journal = {J. Phys. Chem. C},\n"
+    " volume =  127,\n"
+    " pages =   {8704-8713}\n"
+    " year =    2023,\n"
+    "}\n\n";
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/INTERLAYER/pair_ilp_water_2dm.h b/src/INTERLAYER/pair_ilp_water_2dm.h
index c35d757ea0..fad9f99ff1 100644
--- a/src/INTERLAYER/pair_ilp_water_2dm.h
+++ b/src/INTERLAYER/pair_ilp_water_2dm.h
@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -46,22 +46,3 @@ class PairILPWATER2DM : virtual public PairILPTMD {
 
 #endif
 #endif
-
-/* ERROR/WARNING messages:
-
-E: Illegal ... command
-
-Self-explanatory.  Check the input script syntax and compare to the
-documentation for the command.  You can use -echo screen as a
-command-line option when running LAMMPS to see the offending line.
-
-E: Incorrect args for pair coefficients
-
-Self-explanatory.  Check the input script or data file.
-
-E: All pair coeffs are not set
-
-All pair coefficients must be set in the data file or by the
-pair_coeff command before running a simulation.
-
-*/

From 887534fd0211695a2086905ed568d6d0a4da3840 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Thu, 1 Jun 2023 21:12:11 +0800
Subject: [PATCH 141/396] fix checkstyle

---
 src/INTERLAYER/pair_ilp_tmd.cpp       | 10 +++++-----
 src/INTERLAYER/pair_ilp_water_2dm.cpp |  2 +-
 src/OPT/pair_ilp_graphene_hbn_opt.cpp |  3 +--
 src/OPT/pair_ilp_graphene_hbn_opt.h   |  2 +-
 src/OPT/pair_ilp_water_2dm_opt.cpp    |  2 +-
 src/OPT/pair_ilp_water_2dm_opt.h      |  2 +-
 6 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/src/INTERLAYER/pair_ilp_tmd.cpp b/src/INTERLAYER/pair_ilp_tmd.cpp
index f5636ce3fa..c1af7098cd 100644
--- a/src/INTERLAYER/pair_ilp_tmd.cpp
+++ b/src/INTERLAYER/pair_ilp_tmd.cpp
@@ -488,11 +488,11 @@ void PairILPTMD::calc_normal()
           jH2 = atom->map(tag[i] - 2);
           iH1 = map[type[jH1]];
           iH2 = map[type[jH2]];
-          if (strcmp(elements[iH1], "Ow") == 0 ) { 
+          if (strcmp(elements[iH1], "Ow") == 0 ) {
             vect[0][0] = x[jH1][0] - xtp;
             vect[0][1] = x[jH1][1] - ytp;
             vect[0][2] = x[jH1][2] - ztp;
-          } else if (strcmp(elements[iH2], "Ow") == 0 ) { 
+          } else if (strcmp(elements[iH2], "Ow") == 0 ) {
             vect[0][0] = x[jH2][0] - xtp;
             vect[0][1] = x[jH2][1] - ytp;
             vect[0][2] = x[jH2][2] - ztp;
@@ -518,7 +518,7 @@ void PairILPTMD::calc_normal()
         // Calculte dNave/dri, defined as dpvdri
         for (id = 0; id < 3; id++) {
           for (ip = 0; ip < 3; ip++) {
-            if (ip == id) { dpvdri[id][ip] = -1.0;} 
+            if (ip == id) { dpvdri[id][ip] = -1.0;}
             else {dpvdri[id][ip] = 0.0;}
           }
         }
@@ -682,12 +682,12 @@ void PairILPTMD::calc_normal()
           normal[i][2] = Nave[2] / nn;
 
           // derivatives of non-normalized normal vector, dNave:3xcontx3 array
-          // dNave[id][m][ip]: the derivatve of the id component of Nave 
+          // dNave[id][m][ip]: the derivatve of the id component of Nave
           // respect to the ip component of atom m
           for (id = 0; id < 3; id++) {
             for (ip = 0; ip < 3; ip++) {
               for (m = 0; m < cont; m++) {
-                if (ip == id) { dNave[id][m][ip] = 0.5;} 
+                if (ip == id) { dNave[id][m][ip] = 0.5;}
                 else {dNave[id][m][ip] = 0.0;}
               }
             }
diff --git a/src/INTERLAYER/pair_ilp_water_2dm.cpp b/src/INTERLAYER/pair_ilp_water_2dm.cpp
index 2eb50305cc..3747d249de 100644
--- a/src/INTERLAYER/pair_ilp_water_2dm.cpp
+++ b/src/INTERLAYER/pair_ilp_water_2dm.cpp
@@ -40,7 +40,7 @@ using namespace InterLayer;
 #define DELTA 4
 #define PGDELTA 1
 
-static const char cite_ilp_water[] = 
+static const char cite_ilp_water[] =
     "ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464\n"
     "@Article{Feng2023\n"
     " author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},\n"
diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.cpp b/src/OPT/pair_ilp_graphene_hbn_opt.cpp
index 63822ad4c6..e8cb205a52 100644
--- a/src/OPT/pair_ilp_graphene_hbn_opt.cpp
+++ b/src/OPT/pair_ilp_graphene_hbn_opt.cpp
@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@@ -471,7 +471,6 @@ inline void deriv_hat(double dnhatdn[3][3], double *n, double rnnorm, double fac
   dnhatdn[0][2] = -n[0]*n[2]*cfactor;
   dnhatdn[1][2] = -n[1]*n[2]*cfactor;
   dnhatdn[2][2] = (n[0]*n[0]+n[1]*n[1])*cfactor;
-    
 }
 inline double normalize_factor(double *n)
 {
diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.h b/src/OPT/pair_ilp_graphene_hbn_opt.h
index bc22ab22b0..41d2178092 100644
--- a/src/OPT/pair_ilp_graphene_hbn_opt.h
+++ b/src/OPT/pair_ilp_graphene_hbn_opt.h
@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
diff --git a/src/OPT/pair_ilp_water_2dm_opt.cpp b/src/OPT/pair_ilp_water_2dm_opt.cpp
index 6cdac00ed9..316551c345 100644
--- a/src/OPT/pair_ilp_water_2dm_opt.cpp
+++ b/src/OPT/pair_ilp_water_2dm_opt.cpp
@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
diff --git a/src/OPT/pair_ilp_water_2dm_opt.h b/src/OPT/pair_ilp_water_2dm_opt.h
index 25905643af..8062de880a 100644
--- a/src/OPT/pair_ilp_water_2dm_opt.h
+++ b/src/OPT/pair_ilp_water_2dm_opt.h
@@ -1,7 +1,7 @@
   /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

From a4f4f965e3f1688d0e7da135c8809081a4e6083a Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Thu, 1 Jun 2023 21:45:52 +0800
Subject: [PATCH 142/396] fix a bug in the codes

---
 src/INTERLAYER/pair_ilp_graphene_hbn.cpp | 1 +
 src/INTERLAYER/pair_ilp_graphene_hbn.h   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
index 401d7f7b12..6d7526e3dd 100644
--- a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
+++ b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
@@ -59,6 +59,7 @@ static const char cite_ilp[] =
 static std::map<int, std::string> variant_map = {
     {PairILPGrapheneHBN::ILP_GrhBN, "ilp/graphene/hbn"},
     {PairILPGrapheneHBN::ILP_TMD, "ilp/tmd"},
+    {PairILPGrapheneHBN::ILP_WATER_2DM, "ilp/water/2dm"},
     {PairILPGrapheneHBN::SAIP_METAL, "saip/metal"}};
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.h b/src/INTERLAYER/pair_ilp_graphene_hbn.h
index 9987830b1d..e27fce420a 100644
--- a/src/INTERLAYER/pair_ilp_graphene_hbn.h
+++ b/src/INTERLAYER/pair_ilp_graphene_hbn.h
@@ -39,7 +39,7 @@ class PairILPGrapheneHBN : public Pair {
 
   static constexpr int NPARAMS_PER_LINE = 13;
 
-  enum { ILP_GrhBN, ILP_TMD, SAIP_METAL };    // for telling class variants apart in shared code
+  enum { ILP_GrhBN, ILP_TMD, SAIP_METAL, ILP_WATER_2DM };    // for telling class variants apart in shared code
 
  protected:
   int me;

From 08ffd268bff9734217ea14be6d223810fd983991 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Fri, 2 Jun 2023 09:43:58 +0300
Subject: [PATCH 143/396] remove unused symbolic constant

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 071bdf31ee..3ae758b875 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -40,8 +40,6 @@ using namespace LAMMPS_NS;
 enum{X,Y,Z};
 enum{TOTAL,CONF,KIN,PAIR,BOND,ANGLE};
 
-#define BIG 1000000000
-
 /* ---------------------------------------------------------------------- */
 
 ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :

From 8ef4e933b25610a841a8107412cdb7a69cbb50da Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Fri, 2 Jun 2023 10:17:38 -0600
Subject: [PATCH 144/396] Fix bug when Kokkos border comm is on host

---
 src/KOKKOS/comm_kokkos.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp
index 7d007a666c..b0394821fc 100644
--- a/src/KOKKOS/comm_kokkos.cpp
+++ b/src/KOKKOS/comm_kokkos.cpp
@@ -980,9 +980,9 @@ void CommKokkos::borders()
   } else {
     atomKK->sync(Host,ALL_MASK);
     k_sendlist.sync<LMPHostType>();
-    CommBrick::borders();
     k_sendlist.modify<LMPHostType>();
-    atomKK->modified(Host,ALL_MASK);
+    atomKK->modified(Host,ALL_MASK); // needed here for atom map
+    CommBrick::borders();
   }
 
   if (comm->nprocs == 1 && !ghost_velocity && !forward_comm_classic)

From 70507462e9e04e8466e9e7c48a56f065235f871d Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Fri, 2 Jun 2023 19:22:28 +0300
Subject: [PATCH 145/396] Include method for bond contribution & variables to
 compute_stress_mop_profile.h

---
 src/EXTRA-COMPUTE/compute_stress_mop_profile.h | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.h b/src/EXTRA-COMPUTE/compute_stress_mop_profile.h
index b58f762c12..7bb87fa4c6 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.h
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.h
@@ -38,16 +38,20 @@ class ComputeStressMopProfile : public Compute {
 
  private:
   void compute_pairs();
+  void compute_bonds();
   void setup_bins();
 
   int me, nvalues, dir;
   int *which;
 
+  int bondflag;
+
   int originflag;
   double origin, delta, offset, invdelta;
   int nbins;
   double **coord, **coordp;
   double **values_local, **values_global;
+  double **bond_local, **bond_global;
 
   double dt, nktv2p, ftm2v;
   double area;

From e7ae02dd2a53b12f8b6de5eabea4d9750d98b085 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Fri, 2 Jun 2023 19:33:15 +0300
Subject: [PATCH 146/396] Code for bond contribution to stress/mop/profile

---
 .../compute_stress_mop_profile.cpp            | 169 +++++++++++++++++-
 1 file changed, 162 insertions(+), 7 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index ffcc712548..d15067a266 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -19,8 +19,11 @@
 #include "compute_stress_mop_profile.h"
 
 #include "atom.h"
+#include "atom_vec.h"
+#include "bond.h"
 #include "update.h"
 #include "domain.h"
+#include "molecule.h"
 #include "neighbor.h"
 #include "force.h"
 #include "pair.h"
@@ -35,9 +38,7 @@ using namespace LAMMPS_NS;
 
 enum{X,Y,Z};
 enum{LOWER,CENTER,UPPER,COORD};
-enum{TOTAL,CONF,KIN};
-
-#define BIG 1000000000
+enum{TOTAL,CONF,KIN,PAIR,BOND};
 
 /* ---------------------------------------------------------------------- */
 
@@ -48,6 +49,8 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
 
   MPI_Comm_rank(world,&me);
 
+  bondflag = 0;
+
   // set compute mode and direction of plane(s) for pressure calculation
 
   if (strcmp(arg[3],"x")==0) {
@@ -92,6 +95,16 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
         which[nvalues] = TOTAL;
         nvalues++;
       }
+    } else if (strcmp(arg[iarg],"pair") == 0) {
+      for (i=0; i<3; i++) {
+        which[nvalues] = PAIR;
+        nvalues++;
+      }
+    } else if (strcmp(arg[iarg],"bond") == 0) {
+      for (i=0; i<3; i++) {
+        which[nvalues] = PAIR;
+        nvalues++;
+      }
     } else error->all(FLERR, "Illegal compute stress/mop/profile command"); //break;
 
     iarg++;
@@ -114,6 +127,8 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
   nbins = 0;
   coord = coordp = nullptr;
   values_local = values_global = array = nullptr;
+  bond_local = nullptr;
+  bond_global = nullptr;
 
   // bin setup
 
@@ -140,6 +155,8 @@ ComputeStressMopProfile::~ComputeStressMopProfile()
   memory->destroy(coordp);
   memory->destroy(values_local);
   memory->destroy(values_global);
+  memory->destroy(bond_local);
+  memory->destroy(bond_global);
   memory->destroy(array);
 }
 
@@ -185,8 +202,8 @@ void ComputeStressMopProfile::init()
     //Compute stress/mop/profile only accounts for pair interactions.
     // issue an error if any intramolecular potential or Kspace is defined.
 
-    if (force->bond!=nullptr)
-      error->all(FLERR,"compute stress/mop/profile does not account for bond potentials");
+    if (force->bond!=nullptr) bondflag = 1;
+
     if (force->angle!=nullptr)
       error->all(FLERR,"compute stress/mop/profile does not account for angle potentials");
     if (force->dihedral!=nullptr)
@@ -225,6 +242,21 @@ void ComputeStressMopProfile::compute_array()
   MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,
                 MPI_DOUBLE,MPI_SUM,world);
 
+  if (bondflag) {
+    //Compute bond contribution on separate procs
+    compute_bonds();
+  } else {
+    for (int m = 0; m < nbins; m++) {
+      for (int i = 0; i < nvalues; i++) {
+        bond_local[m][i] = 0.0;
+      }
+    }
+  }
+
+  // sum bond contribution over all procs
+  MPI_Allreduce(&bond_local[0][0],&bond_global[0][0],nbins*nvalues,
+                MPI_DOUBLE,MPI_SUM,world);
+
   int ibin,m,mo;
   for (ibin=0; ibin<nbins; ibin++) {
     array[ibin][0] = coord[ibin][0];
@@ -232,7 +264,7 @@ void ComputeStressMopProfile::compute_array()
 
     m = 0;
     while (m<nvalues) {
-      array[ibin][m+mo] = values_global[ibin][m];
+      array[ibin][m+mo] = values_global[ibin][m] + bond_global[ibin][m];
       m++;
     }
   }
@@ -290,7 +322,7 @@ void ComputeStressMopProfile::compute_pairs()
 
   m = 0;
   while (m<nvalues) {
-    if (which[m] == CONF || which[m] == TOTAL) {
+    if (which[m] == CONF || which[m] == TOTAL || which[m] == PAIR) {
 
       // Compute configurational contribution to pressure
 
@@ -452,6 +484,127 @@ void ComputeStressMopProfile::compute_pairs()
   }
 }
 
+/*------------------------------------------------------------------------
+  compute bond contribution to pressure of local proc
+  -------------------------------------------------------------------------*/
+
+void ComputeStressMopProfile::compute_bonds()
+{
+  int i, nb, atom1, atom2, imol, iatom, btype;
+  tagint tagprev;
+  double rsq, fpair;
+
+  double **x = atom->x;
+  tagint *tag = atom->tag;
+  int *num_bond = atom->num_bond;
+  tagint **bond_atom = atom->bond_atom;
+  int **bond_type = atom->bond_type;
+  int *mask = atom->mask;
+
+  int *molindex = atom->molindex;
+  int *molatom = atom->molatom;
+  Molecule **onemols = atom->avec->onemols;
+
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+  int molecular = atom->molecular;
+
+  Bond *bond = force->bond;
+
+  double dx[3] {0};
+  double x_bond_1[3] {0};
+  double x_bond_2[3] {0};
+  double local_contribution[nbins][3] {0};
+
+  // initialization
+  for (int m {0}; m < nbins; m++) {
+    for (int i {0}; i < nvalues; i++) {
+      bond_local[m][i] = 0.0;
+    }
+  }
+
+  // loop over all bonded atoms in the current proc
+  for (atom1 = 0; atom1 < nlocal; atom1++) {
+    if (!(mask[atom1] & groupbit)) continue;
+
+    if (molecular == 1)
+      nb = num_bond[atom1];
+    else {
+      if (molindex[atom1] < 0) continue;
+      imol = molindex[atom1];
+      iatom = molatom[atom1];
+      nb = onemols[imol]->num_bond[iatom];
+    }
+
+    for (i = 0; i < nb; i++) {
+      if (molecular == 1) {
+        btype = bond_type[atom1][i];
+        atom2 = atom->map(bond_atom[atom1][i]);
+      } else {
+        tagprev = tag[atom1] - iatom - 1;
+        btype = onemols[imol]->bond_type[iatom][i];
+        atom2 = atom->map(onemols[imol]->bond_atom[iatom][i] + tagprev);
+      }
+
+      if (atom2 < 0 || !(mask[atom2] & groupbit)) continue;
+      if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
+      if (btype <= 0) continue;
+
+      for (int ibin {0}; ibin<nbins; ibin++) {
+        double pos = coord[ibin][0];
+
+        // minimum image of atom1 with respect to the plane of interest
+        dx[0] = x[atom1][0];
+        dx[1] = x[atom1][1];
+        dx[2] = x[atom1][2];
+        dx[dir] -= pos;
+        domain->minimum_image(dx[0], dx[1], dx[2]);
+        x_bond_1[0] = dx[0];
+        x_bond_1[1] = dx[1];
+        x_bond_1[2] = dx[2];
+        x_bond_1[dir] += pos;
+
+        // minimum image of atom2 with respect to atom1
+        dx[0] = x[atom2][0] - x_bond_1[0];
+        dx[1] = x[atom2][1] - x_bond_1[1];
+        dx[2] = x[atom2][2] - x_bond_1[2];
+        domain->minimum_image(dx[0], dx[1], dx[2]);
+        x_bond_2[0] = x_bond_1[0] + dx[0];
+        x_bond_2[1] = x_bond_1[1] + dx[1];
+        x_bond_2[2] = x_bond_1[2] + dx[2];
+
+        // check if the bond vector crosses the plane of interest
+        double tau = (x_bond_1[dir] - pos) / (x_bond_1[dir] - x_bond_2[dir]);
+        if ((tau <= 1) && (tau >= 0)) {
+          dx[0] = x_bond_1[0] - x_bond_2[0];
+          dx[1] = x_bond_1[1] - x_bond_2[1];
+          dx[2] = x_bond_1[2] - x_bond_2[2];
+          rsq = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
+          bond->single(btype, rsq, atom1, atom2, fpair);
+
+          double sgn = copysign(1.0, x_bond_1[dir] - pos);
+          local_contribution[ibin][0] += sgn*fpair*dx[0]/area*nktv2p;
+          local_contribution[ibin][1] += sgn*fpair*dx[1]/area*nktv2p;
+          local_contribution[ibin][2] += sgn*fpair*dx[2]/area*nktv2p;
+        }
+      }
+    }
+  }
+
+  // loop over the keywords and if necessary add the bond contribution
+  int m {0};
+  while (m<nvalues) {
+    if (which[m] == CONF || which[m] == TOTAL || which[m] == BOND) { // Axel
+      for (int ibin {0}; ibin < nbins; ibin++) {
+        bond_local[ibin][m] = local_contribution[ibin][0];
+        bond_local[ibin][m+1] = local_contribution[ibin][1];
+        bond_local[ibin][m+2] = local_contribution[ibin][2];
+      }
+    }
+    m += 3;
+  }
+} 
+
 /* ----------------------------------------------------------------------
    setup 1d bins and their extent and coordinates
    called at init()
@@ -492,6 +645,8 @@ void ComputeStressMopProfile::setup_bins()
   memory->create(coordp,nbins,1,"stress/mop/profile:coordp");
   memory->create(values_local,nbins,nvalues,"stress/mop/profile:values_local");
   memory->create(values_global,nbins,nvalues,"stress/mop/profile:values_global");
+  memory->create(bond_local,nbins,nvalues,"stress/mop/profile:bond_local");
+  memory->create(bond_global,nbins,nvalues,"stress/mop/profile:bond_global");
 
   // set bin coordinates
   for (i = 0; i < nbins; i++) {

From c30762ca8bfd35bb8554e2024ea57462298fa2e5 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Fri, 2 Jun 2023 19:44:37 +0300
Subject: [PATCH 147/396] Update documentation for compute stress/mop/profile

---
 doc/src/compute_stress_mop.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst
index b4c15257af..e1b151ebbd 100644
--- a/doc/src/compute_stress_mop.rst
+++ b/doc/src/compute_stress_mop.rst
@@ -68,7 +68,7 @@ Between one and six keywords can be used to indicate which
 contributions to the stress must be computed: total stress (total),  kinetic stress (kin),
 configurational stress (conf), stress due to bond stretching (bond),
 stress due to angle bending (angle) and/or due to pairwise non-bonded interactions (pair).
-The last three keywords are currently available only for the stress/mop command and not the stress/mop/profile. 
+The angle keyword is currently available only for the stress/mop command and not the stress/mop/profile. 
 
 NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
 
@@ -120,8 +120,8 @@ size does not change in time, and axis-aligned planes.
 The method only works with two-body pair interactions, because it
 requires the class method pair->single() to be implemented. In
 particular, compute *stress/mop/profile* does not work with more than 
-two-body pair interactions, intra-molecular interactions, and long range 
-(kspace) interactions. Similarly, compute *stress/mop* does not work with more than 
+two-body pair interactions, long range (kspace) interactions and angle/dihedral/improper
+intramolecular interactions. Similarly, compute *stress/mop* does not work with more than 
 two-body pair interactions, long range (kspace) interactions and dihedral/improper
 intramolecular interactions but works with all bond interactions with the class method
 single() implemented and all angle interactions with the class method born_matrix() 

From 28e3a741a8e84d7512e10c34364ac198cf456266 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Fri, 2 Jun 2023 20:02:52 +0300
Subject: [PATCH 148/396] declare local_contribution as pointer in
 compute_stress_mop_profile.h

---
 src/EXTRA-COMPUTE/compute_stress_mop_profile.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.h b/src/EXTRA-COMPUTE/compute_stress_mop_profile.h
index 7bb87fa4c6..1015d6e3eb 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.h
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.h
@@ -52,6 +52,7 @@ class ComputeStressMopProfile : public Compute {
   double **coord, **coordp;
   double **values_local, **values_global;
   double **bond_local, **bond_global;
+  double **local_contribution;
 
   double dt, nktv2p, ftm2v;
   double area;

From 9dc1f45e1e7df4915740479fb29bd1944c99aecf Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Fri, 2 Jun 2023 20:08:59 +0300
Subject: [PATCH 149/396] Create/destroy  local_contribution

---
 src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index d15067a266..3a60342887 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -129,6 +129,7 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
   values_local = values_global = array = nullptr;
   bond_local = nullptr;
   bond_global = nullptr;
+  local_contribution = nullptr;
 
   // bin setup
 
@@ -157,6 +158,7 @@ ComputeStressMopProfile::~ComputeStressMopProfile()
   memory->destroy(values_global);
   memory->destroy(bond_local);
   memory->destroy(bond_global);
+  memory->destroy(local_contribution);
   memory->destroy(array);
 }
 
@@ -514,13 +516,15 @@ void ComputeStressMopProfile::compute_bonds()
   double dx[3] {0};
   double x_bond_1[3] {0};
   double x_bond_2[3] {0};
-  double local_contribution[nbins][3] {0};
 
   // initialization
   for (int m {0}; m < nbins; m++) {
     for (int i {0}; i < nvalues; i++) {
       bond_local[m][i] = 0.0;
     }
+    local_contribution[m][0] = 0.0;
+    local_contribution[m][1] = 0.0;
+    local_contribution[m][2] = 0.0;
   }
 
   // loop over all bonded atoms in the current proc
@@ -647,6 +651,7 @@ void ComputeStressMopProfile::setup_bins()
   memory->create(values_global,nbins,nvalues,"stress/mop/profile:values_global");
   memory->create(bond_local,nbins,nvalues,"stress/mop/profile:bond_local");
   memory->create(bond_global,nbins,nvalues,"stress/mop/profile:bond_global");
+  memory->create(local_contribution,nbins,3,"stress/mop/profile:local_contribution");
 
   // set bin coordinates
   for (i = 0; i < nbins; i++) {

From 390888179fa2282ac9cd60f5eb5745260708d1a3 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Fri, 2 Jun 2023 20:24:32 +0300
Subject: [PATCH 150/396] Update compute_stress_mop_profile.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index 3a60342887..d299633731 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -102,7 +102,7 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
       }
     } else if (strcmp(arg[iarg],"bond") == 0) {
       for (i=0; i<3; i++) {
-        which[nvalues] = PAIR;
+        which[nvalues] = BOND;
         nvalues++;
       }
     } else error->all(FLERR, "Illegal compute stress/mop/profile command"); //break;

From 40cd3bbdc4f976790f484fdb1b560179cfb9096b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 2 Jun 2023 16:29:10 -0400
Subject: [PATCH 151/396] add cache line size padding to avoid false sharing
 with OPENMP package

---
 src/my_page.h | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/my_page.h b/src/my_page.h
index 6c06abd71e..ea19dc8e74 100644
--- a/src/my_page.h
+++ b/src/my_page.h
@@ -104,6 +104,9 @@ template <class T> class MyPage {
   int errorflag;    // flag > 0 if error has occurred
                     // 1 = chunk size exceeded maxchunk
                     // 2 = memory allocation error
+#if defined(_OPENMP)
+  char pad[64];     // to avoid false sharing with multi-threading
+#endif
   void allocate();
   void deallocate();
 };

From 241f3b751e38df598b5d32c6f9bf9812e05c24d2 Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Fri, 2 Jun 2023 15:45:53 -0600
Subject: [PATCH 152/396] Unifying syntax for BPM bond options

---
 doc/src/bond_bpm_rotational.rst | 12 ++++++------
 doc/src/bond_bpm_spring.rst     | 14 +++++++-------
 src/BPM/bond_bpm.cpp            |  8 +++++---
 3 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/doc/src/bond_bpm_rotational.rst b/doc/src/bond_bpm_rotational.rst
index 0baf7e35b1..ca12d86ccc 100644
--- a/doc/src/bond_bpm_rotational.rst
+++ b/doc/src/bond_bpm_rotational.rst
@@ -24,7 +24,7 @@ Syntax
             *x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
             *x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
 
-       *overlay/pair* value = none
+       *overlay/pair* value = *yes* or *no*
           bonded particles will still interact with pair forces
 
        *smooth* value = *yes* or *no*
@@ -33,8 +33,8 @@ Syntax
        *normalize* value = *yes* or *no*
           normalizes normal and shear forces by the reference length
 
-       *break/no*
-          indicates that bonds should not break during a run
+       *break* value = *yes* or *no*
+          indicates whether bonds break during a run
 
 Examples
 """"""""
@@ -144,14 +144,14 @@ by :math:`r_0` such that :math:`k_r` and :math:`k_s` are unit less.
 
 By default, pair forces are not calculated between bonded particles.
 Pair forces can alternatively be overlaid on top of bond forces using
-the *overlay/pair* keyword. These settings require specific
+the *overlay/pair* option. These settings require specific
 :doc:`special_bonds <special_bonds>` settings described in the
 restrictions.  Further details can be found in the `:doc: how to
 <Howto_BPM>` page on BPMs.
 
 .. versionadded:: 28Mar2023
 
-If the *break/no* keyword is used, then LAMMPS assumes bonds should not break
+If the *break* option is used, then LAMMPS assumes bonds should not break
 during a simulation run. This will prevent some unnecessary calculation.
 However, if a bond does break, it will trigger an error.
 
@@ -257,7 +257,7 @@ Related commands
 Default
 """""""
 
-The option defaults are *smooth* = *yes*
+The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
 
 ----------
 
diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst
index 6da0d25a4a..d89035dcad 100644
--- a/doc/src/bond_bpm_spring.rst
+++ b/doc/src/bond_bpm_spring.rst
@@ -24,17 +24,17 @@ Syntax
             *x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
             *x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
 
-       *overlay/pair* value = none
+       *overlay/pair* value = *yes* or *no*
           bonded particles will still interact with pair forces
 
        *smooth* value = *yes* or *no*
           smooths bond forces near the breaking point
 
        *normalize* value = *yes* or *no*
-          normalizes bond forces by their reference length
+          normalizes bond forces by the reference length
 
-       *break/no*
-          indicates that bonds should not break during a run
+       *break* value = *yes* or *no*
+          indicates whether bonds break during a run
 
 Examples
 """"""""
@@ -110,14 +110,14 @@ However, the *normalize* option will normalize the elastic bond force by
 
 By default, pair forces are not calculated between bonded particles.
 Pair forces can alternatively be overlaid on top of bond forces using
-the *overlay/pair* keyword. These settings require specific
+the *overlay/pair* option. These settings require specific
 :doc:`special_bonds <special_bonds>` settings described in the
 restrictions.  Further details can be found in the `:doc: how to
 <Howto_BPM>` page on BPMs.
 
 .. versionadded:: 28Mar2023
 
-If the *break/no* keyword is used, then LAMMPS assumes bonds should not break
+If the *break* option is used, then LAMMPS assumes bonds should not break
 during a simulation run. This will prevent some unnecessary calculation.
 However, if a bond does break, it will trigger an error.
 
@@ -212,7 +212,7 @@ Related commands
 Default
 """""""
 
-The option defaults are *smooth* = *yes*
+The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
 
 ----------
 
diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp
index a68aea3e68..da189ccaf5 100644
--- a/src/BPM/bond_bpm.cpp
+++ b/src/BPM/bond_bpm.cpp
@@ -187,10 +187,12 @@ void BondBPM::settings(int narg, char **arg)
         iarg++;
       }
     } else if (strcmp(arg[iarg], "overlay/pair") == 0) {
-      overlay_flag = 1;
+      if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for overlay/pair");
+      overlay_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
       iarg++;
-    } else if (strcmp(arg[iarg], "break/no") == 0) {
-      break_flag = 0;
+    } else if (strcmp(arg[iarg], "break") == 0) {
+      if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for break");
+      break_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
       iarg++;
     } else {
       leftover_iarg.push_back(iarg);

From a42bfb0e26e8391076719f36a425c5d41ca41a23 Mon Sep 17 00:00:00 2001
From: rohskopf <drew.rohskopf@gmail.com>
Date: Fri, 2 Jun 2023 17:26:40 -0600
Subject: [PATCH 153/396] Make cutoff factor 1 instead of 0 to prevent zero
 valued descriptors

---
 src/KOKKOS/sna_kokkos_impl.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h
index fd58f1c4f3..d5690ea60a 100644
--- a/src/KOKKOS/sna_kokkos_impl.h
+++ b/src/KOKKOS/sna_kokkos_impl.h
@@ -2298,7 +2298,7 @@ void SNAKokkos<DeviceType, real_type, vector_length>::compute_s_dsfac(const real
   constexpr real_type zero = static_cast<real_type>(0.0);
   constexpr real_type onehalf = static_cast<real_type>(0.5);
 
-  if (switch_flag == 0) { sfac_outer = zero; dsfac_outer = zero; }
+  if (switch_flag == 0) { sfac_outer = one; dsfac_outer = zero; }
   else if (switch_flag == 1) {
     if (r <= rmin0) { sfac_outer = one; dsfac_outer = zero; }
     else if (r > rcut) { sfac = zero; dsfac = zero; return; }

From 250eac93dccb4057e2abec357496624e1c3fbbee Mon Sep 17 00:00:00 2001
From: Xin Wu <xin.wu@uni-paderborn.de>
Date: Sat, 3 Jun 2023 07:34:39 +0200
Subject: [PATCH 154/396] fix bug in the reaxff HNS benchmark

---
 examples/reaxff/HNS/in.reaxc.hns | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/reaxff/HNS/in.reaxc.hns b/examples/reaxff/HNS/in.reaxc.hns
index 775a389eca..5b83698917 100644
--- a/examples/reaxff/HNS/in.reaxc.hns
+++ b/examples/reaxff/HNS/in.reaxc.hns
@@ -37,4 +37,4 @@ velocity          all create 300.0 41279 loop geom
 fix               1 all nve
 fix               2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
 
-run               100
+run               $t

From 2e7ca5f65cc8fd421a04b324a6815953e1641d37 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sat, 3 Jun 2023 18:14:45 +0800
Subject: [PATCH 155/396] rename the pair style

---
 .../{pair_ilp_water_2dm.cpp => pair_aip_water_2dm.cpp}          | 0
 src/INTERLAYER/{pair_ilp_water_2dm.h => pair_aip_water_2dm.h}   | 0
 src/INTERLAYER/pair_ilp_graphene_hbn.cpp                        | 2 +-
 src/INTERLAYER/pair_ilp_graphene_hbn.h                          | 2 +-
 4 files changed, 2 insertions(+), 2 deletions(-)
 rename src/INTERLAYER/{pair_ilp_water_2dm.cpp => pair_aip_water_2dm.cpp} (100%)
 rename src/INTERLAYER/{pair_ilp_water_2dm.h => pair_aip_water_2dm.h} (100%)

diff --git a/src/INTERLAYER/pair_ilp_water_2dm.cpp b/src/INTERLAYER/pair_aip_water_2dm.cpp
similarity index 100%
rename from src/INTERLAYER/pair_ilp_water_2dm.cpp
rename to src/INTERLAYER/pair_aip_water_2dm.cpp
diff --git a/src/INTERLAYER/pair_ilp_water_2dm.h b/src/INTERLAYER/pair_aip_water_2dm.h
similarity index 100%
rename from src/INTERLAYER/pair_ilp_water_2dm.h
rename to src/INTERLAYER/pair_aip_water_2dm.h
diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
index 6d7526e3dd..e6711d0f19 100644
--- a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
+++ b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
@@ -59,7 +59,7 @@ static const char cite_ilp[] =
 static std::map<int, std::string> variant_map = {
     {PairILPGrapheneHBN::ILP_GrhBN, "ilp/graphene/hbn"},
     {PairILPGrapheneHBN::ILP_TMD, "ilp/tmd"},
-    {PairILPGrapheneHBN::ILP_WATER_2DM, "ilp/water/2dm"},
+    {PairILPGrapheneHBN::AIP_WATER_2DM, "aip/water/2dm"},
     {PairILPGrapheneHBN::SAIP_METAL, "saip/metal"}};
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.h b/src/INTERLAYER/pair_ilp_graphene_hbn.h
index e27fce420a..e151ecc801 100644
--- a/src/INTERLAYER/pair_ilp_graphene_hbn.h
+++ b/src/INTERLAYER/pair_ilp_graphene_hbn.h
@@ -39,7 +39,7 @@ class PairILPGrapheneHBN : public Pair {
 
   static constexpr int NPARAMS_PER_LINE = 13;
 
-  enum { ILP_GrhBN, ILP_TMD, SAIP_METAL, ILP_WATER_2DM };    // for telling class variants apart in shared code
+  enum { ILP_GrhBN, ILP_TMD, SAIP_METAL, AIP_WATER_2DM };    // for telling class variants apart in shared code
 
  protected:
   int me;

From 8c6e2ca000b7ad201c3c2676582832066343fc00 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sat, 3 Jun 2023 20:34:42 +0800
Subject: [PATCH 156/396] rename the opt pair style

---
 ...2dm_opt.cpp => pair_aip_water_2dm_opt.cpp} |  0
 ...ter_2dm_opt.h => pair_aip_water_2dm_opt.h} |  0
 src/OPT/pair_ilp_graphene_hbn_opt.cpp         | 24 +++++++++----------
 3 files changed, 12 insertions(+), 12 deletions(-)
 rename src/OPT/{pair_ilp_water_2dm_opt.cpp => pair_aip_water_2dm_opt.cpp} (100%)
 rename src/OPT/{pair_ilp_water_2dm_opt.h => pair_aip_water_2dm_opt.h} (100%)

diff --git a/src/OPT/pair_ilp_water_2dm_opt.cpp b/src/OPT/pair_aip_water_2dm_opt.cpp
similarity index 100%
rename from src/OPT/pair_ilp_water_2dm_opt.cpp
rename to src/OPT/pair_aip_water_2dm_opt.cpp
diff --git a/src/OPT/pair_ilp_water_2dm_opt.h b/src/OPT/pair_aip_water_2dm_opt.h
similarity index 100%
rename from src/OPT/pair_ilp_water_2dm_opt.h
rename to src/OPT/pair_aip_water_2dm_opt.h
diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.cpp b/src/OPT/pair_ilp_graphene_hbn_opt.cpp
index e8cb205a52..b2abcec7be 100644
--- a/src/OPT/pair_ilp_graphene_hbn_opt.cpp
+++ b/src/OPT/pair_ilp_graphene_hbn_opt.cpp
@@ -169,33 +169,33 @@ void PairILPGrapheneHBNOpt::compute(int eflag, int vflag)
         }
       }
     }
-  } else if (variant == ILP_WATER_2DM) {
+  } else if (variant == AIP_WATER_2DM) {
     if (eflag_global || eflag_atom) {
       if (vflag_either) {
         if (tap_flag) {
-          eval<6, 1, 1, 1, ILP_WATER_2DM>();
+          eval<6, 1, 1, 1, AIP_WATER_2DM>();
         } else {
-          eval<6, 1, 1, 0, ILP_WATER_2DM>();
+          eval<6, 1, 1, 0, AIP_WATER_2DM>();
         }
       } else {
         if (tap_flag) {
-          eval<6, 1, 0, 1, ILP_WATER_2DM>();
+          eval<6, 1, 0, 1, AIP_WATER_2DM>();
         } else {
-          eval<6, 1, 0, 0, ILP_WATER_2DM>();
+          eval<6, 1, 0, 0, AIP_WATER_2DM>();
         }
       }
     } else {
       if (vflag_either) {
         if (tap_flag) {
-          eval<6, 0, 1, 1, ILP_WATER_2DM>();
+          eval<6, 0, 1, 1, AIP_WATER_2DM>();
         } else {
-          eval<6, 0, 1, 0, ILP_WATER_2DM>();
+          eval<6, 0, 1, 0, AIP_WATER_2DM>();
         }
       } else {
         if (tap_flag) {
-          eval<6, 0, 0, 1, ILP_WATER_2DM>();
+          eval<6, 0, 0, 1, AIP_WATER_2DM>();
         } else {
-          eval<6, 0, 0, 0, ILP_WATER_2DM>();
+          eval<6, 0, 0, 0, AIP_WATER_2DM>();
         }
       }
     }
@@ -286,7 +286,7 @@ void PairILPGrapheneHBNOpt::eval()
       rsq = delx * delx + dely * dely + delz * delz;
 
       if (rsq != 0 && rsq < cutILPsq[itype_map][jtype]) {
-        if ((VARIANT == ILP_TMD || VARIANT == ILP_WATER_2DM) && special_type[itype] == TMD_METAL && itype != type[j]) continue;
+        if ((VARIANT == ILP_TMD || VARIANT == AIP_WATER_2DM) && special_type[itype] == TMD_METAL && itype != type[j]) continue;
         if (ILP_nneigh >= MAX_NNEIGH) {
           error->one(FLERR, "There are too many neighbors for calculating normals");
         }
@@ -519,8 +519,8 @@ void PairILPGrapheneHBNOpt::calc_normal(int i, int itype, int *ILP_neigh, int nn
     vet[jj][2] = x[j][2] - x[i][2];
   }
 
-  //specialize for ILP_WATER_2DM for hydrogen has special normal vector rule
-  if (variant == ILP_WATER_2DM && special_type[itype] == WATER) {
+  //specialize for AIP_WATER_2DM for hydrogen has special normal vector rule
+  if (variant == AIP_WATER_2DM && special_type[itype] == WATER) {
     if (nneigh == 1){
       n[0] = vet[0][0];
       n[1] = vet[0][1];

From a25100120bf59ac93f772b4ae158d9f1a8508304 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sat, 3 Jun 2023 20:36:12 +0800
Subject: [PATCH 157/396] update the doc file

---
 doc/src/{pair_ilp_water_2dm.rst => pair_aip_water_2dm.rst} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename doc/src/{pair_ilp_water_2dm.rst => pair_aip_water_2dm.rst} (100%)

diff --git a/doc/src/pair_ilp_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst
similarity index 100%
rename from doc/src/pair_ilp_water_2dm.rst
rename to doc/src/pair_aip_water_2dm.rst

From d85342cd6da16eded485da0e544bc35eddf35b94 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sat, 3 Jun 2023 16:04:40 +0300
Subject: [PATCH 158/396] Update test_compute_global.cpp

---
 unittest/commands/test_compute_global.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/unittest/commands/test_compute_global.cpp b/unittest/commands/test_compute_global.cpp
index 66a24f049f..04913f51b5 100644
--- a/unittest/commands/test_compute_global.cpp
+++ b/unittest/commands/test_compute_global.cpp
@@ -169,7 +169,7 @@ TEST_F(ComputeGlobalTest, Geometry)
         command("compute mom1 all momentum");
         command("compute mom2 allwater momentum");
         command("compute mop1 all stress/mop x 0.0 total");
-        command("compute mop2 all stress/mop/profile z lower 0.5 kin conf");
+        command("compute mop2 all stress/mop/profile z lower 0.5 kin pair");
         thermo_style += " c_mu1 c_mu2 c_mop1[*] c_mop2[1][1]";
     }
 

From 738a955c4012397c0fadcbac740a6f48ad3d8909 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sat, 3 Jun 2023 22:37:57 +0800
Subject: [PATCH 159/396] fix checkstyle issues

---
 src/INTERLAYER/pair_aip_water_2dm.cpp | 14 +++++++-------
 src/INTERLAYER/pair_aip_water_2dm.h   | 19 +++++--------------
 src/OPT/pair_aip_water_2dm_opt.cpp    | 12 ++++++------
 src/OPT/pair_aip_water_2dm_opt.h      | 12 ++++++------
 4 files changed, 24 insertions(+), 33 deletions(-)

diff --git a/src/INTERLAYER/pair_aip_water_2dm.cpp b/src/INTERLAYER/pair_aip_water_2dm.cpp
index 3747d249de..d88676a6e2 100644
--- a/src/INTERLAYER/pair_aip_water_2dm.cpp
+++ b/src/INTERLAYER/pair_aip_water_2dm.cpp
@@ -18,7 +18,7 @@
    [Feng and Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).]
 ------------------------------------------------------------------------- */
 
-#include "pair_ilp_water_2dm.h"
+#include "pair_aip_water_2dm.h"
 
 #include "atom.h"
 #include "citeme.h"
@@ -40,7 +40,7 @@ using namespace InterLayer;
 #define DELTA 4
 #define PGDELTA 1
 
-static const char cite_ilp_water[] =
+static const char cite_aip_water[] =
     "ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464\n"
     "@Article{Feng2023\n"
     " author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},\n"
@@ -53,26 +53,26 @@ static const char cite_ilp_water[] =
 
 /* ---------------------------------------------------------------------- */
 
-PairILPWATER2DM::PairILPWATER2DM(LAMMPS *lmp) : PairILPGrapheneHBN(lmp), PairILPTMD(lmp)
+PairAIPWATER2DM::PairAIPWATER2DM(LAMMPS *lmp) : PairILPGrapheneHBN(lmp), PairILPTMD(lmp)
 {
-  variant = ILP_WATER_2DM;
+  variant = AIP_WATER_2DM;
   single_enable = 0;
 
   // for TMD, each atom have six neighbors
   Nnei = 6;
 
-  if (lmp->citeme) lmp->citeme->add(cite_ilp_water);
+  if (lmp->citeme) lmp->citeme->add(cite_aip_water);
 }
 
 /* ----------------------------------------------------------------------
    global settings
 ------------------------------------------------------------------------- */
 
-void PairILPWATER2DM::settings(int narg, char **arg)
+void PairAIPWATER2DM::settings(int narg, char **arg)
 {
   if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command");
   if (!utils::strmatch(force->pair_style, "^hybrid/overlay"))
-    error->all(FLERR, "Pair style ilp/water/2dm must be used as sub-style with hybrid/overlay");
+    error->all(FLERR, "Pair style aip/water/2dm must be used as sub-style with hybrid/overlay");
 
   cut_global = utils::numeric(FLERR, arg[0], false, lmp);
   if (narg == 2) tap_flag = utils::numeric(FLERR, arg[1], false, lmp);
diff --git a/src/INTERLAYER/pair_aip_water_2dm.h b/src/INTERLAYER/pair_aip_water_2dm.h
index fad9f99ff1..295cdfffb9 100644
--- a/src/INTERLAYER/pair_aip_water_2dm.h
+++ b/src/INTERLAYER/pair_aip_water_2dm.h
@@ -13,33 +13,24 @@
 
 #ifdef PAIR_CLASS
 // clang-format off
-PairStyle(ilp/water/2dm,PairILPWATER2DM);
+PairStyle(aip/water/2dm,PairAIPWATER2DM);
 // clang-format on
 #else
 
-#ifndef LMP_PAIR_ILP_WATER_2DM_H
-#define LMP_PAIR_ILP_WATER_2DM_H
+#ifndef LMP_PAIR_AIP_WATER_2DM_H
+#define LMP_PAIR_AIP_WATER_2DM_H
 
 #include "pair_ilp_tmd.h"
 
 namespace LAMMPS_NS {
 
-class PairILPWATER2DM : virtual public PairILPTMD {
+class PairAIPWATER2DM : virtual public PairILPTMD {
  public:
-  PairILPWATER2DM(class LAMMPS *);
+  PairAIPWATER2DM(class LAMMPS *);
 
  protected:
   void settings(int, char **) override;
 
-  /**************************************************************/
-  /*       modulo operation with cycling around range           */
-
-  inline int modulo(int k, int range)
-  {
-    if (k < 0) k += range;
-    return k % range;
-  }
-  /**************************************************************/
 };
 
 }    // namespace LAMMPS_NS
diff --git a/src/OPT/pair_aip_water_2dm_opt.cpp b/src/OPT/pair_aip_water_2dm_opt.cpp
index 316551c345..17e981e479 100644
--- a/src/OPT/pair_aip_water_2dm_opt.cpp
+++ b/src/OPT/pair_aip_water_2dm_opt.cpp
@@ -11,7 +11,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   This is an optimized version of ilp/water/2dm based on the contribution of:
+   This is an optimized version of aip/water/2dm based on the contribution of:
      author: Wengen Ouyang (Wuhan University)
      e-mail: w.g.ouyang at gmail dot com
 
@@ -30,7 +30,7 @@
    Potential is described by:
      [Feng and Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).]
 */
-#include "pair_ilp_water_2dm_opt.h"
+#include "pair_aip_water_2dm_opt.h"
 
 #include "atom.h"
 #include "citeme.h"
@@ -49,15 +49,15 @@
 using namespace LAMMPS_NS;
 using namespace InterLayer;
 
-PairILPWATER2DMOpt::PairILPWATER2DMOpt(LAMMPS *lmp) :
-  PairILPGrapheneHBN(lmp), PairILPTMD(lmp), PairILPWATER2DM(lmp), PairILPGrapheneHBNOpt(lmp)
+PairAIPWATER2DMOpt::PairAIPWATER2DMOpt(LAMMPS *lmp) :
+  PairILPGrapheneHBN(lmp), PairILPTMD(lmp), PairAIPWATER2DM(lmp), PairILPGrapheneHBNOpt(lmp)
 {
 }
 
-void PairILPWATER2DMOpt::coeff(int narg, char **args)
+void PairAIPWATER2DMOpt::coeff(int narg, char **args)
 {
   PairILPTMD::coeff(narg, args);
-  memory->create(special_type, atom->ntypes + 1, "PairILPWATER2DMOpt:check_sublayer");
+  memory->create(special_type, atom->ntypes + 1, "PairAIPWATER2DMOpt:check_sublayer");
   for (int i = 1; i <= atom->ntypes; i++) {
     int itype = map[i];
     if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
diff --git a/src/OPT/pair_aip_water_2dm_opt.h b/src/OPT/pair_aip_water_2dm_opt.h
index 8062de880a..46280c2b82 100644
--- a/src/OPT/pair_aip_water_2dm_opt.h
+++ b/src/OPT/pair_aip_water_2dm_opt.h
@@ -13,21 +13,21 @@
 
 #ifdef PAIR_CLASS
 // clang-format off
-PairStyle(ilp/water/2dm/opt,PairILPWATER2DMOpt);
+PairStyle(aip/water/2dm/opt,PairAIPWATER2DMOpt);
 // clang-format on
 #else
 
-#ifndef LMP_PAIR_ILP_WATER_2DM_OPT_H
-#define LMP_PAIR_ILP_WATER_2DM_OPT_H
+#ifndef LMP_PAIR_AIP_WATER_2DM_OPT_H
+#define LMP_PAIR_AIP_WATER_2DM_OPT_H
 
 #include "pair_ilp_graphene_hbn_opt.h"
-#include "pair_ilp_water_2dm.h"
+#include "pair_aip_water_2dm.h"
 
 namespace LAMMPS_NS {
 
-class PairILPWATER2DMOpt : public PairILPWATER2DM, public PairILPGrapheneHBNOpt {
+class PairAIPWATER2DMOpt : public PairAIPWATER2DM, public PairILPGrapheneHBNOpt {
  public:
-  PairILPWATER2DMOpt(class LAMMPS *);
+  PairAIPWATER2DMOpt(class LAMMPS *);
   void coeff(int narg, char **args) override;
 
  protected:

From a40b87b05c1e278b2c836c5d131d8b2a1603cd67 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sat, 3 Jun 2023 22:46:33 +0800
Subject: [PATCH 160/396] rename potential files

---
 potentials/{COH.DMC.ILP => COH.DMC.aip.water.2dm} | 6 +++---
 potentials/{COH.ILP => COH.aip.water.2dm}         | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)
 rename potentials/{COH.DMC.ILP => COH.DMC.aip.water.2dm} (91%)
 mode change 100755 => 100644
 rename potentials/{COH.ILP => COH.aip.water.2dm} (94%)
 mode change 100755 => 100644

diff --git a/potentials/COH.DMC.ILP b/potentials/COH.DMC.aip.water.2dm
old mode 100755
new mode 100644
similarity index 91%
rename from potentials/COH.DMC.ILP
rename to potentials/COH.DMC.aip.water.2dm
index 7235afcdab..f3619dd3f1
--- a/potentials/COH.DMC.ILP
+++ b/potentials/COH.DMC.aip.water.2dm
@@ -1,5 +1,5 @@
-# DATE: 2023-05-18 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com CITATION: Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C 127, 8704 (2023).
-# Interlayer Potential (ILP) for water/graphene heterojunctions
+# DATE: 2022-12-02 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com CITATION: Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C 127, 8704 (2023).
+# Anisotropic Interfacial Potential (AIP) parameters for water/graphene heterojunctions
 # The parameters below are fitted against the DMC reference data that rescaled from PBE+MBD-NL.
 #
 # ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
@@ -25,4 +25,4 @@ Hw H  5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.232494
 Ow Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
 Hw Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
 Ow Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
-Hw Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
\ No newline at end of file
+Hw Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000    1.0     1.2
diff --git a/potentials/COH.ILP b/potentials/COH.aip.water.2dm
old mode 100755
new mode 100644
similarity index 94%
rename from potentials/COH.ILP
rename to potentials/COH.aip.water.2dm
index bd815b5c00..5325399abe
--- a/potentials/COH.ILP
+++ b/potentials/COH.aip.water.2dm
@@ -1,5 +1,5 @@
-# DATE: 2023-05-18 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com CITATION: Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C 127, 8704 (2023).
-# Interlayer Potential (ILP) for water/graphene heterojunctions
+# DATE: 2022-12-02 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com CITATION: Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C 127, 8704 (2023).
+# Anisotropic Interfacial Potential (AIP) parameters for water/graphene heterojunctions
 # The parameters below are fitted against the PBE + MBD-NL DFT reference data from 2.5 A to 15 A.
 #
 # ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************

From f507e30d3698a44103b6acc404d20aa484a977ea Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sat, 3 Jun 2023 22:52:45 +0800
Subject: [PATCH 161/396] update input files of examples

---
 .../aip_water_2dm/COH.aip.water.2dm           |  1 +
 .../gra_water.data                            |  0
 .../in.gr_water                               | 22 +++++++++----------
 .../in.gr_water.opt                           | 22 +++++++++----------
 .../log.18May23.water.g++.1                   |  0
 .../log.18May23.water.g++.4                   |  0
 .../log.18May23.water.opt.g++.1               |  0
 .../log.18May23.water.opt.g++.4               |  0
 .../PACKAGES/interlayer/ilp_water_2dm/COH.ILP |  1 -
 9 files changed, 23 insertions(+), 23 deletions(-)
 create mode 120000 examples/PACKAGES/interlayer/aip_water_2dm/COH.aip.water.2dm
 rename examples/PACKAGES/interlayer/{ilp_water_2dm => aip_water_2dm}/gra_water.data (100%)
 rename examples/PACKAGES/interlayer/{ilp_water_2dm => aip_water_2dm}/in.gr_water (73%)
 rename examples/PACKAGES/interlayer/{ilp_water_2dm => aip_water_2dm}/in.gr_water.opt (73%)
 rename examples/PACKAGES/interlayer/{ilp_water_2dm => aip_water_2dm}/log.18May23.water.g++.1 (100%)
 rename examples/PACKAGES/interlayer/{ilp_water_2dm => aip_water_2dm}/log.18May23.water.g++.4 (100%)
 rename examples/PACKAGES/interlayer/{ilp_water_2dm => aip_water_2dm}/log.18May23.water.opt.g++.1 (100%)
 rename examples/PACKAGES/interlayer/{ilp_water_2dm => aip_water_2dm}/log.18May23.water.opt.g++.4 (100%)
 delete mode 120000 examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP

diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/COH.aip.water.2dm b/examples/PACKAGES/interlayer/aip_water_2dm/COH.aip.water.2dm
new file mode 120000
index 0000000000..fe5cccfcd2
--- /dev/null
+++ b/examples/PACKAGES/interlayer/aip_water_2dm/COH.aip.water.2dm
@@ -0,0 +1 @@
+../../../../potentials/COH.aip.water.2dm
\ No newline at end of file
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/gra_water.data b/examples/PACKAGES/interlayer/aip_water_2dm/gra_water.data
similarity index 100%
rename from examples/PACKAGES/interlayer/ilp_water_2dm/gra_water.data
rename to examples/PACKAGES/interlayer/aip_water_2dm/gra_water.data
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water b/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water
similarity index 73%
rename from examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water
rename to examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water
index 9fccbf733b..9f8e717a7e 100644
--- a/examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water
+++ b/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water
@@ -12,13 +12,13 @@ group 		gr    molecule 1
 group 		water molecule 2
 ######################## Potential defition ##############################
 # Interlayer potential
-pair_style  hybrid/overlay  ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+pair_style  hybrid/overlay  aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
 ####################################################################
 pair_coeff  1 1   none
-pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589          # O-O
 pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
-pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
-pair_coeff  * *   ilp/water/2dm        COH.ILP C Ow Hw    # C-water    
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	          # H-H
+pair_coeff  * *   aip/water/2dm        COH.aip.water.2dm C Ow Hw  # C-H2O    
 # bond and angle
 bond_style  	  harmonic
 bond_coeff  	  1 	0.0  0.9572
@@ -32,7 +32,7 @@ neigh_modify every 1 delay 5 check yes page 1000000 one 100000
 ####################################################################
 # Calculate pair energy
 compute   	1 all pair lj/cut/tip4p/long
-compute   	2 all pair ilp/water/2dm
+compute   	2 all pair aip/water/2dm
 compute		wt water temp
 variable  	TIP4P  equal  c_1
 variable  	EILP   equal  c_2     # total interlayer energy
@@ -42,10 +42,10 @@ thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
 thermo          100
 thermo_modify   lost error
 
-fix				subf gr setforce 0.0 0.0 0.0
-fix 			1 	water shake 0.0001 20 100 b 1 a 1
+fix		subf gr setforce 0.0 0.0 0.0
+fix 		1    water shake 0.0001 20 100 b 1 a 1
 
-timestep  		1e-3  
-velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
-fix				2 water nve
-run			    1000
+timestep	1e-3  
+velocity  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix		2 water nve
+run		1000
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water.opt b/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt
similarity index 73%
rename from examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water.opt
rename to examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt
index 1b38ab6e6e..8494bfcb3e 100644
--- a/examples/PACKAGES/interlayer/ilp_water_2dm/in.gr_water.opt
+++ b/examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt
@@ -12,13 +12,13 @@ group 		gr    molecule 1
 group 		water molecule 2
 ######################## Potential defition ##############################
 # Interlayer potential
-pair_style  hybrid/overlay  ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+pair_style  hybrid/overlay  aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
 ####################################################################
 pair_coeff  1 1   none
-pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589          # O-O
 pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
-pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
-pair_coeff  * *   ilp/water/2dm/opt        COH.ILP C Ow Hw    # C-water    
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	          # H-H
+pair_coeff  * *   aip/water/2dm/opt    COH.aip.water.2dm C Ow Hw  # C-H2O    
 # bond and angle
 bond_style  	  harmonic
 bond_coeff  	  1 	0.0  0.9572
@@ -32,7 +32,7 @@ neigh_modify every 1 delay 5 check yes page 1000000 one 100000
 ####################################################################
 # Calculate pair energy
 compute   	1 all pair lj/cut/tip4p/long
-compute   	2 all pair ilp/water/2dm/opt
+compute   	2 all pair aip/water/2dm/opt
 compute		wt water temp
 variable  	TIP4P  equal  c_1
 variable  	EILP   equal  c_2     # total interlayer energy
@@ -42,10 +42,10 @@ thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
 thermo          100
 thermo_modify   lost error
 
-fix				subf gr setforce 0.0 0.0 0.0
-fix 			1 	water shake 0.0001 20 100 b 1 a 1
+fix		subf gr setforce 0.0 0.0 0.0
+fix 		1    water shake 0.0001 20 100 b 1 a 1
 
-timestep  		1e-3  
-velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
-fix				2 water nve
-run			    1000
+timestep	1e-3  
+velocity  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix		2 water nve
+run		1000
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.1 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.g++.1
similarity index 100%
rename from examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.1
rename to examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.g++.1
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.4 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.g++.4
similarity index 100%
rename from examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.g++.4
rename to examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.g++.4
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.1 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.opt.g++.1
similarity index 100%
rename from examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.1
rename to examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.opt.g++.1
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.4 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.opt.g++.4
similarity index 100%
rename from examples/PACKAGES/interlayer/ilp_water_2dm/log.18May23.water.opt.g++.4
rename to examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.opt.g++.4
diff --git a/examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP b/examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP
deleted file mode 120000
index 526995dae4..0000000000
--- a/examples/PACKAGES/interlayer/ilp_water_2dm/COH.ILP
+++ /dev/null
@@ -1 +0,0 @@
-../../../../potentials/COH.ILP
\ No newline at end of file

From 63f3d183fe57cd035e8989c1df9f28f56d414c1e Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sat, 3 Jun 2023 23:02:45 +0800
Subject: [PATCH 162/396] rename log files of examples

---
 .../{log.18May23.water.g++.1 => log.18May23.gr_water.g++.1}       | 0
 .../{log.18May23.water.g++.4 => log.18May23.gr_water.g++.4}       | 0
 ...log.18May23.water.opt.g++.1 => log.18May23.gr_water.opt.g++.1} | 0
 ...log.18May23.water.opt.g++.4 => log.18May23.gr_water.opt.g++.4} | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 rename examples/PACKAGES/interlayer/aip_water_2dm/{log.18May23.water.g++.1 => log.18May23.gr_water.g++.1} (100%)
 rename examples/PACKAGES/interlayer/aip_water_2dm/{log.18May23.water.g++.4 => log.18May23.gr_water.g++.4} (100%)
 rename examples/PACKAGES/interlayer/aip_water_2dm/{log.18May23.water.opt.g++.1 => log.18May23.gr_water.opt.g++.1} (100%)
 rename examples/PACKAGES/interlayer/aip_water_2dm/{log.18May23.water.opt.g++.4 => log.18May23.gr_water.opt.g++.4} (100%)

diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.g++.1 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1
similarity index 100%
rename from examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.g++.1
rename to examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1
diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.g++.4 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4
similarity index 100%
rename from examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.g++.4
rename to examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4
diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.opt.g++.1 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1
similarity index 100%
rename from examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.opt.g++.1
rename to examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1
diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.opt.g++.4 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4
similarity index 100%
rename from examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.water.opt.g++.4
rename to examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4

From b5ab173763f7c6941c6f6b994f541ef3e9750017 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sat, 3 Jun 2023 23:03:12 +0800
Subject: [PATCH 163/396] update the doc file

---
 doc/src/pair_aip_water_2dm.rst | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/doc/src/pair_aip_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst
index 6a364f38ed..517cc00f4b 100644
--- a/doc/src/pair_aip_water_2dm.rst
+++ b/doc/src/pair_aip_water_2dm.rst
@@ -1,17 +1,17 @@
-.. index:: pair_style ilp/water/2dm
-.. index:: pair_style ilp/water/2dm/opt
+.. index:: pair_style aip/water/2dm
+.. index:: pair_style aip/water/2dm/opt
 
 pair_style ilp/tmd command
 ===================================
 
-Accelerator Variant: *ilp/water/2dm/opt*
+Accelerator Variant: *aip/water/2dm/opt*
 
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   pair_style [hybrid/overlay ...] ilp/tmd cutoff tap_flag
+   pair_style [hybrid/overlay ...] aip/water/2dm cutoff tap_flag
 
 * cutoff = global cutoff (distance units)
 * tap_flag = 0/1 to turn off/on the taper function
@@ -21,22 +21,22 @@ Examples
 
 .. code-block:: LAMMPS
 
-   pair_style  hybrid/overlay ilp/water/2dm 16.0 1
-   pair_coeff  * * ilp/water/2dm  COH.ILP C Ow Hw
+   pair_style  hybrid/overlay aip/water/2dm 16.0 1
+   pair_coeff  * * aip/water/2dm  COH.aip.water.2dm C Ow Hw
 
-   pair_style  hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+   pair_style  hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
    pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
    pair_coeff  2 3   lj/cut/tip4p/long    0.0        0.0     # O-H
    pair_coeff  3 3   lj/cut/tip4p/long    0.0        0.0     # H-H
-   pair_coeff  * *   ilp/water/2dm        COH.ILP    C Ow Hw
+   pair_coeff  * *   aip/water/2dm        COH.aip.water.2dm    C Ow Hw
 
 Description
 """""""""""
 
 .. versionadded:: xxxx2023
 
-The *ilp/water/2dm* style computes the registry-dependent interlayer
-potential (ILP) potential for interfaces of water with two-dimensinal (2D)
+The *aip/water/2dm* style computes the anisotropic interfacial
+potential (AIP) potential for interfaces of water with two-dimensinal (2D)
 materials as described in :ref:`(Feng) <Feng>`.
 
 .. math::
@@ -69,7 +69,7 @@ calculating the normals.
    oxygen-hydrogen bonds and the normal vector of the central oxygen atom
    is defined as their average.
 
-The parameter file (e.g. COH.ILP), is intended for use with *metal*
+The parameter file (e.g. COH.aip.water.2dm), is intended for use with *metal*
 :doc:`units <units>`, with energies in meV. Two additional parameters,
 *S*, and *rcut* are included in the parameter file. *S* is designed to
 facilitate scaling of energies. *rcut* is designed to build the neighbor
@@ -77,7 +77,7 @@ list for calculating the normals for each atom pair.
 
 .. note::
 
-   The parameters presented in the parameter file (e.g. COH.ILP),
+   The parameters presented in the parameter file (e.g. COH.aip.water.2dm),
    are fitted with taper function by setting the cutoff equal to 16.0
    Angstrom.  Using different cutoff or taper function should be careful.
    These parameters provide a good description in both short- and long-range
@@ -100,7 +100,7 @@ headings) the following commands could be included in an input script:
 
 .. code-block:: LAMMPS
 
-   compute 0 all pair ilp/water/2dm
+   compute 0 all pair aip/water/2dm
    variable Evdw  equal c_0[1]
    variable Erep  equal c_0[2]
    thermo_style custom step temp epair v_Erep v_Evdw
@@ -132,10 +132,10 @@ if LAMMPS was built with that package.  See the :doc:`Build package
 This pair style requires the newton setting to be *on* for pair
 interactions.
 
-The COH.ILP potential file provided with LAMMPS (see the potentials
+The COH.aip.water.2dm potential file provided with LAMMPS (see the potentials
 directory) are parameterized for *metal* units.  You can use this
 potential with any LAMMPS units, but you would need to create your
-COH.ILP potential file with coefficients listed in the appropriate
+COH.aip.water.2dm potential file with coefficients listed in the appropriate
 units, if your simulation does not use *metal* units.
 
 Related commands

From 196641927f6973ac76eca00b78b718a0f67cc925 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sat, 3 Jun 2023 23:07:55 +0800
Subject: [PATCH 164/396] correct a typo in the doc file

---
 doc/src/pair_aip_water_2dm.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/pair_aip_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst
index 517cc00f4b..3ae63e1e45 100644
--- a/doc/src/pair_aip_water_2dm.rst
+++ b/doc/src/pair_aip_water_2dm.rst
@@ -1,7 +1,7 @@
 .. index:: pair_style aip/water/2dm
 .. index:: pair_style aip/water/2dm/opt
 
-pair_style ilp/tmd command
+pair_style aip/water/2dm command
 ===================================
 
 Accelerator Variant: *aip/water/2dm/opt*

From bf8a4402cef5d2b9da6c0ffcc0c93e4f03ec0932 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sun, 4 Jun 2023 10:17:21 +0800
Subject: [PATCH 165/396] update log files in the examples

---
 .../aip_water_2dm/log.18May23.gr_water.g++.1  | 83 ++++++++++---------
 .../aip_water_2dm/log.18May23.gr_water.g++.4  | 81 +++++++++---------
 .../log.18May23.gr_water.opt.g++.1            | 83 ++++++++++---------
 .../log.18May23.gr_water.opt.g++.4            | 81 +++++++++---------
 4 files changed, 174 insertions(+), 154 deletions(-)

diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1
index 6e13280f70..c8268c72f6 100644
--- a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1
+++ b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (23 Jun 2022)
+LAMMPS (23 Jun 2022 - Update 4)
 OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
   using 1 OpenMP thread(s) per MPI task
 # Initialization
@@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-3 neighbors
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
-  special bonds CPU = 0.005 seconds
-  read_data CPU = 0.020 seconds
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.012 seconds
 mass            1 12.0107   # carbon   	mass (g/mole)
 mass            2 15.9994   # oxygen    mass (g/mole)
 mass            3 1.008     # hydrogen 	mass (g/mole)
@@ -41,14 +41,14 @@ group 		water molecule 2
 144 atoms in group water
 ######################## Potential defition ##############################
 # Interlayer potential
-pair_style  hybrid/overlay  ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+pair_style  hybrid/overlay  aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
 ####################################################################
 pair_coeff  1 1   none
-pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589          # O-O
 pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
-pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
-pair_coeff  * *   ilp/water/2dm        COH.ILP C Ow Hw    # C-water
-Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	          # H-H
+pair_coeff  * *   aip/water/2dm        COH.aip.water.2dm C Ow Hw  # C-H2O
+Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
 # bond and angle
 bond_style  	  harmonic
 bond_coeff  	  1 	0.0  0.9572
@@ -62,7 +62,7 @@ neigh_modify every 1 delay 5 check yes page 1000000 one 100000
 ####################################################################
 # Calculate pair energy
 compute   	1 all pair lj/cut/tip4p/long
-compute   	2 all pair ilp/water/2dm
+compute   	2 all pair aip/water/2dm
 compute		wt water temp
 variable  	TIP4P  equal  c_1
 variable  	EILP   equal  c_2     # total interlayer energy
@@ -72,18 +72,18 @@ thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
 thermo          100
 thermo_modify   lost error
 
-fix				subf gr setforce 0.0 0.0 0.0
-fix 			1 	water shake 0.0001 20 100 b 1 a 1
+fix		subf gr setforce 0.0 0.0 0.0
+fix 		1    water shake 0.0001 20 100 b 1 a 1
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
       48 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.000 seconds
 
-timestep  		1e-3
-velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
-fix				2 water nve
-run			    1000
+timestep	1e-3
+velocity  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix		2 water nve
+run		1000
 
 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
 
@@ -91,22 +91,24 @@ Your simulation uses code contributions which should be cited:
 
 - ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
 @Article{Ouyang2018
- author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
+ author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
  title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
  journal = {Nano Letters},
  volume =  18,
- pages =   {6009}
+ pages =   6009,
  year =    2018,
 }
 
-- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
+- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
 @Article{Ouyang2021
- author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
- title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
- journal = {J. Chem. Theory Comput.},
- volume =  17,
- pages =   {7237–7245}
- year =    2021,
+  author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
+    A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
+  title = {Anisotropic Interlayer Force Field for Transition
+    Metal Dichalcogenides: The Case of Molybdenum Disulfide},
+  journal = {J.~Chem.\ Theory Comput.},
+ volume   = 17,
+ pages    = {7237--7245}
+ year     = 2021,
 }
 
 - ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@@ -132,6 +134,8 @@ PPPM initialization ...
   using single precision MKL FFT
   3d grid and FFT values/proc = 84320 48000
 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
+WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
+WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
 Neighbor list info ...
   update every 1 steps, delay 5 steps, check yes
   max neighbors/atom: 100000, page size: 1000000
@@ -139,7 +143,7 @@ Neighbor list info ...
   ghost atom cutoff = 18
   binsize = 9, bins = 6 5 23
   3 neighbor lists, perpetual/occasional/extra = 3 0 0
-  (1) pair ilp/water/2dm, perpetual
+  (1) pair aip/water/2dm, perpetual
       attributes: full, newton on, ghost
       pair build: full/bin/ghost
       stencil: full/ghost/bin/3d
@@ -154,10 +158,11 @@ Neighbor list info ...
       pair build: half/bin/newton
       stencil: half/bin/3d
       bin: standard
+WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
 SHAKE stats (type/ave/delta/count) on step 0
 Bond:   1   0.957201  2.19705e-06       96
 Angle:  1   104.52    0.000203056       48
-Per MPI rank memory allocation (min/avg/max) = 33.53 | 33.53 | 33.53 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 32.9 | 32.9 | 32.9 Mbytes
    Step         TotEng         PotEng         KinEng        v_TIP4P         v_EILP       v_temp_wt   
          0  -16.131263     -19.815178      3.6839141      189.37246     -1.903543       300          
 SHAKE stats (type/ave/delta/count) on step 100
@@ -200,22 +205,22 @@ SHAKE stats (type/ave/delta/count) on step 1000
 Bond:   1   0.9572    1.00586e-06       96
 Angle:  1   104.52    0.000111712       48
       1000  -17.498465     -20.331545      2.8330804      188.87473     -1.812177       230.71225    
-Loop time of 20.801 on 1 procs for 1000 steps with 936 atoms
+Loop time of 20.3334 on 1 procs for 1000 steps with 936 atoms
 
-Performance: 4.154 ns/day, 5.778 hours/ns, 48.075 timesteps/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 4.249 ns/day, 5.648 hours/ns, 49.180 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 16.429     | 16.429     | 16.429     |   0.0 | 78.98
-Bond    | 0.0010991  | 0.0010991  | 0.0010991  |   0.0 |  0.01
-Kspace  | 3.4769     | 3.4769     | 3.4769     |   0.0 | 16.72
-Neigh   | 0.83359    | 0.83359    | 0.83359    |   0.0 |  4.01
-Comm    | 0.028825   | 0.028825   | 0.028825   |   0.0 |  0.14
-Output  | 0.00046349 | 0.00046349 | 0.00046349 |   0.0 |  0.00
-Modify  | 0.01943    | 0.01943    | 0.01943    |   0.0 |  0.09
-Other   |            | 0.01154    |            |       |  0.06
+Pair    | 16.179     | 16.179     | 16.179     |   0.0 | 79.57
+Bond    | 0.00021103 | 0.00021103 | 0.00021103 |   0.0 |  0.00
+Kspace  | 3.3118     | 3.3118     | 3.3118     |   0.0 | 16.29
+Neigh   | 0.79017    | 0.79017    | 0.79017    |   0.0 |  3.89
+Comm    | 0.026379   | 0.026379   | 0.026379   |   0.0 |  0.13
+Output  | 0.00046496 | 0.00046496 | 0.00046496 |   0.0 |  0.00
+Modify  | 0.017013   | 0.017013   | 0.017013   |   0.0 |  0.08
+Other   |            | 0.008835   |            |       |  0.04
 
 Nlocal:            936 ave         936 max         936 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -231,4 +236,4 @@ Ave neighs/atom = 460.87821
 Ave special neighs/atom = 0.30769231
 Neighbor list builds = 28
 Dangerous builds = 0
-Total wall time: 0:00:21
+Total wall time: 0:00:20
diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4
index 078ca76e2e..ab28c96657 100644
--- a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4
+++ b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (23 Jun 2022)
+LAMMPS (23 Jun 2022 - Update 4)
 OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
   using 1 OpenMP thread(s) per MPI task
 # Initialization
@@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-3 neighbors
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
-  special bonds CPU = 0.003 seconds
-  read_data CPU = 0.018 seconds
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.017 seconds
 mass            1 12.0107   # carbon   	mass (g/mole)
 mass            2 15.9994   # oxygen    mass (g/mole)
 mass            3 1.008     # hydrogen 	mass (g/mole)
@@ -41,14 +41,14 @@ group 		water molecule 2
 144 atoms in group water
 ######################## Potential defition ##############################
 # Interlayer potential
-pair_style  hybrid/overlay  ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+pair_style  hybrid/overlay  aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
 ####################################################################
 pair_coeff  1 1   none
-pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589          # O-O
 pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
-pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
-pair_coeff  * *   ilp/water/2dm        COH.ILP C Ow Hw    # C-water
-Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	          # H-H
+pair_coeff  * *   aip/water/2dm        COH.aip.water.2dm C Ow Hw  # C-H2O
+Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
 # bond and angle
 bond_style  	  harmonic
 bond_coeff  	  1 	0.0  0.9572
@@ -62,7 +62,7 @@ neigh_modify every 1 delay 5 check yes page 1000000 one 100000
 ####################################################################
 # Calculate pair energy
 compute   	1 all pair lj/cut/tip4p/long
-compute   	2 all pair ilp/water/2dm
+compute   	2 all pair aip/water/2dm
 compute		wt water temp
 variable  	TIP4P  equal  c_1
 variable  	EILP   equal  c_2     # total interlayer energy
@@ -72,18 +72,18 @@ thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
 thermo          100
 thermo_modify   lost error
 
-fix				subf gr setforce 0.0 0.0 0.0
-fix 			1 	water shake 0.0001 20 100 b 1 a 1
+fix		subf gr setforce 0.0 0.0 0.0
+fix 		1    water shake 0.0001 20 100 b 1 a 1
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
       48 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.000 seconds
 
-timestep  		1e-3
-velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
-fix				2 water nve
-run			    1000
+timestep	1e-3
+velocity  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix		2 water nve
+run		1000
 
 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
 
@@ -91,22 +91,24 @@ Your simulation uses code contributions which should be cited:
 
 - ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
 @Article{Ouyang2018
- author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
+ author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
  title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
  journal = {Nano Letters},
  volume =  18,
- pages =   {6009}
+ pages =   6009,
  year =    2018,
 }
 
-- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
+- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
 @Article{Ouyang2021
- author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
- title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
- journal = {J. Chem. Theory Comput.},
- volume =  17,
- pages =   {7237–7245}
- year =    2021,
+  author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
+    A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
+  title = {Anisotropic Interlayer Force Field for Transition
+    Metal Dichalcogenides: The Case of Molybdenum Disulfide},
+  journal = {J.~Chem.\ Theory Comput.},
+ volume   = 17,
+ pages    = {7237--7245}
+ year     = 2021,
 }
 
 - ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@@ -132,6 +134,8 @@ PPPM initialization ...
   using single precision MKL FFT
   3d grid and FFT values/proc = 30685 12480
 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
+WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
+WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
 Neighbor list info ...
   update every 1 steps, delay 5 steps, check yes
   max neighbors/atom: 100000, page size: 1000000
@@ -139,7 +143,7 @@ Neighbor list info ...
   ghost atom cutoff = 18
   binsize = 9, bins = 6 5 23
   3 neighbor lists, perpetual/occasional/extra = 3 0 0
-  (1) pair ilp/water/2dm, perpetual
+  (1) pair aip/water/2dm, perpetual
       attributes: full, newton on, ghost
       pair build: full/bin/ghost
       stencil: full/ghost/bin/3d
@@ -154,10 +158,11 @@ Neighbor list info ...
       pair build: half/bin/newton
       stencil: half/bin/3d
       bin: standard
+WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
 SHAKE stats (type/ave/delta/count) on step 0
 Bond:   1   0.957201  2.19705e-06       96
 Angle:  1   104.52    0.000203056       48
-Per MPI rank memory allocation (min/avg/max) = 25.84 | 25.88 | 25.92 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 25.22 | 25.25 | 25.29 Mbytes
    Step         TotEng         PotEng         KinEng        v_TIP4P         v_EILP       v_temp_wt   
          0  -16.131263     -19.815178      3.6839141      189.37246     -1.903543       300          
 SHAKE stats (type/ave/delta/count) on step 100
@@ -200,22 +205,22 @@ SHAKE stats (type/ave/delta/count) on step 1000
 Bond:   1   0.9572    1.00568e-06       96
 Angle:  1   104.52    0.000111707       48
       1000  -17.498474     -20.331607      2.833133       188.87466     -1.8121689      230.71654    
-Loop time of 9.42273 on 4 procs for 1000 steps with 936 atoms
+Loop time of 9.05361 on 4 procs for 1000 steps with 936 atoms
 
-Performance: 9.169 ns/day, 2.617 hours/ns, 106.126 timesteps/s
-97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 9.543 ns/day, 2.515 hours/ns, 110.453 timesteps/s
+99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.2328     | 4.3228     | 7.5931     | 103.1 | 45.88
-Bond    | 0.00084131 | 0.00088983 | 0.00095229 |   0.0 |  0.01
-Kspace  | 1.3979     | 4.6476     | 6.7252     |  98.8 | 49.32
-Neigh   | 0.34367    | 0.34371    | 0.34376    |   0.0 |  3.65
-Comm    | 0.042806   | 0.062908   | 0.075887   |   5.4 |  0.67
-Output  | 0.00037677 | 0.00041431 | 0.0004619  |   0.0 |  0.00
-Modify  | 0.028432   | 0.031138   | 0.034528   |   1.3 |  0.33
-Other   |            | 0.01321    |            |       |  0.14
+Pair    | 2.462      | 4.2266     | 7.1075     |  89.3 | 46.68
+Bond    | 0.00018424 | 0.00019878 | 0.00022125 |   0.0 |  0.00
+Kspace  | 1.4698     | 4.338      | 6.1001     |  87.8 | 47.91
+Neigh   | 0.39462    | 0.39489    | 0.39518    |   0.0 |  4.36
+Comm    | 0.043753   | 0.055826   | 0.062746   |   3.1 |  0.62
+Output  | 0.00048755 | 0.00053971 | 0.00062785 |   0.0 |  0.01
+Modify  | 0.027255   | 0.028664   | 0.030278   |   0.7 |  0.32
+Other   |            | 0.008904   |            |       |  0.10
 
 Nlocal:            234 ave         302 max         198 min
 Histogram: 2 0 0 1 0 0 0 0 0 1
diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1
index c6a11d209d..c795e85d56 100644
--- a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1
+++ b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (23 Jun 2022)
+LAMMPS (23 Jun 2022 - Update 4)
 OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
   using 1 OpenMP thread(s) per MPI task
 # Initialization
@@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-3 neighbors
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
-  special bonds CPU = 0.005 seconds
-  read_data CPU = 0.020 seconds
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.012 seconds
 mass            1 12.0107   # carbon   	mass (g/mole)
 mass            2 15.9994   # oxygen    mass (g/mole)
 mass            3 1.008     # hydrogen 	mass (g/mole)
@@ -41,14 +41,14 @@ group 		water molecule 2
 144 atoms in group water
 ######################## Potential defition ##############################
 # Interlayer potential
-pair_style  hybrid/overlay  ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+pair_style  hybrid/overlay  aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
 ####################################################################
 pair_coeff  1 1   none
-pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589          # O-O
 pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
-pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
-pair_coeff  * *   ilp/water/2dm/opt        COH.ILP C Ow Hw    # C-water
-Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	          # H-H
+pair_coeff  * *   aip/water/2dm/opt        COH.aip.water.2dm C Ow Hw  # C-H2O
+Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
 # bond and angle
 bond_style  	  harmonic
 bond_coeff  	  1 	0.0  0.9572
@@ -62,7 +62,7 @@ neigh_modify every 1 delay 5 check yes page 1000000 one 100000
 ####################################################################
 # Calculate pair energy
 compute   	1 all pair lj/cut/tip4p/long
-compute   	2 all pair ilp/water/2dm/opt
+compute   	2 all pair aip/water/2dm/opt
 compute		wt water temp
 variable  	TIP4P  equal  c_1
 variable  	EILP   equal  c_2     # total interlayer energy
@@ -72,18 +72,18 @@ thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
 thermo          100
 thermo_modify   lost error
 
-fix				subf gr setforce 0.0 0.0 0.0
-fix 			1 	water shake 0.0001 20 100 b 1 a 1
+fix		subf gr setforce 0.0 0.0 0.0
+fix 		1    water shake 0.0001 20 100 b 1 a 1
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
       48 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.000 seconds
 
-timestep  		1e-3
-velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
-fix				2 water nve
-run			    1000
+timestep	1e-3
+velocity  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix		2 water nve
+run		1000
 
 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
 
@@ -91,22 +91,24 @@ Your simulation uses code contributions which should be cited:
 
 - ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
 @Article{Ouyang2018
- author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
+ author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
  title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
  journal = {Nano Letters},
  volume =  18,
- pages =   {6009}
+ pages =   6009,
  year =    2018,
 }
 
-- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
+- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
 @Article{Ouyang2021
- author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
- title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
- journal = {J. Chem. Theory Comput.},
- volume =  17,
- pages =   {7237–7245}
- year =    2021,
+  author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
+    A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
+  title = {Anisotropic Interlayer Force Field for Transition
+    Metal Dichalcogenides: The Case of Molybdenum Disulfide},
+  journal = {J.~Chem.\ Theory Comput.},
+ volume   = 17,
+ pages    = {7237--7245}
+ year     = 2021,
 }
 
 - ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@@ -149,6 +151,8 @@ PPPM initialization ...
   using single precision MKL FFT
   3d grid and FFT values/proc = 84320 48000
 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
+WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
+WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
 Neighbor list info ...
   update every 1 steps, delay 5 steps, check yes
   max neighbors/atom: 100000, page size: 1000000
@@ -156,7 +160,7 @@ Neighbor list info ...
   ghost atom cutoff = 18
   binsize = 9, bins = 6 5 23
   3 neighbor lists, perpetual/occasional/extra = 3 0 0
-  (1) pair ilp/water/2dm/opt, perpetual
+  (1) pair aip/water/2dm/opt, perpetual
       attributes: full, newton on
       pair build: full/bin
       stencil: full/bin/3d
@@ -171,10 +175,11 @@ Neighbor list info ...
       pair build: halffull/newton
       stencil: none
       bin: none
+WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
 SHAKE stats (type/ave/delta/count) on step 0
 Bond:   1   0.957201  2.19705e-06       96
 Angle:  1   104.52    0.000203056       48
-Per MPI rank memory allocation (min/avg/max) = 25.89 | 25.89 | 25.89 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 25.27 | 25.27 | 25.27 Mbytes
    Step         TotEng         PotEng         KinEng        v_TIP4P         v_EILP       v_temp_wt   
          0  -16.131263     -19.815178      3.6839141      189.37246     -1.903543       300          
 SHAKE stats (type/ave/delta/count) on step 100
@@ -217,22 +222,22 @@ SHAKE stats (type/ave/delta/count) on step 1000
 Bond:   1   0.9572    1.00586e-06       96
 Angle:  1   104.52    0.000111711       48
       1000  -17.498466     -20.331547      2.8330808      188.87473     -1.8121768      230.71228    
-Loop time of 8.95265 on 1 procs for 1000 steps with 936 atoms
+Loop time of 8.11929 on 1 procs for 1000 steps with 936 atoms
 
-Performance: 9.651 ns/day, 2.487 hours/ns, 111.699 timesteps/s
-100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 10.641 ns/day, 2.255 hours/ns, 123.163 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 5.2127     | 5.2127     | 5.2127     |   0.0 | 58.23
-Bond    | 0.00083377 | 0.00083377 | 0.00083377 |   0.0 |  0.01
-Kspace  | 3.5005     | 3.5005     | 3.5005     |   0.0 | 39.10
-Neigh   | 0.17946    | 0.17946    | 0.17946    |   0.0 |  2.00
-Comm    | 0.028553   | 0.028553   | 0.028553   |   0.0 |  0.32
-Output  | 0.00035446 | 0.00035446 | 0.00035446 |   0.0 |  0.00
-Modify  | 0.01889    | 0.01889    | 0.01889    |   0.0 |  0.21
-Other   |            | 0.01135    |            |       |  0.13
+Pair    | 4.6849     | 4.6849     | 4.6849     |   0.0 | 57.70
+Bond    | 0.00017678 | 0.00017678 | 0.00017678 |   0.0 |  0.00
+Kspace  | 3.2098     | 3.2098     | 3.2098     |   0.0 | 39.53
+Neigh   | 0.17546    | 0.17546    | 0.17546    |   0.0 |  2.16
+Comm    | 0.024693   | 0.024693   | 0.024693   |   0.0 |  0.30
+Output  | 0.00037798 | 0.00037798 | 0.00037798 |   0.0 |  0.00
+Modify  | 0.015853   | 0.015853   | 0.015853   |   0.0 |  0.20
+Other   |            | 0.007983   |            |       |  0.10
 
 Nlocal:            936 ave         936 max         936 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -248,4 +253,4 @@ Ave neighs/atom = 460.87821
 Ave special neighs/atom = 0.30769231
 Neighbor list builds = 28
 Dangerous builds = 0
-Total wall time: 0:00:09
+Total wall time: 0:00:08
diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4
index 852c429323..f885c5708d 100644
--- a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4
+++ b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (23 Jun 2022)
+LAMMPS (23 Jun 2022 - Update 4)
 OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
   using 1 OpenMP thread(s) per MPI task
 # Initialization
@@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-3 neighbors
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
-  special bonds CPU = 0.003 seconds
-  read_data CPU = 0.017 seconds
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.014 seconds
 mass            1 12.0107   # carbon   	mass (g/mole)
 mass            2 15.9994   # oxygen    mass (g/mole)
 mass            3 1.008     # hydrogen 	mass (g/mole)
@@ -41,14 +41,14 @@ group 		water molecule 2
 144 atoms in group water
 ######################## Potential defition ##############################
 # Interlayer potential
-pair_style  hybrid/overlay  ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
+pair_style  hybrid/overlay  aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
 ####################################################################
 pair_coeff  1 1   none
-pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589  # O-O
+pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589          # O-O
 pair_coeff  2 3   lj/cut/tip4p/long    0.0 0.0  		  # O-H
-pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	      # H-H
-pair_coeff  * *   ilp/water/2dm/opt        COH.ILP C Ow Hw    # C-water
-Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17
+pair_coeff  3 3   lj/cut/tip4p/long    0.0 0.0  	          # H-H
+pair_coeff  * *   aip/water/2dm/opt        COH.aip.water.2dm C Ow Hw  # C-H2O
+Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
 # bond and angle
 bond_style  	  harmonic
 bond_coeff  	  1 	0.0  0.9572
@@ -62,7 +62,7 @@ neigh_modify every 1 delay 5 check yes page 1000000 one 100000
 ####################################################################
 # Calculate pair energy
 compute   	1 all pair lj/cut/tip4p/long
-compute   	2 all pair ilp/water/2dm/opt
+compute   	2 all pair aip/water/2dm/opt
 compute		wt water temp
 variable  	TIP4P  equal  c_1
 variable  	EILP   equal  c_2     # total interlayer energy
@@ -72,18 +72,18 @@ thermo_style    custom step etotal pe ke v_TIP4P v_EILP  v_temp_wt
 thermo          100
 thermo_modify   lost error
 
-fix				subf gr setforce 0.0 0.0 0.0
-fix 			1 	water shake 0.0001 20 100 b 1 a 1
+fix		subf gr setforce 0.0 0.0 0.0
+fix 		1    water shake 0.0001 20 100 b 1 a 1
        0 = # of size 2 clusters
        0 = # of size 3 clusters
        0 = # of size 4 clusters
       48 = # of frozen angles
-  find clusters CPU = 0.001 seconds
+  find clusters CPU = 0.000 seconds
 
-timestep  		1e-3
-velocity  	  	water create 300.0 12345 dist gaussian mom yes rot yes
-fix				2 water nve
-run			    1000
+timestep	1e-3
+velocity  	water create 300.0 12345 dist gaussian mom yes rot yes
+fix		2 water nve
+run		1000
 
 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
 
@@ -91,22 +91,24 @@ Your simulation uses code contributions which should be cited:
 
 - ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
 @Article{Ouyang2018
- author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},
+ author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
  title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
  journal = {Nano Letters},
  volume =  18,
- pages =   {6009}
+ pages =   6009,
  year =    2018,
 }
 
-- ilp/tmd potential doi/10.1021/acs.jctc.1c00782
+- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
 @Article{Ouyang2021
- author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod},
- title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide},
- journal = {J. Chem. Theory Comput.},
- volume =  17,
- pages =   {7237–7245}
- year =    2021,
+  author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
+    A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
+  title = {Anisotropic Interlayer Force Field for Transition
+    Metal Dichalcogenides: The Case of Molybdenum Disulfide},
+  journal = {J.~Chem.\ Theory Comput.},
+ volume   = 17,
+ pages    = {7237--7245}
+ year     = 2021,
 }
 
 - ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@@ -149,6 +151,8 @@ PPPM initialization ...
   using single precision MKL FFT
   3d grid and FFT values/proc = 30685 12480
 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
+WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
+WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
 Neighbor list info ...
   update every 1 steps, delay 5 steps, check yes
   max neighbors/atom: 100000, page size: 1000000
@@ -156,7 +160,7 @@ Neighbor list info ...
   ghost atom cutoff = 18
   binsize = 9, bins = 6 5 23
   3 neighbor lists, perpetual/occasional/extra = 3 0 0
-  (1) pair ilp/water/2dm/opt, perpetual
+  (1) pair aip/water/2dm/opt, perpetual
       attributes: full, newton on
       pair build: full/bin
       stencil: full/bin/3d
@@ -171,10 +175,11 @@ Neighbor list info ...
       pair build: halffull/newton
       stencil: none
       bin: none
+WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
 SHAKE stats (type/ave/delta/count) on step 0
 Bond:   1   0.957201  2.19705e-06       96
 Angle:  1   104.52    0.000203056       48
-Per MPI rank memory allocation (min/avg/max) = 22.03 | 22.06 | 22.1 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 21.4 | 21.44 | 21.48 Mbytes
    Step         TotEng         PotEng         KinEng        v_TIP4P         v_EILP       v_temp_wt   
          0  -16.131263     -19.815178      3.6839141      189.37246     -1.903543       300          
 SHAKE stats (type/ave/delta/count) on step 100
@@ -217,22 +222,22 @@ SHAKE stats (type/ave/delta/count) on step 1000
 Bond:   1   0.9572    1.00568e-06       96
 Angle:  1   104.52    0.000111707       48
       1000  -17.498472     -20.331605      2.8331335      188.87466     -1.8121689      230.71657    
-Loop time of 4.7828 on 4 procs for 1000 steps with 936 atoms
+Loop time of 4.24862 on 4 procs for 1000 steps with 936 atoms
 
-Performance: 18.065 ns/day, 1.329 hours/ns, 209.082 timesteps/s
-96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 20.336 ns/day, 1.180 hours/ns, 235.370 timesteps/s
+99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.26735    | 1.3839     | 3.2059     |  99.7 | 28.93
-Bond    | 0.00079377 | 0.00086039 | 0.00093529 |   0.0 |  0.02
-Kspace  | 1.4248     | 3.2254     | 4.3332     |  64.6 | 67.44
-Neigh   | 0.061885   | 0.061916   | 0.061951   |   0.0 |  1.29
-Comm    | 0.044281   | 0.065185   | 0.078628   |   5.1 |  1.36
-Output  | 0.0003482  | 0.0003787  | 0.00040746 |   0.0 |  0.01
-Modify  | 0.028727   | 0.031529   | 0.034914   |   1.3 |  0.66
-Other   |            | 0.01367    |            |       |  0.29
+Pair    | 0.25749    | 1.1806     | 2.6872     |  89.0 | 27.79
+Bond    | 0.00018656 | 0.00020786 | 0.00025377 |   0.0 |  0.00
+Kspace  | 1.4259     | 2.9204     | 3.8414     |  56.3 | 68.74
+Neigh   | 0.057504   | 0.057852   | 0.05818    |   0.1 |  1.36
+Comm    | 0.041952   | 0.053593   | 0.05876    |   3.0 |  1.26
+Output  | 0.0004296  | 0.00046809 | 0.00055317 |   0.0 |  0.01
+Modify  | 0.026204   | 0.027251   | 0.028382   |   0.6 |  0.64
+Other   |            | 0.008209   |            |       |  0.19
 
 Nlocal:            234 ave         302 max         198 min
 Histogram: 2 0 0 1 0 0 0 0 0 1

From 3282470cf5b56ae62a0ede29aa8c1519b691d4d3 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Sun, 4 Jun 2023 10:19:13 +0800
Subject: [PATCH 166/396] update the citation information

---
 src/INTERLAYER/pair_aip_water_2dm.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/INTERLAYER/pair_aip_water_2dm.cpp b/src/INTERLAYER/pair_aip_water_2dm.cpp
index d88676a6e2..f2d68f448b 100644
--- a/src/INTERLAYER/pair_aip_water_2dm.cpp
+++ b/src/INTERLAYER/pair_aip_water_2dm.cpp
@@ -41,7 +41,7 @@ using namespace InterLayer;
 #define PGDELTA 1
 
 static const char cite_aip_water[] =
-    "ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464\n"
+    "aip/water/2dm potential doi/10.1021/acs.jpcc.2c08464\n"
     "@Article{Feng2023\n"
     " author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},\n"
     " title = {Registry-Dependent Potential for Interfaces of Water with Graphene},\n"

From a0057d674ff2ef0c7f9e99fb713852f7c1d3ab49 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sun, 4 Jun 2023 13:40:31 +0300
Subject: [PATCH 167/396] Update compute_stress_mop_profile.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index d299633731..99f522096c 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -207,9 +207,11 @@ void ComputeStressMopProfile::init()
     if (force->bond!=nullptr) bondflag = 1;
 
     if (force->angle!=nullptr)
-      error->all(FLERR,"compute stress/mop/profile does not account for angle potentials");
+      if ((strcmp(force->angle_style, "zero") != 0) && (strcmp(force->angle_style, "none") != 0))
+        error->all(FLERR,"compute stress/mop/profile does not account for angle potentials");
     if (force->dihedral!=nullptr)
-      error->all(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
+      if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
+        error->all(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
     if (force->improper!=nullptr)
       error->all(FLERR,"compute stress/mop/profile does not account for improper potentials");
     if (force->kspace!=nullptr)

From d8fad4db1516f2a9a3d5a2ee1e9fda7b6959089c Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sun, 4 Jun 2023 13:45:00 +0300
Subject: [PATCH 168/396] remove white space from compute_stress_mop.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 3ae758b875..c9557a7ef3 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -83,7 +83,7 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
     if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
       error->all(FLERR, "Plane for compute stress/mop is out of bounds");
   }
-     
+
   if (pos < (domain->boxlo[dir]+domain->prd_half[dir])) {
     pos1 = pos + domain->prd[dir];
   } else {
@@ -285,7 +285,7 @@ void ComputeStressMop::compute_vector()
 
   // sum angle contribution over all procs
   MPI_Allreduce(angle_local,angle_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
-   
+
   for (int m=0; m<nvalues; m++) {
     vector[m] = values_global[m] + bond_global[m] + angle_global[m];
   }

From 51851c2f4d0a0fa514e6ef0c4fd91b486fbdd9ff Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sun, 4 Jun 2023 13:45:52 +0300
Subject: [PATCH 169/396] remove whitespace from compute_stress_mop_profile.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index 99f522096c..4f91f8f7fb 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -609,7 +609,7 @@ void ComputeStressMopProfile::compute_bonds()
     }
     m += 3;
   }
-} 
+}
 
 /* ----------------------------------------------------------------------
    setup 1d bins and their extent and coordinates

From 3782eeee2b2bca5435ef51f13082e96a1e0151df Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sun, 4 Jun 2023 13:47:54 +0300
Subject: [PATCH 170/396] remove whitespace from compute_stress_mop.rst

---
 doc/src/compute_stress_mop.rst | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst
index e1b151ebbd..7ab8c58a76 100644
--- a/doc/src/compute_stress_mop.rst
+++ b/doc/src/compute_stress_mop.rst
@@ -68,7 +68,7 @@ Between one and six keywords can be used to indicate which
 contributions to the stress must be computed: total stress (total),  kinetic stress (kin),
 configurational stress (conf), stress due to bond stretching (bond),
 stress due to angle bending (angle) and/or due to pairwise non-bonded interactions (pair).
-The angle keyword is currently available only for the stress/mop command and not the stress/mop/profile. 
+The angle keyword is currently available only for the stress/mop command and not the stress/mop/profile.
 
 NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
 
@@ -119,12 +119,12 @@ size does not change in time, and axis-aligned planes.
 
 The method only works with two-body pair interactions, because it
 requires the class method pair->single() to be implemented. In
-particular, compute *stress/mop/profile* does not work with more than 
+particular, compute *stress/mop/profile* does not work with more than
 two-body pair interactions, long range (kspace) interactions and angle/dihedral/improper
-intramolecular interactions. Similarly, compute *stress/mop* does not work with more than 
+intramolecular interactions. Similarly, compute *stress/mop* does not work with more than
 two-body pair interactions, long range (kspace) interactions and dihedral/improper
 intramolecular interactions but works with all bond interactions with the class method
-single() implemented and all angle interactions with the class method born_matrix() 
+single() implemented and all angle interactions with the class method born_matrix()
 implemented.
 
 Related commands

From c25999d2087c6b79b71ab1d0f6934a7c4598087a Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sun, 4 Jun 2023 16:08:33 +0300
Subject: [PATCH 171/396] Update compute_stress_mop_profile.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index 4f91f8f7fb..2c2260d22c 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -213,7 +213,8 @@ void ComputeStressMopProfile::init()
       if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
         error->all(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
     if (force->improper!=nullptr)
-      error->all(FLERR,"compute stress/mop/profile does not account for improper potentials");
+      if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
+        error->all(FLERR,"compute stress/mop/profile does not account for improper potentials");
     if (force->kspace!=nullptr)
       error->all(FLERR,"compute stress/mop/profile does not account for kspace contributions");
   }

From 0cff31060b5342f69d0b8d382fab423f29677fb4 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Sun, 4 Jun 2023 16:10:24 +0300
Subject: [PATCH 172/396] Update compute_stress_mop.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index c9557a7ef3..50eb3425f8 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -232,9 +232,11 @@ void ComputeStressMop::init()
          angleflag = 1;
       }
     if (force->dihedral!=nullptr)
-      error->all(FLERR,"compute stress/mop does not account for dihedral potentials");
+      if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
+        error->all(FLERR,"compute stress/mop does not account for dihedral potentials");
     if (force->improper!=nullptr)
-      error->all(FLERR,"compute stress/mop does not account for improper potentials");
+      if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
+        error->all(FLERR,"compute stress/mop does not account for improper potentials");
     if (force->kspace!=nullptr)
       error->all(FLERR,"compute stress/mop does not account for kspace contributions");
   }

From ead5a28d354297f20ea40b090aa19f87968a9ce6 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Mon, 5 Jun 2023 18:53:45 +0300
Subject: [PATCH 173/396] Update compute_stress_mop.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 50eb3425f8..e5d0e2ed13 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -227,7 +227,8 @@ void ComputeStressMop::init()
     if (force->bond!=nullptr) bondflag = 1;
     if (force->angle!=nullptr)
       if (force->angle->born_matrix_enable == 0) {
-        error->all(FLERR,"compute stress/mop does not account for angle potentials");
+        if ((strcmp(force->angle_style, "zero") != 0) && (strcmp(force->angle_style, "none") != 0))
+          error->all(FLERR,"compute stress/mop does not account for angle potentials");
       } else {
          angleflag = 1;
       }
@@ -238,7 +239,7 @@ void ComputeStressMop::init()
       if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
         error->all(FLERR,"compute stress/mop does not account for improper potentials");
     if (force->kspace!=nullptr)
-      error->all(FLERR,"compute stress/mop does not account for kspace contributions");
+      error->warning(FLERR,"compute stress/mop does not account for kspace contributions");
   }
 
   // need an occasional half neighbor list

From 8eed55b56c8330e46fd3715fca962140a0691b52 Mon Sep 17 00:00:00 2001
From: Evangelos Voyiatzis <evoyiatzis@gmail.com>
Date: Mon, 5 Jun 2023 18:54:26 +0300
Subject: [PATCH 174/396] Update compute_stress_mop_profile.cpp

---
 src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index 2c2260d22c..807092b37e 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -216,7 +216,7 @@ void ComputeStressMopProfile::init()
       if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
         error->all(FLERR,"compute stress/mop/profile does not account for improper potentials");
     if (force->kspace!=nullptr)
-      error->all(FLERR,"compute stress/mop/profile does not account for kspace contributions");
+      error->warning(FLERR,"compute stress/mop/profile does not account for kspace contributions");
   }
 
   // need an occasional half neighbor list

From a12133ce03fabe7d5746ea8a49905ca1f84267b2 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Mon, 5 Jun 2023 09:59:38 -0600
Subject: [PATCH 175/396] Update Kokkos library in LAMMPS to v3.7.2

---
 lib/kokkos/CHANGELOG.md                       | 23 +++++-
 lib/kokkos/CMakeLists.txt                     |  2 +-
 lib/kokkos/Makefile.kokkos                    |  2 +-
 lib/kokkos/algorithms/src/CMakeLists.txt      |  2 +-
 lib/kokkos/cmake/kokkos_arch.cmake            |  3 +
 lib/kokkos/cmake/kokkos_tribits.cmake         |  7 --
 .../containers/src/Kokkos_DynamicView.hpp     |  4 +-
 .../containers/unit_tests/TestDynamicView.hpp | 77 +++++++++++++++++++
 lib/kokkos/core/perf_test/test_atomic.cpp     |  2 +-
 .../core/src/HIP/Kokkos_HIP_Instance.cpp      |  2 +
 lib/kokkos/core/src/Kokkos_Macros.hpp         |  8 +-
 lib/kokkos/core/src/Kokkos_ScratchSpace.hpp   | 56 +++++++++-----
 lib/kokkos/core/src/Kokkos_Serial.hpp         |  8 --
 lib/kokkos/core/src/Kokkos_View.hpp           | 24 ++++--
 lib/kokkos/core/src/Serial/Kokkos_Serial.cpp  |  8 +-
 .../Serial/Kokkos_Serial_Parallel_MDRange.hpp | 19 ++---
 lib/kokkos/core/src/impl/Kokkos_Core.cpp      |  5 +-
 .../impl/Kokkos_InitializationSettings.hpp    |  4 +-
 lib/kokkos/core/src/impl/Kokkos_Profiling.cpp |  6 +-
 .../unit_test/TestDefaultDeviceTypeInit.hpp   | 24 +++---
 lib/kokkos/core/unit_test/TestSharedAlloc.hpp |  4 +-
 lib/kokkos/core/unit_test/TestTeam.hpp        | 66 +++++++++++++++-
 .../unit_test/cuda/TestCuda_InterOp_Init.cpp  |  4 +-
 .../cuda/TestCuda_InterOp_Streams.cpp         |  4 +-
 .../unit_test/hip/TestHIP_InterOp_Init.cpp    |  4 +-
 .../unit_test/hip/TestHIP_InterOp_Streams.cpp |  4 +-
 .../unit_test/sycl/TestSYCL_InterOp_Init.cpp  |  2 +-
 .../sycl/TestSYCL_InterOp_Init_Context.cpp    |  1 +
 .../sycl/TestSYCL_InterOp_Streams.cpp         |  8 +-
 .../include/desul/atomics/Lock_Array_Cuda.hpp | 49 +++++++-----
 lib/kokkos/tpls/desul/src/Lock_Array_CUDA.cpp |  4 +-
 31 files changed, 312 insertions(+), 124 deletions(-)

diff --git a/lib/kokkos/CHANGELOG.md b/lib/kokkos/CHANGELOG.md
index bdbc75604b..34df76a0fd 100644
--- a/lib/kokkos/CHANGELOG.md
+++ b/lib/kokkos/CHANGELOG.md
@@ -1,4 +1,25 @@
-# Change Log
+# CHANGELOG
+
+## [3.7.02](https://github.com/kokkos/kokkos/tree/3.7.02) (2023-05-17)
+[Full Changelog](https://github.com/kokkos/kokkos/compare/3.7.01...3.7.02)
+
+### Backends and Archs Enhancements:
+#### CUDA
+- Add Hopper support and update nvcc_wrapper to work with CUDA-12 [\#5693](https://github.com/kokkos/kokkos/pull/5693)
+### General Enhancements:
+- sprintf -> snprintf [\#5787](https://github.com/kokkos/kokkos/pull/5787)
+### Build System:
+- Add error message when not using `hipcc` and when `CMAKE_CXX_STANDARD` is not set [\#5945](https://github.com/kokkos/kokkos/pull/5945)
+### Bug Fixes:
+- Fix Scratch allocation alignment issues [\#5692](https://github.com/kokkos/kokkos/pull/5692)
+- Fix Intel Classic Compiler ICE [\#5710](https://github.com/kokkos/kokkos/pull/5710)
+- Don't install std algorithm headers multiple times [\#5711](https://github.com/kokkos/kokkos/pull/5711)
+- Fix static init order issue in InitalizationSettings [\#5721](https://github.com/kokkos/kokkos/pull/5721)
+- Fix src/dst Properties in deep_copy(DynamicView,View) [\#5732](https://github.com/kokkos/kokkos/pull/5732)
+- Fix build on Fedora Rawhide [\#5782](https://github.com/kokkos/kokkos/pull/5782)
+- Finalize HIP lock arrays [\#5694](https://github.com/kokkos/kokkos/pull/5694)
+- Fix CUDA lock arrays for current Desul [\#5812](https://github.com/kokkos/kokkos/pull/5812)
+- Set the correct device/context in InterOp tests [\#5701](https://github.com/kokkos/kokkos/pull/5701)
 
 ## [3.7.01](https://github.com/kokkos/kokkos/tree/3.7.01) (2022-12-01)
 [Full Changelog](https://github.com/kokkos/kokkos/compare/3.7.00...3.7.01)
diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt
index 7b78f29d73..404aad8065 100644
--- a/lib/kokkos/CMakeLists.txt
+++ b/lib/kokkos/CMakeLists.txt
@@ -129,7 +129,7 @@ ENDIF()
 
 set(Kokkos_VERSION_MAJOR 3)
 set(Kokkos_VERSION_MINOR 7)
-set(Kokkos_VERSION_PATCH 01)
+set(Kokkos_VERSION_PATCH 02)
 set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}")
 math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}")
 
diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos
index b873fd1e06..361995d847 100644
--- a/lib/kokkos/Makefile.kokkos
+++ b/lib/kokkos/Makefile.kokkos
@@ -12,7 +12,7 @@ endif
 
 KOKKOS_VERSION_MAJOR = 3
 KOKKOS_VERSION_MINOR = 7
-KOKKOS_VERSION_PATCH = 01
+KOKKOS_VERSION_PATCH = 02
 KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc)
 
 # Options: Cuda,HIP,SYCL,OpenMPTarget,OpenMP,Threads,Serial
diff --git a/lib/kokkos/algorithms/src/CMakeLists.txt b/lib/kokkos/algorithms/src/CMakeLists.txt
index 597626b111..606d83d18b 100644
--- a/lib/kokkos/algorithms/src/CMakeLists.txt
+++ b/lib/kokkos/algorithms/src/CMakeLists.txt
@@ -25,7 +25,7 @@ INSTALL (
 # These will get ignored for standalone CMake and a true interface library made
 KOKKOS_ADD_INTERFACE_LIBRARY(
   kokkosalgorithms
-  HEADERS ${ALGO_HEADERS}
+  NOINSTALLHEADERS ${ALGO_HEADERS}
   SOURCES ${ALGO_SOURCES}
 )
 KOKKOS_LIB_INCLUDE_DIRECTORIES(kokkosalgorithms
diff --git a/lib/kokkos/cmake/kokkos_arch.cmake b/lib/kokkos/cmake/kokkos_arch.cmake
index f20a91e42f..3aff6857a3 100644
--- a/lib/kokkos/cmake/kokkos_arch.cmake
+++ b/lib/kokkos/cmake/kokkos_arch.cmake
@@ -214,6 +214,9 @@ GLOBAL_SET(KOKKOS_AMDGPU_OPTIONS)
 IF(KOKKOS_ENABLE_HIP)
   SET(AMDGPU_ARCH_FLAG "--offload-arch")
   IF(NOT KOKKOS_CXX_COMPILER_ID STREQUAL HIPCC)
+    IF(KOKKOS_CXX_STANDARD STREQUAL 14 AND NOT CMAKE_CXX_STANDARD)
+      message(FATAL_ERROR "Set CMAKE_CXX_STANDARD to 14")
+    ENDIF()
     GLOBAL_APPEND(KOKKOS_AMDGPU_OPTIONS -x hip)
     IF(DEFINED ENV{ROCM_PATH})
       GLOBAL_APPEND(KOKKOS_AMDGPU_OPTIONS --rocm-path=$ENV{ROCM_PATH})
diff --git a/lib/kokkos/cmake/kokkos_tribits.cmake b/lib/kokkos/cmake/kokkos_tribits.cmake
index 34e45ecf72..9a55d2a5e9 100644
--- a/lib/kokkos/cmake/kokkos_tribits.cmake
+++ b/lib/kokkos/cmake/kokkos_tribits.cmake
@@ -534,13 +534,6 @@ FUNCTION(KOKKOS_ADD_INTERFACE_LIBRARY NAME)
 IF (KOKKOS_HAS_TRILINOS)
   TRIBITS_ADD_LIBRARY(${NAME} ${ARGN})
 ELSE()
-  CMAKE_PARSE_ARGUMENTS(PARSE
-    ""
-    ""
-    "HEADERS;SOURCES"
-    ${ARGN}
-  )
-
   ADD_LIBRARY(${NAME} INTERFACE)
   KOKKOS_INTERNAL_ADD_LIBRARY_INSTALL(${NAME})
 ENDIF()
diff --git a/lib/kokkos/containers/src/Kokkos_DynamicView.hpp b/lib/kokkos/containers/src/Kokkos_DynamicView.hpp
index a2b68064de..8450c06077 100644
--- a/lib/kokkos/containers/src/Kokkos_DynamicView.hpp
+++ b/lib/kokkos/containers/src/Kokkos_DynamicView.hpp
@@ -915,8 +915,8 @@ inline void deep_copy(const View<T, DP...>& dst,
 template <class T, class... DP, class... SP>
 inline void deep_copy(const Kokkos::Experimental::DynamicView<T, DP...>& dst,
                       const View<T, SP...>& src) {
-  using dst_type = Kokkos::Experimental::DynamicView<T, SP...>;
-  using src_type = View<T, DP...>;
+  using dst_type = Kokkos::Experimental::DynamicView<T, DP...>;
+  using src_type = View<T, SP...>;
 
   using dst_execution_space = typename ViewTraits<T, DP...>::execution_space;
   using src_memory_space    = typename ViewTraits<T, SP...>::memory_space;
diff --git a/lib/kokkos/containers/unit_tests/TestDynamicView.hpp b/lib/kokkos/containers/unit_tests/TestDynamicView.hpp
index 5345f8ea24..303e3643c9 100644
--- a/lib/kokkos/containers/unit_tests/TestDynamicView.hpp
+++ b/lib/kokkos/containers/unit_tests/TestDynamicView.hpp
@@ -240,6 +240,83 @@ struct TestDynamicView {
       ASSERT_EQ(new_result_sum, (value_type)(da_resize * (da_resize - 1) / 2));
 #endif
     }  // end scope
+
+    // Test: Reproducer to demonstrate compile-time error of deep_copy
+    // of DynamicView to/from on-host View.
+    //   Case 4:
+    {
+      using device_view_type = Kokkos::View<Scalar*, Space>;
+      using host_view_type = typename Kokkos::View<Scalar*, Space>::HostMirror;
+
+      view_type device_dynamic_view("on-device DynamicView", 1024,
+                                    arg_total_size);
+      device_view_type device_view("on-device View", arg_total_size);
+      host_view_type host_view("on-host View", arg_total_size);
+
+      unsigned da_size = arg_total_size / 8;
+      device_dynamic_view.resize_serial(da_size);
+
+      // Use parallel_for to populate device_dynamic_view and verify values
+#if defined(KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA)
+      Kokkos::parallel_for(
+          Kokkos::RangePolicy<execution_space>(0, da_size),
+          KOKKOS_LAMBDA(const int i) { device_dynamic_view(i) = Scalar(i); });
+
+      value_type result_sum = 0.0;
+      Kokkos::parallel_reduce(
+          Kokkos::RangePolicy<execution_space>(0, da_size),
+          KOKKOS_LAMBDA(const int i, value_type& partial_sum) {
+            partial_sum += (value_type)device_dynamic_view(i);
+          },
+          result_sum);
+
+      ASSERT_EQ(result_sum, (value_type)(da_size * (da_size - 1) / 2));
+#endif
+
+      // Use an on-device View as intermediate to deep_copy the
+      // device_dynamic_view to host, zero out the device_dynamic_view,
+      // deep_copy from host back to the device_dynamic_view and verify
+      Kokkos::deep_copy(device_view, device_dynamic_view);
+      Kokkos::deep_copy(host_view, device_view);
+      Kokkos::deep_copy(device_view, host_view);
+#if defined(KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA)
+      Kokkos::parallel_for(
+          Kokkos::RangePolicy<execution_space>(0, da_size),
+          KOKKOS_LAMBDA(const int i) { device_dynamic_view(i) = Scalar(0); });
+#endif
+      Kokkos::deep_copy(device_dynamic_view, device_view);
+#if defined(KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA)
+      value_type new_result_sum = 0.0;
+      Kokkos::parallel_reduce(
+          Kokkos::RangePolicy<execution_space>(0, da_size),
+          KOKKOS_LAMBDA(const int i, value_type& partial_sum) {
+            partial_sum += (value_type)device_dynamic_view(i);
+          },
+          new_result_sum);
+
+      ASSERT_EQ(new_result_sum, (value_type)(da_size * (da_size - 1) / 2));
+#endif
+
+      // Try to deep_copy device_dynamic_view directly to/from host.
+      // host-to-device currently fails to compile because DP and SP are
+      // swapped in the deep_copy implementation.
+      // Once that's fixed, both deep_copy's will fail at runtime because the
+      // destination execution space cannot access the source memory space.
+      try {
+        Kokkos::deep_copy(host_view, device_dynamic_view);
+      } catch (std::runtime_error const& error) {
+        std::string msg = error.what();
+        std::cerr << "Copy from on-device DynamicView to on-host View failed:\n"
+                  << msg << std::endl;
+      }
+      try {
+        Kokkos::deep_copy(device_dynamic_view, host_view);
+      } catch (std::runtime_error const& error) {
+        std::string msg = error.what();
+        std::cerr << "Copy from on-host View to on-device DynamicView failed:\n"
+                  << msg << std::endl;
+      }
+    }
   }
 };
 
diff --git a/lib/kokkos/core/perf_test/test_atomic.cpp b/lib/kokkos/core/perf_test/test_atomic.cpp
index 54824e5b39..094c40bfa7 100644
--- a/lib/kokkos/core/perf_test/test_atomic.cpp
+++ b/lib/kokkos/core/perf_test/test_atomic.cpp
@@ -73,7 +73,7 @@ void textcolor(int attr, int fg, int bg) {
   char command[40];
 
   /* Command is the control command to the terminal */
-  sprintf(command, "%c[%d;%d;%dm", 0x1B, attr, fg + 30, bg + 40);
+  snprintf(command, 40, "%c[%d;%d;%dm", 0x1B, attr, fg + 30, bg + 40);
   printf("%s", command);
 }
 void textcolor_standard() { textcolor(RESET, BLACK, WHITE); }
diff --git a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp
index 3785cfe80b..bdba322fcc 100644
--- a/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp
+++ b/lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.cpp
@@ -428,6 +428,8 @@ void HIPInternal::finalize() {
 
   if (this == &singleton()) {
     (void)Kokkos::Impl::hip_global_unique_token_locks(true);
+    Kokkos::Impl::finalize_host_hip_lock_arrays();
+
     KOKKOS_IMPL_HIP_SAFE_CALL(hipHostFree(constantMemHostStaging));
     KOKKOS_IMPL_HIP_SAFE_CALL(hipEventDestroy(constantMemReusable));
   }
diff --git a/lib/kokkos/core/src/Kokkos_Macros.hpp b/lib/kokkos/core/src/Kokkos_Macros.hpp
index e42944d819..8d2aa4d188 100644
--- a/lib/kokkos/core/src/Kokkos_Macros.hpp
+++ b/lib/kokkos/core/src/Kokkos_Macros.hpp
@@ -228,11 +228,6 @@
 #define KOKKOS_ENABLE_PRAGMA_SIMD 1
 #endif
 
-// FIXME Workaround for ICE with intel 17,18,19,20,21 in Trilinos
-#if (KOKKOS_COMPILER_INTEL <= 2100)
-#define KOKKOS_IMPL_WORKAROUND_ICE_IN_TRILINOS_WITH_OLD_INTEL_COMPILERS
-#endif
-
 // FIXME_SYCL
 #if !defined(KOKKOS_ENABLE_SYCL)
 #define KOKKOS_ENABLE_PRAGMA_IVDEP 1
@@ -653,7 +648,8 @@ static constexpr bool kokkos_omp_on_host() { return false; }
 #if (defined(KOKKOS_COMPILER_GNU) || defined(KOKKOS_COMPILER_CLANG) ||  \
      defined(KOKKOS_COMPILER_INTEL) || defined(KOKKOS_COMPILER_PGI)) && \
     !defined(_WIN32)
-#if (!defined(__linux__) || defined(__GLIBC_MINOR__))
+// disable stacktrace for musl-libc
+#if !defined(__linux__) || defined(__GLIBC_MINOR__)
 #define KOKKOS_IMPL_ENABLE_STACKTRACE
 #endif
 #define KOKKOS_IMPL_ENABLE_CXXABI
diff --git a/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp b/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp
index 3e37eb61dc..a1d77071f5 100644
--- a/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp
+++ b/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp
@@ -73,9 +73,8 @@ class ScratchMemorySpace {
       "Instantiating ScratchMemorySpace on non-execution-space type.");
 
  public:
-  // Alignment of memory chunks returned by 'get'
-  // must be a power of two
-  enum { ALIGN = 8 };
+  // Minimal overalignment used by view scratch allocations
+  constexpr static int ALIGN = 8;
 
  private:
   mutable char* m_iter_L0 = nullptr;
@@ -87,7 +86,9 @@ class ScratchMemorySpace {
   mutable int m_offset        = 0;
   mutable int m_default_level = 0;
 
-  enum { MASK = ALIGN - 1 };  // Alignment used by View::shmem_size
+#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4
+  constexpr static int DEFAULT_ALIGNMENT_MASK = ALIGN - 1;
+#endif
 
  public:
   //! Tag this class as a memory space
@@ -101,39 +102,59 @@ class ScratchMemorySpace {
 
   static constexpr const char* name() { return "ScratchMemorySpace"; }
 
+#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4
+  // This function is unused
   template <typename IntType>
-  KOKKOS_INLINE_FUNCTION static IntType align(const IntType& size) {
-    return (size + MASK) & ~MASK;
+  KOKKOS_DEPRECATED KOKKOS_INLINE_FUNCTION static constexpr IntType align(
+      const IntType& size) {
+    return (size + DEFAULT_ALIGNMENT_MASK) & ~DEFAULT_ALIGNMENT_MASK;
   }
+#endif
 
   template <typename IntType>
   KOKKOS_INLINE_FUNCTION void* get_shmem(const IntType& size,
                                          int level = -1) const {
-    return get_shmem_common</*aligned*/ false>(size, 1, level);
+    return get_shmem_common</*alignment_requested*/ false>(size, 1, level);
   }
 
   template <typename IntType>
   KOKKOS_INLINE_FUNCTION void* get_shmem_aligned(const IntType& size,
                                                  const ptrdiff_t alignment,
                                                  int level = -1) const {
-    return get_shmem_common</*aligned*/ true>(size, alignment, level);
+    return get_shmem_common</*alignment_requested*/ true>(size, alignment,
+                                                          level);
   }
 
  private:
-  template <bool aligned, typename IntType>
+  template <bool alignment_requested, typename IntType>
   KOKKOS_INLINE_FUNCTION void* get_shmem_common(const IntType& size,
                                                 const ptrdiff_t alignment,
                                                 int level = -1) const {
     if (level == -1) level = m_default_level;
-    auto& m_iter              = (level == 0) ? m_iter_L0 : m_iter_L1;
-    auto& m_end               = (level == 0) ? m_end_L0 : m_end_L1;
-    char* previous            = m_iter;
-    const ptrdiff_t missalign = size_t(m_iter) % alignment;
-    if (missalign) m_iter += alignment - missalign;
+    auto& m_iter = (level == 0) ? m_iter_L0 : m_iter_L1;
+    auto& m_end  = (level == 0) ? m_end_L0 : m_end_L1;
 
-    void* tmp = m_iter + m_offset * (aligned ? size : align(size));
-    if (m_end < (m_iter += (aligned ? size : align(size)) * m_multiplier)) {
-      m_iter = previous;  // put it back like it was
+    if (alignment_requested) {
+      const ptrdiff_t missalign = size_t(m_iter) % alignment;
+      if (missalign) m_iter += alignment - missalign;
+    }
+
+    // This is each thread's start pointer for its allocation
+    // Note: for team scratch m_offset is 0, since every
+    // thread will get back the same shared pointer
+    void* tmp           = m_iter + m_offset * size;
+    ptrdiff_t increment = size * m_multiplier;
+
+    // increment m_iter first and decrement it again if not
+    // enough memory was available. In the non-failing path
+    // this will save instructions.
+    m_iter += increment;
+
+    if (m_end < m_iter) {
+      // Request did overflow: reset the base team ptr, and
+      // return nullptr
+      m_iter -= increment;
+      tmp = nullptr;
 #ifdef KOKKOS_ENABLE_DEBUG
       // mfh 23 Jun 2015: printf call consumes 25 registers
       // in a CUDA build, so only print in debug mode.  The
@@ -143,7 +164,6 @@ class ScratchMemorySpace {
           "%ld byte(s); remaining capacity is %ld byte(s)\n",
           long(size), long(m_end - m_iter));
 #endif  // KOKKOS_ENABLE_DEBUG
-      tmp = nullptr;
     }
     return tmp;
   }
diff --git a/lib/kokkos/core/src/Kokkos_Serial.hpp b/lib/kokkos/core/src/Kokkos_Serial.hpp
index ffdd1e9fc8..b0d1d693fc 100644
--- a/lib/kokkos/core/src/Kokkos_Serial.hpp
+++ b/lib/kokkos/core/src/Kokkos_Serial.hpp
@@ -203,19 +203,11 @@ class Serial {
   static const char* name();
 
   Impl::SerialInternal* impl_internal_space_instance() const {
-#ifdef KOKKOS_IMPL_WORKAROUND_ICE_IN_TRILINOS_WITH_OLD_INTEL_COMPILERS
-    return m_space_instance;
-#else
     return m_space_instance.get();
-#endif
   }
 
  private:
-#ifdef KOKKOS_IMPL_WORKAROUND_ICE_IN_TRILINOS_WITH_OLD_INTEL_COMPILERS
-  Impl::SerialInternal* m_space_instance;
-#else
   Kokkos::Impl::HostSharedPtr<Impl::SerialInternal> m_space_instance;
-#endif
   //--------------------------------------------------------------------------
 };
 
diff --git a/lib/kokkos/core/src/Kokkos_View.hpp b/lib/kokkos/core/src/Kokkos_View.hpp
index f8dcfc869e..795ef91e6a 100644
--- a/lib/kokkos/core/src/Kokkos_View.hpp
+++ b/lib/kokkos/core/src/Kokkos_View.hpp
@@ -67,6 +67,8 @@ KOKKOS_IMPL_WARNING("Including non-public Kokkos header files is not allowed.")
 
 #include <impl/Kokkos_Tools.hpp>
 
+#include <Kokkos_MinMaxClamp.hpp>
+
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
@@ -1692,19 +1694,27 @@ class View : public ViewTraits<DataType, Properties...> {
         arg_N0, arg_N1, arg_N2, arg_N3, arg_N4, arg_N5, arg_N6, arg_N7));
   }
 
+ private:
+  // Want to be able to align to minimum scratch alignment or sizeof or alignof
+  // elements
+  static constexpr size_t scratch_value_alignment =
+      ::Kokkos::max(::Kokkos::max(sizeof(typename traits::value_type),
+                                  alignof(typename traits::value_type)),
+                    static_cast<size_t>(
+                        traits::execution_space::scratch_memory_space::ALIGN));
+
+ public:
   static KOKKOS_INLINE_FUNCTION size_t
   shmem_size(typename traits::array_layout const& arg_layout) {
-    return map_type::memory_span(arg_layout) +
-           sizeof(typename traits::value_type);
+    return map_type::memory_span(arg_layout) + scratch_value_alignment;
   }
 
   explicit KOKKOS_INLINE_FUNCTION View(
       const typename traits::execution_space::scratch_memory_space& arg_space,
       const typename traits::array_layout& arg_layout)
-      : View(Impl::ViewCtorProp<pointer_type>(
-                 reinterpret_cast<pointer_type>(arg_space.get_shmem_aligned(
-                     map_type::memory_span(arg_layout),
-                     sizeof(typename traits::value_type)))),
+      : View(Impl::ViewCtorProp<pointer_type>(reinterpret_cast<pointer_type>(
+                 arg_space.get_shmem_aligned(map_type::memory_span(arg_layout),
+                                             scratch_value_alignment))),
              arg_layout) {}
 
   explicit KOKKOS_INLINE_FUNCTION View(
@@ -1722,7 +1732,7 @@ class View : public ViewTraits<DataType, Properties...> {
                      map_type::memory_span(typename traits::array_layout(
                          arg_N0, arg_N1, arg_N2, arg_N3, arg_N4, arg_N5, arg_N6,
                          arg_N7)),
-                     sizeof(typename traits::value_type)))),
+                     scratch_value_alignment))),
              typename traits::array_layout(arg_N0, arg_N1, arg_N2, arg_N3,
                                            arg_N4, arg_N5, arg_N6, arg_N7),
              check_input_args::yes) {
diff --git a/lib/kokkos/core/src/Serial/Kokkos_Serial.cpp b/lib/kokkos/core/src/Serial/Kokkos_Serial.cpp
index 9205e82560..25d220e45d 100644
--- a/lib/kokkos/core/src/Serial/Kokkos_Serial.cpp
+++ b/lib/kokkos/core/src/Serial/Kokkos_Serial.cpp
@@ -173,14 +173,8 @@ void SerialInternal::resize_thread_team_data(size_t pool_reduce_bytes,
 }  // namespace Impl
 
 Serial::Serial()
-#ifdef KOKKOS_IMPL_WORKAROUND_ICE_IN_TRILINOS_WITH_OLD_INTEL_COMPILERS
-    : m_space_instance(&Impl::SerialInternal::singleton()) {
-}
-#else
     : m_space_instance(&Impl::SerialInternal::singleton(),
-                       [](Impl::SerialInternal*) {}) {
-}
-#endif
+                       [](Impl::SerialInternal*) {}) {}
 
 void Serial::print_configuration(std::ostream& os, bool /*verbose*/) const {
   os << "Host Serial Execution Space:\n";
diff --git a/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_MDRange.hpp b/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_MDRange.hpp
index d726a86f76..c3e28c59f4 100644
--- a/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_MDRange.hpp
+++ b/lib/kokkos/core/src/Serial/Kokkos_Serial_Parallel_MDRange.hpp
@@ -63,11 +63,10 @@ class ParallelFor<FunctorType, Kokkos::MDRangePolicy<Traits...>,
 
   const FunctorType m_functor;
   const MDRangePolicy m_mdr_policy;
-  const Policy m_policy;
 
   void exec() const {
-    const typename Policy::member_type e = m_policy.end();
-    for (typename Policy::member_type i = m_policy.begin(); i < e; ++i) {
+    const typename Policy::member_type e = m_mdr_policy.m_num_tiles;
+    for (typename Policy::member_type i = 0; i < e; ++i) {
       iterate_type(m_mdr_policy, m_functor)(i);
     }
   }
@@ -85,9 +84,7 @@ class ParallelFor<FunctorType, Kokkos::MDRangePolicy<Traits...>,
   }
   inline ParallelFor(const FunctorType& arg_functor,
                      const MDRangePolicy& arg_policy)
-      : m_functor(arg_functor),
-        m_mdr_policy(arg_policy),
-        m_policy(Policy(0, m_mdr_policy.m_num_tiles).set_chunk_size(1)) {}
+      : m_functor(arg_functor), m_mdr_policy(arg_policy) {}
 };
 
 template <class FunctorType, class ReducerType, class... Traits>
@@ -120,13 +117,12 @@ class ParallelReduce<FunctorType, Kokkos::MDRangePolicy<Traits...>, ReducerType,
 
   const FunctorType m_functor;
   const MDRangePolicy m_mdr_policy;
-  const Policy m_policy;
   const ReducerType m_reducer;
   const pointer_type m_result_ptr;
 
   inline void exec(reference_type update) const {
-    const typename Policy::member_type e = m_policy.end();
-    for (typename Policy::member_type i = m_policy.begin(); i < e; ++i) {
+    const typename Policy::member_type e = m_mdr_policy.m_num_tiles;
+    for (typename Policy::member_type i = 0; i < e; ++i) {
       iterate_type(m_mdr_policy, m_functor, update)(i);
     }
   }
@@ -148,7 +144,8 @@ class ParallelReduce<FunctorType, Kokkos::MDRangePolicy<Traits...>, ReducerType,
     const size_t team_shared_size  = 0;  // Never shrinks
     const size_t thread_local_size = 0;  // Never shrinks
 
-    auto* internal_instance = m_policy.space().impl_internal_space_instance();
+    auto* internal_instance =
+        m_mdr_policy.space().impl_internal_space_instance();
     // Need to lock resize_thread_team_data
     std::lock_guard<std::mutex> lock(
         internal_instance->m_thread_team_data_mutex);
@@ -181,7 +178,6 @@ class ParallelReduce<FunctorType, Kokkos::MDRangePolicy<Traits...>, ReducerType,
                                   void*> = nullptr)
       : m_functor(arg_functor),
         m_mdr_policy(arg_policy),
-        m_policy(Policy(0, m_mdr_policy.m_num_tiles).set_chunk_size(1)),
         m_reducer(InvalidType()),
         m_result_ptr(arg_result_view.data()) {
     static_assert(Kokkos::is_view<HostViewType>::value,
@@ -197,7 +193,6 @@ class ParallelReduce<FunctorType, Kokkos::MDRangePolicy<Traits...>, ReducerType,
                         MDRangePolicy arg_policy, const ReducerType& reducer)
       : m_functor(arg_functor),
         m_mdr_policy(arg_policy),
-        m_policy(Policy(0, m_mdr_policy.m_num_tiles).set_chunk_size(1)),
         m_reducer(reducer),
         m_result_ptr(reducer.view().data()) {
     /*static_assert( std::is_same< typename ViewType::memory_space
diff --git a/lib/kokkos/core/src/impl/Kokkos_Core.cpp b/lib/kokkos/core/src/impl/Kokkos_Core.cpp
index a5bd003237..fc89e485fd 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Core.cpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Core.cpp
@@ -1165,6 +1165,5 @@ void _kokkos_pgi_compiler_bug_workaround() {}
 #endif
 }  // namespace Kokkos
 
-Kokkos::Impl::InitializationSettingsHelper<std::string>::storage_type const
-    Kokkos::Impl::InitializationSettingsHelper<std::string>::unspecified =
-        "some string we don't expect user would ever provide";
+constexpr char
+    Kokkos::Impl::InitializationSettingsHelper<std::string>::unspecified[];
diff --git a/lib/kokkos/core/src/impl/Kokkos_InitializationSettings.hpp b/lib/kokkos/core/src/impl/Kokkos_InitializationSettings.hpp
index ceb35f0247..00b2335fd7 100644
--- a/lib/kokkos/core/src/impl/Kokkos_InitializationSettings.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_InitializationSettings.hpp
@@ -104,7 +104,9 @@ struct InitializationSettingsHelper<std::string> {
   using value_type   = std::string;
   using storage_type = std::string;
 
-  static storage_type const unspecified;
+  // prefer c-string to avoid static initialization order nightmare
+  static constexpr char unspecified[] =
+      "some string we don't expect user would ever provide";
 };
 }  // namespace Impl
 
diff --git a/lib/kokkos/core/src/impl/Kokkos_Profiling.cpp b/lib/kokkos/core/src/impl/Kokkos_Profiling.cpp
index 480b1a392b..796552cead 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Profiling.cpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Profiling.cpp
@@ -655,9 +655,9 @@ void initialize(const std::string& profileLibrary) {
 
   char* envProfileLibrary = const_cast<char*>(profileLibrary.c_str());
 
-  const auto envProfileCopy =
-      std::make_unique<char[]>(strlen(envProfileLibrary) + 1);
-  sprintf(envProfileCopy.get(), "%s", envProfileLibrary);
+  const size_t envProfileLen = strlen(envProfileLibrary) + 1;
+  const auto envProfileCopy  = std::make_unique<char[]>(envProfileLen);
+  snprintf(envProfileCopy.get(), envProfileLen, "%s", envProfileLibrary);
 
   char* profileLibraryName = strtok(envProfileCopy.get(), ";");
 
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp
index d915b7e472..55a29f1128 100644
--- a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp
@@ -69,9 +69,10 @@ char** init_kokkos_args(bool do_threads, bool do_numa, bool do_device,
   nargs = (do_threads ? 1 : 0) + (do_numa ? 1 : 0) + (do_device ? 1 : 0) +
           (do_other ? 4 : 0) + (do_tune ? 1 : 0);
 
-  char** args_kokkos = new char*[nargs];
+  char** args_kokkos      = new char*[nargs];
+  const int max_args_size = 45;
   for (int i = 0; i < nargs; i++) {
-    args_kokkos[i] = new char[45];
+    args_kokkos[i] = new char[max_args_size];
     delete_these.insert(args_kokkos[i]);
   }
 
@@ -112,7 +113,7 @@ char** init_kokkos_args(bool do_threads, bool do_numa, bool do_device,
 #endif
 
     init_args.num_threads = nthreads;
-    sprintf(args_kokkos[threads_idx], "--threads=%i", nthreads);
+    snprintf(args_kokkos[threads_idx], max_args_size, "--threads=%i", nthreads);
   }
 
   if (do_numa) {
@@ -130,24 +131,27 @@ char** init_kokkos_args(bool do_threads, bool do_numa, bool do_device,
 #endif
 
     init_args.num_numa = numa;
-    sprintf(args_kokkos[numa_idx], "--numa=%i", numa);
+    snprintf(args_kokkos[numa_idx], max_args_size, "--numa=%i", numa);
   }
 
   if (do_device) {
     init_args.device_id = 0;
-    sprintf(args_kokkos[device_idx], "--device-id=%i", 0);
+    snprintf(args_kokkos[device_idx], max_args_size, "--device-id=%i", 0);
   }
 
   if (do_other) {
-    sprintf(args_kokkos[0], "--dummyarg=1");
-    sprintf(args_kokkos[threads_idx + (do_threads ? 1 : 0)], "--dummy2arg");
-    sprintf(args_kokkos[threads_idx + (do_threads ? 1 : 0) + 1], "dummy3arg");
-    sprintf(args_kokkos[device_idx + (do_device ? 1 : 0)], "dummy4arg=1");
+    snprintf(args_kokkos[0], max_args_size, "--dummyarg=1");
+    snprintf(args_kokkos[threads_idx + (do_threads ? 1 : 0)], max_args_size,
+             "--dummy2arg");
+    snprintf(args_kokkos[threads_idx + (do_threads ? 1 : 0) + 1], max_args_size,
+             "dummy3arg");
+    snprintf(args_kokkos[device_idx + (do_device ? 1 : 0)], max_args_size,
+             "dummy4arg=1");
   }
 
   if (do_tune) {
     init_args.tune_internals = true;
-    sprintf(args_kokkos[tune_idx], "--kokkos-tune-internals");
+    snprintf(args_kokkos[tune_idx], max_args_size, "--kokkos-tune-internals");
   }
 
   return args_kokkos;
diff --git a/lib/kokkos/core/unit_test/TestSharedAlloc.hpp b/lib/kokkos/core/unit_test/TestSharedAlloc.hpp
index f66b35dc9f..18f3c9a777 100644
--- a/lib/kokkos/core/unit_test/TestSharedAlloc.hpp
+++ b/lib/kokkos/core/unit_test/TestSharedAlloc.hpp
@@ -91,7 +91,7 @@ void test_shared_alloc() {
     // Since always executed on host space, leave [=]
     Kokkos::parallel_for(range, [=](int i) {
       char name[64];
-      sprintf(name, "test_%.2d", i);
+      snprintf(name, 64, "test_%.2d", i);
 
       r[i] = RecordMemS::allocate(s, name, size * (i + 1));
       h[i] = Header::get_header(r[i]->data());
@@ -135,7 +135,7 @@ void test_shared_alloc() {
 
     Kokkos::parallel_for(range, [=](size_t i) {
       char name[64];
-      sprintf(name, "test_%.2d", int(i));
+      snprintf(name, 64, "test_%.2d", int(i));
 
       RecordFull* rec = RecordFull::allocate(s, name, size * (i + 1));
 
diff --git a/lib/kokkos/core/unit_test/TestTeam.hpp b/lib/kokkos/core/unit_test/TestTeam.hpp
index 3f05b2ef66..58db4360e5 100644
--- a/lib/kokkos/core/unit_test/TestTeam.hpp
+++ b/lib/kokkos/core/unit_test/TestTeam.hpp
@@ -1551,14 +1551,16 @@ struct TestScratchAlignment {
     double x, y, z;
   };
   TestScratchAlignment() {
-    test(true);
-    test(false);
+    test_view(true);
+    test_view(false);
+    test_minimal();
+    test_raw();
   }
   using ScratchView =
       Kokkos::View<TestScalar *, typename ExecSpace::scratch_memory_space>;
   using ScratchViewInt =
       Kokkos::View<int *, typename ExecSpace::scratch_memory_space>;
-  void test(bool allocate_small) {
+  void test_view(bool allocate_small) {
     int shmem_size = ScratchView::shmem_size(11);
 #ifdef KOKKOS_ENABLE_OPENMPTARGET
     int team_size =
@@ -1580,12 +1582,68 @@ struct TestScratchAlignment {
         });
     Kokkos::fence();
   }
+
+  void test_minimal() {
+    using member_type = typename Kokkos::TeamPolicy<ExecSpace>::member_type;
+    Kokkos::TeamPolicy<ExecSpace> policy(1, 1);
+    size_t scratch_size = sizeof(int);
+    Kokkos::View<int, ExecSpace> flag("Flag");
+
+    Kokkos::parallel_for(
+        policy.set_scratch_size(0, Kokkos::PerTeam(scratch_size)),
+        KOKKOS_LAMBDA(const member_type &team) {
+          int *scratch_ptr = (int *)team.team_shmem().get_shmem(scratch_size);
+          if (scratch_ptr == nullptr) flag() = 1;
+        });
+    Kokkos::fence();
+    int minimal_scratch_allocation_failed = 0;
+    Kokkos::deep_copy(minimal_scratch_allocation_failed, flag);
+    ASSERT_TRUE(minimal_scratch_allocation_failed == 0);
+  }
+
+  void test_raw() {
+    using member_type = typename Kokkos::TeamPolicy<ExecSpace>::member_type;
+    Kokkos::TeamPolicy<ExecSpace> policy(1, 1);
+    Kokkos::View<int, ExecSpace> flag("Flag");
+
+    Kokkos::parallel_for(
+        policy.set_scratch_size(0, Kokkos::PerTeam(1024)),
+        KOKKOS_LAMBDA(const member_type &team) {
+          int *scratch_ptr1 = (int *)team.team_shmem().get_shmem(24);
+          int *scratch_ptr2 = (int *)team.team_shmem().get_shmem(32);
+          int *scratch_ptr3 = (int *)team.team_shmem().get_shmem(12);
+
+          if ((int(scratch_ptr2 - scratch_ptr1) != 6) ||
+              (int(scratch_ptr3 - scratch_ptr2) != 8))
+            flag() = 1;
+
+          if (((scratch_ptr3 - static_cast<int *>(nullptr)) + 3) % 2 == 1)
+            scratch_ptr1 = (int *)team.team_shmem().get_shmem_aligned(24, 4);
+          else {
+            scratch_ptr1 = (int *)team.team_shmem().get_shmem_aligned(12, 4);
+          }
+          scratch_ptr2 = (int *)team.team_shmem().get_shmem_aligned(32, 8);
+          scratch_ptr3 = (int *)team.team_shmem().get_shmem_aligned(8, 4);
+
+          if ((int(scratch_ptr2 - scratch_ptr1) != 7) &&
+              (int(scratch_ptr2 - scratch_ptr1) != 4))
+            flag() = 1;
+          if (int(scratch_ptr3 - scratch_ptr2) != 8) flag() = 1;
+          if ((int(size_t(scratch_ptr1) % 4) != 0) ||
+              (int(size_t(scratch_ptr2) % 8) != 0) ||
+              (int(size_t(scratch_ptr3) % 4) != 0))
+            flag() = 1;
+        });
+    Kokkos::fence();
+    int raw_get_shmem_alignment_failed = 0;
+    Kokkos::deep_copy(raw_get_shmem_alignment_failed, flag);
+    ASSERT_TRUE(raw_get_shmem_alignment_failed == 0);
+  }
 };
 
 }  // namespace
 
 namespace {
-
 template <class ExecSpace>
 struct TestTeamPolicyHandleByValue {
   using scalar     = double;
diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_Init.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_Init.cpp
index 31fd63f084..c4381b29e7 100644
--- a/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_Init.cpp
+++ b/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_Init.cpp
@@ -59,9 +59,11 @@ __global__ void offset(int* p) {
 // Test whether allocations survive Kokkos initialize/finalize if done via Raw
 // Cuda.
 TEST(cuda, raw_cuda_interop) {
+  // Make sure that we use the same device for all allocations
+  Kokkos::initialize();
+
   int* p;
   KOKKOS_IMPL_CUDA_SAFE_CALL(cudaMalloc(&p, sizeof(int) * 100));
-  Kokkos::initialize();
 
   Kokkos::View<int*, Kokkos::MemoryTraits<Kokkos::Unmanaged>> v(p, 100);
   Kokkos::deep_copy(v, 5);
diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_Streams.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_Streams.cpp
index f11f657e00..69aef6f8d8 100644
--- a/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_Streams.cpp
+++ b/lib/kokkos/core/unit_test/cuda/TestCuda_InterOp_Streams.cpp
@@ -48,9 +48,11 @@
 namespace Test {
 // Test Interoperability with Cuda Streams
 TEST(cuda, raw_cuda_streams) {
+  // Make sure that we use the same device for all allocations
+  Kokkos::initialize();
+
   cudaStream_t stream;
   cudaStreamCreate(&stream);
-  Kokkos::initialize();
   int* p;
   cudaMalloc(&p, sizeof(int) * 100);
   using MemorySpace = typename TEST_EXECSPACE::memory_space;
diff --git a/lib/kokkos/core/unit_test/hip/TestHIP_InterOp_Init.cpp b/lib/kokkos/core/unit_test/hip/TestHIP_InterOp_Init.cpp
index af20e753d4..ce76076f9b 100644
--- a/lib/kokkos/core/unit_test/hip/TestHIP_InterOp_Init.cpp
+++ b/lib/kokkos/core/unit_test/hip/TestHIP_InterOp_Init.cpp
@@ -59,9 +59,11 @@ __global__ void offset(int* p) {
 // Test whether allocations survive Kokkos initialize/finalize if done via Raw
 // HIP.
 TEST(hip, raw_hip_interop) {
+  // Make sure that we use the same device for all allocations
+  Kokkos::initialize();
+
   int* p;
   KOKKOS_IMPL_HIP_SAFE_CALL(hipMalloc(&p, sizeof(int) * 100));
-  Kokkos::initialize();
 
   Kokkos::View<int*, Kokkos::MemoryTraits<Kokkos::Unmanaged>> v(p, 100);
   Kokkos::deep_copy(v, 5);
diff --git a/lib/kokkos/core/unit_test/hip/TestHIP_InterOp_Streams.cpp b/lib/kokkos/core/unit_test/hip/TestHIP_InterOp_Streams.cpp
index 95d102d4d1..6c7fdd7044 100644
--- a/lib/kokkos/core/unit_test/hip/TestHIP_InterOp_Streams.cpp
+++ b/lib/kokkos/core/unit_test/hip/TestHIP_InterOp_Streams.cpp
@@ -50,9 +50,11 @@ namespace Test {
 // The difference with the CUDA tests are: raw HIP vs raw CUDA and no launch
 // bound in HIP due to an error when computing the block size.
 TEST(hip, raw_hip_streams) {
+  // Make sure that we use the same device for all allocations
+  Kokkos::initialize();
+
   hipStream_t stream;
   KOKKOS_IMPL_HIP_SAFE_CALL(hipStreamCreate(&stream));
-  Kokkos::initialize();
   int* p;
   KOKKOS_IMPL_HIP_SAFE_CALL(hipMalloc(&p, sizeof(int) * 100));
   using MemorySpace = typename TEST_EXECSPACE::memory_space;
diff --git a/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Init.cpp b/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Init.cpp
index e45d990745..1189aba26f 100644
--- a/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Init.cpp
+++ b/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Init.cpp
@@ -52,8 +52,8 @@ namespace Test {
 // Test whether allocations survive Kokkos initialize/finalize if done via Raw
 // SYCL.
 TEST(sycl, raw_sycl_interop) {
+  // Make sure all queues use the same context
   Kokkos::initialize();
-
   Kokkos::Experimental::SYCL default_space;
   sycl::context default_context = default_space.sycl_queue().get_context();
 
diff --git a/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Init_Context.cpp b/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Init_Context.cpp
index 114d2a4aa2..7b9a664304 100644
--- a/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Init_Context.cpp
+++ b/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Init_Context.cpp
@@ -51,6 +51,7 @@ namespace Test {
 
 // Test whether external allocations can be accessed by the default queue.
 TEST(sycl, raw_sycl_interop_context_1) {
+  // Make sure all queues use the same context
   Kokkos::Experimental::SYCL default_space;
   sycl::context default_context = default_space.sycl_queue().get_context();
 
diff --git a/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Streams.cpp b/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Streams.cpp
index 8ffada1dab..be093d8edc 100644
--- a/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Streams.cpp
+++ b/lib/kokkos/core/unit_test/sycl/TestSYCL_InterOp_Streams.cpp
@@ -48,9 +48,13 @@
 namespace Test {
 // Test Interoperability with SYCL Streams
 TEST(sycl, raw_sycl_queues) {
-  sycl::default_selector device_selector;
-  sycl::queue queue(device_selector);
+  // Make sure all queues use the same context
   Kokkos::initialize();
+  Kokkos::Experimental::SYCL default_space;
+  sycl::context default_context = default_space.sycl_queue().get_context();
+
+  sycl::default_selector device_selector;
+  sycl::queue queue(default_context, device_selector);
   int* p            = sycl::malloc_device<int>(100, queue);
   using MemorySpace = typename TEST_EXECSPACE::memory_space;
 
diff --git a/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Array_Cuda.hpp b/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Array_Cuda.hpp
index 1815adb4a7..b55be52264 100644
--- a/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Array_Cuda.hpp
+++ b/lib/kokkos/tpls/desul/include/desul/atomics/Lock_Array_Cuda.hpp
@@ -76,7 +76,7 @@ namespace Impl {
 /// instances in other translation units, we must update this CUDA global
 /// variable based on the Host global variable prior to running any kernels
 /// that will use it.
-/// That is the purpose of the KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE macro.
+/// That is the purpose of the ensure_cuda_lock_arrays_on_device function.
 __device__
 #ifdef __CUDACC_RDC__
     __constant__ extern
@@ -138,33 +138,42 @@ namespace {
 static int lock_array_copied = 0;
 inline int eliminate_warning_for_lock_array() { return lock_array_copied; }
 }  // namespace
+
+#ifdef __CUDACC_RDC__
+inline
+#else
+inline static
+#endif
+    void
+    copy_cuda_lock_arrays_to_device() {
+  if (lock_array_copied == 0) {
+    cudaMemcpyToSymbol(CUDA_SPACE_ATOMIC_LOCKS_DEVICE,
+                       &CUDA_SPACE_ATOMIC_LOCKS_DEVICE_h,
+                       sizeof(int32_t*));
+    cudaMemcpyToSymbol(CUDA_SPACE_ATOMIC_LOCKS_NODE,
+                       &CUDA_SPACE_ATOMIC_LOCKS_NODE_h,
+                       sizeof(int32_t*));
+  }
+  lock_array_copied = 1;
+}
+
 }  // namespace Impl
 }  // namespace desul
-/* It is critical that this code be a macro, so that it will
-   capture the right address for desul::Impl::CUDA_SPACE_ATOMIC_LOCKS_DEVICE
-   putting this in an inline function will NOT do the right thing! */
-#define DESUL_IMPL_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE()                       \
-  {                                                                        \
-    if (::desul::Impl::lock_array_copied == 0) {                           \
-      cudaMemcpyToSymbol(::desul::Impl::CUDA_SPACE_ATOMIC_LOCKS_DEVICE,    \
-                         &::desul::Impl::CUDA_SPACE_ATOMIC_LOCKS_DEVICE_h, \
-                         sizeof(int32_t*));                                \
-      cudaMemcpyToSymbol(::desul::Impl::CUDA_SPACE_ATOMIC_LOCKS_NODE,      \
-                         &::desul::Impl::CUDA_SPACE_ATOMIC_LOCKS_NODE_h,   \
-                         sizeof(int32_t*));                                \
-    }                                                                      \
-    ::desul::Impl::lock_array_copied = 1;                                  \
-  }
 
 #endif /* defined( __CUDACC__ ) */
 
 #endif /* defined( DESUL_HAVE_CUDA_ATOMICS ) */
 
+namespace desul {
+
 #if defined(__CUDACC_RDC__) || (!defined(__CUDACC__))
-#define DESUL_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE()
+inline void ensure_cuda_lock_arrays_on_device() {}
 #else
-#define DESUL_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE() \
-  DESUL_IMPL_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE()
+static inline void ensure_cuda_lock_arrays_on_device() {
+  Impl::copy_cuda_lock_arrays_to_device();
+}
 #endif
 
-#endif /* #ifndef KOKKOS_CUDA_LOCKS_HPP_ */
+}  // namespace desul
+
+#endif /* #ifndef DESUL_ATOMICS_LOCK_ARRAY_CUDA_HPP_ */
diff --git a/lib/kokkos/tpls/desul/src/Lock_Array_CUDA.cpp b/lib/kokkos/tpls/desul/src/Lock_Array_CUDA.cpp
index cb8482c5da..19944b378e 100644
--- a/lib/kokkos/tpls/desul/src/Lock_Array_CUDA.cpp
+++ b/lib/kokkos/tpls/desul/src/Lock_Array_CUDA.cpp
@@ -70,7 +70,7 @@ void init_lock_arrays_cuda() {
                              "init_lock_arrays_cuda: cudaMalloc host locks");
 
   auto error_sync1 = cudaDeviceSynchronize();
-  DESUL_IMPL_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE();
+  copy_cuda_lock_arrays_to_device();
   check_error_and_throw_cuda(error_sync1, "init_lock_arrays_cuda: post mallocs");
   init_lock_arrays_cuda_kernel<<<(CUDA_SPACE_ATOMIC_MASK + 1 + 255) / 256, 256>>>();
   auto error_sync2 = cudaDeviceSynchronize();
@@ -85,7 +85,7 @@ void finalize_lock_arrays_cuda() {
   CUDA_SPACE_ATOMIC_LOCKS_DEVICE_h = nullptr;
   CUDA_SPACE_ATOMIC_LOCKS_NODE_h = nullptr;
 #ifdef __CUDACC_RDC__
-  DESUL_IMPL_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE();
+  copy_cuda_lock_arrays_to_device();
 #endif
 }
 

From 2e09ba2702639ca5c5ac311e624249ac1f682d42 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Mon, 5 Jun 2023 10:08:20 -0600
Subject: [PATCH 176/396] Update CMake

---
 cmake/Modules/Packages/KOKKOS.cmake | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake
index aa93e0cd7c..8b695667ae 100644
--- a/cmake/Modules/Packages/KOKKOS.cmake
+++ b/cmake/Modules/Packages/KOKKOS.cmake
@@ -49,8 +49,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "f140e02b826223b1045207d9bc10d404" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.02.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "34d7860d548c06a4040236d959c9f99a" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -75,7 +75,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.7.01 REQUIRED CONFIG)
+  find_package(Kokkos 3.7.02 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

From 966efd8bd53cf170e90a809af696077f6b8b3351 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Mon, 5 Jun 2023 10:33:30 -0600
Subject: [PATCH 177/396] Add missed changes

---
 .../src/Cuda/Kokkos_Cuda_KernelLaunch.hpp     |  2 +-
 .../core/src/Cuda/Kokkos_Cuda_Locks.cpp       |  7 +--
 .../core/src/Cuda/Kokkos_Cuda_Locks.hpp       | 58 ++++++++++---------
 3 files changed, 34 insertions(+), 33 deletions(-)

diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp
index ba43e362bb..a91d0eb313 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_KernelLaunch.hpp
@@ -710,7 +710,7 @@ struct CudaParallelLaunchImpl<
                     " occupancy requests are currently broken."));
       }
 
-      KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE();
+      ensure_cuda_lock_arrays_on_device();
 
       // Invoke the driver function on the device
       base_t::invoke_kernel(driver, grid, block, shmem, cuda_instance);
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.cpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.cpp
index 84d4307cfd..3796534816 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.cpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.cpp
@@ -79,8 +79,7 @@ CudaLockArrays g_host_cuda_lock_arrays = {nullptr, 0};
 void initialize_host_cuda_lock_arrays() {
 #ifdef KOKKOS_ENABLE_IMPL_DESUL_ATOMICS
   desul::Impl::init_lock_arrays();
-
-  DESUL_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE();
+  desul::ensure_cuda_lock_arrays_on_device();
 #endif
   if (g_host_cuda_lock_arrays.atomic != nullptr) return;
   KOKKOS_IMPL_CUDA_SAFE_CALL(
@@ -89,7 +88,7 @@ void initialize_host_cuda_lock_arrays() {
   Impl::cuda_device_synchronize(
       "Kokkos::Impl::initialize_host_cuda_lock_arrays: Pre Init Lock Arrays");
   g_host_cuda_lock_arrays.n = Cuda::concurrency();
-  KOKKOS_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE();
+  copy_cuda_lock_arrays_to_device();
   init_lock_array_kernel_atomic<<<(CUDA_SPACE_ATOMIC_MASK + 1 + 255) / 256,
                                   256>>>();
   Impl::cuda_device_synchronize(
@@ -106,7 +105,7 @@ void finalize_host_cuda_lock_arrays() {
   g_host_cuda_lock_arrays.atomic = nullptr;
   g_host_cuda_lock_arrays.n      = 0;
 #ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE
-  KOKKOS_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE();
+  copy_cuda_lock_arrays_to_device();
 #endif
 }
 
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp
index bdb7723985..84bfc953fd 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp
@@ -67,7 +67,7 @@ struct CudaLockArrays {
 
 /// \brief This global variable in Host space is the central definition
 ///        of these arrays.
-extern Kokkos::Impl::CudaLockArrays g_host_cuda_lock_arrays;
+extern CudaLockArrays g_host_cuda_lock_arrays;
 
 /// \brief After this call, the g_host_cuda_lock_arrays variable has
 ///        valid, initialized arrays.
@@ -105,12 +105,12 @@ namespace Impl {
 /// instances in other translation units, we must update this CUDA global
 /// variable based on the Host global variable prior to running any kernels
 /// that will use it.
-/// That is the purpose of the KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE macro.
+/// That is the purpose of the ensure_cuda_lock_arrays_on_device function.
 __device__
 #ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE
     __constant__ extern
 #endif
-    Kokkos::Impl::CudaLockArrays g_device_cuda_lock_arrays;
+    CudaLockArrays g_device_cuda_lock_arrays;
 
 #define CUDA_SPACE_ATOMIC_MASK 0x1FFFF
 
@@ -123,9 +123,7 @@ __device__ inline bool lock_address_cuda_space(void* ptr) {
   size_t offset = size_t(ptr);
   offset        = offset >> 2;
   offset        = offset & CUDA_SPACE_ATOMIC_MASK;
-  return (
-      0 ==
-      atomicCAS(&Kokkos::Impl::g_device_cuda_lock_arrays.atomic[offset], 0, 1));
+  return (0 == atomicCAS(&g_device_cuda_lock_arrays.atomic[offset], 0, 1));
 }
 
 /// \brief Release lock for the address
@@ -138,7 +136,7 @@ __device__ inline void unlock_address_cuda_space(void* ptr) {
   size_t offset = size_t(ptr);
   offset        = offset >> 2;
   offset        = offset & CUDA_SPACE_ATOMIC_MASK;
-  atomicExch(&Kokkos::Impl::g_device_cuda_lock_arrays.atomic[offset], 0);
+  atomicExch(&g_device_cuda_lock_arrays.atomic[offset], 0);
 }
 
 }  // namespace Impl
@@ -151,45 +149,49 @@ namespace {
 static int lock_array_copied = 0;
 inline int eliminate_warning_for_lock_array() { return lock_array_copied; }
 }  // namespace
-}  // namespace Impl
-}  // namespace Kokkos
 
-/* Dan Ibanez: it is critical that this code be a macro, so that it will
-   capture the right address for Kokkos::Impl::g_device_cuda_lock_arrays!
-   putting this in an inline function will NOT do the right thing! */
-#define KOKKOS_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE()                      \
-  {                                                                   \
-    if (::Kokkos::Impl::lock_array_copied == 0) {                     \
-      KOKKOS_IMPL_CUDA_SAFE_CALL(                                     \
-          cudaMemcpyToSymbol(Kokkos::Impl::g_device_cuda_lock_arrays, \
-                             &Kokkos::Impl::g_host_cuda_lock_arrays,  \
-                             sizeof(Kokkos::Impl::CudaLockArrays)));  \
-    }                                                                 \
-    lock_array_copied = 1;                                            \
+#ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE
+inline
+#else
+inline static
+#endif
+    void
+    copy_cuda_lock_arrays_to_device() {
+  if (lock_array_copied == 0) {
+    KOKKOS_IMPL_CUDA_SAFE_CALL(cudaMemcpyToSymbol(g_device_cuda_lock_arrays,
+                                                  &g_host_cuda_lock_arrays,
+                                                  sizeof(CudaLockArrays)));
   }
+  lock_array_copied = 1;
+}
 
 #ifndef KOKKOS_ENABLE_IMPL_DESUL_ATOMICS
 
 #ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE
-#define KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE()
+inline void ensure_cuda_lock_arrays_on_device() {}
 #else
-#define KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE() \
-  KOKKOS_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE()
+inline static void ensure_cuda_lock_arrays_on_device() {
+  copy_cuda_lock_arrays_to_device();
+}
 #endif
 
 #else
 
 #ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE
-#define KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE()
+inline void ensure_cuda_lock_arrays_on_device() {}
 #else
 // Still Need COPY_CUDA_LOCK_ARRAYS for team scratch etc.
-#define KOKKOS_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE() \
-  KOKKOS_COPY_CUDA_LOCK_ARRAYS_TO_DEVICE()         \
-  DESUL_ENSURE_CUDA_LOCK_ARRAYS_ON_DEVICE()
+inline static void ensure_cuda_lock_arrays_on_device() {
+  copy_cuda_lock_arrays_to_device();
+  desul::ensure_cuda_lock_arrays_on_device();
+}
 #endif
 
 #endif /* defined( KOKKOS_ENABLE_IMPL_DESUL_ATOMICS ) */
 
+}  // namespace Impl
+}  // namespace Kokkos
+
 #endif /* defined( KOKKOS_ENABLE_CUDA ) */
 
 #endif /* #ifndef KOKKOS_CUDA_LOCKS_HPP */

From c558de3ce003e2f77744d82f30d3f967df7be81d Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Tue, 6 Jun 2023 08:27:14 +0800
Subject: [PATCH 178/396] remove the fprintf debug outputs

---
 src/INTERLAYER/pair_ilp_tmd.cpp | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/src/INTERLAYER/pair_ilp_tmd.cpp b/src/INTERLAYER/pair_ilp_tmd.cpp
index c1af7098cd..f0d618687a 100644
--- a/src/INTERLAYER/pair_ilp_tmd.cpp
+++ b/src/INTERLAYER/pair_ilp_tmd.cpp
@@ -336,9 +336,6 @@ void PairILPTMD::ILP_neigh()
           }
         }    // end of idenfying the first neighbor
       } else if (n > Nnei) {
-        fprintf(screen, "Molecule ID = %d\n", imol);
-        fprintf(screen, "Atom Type = %d\n", type[i]);
-        fprintf(screen, "Neinum = %d\n", n);
         error->one(FLERR,
                    "There are too many neighbors for TMD atoms, please check your configuration");
       }
@@ -497,9 +494,6 @@ void PairILPTMD::calc_normal()
             vect[0][1] = x[jH2][1] - ytp;
             vect[0][2] = x[jH2][2] - ztp;
           } else {
-            fprintf(screen, "jH1 jH2 = %d %d\n", jH1,jH2);
-            fprintf(screen, "Atom Type = %d %d\n", type[jH1],type[jH2]);
-            fprintf(screen, "For atom i = %d %d\n", tag[i],type[i]);
             error->one(FLERR, "The order of atoms in water molecule should be O H H !");
           }
         }
@@ -662,9 +656,6 @@ void PairILPTMD::calc_normal()
 
             cont = 2;
           } else {
-            fprintf(screen, "jH1 jH2 = %d %d\n", jH1,jH2);
-            fprintf(screen, "Atom Type = %d %d\n", type[jH1],type[jH2]);
-            fprintf(screen, "ID and type of atom i = %d %d\n", tag[i],type[i]);
             error->one(FLERR, "The order of atoms in water molecule should be O H H !");
           }
         }
@@ -728,11 +719,6 @@ void PairILPTMD::calc_normal()
               dnormdri[i][id][ip] = dpvdri[id][ip] / nn - Nave[id] * dni[ip] / nn2;
             }
           }
-          // printf("%4d:\t%e %e %e\n\t%e %e %e\n\t%e %e %e\n",
-          //        i, dnormdri[i][0][0], dnormdri[i][0][1], dnormdri[i][0][2],
-          //        dnormdri[i][1][0],dnormdri[i][1][1],dnormdri[i][1][2],
-          //        dnormdri[i][2][0],dnormdri[i][2][1],dnormdri[i][2][2]);
-          // exit(0);
         }
         else if (cont >= 3) {
           error->one(FLERR,

From 409bced5fd74e2c9b75a1e153ee126a5507605ca Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Tue, 6 Jun 2023 08:35:42 +0800
Subject: [PATCH 179/396] update affiliations

---
 src/INTERLAYER/pair_coul_shield.cpp            | 2 +-
 src/INTERLAYER/pair_ilp_graphene_hbn.cpp       | 4 ++--
 src/INTERLAYER/pair_kolmogorov_crespi_full.cpp | 2 +-
 src/MANYBODY/pair_tersoff.cpp                  | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/INTERLAYER/pair_coul_shield.cpp b/src/INTERLAYER/pair_coul_shield.cpp
index e647e1ea91..a5e3e63442 100644
--- a/src/INTERLAYER/pair_coul_shield.cpp
+++ b/src/INTERLAYER/pair_coul_shield.cpp
@@ -11,7 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 /* ----------------------------------------------------------------------
-   Contributing author: Wengen Ouyang (Tel Aviv University)
+   Contributing author: Wengen Ouyang (Wuhan University)
    e-mail: w.g.ouyang at gmail dot com
 
    This is a Coulomb potential described in
diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
index e6711d0f19..eb37b39864 100644
--- a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
+++ b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
@@ -11,11 +11,11 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing author: Wengen Ouyang (Tel Aviv University)
+   Contributing author: Wengen Ouyang (Wuhan University)
    e-mail: w.g.ouyang at gmail dot com
 
    This is a full version of the potential described in
-   [Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)]
+   [Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020)]
    The definition of normals are the same as that in
    [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
 ------------------------------------------------------------------------- */
diff --git a/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp b/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp
index b2eba787b1..b497ae3568 100644
--- a/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp
+++ b/src/INTERLAYER/pair_kolmogorov_crespi_full.cpp
@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing author: Wengen Ouyang (Tel Aviv University)
+   Contributing author: Wengen Ouyang (Wuhan University)
    e-mail: w.g.ouyang at gmail dot com
    based on previous versions by Jaap Kroes
 
diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp
index f38ba00861..c7c45bc865 100644
--- a/src/MANYBODY/pair_tersoff.cpp
+++ b/src/MANYBODY/pair_tersoff.cpp
@@ -14,7 +14,7 @@
 
 /* ----------------------------------------------------------------------
    Contributing author: Aidan Thompson (SNL) - original Tersoff implementation
-                        Wengen Ouyang (TAU)  - Shift addition
+                        Wengen Ouyang (WHU)  - Shift addition
 ------------------------------------------------------------------------- */
 
 #include "pair_tersoff.h"

From 0ef0419a98adb1d804c17efc0c3d78cb2d549275 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Tue, 6 Jun 2023 21:45:51 +0800
Subject: [PATCH 180/396] rename function names in opt version

---
 src/OPT/pair_aip_water_2dm_opt.cpp    |  2 +-
 src/OPT/pair_ilp_graphene_hbn_opt.cpp | 51 +++++++++++++++++----------
 src/OPT/pair_ilp_graphene_hbn_opt.h   |  2 +-
 src/OPT/pair_ilp_tmd_opt.cpp          |  2 +-
 4 files changed, 35 insertions(+), 22 deletions(-)

diff --git a/src/OPT/pair_aip_water_2dm_opt.cpp b/src/OPT/pair_aip_water_2dm_opt.cpp
index 17e981e479..3aba5b9dbd 100644
--- a/src/OPT/pair_aip_water_2dm_opt.cpp
+++ b/src/OPT/pair_aip_water_2dm_opt.cpp
@@ -23,7 +23,7 @@
      e-mail: qdgaoping at gmail dot com
 
    Optimizations are described in:
-     Gao, Ping and Duan, Xiaohui, et al:
+     Gao, Ping and Duan, Xiaohui, et al.:
        LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
      DOI: 10.1145/3458817.3476137
 
diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.cpp b/src/OPT/pair_ilp_graphene_hbn_opt.cpp
index b2abcec7be..5bf21e5c24 100644
--- a/src/OPT/pair_ilp_graphene_hbn_opt.cpp
+++ b/src/OPT/pair_ilp_graphene_hbn_opt.cpp
@@ -11,12 +11,24 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Optimization author1: Ping Gao (National Supercomputing Center in Wuxi, China)
-   e-mail: qdgaoping at gmail dot com
-   Optimization author2: Xiaohui Duan (National Supercomputing Center in Wuxi, China)
-   e-mail: sunrise_duan at 126 dot com
+   This is an optimized version of ilp/graphene/hbn based on the contribution of:
+     author: Wengen Ouyang (Wuhan University)
+     e-mail: w.g.ouyang at gmail dot com
 
-   Provides some bugfixes and performance optimizations in this potential.
+   Optimizations are done by:
+     author1: Ping Gao (National Supercomputing Center in Wuxi, China)
+     e-mail: qdgaoping at gmail dot com
+
+     author2: Xiaohui Duan (National Supercomputing Center in Wuxi, China)
+     e-mail: sunrise_duan at 126 dot com
+
+   Optimizations are described in:
+     Gao, Ping and Duan, Xiaohui, et al.:
+       LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
+     DOI: 10.1145/3458817.3476137
+
+   Potential is described by:
+     [Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020)]
 */
 
 #include "pair_ilp_graphene_hbn_opt.h"
@@ -169,33 +181,33 @@ void PairILPGrapheneHBNOpt::compute(int eflag, int vflag)
         }
       }
     }
-  } else if (variant == AIP_WATER_2DM) {
+  } else if (variant == ILP_WATER_2DM) {
     if (eflag_global || eflag_atom) {
       if (vflag_either) {
         if (tap_flag) {
-          eval<6, 1, 1, 1, AIP_WATER_2DM>();
+          eval<6, 1, 1, 1, ILP_WATER_2DM>();
         } else {
-          eval<6, 1, 1, 0, AIP_WATER_2DM>();
+          eval<6, 1, 1, 0, ILP_WATER_2DM>();
         }
       } else {
         if (tap_flag) {
-          eval<6, 1, 0, 1, AIP_WATER_2DM>();
+          eval<6, 1, 0, 1, ILP_WATER_2DM>();
         } else {
-          eval<6, 1, 0, 0, AIP_WATER_2DM>();
+          eval<6, 1, 0, 0, ILP_WATER_2DM>();
         }
       }
     } else {
       if (vflag_either) {
         if (tap_flag) {
-          eval<6, 0, 1, 1, AIP_WATER_2DM>();
+          eval<6, 0, 1, 1, ILP_WATER_2DM>();
         } else {
-          eval<6, 0, 1, 0, AIP_WATER_2DM>();
+          eval<6, 0, 1, 0, ILP_WATER_2DM>();
         }
       } else {
         if (tap_flag) {
-          eval<6, 0, 0, 1, AIP_WATER_2DM>();
+          eval<6, 0, 0, 1, ILP_WATER_2DM>();
         } else {
-          eval<6, 0, 0, 0, AIP_WATER_2DM>();
+          eval<6, 0, 0, 0, ILP_WATER_2DM>();
         }
       }
     }
@@ -286,7 +298,7 @@ void PairILPGrapheneHBNOpt::eval()
       rsq = delx * delx + dely * dely + delz * delz;
 
       if (rsq != 0 && rsq < cutILPsq[itype_map][jtype]) {
-        if ((VARIANT == ILP_TMD || VARIANT == AIP_WATER_2DM) && special_type[itype] == TMD_METAL && itype != type[j]) continue;
+        if ((VARIANT == ILP_TMD || VARIANT == ILP_WATER_2DM) && special_type[itype] == TMD_METAL && itype != type[j]) continue;
         if (ILP_nneigh >= MAX_NNEIGH) {
           error->one(FLERR, "There are too many neighbors for calculating normals");
         }
@@ -301,7 +313,7 @@ void PairILPGrapheneHBNOpt::eval()
 
     double norm[3], dnormdxi[3][3], dnormdxk[MAX_NNEIGH][3][3];
 
-    calc_normal<MAX_NNEIGH>(i, itype, ILP_neigh, ILP_nneigh, norm, dnormdxi, dnormdxk);
+    calc_atom_normal<MAX_NNEIGH>(i, itype, ILP_neigh, ILP_nneigh, norm, dnormdxi, dnormdxk);
 
     for (jj = 0; jj < jnum_inter; jj++) {
       j = jlist_inter[jj];
@@ -471,6 +483,7 @@ inline void deriv_hat(double dnhatdn[3][3], double *n, double rnnorm, double fac
   dnhatdn[0][2] = -n[0]*n[2]*cfactor;
   dnhatdn[1][2] = -n[1]*n[2]*cfactor;
   dnhatdn[2][2] = (n[0]*n[0]+n[1]*n[1])*cfactor;
+
 }
 inline double normalize_factor(double *n)
 {
@@ -485,7 +498,7 @@ inline double normalize_factor(double *n)
   Yet another normal calculation method for simpiler code.
  */
 template <int MAX_NNEIGH>
-void PairILPGrapheneHBNOpt::calc_normal(int i, int itype, int *ILP_neigh, int nneigh, double *n,
+void PairILPGrapheneHBNOpt::calc_atom_normal(int i, int itype, int *ILP_neigh, int nneigh, double *n,
                                         double (*dnormdri)[3], double (*dnormdrk)[3][3])
 {
   double **x = atom->x;
@@ -519,8 +532,8 @@ void PairILPGrapheneHBNOpt::calc_normal(int i, int itype, int *ILP_neigh, int nn
     vet[jj][2] = x[j][2] - x[i][2];
   }
 
-  //specialize for AIP_WATER_2DM for hydrogen has special normal vector rule
-  if (variant == AIP_WATER_2DM && special_type[itype] == WATER) {
+  //specialize for ILP_WATER_2DM for hydrogen has special normal vector rule
+  if (variant == ILP_WATER_2DM && special_type[itype] == WATER) {
     if (nneigh == 1){
       n[0] = vet[0][0];
       n[1] = vet[0][1];
diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.h b/src/OPT/pair_ilp_graphene_hbn_opt.h
index 41d2178092..01b66bb2fa 100644
--- a/src/OPT/pair_ilp_graphene_hbn_opt.h
+++ b/src/OPT/pair_ilp_graphene_hbn_opt.h
@@ -35,7 +35,7 @@ class PairILPGrapheneHBNOpt : virtual public PairILPGrapheneHBN {
  protected:
   void update_internal_list();
   template <int MAX_NNEIGH>
-  void calc_normal(int i, int itype, int *ILP_neigh, int nneigh, double *normal, double (*dnormdri)[3],
+  void calc_atom_normal(int i, int itype, int *ILP_neigh, int nneigh, double *normal, double (*dnormdri)[3],
                    double (*dnormdrk)[3][3]);
   template <int MAX_NNEIGH, int EFLAG, int VFLAG_EITHER, int TAP_FLAG, int VARIANT = ILP_GrhBN>
   void eval();
diff --git a/src/OPT/pair_ilp_tmd_opt.cpp b/src/OPT/pair_ilp_tmd_opt.cpp
index 834f2a0c9f..3fa95b7e10 100644
--- a/src/OPT/pair_ilp_tmd_opt.cpp
+++ b/src/OPT/pair_ilp_tmd_opt.cpp
@@ -23,7 +23,7 @@
      e-mail: qdgaoping at gmail dot com
 
    Optimizations are described in:
-     Gao, Ping and Duan, Xiaohui, et al:
+     Gao, Ping and Duan, Xiaohui, et al.:
        LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
      DOI: 10.1145/3458817.3476137
 

From f85474c9ecc64532c5197b96ba0d38c80547a729 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Tue, 6 Jun 2023 22:03:33 +0800
Subject: [PATCH 181/396] fix a typo

---
 src/OPT/pair_aip_water_2dm_opt.h      |  1 -
 src/OPT/pair_ilp_graphene_hbn_opt.cpp | 48 +++++++++++++--------------
 2 files changed, 23 insertions(+), 26 deletions(-)

diff --git a/src/OPT/pair_aip_water_2dm_opt.h b/src/OPT/pair_aip_water_2dm_opt.h
index 46280c2b82..50b5043360 100644
--- a/src/OPT/pair_aip_water_2dm_opt.h
+++ b/src/OPT/pair_aip_water_2dm_opt.h
@@ -36,4 +36,3 @@ class PairAIPWATER2DMOpt : public PairAIPWATER2DM, public PairILPGrapheneHBNOpt
 }    // namespace LAMMPS_NS
 #endif
 #endif
-
diff --git a/src/OPT/pair_ilp_graphene_hbn_opt.cpp b/src/OPT/pair_ilp_graphene_hbn_opt.cpp
index 5bf21e5c24..5cb896223e 100644
--- a/src/OPT/pair_ilp_graphene_hbn_opt.cpp
+++ b/src/OPT/pair_ilp_graphene_hbn_opt.cpp
@@ -11,31 +11,30 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   This is an optimized version of ilp/graphene/hbn based on the contribution of:
-     author: Wengen Ouyang (Wuhan University)
-     e-mail: w.g.ouyang at gmail dot com
+   This is an optimized version of ilp/graphene/hbn based on the contirubtion of:
+   author: Wengen Ouyang (Wuhan University, China)
+   e-mail: w.g.ouyang at gmail dot com
 
    Optimizations are done by:
-     author1: Ping Gao (National Supercomputing Center in Wuxi, China)
-     e-mail: qdgaoping at gmail dot com
+   author1: Ping Gao (National Supercomputing Center in Wuxi, China) implements the base ILP potential.
+   e-mail: qdgaoping at gmail dot com
 
-     author2: Xiaohui Duan (National Supercomputing Center in Wuxi, China)
-     e-mail: sunrise_duan at 126 dot com
+   author2: Xiaohui Duan (Shandong University, China) adjusts the framework to adopt SAIP, TMD, WATER2DM, etc.
+   e-mail: sunrise_duan at 126 dot com
 
    Optimizations are described in:
-     Gao, Ping and Duan, Xiaohui, et al.:
-       LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
-     DOI: 10.1145/3458817.3476137
+   Gao, Ping and Duan, Xiaohui, et al:
+   LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
+   DOI: 10.1145/3458817.3476137
 
    Potential is described by:
-     [Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020)]
+   [Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020)]
 */
 
 #include "pair_ilp_graphene_hbn_opt.h"
 
 #include "atom.h"
 #include "citeme.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "interlayer_taper.h"
@@ -181,33 +180,33 @@ void PairILPGrapheneHBNOpt::compute(int eflag, int vflag)
         }
       }
     }
-  } else if (variant == ILP_WATER_2DM) {
+  } else if (variant == AIP_WATER_2DM) {
     if (eflag_global || eflag_atom) {
       if (vflag_either) {
         if (tap_flag) {
-          eval<6, 1, 1, 1, ILP_WATER_2DM>();
+          eval<6, 1, 1, 1, AIP_WATER_2DM>();
         } else {
-          eval<6, 1, 1, 0, ILP_WATER_2DM>();
+          eval<6, 1, 1, 0, AIP_WATER_2DM>();
         }
       } else {
         if (tap_flag) {
-          eval<6, 1, 0, 1, ILP_WATER_2DM>();
+          eval<6, 1, 0, 1, AIP_WATER_2DM>();
         } else {
-          eval<6, 1, 0, 0, ILP_WATER_2DM>();
+          eval<6, 1, 0, 0, AIP_WATER_2DM>();
         }
       }
     } else {
       if (vflag_either) {
         if (tap_flag) {
-          eval<6, 0, 1, 1, ILP_WATER_2DM>();
+          eval<6, 0, 1, 1, AIP_WATER_2DM>();
         } else {
-          eval<6, 0, 1, 0, ILP_WATER_2DM>();
+          eval<6, 0, 1, 0, AIP_WATER_2DM>();
         }
       } else {
         if (tap_flag) {
-          eval<6, 0, 0, 1, ILP_WATER_2DM>();
+          eval<6, 0, 0, 1, AIP_WATER_2DM>();
         } else {
-          eval<6, 0, 0, 0, ILP_WATER_2DM>();
+          eval<6, 0, 0, 0, AIP_WATER_2DM>();
         }
       }
     }
@@ -298,7 +297,7 @@ void PairILPGrapheneHBNOpt::eval()
       rsq = delx * delx + dely * dely + delz * delz;
 
       if (rsq != 0 && rsq < cutILPsq[itype_map][jtype]) {
-        if ((VARIANT == ILP_TMD || VARIANT == ILP_WATER_2DM) && special_type[itype] == TMD_METAL && itype != type[j]) continue;
+        if ((VARIANT == ILP_TMD || VARIANT == AIP_WATER_2DM) && special_type[itype] == TMD_METAL && itype != type[j]) continue;
         if (ILP_nneigh >= MAX_NNEIGH) {
           error->one(FLERR, "There are too many neighbors for calculating normals");
         }
@@ -483,7 +482,6 @@ inline void deriv_hat(double dnhatdn[3][3], double *n, double rnnorm, double fac
   dnhatdn[0][2] = -n[0]*n[2]*cfactor;
   dnhatdn[1][2] = -n[1]*n[2]*cfactor;
   dnhatdn[2][2] = (n[0]*n[0]+n[1]*n[1])*cfactor;
-
 }
 inline double normalize_factor(double *n)
 {
@@ -532,8 +530,8 @@ void PairILPGrapheneHBNOpt::calc_atom_normal(int i, int itype, int *ILP_neigh, i
     vet[jj][2] = x[j][2] - x[i][2];
   }
 
-  //specialize for ILP_WATER_2DM for hydrogen has special normal vector rule
-  if (variant == ILP_WATER_2DM && special_type[itype] == WATER) {
+  //specialize for AIP_WATER_2DM for hydrogen has special normal vector rule
+  if (variant == AIP_WATER_2DM && special_type[itype] == WATER) {
     if (nneigh == 1){
       n[0] = vet[0][0];
       n[1] = vet[0][1];

From 51b45d683071f1985d59a9a25b1ebc8f29739017 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Tue, 6 Jun 2023 22:16:41 +0800
Subject: [PATCH 182/396] fix small format issues

---
 src/INTERLAYER/pair_ilp_graphene_hbn.cpp | 2 --
 src/INTERLAYER/pair_ilp_tmd.cpp          | 2 +-
 src/INTERLAYER/pair_saip_metal.cpp       | 2 +-
 3 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
index eb37b39864..69896d7c0b 100644
--- a/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
+++ b/src/INTERLAYER/pair_ilp_graphene_hbn.cpp
@@ -16,8 +16,6 @@
 
    This is a full version of the potential described in
    [Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020)]
-   The definition of normals are the same as that in
-   [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
 ------------------------------------------------------------------------- */
 
 #include "pair_ilp_graphene_hbn.h"
diff --git a/src/INTERLAYER/pair_ilp_tmd.cpp b/src/INTERLAYER/pair_ilp_tmd.cpp
index f0d618687a..f29ee34180 100644
--- a/src/INTERLAYER/pair_ilp_tmd.cpp
+++ b/src/INTERLAYER/pair_ilp_tmd.cpp
@@ -15,7 +15,7 @@
    e-mail: w.g.ouyang at gmail dot com
 
    This is a full version of the potential described in
-   [Ouyang et al, J. Chem. Theory Comput. 17, 7237 (2021).]
+   [Ouyang et al., J. Chem. Theory Comput. 17, 7237 (2021).]
 ------------------------------------------------------------------------- */
 
 #include "pair_ilp_tmd.h"
diff --git a/src/INTERLAYER/pair_saip_metal.cpp b/src/INTERLAYER/pair_saip_metal.cpp
index 05fbfbf7f4..bd327391a4 100644
--- a/src/INTERLAYER/pair_saip_metal.cpp
+++ b/src/INTERLAYER/pair_saip_metal.cpp
@@ -15,7 +15,7 @@
    e-mail: w.g.ouyang at gmail dot com
 
    This is a full version of the potential described in
-   [Ouyang et al, J. Chem. Theory Comput. 17, 7215-7223 (2021)]
+   [Ouyang et al., J. Chem. Theory Comput. 17, 7215-7223 (2021)]
 ------------------------------------------------------------------------- */
 
 #include "pair_saip_metal.h"

From c4d49324b52f708d9e0d8fc6ef123cee84f68845 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Jun 2023 16:08:50 -0400
Subject: [PATCH 183/396] various documentation updates

- spelling fixes
- formatting conventions
- grammar fixes and clarifications
- full integration into manual build procedure
---
 doc/src/Commands_pair.rst                   |  1 +
 doc/src/pair_aip_water_2dm.rst              | 64 +++++++++++----------
 doc/src/pair_style.rst                      |  1 +
 doc/utils/sphinx-config/false_positives.txt |  3 +
 4 files changed, 39 insertions(+), 30 deletions(-)

diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index 5f79015aaf..87d3129880 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -37,6 +37,7 @@ OPT.
    *
    * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
+   * :doc:`aip/water/2dm (o) <pair_aip_water_2dm>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/morse (io) <pair_airebo>`
    * :doc:`amoeba (g) <pair_amoeba>`
diff --git a/doc/src/pair_aip_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst
index 3ae63e1e45..5218db9c37 100644
--- a/doc/src/pair_aip_water_2dm.rst
+++ b/doc/src/pair_aip_water_2dm.rst
@@ -35,8 +35,8 @@ Description
 
 .. versionadded:: xxxx2023
 
-The *aip/water/2dm* style computes the anisotropic interfacial
-potential (AIP) potential for interfaces of water with two-dimensinal (2D)
+The *aip/water/2dm* style computes the anisotropic interfacial potential
+(AIP) potential for interfaces of water with two-dimensional (2D)
 materials as described in :ref:`(Feng) <Feng>`.
 
 .. math::
@@ -56,41 +56,45 @@ materials as described in :ref:`(Feng) <Feng>`.
 
 Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides
 a continuous cutoff (up to third derivative) for interatomic separations
-larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`.
+larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn
+<pair_ilp_graphene_hbn>`.
 
 It is important to include all the pairs to build the neighbor list for
 calculating the normals.
 
 .. note::
 
-   Since each water molecule contains one oxygen atom and two hydrogen atoms,
-   a new definition is proposed (see In :ref:`(Feng) <Feng>`),the atomic
-   normal vectors of hydrogen atoms are assumed to lie along the corresponding
-   oxygen-hydrogen bonds and the normal vector of the central oxygen atom
-   is defined as their average.
+   Since each water molecule contains one oxygen atom and two hydrogen
+   atoms, a new definition is proposed (see In :ref:`(Feng) <Feng>`),the
+   atomic normal vectors of hydrogen atoms are assumed to lie along the
+   corresponding oxygen-hydrogen bonds and the normal vector of the
+   central oxygen atom is defined as their average.
 
-The parameter file (e.g. COH.aip.water.2dm), is intended for use with *metal*
-:doc:`units <units>`, with energies in meV. Two additional parameters,
-*S*, and *rcut* are included in the parameter file. *S* is designed to
-facilitate scaling of energies. *rcut* is designed to build the neighbor
-list for calculating the normals for each atom pair.
+The provided parameter file, ``COH.aip.water.2dm``, is intended for use
+with *metal* :doc:`units <units>`, with energies in meV.  Two additional
+parameters, *S*, and *rcut* are included in the parameter file. *S* is
+designed to facilitate scaling of energies; *rcut* is designed to build
+the neighbor list for calculating the normals for each atom pair.
 
 .. note::
 
-   The parameters presented in the parameter file (e.g. COH.aip.water.2dm),
-   are fitted with taper function by setting the cutoff equal to 16.0
-   Angstrom.  Using different cutoff or taper function should be careful.
-   These parameters provide a good description in both short- and long-range
-   interaction regimes. This feature is essential for simulations in high pressure
-   regime (i.e., the interlayer distance is smaller than the equilibrium
-   distance).
+   The parameters presented in the provided parameter file,
+   ``COH.aip.water.2dm``, are fitted with the taper function enabled by
+   setting the cutoff equal to 16.0 Angstrom.  Using a different cutoff
+   or taper function setting should be carefully checked as they can
+   lead to significant errors.  These parameters provide a good
+   description in both short- and long-range interaction regimes.  This
+   feature is essential for simulations in high pressure regime (i.e.,
+   the interlayer distance is smaller than the equilibrium distance).
 
-This potential must be used in combination with hybrid/overlay.
-Other interactions can be set to zero using pair_style *none*\ .
+This potential must be used in combination with hybrid/overlay.  Other
+interactions can be set to zero using :doc:`pair_coeff settings
+<pair_coeff>` with the pair style set to *none*\ .
 
 This pair style tallies a breakdown of the total interlayer potential
-energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 2.
-The 2 values correspond to the following sub-categories:
+energy into sub-categories, which can be accessed via the :doc:`compute
+pair <compute_pair>` command as a vector of values of length 2.  The 2
+values correspond to the following sub-categories:
 
 1. *E_vdW* = vdW (attractive) energy
 2. *E_Rep* = Repulsive energy
@@ -132,11 +136,11 @@ if LAMMPS was built with that package.  See the :doc:`Build package
 This pair style requires the newton setting to be *on* for pair
 interactions.
 
-The COH.aip.water.2dm potential file provided with LAMMPS (see the potentials
-directory) are parameterized for *metal* units.  You can use this
-potential with any LAMMPS units, but you would need to create your
-COH.aip.water.2dm potential file with coefficients listed in the appropriate
-units, if your simulation does not use *metal* units.
+The ``COH.aip.water.2dm`` potential file provided with LAMMPS is
+parameterized for *metal* units.  You can use this pair style with any
+LAMMPS units, but you would need to create your own potential file with
+parameters in the appropriate units, if your simulation does not use
+*metal* units.
 
 Related commands
 """"""""""""""""
@@ -158,8 +162,8 @@ Default
 
 tap_flag = 1
 
-
 ----------
 
 .. _Feng:
+
 **(Feng)** Z. Feng and W. Ouyang et al., J. Phys. Chem. C. 127, 8704-8713 (2023).
diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst
index 441313b0b8..494a26aacf 100644
--- a/doc/src/pair_style.rst
+++ b/doc/src/pair_style.rst
@@ -114,6 +114,7 @@ accelerated styles exist.
 
 * :doc:`adp <pair_adp>` - angular dependent potential (ADP) of Mishin
 * :doc:`agni <pair_agni>` - AGNI machine-learning potential
+* :doc:`aip/water/2dm <pair_aip_water_2dm>` - anisotropic interfacial potential for water in 2d geometries
 * :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
 * :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
 * :doc:`amoeba <pair_amoeba>` -
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index d2d15633af..ad2a255447 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -55,6 +55,7 @@ Ai
 Aidan
 aij
 aimd
+aip
 airebo
 Aj
 ajaramil
@@ -528,6 +529,7 @@ collisional
 Columic
 colvars
 Colvars
+COH
 COLVARS
 comID
 Commun
@@ -1090,6 +1092,7 @@ Fellinger
 femtosecond
 femtoseconds
 fene
+Feng
 Fennell
 fep
 FEP

From eafabf0fb1d0818b675953a7e5a56f044044491b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Jun 2023 16:10:11 -0400
Subject: [PATCH 184/396] update .gitignore

---
 src/.gitignore | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/.gitignore b/src/.gitignore
index 204eec5e0b..2db7bb4663 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -1058,6 +1058,10 @@
 /pair_adp.h
 /pair_agni.cpp
 /pair_agni.h
+/pair_aip_water_2dm.cpp
+/pair_aip_water_2dm.h
+/pair_aip_water_2dm_opt.cpp
+/pair_aip_water_2dm_opt.h
 /pair_airebo.cpp
 /pair_airebo.h
 /pair_airebo_morse.cpp

From e954d8f0507bc31869f083777e412e5b1ed1aaed Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Jun 2023 16:11:03 -0400
Subject: [PATCH 185/396] correctly indicate OPT package version of pair style

---
 doc/src/Commands_pair.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index 87d3129880..c45a1d778c 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -37,7 +37,7 @@ OPT.
    *
    * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
-   * :doc:`aip/water/2dm (o) <pair_aip_water_2dm>`
+   * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/morse (io) <pair_airebo>`
    * :doc:`amoeba (g) <pair_amoeba>`

From ee6b12ee300c8adb1c8cd62ba6f703b4a6bb73b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Yifan=20Li=E6=9D=8E=E4=B8=80=E5=B8=86?=
 <yifanl0716@gmail.com>
Date: Tue, 6 Jun 2023 18:04:26 -0400
Subject: [PATCH 186/396] Correct reference info

---
 doc/src/fix_pimd.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index 22c064b60b..c08a4005f5 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -445,7 +445,7 @@ Path Integrals, McGraw-Hill, New York (1965).
 
 **(Bussi)** G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
 
-.. _Ceriotti2:
+.. _Ceriotti3:
 
 **(Ceriotti)** M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
 

From a415d732fc354ba7af12c438ad869f5f9f5484c4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Yifan=20Li=E6=9D=8E=E4=B8=80=E5=B8=86?=
 <yifanl0716@gmail.com>
Date: Tue, 6 Jun 2023 18:11:01 -0400
Subject: [PATCH 187/396] rename Langevin init

---
 src/REPLICA/fix_pimd_langevin.cpp | 4 ++--
 src/REPLICA/fix_pimd_langevin.h   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 2e4b1c17b8..17ea07c845 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -451,7 +451,7 @@ void FixPIMDLangevin::init()
 
   nmpimd_init();
 
-  Langevin_init();
+  langevin_init();
 
   c_pe = modify->get_compute_by_id(id_pe);
   c_press = modify->get_compute_by_id(id_press);
@@ -888,7 +888,7 @@ void FixPIMDLangevin::press_o_step()
 
 /* ---------------------------------------------------------------------- */
 
-void FixPIMDLangevin::Langevin_init()
+void FixPIMDLangevin::langevin_init()
 {
   double beta = 1.0 / kBT;
   _omega_np = np / beta / hbar;
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 79a2ee7477..1ef1dfae52 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -115,7 +115,7 @@ class FixPIMDLangevin : public Fix {
   class RanMars *random;
 
   int tstat_flag;    // tstat_flat = 1 if thermostat if used
-  void Langevin_init();
+  void langevin_init();
   void b_step();    // integrate for dt/2 according to B part (v <- v + f * dt/2)
   void a_step();    // integrate for dt/2 according to A part (non-centroid mode, harmonic force between replicas)
   void qc_step();    // integrate for dt/2 for the centroid mode (x <- x + v * dt/2)

From 5ff6fd9aad41084521a1a48381c6ebba6f584426 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Yifan=20Li=E6=9D=8E=E4=B8=80=E5=B8=86?=
 <yifanl0716@gmail.com>
Date: Tue, 6 Jun 2023 18:14:28 -0400
Subject: [PATCH 188/396] rename kBT to kt

---
 src/REPLICA/fix_pimd_langevin.cpp | 16 ++++++++--------
 src/REPLICA/fix_pimd_langevin.h   |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 17ea07c845..c85edc99f9 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -257,7 +257,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
     }
   }
   extvector = 1;
-  kBT = force->boltz * temp;
+  kt = force->boltz * temp;
   if (pstat_flag) baro_init();
 
   // some initilizations
@@ -800,10 +800,10 @@ void FixPIMDLangevin::baro_init()
 {
   vw[0] = vw[1] = vw[2] = vw[3] = vw[4] = vw[5] = 0.0;
   if (pstyle == ISO) {
-    W = 3 * (atom->natoms) * tau_p * tau_p * np * kBT;
+    W = 3 * (atom->natoms) * tau_p * tau_p * np * kt;
   }    // consistent with the definition in i-Pi
   else if (pstyle == ANISO) {
-    W = atom->natoms * tau_p * tau_p * np * kBT;
+    W = atom->natoms * tau_p * tau_p * np * kt;
   }
   Vcoeff = 1.0;
   std::string out = fmt::format("\nInitializing PIMD {:s} barostat...\n", Barostats[barostat]);
@@ -890,7 +890,7 @@ void FixPIMDLangevin::press_o_step()
 
 void FixPIMDLangevin::langevin_init()
 {
-  double beta = 1.0 / kBT;
+  double beta = 1.0 / kt;
   _omega_np = np / beta / hbar;
   double _omega_np_dt_half = _omega_np * update->dt * 0.5;
 
@@ -1394,11 +1394,11 @@ void FixPIMDLangevin::compute_totenthalpy()
   if (barostat == BZP) {
     if (pstyle == ISO) {
       totenthalpy = tote + 0.5 * W * vw[0] * vw[0] * inverse_np + p_hydro * volume / force->nktv2p -
-          Vcoeff * kBT * log(volume);
+          Vcoeff * kt * log(volume);
     } else if (pstyle == ANISO) {
       totenthalpy = tote + 0.5 * W * vw[0] * vw[0] * inverse_np +
           0.5 * W * vw[1] * vw[1] * inverse_np + 0.5 * W * vw[2] * vw[2] * inverse_np +
-          p_hydro * volume / force->nktv2p - Vcoeff * kBT * log(volume);
+          p_hydro * volume / force->nktv2p - Vcoeff * kt * log(volume);
     }
   } else if (barostat == MTTK)
     totenthalpy = tote + 1.5 * W * vw[0] * vw[0] * inverse_np + p_hydro * (volume - vol0);
@@ -1477,7 +1477,7 @@ double FixPIMDLangevin::compute_vector(int n)
         if (n == 11) return 1.5 * W * vw[0] * vw[0];
       }
       if (n == 12) { return np * Pext * volume / force->nktv2p; }
-      if (n == 13) { return -Vcoeff * np * kBT * log(volume); }
+      if (n == 13) { return -Vcoeff * np * kt * log(volume); }
       if (n == 14) return totenthalpy;
     } else if (pstyle == ANISO) {
       if (n == 10) return vw[0];
@@ -1487,7 +1487,7 @@ double FixPIMDLangevin::compute_vector(int n)
       if (n == 14) { return np * Pext * volume / force->nktv2p; }
       if (n == 15) {
         volume = domain->xprd * domain->yprd * domain->zprd;
-        return -Vcoeff * np * kBT * log(volume);
+        return -Vcoeff * np * kt * log(volume);
       }
       if (n == 16) return totenthalpy;
     }
diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index 1ef1dfae52..dc48832855 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -51,7 +51,7 @@ class FixPIMDLangevin : public Fix {
   double lj_epsilon, lj_sigma, lj_mass;    // LJ unit energy, length, and mass scales
   double other_planck;
   double other_mvv2e;
-  double kBT;              // k_B * temp
+  double kt;              // k_B * temp
   double beta, beta_np;    // beta = 1./kBT beta_np = 1./kBT/np
   int thermostat;          // NHC or PILE_L
   int barostat;            // BZP

From f83867787c6eb7ed8b509a54be25b3ee46e7290d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Yifan=20Li=E6=9D=8E=E4=B8=80=E5=B8=86?=
 <yifanl0716@gmail.com>
Date: Tue, 6 Jun 2023 18:17:39 -0400
Subject: [PATCH 189/396] update error message

---
 src/REPLICA/fix_pimd_langevin.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index c85edc99f9..0af08b43b3 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -155,7 +155,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         pstat_flag = 1;
       } else
         error->universe_all(FLERR,
-                            "Unknown ensemble parameter for fix pimd/langevin. Only nve and nvt "
+                            "Unknown ensemble parameter for fix pimd/langevin. Only nve, nvt, nph, and npt "
                             "ensembles are supported!");
     } else if (strcmp(arg[i], "fmass") == 0) {
       fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);

From 14acb3e0ca5aa77662fbe4d96fc6463909e52be5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Jun 2023 20:38:15 -0400
Subject: [PATCH 190/396] add multitype data type and unittest (including tests
 for ubuf)

---
 src/lmptype.h                   | 82 +++++++++++++++++++++++++++++++-
 unittest/utils/CMakeLists.txt   |  4 ++
 unittest/utils/test_lmptype.cpp | 84 +++++++++++++++++++++++++++++++++
 3 files changed, 168 insertions(+), 2 deletions(-)
 create mode 100644 unittest/utils/test_lmptype.cpp

diff --git a/src/lmptype.h b/src/lmptype.h
index ecd6ee5761..6e0b54d988 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -95,7 +95,7 @@ typedef int64_t bigint;
 #define MAXSMALLINT INT_MAX
 #define MAXTAGINT INT_MAX
 #define MAXBIGINT INT64_MAX
-#define MAXDOUBLEINT 9007199254740992   // 2^53
+#define MAXDOUBLEINT 9007199254740992    // 2^53
 
 #define MPI_LMP_TAGINT MPI_INT
 #define MPI_LMP_IMAGEINT MPI_INT
@@ -133,7 +133,7 @@ typedef int64_t bigint;
 #define MAXSMALLINT INT_MAX
 #define MAXTAGINT INT64_MAX
 #define MAXBIGINT INT64_MAX
-#define MAXDOUBLEINT 9007199254740992   // 2^53
+#define MAXDOUBLEINT 9007199254740992    // 2^53
 
 #define MPI_LMP_TAGINT MPI_LL
 #define MPI_LMP_IMAGEINT MPI_LL
@@ -232,6 +232,84 @@ union ubuf {
   ubuf(const int64_t &arg) : i(arg) {}
   ubuf(const int &arg) : i(arg) {}
 };
+
+/** Data structure for dynamic typing of int, bigint, and double
+ *
+ * Using this union allows to store any of the supported data types
+ * in the same container and allows to "see" its current type.
+\verbatim embed:rst
+
+**Usage:**
+
+.. code-block:: c++
+   :caption: To store data in multitype array:
+
+   multitype m[5];
+   int    foo = 1;
+   double bar = 2.5;
+   bigint baz = 1<<40 - 1;
+   m[0] = foo;
+   m[1] = bar;
+   m[2] = -1;
+   m[3] = 2.0;
+   m[4] = baz;
+
+.. code-block:: c++
+   :caption: To format data from multitype array into a space separated string:
+
+   std::string str;
+   for (int i = 0; i < 5; ++i) {
+       switch (m[i].type) {
+           case multitype::DOUBLE:
+               str += std::to_string(m[i].data.d) + ' ';
+               break;
+           case multitype::INT:
+               str += std::to_string(m[i].data.i) + ' ';
+               break;
+           case multitype::BIGINT:
+               str += std::to_string(m[i].data.b) + ' ';
+               break;
+           default:
+               break;
+       }
+   }
+\endverbatim
+  */
+struct multitype {
+  enum { NONE, DOUBLE, INT, BIGINT };
+
+  int type;
+  union {
+    double d;
+    int i;
+    int64_t b;
+  } data;
+
+  multitype() : type(NONE) { data.d = 0.0; }
+  multitype(const multitype &) = default;
+  multitype(multitype &&) = default;
+  ~multitype() = default;
+
+  multitype &operator=(const double &_d)
+  {
+    type = DOUBLE;
+    data.d = _d;
+    return *this;
+  }
+  multitype &operator=(const int &_i)
+  {
+    type = INT;
+    data.i = _i;
+    return *this;
+  }
+  multitype &operator=(const int64_t &_b)
+  {
+    type = BIGINT;
+    data.b = _b;
+    return *this;
+  }
+};
+
 }    // namespace LAMMPS_NS
 
 // preprocessor macros for compiler specific settings
diff --git a/unittest/utils/CMakeLists.txt b/unittest/utils/CMakeLists.txt
index a6d5545873..8c1a5a3f6a 100644
--- a/unittest/utils/CMakeLists.txt
+++ b/unittest/utils/CMakeLists.txt
@@ -7,6 +7,10 @@ add_executable(test_mempool test_mempool.cpp)
 target_link_libraries(test_mempool PRIVATE lammps GTest::GMockMain)
 add_test(NAME MemPool COMMAND test_mempool)
 
+add_executable(test_lmptype test_lmptype.cpp)
+target_link_libraries(test_lmptype PRIVATE lammps GTest::GMockMain)
+add_test(NAME LmpType COMMAND test_lmptype)
+
 add_executable(test_argutils test_argutils.cpp)
 target_link_libraries(test_argutils PRIVATE lammps GTest::GMockMain)
 add_test(NAME ArgUtils COMMAND test_argutils)
diff --git a/unittest/utils/test_lmptype.cpp b/unittest/utils/test_lmptype.cpp
new file mode 100644
index 0000000000..6db340fddf
--- /dev/null
+++ b/unittest/utils/test_lmptype.cpp
@@ -0,0 +1,84 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS Development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "lmptype.h"
+
+#include "gmock/gmock.h"
+#include "gtest/gtest.h"
+
+#include <string>
+
+using namespace LAMMPS_NS;
+
+TEST(Types, ubuf)
+{
+    double buf[3];
+    double d1 = 0.1;
+    int i1 = -10;
+#if defined(LAMMPS_SMALLSMALL)
+    bigint b1 = 2048;
+#else
+    bigint b1 = (1L << 58) + (1L << 50);
+#endif
+    buf[0] = d1;
+    buf[1] = ubuf(i1).d;
+    buf[2] = ubuf(b1).d;
+
+    EXPECT_EQ(d1, buf[0]);
+    EXPECT_EQ(i1, (int)ubuf(buf[1]).i);
+    EXPECT_EQ(b1, (bigint)ubuf(buf[2]).i);
+}
+
+TEST(Types, multitype)
+{
+    multitype m[6];
+    int64_t b1 = (3L << 48) - 1;
+    int i1    = 20;
+    double d1 = 0.1;
+
+    m[0] = b1;
+    m[1] = i1;
+    m[2] = d1;
+
+#if !defined(LAMMPS_SMALLSMALL)
+    m[3] = -((1L << 40) + (1L << 50));
+#endif
+    m[4] = -1023;
+    m[5] = -2.225;
+
+#if defined(LAMMPS_SMALLSMALL)
+    EXPECT_EQ(m[0].type, multitype::INT);
+#else
+    EXPECT_EQ(m[0].type, multitype::BIGINT);
+#endif
+    EXPECT_EQ(m[1].type, multitype::INT);
+    EXPECT_EQ(m[2].type, multitype::DOUBLE);
+
+#if defined(LAMMPS_SMALLSMALL)
+    EXPECT_EQ(m[3].type, multitype::NONE);
+#else
+    EXPECT_EQ(m[3].type, multitype::BIGINT);
+#endif
+    EXPECT_EQ(m[4].type, multitype::INT);
+    EXPECT_EQ(m[5].type, multitype::DOUBLE);
+
+    EXPECT_EQ(m[0].data.b, b1);
+    EXPECT_EQ(m[1].data.i, i1);
+    EXPECT_EQ(m[2].data.d, d1);
+
+#if !defined(LAMMPS_SMALLSMALL)
+    EXPECT_EQ(m[3].data.b,  -((1L << 40) + (1L << 50)));
+#endif
+    EXPECT_EQ(m[4].data.i, -1023);
+    EXPECT_EQ(m[5].data.d, -2.225);
+}

From b81b1f5ecc587289538ee24160c6b23e45b92d8e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Jun 2023 22:40:13 -0400
Subject: [PATCH 191/396] switch dump yaml/netcdf thermo output to use new
 caching API. remove old API.

---
 doc/src/dump_modify.rst          |  9 +++--
 src/EXTRA-DUMP/dump_yaml.cpp     | 31 ++++++++++-------
 src/NETCDF/dump_netcdf.cpp       | 58 ++++++++++++++------------------
 src/NETCDF/dump_netcdf_mpiio.cpp | 54 ++++++++++++++---------------
 src/thermo.cpp                   | 17 ++++------
 src/thermo.h                     | 11 +++---
 6 files changed, 87 insertions(+), 93 deletions(-)

diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst
index f00cc339cc..89b3766083 100644
--- a/doc/src/dump_modify.rst
+++ b/doc/src/dump_modify.rst
@@ -753,9 +753,12 @@ run, this option is ignored since the output is already balanced.
 ----------
 
 The *thermo* keyword only applies the dump styles *netcdf* and *yaml*.
-It triggers writing of :doc:`thermo <thermo>` information to the dump file
-alongside per-atom data.  The values included in the dump file are
-identical to the values specified by :doc:`thermo_style <thermo_style>`.
+It triggers writing of :doc:`thermo <thermo>` information to the dump
+file alongside per-atom data.  The values included in the dump file are
+cached values from the last thermo output and include the exact same the
+values as specified by the :doc:`thermo_style <thermo_style>` command.
+Because these are cached values, they are only up-to-date when dump
+output is on a timestep that also has thermo output.
 
 ----------
 
diff --git a/src/EXTRA-DUMP/dump_yaml.cpp b/src/EXTRA-DUMP/dump_yaml.cpp
index 3c35ec43ba..029415164f 100644
--- a/src/EXTRA-DUMP/dump_yaml.cpp
+++ b/src/EXTRA-DUMP/dump_yaml.cpp
@@ -60,21 +60,26 @@ void DumpYAML::write_header(bigint ndump)
   std::string thermo_data;
   if (thermo) {
     Thermo *th = output->thermo;
-    thermo_data += "thermo:\n  - keywords: [ ";
-    for (int i = 0; i < th->nfield; ++i) thermo_data += fmt::format("{}, ", th->keyword[i]);
-    thermo_data += "]\n  - data: [ ";
+    // output thermo data only on timesteps where it was computed
+    if (update->ntimestep == th->get_timestep()) {
 
-    for (int i = 0; i < th->nfield; ++i) {
-      th->call_vfunc(i);
-      if (th->vtype[i] == Thermo::FLOAT)
-        thermo_data += fmt::format("{}, ", th->dvalue);
-      else if (th->vtype[i] == Thermo::INT)
-        thermo_data += fmt::format("{}, ", th->ivalue);
-      else if (th->vtype[i] == Thermo::BIGINT)
-        thermo_data += fmt::format("{}, ", th->bivalue);
+      thermo_data += "thermo:\n  - keywords: [ ";
+      for (auto key : th->get_keywords()) thermo_data += fmt::format("{}, ", key);
+      thermo_data += "]\n  - data: [ ";
+
+      for (auto val : th->get_fields()) {
+        if (val.type == multitype::DOUBLE)
+          thermo_data += fmt::format("{}, ", val.data.d);
+        else if (val.type == multitype::INT)
+          thermo_data += fmt::format("{}, ", val.data.i);
+        else if (val.type == multitype::BIGINT)
+          thermo_data += fmt::format("{}, ", val.data.b);
+        else
+          thermo_data += ", ";
+      }
+      thermo_data += "]\n";
+      MPI_Barrier(world);
     }
-    thermo_data += "]\n";
-    MPI_Barrier(world);
   }
 
   if (comm->me == 0) {
diff --git a/src/NETCDF/dump_netcdf.cpp b/src/NETCDF/dump_netcdf.cpp
index 6fecf7f41b..cb6aea16cf 100644
--- a/src/NETCDF/dump_netcdf.cpp
+++ b/src/NETCDF/dump_netcdf.cpp
@@ -223,7 +223,7 @@ void DumpNetCDF::openfile()
 
   if (thermo && !singlefile_opened) {
     delete[] thermovar;
-    thermovar = new int[output->thermo->nfield];
+    thermovar = new int[output->thermo->get_keywords().size()];
   }
 
   // now the computes and fixes have been initialized, so we can query
@@ -320,9 +320,10 @@ void DumpNetCDF::openfile()
 
       // perframe variables
       if (thermo) {
-        Thermo *th = output->thermo;
-        for (int i = 0; i < th->nfield; i++) {
-          NCERRX( nc_inq_varid(ncid, th->keyword[i].c_str(), &thermovar[i]), th->keyword[i].c_str() );
+        auto keywords = output->thermo->get_keywords();
+        int nfield = keywords.size();
+        for (int i = 0; i < nfield; i++) {
+          NCERRX( nc_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
         }
       }
 
@@ -432,22 +433,16 @@ void DumpNetCDF::openfile()
 
       // perframe variables
       if (thermo) {
-        Thermo *th = output->thermo;
-        for (int i = 0; i < th->nfield; i++) {
-          if (th->vtype[i] == Thermo::FLOAT) {
-            NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), type_nc_real, 1, dims,
-                               &thermovar[i]), th->keyword[i].c_str() );
-          } else if (th->vtype[i] == Thermo::INT) {
-            NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), NC_INT, 1, dims,
-                               &thermovar[i]), th->keyword[i].c_str() );
-          } else if (th->vtype[i] == Thermo::BIGINT) {
-#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
-            NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), NC_INT64, 1, dims,
-                               &thermovar[i]), th->keyword[i].c_str() );
-#else
-            NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), NC_LONG, 1, dims,
-                               &thermovar[i]), th->keyword[i].c_str() );
-#endif
+        auto fields = output->thermo->get_fields();
+        auto keywords = output->thermo->get_keywords();
+        int nfield = fields.size();
+        for (int i = 0; i < nfield; i++) {
+          if (fields[i].type == multitype::DOUBLE) {
+            NCERRX( nc_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
+          } else if (fields[i].type == multitype::INT) {
+            NCERRX( nc_def_var(ncid, keywords[i].c_str(), NC_INT, 1, dims, &thermovar[i]), keywords[i].c_str() );
+          } else if (fields[i].type == multitype::BIGINT) {
+            NCERRX( nc_def_var(ncid, keywords[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), keywords[i].c_str() );
           }
         }
       }
@@ -605,20 +600,17 @@ void DumpNetCDF::write()
   start[1] = 0;
 
   if (thermo) {
-    Thermo *th = output->thermo;
-    for (int i = 0; i < th->nfield; i++) {
-      th->call_vfunc(i);
+    auto keywords = output->thermo->get_keywords();
+    auto fields = output->thermo->get_fields();
+    int nfield = fields.size();
+    for (int i = 0; i < nfield; i++) {
       if (filewriter) {
-        if (th->vtype[i] == Thermo::FLOAT) {
-          NCERRX( nc_put_var1_double(ncid, thermovar[i], start,
-                                     &th->dvalue),
-                  th->keyword[i].c_str() );
-        } else if (th->vtype[i] == Thermo::INT) {
-          NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->ivalue),
-                  th->keyword[i].c_str() );
-        } else if (th->vtype[i] == Thermo::BIGINT) {
-          NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
-                  th->keyword[i].c_str() );
+        if (fields[i].type == multitype::DOUBLE) {
+          NCERRX( nc_put_var1_double(ncid, thermovar[i], start, &fields[i].data.d), keywords[i].c_str() );
+        } else if (fields[i].type == multitype::INT) {
+          NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &fields[i].data.i), keywords[i].c_str() );
+        } else if (fields[i].type == multitype::BIGINT) {
+          NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &fields[i].data.b), keywords[i].c_str() );
         }
       }
     }
diff --git a/src/NETCDF/dump_netcdf_mpiio.cpp b/src/NETCDF/dump_netcdf_mpiio.cpp
index 0282903d77..fdcd03470e 100644
--- a/src/NETCDF/dump_netcdf_mpiio.cpp
+++ b/src/NETCDF/dump_netcdf_mpiio.cpp
@@ -220,7 +220,7 @@ void DumpNetCDFMPIIO::openfile()
 
   if (thermo && !singlefile_opened) {
     delete[] thermovar;
-    thermovar = new int[output->thermo->nfield];
+    thermovar = new int[output->thermo->get_keywords().size()];
   }
 
   // now the computes and fixes have been initialized, so we can query
@@ -318,9 +318,10 @@ void DumpNetCDFMPIIO::openfile()
 
     // perframe variables
     if (thermo) {
-      Thermo *th = output->thermo;
-      for (int i = 0; i < th->nfield; i++) {
-        NCERRX( ncmpi_inq_varid(ncid, th->keyword[i].c_str(), &thermovar[i]), th->keyword[i].c_str() );
+      auto keywords = output->thermo->get_keywords();
+      int nfield = keywords.size();
+      for (int i = 0; i < nfield; i++) {
+        NCERRX( ncmpi_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
       }
     }
 
@@ -422,18 +423,16 @@ void DumpNetCDFMPIIO::openfile()
 
     // perframe variables
     if (thermo) {
-      Thermo *th = output->thermo;
-      for (int i = 0; i < th->nfield; i++) {
-        if (th->vtype[i] == Thermo::FLOAT) {
-          NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
-        } else if (th->vtype[i] == Thermo::INT) {
-          NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), NC_INT, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
-        } else if (th->vtype[i] == Thermo::BIGINT) {
-#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
-          NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
-#else
-          NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), NC_LONG, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
-#endif
+      auto fields = output->thermo->get_fields();
+      auto keywords = output->thermo->get_keywords();
+      int nfield = fields.size();
+      for (int i = 0; i < nfield; i++) {
+        if (fields[i].type == multitype::DOUBLE) {
+          NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
+        } else if (fields[i].type == multitype::INT) {
+          NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), NC_INT, 1, dims, &thermovar[i]), keywords[i].c_str() );
+        } else if (fields[i].type == multitype::BIGINT) {
+          NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), keywords[i].c_str() );
         }
       }
     }
@@ -594,20 +593,17 @@ void DumpNetCDFMPIIO::write()
   NCERR( ncmpi_begin_indep_data(ncid) );
 
   if (thermo) {
-    Thermo *th = output->thermo;
-    for (int i = 0; i < th->nfield; i++) {
-      th->call_vfunc(i);
+    auto keywords = output->thermo->get_keywords();
+    auto fields = output->thermo->get_fields();
+    int nfield = fields.size();
+    for (int i = 0; i < nfield; i++) {
       if (filewriter) {
-        if (th->vtype[i] == Thermo::FLOAT) {
-          NCERRX( ncmpi_put_var1_double(ncid, thermovar[i], start,
-                                        &th->dvalue),
-                  th->keyword[i].c_str() );
-        } else if (th->vtype[i] == Thermo::INT) {
-          NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &th->ivalue),
-                  th->keyword[i].c_str() );
-        } else if (th->vtype[i] == Thermo::BIGINT) {
-          NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
-                  th->keyword[i].c_str() );
+        if (fields[i].type == multitype::DOUBLE) {
+          NCERRX( ncmpi_put_var1_double(ncid, thermovar[i], start, &fields[i].data.d), keywords[i].c_str() );
+        } else if (fields[i].type == multitype::INT) {
+          NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &fields[i].data.i), keywords[i].c_str() );
+        } else if (fields[i].type == multitype::BIGINT) {
+          NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &fields[i].data.b), keywords[i].c_str() );
         }
       }
     }
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 0503018a3a..31c19fbdc2 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -361,7 +361,7 @@ void Thermo::compute(int flag)
   int i;
 
   firststep = flag;
-  bigint ntimestep = update->ntimestep;
+  ntimestep = update->ntimestep;
 
   // check for lost atoms
   // turn off normflag if natoms = 0 to avoid divide by 0
@@ -405,18 +405,23 @@ void Thermo::compute(int flag)
   }
 
   // add each thermo value to line with its specific format
+  field_data.clear();
+  field_data.resize(nfield);
 
   for (ifield = 0; ifield < nfield; ifield++) {
     (this->*vfunc[ifield])();
     if (vtype[ifield] == FLOAT) {
       snprintf(fmtbuf, sizeof(fmtbuf), format[ifield].c_str(), dvalue);
       line += fmtbuf;
+      field_data[ifield] = dvalue;
     } else if (vtype[ifield] == INT) {
       snprintf(fmtbuf, sizeof(fmtbuf), format[ifield].c_str(), ivalue);
       line += fmtbuf;
+      field_data[ifield] = ivalue;
     } else if (vtype[ifield] == BIGINT) {
       snprintf(fmtbuf, sizeof(fmtbuf), format[ifield].c_str(), bivalue);
       line += fmtbuf;
+      field_data[ifield] = bivalue;
     }
   }
 
@@ -433,16 +438,6 @@ void Thermo::compute(int flag)
   firststep = 1;
 }
 
-/* ----------------------------------------------------------------------
-   call function to compute property
-------------------------------------------------------------------------- */
-
-void Thermo::call_vfunc(int ifield_in)
-{
-  ifield = ifield_in;
-  (this->*vfunc[ifield])();
-}
-
 /* ----------------------------------------------------------------------
    check for lost atoms, return current number of atoms
    also could number of warnings across MPI ranks and update total
diff --git a/src/thermo.h b/src/thermo.h
index eaec3eb9f8..8a5cba29d7 100644
--- a/src/thermo.h
+++ b/src/thermo.h
@@ -21,9 +21,6 @@ namespace LAMMPS_NS {
 
 class Thermo : protected Pointers {
   friend class MinCG;              // accesses compute_pe
-  friend class DumpNetCDF;         // accesses thermo properties
-  friend class DumpNetCDFMPIIO;    // accesses thermo properties
-  friend class DumpYAML;           // accesses thermo properties
 
  public:
   char *style;
@@ -45,6 +42,11 @@ class Thermo : protected Pointers {
   void compute(int);
   int evaluate_keyword(const std::string &, double *);
 
+  // for accessing cached thermo data
+  bigint get_timestep() const { return ntimestep; }
+  const std::vector<multitype> &get_fields() const { return field_data; }
+  const std::vector<std::string> &get_keywords() const { return keyword; }
+
  private:
   int nfield, nfield_initial;
   int *vtype;
@@ -52,6 +54,7 @@ class Thermo : protected Pointers {
   std::vector<std::string> keyword, format, format_column_user, keyword_user;
   std::string format_line_user, format_float_user, format_int_user, format_bigint_user;
   std::map<std::string, int> key2col;
+  std::vector<multitype> field_data;
 
   int normvalue;       // use this for normflag unless natoms = 0
   int normuserflag;    // 0 if user has not set, 1 if has
@@ -66,6 +69,7 @@ class Thermo : protected Pointers {
   bigint last_step;
 
   bigint natoms;
+  bigint ntimestep;
 
   // data used by routines that compute single values
   int ivalue;          // integer value to print
@@ -114,7 +118,6 @@ class Thermo : protected Pointers {
   typedef void (Thermo::*FnPtr)();
   void addfield(const char *, FnPtr, int);
   FnPtr *vfunc;    // list of ptrs to functions
-  void call_vfunc(int ifield);
 
   void compute_compute();    // functions that compute a single value
   void compute_fix();        // via calls to  Compute,Fix,Variable classes

From bbfd909be64c3d6836f22d07c5049e9600a279ff Mon Sep 17 00:00:00 2001
From: "W. Michael Brown" <michael.w.brown@intel.com>
Date: Tue, 6 Jun 2023 23:56:16 -0700
Subject: [PATCH 192/396] Adding redundant call to sync Intel package arrays
 with native arrays for methods such as MC that do not need pre_reverse.

---
 src/INTEL/fix_intel.cpp | 22 +++++++++++++---------
 src/INTEL/fix_intel.h   |  2 +-
 src/MC/fix_gcmc.cpp     |  6 ------
 src/MC/fix_widom.cpp    |  8 +-------
 4 files changed, 15 insertions(+), 23 deletions(-)

diff --git a/src/INTEL/fix_intel.cpp b/src/INTEL/fix_intel.cpp
index 1ce0b41338..89775108cb 100644
--- a/src/INTEL/fix_intel.cpp
+++ b/src/INTEL/fix_intel.cpp
@@ -275,10 +275,8 @@ int FixIntel::setmask()
   int mask = 0;
   mask |= PRE_REVERSE;
   mask |= MIN_PRE_REVERSE;
-  #ifdef _LMP_INTEL_OFFLOAD
   mask |= POST_FORCE;
   mask |= MIN_POST_FORCE;
-  #endif
   mask |= POST_RUN;
   return mask;
 }
@@ -597,6 +595,19 @@ void FixIntel::pre_reverse(int /*eflag*/, int /*vflag*/)
 
 /* ---------------------------------------------------------------------- */
 
+void FixIntel::post_force(int vflag)
+{
+  // Redundant call to sync Intel data structs with native for methods that
+  // call force compute but do not call prereverse
+  _sync_main_arrays(1);
+
+  #ifdef LMP_INTEL_OFFLOAD
+  if (_sync_mode == 2) sync_coprocessor();
+  #endif
+}
+
+/* ---------------------------------------------------------------------- */
+
 template <class acc_t>
 void FixIntel::reduce_results(acc_t * _noalias const f_scalar)
 {
@@ -883,13 +894,6 @@ double FixIntel::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void FixIntel::post_force(int vflag)
-{
-  if (_sync_mode == 2) sync_coprocessor();
-}
-
-/* ---------------------------------------------------------------------- */
-
 template <class ft, class acc_t>
 void FixIntel::add_off_results(const ft * _noalias const f_in,
                                const acc_t * _noalias const ev_global) {
diff --git a/src/INTEL/fix_intel.h b/src/INTEL/fix_intel.h
index 9214fe3419..1960a6d802 100644
--- a/src/INTEL/fix_intel.h
+++ b/src/INTEL/fix_intel.h
@@ -55,6 +55,7 @@ class FixIntel : public Fix {
   void pre_reverse(int eflag = 0, int vflag = 0) override;
   inline void min_pre_reverse(int eflag = 0, int vflag = 0) override { pre_reverse(eflag, vflag); }
 
+  void post_force(int vflag) override;
   void post_run() override { _print_pkg_info = 1; }
 
   // Get all forces, calculation results from coprocesser
@@ -132,7 +133,6 @@ class FixIntel : public Fix {
   inline void get_buffern(const int offload, int &nlocal, int &nall, int &minlocal);
 
 #ifdef _LMP_INTEL_OFFLOAD
-  void post_force(int vflag);
   inline int coprocessor_number() { return _cop; }
   inline int full_host_list() { return _full_host_list; }
   void set_offload_affinity();
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index 634b512936..21fb4431e1 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -2352,12 +2352,6 @@ double FixGCMC::energy_full()
 
   if (force->kspace) force->kspace->compute(eflag,vflag);
 
-  // unlike Verlet, not performing a reverse_comm() or forces here
-  // b/c GCMC does not care about forces
-  // don't think it will mess up energy due to any post_force() fixes
-  // but Modify::pre_reverse() is needed for INTEL
-
-  if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag);
   if (modify->n_post_force_any) modify->post_force(vflag);
 
   // NOTE: all fixes with energy_global_flag set and which
diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp
index a98f29da5e..cc2f1bc94d 100644
--- a/src/MC/fix_widom.cpp
+++ b/src/MC/fix_widom.cpp
@@ -1050,13 +1050,7 @@ double FixWidom::energy_full()
 
   if (force->kspace) force->kspace->compute(eflag,vflag);
 
-  // unlike Verlet, not performing a reverse_comm() or forces here
-  // b/c Widom does not care about forces
-  // don't think it will mess up energy due to any post_force() fixes
-  // but Modify::pre_reverse() is needed for INTEL
-
-  if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag);
-  if (modify->n_pre_force) modify->pre_force(vflag);
+  if (modify->n_post_force_any) modify->post_force(vflag);
 
   // NOTE: all fixes with energy_global_flag set and which
   //   operate at pre_force() or post_force()

From 6c7a5d2f1efc77fcdf33ee30214a4faa6e0f9215 Mon Sep 17 00:00:00 2001
From: "W. Michael Brown" <michael.w.brown@intel.com>
Date: Tue, 6 Jun 2023 23:56:31 -0700
Subject: [PATCH 193/396] Using bigint for Intel package neighbor overflow
 detection for large local sizes.

---
 src/INTEL/npair_full_bin_ghost_intel.cpp | 7 ++++---
 src/INTEL/npair_intel.cpp                | 9 +++++----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/INTEL/npair_full_bin_ghost_intel.cpp b/src/INTEL/npair_full_bin_ghost_intel.cpp
index b7b9ee4aea..381db62c08 100644
--- a/src/INTEL/npair_full_bin_ghost_intel.cpp
+++ b/src/INTEL/npair_full_bin_ghost_intel.cpp
@@ -292,12 +292,13 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
       else ito -= wlocal - nlocal;
 
       int e_ito = ito;
-      const int list_size = (e_ito + tid * 2 + 2) * maxnbors;
+      const bigint list_size = (bigint)(e_ito + tid * 2 + 2) *
+        (bigint)maxnbors;
 
       int pack_offset = maxnbors;
-      int ct = (ifrom + tid * 2) * maxnbors;
+      bigint ct = (bigint)(ifrom + tid * 2) * (bigint)maxnbors;
       int * _noalias neighptr = intel_list + ct;
-      const int obound = pack_offset + maxnbors * 2;
+      const bigint obound = pack_offset + maxnbors * 2;
 
       const int toffs = tid * ncache_stride;
       flt_t * _noalias const tx = ncachex + toffs;
diff --git a/src/INTEL/npair_intel.cpp b/src/INTEL/npair_intel.cpp
index b85873f677..8b05aa38aa 100644
--- a/src/INTEL/npair_intel.cpp
+++ b/src/INTEL/npair_intel.cpp
@@ -287,16 +287,17 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
         if (imod) e_ito += pack_width - imod;
       }
       #endif
-      const int list_size = (e_ito + tid * 2 + 2) * maxnbors;
+      const bigint list_size = (bigint)(e_ito + tid * 2 + 2) *
+        (bigint)maxnbors;
 
       #ifdef LMP_INTEL_3BODY_FAST
       const int pack_offset = maxnbors * pack_width;
-      const int obound = pack_offset + maxnbors * 2;
+      const bigint obound = pack_offset + maxnbors * 2;
       #else
       const int pack_offset = 0;
-      const int obound = maxnbors * 3;
+      const bigint obound = maxnbors * 3;
       #endif
-      int ct = (ifrom + tid * 2) * maxnbors;
+      bigint ct = (bigint)(ifrom + tid * 2) * (bigint)maxnbors;
       int * _noalias neighptr = intel_list + ct;
       int * _noalias neighptr2;
       if (THREE) neighptr2 = neighptr;

From 0f925f7a39ea4fccd20e5bd35cf81dc56dd00296 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 04:33:08 -0400
Subject: [PATCH 194/396] reformat, add versionadded marker

---
 doc/src/compute_stress_mop.rst | 123 ++++++++++++++++++---------------
 1 file changed, 69 insertions(+), 54 deletions(-)

diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst
index 7ab8c58a76..5662fc76d4 100644
--- a/doc/src/compute_stress_mop.rst
+++ b/doc/src/compute_stress_mop.rst
@@ -45,92 +45,107 @@ Examples
 Description
 """""""""""
 
-Compute *stress/mop* and compute *stress/mop/profile* define computations that
-calculate components of the local stress tensor using the method of
-planes :ref:`(Todd) <mop-todd>`.  Specifically in compute *stress/mop* calculates 3
-components are computed in directions *dir*,\ *x*\ ; *dir*,\ *y*\ ; and
-*dir*,\ *z*\ ; where *dir* is the direction normal to the plane, while
-in compute *stress/mop/profile* the profile of the stress is computed.
+Compute *stress/mop* and compute *stress/mop/profile* define
+computations that calculate components of the local stress tensor using
+the method of planes :ref:`(Todd) <mop-todd>`.  Specifically in compute
+*stress/mop* calculates 3 components are computed in directions *dir*,\
+*x*\ ; *dir*,\ *y*\ ; and *dir*,\ *z*\ ; where *dir* is the direction
+normal to the plane, while in compute *stress/mop/profile* the profile
+of the stress is computed.
 
 Contrary to methods based on histograms of atomic stress (i.e., using
-:doc:`compute stress/atom <compute_stress_atom>`), the method of planes is
-compatible with mechanical balance in heterogeneous systems and at
+:doc:`compute stress/atom <compute_stress_atom>`), the method of planes
+is compatible with mechanical balance in heterogeneous systems and at
 interfaces :ref:`(Todd) <mop-todd>`.
 
 The stress tensor is the sum of a kinetic term and a configurational
 term, which are given respectively by Eq. (21) and Eq. (16) in
-:ref:`(Todd) <mop-todd>`. For the kinetic part, the algorithm considers that
-atoms have crossed the plane if their positions at times :math:`t-\Delta t`
-and :math:`t` are one on either side of the plane, and uses the velocity at
-time :math:`t-\Delta t/2` given by the velocity Verlet algorithm.
+:ref:`(Todd) <mop-todd>`. For the kinetic part, the algorithm considers
+that atoms have crossed the plane if their positions at times
+:math:`t-\Delta t` and :math:`t` are one on either side of the plane,
+and uses the velocity at time :math:`t-\Delta t/2` given by the velocity
+Verlet algorithm.
 
-Between one and six keywords can be used to indicate which
-contributions to the stress must be computed: total stress (total),  kinetic stress (kin),
-configurational stress (conf), stress due to bond stretching (bond),
-stress due to angle bending (angle) and/or due to pairwise non-bonded interactions (pair).
-The angle keyword is currently available only for the stress/mop command and not the stress/mop/profile.
+.. versionadded:: TBD
 
-NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
+   contributions from bond and angle potentials
+
+Between one and six keywords can be used to indicate which contributions
+to the stress must be computed: total stress (total), kinetic stress
+(kin), configurational stress (conf), stress due to bond stretching
+(bond), stress due to angle bending (angle) and/or due to pairwise
+non-bonded interactions (pair).  The angle keyword is currently
+available only for the *stress/mop* command and **not** the
+*stress/mop/profile* command.
+
+NOTE 1: The configurational stress is computed considering all pairs of
+atoms where at least one atom belongs to group group-ID.
 
 NOTE 2: The local stress does not include any Lennard-Jones tail
-corrections to the stress added by the :doc:`pair_modify tail yes <pair_modify>`
-command, since those are contributions to the global system pressure.
+corrections to the stress added by the :doc:`pair_modify tail yes
+<pair_modify>` command, since those are contributions to the global
+system pressure.
 
-NOTE 3: The local stress profile generated by compute *stress/mop/profile*
-is similar to that obtained by compute
-:doc:`stress/cartesian <compute_stress_profile>`.
-A key difference is that compute *stress/mop/profile* considers particles
-crossing a set of planes, while compute *stress/cartesian* computes averages
-for a set of small volumes.  More information
-on the similarities and differences can be found in
-:ref:`(Ikeshoji)<Ikeshoji2>`.
+NOTE 3: The local stress profile generated by compute
+*stress/mop/profile* is similar to that obtained by compute
+:doc:`stress/cartesian <compute_stress_profile>`.  A key difference is
+that compute *stress/mop/profile* considers particles crossing a set of
+planes, while compute *stress/cartesian* computes averages for a set of
+small volumes.  More information on the similarities and differences can
+be found in :ref:`(Ikeshoji)<Ikeshoji2>`.
 
 Output info
 """""""""""
 
-Compute *stress/mop* calculates a global vector (indices starting at 1), with 3
-values for each declared keyword (in the order the keywords have been
-declared). For each keyword, the stress tensor components are ordered as
-follows: stress_dir,x, stress_dir,y, and stress_dir,z.
+Compute *stress/mop* calculates a global vector (indices starting at 1),
+with 3 values for each declared keyword (in the order the keywords have
+been declared). For each keyword, the stress tensor components are
+ordered as follows: stress_dir,x, stress_dir,y, and stress_dir,z.
 
-Compute *stress/mop/profile* instead calculates a global array, with 1 column
-giving the position of the planes where the stress tensor was computed,
-and with 3 columns of values for each declared keyword (in the order the
-keywords have been declared). For each keyword, the profiles of stress
-tensor components are ordered as follows: stress_dir,x; stress_dir,y;
-and stress_dir,z.
+Compute *stress/mop/profile* instead calculates a global array, with 1
+column giving the position of the planes where the stress tensor was
+computed, and with 3 columns of values for each declared keyword (in the
+order the keywords have been declared). For each keyword, the profiles
+of stress tensor components are ordered as follows: stress_dir,x;
+stress_dir,y; and stress_dir,z.
 
 The values are in pressure :doc:`units <units>`.
 
-The values produced by this compute can be accessed by various :doc:`output commands <Howto_output>`.
-For instance, the results can be written to a file using the
-:doc:`fix ave/time <fix_ave_time>` command. Please see the example
-in the examples/PACKAGES/mop folder.
+The values produced by this compute can be accessed by various
+:doc:`output commands <Howto_output>`.  For instance, the results can be
+written to a file using the :doc:`fix ave/time <fix_ave_time>`
+command. Please see the example in the examples/PACKAGES/mop folder.
 
 Restrictions
 """"""""""""
 
-These styles are part of the EXTRA-COMPUTE package. They are only enabled if
-LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
-doc page on for more info.
+These styles are part of the EXTRA-COMPUTE package. They are only
+enabled if LAMMPS is built with that package. See the :doc:`Build
+package <Build_package>` doc page on for more info.
 
 The method is only implemented for 3d orthogonal simulation boxes whose
 size does not change in time, and axis-aligned planes.
 
 The method only works with two-body pair interactions, because it
-requires the class method pair->single() to be implemented. In
-particular, compute *stress/mop/profile* does not work with more than
-two-body pair interactions, long range (kspace) interactions and angle/dihedral/improper
-intramolecular interactions. Similarly, compute *stress/mop* does not work with more than
-two-body pair interactions, long range (kspace) interactions and dihedral/improper
-intramolecular interactions but works with all bond interactions with the class method
-single() implemented and all angle interactions with the class method born_matrix()
-implemented.
+requires the class method ``Pair::single()`` to be implemented, which is
+not possible for manybody potentials.  In particular, compute
+*stress/mop/profile* does not work with more than two-body pair
+interactions, long range (kspace) interactions and
+angle/dihedral/improper intramolecular interactions. Similarly, compute
+*stress/mop* does not work with more than two-body pair interactions,
+long range (kspace) interactions and dihedral/improper intramolecular
+interactions but works with all bond interactions with the class method
+single() implemented and all angle interactions with the class method
+born_matrix() implemented.
 
 Related commands
 """"""""""""""""
 
-:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_profile>`, :doc:`compute stress/cylinder <compute_stress_profile>`, :doc:`compute stress/spherical <compute_stress_profile>`
+:doc:`compute stress/atom <compute_stress_atom>`,
+:doc:`compute pressure <compute_pressure>`,
+:doc:`compute stress/cartesian <compute_stress_profile>`,
+:doc:`compute stress/cylinder <compute_stress_profile>`,
+:doc:`compute stress/spherical <compute_stress_profile>`
 
 Default
 """""""

From 045b230587c3fcf1eb4ea7a0fcf00f0f08b1d19c Mon Sep 17 00:00:00 2001
From: Lars Veldscholte <lars@tuxplace.nl>
Date: Wed, 7 Jun 2023 10:43:57 +0200
Subject: [PATCH 195/396] Fix shifted coordinates:

Add `boxlo` to the bin centers
---
 src/EXTRA-COMPUTE/compute_stress_cartesian.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
index 106ffef8fb..0aae797111 100644
--- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
@@ -399,8 +399,8 @@ void ComputeStressCartesian::compute_array()
 
   // populate array to output.
   for (int bin = 0; bin < nbins1 * nbins2; bin++) {
-    array[bin][0] = (bin % nbins1 + 0.5) * bin_width1;
-    if (dims == 2) array[bin][1] = ((int) (bin / nbins1) + 0.5) * bin_width2;
+    array[bin][0] = (bin % nbins1 + 0.5) * bin_width1 + boxlo[dir1];
+    if (dims == 2) array[bin][1] = ((int) (bin / nbins1) + 0.5) * bin_width2 + boxlo[dir2];
     array[bin][0 + dims] = dens[bin];
     array[bin][1 + dims] = pkxx[bin];
     array[bin][2 + dims] = pkyy[bin];

From 53b1af7720c9246eec9cbadf6ef0cb39bcc30fad Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 05:11:53 -0400
Subject: [PATCH 196/396] LAMMPS programming style/conventions updates

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp      | 171 ++++++++----------
 src/EXTRA-COMPUTE/compute_stress_mop.h        |   2 +-
 .../compute_stress_mop_profile.cpp            |  96 +++++-----
 .../compute_stress_mop_profile.h              |   2 +-
 4 files changed, 126 insertions(+), 145 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index e5d0e2ed13..98e3bf7043 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,6 +13,7 @@
 
 /*------------------------------------------------------------------------
   Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+  Support for bonds and angles added by : Evangelos Voyiatzis (NovaMechanics)
   --------------------------------------------------------------------------*/
 
 #include "compute_stress_mop.h"
@@ -22,6 +22,7 @@
 #include "atom.h"
 #include "atom_vec.h"
 #include "bond.h"
+#include "comm.h"
 #include "domain.h"
 #include "error.h"
 #include "force.h"
@@ -37,50 +38,49 @@
 
 using namespace LAMMPS_NS;
 
-enum{X,Y,Z};
-enum{TOTAL,CONF,KIN,PAIR,BOND,ANGLE};
+enum { X, Y, Z };
+enum { TOTAL, CONF, KIN, PAIR, BOND, ANGLE };
 
+// clang-format off
 /* ---------------------------------------------------------------------- */
 
 ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg)
 {
-  if (narg < 6) error->all(FLERR,"Illegal compute stress/mop command");
-
-  MPI_Comm_rank(world,&me);
+  if (narg < 6) utils::missing_cmd_args(FLERR, "compute stress/mop", error);
 
   bondflag = 0;
   angleflag = 0;
 
   // set compute mode and direction of plane(s) for pressure calculation
 
-  if (strcmp(arg[3],"x")==0) {
+  if (strcmp(arg[3],"x") == 0) {
     dir = X;
-  } else if (strcmp(arg[3],"y")==0) {
+  } else if (strcmp(arg[3],"y") == 0) {
     dir = Y;
-  } else if (strcmp(arg[3],"z")==0) {
+  } else if (strcmp(arg[3],"z") == 0) {
     dir = Z;
   } else error->all(FLERR,"Illegal compute stress/mop command");
 
   // Position of the plane
 
-  if (strcmp(arg[4],"lower")==0) {
+  if (strcmp(arg[4],"lower") == 0) {
     pos = domain->boxlo[dir];
-  } else if (strcmp(arg[4],"upper")==0) {
+  } else if (strcmp(arg[4],"upper") == 0) {
     pos = domain->boxhi[dir];
-  } else if (strcmp(arg[4],"center")==0) {
+  } else if (strcmp(arg[4],"center") == 0) {
     pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]);
   } else pos = utils::numeric(FLERR,arg[4],false,lmp);
 
   // plane inside the box
-  if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir]) {
-    error->warning(FLERR,"The specified initial plane lies outside of the simulation box");
-    double dx[3] {0};
+  if ((pos > domain->boxhi[dir]) || (pos < domain->boxlo[dir])) {
+    error->warning(FLERR, "The specified initial plane lies outside of the simulation box");
+    double dx[3] = {0.0, 0.0, 0.0};
     dx[dir] = pos - 0.5*(domain->boxhi[dir] + domain->boxlo[dir]);
     domain->minimum_image(dx[0], dx[1], dx[2]);
     pos = 0.5*(domain->boxhi[dir] + domain->boxlo[dir]) + dx[dir];
 
-    if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
+    if ((pos > domain->boxhi[dir]) || (pos < domain->boxlo[dir]))
       error->all(FLERR, "Plane for compute stress/mop is out of bounds");
   }
 
@@ -133,15 +133,15 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
     iarg++;
   }
 
-  // Error check
+  // Error checks
   // 3D only
 
-  if (domain->dimension < 3)
-    error->all(FLERR, "Compute stress/mop incompatible with simulation dimension");
+  if (domain->dimension != 3)
+    error->all(FLERR, "Compute stress/mop requires a 3d system");
 
   // orthogonal simulation box
   if (domain->triclinic != 0)
-    error->all(FLERR, "Compute stress/mop incompatible with triclinic simulation box");
+    error->all(FLERR, "Compute stress/mop is incompatible with triclinic simulation box");
 
   // Initialize some variables
 
@@ -154,12 +154,12 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
   // this fix produces a global vector
 
   memory->create(vector,nvalues,"stress/mop:vector");
-  memory->create(values_local,nvalues,"stress/mop/spatial:values_local");
-  memory->create(values_global,nvalues,"stress/mop/spatial:values_global");
-  memory->create(bond_local,nvalues,"stress/mop/spatial:bond_local");
-  memory->create(bond_global,nvalues,"stress/mop/spatial:bond_global");
-  memory->create(angle_local,nvalues,"stress/mop/spatial:angle_local");
-  memory->create(angle_global,nvalues,"stress/mop/spatial:angle_global");
+  memory->create(values_local,nvalues,"stress/mop:values_local");
+  memory->create(values_global,nvalues,"stress/mop:values_global");
+  memory->create(bond_local,nvalues,"stress/mop:bond_local");
+  memory->create(bond_global,nvalues,"stress/mop:bond_global");
+  memory->create(angle_local,nvalues,"stress/mop:angle_local");
+  memory->create(angle_global,nvalues,"stress/mop:angle_global");
   size_vector = nvalues;
 
   vector_flag = 1;
@@ -171,8 +171,7 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeStressMop::~ComputeStressMop()
 {
-
-  delete [] which;
+  delete[] which;
 
   memory->destroy(values_local);
   memory->destroy(values_global);
@@ -209,36 +208,39 @@ void ComputeStressMop::init()
 
   // Compute stress/mop requires fixed simulation box
   if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
-    error->all(FLERR, "Compute stress/mop requires a fixed simulation box");
+    error->all(FLERR, "Compute stress/mop requires a fixed size simulation box");
 
   // This compute requires a pair style with pair_single method implemented
 
-  if (force->pair == nullptr)
+  if (!force->pair)
     error->all(FLERR,"No pair style is defined for compute stress/mop");
   if (force->pair->single_enable == 0)
     error->all(FLERR,"Pair style does not support compute stress/mop");
 
   // Errors
 
-  if (me==0) {
+  if (comm->me == 0) {
 
     // issue an error for unimplemented intramolecular potentials or Kspace.
 
-    if (force->bond!=nullptr) bondflag = 1;
-    if (force->angle!=nullptr)
+    if (force->bond) bondflag = 1;
+    if (force->angle) {
       if (force->angle->born_matrix_enable == 0) {
         if ((strcmp(force->angle_style, "zero") != 0) && (strcmp(force->angle_style, "none") != 0))
           error->all(FLERR,"compute stress/mop does not account for angle potentials");
       } else {
          angleflag = 1;
       }
-    if (force->dihedral!=nullptr)
+    }
+    if (force->dihedral) {
       if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
         error->all(FLERR,"compute stress/mop does not account for dihedral potentials");
-    if (force->improper!=nullptr)
+    }
+    if (force->improper) {
       if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
         error->all(FLERR,"compute stress/mop does not account for improper potentials");
-    if (force->kspace!=nullptr)
+    }
+    if (force->kspace)
       error->warning(FLERR,"compute stress/mop does not account for kspace contributions");
   }
 
@@ -266,8 +268,7 @@ void ComputeStressMop::compute_vector()
   compute_pairs();
 
   // sum pressure contributions over all procs
-  MPI_Allreduce(values_local,values_global,nvalues,
-                MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(values_local,values_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
 
   if (bondflag) {
     //Compute bond contribution on separate procs
@@ -292,7 +293,6 @@ void ComputeStressMop::compute_vector()
   for (int m=0; m<nvalues; m++) {
     vector[m] = values_global[m] + bond_global[m] + angle_global[m];
   }
-
 }
 
 
@@ -344,8 +344,8 @@ void ComputeStressMop::compute_pairs()
   double xj[3];
 
   m = 0;
-  while (m<nvalues) {
-    if (which[m] == CONF || which[m] == TOTAL || which[m] == PAIR) {
+  while (m < nvalues) {
+    if ((which[m] == CONF) || (which[m] == TOTAL) || (which[m] == PAIR)) {
 
       //Compute configurational contribution to pressure
       for (ii = 0; ii < inum; ii++) {
@@ -380,47 +380,34 @@ void ComputeStressMop::compute_pairs()
           if (newton_pair || j < nlocal) {
 
             //check if ij pair is across plane, add contribution to pressure
-            if (((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1))) {
-
+            if (((xi[dir] > pos) && (xj[dir] < pos)) || ((xi[dir] > pos1) && (xj[dir] < pos1))) {
               pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
               values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
               values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
               values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
-            }
-            else if (((xi[dir]<pos) && (xj[dir]>pos)) || ((xi[dir]<pos1) && (xj[dir]>pos1))) {
-
+            } else if (((xi[dir] < pos) && (xj[dir] > pos)) || ((xi[dir] < pos1) && (xj[dir] > pos1))) {
               pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
               values_local[m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
               values_local[m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
               values_local[m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
             }
-
           } else {
-
-            if (((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1))) {
-
+            if (((xi[dir] > pos) && (xj[dir] < pos)) || ((xi[dir] > pos1) && (xj[dir] < pos1))) {
               pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
               values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
               values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
               values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
             }
-
           }
-
         }
-
       }
-
     }
 
 
     // Compute kinetic contribution to pressure
     // counts local particles transfers across the plane
 
-    if (which[m] == KIN || which[m] == TOTAL) {
+    if ((which[m] == KIN) || (which[m] == TOTAL)) {
       double sgn;
 
       for (int i = 0; i < nlocal; i++) {
@@ -447,13 +434,13 @@ void ComputeStressMop::compute_pairs()
 
           //coordinates at t-dt (based on Velocity-Verlet alg.)
           if (rmass) {
-            xj[0] = xi[0]-vi[0]*dt+fi[0]/2/rmass[i]*dt*dt*ftm2v;
-            xj[1] = xi[1]-vi[1]*dt+fi[1]/2/rmass[i]*dt*dt*ftm2v;
-            xj[2] = xi[2]-vi[2]*dt+fi[2]/2/rmass[i]*dt*dt*ftm2v;
+            xj[0] = xi[0]-vi[0]*dt+fi[0]/2.0/rmass[i]*dt*dt*ftm2v;
+            xj[1] = xi[1]-vi[1]*dt+fi[1]/2.0/rmass[i]*dt*dt*ftm2v;
+            xj[2] = xi[2]-vi[2]*dt+fi[2]/2.0/rmass[i]*dt*dt*ftm2v;
           } else {
-            xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
-            xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
-            xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
+            xj[0] = xi[0]-vi[0]*dt+fi[0]/2.0/mass[itype]*dt*dt*ftm2v;
+            xj[1] = xi[1]-vi[1]*dt+fi[1]/2.0/mass[itype]*dt*dt*ftm2v;
+            xj[2] = xi[2]-vi[2]*dt+fi[2]/2.0/mass[itype]*dt*dt*ftm2v;
           }
 
           // because LAMMPS does not put atoms back in the box
@@ -463,21 +450,21 @@ void ComputeStressMop::compute_pairs()
           double pos_temp = pos+copysign(1.0,domain->prd_half[dir]-pos)*domain->prd[dir];
           if (fabs(xi[dir]-pos)<fabs(xi[dir]-pos_temp)) pos_temp = pos;
 
-          if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)<0)) {
+          if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)) < 0) {
 
-            //sgn = copysign(1.0,vi[dir]-vcm[dir]);
+            // sgn = copysign(1.0,vi[dir]-vcm[dir]);
             sgn = copysign(1.0,vi[dir]);
 
-            //approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
+            // approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
             double vcross[3];
             if (rmass) {
-              vcross[0] = vi[0]-fi[0]/rmass[i]/2*ftm2v*dt;
-              vcross[1] = vi[1]-fi[1]/rmass[i]/2*ftm2v*dt;
-              vcross[2] = vi[2]-fi[2]/rmass[i]/2*ftm2v*dt;
+              vcross[0] = vi[0]-fi[0]/rmass[i]/2.0*ftm2v*dt;
+              vcross[1] = vi[1]-fi[1]/rmass[i]/2.0*ftm2v*dt;
+              vcross[2] = vi[2]-fi[2]/rmass[i]/2.0*ftm2v*dt;
             } else {
-              vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
-              vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
-              vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
+              vcross[0] = vi[0]-fi[0]/mass[itype]/2.0*ftm2v*dt;
+              vcross[1] = vi[1]-fi[1]/mass[itype]/2.0*ftm2v*dt;
+              vcross[2] = vi[2]-fi[2]/mass[itype]/2.0*ftm2v*dt;
             }
 
             values_local[m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
@@ -487,13 +474,13 @@ void ComputeStressMop::compute_pairs()
         }
       }
     }
-    m+=3;
+    m += 3;
   }
 }
 
 /*------------------------------------------------------------------------
  *   compute bond contribution to pressure of local proc
- *     -------------------------------------------------------------------------*/
+ *-------------------------------------------------------------------------*/
 
 void ComputeStressMop::compute_bonds()
 {
@@ -518,13 +505,13 @@ void ComputeStressMop::compute_bonds()
 
   Bond *bond = force->bond;
 
-  double dx[3] {0};
-  double x_bond_1[3] {0};
-  double x_bond_2[3] {0};
-  double local_contribution[3] {0};
+  double dx[3] = {0.0, 0.0, 0.0};
+  double x_bond_1[3] = {0.0, 0.0, 0.0};
+  double x_bond_2[3] = {0.0, 0.0, 0.0};
+  double local_contribution[3] = {0.0, 0.0, 0.0};
 
   // initialization
-  for (int i {0}; i < nvalues; i++) bond_local[i] = 0.0;
+  for (int i = 0; i < nvalues; i++) bond_local[i] = 0.0;
 
   // loop over all bonded atoms in the current proc
   for (atom1 = 0; atom1 < nlocal; atom1++) {
@@ -591,7 +578,7 @@ void ComputeStressMop::compute_bonds()
   }
 
   // loop over the keywords and if necessary add the bond contribution
-  int m {0};
+  int m = 0;
   while (m<nvalues) {
     if (which[m] == CONF || which[m] == TOTAL || which[m] == BOND) {
       bond_local[m] = local_contribution[0];
@@ -633,17 +620,17 @@ void ComputeStressMop::compute_angles()
   Angle *angle = force->angle;
 
   double duang, du2ang;
-  double dx[3] {0};
-  double dx_left[3] {0};
-  double dx_right[3] {0};
-  double x_angle_left[3] {0};
-  double x_angle_middle[3] {0};
-  double x_angle_right[3] {0};
-  double dcos_theta[3] {0};
-  double local_contribution[3] {0};
+  double dx[3] = {0.0, 0.0, 0.0};
+  double dx_left[3] = {0.0, 0.0, 0.0};
+  double dx_right[3] = {0.0, 0.0, 0.0};
+  double x_angle_left[3] = {0.0, 0.0, 0.0};
+  double x_angle_middle[3] = {0.0, 0.0, 0.0};
+  double x_angle_right[3] = {0.0, 0.0, 0.0};
+  double dcos_theta[3] = {0.0, 0.0, 0.0};
+  double local_contribution[3] = {0.0, 0.0, 0.0};
 
   // initialization
-  for (int i {0}; i < nvalues; i++) angle_local[i] = 0.0;
+  for (int i = 0; i < nvalues; i++) angle_local[i] = 0.0;
 
   for (atom2 = 0; atom2 < nlocal; atom2++) {
     if (!(mask[atom2] & groupbit)) continue;
@@ -762,8 +749,8 @@ void ComputeStressMop::compute_angles()
     }
   }
   // loop over the keywords and if necessary add the angle contribution
-  int m {0};
-  while (m<nvalues) {
+  int m = 0;
+  while (m < nvalues) {
     if (which[m] == CONF || which[m] == TOTAL || which[m] == ANGLE) {
       angle_local[m] = local_contribution[0];
       angle_local[m+1] = local_contribution[1];
diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.h b/src/EXTRA-COMPUTE/compute_stress_mop.h
index 791e18d624..86140dc278 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.h
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.h
@@ -41,7 +41,7 @@ class ComputeStressMop : public Compute {
   void compute_bonds();
   void compute_angles();
 
-  int me, nvalues, dir;
+  int nvalues, dir;
   int *which;
 
   int bondflag, angleflag;
diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index 807092b37e..1f1dc30733 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,6 +13,7 @@
 
 /*------------------------------------------------------------------------
   Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+  Support for bonds added by : Evangelos Voyiatzis (NovaMechanics)
   --------------------------------------------------------------------------*/
 
 #include "compute_stress_mop_profile.h"
@@ -21,43 +21,43 @@
 #include "atom.h"
 #include "atom_vec.h"
 #include "bond.h"
-#include "update.h"
+#include "comm.h"
 #include "domain.h"
-#include "molecule.h"
-#include "neighbor.h"
-#include "force.h"
-#include "pair.h"
-#include "neigh_list.h"
 #include "error.h"
+#include "force.h"
 #include "memory.h"
+#include "molecule.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "update.h"
 
 #include <cmath>
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
-enum{X,Y,Z};
-enum{LOWER,CENTER,UPPER,COORD};
-enum{TOTAL,CONF,KIN,PAIR,BOND};
+enum { X, Y, Z };
+enum { LOWER, CENTER, UPPER, COORD };
+enum { TOTAL, CONF, KIN, PAIR, BOND };
 
+// clang-format off
 /* ---------------------------------------------------------------------- */
 
 ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg)
 {
-  if (narg < 7) error->all(FLERR,"Illegal compute stress/mop/profile command");
-
-  MPI_Comm_rank(world,&me);
+  if (narg < 7) utils::missing_cmd_args(FLERR, "compute stress/mop/profile", error);
 
   bondflag = 0;
 
   // set compute mode and direction of plane(s) for pressure calculation
 
-  if (strcmp(arg[3],"x")==0) {
+  if (strcmp(arg[3],"x") == 0) {
     dir = X;
-  } else if (strcmp(arg[3],"y")==0) {
+  } else if (strcmp(arg[3],"y") == 0) {
     dir = Y;
-  } else if (strcmp(arg[3],"z")==0) {
+  } else if (strcmp(arg[3],"z") == 0) {
     dir = Z;
   } else error->all(FLERR,"Illegal compute stress/mop/profile command");
 
@@ -67,8 +67,7 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
   else if (strcmp(arg[4],"center") == 0) originflag = CENTER;
   else if (strcmp(arg[4],"upper") == 0) originflag = UPPER;
   else originflag = COORD;
-  if (originflag == COORD)
-    origin = utils::numeric(FLERR,arg[4],false,lmp);
+  if (originflag == COORD) origin = utils::numeric(FLERR,arg[4],false,lmp);
   delta = utils::numeric(FLERR,arg[5],false,lmp);
   invdelta = 1.0/delta;
 
@@ -149,8 +148,7 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
 
 ComputeStressMopProfile::~ComputeStressMopProfile()
 {
-
-  delete [] which;
+  delete[] which;
 
   memory->destroy(coord);
   memory->destroy(coordp);
@@ -166,7 +164,6 @@ ComputeStressMopProfile::~ComputeStressMopProfile()
 
 void ComputeStressMopProfile::init()
 {
-
   // conversion constants
 
   nktv2p = force->nktv2p;
@@ -192,30 +189,30 @@ void ComputeStressMopProfile::init()
 
   //This compute requires a pair style with pair_single method implemented
 
-  if (force->pair == nullptr)
+  if (!force->pair)
     error->all(FLERR,"No pair style is defined for compute stress/mop/profile");
   if (force->pair->single_enable == 0)
     error->all(FLERR,"Pair style does not support compute stress/mop/profile");
 
   // Errors
 
-  if (me==0) {
+  if (comm->me == 0) {
 
     //Compute stress/mop/profile only accounts for pair interactions.
     // issue an error if any intramolecular potential or Kspace is defined.
 
-    if (force->bond!=nullptr) bondflag = 1;
+    if (force->bond) bondflag = 1;
 
-    if (force->angle!=nullptr)
+    if (force->angle)
       if ((strcmp(force->angle_style, "zero") != 0) && (strcmp(force->angle_style, "none") != 0))
         error->all(FLERR,"compute stress/mop/profile does not account for angle potentials");
-    if (force->dihedral!=nullptr)
+    if (force->dihedral)
       if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
         error->all(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
-    if (force->improper!=nullptr)
+    if (force->improper)
       if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
         error->all(FLERR,"compute stress/mop/profile does not account for improper potentials");
-    if (force->kspace!=nullptr)
+    if (force->kspace)
       error->warning(FLERR,"compute stress/mop/profile does not account for kspace contributions");
   }
 
@@ -244,8 +241,7 @@ void ComputeStressMopProfile::compute_array()
   compute_pairs();
 
   // sum pressure contributions over all procs
-  MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,
-                MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,MPI_DOUBLE,MPI_SUM,world);
 
   if (bondflag) {
     //Compute bond contribution on separate procs
@@ -259,16 +255,14 @@ void ComputeStressMopProfile::compute_array()
   }
 
   // sum bond contribution over all procs
-  MPI_Allreduce(&bond_local[0][0],&bond_global[0][0],nbins*nvalues,
-                MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&bond_local[0][0],&bond_global[0][0],nbins*nvalues,MPI_DOUBLE,MPI_SUM,world);
 
-  int ibin,m,mo;
-  for (ibin=0; ibin<nbins; ibin++) {
+  for (int ibin=0; ibin<nbins; ibin++) {
     array[ibin][0] = coord[ibin][0];
-    mo=1;
 
-    m = 0;
-    while (m<nvalues) {
+    int mo = 1;
+    int m = 0;
+    while (m < nvalues) {
       array[ibin][m+mo] = values_global[ibin][m] + bond_global[ibin][m];
       m++;
     }
@@ -326,8 +320,8 @@ void ComputeStressMopProfile::compute_pairs()
   double xj[3];
 
   m = 0;
-  while (m<nvalues) {
-    if (which[m] == CONF || which[m] == TOTAL || which[m] == PAIR) {
+  while (m < nvalues) {
+    if ((which[m] == CONF) || (which[m] == TOTAL) || (which[m] == PAIR)) {
 
       // Compute configurational contribution to pressure
 
@@ -414,7 +408,7 @@ void ComputeStressMopProfile::compute_pairs()
     // compute kinetic contribution to pressure
     // counts local particles transfers across the plane
 
-    if (which[m] == KIN || which[m] == TOTAL) {
+    if ((which[m] == KIN) || (which[m] == TOTAL)) {
 
       double sgn;
 
@@ -452,7 +446,7 @@ void ComputeStressMopProfile::compute_pairs()
             xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
           }
 
-          for (ibin=0;ibin<nbins;ibin++) {
+          for (ibin = 0; ibin < nbins; ibin++) {
             pos = coord[ibin][0];
             pos1 = coordp[ibin][0];
 
@@ -516,13 +510,13 @@ void ComputeStressMopProfile::compute_bonds()
 
   Bond *bond = force->bond;
 
-  double dx[3] {0};
-  double x_bond_1[3] {0};
-  double x_bond_2[3] {0};
+  double dx[3] = {0.0, 0.0, 0.0};
+  double x_bond_1[3] = {0.0, 0.0, 0.0};
+  double x_bond_2[3] = {0.0, 0.0, 0.0};
 
   // initialization
-  for (int m {0}; m < nbins; m++) {
-    for (int i {0}; i < nvalues; i++) {
+  for (int m = 0; m < nbins; m++) {
+    for (int i = 0; i < nvalues; i++) {
       bond_local[m][i] = 0.0;
     }
     local_contribution[m][0] = 0.0;
@@ -557,7 +551,7 @@ void ComputeStressMopProfile::compute_bonds()
       if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
       if (btype <= 0) continue;
 
-      for (int ibin {0}; ibin<nbins; ibin++) {
+      for (int ibin = 0; ibin<nbins; ibin++) {
         double pos = coord[ibin][0];
 
         // minimum image of atom1 with respect to the plane of interest
@@ -599,10 +593,10 @@ void ComputeStressMopProfile::compute_bonds()
   }
 
   // loop over the keywords and if necessary add the bond contribution
-  int m {0};
-  while (m<nvalues) {
-    if (which[m] == CONF || which[m] == TOTAL || which[m] == BOND) { // Axel
-      for (int ibin {0}; ibin < nbins; ibin++) {
+  int m = 0;
+  while (m < nvalues) {
+    if ((which[m] == CONF) || (which[m] == TOTAL) || (which[m] == BOND)) {
+      for (int ibin = 0; ibin < nbins; ibin++) {
         bond_local[ibin][m] = local_contribution[ibin][0];
         bond_local[ibin][m+1] = local_contribution[ibin][1];
         bond_local[ibin][m+2] = local_contribution[ibin][2];
diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.h b/src/EXTRA-COMPUTE/compute_stress_mop_profile.h
index 1015d6e3eb..2b0ffef0f8 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.h
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.h
@@ -41,7 +41,7 @@ class ComputeStressMopProfile : public Compute {
   void compute_bonds();
   void setup_bins();
 
-  int me, nvalues, dir;
+  int nvalues, dir;
   int *which;
 
   int bondflag;

From bd3e7882e64c50b50a6cee1f3b1c98fdc461eb04 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 06:20:24 -0400
Subject: [PATCH 197/396] remove unused include and related statements

---
 src/INTERLAYER/pair_aip_water_2dm.cpp |  7 -------
 src/INTERLAYER/pair_ilp_tmd.cpp       |  4 ----
 src/OPT/pair_aip_water_2dm_opt.cpp    | 10 ----------
 3 files changed, 21 deletions(-)

diff --git a/src/INTERLAYER/pair_aip_water_2dm.cpp b/src/INTERLAYER/pair_aip_water_2dm.cpp
index f2d68f448b..6e2bf7228d 100644
--- a/src/INTERLAYER/pair_aip_water_2dm.cpp
+++ b/src/INTERLAYER/pair_aip_water_2dm.cpp
@@ -20,21 +20,14 @@
 
 #include "pair_aip_water_2dm.h"
 
-#include "atom.h"
 #include "citeme.h"
 #include "error.h"
 #include "force.h"
-#include "interlayer_taper.h"
-#include "memory.h"
-#include "my_page.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 
 #include <cmath>
 #include <cstring>
 
 using namespace LAMMPS_NS;
-using namespace InterLayer;
 
 #define MAXLINE 1024
 #define DELTA 4
diff --git a/src/INTERLAYER/pair_ilp_tmd.cpp b/src/INTERLAYER/pair_ilp_tmd.cpp
index f29ee34180..fd3a2f8c6f 100644
--- a/src/INTERLAYER/pair_ilp_tmd.cpp
+++ b/src/INTERLAYER/pair_ilp_tmd.cpp
@@ -35,10 +35,6 @@
 using namespace LAMMPS_NS;
 using namespace InterLayer;
 
-#define MAXLINE 1024
-#define DELTA 4
-#define PGDELTA 1
-
 static const char cite_ilp_tmd[] =
     "ilp/tmd potential doi:10.1021/acs.jctc.1c00782\n"
     "@Article{Ouyang2021\n"
diff --git a/src/OPT/pair_aip_water_2dm_opt.cpp b/src/OPT/pair_aip_water_2dm_opt.cpp
index 3aba5b9dbd..47c8c395db 100644
--- a/src/OPT/pair_aip_water_2dm_opt.cpp
+++ b/src/OPT/pair_aip_water_2dm_opt.cpp
@@ -33,21 +33,11 @@
 #include "pair_aip_water_2dm_opt.h"
 
 #include "atom.h"
-#include "citeme.h"
-#include "comm.h"
-#include "error.h"
-#include "force.h"
-#include "interlayer_taper.h"
 #include "memory.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "neighbor.h"
 
-#include <cmath>
 #include <cstring>
 
 using namespace LAMMPS_NS;
-using namespace InterLayer;
 
 PairAIPWATER2DMOpt::PairAIPWATER2DMOpt(LAMMPS *lmp) :
   PairILPGrapheneHBN(lmp), PairILPTMD(lmp), PairAIPWATER2DM(lmp), PairILPGrapheneHBNOpt(lmp)

From 37d894db51074724b20ff1e6befe8c4f7099320f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 06:30:07 -0400
Subject: [PATCH 198/396] update/clarify docs

---
 doc/src/pair_aip_water_2dm.rst | 24 +++++++++++-------------
 1 file changed, 11 insertions(+), 13 deletions(-)

diff --git a/doc/src/pair_aip_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst
index 5218db9c37..f57e4b33fb 100644
--- a/doc/src/pair_aip_water_2dm.rst
+++ b/doc/src/pair_aip_water_2dm.rst
@@ -59,22 +59,20 @@ a continuous cutoff (up to third derivative) for interatomic separations
 larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn
 <pair_ilp_graphene_hbn>`.
 
-It is important to include all the pairs to build the neighbor list for
-calculating the normals.
-
 .. note::
 
-   Since each water molecule contains one oxygen atom and two hydrogen
-   atoms, a new definition is proposed (see In :ref:`(Feng) <Feng>`),the
-   atomic normal vectors of hydrogen atoms are assumed to lie along the
-   corresponding oxygen-hydrogen bonds and the normal vector of the
-   central oxygen atom is defined as their average.
+   This pair style uses the atomic normal vector definition from
+   :ref:`(Feng) <Feng>`), where the atomic normal vectors of the
+   hydrogen atoms are assumed to lie along the corresponding
+   oxygen-hydrogen bonds and the normal vector of the central oxygen
+   atom is defined as their average.
 
 The provided parameter file, ``COH.aip.water.2dm``, is intended for use
 with *metal* :doc:`units <units>`, with energies in meV.  Two additional
 parameters, *S*, and *rcut* are included in the parameter file. *S* is
-designed to facilitate scaling of energies; *rcut* is designed to build
-the neighbor list for calculating the normals for each atom pair.
+designed to facilitate scaling of energies; *rcut* is the cutoff for an
+internal, short distance neighbor list that is generated for speeding up
+the calculation of the normals for all atom pairs.
 
 .. note::
 
@@ -83,9 +81,9 @@ the neighbor list for calculating the normals for each atom pair.
    setting the cutoff equal to 16.0 Angstrom.  Using a different cutoff
    or taper function setting should be carefully checked as they can
    lead to significant errors.  These parameters provide a good
-   description in both short- and long-range interaction regimes.  This
-   feature is essential for simulations in high pressure regime (i.e.,
-   the interlayer distance is smaller than the equilibrium distance).
+   description in both short- and long-range interaction regimes. This
+   is essential for simulations in high pressure regime (i.e., the
+   interlayer distance is smaller than the equilibrium distance).
 
 This potential must be used in combination with hybrid/overlay.  Other
 interactions can be set to zero using :doc:`pair_coeff settings

From 57f166670f08fe7a683306172ca4d5527e6564cb Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 06:38:52 -0400
Subject: [PATCH 199/396] fix versionadded macro so it is detected when actual
 version is added

---
 doc/src/pair_aip_water_2dm.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/pair_aip_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst
index f57e4b33fb..532ee8f8f6 100644
--- a/doc/src/pair_aip_water_2dm.rst
+++ b/doc/src/pair_aip_water_2dm.rst
@@ -33,7 +33,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: xxxx2023
+.. versionadded:: TBD
 
 The *aip/water/2dm* style computes the anisotropic interfacial potential
 (AIP) potential for interfaces of water with two-dimensional (2D)

From f2f8e139d8c23e750ce603ef4cd2a95b245bdb5a Mon Sep 17 00:00:00 2001
From: Lars Veldscholte <lars@tuxplace.nl>
Date: Wed, 7 Jun 2023 16:03:32 +0200
Subject: [PATCH 200/396] Add optional keywords to arguments for ke/pair/bond
 forces

---
 .../compute_stress_cartesian.cpp              | 232 ++++++++++--------
 src/EXTRA-COMPUTE/compute_stress_cartesian.h  |   3 +
 2 files changed, 130 insertions(+), 105 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
index 0aae797111..3835b8bea9 100644
--- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
@@ -62,14 +62,12 @@ ComputeStressCartesian::ComputeStressCartesian(LAMMPS *lmp, int narg, char **arg
 {
   if (lmp->citeme) lmp->citeme->add(cite_compute_stress_cartesian);
 
-  // narg == 5 for one-dimensional and narg == 7 for two-dimensional
-  if (narg == 5)
-    dims = 1;
-  else if (narg == 7)
-    dims = 2;
-  else
-    error->all(FLERR, "Illegal compute stress/cartesian command. Illegal number of arguments.");
+  if (narg < 7) error->all(FLERR, "Illegal compute stress/cartesian command: illegal number of arguments.");
 
+  // no triclinic boxes
+  if (domain->triclinic) error->all(FLERR, "Compute stress/cartesian requires an orthogonal box");
+
+  // Direction of first dimension
   if (strcmp(arg[3], "x") == 0)
     dir1 = 0;
   else if (strcmp(arg[3], "y") == 0)
@@ -79,14 +77,8 @@ ComputeStressCartesian::ComputeStressCartesian(LAMMPS *lmp, int narg, char **arg
   else
     error->all(FLERR, "Illegal compute stress/cartesian direction: {}", arg[3]);
 
-  dir2 = 0;
   bin_width1 = utils::numeric(FLERR, arg[4], false, lmp);
-  bin_width2 = domain->boxhi[dir2] - domain->boxlo[dir2];
   nbins1 = (int) ((domain->boxhi[dir1] - domain->boxlo[dir1]) / bin_width1);
-  nbins2 = 1;
-
-  // no triclinic boxes
-  if (domain->triclinic) error->all(FLERR, "Compute stress/cartesian requires an orthogonal box");
 
   // adjust bin width if not a perfect match
   double tmp_binwidth = (domain->boxhi[dir1] - domain->boxlo[dir1]) / nbins1;
@@ -94,14 +86,23 @@ ComputeStressCartesian::ComputeStressCartesian(LAMMPS *lmp, int narg, char **arg
     utils::logmesg(lmp, "Adjusting first bin width for compute {} from {:.6f} to {:.6f}\n", style,
                    bin_width1, tmp_binwidth);
   bin_width1 = tmp_binwidth;
+  invV = bin_width1;
 
   if (bin_width1 <= 0.0)
     error->all(FLERR, "Illegal compute stress/cartesian command. First bin width must be > 0");
   else if (bin_width1 > domain->boxhi[dir1] - domain->boxlo[dir1])
     error->all(FLERR, "Illegal compute stress/cartesian command. First bin width > box.");
 
-  invV = bin_width1;
-  if (dims == 2) {
+  // Direction of second dimension
+  if (strcmp(arg[5], "NULL") == 0) {
+    dims = 1;
+    dir2 = 0;
+    bin_width2 = domain->boxhi[dir2] - domain->boxlo[dir2];
+    nbins2 = 1;
+  } else {
+    dims = 2;
+
+    // Direction of first dimension
     if (strcmp(arg[5], "x") == 0)
       dir2 = 0;
     else if (strcmp(arg[5], "y") == 0)
@@ -150,6 +151,21 @@ ComputeStressCartesian::ComputeStressCartesian(LAMMPS *lmp, int narg, char **arg
   if (box_incompatible)
     error->all(FLERR, "Must not use compute stress/cartesian on variable box dimension");
 
+  // process optional args
+  if (narg > 7) {
+    compute_ke = false;
+    compute_pair = false;
+    compute_bond = false;
+    int iarg = 7;
+    while (iarg < narg) {
+      if (strcmp(arg[iarg], "ke") == 0)        compute_ke = true;
+      else if (strcmp(arg[iarg], "pair") == 0) compute_pair = true;
+      else if (strcmp(arg[iarg], "bond") == 0) compute_bond = true;
+      else error->all(FLERR, "Illegal compute stress/atom command");
+      iarg++;
+    }
+  }
+
   for (int i = 0; i < 3; i++)
     if ((dims == 1 && i != dir1) || (dims == 2 && (i != dir1 && i != dir2)))
       invV *= domain->boxhi[i] - domain->boxlo[i];
@@ -262,119 +278,125 @@ void ComputeStressCartesian::compute_array()
   }
 
   // calculate number density and kinetic contribution to pressure
-  for (int i = 0; i < nlocal; i++) {
-    int bin1 = (int) ((x[i][dir1] - boxlo[dir1]) / bin_width1) % nbins1;
-    int bin2 = 0;
-    if (dims == 2) bin2 = (int) ((x[i][dir2] - boxlo[dir2]) / bin_width2) % nbins2;
+  if (compute_ke) {
+    for (int i = 0; i < nlocal; i++) {
+      int bin1 = (int) ((x[i][dir1] - boxlo[dir1]) / bin_width1) % nbins1;
+      int bin2 = 0;
+      if (dims == 2) bin2 = (int) ((x[i][dir2] - boxlo[dir2]) / bin_width2) % nbins2;
 
-    // Apply periodic boundary conditions and avoid out of range access
-    if (domain->periodicity[dir1] == 1) {
-      if (bin1 < 0)
-        bin1 = (bin1 + nbins1) % nbins1;
+      // Apply periodic boundary conditions and avoid out of range access
+      if (domain->periodicity[dir1] == 1) {
+        if (bin1 < 0)
+          bin1 = (bin1 + nbins1) % nbins1;
+        else if (bin1 >= nbins1)
+          bin1 = (bin1 - nbins1) % nbins1;
+      } else if (bin1 < 0)
+        bin1 = 0;
       else if (bin1 >= nbins1)
-        bin1 = (bin1 - nbins1) % nbins1;
-    } else if (bin1 < 0)
-      bin1 = 0;
-    else if (bin1 >= nbins1)
-      bin1 = nbins1 - 1;
+        bin1 = nbins1 - 1;
 
-    if (domain->periodicity[dir2] == 1) {
-      if (bin2 < 0)
-        bin2 = (bin2 + nbins2) % nbins2;
+      if (domain->periodicity[dir2] == 1) {
+        if (bin2 < 0)
+          bin2 = (bin2 + nbins2) % nbins2;
+        else if (bin2 >= nbins2)
+          bin2 = (bin2 - nbins2) % nbins2;
+      } else if (bin2 < 0)
+        bin2 = 0;
       else if (bin2 >= nbins2)
-        bin2 = (bin2 - nbins2) % nbins2;
-    } else if (bin2 < 0)
-      bin2 = 0;
-    else if (bin2 >= nbins2)
-      bin2 = nbins2 - 1;
+        bin2 = nbins2 - 1;
 
-    int j = bin1 + bin2 * nbins1;
-    tdens[j] += 1;
-    tpkxx[j] += mass[type[i]] * v[i][0] * v[i][0];
-    tpkyy[j] += mass[type[i]] * v[i][1] * v[i][1];
-    tpkzz[j] += mass[type[i]] * v[i][2] * v[i][2];
+      int j = bin1 + bin2 * nbins1;
+      tdens[j] += 1;
+      tpkxx[j] += mass[type[i]] * v[i][0] * v[i][0];
+      tpkyy[j] += mass[type[i]] * v[i][1] * v[i][1];
+      tpkzz[j] += mass[type[i]] * v[i][2] * v[i][2];
+    }
   }
 
   // loop over neighbors of my atoms
-  for (int ii = 0; ii < inum; ii++) {
-    int i = ilist[ii];
+  if (compute_pair && force->pair) {
+    for (int ii = 0; ii < inum; ii++) {
+      int i = ilist[ii];
 
-    // skip if I or J are not in group
-    if (!(mask[i] & groupbit)) continue;
+      // skip if I or J are not in group
+      if (!(mask[i] & groupbit)) continue;
 
-    double xi1 = x[i][dir1] - boxlo[dir1];
-    double xi2 = x[i][dir2] - boxlo[dir2];
+      double xi1 = x[i][dir1] - boxlo[dir1];
+      double xi2 = x[i][dir2] - boxlo[dir2];
 
-    for (int jj = 0; jj < numneigh[i]; jj++) {
-      int j = firstneigh[i][jj];
-      double factor_lj = special_lj[sbmask(j)];
-      double factor_coul = special_coul[sbmask(j)];
-      j &= NEIGHMASK;
-      if (!(mask[j] & groupbit)) continue;
+      for (int jj = 0; jj < numneigh[i]; jj++) {
+        int j = firstneigh[i][jj];
+        double factor_lj = special_lj[sbmask(j)];
+        double factor_coul = special_coul[sbmask(j)];
+        j &= NEIGHMASK;
+        if (!(mask[j] & groupbit)) continue;
 
-      // for newton = 0 and J = ghost atom, need to ensure I,J pair is only output by one proc
-      // use same tag[i],tag[j] logic as in Neighbor::neigh_half_nsq()
-      if (newton_pair == 0 && j >= nlocal) {
-        if (tag[i] > tag[j]) {
-          if ((tag[i] + tag[j]) % 2 == 0) continue;
-        } else if (tag[i] < tag[j]) {
-          if ((tag[i] + tag[j]) % 2 == 1) continue;
-        } else {
-          // tag[i] = tag[j] is possible for long cutoffs that include images of self
-          if (x[j][2] < x[i][2]) continue;
-          if (x[j][2] == x[i][2]) {
-            if (x[j][1] < x[i][1]) continue;
-            if (x[j][1] == x[i][1] && x[j][0] < x[i][0]) continue;
+        // for newton = 0 and J = ghost atom, need to ensure I,J pair is only output by one proc
+        // use same tag[i],tag[j] logic as in Neighbor::neigh_half_nsq()
+        if (newton_pair == 0 && j >= nlocal) {
+          if (tag[i] > tag[j]) {
+            if ((tag[i] + tag[j]) % 2 == 0) continue;
+          } else if (tag[i] < tag[j]) {
+            if ((tag[i] + tag[j]) % 2 == 1) continue;
+          } else {
+            // tag[i] = tag[j] is possible for long cutoffs that include images of self
+            if (x[j][2] < x[i][2]) continue;
+            if (x[j][2] == x[i][2]) {
+              if (x[j][1] < x[i][1]) continue;
+              if (x[j][1] == x[i][1] && x[j][0] < x[i][0]) continue;
+            }
           }
         }
+
+        double delx = x[j][0] - x[i][0];
+        double dely = x[j][1] - x[i][1];
+        double delz = x[j][2] - x[i][2];
+        double rsq = delx * delx + dely * dely + delz * delz;
+
+        // Check if inside cut-off
+        int itype = type[i];
+        int jtype = type[j];
+        if (rsq >= force->pair->cutsq[itype][jtype]) continue;
+
+        double fpair;
+        force->pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
+        compute_pressure(fpair, xi1, xi2, delx, dely, delz);
       }
-
-      double delx = x[j][0] - x[i][0];
-      double dely = x[j][1] - x[i][1];
-      double delz = x[j][2] - x[i][2];
-      double rsq = delx * delx + dely * dely + delz * delz;
-
-      // Check if inside cut-off
-      int itype = type[i];
-      int jtype = type[j];
-      if (rsq >= force->pair->cutsq[itype][jtype]) continue;
-
-      double fpair;
-      force->pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
-      compute_pressure(fpair, xi1, xi2, delx, dely, delz);
     }
   }
 
   // Loop over all bonds
-  for (int i_bond = 0; i_bond < neighbor->nbondlist; i_bond++) {
-    // i == atom1, j == atom2
-    int i = neighbor->bondlist[i_bond][0];
-    int j = neighbor->bondlist[i_bond][1];
-    int btype  = neighbor->bondlist[i_bond][2];
+  if (compute_bond && force->bond) {
+    for (int i_bond = 0; i_bond < neighbor->nbondlist; i_bond++) {
+      // i == atom1, j == atom2
+      int i = neighbor->bondlist[i_bond][0];
+      int j = neighbor->bondlist[i_bond][1];
+      int btype  = neighbor->bondlist[i_bond][2];
 
-    // Skip if one of both atoms is not in group
-    if (!(mask[i] & groupbit)) continue;
-    if (!(mask[j] & groupbit)) continue;
+      // Skip if one of both atoms is not in group
+      if (!(mask[i] & groupbit)) continue;
+      if (!(mask[j] & groupbit)) continue;
 
-    // if newton_bond is off and atom2 is a ghost atom, only compute this on one processor
-    if (!force->newton_bond && j >= nlocal) {
-      if (tag[i] > tag[j]) {
-        if ((tag[i] + tag[j]) % 2 == 0) continue;
-      } else if (tag[i] < tag[j]) {
-        if ((tag[i] < tag[j]) % 2 == 1) continue;
+      // if newton_bond is off and atom2 is a ghost atom, only compute this on one processor
+      if (!force->newton_bond && j >= nlocal) {
+        if (tag[i] > tag[j]) {
+          if ((tag[i] + tag[j]) % 2 == 0) continue;
+        } else if (tag[i] < tag[j]) {
+          if ((tag[i] < tag[j]) % 2 == 1) continue;
+        }
       }
+
+      double dx = x[j][0] - x[i][0];
+      double dy = x[j][1] - x[i][1];
+      double dz = x[j][2] - x[i][2];
+      double rsq = dx*dx + dy*dy + dz*dz;
+      double xi = x[i][dir1] - boxlo[dir1];
+      double yi = x[i][dir2] - boxlo[dir2];
+
+      double fbond;
+      force->bond->single(btype, rsq, i, j, fbond);
+      compute_pressure(fbond, xi, yi, dx, dy, dz);
     }
-
-    double dx = x[j][0] - x[i][0];
-    double dy = x[j][1] - x[i][1];
-    double dz = x[j][2] - x[i][2];
-    double rsq = dx*dx + dy*dy + dz*dz;
-    double xi = x[i][dir1] - boxlo[dir1];
-    double yi = x[i][dir2] - boxlo[dir2];
-
-    double fbond;
-    force->bond->single(btype, rsq, i, j, fbond);
-    compute_pressure(fbond, xi, yi, dx, dy, dz);
   }
 
   // normalize pressure
diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.h b/src/EXTRA-COMPUTE/compute_stress_cartesian.h
index 0954d9ca71..40f2e9d4af 100644
--- a/src/EXTRA-COMPUTE/compute_stress_cartesian.h
+++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.h
@@ -36,6 +36,9 @@ class ComputeStressCartesian : public Compute {
  private:
   int nbins1, nbins2, dir1, dir2, dims;
   double bin_width1, bin_width2, invV;
+  bool compute_ke = true;
+  bool compute_pair = true;
+  bool compute_bond = true;
 
   // Number density, kinetic and configurational contribution to the pressure.
   double *dens, *pkxx, *pkyy, *pkzz, *pcxx, *pcyy, *pczz;

From 2f88153f060f8bac8a98108b86cd298403a1c5a6 Mon Sep 17 00:00:00 2001
From: "W. Michael Brown" <michael.w.brown@intel.com>
Date: Wed, 7 Jun 2023 10:43:51 -0700
Subject: [PATCH 201/396] Implementing feature request for runtime control of
 pppm_table in Intel package.

---
 doc/src/package.rst          | 19 +++++++++++--------
 src/INTEL/fix_intel.cpp      |  8 ++++++--
 src/INTEL/fix_intel.h        |  4 ++--
 src/INTEL/intel_preprocess.h |  2 --
 4 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/doc/src/package.rst b/doc/src/package.rst
index 6d425b63dd..ce45a1eb79 100644
--- a/doc/src/package.rst
+++ b/doc/src/package.rst
@@ -68,6 +68,9 @@ Syntax
              Ntpc = max number of co-processor threads per co-processor core (default = 4)
            *tptask* value = Ntptask
              Ntptask = max number of co-processor threads per MPI task (default = 240)
+           *pppm_table* value = *yes* or *no*
+             *yes* = Precompute pppm values in table (doesn't change accuracy)
+             *no* = Compute pppm values on the fly
            *no_affinity* values = none
        *kokkos* args = keyword value ...
          zero or more keyword/value pairs may be appended
@@ -708,14 +711,14 @@ in your input script or via the "-pk gpu" :doc:`command-line switch <Run_options
 
 For the INTEL package, the default is Nphi = 1 and the option
 defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4,
-tptask = 240.  The default ghost option is determined by the pair
-style being used.  This value is output to the screen in the offload
-report at the end of each run.  Note that all of these settings,
-except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
-Phi co-processor support.  These settings are made automatically if the
-"-sf intel" :doc:`command-line switch <Run_options>` is used.  If it is
-not used, you must invoke the package intel command in your input
-script or via the "-pk intel" :doc:`command-line switch <Run_options>`.
+tptask = 240, pppm_table = yes.  The default ghost option is determined
+by the pair style being used.  This value is output to the screen in
+the offload report at the end of each run.  Note that all of these
+settings, except "omp" and "mode", are ignored if LAMMPS was not built
+with Xeon Phi co-processor support.  These settings are made
+automatically if the "-sf intel" :doc:`command-line switch <Run_options>`
+is used.  If it is not used, you must invoke the package intel command
+in your input script or via the "-pk intel" :doc:`command-line switch <Run_options>`.
 
 For the KOKKOS package, the option defaults for GPUs are neigh = full,
 neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default
diff --git a/src/INTEL/fix_intel.cpp b/src/INTEL/fix_intel.cpp
index 89775108cb..2b786b6eed 100644
--- a/src/INTEL/fix_intel.cpp
+++ b/src/INTEL/fix_intel.cpp
@@ -95,6 +95,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) :  Fix(lmp, narg, arg)
   _allow_separate_buffers = 1;
   _offload_ghost = -1;
   _lrt = 0;
+  _p3m_table = 1;
 
   int iarg = 4;
   while (iarg < narg) {
@@ -135,11 +136,14 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) :  Fix(lmp, narg, arg)
       if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
       _lrt = utils::logical(FLERR,arg[iarg+1],false,lmp);
       iarg += 2;
-    }
+    } else if (strcmp(arg[iarg], "pppm_table") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
+      _p3m_table = utils::logical(FLERR,arg[iarg+1],false,lmp);
+      iarg += 2;
 
     // undocumented options
 
-    else if (strcmp(arg[iarg],"offload_affinity_balanced") == 0) {
+    } else if (strcmp(arg[iarg],"offload_affinity_balanced") == 0) {
       _offload_affinity_balanced = 1;
       iarg++;
     } else if (strcmp(arg[iarg],"buffers") == 0) {
diff --git a/src/INTEL/fix_intel.h b/src/INTEL/fix_intel.h
index 1960a6d802..050b27c313 100644
--- a/src/INTEL/fix_intel.h
+++ b/src/INTEL/fix_intel.h
@@ -103,7 +103,7 @@ class FixIntel : public Fix {
   inline int pppm_table()
   {
     if (force->kspace_match("^pppm/.*intel$", 0))
-      return INTEL_P3M_TABLE;
+      return _p3m_table;
     else
       return 0;
   }
@@ -194,7 +194,7 @@ class FixIntel : public Fix {
  protected:
   int _overflow_flag[5];
   _alignvar(int _off_overflow_flag[5], 64);
-  int _allow_separate_buffers, _offload_ghost, _lrt;
+  int _allow_separate_buffers, _offload_ghost, _lrt, _p3m_table;
 
   IntelBuffers<float, float>::vec3_acc_t *_force_array_s;
   IntelBuffers<float, double>::vec3_acc_t *_force_array_m;
diff --git a/src/INTEL/intel_preprocess.h b/src/INTEL/intel_preprocess.h
index a3c961f436..2c4b9a0c1b 100644
--- a/src/INTEL/intel_preprocess.h
+++ b/src/INTEL/intel_preprocess.h
@@ -86,8 +86,6 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
 #define INTEL_MAX_STENCIL_CHECK 4096
 #define INTEL_P3M_MAXORDER 8
 #define INTEL_P3M_ALIGNED_MAXORDER 8
-// PRECOMPUTE VALUES IN TABLE (DOESN'T AFFECT ACCURACY)
-#define INTEL_P3M_TABLE 1
 
 #ifdef __INTEL_COMPILER
 #ifdef __AVX__

From 6360c02daaa882c73770aaebd3a11f1239b398f6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 14:04:41 -0400
Subject: [PATCH 202/396] use explicit const references

---
 src/EXTRA-DUMP/dump_yaml.cpp     |  6 +++---
 src/NETCDF/dump_netcdf.cpp       | 10 +++++-----
 src/NETCDF/dump_netcdf_mpiio.cpp | 10 +++++-----
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/EXTRA-DUMP/dump_yaml.cpp b/src/EXTRA-DUMP/dump_yaml.cpp
index 029415164f..ec7d26af31 100644
--- a/src/EXTRA-DUMP/dump_yaml.cpp
+++ b/src/EXTRA-DUMP/dump_yaml.cpp
@@ -64,10 +64,10 @@ void DumpYAML::write_header(bigint ndump)
     if (update->ntimestep == th->get_timestep()) {
 
       thermo_data += "thermo:\n  - keywords: [ ";
-      for (auto key : th->get_keywords()) thermo_data += fmt::format("{}, ", key);
+      for (const auto &key : th->get_keywords()) thermo_data += fmt::format("{}, ", key);
       thermo_data += "]\n  - data: [ ";
 
-      for (auto val : th->get_fields()) {
+      for (const auto &val : th->get_fields()) {
         if (val.type == multitype::DOUBLE)
           thermo_data += fmt::format("{}, ", val.data.d);
         else if (val.type == multitype::INT)
@@ -90,7 +90,7 @@ void DumpYAML::write_header(bigint ndump)
 
     fmt::print(fp, "natoms: {}\n", ndump);
     fputs("boundary: [ ", fp);
-    for (const auto bflag : boundary) {
+    for (const auto &bflag : boundary) {
       if (bflag == ' ') continue;
       fmt::print(fp, "{}, ", bflag);
     }
diff --git a/src/NETCDF/dump_netcdf.cpp b/src/NETCDF/dump_netcdf.cpp
index cb6aea16cf..8c99ff1f70 100644
--- a/src/NETCDF/dump_netcdf.cpp
+++ b/src/NETCDF/dump_netcdf.cpp
@@ -320,7 +320,7 @@ void DumpNetCDF::openfile()
 
       // perframe variables
       if (thermo) {
-        auto keywords = output->thermo->get_keywords();
+        const auto &keywords = output->thermo->get_keywords();
         int nfield = keywords.size();
         for (int i = 0; i < nfield; i++) {
           NCERRX( nc_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
@@ -433,8 +433,8 @@ void DumpNetCDF::openfile()
 
       // perframe variables
       if (thermo) {
-        auto fields = output->thermo->get_fields();
-        auto keywords = output->thermo->get_keywords();
+        const auto &fields = output->thermo->get_fields();
+        const auto &keywords = output->thermo->get_keywords();
         int nfield = fields.size();
         for (int i = 0; i < nfield; i++) {
           if (fields[i].type == multitype::DOUBLE) {
@@ -600,8 +600,8 @@ void DumpNetCDF::write()
   start[1] = 0;
 
   if (thermo) {
-    auto keywords = output->thermo->get_keywords();
-    auto fields = output->thermo->get_fields();
+    const auto &keywords = output->thermo->get_keywords();
+    const auto &fields = output->thermo->get_fields();
     int nfield = fields.size();
     for (int i = 0; i < nfield; i++) {
       if (filewriter) {
diff --git a/src/NETCDF/dump_netcdf_mpiio.cpp b/src/NETCDF/dump_netcdf_mpiio.cpp
index fdcd03470e..3aec34dd40 100644
--- a/src/NETCDF/dump_netcdf_mpiio.cpp
+++ b/src/NETCDF/dump_netcdf_mpiio.cpp
@@ -318,7 +318,7 @@ void DumpNetCDFMPIIO::openfile()
 
     // perframe variables
     if (thermo) {
-      auto keywords = output->thermo->get_keywords();
+      const auto &keywords = output->thermo->get_keywords();
       int nfield = keywords.size();
       for (int i = 0; i < nfield; i++) {
         NCERRX( ncmpi_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
@@ -423,8 +423,8 @@ void DumpNetCDFMPIIO::openfile()
 
     // perframe variables
     if (thermo) {
-      auto fields = output->thermo->get_fields();
-      auto keywords = output->thermo->get_keywords();
+      const auto &fields = output->thermo->get_fields();
+      const auto &keywords = output->thermo->get_keywords();
       int nfield = fields.size();
       for (int i = 0; i < nfield; i++) {
         if (fields[i].type == multitype::DOUBLE) {
@@ -593,8 +593,8 @@ void DumpNetCDFMPIIO::write()
   NCERR( ncmpi_begin_indep_data(ncid) );
 
   if (thermo) {
-    auto keywords = output->thermo->get_keywords();
-    auto fields = output->thermo->get_fields();
+    const auto &keywords = output->thermo->get_keywords();
+    const auto &fields = output->thermo->get_fields();
     int nfield = fields.size();
     for (int i = 0; i < nfield; i++) {
       if (filewriter) {

From b7afe412dc939876b0165eaa7325c8bed9e0e56c Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Wed, 7 Jun 2023 13:08:46 -0600
Subject: [PATCH 203/396] Updating SDPD examples

---
 .../2d-diffusion-in-shear-flow/in.lammps      |   6 +-
 ...g.24Oct18.2d-diffusion-in-shear-flow.g++.1 | 247 -----------------
 ...g.24Oct18.2d-diffusion-in-shear-flow.g++.4 | 247 -----------------
 ...g.28Mar23.2d-diffusion-in-shear-flow.g++.1 | 253 ++++++++++++++++++
 ...g.28Mar23.2d-diffusion-in-shear-flow.g++.4 | 253 ++++++++++++++++++
 .../dpd-smooth/2d-diffusion/in.lammps         |   6 +-
 .../log.24Oct18.2d-diffusion.g++.1            | 226 ----------------
 .../log.24Oct18.2d-diffusion.g++.4            | 226 ----------------
 .../log.28Mar23.2d-diffusion.g++.1            | 230 ++++++++++++++++
 .../log.28Mar23.2d-diffusion.g++.4            | 230 ++++++++++++++++
 .../equipartition-verification/in.lammps      |   6 +-
 ....g++.1 => log.28Mar23.equipartition.g++.1} |  91 ++++---
 ....g++.4 => log.28Mar23.equipartition.g++.4} |  91 ++++---
 13 files changed, 1069 insertions(+), 1043 deletions(-)
 delete mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1
 delete mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4
 create mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.1
 create mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.4
 delete mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.1
 delete mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.4
 create mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.1
 create mode 100644 examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.4
 rename examples/PACKAGES/dpd-smooth/equipartition-verification/{log.24Oct18.equipartition.g++.1 => log.28Mar23.equipartition.g++.1} (58%)
 rename examples/PACKAGES/dpd-smooth/equipartition-verification/{log.24Oct18.equipartition.g++.4 => log.28Mar23.equipartition.g++.4} (58%)

diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps
index 138f7b5338..dd50a5e69f 100644
--- a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps
+++ b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps
@@ -1,6 +1,6 @@
 dimension       2
 units           micro
-atom_style      meso
+atom_style      sph
 
 variable        R equal 0.5             # radius of sphere          micrometers
 variable        a equal $R/5            # lattice spacing           micrometers
@@ -37,12 +37,12 @@ group           upper_wall type 3
 group           lower_wall type 4
 
 mass            * ${mass}
-set             group all meso/rho ${rho_0}
+set             group all sph/rho ${rho_0}
 
 pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
 pair_coeff      * * ${rho_0} ${c_0} ${h}
 
-fix             1 fluid meso
+fix             1 fluid sph
 fix             2 sphere rigid/meso single
 fix             3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
 fix             4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1
deleted file mode 100644
index cd01601292..0000000000
--- a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1
+++ /dev/null
@@ -1,247 +0,0 @@
-LAMMPS (24 Oct 2018)
-dimension       2
-units           micro
-atom_style      meso
-
-variable        R equal 0.5             # radius of sphere          micrometers
-variable        a equal $R/5            # lattice spacing           micrometers
-variable        a equal 0.5/5            
-variable        Lf equal $R*3
-variable        Lf equal 0.5*3
-variable        Lb equal $R*4
-variable        Lb equal 0.5*4
-variable        wall_velocity equal 0.01                          # micrometers/microsecond
-variable        T equal 300.
-variable        rho_0 equal 1.          # density                   picograms/micrometer^3
-variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
-variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
-variable        h equal $a*4.5          # kernel function cutoff    micrometers
-variable        h equal 0.1*4.5          
-variable        mass equal $a*$a*$a*${rho_0}
-variable        mass equal 0.1*$a*$a*${rho_0}
-variable        mass equal 0.1*0.1*$a*${rho_0}
-variable        mass equal 0.1*0.1*0.1*${rho_0}
-variable        mass equal 0.1*0.1*0.1*1
-variable        dt equal 1e-3           # timestep                  microseconds
-variable        skin equal 0.2*$h
-variable        skin equal 0.2*0.45
-
-region          box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
-region          box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
-region          box block -2 2 -${Lb} ${Lb} 0 ${a} units box
-region          box block -2 2 -2 ${Lb} 0 ${a} units box
-region          box block -2 2 -2 2 0 ${a} units box
-region          box block -2 2 -2 2 0 0.1 units box
-create_box      4 box
-Created orthogonal box = (-2 -2 0) to (2 2 0.1)
-  1 by 1 by 1 MPI processor grid
-lattice         sq $a
-lattice         sq 0.1
-Lattice spacing in x,y,z = 0.1 0.1 0.1
-
-create_atoms    1 box
-Created 1600 atoms
-  Time spent = 0.00169706 secs
-
-region          sphere sphere 0 0 0 $R units box
-region          sphere sphere 0 0 0 0.5 units box
-set             region sphere type 2
-  81 settings made for type
-
-region          upper_wall block INF INF +${Lf} INF INF INF units box
-region          upper_wall block INF INF +1.5 INF INF INF units box
-set             region upper_wall type 3
-  200 settings made for type
-
-region          lower_wall block INF INF INF -${Lf} INF INF units box
-region          lower_wall block INF INF INF -1.5 INF INF units box
-set             region lower_wall type 4
-  240 settings made for type
-
-group           fluid type 1
-1079 atoms in group fluid
-group           sphere type 2
-81 atoms in group sphere
-group           upper_wall type 3
-200 atoms in group upper_wall
-group           lower_wall type 4
-240 atoms in group lower_wall
-
-mass            * ${mass}
-mass            * 0.001
-set             group all meso/rho ${rho_0}
-set             group all meso/rho 1
-  1600 settings made for meso/rho
-
-pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
-pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
-pair_style      sdpd/taitwater/isothermal 300 1 76787    
-pair_coeff      * * ${rho_0} ${c_0} ${h}
-pair_coeff      * * 1 ${c_0} ${h}
-pair_coeff      * * 1 100 ${h}
-pair_coeff      * * 1 100 0.45
-
-fix             1 fluid meso
-fix             2 sphere rigid/meso single
-1 rigid bodies with 81 atoms
-fix             3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
-fix             3 upper_wall meso/move linear +0.01 0 0 units box
-fix             4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
-fix             4 lower_wall meso/move linear -0.01 0 0 units box
-
-fix             2d all enforce2d
-
-neighbor        ${skin} bin
-neighbor        0.09 bin
-neigh_modify	delay 0 every 1 check yes
-timestep        ${dt}
-timestep        0.001
-
-dump            dump_id all atom 100 dump.lammpstrj
-
-thermo          100
-thermo_style    custom step time nbuild ndanger
-
-run             10000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 0.54
-  ghost atom cutoff = 0.54
-  binsize = 0.27, bins = 15 15 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair sdpd/taitwater/isothermal, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.937 | 6.937 | 6.937 Mbytes
-Step Time Nbuild Ndanger 
-       0            0        0        0 
-     100          0.1        0        0 
-     200          0.2        0        0 
-     300          0.3        0        0 
-     400          0.4        0        0 
-     500          0.5        1        0 
-     600          0.6        1        0 
-     700          0.7        2        0 
-     800          0.8        2        0 
-     900          0.9        2        0 
-    1000            1        3        0 
-    1100          1.1        3        0 
-    1200          1.2        3        0 
-    1300          1.3        4        0 
-    1400          1.4        4        0 
-    1500          1.5        4        0 
-    1600          1.6        5        0 
-    1700          1.7        5        0 
-    1800          1.8        5        0 
-    1900          1.9        6        0 
-    2000            2        6        0 
-    2100          2.1        6        0 
-    2200          2.2        7        0 
-    2300          2.3        7        0 
-    2400          2.4        7        0 
-    2500          2.5        8        0 
-    2600          2.6        8        0 
-    2700          2.7        8        0 
-    2800          2.8        9        0 
-    2900          2.9        9        0 
-    3000            3        9        0 
-    3100          3.1       10        0 
-    3200          3.2       10        0 
-    3300          3.3       10        0 
-    3400          3.4       11        0 
-    3500          3.5       11        0 
-    3600          3.6       11        0 
-    3700          3.7       12        0 
-    3800          3.8       12        0 
-    3900          3.9       12        0 
-    4000            4       13        0 
-    4100          4.1       13        0 
-    4200          4.2       14        0 
-    4300          4.3       14        0 
-    4400          4.4       14        0 
-    4500          4.5       15        0 
-    4600          4.6       15        0 
-    4700          4.7       15        0 
-    4800          4.8       16        0 
-    4900          4.9       16        0 
-    5000            5       16        0 
-    5100          5.1       17        0 
-    5200          5.2       17        0 
-    5300          5.3       17        0 
-    5400          5.4       17        0 
-    5500          5.5       18        0 
-    5600          5.6       18        0 
-    5700          5.7       19        0 
-    5800          5.8       19        0 
-    5900          5.9       19        0 
-    6000            6       20        0 
-    6100          6.1       20        0 
-    6200          6.2       21        0 
-    6300          6.3       21        0 
-    6400          6.4       21        0 
-    6500          6.5       22        0 
-    6600          6.6       22        0 
-    6700          6.7       22        0 
-    6800          6.8       23        0 
-    6900          6.9       23        0 
-    7000            7       23        0 
-    7100          7.1       24        0 
-    7200          7.2       24        0 
-    7300          7.3       25        0 
-    7400          7.4       25        0 
-    7500          7.5       25        0 
-    7600          7.6       26        0 
-    7700          7.7       26        0 
-    7800          7.8       26        0 
-    7900          7.9       27        0 
-    8000            8       27        0 
-    8100          8.1       27        0 
-    8200          8.2       28        0 
-    8300          8.3       28        0 
-    8400          8.4       28        0 
-    8500          8.5       29        0 
-    8600          8.6       29        0 
-    8700          8.7       30        0 
-    8800          8.8       30        0 
-    8900          8.9       30        0 
-    9000            9       31        0 
-    9100          9.1       31        0 
-    9200          9.2       31        0 
-    9300          9.3       32        0 
-    9400          9.4       32        0 
-    9500          9.5       32        0 
-    9600          9.6       33        0 
-    9700          9.7       33        0 
-    9800          9.8       33        0 
-    9900          9.9       34        0 
-   10000           10       34        0 
-Loop time of 144.208 on 1 procs for 10000 steps with 1600 atoms
-
-Performance: 5991348.580 ns/day, 0.000 hours/ns, 69.344 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 143.08     | 143.08     | 143.08     |   0.0 | 99.22
-Neigh   | 0.033195   | 0.033195   | 0.033195   |   0.0 |  0.02
-Comm    | 0.24139    | 0.24139    | 0.24139    |   0.0 |  0.17
-Output  | 0.11687    | 0.11687    | 0.11687    |   0.0 |  0.08
-Modify  | 0.61566    | 0.61566    | 0.61566    |   0.0 |  0.43
-Other   |            | 0.117      |            |       |  0.08
-
-Nlocal:    1600 ave 1600 max 1600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    993 ave 993 max 993 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    73236 ave 73236 max 73236 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 73236
-Ave neighs/atom = 45.7725
-Neighbor list builds = 34
-Dangerous builds = 0
-Total wall time: 0:02:24
diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4
deleted file mode 100644
index 77823e00fc..0000000000
--- a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4
+++ /dev/null
@@ -1,247 +0,0 @@
-LAMMPS (24 Oct 2018)
-dimension       2
-units           micro
-atom_style      meso
-
-variable        R equal 0.5             # radius of sphere          micrometers
-variable        a equal $R/5            # lattice spacing           micrometers
-variable        a equal 0.5/5            
-variable        Lf equal $R*3
-variable        Lf equal 0.5*3
-variable        Lb equal $R*4
-variable        Lb equal 0.5*4
-variable        wall_velocity equal 0.01                          # micrometers/microsecond
-variable        T equal 300.
-variable        rho_0 equal 1.          # density                   picograms/micrometer^3
-variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
-variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
-variable        h equal $a*4.5          # kernel function cutoff    micrometers
-variable        h equal 0.1*4.5          
-variable        mass equal $a*$a*$a*${rho_0}
-variable        mass equal 0.1*$a*$a*${rho_0}
-variable        mass equal 0.1*0.1*$a*${rho_0}
-variable        mass equal 0.1*0.1*0.1*${rho_0}
-variable        mass equal 0.1*0.1*0.1*1
-variable        dt equal 1e-3           # timestep                  microseconds
-variable        skin equal 0.2*$h
-variable        skin equal 0.2*0.45
-
-region          box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
-region          box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
-region          box block -2 2 -${Lb} ${Lb} 0 ${a} units box
-region          box block -2 2 -2 ${Lb} 0 ${a} units box
-region          box block -2 2 -2 2 0 ${a} units box
-region          box block -2 2 -2 2 0 0.1 units box
-create_box      4 box
-Created orthogonal box = (-2 -2 0) to (2 2 0.1)
-  2 by 2 by 1 MPI processor grid
-lattice         sq $a
-lattice         sq 0.1
-Lattice spacing in x,y,z = 0.1 0.1 0.1
-
-create_atoms    1 box
-Created 1600 atoms
-  Time spent = 0.000589566 secs
-
-region          sphere sphere 0 0 0 $R units box
-region          sphere sphere 0 0 0 0.5 units box
-set             region sphere type 2
-  81 settings made for type
-
-region          upper_wall block INF INF +${Lf} INF INF INF units box
-region          upper_wall block INF INF +1.5 INF INF INF units box
-set             region upper_wall type 3
-  200 settings made for type
-
-region          lower_wall block INF INF INF -${Lf} INF INF units box
-region          lower_wall block INF INF INF -1.5 INF INF units box
-set             region lower_wall type 4
-  240 settings made for type
-
-group           fluid type 1
-1079 atoms in group fluid
-group           sphere type 2
-81 atoms in group sphere
-group           upper_wall type 3
-200 atoms in group upper_wall
-group           lower_wall type 4
-240 atoms in group lower_wall
-
-mass            * ${mass}
-mass            * 0.001
-set             group all meso/rho ${rho_0}
-set             group all meso/rho 1
-  1600 settings made for meso/rho
-
-pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
-pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
-pair_style      sdpd/taitwater/isothermal 300 1 76787    
-pair_coeff      * * ${rho_0} ${c_0} ${h}
-pair_coeff      * * 1 ${c_0} ${h}
-pair_coeff      * * 1 100 ${h}
-pair_coeff      * * 1 100 0.45
-
-fix             1 fluid meso
-fix             2 sphere rigid/meso single
-1 rigid bodies with 81 atoms
-fix             3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
-fix             3 upper_wall meso/move linear +0.01 0 0 units box
-fix             4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
-fix             4 lower_wall meso/move linear -0.01 0 0 units box
-
-fix             2d all enforce2d
-
-neighbor        ${skin} bin
-neighbor        0.09 bin
-neigh_modify	delay 0 every 1 check yes
-timestep        ${dt}
-timestep        0.001
-
-dump            dump_id all atom 100 dump.lammpstrj
-
-thermo          100
-thermo_style    custom step time nbuild ndanger
-
-run             10000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 0.54
-  ghost atom cutoff = 0.54
-  binsize = 0.27, bins = 15 15 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair sdpd/taitwater/isothermal, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.854 | 6.854 | 6.854 Mbytes
-Step Time Nbuild Ndanger 
-       0            0        0        0 
-     100          0.1        0        0 
-     200          0.2        0        0 
-     300          0.3        0        0 
-     400          0.4        1        0 
-     500          0.5        1        0 
-     600          0.6        1        0 
-     700          0.7        2        0 
-     800          0.8        2        0 
-     900          0.9        2        0 
-    1000            1        3        0 
-    1100          1.1        3        0 
-    1200          1.2        4        0 
-    1300          1.3        4        0 
-    1400          1.4        4        0 
-    1500          1.5        4        0 
-    1600          1.6        5        0 
-    1700          1.7        5        0 
-    1800          1.8        5        0 
-    1900          1.9        6        0 
-    2000            2        6        0 
-    2100          2.1        6        0 
-    2200          2.2        6        0 
-    2300          2.3        7        0 
-    2400          2.4        7        0 
-    2500          2.5        7        0 
-    2600          2.6        8        0 
-    2700          2.7        8        0 
-    2800          2.8        8        0 
-    2900          2.9        9        0 
-    3000            3        9        0 
-    3100          3.1        9        0 
-    3200          3.2       10        0 
-    3300          3.3       10        0 
-    3400          3.4       10        0 
-    3500          3.5       11        0 
-    3600          3.6       11        0 
-    3700          3.7       11        0 
-    3800          3.8       12        0 
-    3900          3.9       12        0 
-    4000            4       12        0 
-    4100          4.1       13        0 
-    4200          4.2       13        0 
-    4300          4.3       13        0 
-    4400          4.4       14        0 
-    4500          4.5       14        0 
-    4600          4.6       15        0 
-    4700          4.7       15        0 
-    4800          4.8       15        0 
-    4900          4.9       16        0 
-    5000            5       16        0 
-    5100          5.1       17        0 
-    5200          5.2       17        0 
-    5300          5.3       17        0 
-    5400          5.4       17        0 
-    5500          5.5       18        0 
-    5600          5.6       18        0 
-    5700          5.7       18        0 
-    5800          5.8       19        0 
-    5900          5.9       19        0 
-    6000            6       20        0 
-    6100          6.1       20        0 
-    6200          6.2       20        0 
-    6300          6.3       21        0 
-    6400          6.4       21        0 
-    6500          6.5       21        0 
-    6600          6.6       22        0 
-    6700          6.7       22        0 
-    6800          6.8       22        0 
-    6900          6.9       23        0 
-    7000            7       23        0 
-    7100          7.1       23        0 
-    7200          7.2       24        0 
-    7300          7.3       24        0 
-    7400          7.4       25        0 
-    7500          7.5       25        0 
-    7600          7.6       25        0 
-    7700          7.7       25        0 
-    7800          7.8       26        0 
-    7900          7.9       26        0 
-    8000            8       26        0 
-    8100          8.1       27        0 
-    8200          8.2       27        0 
-    8300          8.3       27        0 
-    8400          8.4       28        0 
-    8500          8.5       28        0 
-    8600          8.6       28        0 
-    8700          8.7       29        0 
-    8800          8.8       29        0 
-    8900          8.9       29        0 
-    9000            9       30        0 
-    9100          9.1       30        0 
-    9200          9.2       31        0 
-    9300          9.3       31        0 
-    9400          9.4       31        0 
-    9500          9.5       32        0 
-    9600          9.6       32        0 
-    9700          9.7       32        0 
-    9800          9.8       32        0 
-    9900          9.9       33        0 
-   10000           10       33        0 
-Loop time of 63.2372 on 4 procs for 10000 steps with 1600 atoms
-
-Performance: 13662841.706 ns/day, 0.000 hours/ns, 158.135 timesteps/s
-94.3% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 51.576     | 53.662     | 55.484     |  23.9 | 84.86
-Neigh   | 0.011519   | 0.012395   | 0.013405   |   0.7 |  0.02
-Comm    | 6.8389     | 8.5423     | 10.517     |  56.1 | 13.51
-Output  | 0.12342    | 0.12513    | 0.1302     |   0.8 |  0.20
-Modify  | 0.58708    | 0.69128    | 0.78806    |  11.3 |  1.09
-Other   |            | 0.2038     |            |       |  0.32
-
-Nlocal:    400 ave 411 max 388 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Nghost:    552.25 ave 567 max 539 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs:    18298.8 ave 18781 max 17829 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 73195
-Ave neighs/atom = 45.7469
-Neighbor list builds = 33
-Dangerous builds = 0
-Total wall time: 0:01:03
diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.1 b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.1
new file mode 100644
index 0000000000..c4c11205e1
--- /dev/null
+++ b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.1
@@ -0,0 +1,253 @@
+LAMMPS (28 Mar 2023 - Development)
+dimension       2
+units           micro
+atom_style      sph
+
+variable        R equal 0.5             # radius of sphere          micrometers
+variable        a equal $R/5            # lattice spacing           micrometers
+variable        a equal 0.5/5            
+variable        Lf equal $R*3
+variable        Lf equal 0.5*3
+variable        Lb equal $R*4
+variable        Lb equal 0.5*4
+variable        wall_velocity equal 0.01                          # micrometers/microsecond
+variable        T equal 300.
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.5          # kernel function cutoff    micrometers
+variable        h equal 0.1*4.5          
+variable        mass equal $a*$a*$a*${rho_0}
+variable        mass equal 0.1*$a*$a*${rho_0}
+variable        mass equal 0.1*0.1*$a*${rho_0}
+variable        mass equal 0.1*0.1*0.1*${rho_0}
+variable        mass equal 0.1*0.1*0.1*1
+variable        dt equal 1e-3           # timestep                  microseconds
+variable        skin equal 0.2*$h
+variable        skin equal 0.2*0.45
+
+region          box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 2 -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 2 -2 ${Lb} 0 ${a} units box
+region          box block -2 2 -2 2 0 ${a} units box
+region          box block -2 2 -2 2 0 0.1 units box
+create_box      4 box
+Created orthogonal box = (-2 -2 0) to (2 2 0.1)
+  1 by 1 by 1 MPI processor grid
+lattice         sq $a
+lattice         sq 0.1
+Lattice spacing in x,y,z = 0.1 0.1 0.1
+
+create_atoms    1 box
+Created 1600 atoms
+  using lattice units in orthogonal box = (-2 -2 0) to (2 2 0.1)
+  create_atoms CPU = 0.001 seconds
+
+region          sphere sphere 0 0 0 $R units box
+region          sphere sphere 0 0 0 0.5 units box
+set             region sphere type 2
+Setting atom values ...
+  81 settings made for type
+
+region          upper_wall block INF INF +${Lf} INF INF INF units box
+region          upper_wall block INF INF +1.5 INF INF INF units box
+set             region upper_wall type 3
+Setting atom values ...
+  200 settings made for type
+
+region          lower_wall block INF INF INF -${Lf} INF INF units box
+region          lower_wall block INF INF INF -1.5 INF INF units box
+set             region lower_wall type 4
+Setting atom values ...
+  240 settings made for type
+
+group           fluid type 1
+1079 atoms in group fluid
+group           sphere type 2
+81 atoms in group sphere
+group           upper_wall type 3
+200 atoms in group upper_wall
+group           lower_wall type 4
+240 atoms in group lower_wall
+
+mass            * ${mass}
+mass            * 0.001
+set             group all sph/rho ${rho_0}
+set             group all sph/rho 1
+Setting atom values ...
+  1600 settings made for sph/rho
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
+pair_style      sdpd/taitwater/isothermal 300 1 76787    
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+pair_coeff      * * 1 ${c_0} ${h}
+pair_coeff      * * 1 100 ${h}
+pair_coeff      * * 1 100 0.45
+
+fix             1 fluid sph
+fix             2 sphere rigid/meso single
+  1 rigid bodies with 81 atoms
+fix             3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
+fix             3 upper_wall meso/move linear +0.01 0 0 units box
+fix             4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
+fix             4 lower_wall meso/move linear -0.01 0 0 units box
+
+fix             2d all enforce2d
+
+neighbor        ${skin} bin
+neighbor        0.09 bin
+neigh_modify	delay 0 every 1 check yes
+timestep        ${dt}
+timestep        0.001
+
+dump            dump_id all atom 100 dump.lammpstrj
+
+thermo          100
+thermo_style    custom step time nbuild ndanger
+
+run             10000
+Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0.54
+  ghost atom cutoff = 0.54
+  binsize = 0.27, bins = 15 15 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sdpd/taitwater/isothermal, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.313 | 7.313 Mbytes
+   Step          Time        Nbuild      Ndanger  
+         0   0                      0           0 
+       100   0.1                    0           0 
+       200   0.2                    0           0 
+       300   0.3                    0           0 
+       400   0.4                    0           0 
+       500   0.5                    1           0 
+       600   0.6                    1           0 
+       700   0.7                    2           0 
+       800   0.8                    2           0 
+       900   0.9                    2           0 
+      1000   1                      3           0 
+      1100   1.1                    3           0 
+      1200   1.2                    3           0 
+      1300   1.3                    4           0 
+      1400   1.4                    4           0 
+      1500   1.5                    4           0 
+      1600   1.6                    5           0 
+      1700   1.7                    5           0 
+      1800   1.8                    5           0 
+      1900   1.9                    6           0 
+      2000   2                      6           0 
+      2100   2.1                    6           0 
+      2200   2.2                    7           0 
+      2300   2.3                    7           0 
+      2400   2.4                    7           0 
+      2500   2.5                    8           0 
+      2600   2.6                    8           0 
+      2700   2.7                    8           0 
+      2800   2.8                    9           0 
+      2900   2.9                    9           0 
+      3000   3                      9           0 
+      3100   3.1                   10           0 
+      3200   3.2                   10           0 
+      3300   3.3                   10           0 
+      3400   3.4                   11           0 
+      3500   3.5                   11           0 
+      3600   3.6                   11           0 
+      3700   3.7                   12           0 
+      3800   3.8                   12           0 
+      3900   3.9                   12           0 
+      4000   4                     13           0 
+      4100   4.1                   13           0 
+      4200   4.2                   14           0 
+      4300   4.3                   14           0 
+      4400   4.4                   14           0 
+      4500   4.5                   15           0 
+      4600   4.6                   15           0 
+      4700   4.7                   15           0 
+      4800   4.8                   16           0 
+      4900   4.9                   16           0 
+      5000   5                     16           0 
+      5100   5.1                   17           0 
+      5200   5.2                   17           0 
+      5300   5.3                   17           0 
+      5400   5.4                   17           0 
+      5500   5.5                   18           0 
+      5600   5.6                   18           0 
+      5700   5.7                   19           0 
+      5800   5.8                   19           0 
+      5900   5.9                   19           0 
+      6000   6                     20           0 
+      6100   6.1                   20           0 
+      6200   6.2                   21           0 
+      6300   6.3                   21           0 
+      6400   6.4                   21           0 
+      6500   6.5                   22           0 
+      6600   6.6                   22           0 
+      6700   6.7                   22           0 
+      6800   6.8                   23           0 
+      6900   6.9                   23           0 
+      7000   7                     23           0 
+      7100   7.1                   24           0 
+      7200   7.2                   24           0 
+      7300   7.3                   25           0 
+      7400   7.4                   25           0 
+      7500   7.5                   25           0 
+      7600   7.6                   26           0 
+      7700   7.7                   26           0 
+      7800   7.8                   26           0 
+      7900   7.9                   27           0 
+      8000   8                     27           0 
+      8100   8.1                   27           0 
+      8200   8.2                   28           0 
+      8300   8.3                   28           0 
+      8400   8.4                   28           0 
+      8500   8.5                   29           0 
+      8600   8.6                   29           0 
+      8700   8.7                   30           0 
+      8800   8.8                   30           0 
+      8900   8.9                   30           0 
+      9000   9                     31           0 
+      9100   9.1                   31           0 
+      9200   9.2                   31           0 
+      9300   9.3                   32           0 
+      9400   9.4                   32           0 
+      9500   9.5                   32           0 
+      9600   9.6                   33           0 
+      9700   9.7                   33           0 
+      9800   9.8                   33           0 
+      9900   9.9                   34           0 
+     10000   10                    34           0 
+Loop time of 131.724 on 1 procs for 10000 steps with 1600 atoms
+
+Performance: 6559168.339 ns/day, 0.000 hours/ns, 75.916 timesteps/s, 121.466 katom-step/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 130.89     | 130.89     | 130.89     |   0.0 | 99.37
+Neigh   | 0.02884    | 0.02884    | 0.02884    |   0.0 |  0.02
+Comm    | 0.17863    | 0.17863    | 0.17863    |   0.0 |  0.14
+Output  | 0.095497   | 0.095497   | 0.095497   |   0.0 |  0.07
+Modify  | 0.42063    | 0.42063    | 0.42063    |   0.0 |  0.32
+Other   |            | 0.1069     |            |       |  0.08
+
+Nlocal:           1600 ave        1600 max        1600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            993 ave         993 max         993 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          73236 ave       73236 max       73236 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 73236
+Ave neighs/atom = 45.7725
+Neighbor list builds = 34
+Dangerous builds = 0
+Total wall time: 0:02:11
diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.4 b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.4
new file mode 100644
index 0000000000..6cb58bc233
--- /dev/null
+++ b/examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.4
@@ -0,0 +1,253 @@
+LAMMPS (28 Mar 2023 - Development)
+dimension       2
+units           micro
+atom_style      sph
+
+variable        R equal 0.5             # radius of sphere          micrometers
+variable        a equal $R/5            # lattice spacing           micrometers
+variable        a equal 0.5/5            
+variable        Lf equal $R*3
+variable        Lf equal 0.5*3
+variable        Lb equal $R*4
+variable        Lb equal 0.5*4
+variable        wall_velocity equal 0.01                          # micrometers/microsecond
+variable        T equal 300.
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.5          # kernel function cutoff    micrometers
+variable        h equal 0.1*4.5          
+variable        mass equal $a*$a*$a*${rho_0}
+variable        mass equal 0.1*$a*$a*${rho_0}
+variable        mass equal 0.1*0.1*$a*${rho_0}
+variable        mass equal 0.1*0.1*0.1*${rho_0}
+variable        mass equal 0.1*0.1*0.1*1
+variable        dt equal 1e-3           # timestep                  microseconds
+variable        skin equal 0.2*$h
+variable        skin equal 0.2*0.45
+
+region          box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 2 -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 2 -2 ${Lb} 0 ${a} units box
+region          box block -2 2 -2 2 0 ${a} units box
+region          box block -2 2 -2 2 0 0.1 units box
+create_box      4 box
+Created orthogonal box = (-2 -2 0) to (2 2 0.1)
+  2 by 2 by 1 MPI processor grid
+lattice         sq $a
+lattice         sq 0.1
+Lattice spacing in x,y,z = 0.1 0.1 0.1
+
+create_atoms    1 box
+Created 1600 atoms
+  using lattice units in orthogonal box = (-2 -2 0) to (2 2 0.1)
+  create_atoms CPU = 0.001 seconds
+
+region          sphere sphere 0 0 0 $R units box
+region          sphere sphere 0 0 0 0.5 units box
+set             region sphere type 2
+Setting atom values ...
+  81 settings made for type
+
+region          upper_wall block INF INF +${Lf} INF INF INF units box
+region          upper_wall block INF INF +1.5 INF INF INF units box
+set             region upper_wall type 3
+Setting atom values ...
+  200 settings made for type
+
+region          lower_wall block INF INF INF -${Lf} INF INF units box
+region          lower_wall block INF INF INF -1.5 INF INF units box
+set             region lower_wall type 4
+Setting atom values ...
+  240 settings made for type
+
+group           fluid type 1
+1079 atoms in group fluid
+group           sphere type 2
+81 atoms in group sphere
+group           upper_wall type 3
+200 atoms in group upper_wall
+group           lower_wall type 4
+240 atoms in group lower_wall
+
+mass            * ${mass}
+mass            * 0.001
+set             group all sph/rho ${rho_0}
+set             group all sph/rho 1
+Setting atom values ...
+  1600 settings made for sph/rho
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
+pair_style      sdpd/taitwater/isothermal 300 1 76787    
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+pair_coeff      * * 1 ${c_0} ${h}
+pair_coeff      * * 1 100 ${h}
+pair_coeff      * * 1 100 0.45
+
+fix             1 fluid sph
+fix             2 sphere rigid/meso single
+  1 rigid bodies with 81 atoms
+fix             3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
+fix             3 upper_wall meso/move linear +0.01 0 0 units box
+fix             4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
+fix             4 lower_wall meso/move linear -0.01 0 0 units box
+
+fix             2d all enforce2d
+
+neighbor        ${skin} bin
+neighbor        0.09 bin
+neigh_modify	delay 0 every 1 check yes
+timestep        ${dt}
+timestep        0.001
+
+dump            dump_id all atom 100 dump.lammpstrj
+
+thermo          100
+thermo_style    custom step time nbuild ndanger
+
+run             10000
+Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0.54
+  ghost atom cutoff = 0.54
+  binsize = 0.27, bins = 15 15 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sdpd/taitwater/isothermal, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.23 | 7.23 | 7.23 Mbytes
+   Step          Time        Nbuild      Ndanger  
+         0   0                      0           0 
+       100   0.1                    0           0 
+       200   0.2                    0           0 
+       300   0.3                    0           0 
+       400   0.4                    1           0 
+       500   0.5                    1           0 
+       600   0.6                    1           0 
+       700   0.7                    2           0 
+       800   0.8                    2           0 
+       900   0.9                    2           0 
+      1000   1                      3           0 
+      1100   1.1                    3           0 
+      1200   1.2                    3           0 
+      1300   1.3                    4           0 
+      1400   1.4                    4           0 
+      1500   1.5                    4           0 
+      1600   1.6                    5           0 
+      1700   1.7                    5           0 
+      1800   1.8                    5           0 
+      1900   1.9                    6           0 
+      2000   2                      6           0 
+      2100   2.1                    6           0 
+      2200   2.2                    7           0 
+      2300   2.3                    7           0 
+      2400   2.4                    7           0 
+      2500   2.5                    8           0 
+      2600   2.6                    8           0 
+      2700   2.7                    8           0 
+      2800   2.8                    9           0 
+      2900   2.9                    9           0 
+      3000   3                      9           0 
+      3100   3.1                   10           0 
+      3200   3.2                   10           0 
+      3300   3.3                   10           0 
+      3400   3.4                   11           0 
+      3500   3.5                   11           0 
+      3600   3.6                   11           0 
+      3700   3.7                   12           0 
+      3800   3.8                   12           0 
+      3900   3.9                   12           0 
+      4000   4                     13           0 
+      4100   4.1                   13           0 
+      4200   4.2                   13           0 
+      4300   4.3                   14           0 
+      4400   4.4                   14           0 
+      4500   4.5                   14           0 
+      4600   4.6                   14           0 
+      4700   4.7                   15           0 
+      4800   4.8                   15           0 
+      4900   4.9                   16           0 
+      5000   5                     16           0 
+      5100   5.1                   16           0 
+      5200   5.2                   17           0 
+      5300   5.3                   17           0 
+      5400   5.4                   17           0 
+      5500   5.5                   18           0 
+      5600   5.6                   18           0 
+      5700   5.7                   18           0 
+      5800   5.8                   19           0 
+      5900   5.9                   19           0 
+      6000   6                     20           0 
+      6100   6.1                   20           0 
+      6200   6.2                   20           0 
+      6300   6.3                   21           0 
+      6400   6.4                   21           0 
+      6500   6.5                   21           0 
+      6600   6.6                   22           0 
+      6700   6.7                   22           0 
+      6800   6.8                   22           0 
+      6900   6.9                   23           0 
+      7000   7                     23           0 
+      7100   7.1                   23           0 
+      7200   7.2                   24           0 
+      7300   7.3                   24           0 
+      7400   7.4                   24           0 
+      7500   7.5                   25           0 
+      7600   7.6                   25           0 
+      7700   7.7                   25           0 
+      7800   7.8                   25           0 
+      7900   7.9                   26           0 
+      8000   8                     26           0 
+      8100   8.1                   26           0 
+      8200   8.2                   27           0 
+      8300   8.3                   27           0 
+      8400   8.4                   28           0 
+      8500   8.5                   28           0 
+      8600   8.6                   28           0 
+      8700   8.7                   29           0 
+      8800   8.8                   29           0 
+      8900   8.9                   29           0 
+      9000   9                     30           0 
+      9100   9.1                   30           0 
+      9200   9.2                   30           0 
+      9300   9.3                   31           0 
+      9400   9.4                   31           0 
+      9500   9.5                   31           0 
+      9600   9.6                   32           0 
+      9700   9.7                   32           0 
+      9800   9.8                   32           0 
+      9900   9.9                   32           0 
+     10000   10                    33           0 
+Loop time of 24.8261 on 4 procs for 10000 steps with 1600 atoms
+
+Performance: 34802055.618 ns/day, 0.000 hours/ns, 402.802 timesteps/s, 644.483 katom-step/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 21.84      | 22.879     | 23.944     |  21.4 | 92.16
+Neigh   | 0.007446   | 0.0079435  | 0.0084435  |   0.6 |  0.03
+Comm    | 0.5271     | 1.5894     | 2.6259     |  80.9 |  6.40
+Output  | 0.034799   | 0.035302   | 0.036437   |   0.4 |  0.14
+Modify  | 0.20079    | 0.21033    | 0.2202     |   1.7 |  0.85
+Other   |            | 0.1041     |            |       |  0.42
+
+Nlocal:            400 ave         414 max         390 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Nghost:          555.5 ave         564 max         543 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Neighs:        18299.2 ave       18820 max       17906 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 73197
+Ave neighs/atom = 45.748125
+Neighbor list builds = 33
+Dangerous builds = 0
+Total wall time: 0:00:24
diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps b/examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps
index 6ef36a0cf6..2e0e821480 100644
--- a/examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps
+++ b/examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps
@@ -1,6 +1,6 @@
 dimension       2
 units           micro
-atom_style      meso
+atom_style      sph
 
 variable        R equal 0.5             # radius of sphere          micrometers
 variable        a equal $R/5            # lattice spacing           micrometers
@@ -27,12 +27,12 @@ group           fluid type 1
 group           sphere type 2
 
 mass            * ${mass}
-set             group all meso/rho ${rho_0}
+set             group all sph/rho ${rho_0}
 
 pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
 pair_coeff      * * ${rho_0} ${c_0} ${h}
 
-fix             1 fluid meso
+fix             1 fluid sph
 fix             2 sphere rigid/meso single
 
 fix             2d all enforce2d
diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.1
deleted file mode 100644
index d44c0fd6f4..0000000000
--- a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.1
+++ /dev/null
@@ -1,226 +0,0 @@
-LAMMPS (24 Oct 2018)
-dimension       2
-units           micro
-atom_style      meso
-
-variable        R equal 0.5             # radius of sphere          micrometers
-variable        a equal $R/5            # lattice spacing           micrometers
-variable        a equal 0.5/5            
-variable        L equal $R*3
-variable        L equal 0.5*3
-variable        T equal 300.
-variable        rho_0 equal 1.          # density                   picograms/micrometer^3
-variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
-variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
-variable        h equal $a*4.5          # kernel function cutoff    micrometers
-variable        h equal 0.1*4.5          
-variable        mass equal $a*$a*$a*${rho_0}
-variable        mass equal 0.1*$a*$a*${rho_0}
-variable        mass equal 0.1*0.1*$a*${rho_0}
-variable        mass equal 0.1*0.1*0.1*${rho_0}
-variable        mass equal 0.1*0.1*0.1*1
-variable        dt equal 1e-3           # timestep                  microseconds
-variable        skin equal 0.2*$h
-variable        skin equal 0.2*0.45
-
-region          box block -$L $L -$L $L 0 $a units box
-region          box block -1.5 $L -$L $L 0 $a units box
-region          box block -1.5 1.5 -$L $L 0 $a units box
-region          box block -1.5 1.5 -1.5 $L 0 $a units box
-region          box block -1.5 1.5 -1.5 1.5 0 $a units box
-region          box block -1.5 1.5 -1.5 1.5 0 0.1 units box
-create_box      2 box
-Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
-  1 by 1 by 1 MPI processor grid
-lattice         sq $a
-lattice         sq 0.1
-Lattice spacing in x,y,z = 0.1 0.1 0.1
-
-create_atoms    1 box
-Created 900 atoms
-  Time spent = 0.0015769 secs
-
-region          sphere sphere 0 0 0 $R units box
-region          sphere sphere 0 0 0 0.5 units box
-set             region sphere type 2
-  81 settings made for type
-
-group           fluid type 1
-819 atoms in group fluid
-group           sphere type 2
-81 atoms in group sphere
-
-mass            * ${mass}
-mass            * 0.001
-set             group all meso/rho ${rho_0}
-set             group all meso/rho 1
-  900 settings made for meso/rho
-
-pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
-pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
-pair_style      sdpd/taitwater/isothermal 300 1 76787    
-pair_coeff      * * ${rho_0} ${c_0} ${h}
-pair_coeff      * * 1 ${c_0} ${h}
-pair_coeff      * * 1 100 ${h}
-pair_coeff      * * 1 100 0.45
-
-fix             1 fluid meso
-fix             2 sphere rigid/meso single
-1 rigid bodies with 81 atoms
-
-fix             2d all enforce2d
-
-neighbor        ${skin} bin
-neighbor        0.09 bin
-neigh_modify	delay 0 every 1 check yes
-timestep        ${dt}
-timestep        0.001
-
-dump            dump_id all atom 100 dump.lammpstrj
-
-thermo          100
-thermo_style    custom step time nbuild ndanger
-
-run             10000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 0.54
-  ghost atom cutoff = 0.54
-  binsize = 0.27, bins = 12 12 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair sdpd/taitwater/isothermal, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.137 | 6.137 | 6.137 Mbytes
-Step Time Nbuild Ndanger 
-       0            0        0        0 
-     100          0.1        0        0 
-     200          0.2        0        0 
-     300          0.3        0        0 
-     400          0.4        1        0 
-     500          0.5        1        0 
-     600          0.6        1        0 
-     700          0.7        2        0 
-     800          0.8        2        0 
-     900          0.9        2        0 
-    1000            1        3        0 
-    1100          1.1        3        0 
-    1200          1.2        3        0 
-    1300          1.3        4        0 
-    1400          1.4        4        0 
-    1500          1.5        4        0 
-    1600          1.6        5        0 
-    1700          1.7        5        0 
-    1800          1.8        6        0 
-    1900          1.9        6        0 
-    2000            2        6        0 
-    2100          2.1        7        0 
-    2200          2.2        7        0 
-    2300          2.3        7        0 
-    2400          2.4        7        0 
-    2500          2.5        8        0 
-    2600          2.6        8        0 
-    2700          2.7        8        0 
-    2800          2.8        9        0 
-    2900          2.9        9        0 
-    3000            3       10        0 
-    3100          3.1       10        0 
-    3200          3.2       10        0 
-    3300          3.3       11        0 
-    3400          3.4       11        0 
-    3500          3.5       11        0 
-    3600          3.6       12        0 
-    3700          3.7       12        0 
-    3800          3.8       12        0 
-    3900          3.9       13        0 
-    4000            4       13        0 
-    4100          4.1       13        0 
-    4200          4.2       14        0 
-    4300          4.3       14        0 
-    4400          4.4       14        0 
-    4500          4.5       15        0 
-    4600          4.6       15        0 
-    4700          4.7       15        0 
-    4800          4.8       16        0 
-    4900          4.9       16        0 
-    5000            5       17        0 
-    5100          5.1       17        0 
-    5200          5.2       17        0 
-    5300          5.3       17        0 
-    5400          5.4       18        0 
-    5500          5.5       18        0 
-    5600          5.6       18        0 
-    5700          5.7       19        0 
-    5800          5.8       19        0 
-    5900          5.9       19        0 
-    6000            6       19        0 
-    6100          6.1       20        0 
-    6200          6.2       20        0 
-    6300          6.3       20        0 
-    6400          6.4       21        0 
-    6500          6.5       21        0 
-    6600          6.6       21        0 
-    6700          6.7       21        0 
-    6800          6.8       22        0 
-    6900          6.9       22        0 
-    7000            7       22        0 
-    7100          7.1       23        0 
-    7200          7.2       23        0 
-    7300          7.3       23        0 
-    7400          7.4       24        0 
-    7500          7.5       24        0 
-    7600          7.6       24        0 
-    7700          7.7       25        0 
-    7800          7.8       25        0 
-    7900          7.9       26        0 
-    8000            8       26        0 
-    8100          8.1       26        0 
-    8200          8.2       26        0 
-    8300          8.3       27        0 
-    8400          8.4       27        0 
-    8500          8.5       27        0 
-    8600          8.6       28        0 
-    8700          8.7       28        0 
-    8800          8.8       28        0 
-    8900          8.9       29        0 
-    9000            9       29        0 
-    9100          9.1       29        0 
-    9200          9.2       30        0 
-    9300          9.3       30        0 
-    9400          9.4       30        0 
-    9500          9.5       30        0 
-    9600          9.6       31        0 
-    9700          9.7       31        0 
-    9800          9.8       32        0 
-    9900          9.9       32        0 
-   10000           10       32        0 
-Loop time of 80.9456 on 1 procs for 10000 steps with 900 atoms
-
-Performance: 10673829.855 ns/day, 0.000 hours/ns, 123.540 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 80.306     | 80.306     | 80.306     |   0.0 | 99.21
-Neigh   | 0.017418   | 0.017418   | 0.017418   |   0.0 |  0.02
-Comm    | 0.16939    | 0.16939    | 0.16939    |   0.0 |  0.21
-Output  | 0.070281   | 0.070281   | 0.070281   |   0.0 |  0.09
-Modify  | 0.3154     | 0.3154     | 0.3154     |   0.0 |  0.39
-Other   |            | 0.067      |            |       |  0.08
-
-Nlocal:    900 ave 900 max 900 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    762 ave 762 max 762 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    40697 ave 40697 max 40697 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 40697
-Ave neighs/atom = 45.2189
-Neighbor list builds = 32
-Dangerous builds = 0
-Total wall time: 0:01:20
diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.4
deleted file mode 100644
index f904b78ab4..0000000000
--- a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.24Oct18.2d-diffusion.g++.4
+++ /dev/null
@@ -1,226 +0,0 @@
-LAMMPS (24 Oct 2018)
-dimension       2
-units           micro
-atom_style      meso
-
-variable        R equal 0.5             # radius of sphere          micrometers
-variable        a equal $R/5            # lattice spacing           micrometers
-variable        a equal 0.5/5            
-variable        L equal $R*3
-variable        L equal 0.5*3
-variable        T equal 300.
-variable        rho_0 equal 1.          # density                   picograms/micrometer^3
-variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
-variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
-variable        h equal $a*4.5          # kernel function cutoff    micrometers
-variable        h equal 0.1*4.5          
-variable        mass equal $a*$a*$a*${rho_0}
-variable        mass equal 0.1*$a*$a*${rho_0}
-variable        mass equal 0.1*0.1*$a*${rho_0}
-variable        mass equal 0.1*0.1*0.1*${rho_0}
-variable        mass equal 0.1*0.1*0.1*1
-variable        dt equal 1e-3           # timestep                  microseconds
-variable        skin equal 0.2*$h
-variable        skin equal 0.2*0.45
-
-region          box block -$L $L -$L $L 0 $a units box
-region          box block -1.5 $L -$L $L 0 $a units box
-region          box block -1.5 1.5 -$L $L 0 $a units box
-region          box block -1.5 1.5 -1.5 $L 0 $a units box
-region          box block -1.5 1.5 -1.5 1.5 0 $a units box
-region          box block -1.5 1.5 -1.5 1.5 0 0.1 units box
-create_box      2 box
-Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
-  2 by 2 by 1 MPI processor grid
-lattice         sq $a
-lattice         sq 0.1
-Lattice spacing in x,y,z = 0.1 0.1 0.1
-
-create_atoms    1 box
-Created 900 atoms
-  Time spent = 0.0010246 secs
-
-region          sphere sphere 0 0 0 $R units box
-region          sphere sphere 0 0 0 0.5 units box
-set             region sphere type 2
-  81 settings made for type
-
-group           fluid type 1
-819 atoms in group fluid
-group           sphere type 2
-81 atoms in group sphere
-
-mass            * ${mass}
-mass            * 0.001
-set             group all meso/rho ${rho_0}
-set             group all meso/rho 1
-  900 settings made for meso/rho
-
-pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
-pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
-pair_style      sdpd/taitwater/isothermal 300 1 76787    
-pair_coeff      * * ${rho_0} ${c_0} ${h}
-pair_coeff      * * 1 ${c_0} ${h}
-pair_coeff      * * 1 100 ${h}
-pair_coeff      * * 1 100 0.45
-
-fix             1 fluid meso
-fix             2 sphere rigid/meso single
-1 rigid bodies with 81 atoms
-
-fix             2d all enforce2d
-
-neighbor        ${skin} bin
-neighbor        0.09 bin
-neigh_modify	delay 0 every 1 check yes
-timestep        ${dt}
-timestep        0.001
-
-dump            dump_id all atom 100 dump.lammpstrj
-
-thermo          100
-thermo_style    custom step time nbuild ndanger
-
-run             10000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 0.54
-  ghost atom cutoff = 0.54
-  binsize = 0.27, bins = 12 12 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair sdpd/taitwater/isothermal, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.087 | 6.087 | 6.087 Mbytes
-Step Time Nbuild Ndanger 
-       0            0        0        0 
-     100          0.1        0        0 
-     200          0.2        0        0 
-     300          0.3        0        0 
-     400          0.4        1        0 
-     500          0.5        1        0 
-     600          0.6        1        0 
-     700          0.7        2        0 
-     800          0.8        2        0 
-     900          0.9        2        0 
-    1000            1        3        0 
-    1100          1.1        3        0 
-    1200          1.2        3        0 
-    1300          1.3        4        0 
-    1400          1.4        4        0 
-    1500          1.5        5        0 
-    1600          1.6        5        0 
-    1700          1.7        5        0 
-    1800          1.8        6        0 
-    1900          1.9        6        0 
-    2000            2        6        0 
-    2100          2.1        7        0 
-    2200          2.2        7        0 
-    2300          2.3        7        0 
-    2400          2.4        8        0 
-    2500          2.5        8        0 
-    2600          2.6        8        0 
-    2700          2.7        9        0 
-    2800          2.8        9        0 
-    2900          2.9        9        0 
-    3000            3        9        0 
-    3100          3.1       10        0 
-    3200          3.2       10        0 
-    3300          3.3       10        0 
-    3400          3.4       11        0 
-    3500          3.5       11        0 
-    3600          3.6       11        0 
-    3700          3.7       12        0 
-    3800          3.8       12        0 
-    3900          3.9       12        0 
-    4000            4       13        0 
-    4100          4.1       13        0 
-    4200          4.2       13        0 
-    4300          4.3       14        0 
-    4400          4.4       14        0 
-    4500          4.5       15        0 
-    4600          4.6       15        0 
-    4700          4.7       15        0 
-    4800          4.8       16        0 
-    4900          4.9       16        0 
-    5000            5       16        0 
-    5100          5.1       16        0 
-    5200          5.2       17        0 
-    5300          5.3       17        0 
-    5400          5.4       18        0 
-    5500          5.5       18        0 
-    5600          5.6       19        0 
-    5700          5.7       19        0 
-    5800          5.8       19        0 
-    5900          5.9       20        0 
-    6000            6       20        0 
-    6100          6.1       20        0 
-    6200          6.2       21        0 
-    6300          6.3       21        0 
-    6400          6.4       21        0 
-    6500          6.5       22        0 
-    6600          6.6       22        0 
-    6700          6.7       22        0 
-    6800          6.8       23        0 
-    6900          6.9       23        0 
-    7000            7       23        0 
-    7100          7.1       24        0 
-    7200          7.2       24        0 
-    7300          7.3       24        0 
-    7400          7.4       25        0 
-    7500          7.5       25        0 
-    7600          7.6       25        0 
-    7700          7.7       26        0 
-    7800          7.8       26        0 
-    7900          7.9       26        0 
-    8000            8       27        0 
-    8100          8.1       27        0 
-    8200          8.2       27        0 
-    8300          8.3       28        0 
-    8400          8.4       28        0 
-    8500          8.5       28        0 
-    8600          8.6       28        0 
-    8700          8.7       29        0 
-    8800          8.8       29        0 
-    8900          8.9       29        0 
-    9000            9       30        0 
-    9100          9.1       30        0 
-    9200          9.2       31        0 
-    9300          9.3       31        0 
-    9400          9.4       31        0 
-    9500          9.5       31        0 
-    9600          9.6       32        0 
-    9700          9.7       32        0 
-    9800          9.8       32        0 
-    9900          9.9       33        0 
-   10000           10       33        0 
-Loop time of 69.01 on 4 procs for 10000 steps with 900 atoms
-
-Performance: 12519931.275 ns/day, 0.000 hours/ns, 144.907 timesteps/s
-48.7% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 56.528     | 57.936     | 58.729     |  11.0 | 83.95
-Neigh   | 0.013157   | 0.013382   | 0.013551   |   0.1 |  0.02
-Comm    | 8.9594     | 9.7555     | 11.113     |  26.7 | 14.14
-Output  | 0.14644    | 0.15009    | 0.15809    |   1.2 |  0.22
-Modify  | 0.72913    | 0.91574    | 1.0524     |  12.4 |  1.33
-Other   |            | 0.2389     |            |       |  0.35
-
-Nlocal:    225 ave 229 max 223 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-Nghost:    442 ave 444 max 439 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Neighs:    10188.8 ave 10437 max 9932 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-
-Total # of neighbors = 40755
-Ave neighs/atom = 45.2833
-Neighbor list builds = 33
-Dangerous builds = 0
-Total wall time: 0:01:09
diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.1 b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.1
new file mode 100644
index 0000000000..30bf43dcf6
--- /dev/null
+++ b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.1
@@ -0,0 +1,230 @@
+LAMMPS (28 Mar 2023 - Development)
+dimension       2
+units           micro
+atom_style      sph
+
+variable        R equal 0.5             # radius of sphere          micrometers
+variable        a equal $R/5            # lattice spacing           micrometers
+variable        a equal 0.5/5            
+variable        L equal $R*3
+variable        L equal 0.5*3
+variable        T equal 300.
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.5          # kernel function cutoff    micrometers
+variable        h equal 0.1*4.5          
+variable        mass equal $a*$a*$a*${rho_0}
+variable        mass equal 0.1*$a*$a*${rho_0}
+variable        mass equal 0.1*0.1*$a*${rho_0}
+variable        mass equal 0.1*0.1*0.1*${rho_0}
+variable        mass equal 0.1*0.1*0.1*1
+variable        dt equal 1e-3           # timestep                  microseconds
+variable        skin equal 0.2*$h
+variable        skin equal 0.2*0.45
+
+region          box block -$L $L -$L $L 0 $a units box
+region          box block -1.5 $L -$L $L 0 $a units box
+region          box block -1.5 1.5 -$L $L 0 $a units box
+region          box block -1.5 1.5 -1.5 $L 0 $a units box
+region          box block -1.5 1.5 -1.5 1.5 0 $a units box
+region          box block -1.5 1.5 -1.5 1.5 0 0.1 units box
+create_box      2 box
+Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
+  1 by 1 by 1 MPI processor grid
+lattice         sq $a
+lattice         sq 0.1
+Lattice spacing in x,y,z = 0.1 0.1 0.1
+
+create_atoms    1 box
+Created 900 atoms
+  using lattice units in orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
+  create_atoms CPU = 0.001 seconds
+
+region          sphere sphere 0 0 0 $R units box
+region          sphere sphere 0 0 0 0.5 units box
+set             region sphere type 2
+Setting atom values ...
+  81 settings made for type
+
+group           fluid type 1
+819 atoms in group fluid
+group           sphere type 2
+81 atoms in group sphere
+
+mass            * ${mass}
+mass            * 0.001
+set             group all sph/rho ${rho_0}
+set             group all sph/rho 1
+Setting atom values ...
+  900 settings made for sph/rho
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
+pair_style      sdpd/taitwater/isothermal 300 1 76787    
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+pair_coeff      * * 1 ${c_0} ${h}
+pair_coeff      * * 1 100 ${h}
+pair_coeff      * * 1 100 0.45
+
+fix             1 fluid sph
+fix             2 sphere rigid/meso single
+  1 rigid bodies with 81 atoms
+
+fix             2d all enforce2d
+
+neighbor        ${skin} bin
+neighbor        0.09 bin
+neigh_modify	delay 0 every 1 check yes
+timestep        ${dt}
+timestep        0.001
+
+dump            dump_id all atom 100 dump.lammpstrj
+
+thermo          100
+thermo_style    custom step time nbuild ndanger
+
+run             10000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0.54
+  ghost atom cutoff = 0.54
+  binsize = 0.27, bins = 12 12 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sdpd/taitwater/isothermal, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.512 | 6.512 | 6.512 Mbytes
+   Step          Time        Nbuild      Ndanger  
+         0   0                      0           0 
+       100   0.1                    0           0 
+       200   0.2                    0           0 
+       300   0.3                    0           0 
+       400   0.4                    1           0 
+       500   0.5                    1           0 
+       600   0.6                    1           0 
+       700   0.7                    2           0 
+       800   0.8                    2           0 
+       900   0.9                    2           0 
+      1000   1                      3           0 
+      1100   1.1                    3           0 
+      1200   1.2                    3           0 
+      1300   1.3                    4           0 
+      1400   1.4                    4           0 
+      1500   1.5                    4           0 
+      1600   1.6                    5           0 
+      1700   1.7                    5           0 
+      1800   1.8                    6           0 
+      1900   1.9                    6           0 
+      2000   2                      6           0 
+      2100   2.1                    7           0 
+      2200   2.2                    7           0 
+      2300   2.3                    7           0 
+      2400   2.4                    7           0 
+      2500   2.5                    8           0 
+      2600   2.6                    8           0 
+      2700   2.7                    8           0 
+      2800   2.8                    9           0 
+      2900   2.9                    9           0 
+      3000   3                     10           0 
+      3100   3.1                   10           0 
+      3200   3.2                   10           0 
+      3300   3.3                   11           0 
+      3400   3.4                   11           0 
+      3500   3.5                   11           0 
+      3600   3.6                   12           0 
+      3700   3.7                   12           0 
+      3800   3.8                   12           0 
+      3900   3.9                   13           0 
+      4000   4                     13           0 
+      4100   4.1                   13           0 
+      4200   4.2                   14           0 
+      4300   4.3                   14           0 
+      4400   4.4                   14           0 
+      4500   4.5                   15           0 
+      4600   4.6                   15           0 
+      4700   4.7                   15           0 
+      4800   4.8                   16           0 
+      4900   4.9                   16           0 
+      5000   5                     17           0 
+      5100   5.1                   17           0 
+      5200   5.2                   17           0 
+      5300   5.3                   17           0 
+      5400   5.4                   18           0 
+      5500   5.5                   18           0 
+      5600   5.6                   18           0 
+      5700   5.7                   19           0 
+      5800   5.8                   19           0 
+      5900   5.9                   19           0 
+      6000   6                     19           0 
+      6100   6.1                   20           0 
+      6200   6.2                   20           0 
+      6300   6.3                   20           0 
+      6400   6.4                   21           0 
+      6500   6.5                   21           0 
+      6600   6.6                   21           0 
+      6700   6.7                   21           0 
+      6800   6.8                   22           0 
+      6900   6.9                   22           0 
+      7000   7                     22           0 
+      7100   7.1                   23           0 
+      7200   7.2                   23           0 
+      7300   7.3                   23           0 
+      7400   7.4                   24           0 
+      7500   7.5                   24           0 
+      7600   7.6                   24           0 
+      7700   7.7                   25           0 
+      7800   7.8                   25           0 
+      7900   7.9                   26           0 
+      8000   8                     26           0 
+      8100   8.1                   26           0 
+      8200   8.2                   26           0 
+      8300   8.3                   27           0 
+      8400   8.4                   27           0 
+      8500   8.5                   27           0 
+      8600   8.6                   28           0 
+      8700   8.7                   28           0 
+      8800   8.8                   28           0 
+      8900   8.9                   29           0 
+      9000   9                     29           0 
+      9100   9.1                   29           0 
+      9200   9.2                   30           0 
+      9300   9.3                   30           0 
+      9400   9.4                   30           0 
+      9500   9.5                   30           0 
+      9600   9.6                   31           0 
+      9700   9.7                   31           0 
+      9800   9.8                   32           0 
+      9900   9.9                   32           0 
+     10000   10                    32           0 
+Loop time of 78.0094 on 1 procs for 10000 steps with 900 atoms
+
+Performance: 11075589.479 ns/day, 0.000 hours/ns, 128.190 timesteps/s, 115.371 katom-step/s
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 77.441     | 77.441     | 77.441     |   0.0 | 99.27
+Neigh   | 0.016471   | 0.016471   | 0.016471   |   0.0 |  0.02
+Comm    | 0.14821    | 0.14821    | 0.14821    |   0.0 |  0.19
+Output  | 0.062415   | 0.062415   | 0.062415   |   0.0 |  0.08
+Modify  | 0.25323    | 0.25323    | 0.25323    |   0.0 |  0.32
+Other   |            | 0.0877     |            |       |  0.11
+
+Nlocal:            900 ave         900 max         900 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            762 ave         762 max         762 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          40697 ave       40697 max       40697 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 40697
+Ave neighs/atom = 45.218889
+Neighbor list builds = 32
+Dangerous builds = 0
+Total wall time: 0:01:18
diff --git a/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.4 b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.4
new file mode 100644
index 0000000000..03f5ed01bb
--- /dev/null
+++ b/examples/PACKAGES/dpd-smooth/2d-diffusion/log.28Mar23.2d-diffusion.g++.4
@@ -0,0 +1,230 @@
+LAMMPS (28 Mar 2023 - Development)
+dimension       2
+units           micro
+atom_style      sph
+
+variable        R equal 0.5             # radius of sphere          micrometers
+variable        a equal $R/5            # lattice spacing           micrometers
+variable        a equal 0.5/5            
+variable        L equal $R*3
+variable        L equal 0.5*3
+variable        T equal 300.
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.5          # kernel function cutoff    micrometers
+variable        h equal 0.1*4.5          
+variable        mass equal $a*$a*$a*${rho_0}
+variable        mass equal 0.1*$a*$a*${rho_0}
+variable        mass equal 0.1*0.1*$a*${rho_0}
+variable        mass equal 0.1*0.1*0.1*${rho_0}
+variable        mass equal 0.1*0.1*0.1*1
+variable        dt equal 1e-3           # timestep                  microseconds
+variable        skin equal 0.2*$h
+variable        skin equal 0.2*0.45
+
+region          box block -$L $L -$L $L 0 $a units box
+region          box block -1.5 $L -$L $L 0 $a units box
+region          box block -1.5 1.5 -$L $L 0 $a units box
+region          box block -1.5 1.5 -1.5 $L 0 $a units box
+region          box block -1.5 1.5 -1.5 1.5 0 $a units box
+region          box block -1.5 1.5 -1.5 1.5 0 0.1 units box
+create_box      2 box
+Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
+  2 by 2 by 1 MPI processor grid
+lattice         sq $a
+lattice         sq 0.1
+Lattice spacing in x,y,z = 0.1 0.1 0.1
+
+create_atoms    1 box
+Created 900 atoms
+  using lattice units in orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
+  create_atoms CPU = 0.001 seconds
+
+region          sphere sphere 0 0 0 $R units box
+region          sphere sphere 0 0 0 0.5 units box
+set             region sphere type 2
+Setting atom values ...
+  81 settings made for type
+
+group           fluid type 1
+819 atoms in group fluid
+group           sphere type 2
+81 atoms in group sphere
+
+mass            * ${mass}
+mass            * 0.001
+set             group all sph/rho ${rho_0}
+set             group all sph/rho 1
+Setting atom values ...
+  900 settings made for sph/rho
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
+pair_style      sdpd/taitwater/isothermal 300 1 76787    
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+pair_coeff      * * 1 ${c_0} ${h}
+pair_coeff      * * 1 100 ${h}
+pair_coeff      * * 1 100 0.45
+
+fix             1 fluid sph
+fix             2 sphere rigid/meso single
+  1 rigid bodies with 81 atoms
+
+fix             2d all enforce2d
+
+neighbor        ${skin} bin
+neighbor        0.09 bin
+neigh_modify	delay 0 every 1 check yes
+timestep        ${dt}
+timestep        0.001
+
+dump            dump_id all atom 100 dump.lammpstrj
+
+thermo          100
+thermo_style    custom step time nbuild ndanger
+
+run             10000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0.54
+  ghost atom cutoff = 0.54
+  binsize = 0.27, bins = 12 12 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sdpd/taitwater/isothermal, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.463 | 6.463 | 6.463 Mbytes
+   Step          Time        Nbuild      Ndanger  
+         0   0                      0           0 
+       100   0.1                    0           0 
+       200   0.2                    0           0 
+       300   0.3                    0           0 
+       400   0.4                    1           0 
+       500   0.5                    1           0 
+       600   0.6                    1           0 
+       700   0.7                    2           0 
+       800   0.8                    2           0 
+       900   0.9                    2           0 
+      1000   1                      3           0 
+      1100   1.1                    3           0 
+      1200   1.2                    3           0 
+      1300   1.3                    4           0 
+      1400   1.4                    4           0 
+      1500   1.5                    4           0 
+      1600   1.6                    5           0 
+      1700   1.7                    5           0 
+      1800   1.8                    5           0 
+      1900   1.9                    6           0 
+      2000   2                      6           0 
+      2100   2.1                    6           0 
+      2200   2.2                    7           0 
+      2300   2.3                    7           0 
+      2400   2.4                    7           0 
+      2500   2.5                    8           0 
+      2600   2.6                    8           0 
+      2700   2.7                    8           0 
+      2800   2.8                    9           0 
+      2900   2.9                    9           0 
+      3000   3                      9           0 
+      3100   3.1                   10           0 
+      3200   3.2                   10           0 
+      3300   3.3                   11           0 
+      3400   3.4                   11           0 
+      3500   3.5                   11           0 
+      3600   3.6                   12           0 
+      3700   3.7                   12           0 
+      3800   3.8                   12           0 
+      3900   3.9                   12           0 
+      4000   4                     13           0 
+      4100   4.1                   13           0 
+      4200   4.2                   14           0 
+      4300   4.3                   14           0 
+      4400   4.4                   14           0 
+      4500   4.5                   15           0 
+      4600   4.6                   15           0 
+      4700   4.7                   15           0 
+      4800   4.8                   16           0 
+      4900   4.9                   16           0 
+      5000   5                     16           0 
+      5100   5.1                   17           0 
+      5200   5.2                   17           0 
+      5300   5.3                   17           0 
+      5400   5.4                   17           0 
+      5500   5.5                   18           0 
+      5600   5.6                   18           0 
+      5700   5.7                   18           0 
+      5800   5.8                   19           0 
+      5900   5.9                   19           0 
+      6000   6                     19           0 
+      6100   6.1                   20           0 
+      6200   6.2                   20           0 
+      6300   6.3                   20           0 
+      6400   6.4                   21           0 
+      6500   6.5                   21           0 
+      6600   6.6                   21           0 
+      6700   6.7                   22           0 
+      6800   6.8                   22           0 
+      6900   6.9                   22           0 
+      7000   7                     23           0 
+      7100   7.1                   23           0 
+      7200   7.2                   23           0 
+      7300   7.3                   24           0 
+      7400   7.4                   24           0 
+      7500   7.5                   24           0 
+      7600   7.6                   25           0 
+      7700   7.7                   25           0 
+      7800   7.8                   26           0 
+      7900   7.9                   26           0 
+      8000   8                     26           0 
+      8100   8.1                   26           0 
+      8200   8.2                   27           0 
+      8300   8.3                   27           0 
+      8400   8.4                   28           0 
+      8500   8.5                   28           0 
+      8600   8.6                   28           0 
+      8700   8.7                   29           0 
+      8800   8.8                   29           0 
+      8900   8.9                   29           0 
+      9000   9                     30           0 
+      9100   9.1                   30           0 
+      9200   9.2                   30           0 
+      9300   9.3                   30           0 
+      9400   9.4                   31           0 
+      9500   9.5                   31           0 
+      9600   9.6                   31           0 
+      9700   9.7                   32           0 
+      9800   9.8                   32           0 
+      9900   9.9                   32           0 
+     10000   10                    33           0 
+Loop time of 13.5306 on 4 procs for 10000 steps with 900 atoms
+
+Performance: 63855371.888 ns/day, 0.000 hours/ns, 739.067 timesteps/s, 665.160 katom-step/s
+98.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 12.327     | 12.56      | 12.738     |   4.3 | 92.83
+Neigh   | 0.0043391  | 0.0044297  | 0.0045381  |   0.1 |  0.03
+Comm    | 0.53746    | 0.71463    | 0.94685    |  18.1 |  5.28
+Output  | 0.021884   | 0.02228    | 0.023428   |   0.4 |  0.16
+Modify  | 0.14457    | 0.14548    | 0.14643    |   0.2 |  1.08
+Other   |            | 0.08351    |            |       |  0.62
+
+Nlocal:            225 ave         228 max         222 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:         438.25 ave         442 max         434 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Neighs:        10152.2 ave       10328 max        9853 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 40609
+Ave neighs/atom = 45.121111
+Neighbor list builds = 33
+Dangerous builds = 0
+Total wall time: 0:00:13
diff --git a/examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps b/examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps
index 0d06723f59..59359d4b38 100644
--- a/examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps
+++ b/examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps
@@ -1,6 +1,6 @@
 dimension       3
 units           micro
-atom_style      meso
+atom_style      sph
 
 variable        a equal 0.1             # lattice spacing         micrometers
 variable        L equal $a*10
@@ -21,7 +21,7 @@ lattice         sc $a
 create_atoms    1 box
 
 mass            * ${mass}
-set             group all meso/rho ${rho_0}
+set             group all sph/rho ${rho_0}
 
 pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
 pair_coeff      * * ${rho_0} ${c_0} ${h}
@@ -34,7 +34,7 @@ variable        vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
 variable        vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
 variable        vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
 
-fix             1 all meso
+fix             1 all sph
 
 neighbor        ${skin} bin
 timestep        ${dt}
diff --git a/examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.1 b/examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.1
similarity index 58%
rename from examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.1
rename to examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.1
index 06ffd699bc..2fa4771a74 100644
--- a/examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.1
+++ b/examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.1
@@ -1,7 +1,7 @@
-LAMMPS (24 Oct 2018)
+LAMMPS (28 Mar 2023 - Development)
 dimension       3
 units           micro
-atom_style      meso
+atom_style      sph
 
 variable        a equal 0.1             # lattice spacing         micrometers
 variable        L equal $a*10
@@ -38,13 +38,15 @@ Lattice spacing in x,y,z = 0.1 0.1 0.1
 
 create_atoms    1 box
 Created 8000 atoms
-  Time spent = 0.00285411 secs
+  using lattice units in orthogonal box = (-1 -1 -1) to (1 1 1)
+  create_atoms CPU = 0.002 seconds
 
 mass            * ${mass}
 mass            * 0.001
-set             group all meso/rho ${rho_0}
-set             group all meso/rho 1
-  8000 settings made for meso/rho
+set             group all sph/rho ${rho_0}
+set             group all sph/rho 1
+Setting atom values ...
+  8000 settings made for sph/rho
 
 pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
 pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
@@ -71,7 +73,7 @@ variable        vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
 variable        vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
 variable        vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
 
-fix             1 all meso
+fix             1 all sph
 
 neighbor        ${skin} bin
 neighbor        0.04 bin
@@ -82,8 +84,9 @@ thermo          10
 thermo_style    custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
 
 run             200
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 0.44
   ghost atom cutoff = 0.44
@@ -92,55 +95,55 @@ Neighbor list info ...
   (1) pair sdpd/taitwater/isothermal, perpetual
       attributes: half, newton on
       pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
+      stencil: half/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 13.54 | 13.54 | 13.54 Mbytes
-Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check 
-       0            0            0            0            0 
-      10        0.005   0.70973271   0.71495693   0.71910087 
-      20         0.01   0.90418096   0.88845437   0.89659567 
-      30        0.015    0.9590736   0.97880338    0.9619016 
-      40         0.02   0.98533774   0.96057682   0.95600448 
-      50        0.025   0.96433662   0.96650071   0.95509683 
-      60         0.03   0.96598029   0.96373656   0.96734888 
-      70        0.035   0.95433045   0.98004764   0.96255924 
-      80         0.04   0.97872906   0.95987289   0.96623598 
-      90        0.045   0.99913888   0.99255731   0.95616142 
-     100         0.05   0.98872675   0.97141018   0.95338841 
-     110        0.055   0.97794592   0.97389258   0.98473719 
-     120         0.06   0.98389266   0.96716284   0.95504862 
-     130        0.065   0.98572886   0.96680923   0.95599065 
-     140         0.07   0.97602684   0.97580081    0.9886878 
-     150        0.075   0.99172003   0.95027467   0.96028033 
-     160         0.08   0.96793247   0.94590928   0.95644301 
-     170        0.085   0.94167619   0.98048861   0.93439426 
-     180         0.09   0.97277934   0.97383622   0.96900866 
-     190        0.095   0.96647288    1.0027643   0.96230782 
-     200          0.1   0.94864291   0.95902585   0.96398175 
-Loop time of 60.1095 on 1 procs for 200 steps with 8000 atoms
+Per MPI rank memory allocation (min/avg/max) = 14.29 | 14.29 | 14.29 Mbytes
+   Step          Time      v_vx_sq_check  v_vy_sq_check  v_vz_sq_check 
+         0   0              0              0              0            
+        10   0.005          0.70973271     0.71495693     0.71910087   
+        20   0.01           0.90418096     0.88845437     0.89659567   
+        30   0.015          0.9590736      0.97880338     0.9619016    
+        40   0.02           0.98533774     0.96057682     0.95600448   
+        50   0.025          0.96433662     0.96650071     0.95509683   
+        60   0.03           0.96598029     0.96373656     0.96734888   
+        70   0.035          0.95433045     0.98004764     0.96255924   
+        80   0.04           0.97872906     0.95987289     0.96623598   
+        90   0.045          0.99913888     0.99255731     0.95616142   
+       100   0.05           0.98872675     0.97141018     0.95338841   
+       110   0.055          0.97794592     0.97389258     0.98473719   
+       120   0.06           0.98389266     0.96716284     0.95504862   
+       130   0.065          0.98572886     0.96680923     0.95599065   
+       140   0.07           0.97602684     0.97580081     0.9886878    
+       150   0.075          0.99172003     0.95027467     0.96028033   
+       160   0.08           0.96793247     0.94590928     0.95644301   
+       170   0.085          0.94167619     0.98048861     0.93439426   
+       180   0.09           0.97277934     0.97383622     0.96900866   
+       190   0.095          0.96647288     1.0027643      0.96230782   
+       200   0.1            0.94864291     0.95902585     0.96398175   
+Loop time of 55.7542 on 1 procs for 200 steps with 8000 atoms
 
-Performance: 143737.595 ns/day, 0.000 hours/ns, 3.327 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 154965.922 ns/day, 0.000 hours/ns, 3.587 timesteps/s, 28.697 katom-step/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 59.92      | 59.92      | 59.92      |   0.0 | 99.68
+Pair    | 55.642     | 55.642     | 55.642     |   0.0 | 99.80
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.11154    | 0.11154    | 0.11154    |   0.0 |  0.19
-Output  | 0.0063498  | 0.0063498  | 0.0063498  |   0.0 |  0.01
-Modify  | 0.043546   | 0.043546   | 0.043546   |   0.0 |  0.07
-Other   |            | 0.02811    |            |       |  0.05
+Comm    | 0.060977   | 0.060977   | 0.060977   |   0.0 |  0.11
+Output  | 0.0066393  | 0.0066393  | 0.0066393  |   0.0 |  0.01
+Modify  | 0.028354   | 0.028354   | 0.028354   |   0.0 |  0.05
+Other   |            | 0.01623    |            |       |  0.03
 
-Nlocal:    8000 ave 8000 max 8000 min
+Nlocal:           8000 ave        8000 max        8000 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    16389 ave 16389 max 16389 min
+Nghost:          16389 ave       16389 max       16389 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    1.456e+06 ave 1.456e+06 max 1.456e+06 min
+Neighs:      1.456e+06 ave   1.456e+06 max   1.456e+06 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 1456000
 Ave neighs/atom = 182
 Neighbor list builds = 0
 Dangerous builds = 0
-Total wall time: 0:01:00
+Total wall time: 0:00:56
diff --git a/examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.4 b/examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.4
similarity index 58%
rename from examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.4
rename to examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.4
index 88509f0fd1..e4f11d305e 100644
--- a/examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.4
+++ b/examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.4
@@ -1,7 +1,7 @@
-LAMMPS (24 Oct 2018)
+LAMMPS (28 Mar 2023 - Development)
 dimension       3
 units           micro
-atom_style      meso
+atom_style      sph
 
 variable        a equal 0.1             # lattice spacing         micrometers
 variable        L equal $a*10
@@ -38,13 +38,15 @@ Lattice spacing in x,y,z = 0.1 0.1 0.1
 
 create_atoms    1 box
 Created 8000 atoms
-  Time spent = 0.00252754 secs
+  using lattice units in orthogonal box = (-1 -1 -1) to (1 1 1)
+  create_atoms CPU = 0.001 seconds
 
 mass            * ${mass}
 mass            * 0.001
-set             group all meso/rho ${rho_0}
-set             group all meso/rho 1
-  8000 settings made for meso/rho
+set             group all sph/rho ${rho_0}
+set             group all sph/rho 1
+Setting atom values ...
+  8000 settings made for sph/rho
 
 pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
 pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
@@ -71,7 +73,7 @@ variable        vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
 variable        vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
 variable        vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
 
-fix             1 all meso
+fix             1 all sph
 
 neighbor        ${skin} bin
 neighbor        0.04 bin
@@ -82,8 +84,9 @@ thermo          10
 thermo_style    custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
 
 run             200
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
   master list distance cutoff = 0.44
   ghost atom cutoff = 0.44
@@ -92,55 +95,55 @@ Neighbor list info ...
   (1) pair sdpd/taitwater/isothermal, perpetual
       attributes: half, newton on
       pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
+      stencil: half/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes
-Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check 
-       0            0            0            0            0 
-      10        0.005   0.71224819   0.71470372    0.7008956 
-      20         0.01   0.90627589   0.90683966   0.90116506 
-      30        0.015     0.938505   0.95884272   0.93337542 
-      40         0.02   0.94394649   0.93668038   0.96468004 
-      50        0.025   0.97152309   0.97546161   0.95107762 
-      60         0.03   0.94710871   0.95678322   0.97285504 
-      70        0.035   0.96253148   0.95838642   0.95450883 
-      80         0.04   0.97581495   0.95278681   0.95099478 
-      90        0.045   0.96251614    0.9740684   0.96081505 
-     100         0.05   0.94191275   0.97137523   0.94084858 
-     110        0.055     0.953406   0.95739684   0.98574522 
-     120         0.06   0.99001614   0.99608287    0.9839996 
-     130        0.065   0.96575225   0.94309655   0.92847798 
-     140         0.07   0.97642687   0.97458638   0.94696406 
-     150        0.075   0.99316381   0.96876814   0.95440106 
-     160         0.08   0.94589744   0.95264791   0.95495169 
-     170        0.085   0.97599092   0.95336014   0.97687718 
-     180         0.09   0.97214242    0.9726305    0.9726035 
-     190        0.095   0.97577583   0.96523645    0.9756968 
-     200          0.1   0.96386053   0.97268854   0.94582436 
-Loop time of 32.5247 on 4 procs for 200 steps with 8000 atoms
+Per MPI rank memory allocation (min/avg/max) = 6.172 | 6.172 | 6.172 Mbytes
+   Step          Time      v_vx_sq_check  v_vy_sq_check  v_vz_sq_check 
+         0   0              0              0              0            
+        10   0.005          0.71224819     0.71470372     0.7008956    
+        20   0.01           0.90627589     0.90683966     0.90116506   
+        30   0.015          0.938505       0.95884272     0.93337542   
+        40   0.02           0.94394649     0.93668038     0.96468004   
+        50   0.025          0.97152309     0.97546161     0.95107762   
+        60   0.03           0.94710871     0.95678322     0.97285504   
+        70   0.035          0.96253148     0.95838642     0.95450883   
+        80   0.04           0.97581495     0.95278681     0.95099478   
+        90   0.045          0.96251614     0.9740684      0.96081505   
+       100   0.05           0.94191275     0.97137523     0.94084858   
+       110   0.055          0.953406       0.95739684     0.98574522   
+       120   0.06           0.99001614     0.99608287     0.9839996    
+       130   0.065          0.96575225     0.94309655     0.92847798   
+       140   0.07           0.97642687     0.97458638     0.94696406   
+       150   0.075          0.99316381     0.96876814     0.95440106   
+       160   0.08           0.94589744     0.95264791     0.95495169   
+       170   0.085          0.97599092     0.95336014     0.97687718   
+       180   0.09           0.97214242     0.9726305      0.9726035    
+       190   0.095          0.97577583     0.96523645     0.9756968    
+       200   0.1            0.96386053     0.97268854     0.94582436   
+Loop time of 9.59181 on 4 procs for 200 steps with 8000 atoms
 
-Performance: 265644.515 ns/day, 0.000 hours/ns, 6.149 timesteps/s
-73.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 900768.333 ns/day, 0.000 hours/ns, 20.851 timesteps/s, 166.809 katom-step/s
+98.1% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 27.385     | 28.409     | 28.761     |  11.1 | 87.34
+Pair    | 8.9729     | 9.2147     | 9.4383     |   5.5 | 96.07
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 3.582      | 3.9343     | 4.9531     |  29.7 | 12.10
-Output  | 0.022267   | 0.026073   | 0.033141   |   2.7 |  0.08
-Modify  | 0.031714   | 0.033134   | 0.034367   |   0.6 |  0.10
-Other   |            | 0.1226     |            |       |  0.38
+Comm    | 0.13739    | 0.36068    | 0.60216    |  27.6 |  3.76
+Output  | 0.0022724  | 0.002394   | 0.0026506  |   0.3 |  0.02
+Modify  | 0.0068559  | 0.0069926  | 0.0070974  |   0.1 |  0.07
+Other   |            | 0.007004   |            |       |  0.07
 
-Nlocal:    2000 ave 2000 max 2000 min
+Nlocal:           2000 ave        2000 max        2000 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    8469 ave 8469 max 8469 min
+Nghost:           8469 ave        8469 max        8469 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    364000 ave 376628 max 351184 min
+Neighs:         364000 ave      376628 max      351184 min
 Histogram: 1 0 1 0 0 0 0 1 0 1
 
 Total # of neighbors = 1456000
 Ave neighs/atom = 182
 Neighbor list builds = 0
 Dangerous builds = 0
-Total wall time: 0:00:32
+Total wall time: 0:00:09

From 620cca34d4f840722fefaeca35c3548200dadce0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 15:19:13 -0400
Subject: [PATCH 204/396] add accessor to nfield, make certain field types are
 initialized early

---
 src/thermo.cpp | 10 ++++++++++
 src/thermo.h   |  1 +
 2 files changed, 11 insertions(+)

diff --git a/src/thermo.cpp b/src/thermo.cpp
index 31c19fbdc2..1c07da695f 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -201,6 +201,8 @@ void Thermo::init()
   ValueTokenizer *format_line = nullptr;
   if (format_line_user.size()) format_line = new ValueTokenizer(format_line_user);
 
+  field_data.clear();
+  field_data.resize(nfield);
   std::string format_this, format_line_user_def;
   for (int i = 0; i < nfield; i++) {
 
@@ -208,6 +210,14 @@ void Thermo::init()
     format_this.clear();
     format_line_user_def.clear();
 
+    if (vtype[i] == FLOAT) {
+      field_data[i] = (double) 0.0;
+    } else if (vtype[i] == INT) {
+      field_data[i] = (int) 0;
+    } else if (vtype[i] == BIGINT) {
+      field_data[i] = (bigint) 0;
+    }
+
     if ((lineflag == MULTILINE) && ((i % 3) == 0)) format[i] += "\n";
     if ((lineflag == YAMLLINE) && (i == 0)) format[i] += "  - [";
     if (format_line) format_line_user_def = format_line->next_string();
diff --git a/src/thermo.h b/src/thermo.h
index 8a5cba29d7..f22f3103b0 100644
--- a/src/thermo.h
+++ b/src/thermo.h
@@ -43,6 +43,7 @@ class Thermo : protected Pointers {
   int evaluate_keyword(const std::string &, double *);
 
   // for accessing cached thermo data
+  int get_nfield() const { return nfield; }
   bigint get_timestep() const { return ntimestep; }
   const std::vector<multitype> &get_fields() const { return field_data; }
   const std::vector<std::string> &get_keywords() const { return keyword; }

From 30e6b8b9b6405cd979b87d4abb951ae5ca4e0a46 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 15:19:58 -0400
Subject: [PATCH 205/396] make more reliable with explicit loops using exported
 nfield value

---
 src/EXTRA-DUMP/dump_yaml.cpp     | 19 +++++++++-------
 src/NETCDF/dump_netcdf.cpp       | 37 ++++++++++++++++++++++--------
 src/NETCDF/dump_netcdf.h         |  1 +
 src/NETCDF/dump_netcdf_mpiio.cpp | 39 ++++++++++++++++++++++++--------
 src/NETCDF/dump_netcdf_mpiio.h   |  1 +
 5 files changed, 70 insertions(+), 27 deletions(-)

diff --git a/src/EXTRA-DUMP/dump_yaml.cpp b/src/EXTRA-DUMP/dump_yaml.cpp
index ec7d26af31..f8d2fb2264 100644
--- a/src/EXTRA-DUMP/dump_yaml.cpp
+++ b/src/EXTRA-DUMP/dump_yaml.cpp
@@ -62,18 +62,21 @@ void DumpYAML::write_header(bigint ndump)
     Thermo *th = output->thermo;
     // output thermo data only on timesteps where it was computed
     if (update->ntimestep == th->get_timestep()) {
+      int nfield = th->get_nfield();
+      const auto &keywords = th->get_keywords();
+      const auto &fields = th->get_fields();
 
       thermo_data += "thermo:\n  - keywords: [ ";
-      for (const auto &key : th->get_keywords()) thermo_data += fmt::format("{}, ", key);
+      for (int i = 0; i < nfield; ++i) thermo_data += fmt::format("{}, ", keywords[i]);
       thermo_data += "]\n  - data: [ ";
 
-      for (const auto &val : th->get_fields()) {
-        if (val.type == multitype::DOUBLE)
-          thermo_data += fmt::format("{}, ", val.data.d);
-        else if (val.type == multitype::INT)
-          thermo_data += fmt::format("{}, ", val.data.i);
-        else if (val.type == multitype::BIGINT)
-          thermo_data += fmt::format("{}, ", val.data.b);
+      for (int i = 0; i < nfield; ++i) {
+        if (fields[i].type == multitype::DOUBLE)
+          thermo_data += fmt::format("{}, ", fields[i].data.d);
+        else if (fields[i].type == multitype::INT)
+          thermo_data += fmt::format("{}, ", fields[i].data.i);
+        else if (fields[i].type == multitype::BIGINT)
+          thermo_data += fmt::format("{}, ", fields[i].data.b);
         else
           thermo_data += ", ";
       }
diff --git a/src/NETCDF/dump_netcdf.cpp b/src/NETCDF/dump_netcdf.cpp
index 8c99ff1f70..2b064edeae 100644
--- a/src/NETCDF/dump_netcdf.cpp
+++ b/src/NETCDF/dump_netcdf.cpp
@@ -195,6 +195,7 @@ DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) :
   type_nc_real = NC_FLOAT;
 
   thermo = false;
+  thermo_warn = true;
   thermovar = nullptr;
 
   framei = 0;
@@ -223,7 +224,7 @@ void DumpNetCDF::openfile()
 
   if (thermo && !singlefile_opened) {
     delete[] thermovar;
-    thermovar = new int[output->thermo->get_keywords().size()];
+    thermovar = new int[output->thermo->get_nfield()];
   }
 
   // now the computes and fixes have been initialized, so we can query
@@ -320,8 +321,10 @@ void DumpNetCDF::openfile()
 
       // perframe variables
       if (thermo) {
-        const auto &keywords = output->thermo->get_keywords();
-        int nfield = keywords.size();
+        Thermo *th = output->thermo;
+        const auto &keywords = th->get_keywords();
+        const int nfield = th->get_nfield();
+
         for (int i = 0; i < nfield; i++) {
           NCERRX( nc_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
         }
@@ -433,9 +436,11 @@ void DumpNetCDF::openfile()
 
       // perframe variables
       if (thermo) {
-        const auto &fields = output->thermo->get_fields();
-        const auto &keywords = output->thermo->get_keywords();
-        int nfield = fields.size();
+        Thermo *th = output->thermo;
+        const auto &fields = th->get_fields();
+        const auto &keywords = th->get_keywords();
+        const int nfield = th->get_nfield();
+
         for (int i = 0; i < nfield; i++) {
           if (fields[i].type == multitype::DOUBLE) {
             NCERRX( nc_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
@@ -600,9 +605,23 @@ void DumpNetCDF::write()
   start[1] = 0;
 
   if (thermo) {
-    const auto &keywords = output->thermo->get_keywords();
-    const auto &fields = output->thermo->get_fields();
-    int nfield = fields.size();
+    Thermo *th = output->thermo;
+
+    // will output current thermo data only on timesteps where it was computed.
+    // warn (once) about using cached copy from old timestep.
+
+    if (thermo_warn && (update->ntimestep != th->get_timestep())) {
+      thermo_warn = false;
+      if (comm->me == 0) {
+        error->warning(FLERR, "Dump {} output on incompatible timestep with thermo output: {} vs {} \n"
+                       "         Dump netcdf always stores thermo data from last thermo output",
+                       id, th->get_timestep(), update->ntimestep);
+      }
+    }
+
+    const auto &keywords = th->get_keywords();
+    const auto &fields = th->get_fields();
+    int nfield = th->get_nfield();
     for (int i = 0; i < nfield; i++) {
       if (filewriter) {
         if (fields[i].type == multitype::DOUBLE) {
diff --git a/src/NETCDF/dump_netcdf.h b/src/NETCDF/dump_netcdf.h
index 20c60ef104..982cd99fb5 100644
--- a/src/NETCDF/dump_netcdf.h
+++ b/src/NETCDF/dump_netcdf.h
@@ -65,6 +65,7 @@ class DumpNetCDF : public DumpCustom {
 
   int type_nc_real;    // netcdf type to use for real variables: float or double
   bool thermo;         // write thermo output to netcdf file
+  bool thermo_warn;    // warn (once) that thermo output is on incompatible step
 
   bigint n_buffer;          // size of buffer
   bigint *int_buffer;       // buffer for passing data to netcdf
diff --git a/src/NETCDF/dump_netcdf_mpiio.cpp b/src/NETCDF/dump_netcdf_mpiio.cpp
index 3aec34dd40..4a34f11ab4 100644
--- a/src/NETCDF/dump_netcdf_mpiio.cpp
+++ b/src/NETCDF/dump_netcdf_mpiio.cpp
@@ -192,6 +192,7 @@ DumpNetCDFMPIIO::DumpNetCDFMPIIO(LAMMPS *lmp, int narg, char **arg) :
   type_nc_real = NC_FLOAT;
 
   thermo = false;
+  thermo_warn = true;
   thermovar = nullptr;
 
   framei = 0;
@@ -220,7 +221,7 @@ void DumpNetCDFMPIIO::openfile()
 
   if (thermo && !singlefile_opened) {
     delete[] thermovar;
-    thermovar = new int[output->thermo->get_keywords().size()];
+    thermovar = new int[output->thermo->get_nfield()];
   }
 
   // now the computes and fixes have been initialized, so we can query
@@ -318,8 +319,10 @@ void DumpNetCDFMPIIO::openfile()
 
     // perframe variables
     if (thermo) {
-      const auto &keywords = output->thermo->get_keywords();
-      int nfield = keywords.size();
+      Thermo *th = output->thermo;
+      const auto &keywords = th->get_keywords();
+      const int nfield = th->get_nfield();
+
       for (int i = 0; i < nfield; i++) {
         NCERRX( ncmpi_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
       }
@@ -423,9 +426,11 @@ void DumpNetCDFMPIIO::openfile()
 
     // perframe variables
     if (thermo) {
-      const auto &fields = output->thermo->get_fields();
-      const auto &keywords = output->thermo->get_keywords();
-      int nfield = fields.size();
+      Thermo *th = output->thermo;
+      const auto &fields = th->get_fields();
+      const auto &keywords = th->get_keywords();
+      const int nfield = th->get_nfield();
+
       for (int i = 0; i < nfield; i++) {
         if (fields[i].type == multitype::DOUBLE) {
           NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
@@ -593,9 +598,23 @@ void DumpNetCDFMPIIO::write()
   NCERR( ncmpi_begin_indep_data(ncid) );
 
   if (thermo) {
-    const auto &keywords = output->thermo->get_keywords();
-    const auto &fields = output->thermo->get_fields();
-    int nfield = fields.size();
+    Thermo *th = output->thermo;
+
+    // will output current thermo data only on timesteps where it was computed.
+    // warn (once) about using cached copy from old timestep.
+
+    if (thermo_warn && (update->ntimestep != th->get_timestep())) {
+      thermo_warn = false;
+      if (comm->me == 0) {
+        error->warning(FLERR, "Dump {} output on incompatible timestep with thermo output: {} vs {} \n"
+                       "         Dump netcdf/mpiio always stores thermo data from last thermo output",
+                       id, th->get_timestep(), update->ntimestep);
+      }
+    }
+
+    const auto &keywords = th->get_keywords();
+    const auto &fields = th->get_fields();
+    int nfield = th->get_nfield();
     for (int i = 0; i < nfield; i++) {
       if (filewriter) {
         if (fields[i].type == multitype::DOUBLE) {
@@ -609,7 +628,7 @@ void DumpNetCDFMPIIO::write()
     }
   }
 
- // write timestep header
+  // write timestep header
 
   write_time_and_cell();
 
diff --git a/src/NETCDF/dump_netcdf_mpiio.h b/src/NETCDF/dump_netcdf_mpiio.h
index 5948dc272b..14ee930e26 100644
--- a/src/NETCDF/dump_netcdf_mpiio.h
+++ b/src/NETCDF/dump_netcdf_mpiio.h
@@ -62,6 +62,7 @@ class DumpNetCDFMPIIO : public DumpCustom {
 
   int type_nc_real;    // netcdf type to use for real variables: float or double
   bool thermo;         // write thermo output to netcdf file
+  bool thermo_warn;    // warn (once) that thermo output is on incompatible step
 
   bigint n_buffer;          // size of buffer
   bigint *int_buffer;       // buffer for passing data to netcdf

From de561737a3be4a0c3554b544273110c7be46e16e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 15:28:35 -0400
Subject: [PATCH 206/396] update docs

---
 doc/src/dump_modify.rst | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst
index 89b3766083..0ac2afbeee 100644
--- a/doc/src/dump_modify.rst
+++ b/doc/src/dump_modify.rst
@@ -758,7 +758,8 @@ file alongside per-atom data.  The values included in the dump file are
 cached values from the last thermo output and include the exact same the
 values as specified by the :doc:`thermo_style <thermo_style>` command.
 Because these are cached values, they are only up-to-date when dump
-output is on a timestep that also has thermo output.
+output is on a timestep that also has thermo output. Dump style *yaml*
+will skip thermo output on incompatible steps.
 
 ----------
 

From 491e152289e3abf267f4ebee6cddda7ba797591f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 16:21:01 -0400
Subject: [PATCH 207/396] add API to library interface to access last thermo
 data

---
 src/EXTRA-DUMP/dump_yaml.cpp     |  4 +-
 src/NETCDF/dump_netcdf.cpp       | 12 ++--
 src/NETCDF/dump_netcdf_mpiio.cpp | 12 ++--
 src/library.cpp                  | 99 +++++++++++++++++++++++++++++++-
 src/library.h                    |  1 +
 src/thermo.cpp                   |  1 +
 src/thermo.h                     |  4 +-
 7 files changed, 116 insertions(+), 17 deletions(-)

diff --git a/src/EXTRA-DUMP/dump_yaml.cpp b/src/EXTRA-DUMP/dump_yaml.cpp
index f8d2fb2264..47cab1ee02 100644
--- a/src/EXTRA-DUMP/dump_yaml.cpp
+++ b/src/EXTRA-DUMP/dump_yaml.cpp
@@ -61,8 +61,8 @@ void DumpYAML::write_header(bigint ndump)
   if (thermo) {
     Thermo *th = output->thermo;
     // output thermo data only on timesteps where it was computed
-    if (update->ntimestep == th->get_timestep()) {
-      int nfield = th->get_nfield();
+    if (update->ntimestep == *th->get_timestep()) {
+      int nfield = *th->get_nfield();
       const auto &keywords = th->get_keywords();
       const auto &fields = th->get_fields();
 
diff --git a/src/NETCDF/dump_netcdf.cpp b/src/NETCDF/dump_netcdf.cpp
index 2b064edeae..0115c0bbe9 100644
--- a/src/NETCDF/dump_netcdf.cpp
+++ b/src/NETCDF/dump_netcdf.cpp
@@ -224,7 +224,7 @@ void DumpNetCDF::openfile()
 
   if (thermo && !singlefile_opened) {
     delete[] thermovar;
-    thermovar = new int[output->thermo->get_nfield()];
+    thermovar = new int[*output->thermo->get_nfield()];
   }
 
   // now the computes and fixes have been initialized, so we can query
@@ -323,7 +323,7 @@ void DumpNetCDF::openfile()
       if (thermo) {
         Thermo *th = output->thermo;
         const auto &keywords = th->get_keywords();
-        const int nfield = th->get_nfield();
+        const int nfield = *th->get_nfield();
 
         for (int i = 0; i < nfield; i++) {
           NCERRX( nc_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
@@ -439,7 +439,7 @@ void DumpNetCDF::openfile()
         Thermo *th = output->thermo;
         const auto &fields = th->get_fields();
         const auto &keywords = th->get_keywords();
-        const int nfield = th->get_nfield();
+        const int nfield = *th->get_nfield();
 
         for (int i = 0; i < nfield; i++) {
           if (fields[i].type == multitype::DOUBLE) {
@@ -610,18 +610,18 @@ void DumpNetCDF::write()
     // will output current thermo data only on timesteps where it was computed.
     // warn (once) about using cached copy from old timestep.
 
-    if (thermo_warn && (update->ntimestep != th->get_timestep())) {
+    if (thermo_warn && (update->ntimestep != *th->get_timestep())) {
       thermo_warn = false;
       if (comm->me == 0) {
         error->warning(FLERR, "Dump {} output on incompatible timestep with thermo output: {} vs {} \n"
                        "         Dump netcdf always stores thermo data from last thermo output",
-                       id, th->get_timestep(), update->ntimestep);
+                       id, *th->get_timestep(), update->ntimestep);
       }
     }
 
     const auto &keywords = th->get_keywords();
     const auto &fields = th->get_fields();
-    int nfield = th->get_nfield();
+    int nfield = *th->get_nfield();
     for (int i = 0; i < nfield; i++) {
       if (filewriter) {
         if (fields[i].type == multitype::DOUBLE) {
diff --git a/src/NETCDF/dump_netcdf_mpiio.cpp b/src/NETCDF/dump_netcdf_mpiio.cpp
index 4a34f11ab4..f9382dacef 100644
--- a/src/NETCDF/dump_netcdf_mpiio.cpp
+++ b/src/NETCDF/dump_netcdf_mpiio.cpp
@@ -221,7 +221,7 @@ void DumpNetCDFMPIIO::openfile()
 
   if (thermo && !singlefile_opened) {
     delete[] thermovar;
-    thermovar = new int[output->thermo->get_nfield()];
+    thermovar = new int[*output->thermo->get_nfield()];
   }
 
   // now the computes and fixes have been initialized, so we can query
@@ -321,7 +321,7 @@ void DumpNetCDFMPIIO::openfile()
     if (thermo) {
       Thermo *th = output->thermo;
       const auto &keywords = th->get_keywords();
-      const int nfield = th->get_nfield();
+      const int nfield = *th->get_nfield();
 
       for (int i = 0; i < nfield; i++) {
         NCERRX( ncmpi_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
@@ -429,7 +429,7 @@ void DumpNetCDFMPIIO::openfile()
       Thermo *th = output->thermo;
       const auto &fields = th->get_fields();
       const auto &keywords = th->get_keywords();
-      const int nfield = th->get_nfield();
+      const int nfield = *th->get_nfield();
 
       for (int i = 0; i < nfield; i++) {
         if (fields[i].type == multitype::DOUBLE) {
@@ -603,18 +603,18 @@ void DumpNetCDFMPIIO::write()
     // will output current thermo data only on timesteps where it was computed.
     // warn (once) about using cached copy from old timestep.
 
-    if (thermo_warn && (update->ntimestep != th->get_timestep())) {
+    if (thermo_warn && (update->ntimestep != *th->get_timestep())) {
       thermo_warn = false;
       if (comm->me == 0) {
         error->warning(FLERR, "Dump {} output on incompatible timestep with thermo output: {} vs {} \n"
                        "         Dump netcdf/mpiio always stores thermo data from last thermo output",
-                       id, th->get_timestep(), update->ntimestep);
+                       id, *th->get_timestep(), update->ntimestep);
       }
     }
 
     const auto &keywords = th->get_keywords();
     const auto &fields = th->get_fields();
-    int nfield = th->get_nfield();
+    int nfield = *th->get_nfield();
     for (int i = 0; i < nfield; i++) {
       if (filewriter) {
         if (fields[i].type == multitype::DOUBLE) {
diff --git a/src/library.cpp b/src/library.cpp
index 33f49a4e53..6b079b4a93 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -719,7 +719,7 @@ double lammps_get_natoms(void *handle)
 
 /* ---------------------------------------------------------------------- */
 
-/** Get current value of a thermo keyword.
+/** Evaluate a thermo keyword.
  *
 \verbatim embed:rst
 
@@ -750,6 +750,103 @@ double lammps_get_thermo(void *handle, const char *keyword)
 
 /* ---------------------------------------------------------------------- */
 
+/** Access cached data from last thermo output
+ *
+\verbatim embed:rst
+
+This function provides access to cached data from the last thermo
+output.  This differs from :cpp:func:`lammps_get_thermo` in that it does
+not trigger an evaluation.  It provides direct access to a a read-only
+location of the last thermo output data and the corresponding keyword
+strings. The output depends on the value of the *what* argument string.
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Value of *what
+     - Description of return value
+     - Data type
+     - Uses index
+   * - step
+     - timestep when the last thermo output was generated or -1 when no data available
+     - pointer to bigint cast to void pointer
+     - no
+   * - num
+     - number of fields in thermo output
+     - pointer to int cast to void pointer
+     - no
+   * - keyword
+     - column keyword for thermo output
+     - const char pointer cast to void pointer
+     - yes
+   * - type
+     - data type of thermo output column. LAMMPS_INT, LAMMPS_DOUBLE, or LAMMPS_INT64
+     - const int cast to void pointer
+     - yes
+   * - data
+     - actual field data for column
+     - pointer to either int, int64_t or double cast to void pointer
+     - yes
+     
+\endverbatim
+ *
+ * \param  handle   pointer to a previously created LAMMPS instance
+ * \param  what     string with the kind of data requested
+ * \param  idx      integer with index into data arrays, ignored for scalar data
+ * \return          pointer to location of requested data cast to void or NULL */
+
+void *lammps_last_thermo(void *handle, const char *what, int idx)
+{
+  auto lmp = (LAMMPS *) handle;
+  void *val = nullptr;
+  Thermo *th = lmp->output->thermo;
+  if (!th) return nullptr;
+  const int nfield = *th->get_nfield();
+
+  BEGIN_CAPTURE
+  {
+    if (strcmp(what, "step") == 0) {
+      val = (void *) th->get_timestep();
+
+    } else if (strcmp(what, "num") == 0) {
+      val = (void *) th->get_nfield();
+
+    } else if (strcmp(what, "keyword") == 0) {
+      if ((idx < 0) || (idx >= nfield)) return nullptr;
+      const auto &keywords = th->get_keywords();
+      val = (void *) keywords[idx].c_str();
+
+    } else if (strcmp(what, "type") == 0) {
+      if ((idx < 0) || (idx >= nfield)) return nullptr;
+      const auto &field = th->get_fields()[idx];
+      if (field.type == multitype::INT) {
+        val = (void *) LAMMPS_INT;
+      } else if (field.type == multitype::BIGINT) {
+        val = (void *) LAMMPS_INT64;
+      } else if (field.type == multitype::DOUBLE) {
+        val = (void *) LAMMPS_DOUBLE;
+      }
+
+    } else if (strcmp(what, "data") == 0) {
+      if ((idx < 0) || (idx >= nfield)) return nullptr;
+      const auto &field = th->get_fields()[idx];
+      if (field.type == multitype::INT) {
+        val = (void *) &field.data.i;
+      } else if (field.type == multitype::BIGINT) {
+        val = (void *) &field.data.b;
+      } else if (field.type == multitype::DOUBLE) {
+        val = (void *) &field.data.d;
+      }
+
+    } else val = nullptr;
+  }
+  END_CAPTURE
+  return val;
+}
+
+/* ---------------------------------------------------------------------- */
+
 /** Extract simulation box parameters.
  *
 \verbatim embed:rst
diff --git a/src/library.h b/src/library.h
index 340b0edb7b..4c2530210c 100644
--- a/src/library.h
+++ b/src/library.h
@@ -148,6 +148,7 @@ void lammps_commands_string(void *handle, const char *str);
 
 double lammps_get_natoms(void *handle);
 double lammps_get_thermo(void *handle, const char *keyword);
+void *lammps_last_thermo(void *handle, const char *what, int idx);
 
 void lammps_extract_box(void *handle, double *boxlo, double *boxhi, double *xy, double *yz,
                         double *xz, int *pflags, int *boxflag);
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 1c07da695f..c6e71354ff 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -111,6 +111,7 @@ Thermo::Thermo(LAMMPS *_lmp, int narg, char **arg) :
   lostflag = lostbond = Thermo::ERROR;
   lostbefore = warnbefore = 0;
   flushflag = 0;
+  ntimestep = -1;
 
   // set style and corresponding lineflag
   // custom style builds its own line of keywords, including wildcard expansion
diff --git a/src/thermo.h b/src/thermo.h
index f22f3103b0..333a282ca0 100644
--- a/src/thermo.h
+++ b/src/thermo.h
@@ -43,8 +43,8 @@ class Thermo : protected Pointers {
   int evaluate_keyword(const std::string &, double *);
 
   // for accessing cached thermo data
-  int get_nfield() const { return nfield; }
-  bigint get_timestep() const { return ntimestep; }
+  const int *get_nfield() const { return &nfield; }
+  const bigint *get_timestep() const { return &ntimestep; }
   const std::vector<multitype> &get_fields() const { return field_data; }
   const std::vector<std::string> &get_keywords() const { return keyword; }
 

From f3ff8dac6626add46564385dcc39c622cc09546b Mon Sep 17 00:00:00 2001
From: jbcouli <jbcouli@sandia.gov>
Date: Wed, 7 Jun 2023 16:23:06 -0600
Subject: [PATCH 208/396] clean up documentation for BPM bond styles

---
 doc/src/bond_bpm_rotational.rst | 45 +++++++++++++++++----------------
 doc/src/bond_bpm_spring.rst     | 37 ++++++++++++++-------------
 2 files changed, 42 insertions(+), 40 deletions(-)

diff --git a/doc/src/bond_bpm_rotational.rst b/doc/src/bond_bpm_rotational.rst
index ca12d86ccc..cfacfde2cd 100644
--- a/doc/src/bond_bpm_rotational.rst
+++ b/doc/src/bond_bpm_rotational.rst
@@ -10,7 +10,7 @@ Syntax
 
    bond_style bpm/rotational keyword value attribute1 attribute2 ...
 
-* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break/no*
+* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
 
   .. parsed-literal::
 
@@ -80,32 +80,32 @@ respectively.  Details on the calculations of shear displacements and
 angular displacements can be found in :ref:`(Wang) <Wang2009>` and
 :ref:`(Wang and Mora) <Wang2009b>`.
 
-Bonds will break under sufficient stress. A breaking criteria is calculated
+Bonds will break under sufficient stress. A breaking criterion is calculated
 
 .. math::
 
-   B = \mathrm{max}\{0, \frac{f_r}{f_{r,c}} + \frac{|f_s|}{f_{s,c}} +
-       \frac{|\tau_b|}{\tau_{b,c}} + \frac{|\tau_t|}{\tau_{t,c}} \}
+   B = \mathrm{max}\left\{0, \frac{f_r}{f_{r,c}} + \frac{|f_s|}{f_{s,c}} +
+       \frac{|\tau_b|}{\tau_{b,c}} + \frac{|\tau_t|}{\tau_{t,c}} \right\}
 
 where :math:`|f_s|` is the magnitude of the shear force and
 :math:`|\tau_b|` and :math:`|\tau_t|` are the magnitudes of the
-bending and twisting forces, respectively. The corresponding variables
+bending and twisting torques, respectively. The corresponding variables
 :math:`f_{r,c}` :math:`f_{s,c}`, :math:`\tau_{b,c}`, and
 :math:`\tau_{t,c}` are critical limits to each force or torque.  If
 :math:`B` is ever equal to or exceeds one, the bond will break.  This
-is done by setting by setting its type to 0 such that forces and
+is done by setting the bond type to 0 such that forces and
 torques are no longer computed.
 
 After computing the base magnitudes of the forces and torques, they
 can be optionally multiplied by an extra factor :math:`w` to smoothly
 interpolate forces and torques to zero as the bond breaks. This term
-is calculated as :math:`w = (1.0 - B^4)`. This smoothing factor can be
-added or removed using the *smooth* keyword.
+is calculated as :math:`w = (1.0 - B^4)`. This smoothing factor can be added
+or removed by setting the *smooth* keyword to *yes* or *no*, respectively.
 
 Finally, additional damping forces and torques are applied to the two
 particles. A force is applied proportional to the difference in the
 normal velocity of particles using a similar construction as
-dissipative particle dynamics (:ref:`(Groot) <Groot3>`):
+dissipative particle dynamics :ref:`(Groot) <Groot3>`:
 
 .. math::
 
@@ -115,8 +115,8 @@ where :math:`\gamma_n` is the damping strength, :math:`\hat{r}` is the
 radial normal vector, and :math:`\vec{v}` is the velocity difference
 between the two particles. Similarly, tangential forces are applied to
 each atom proportional to the relative differences in sliding
-velocities with a constant prefactor :math:`\gamma_s` (:ref:`(Wang et
-al.) <Wang20152>`) along with their associated torques. The rolling and
+velocities with a constant prefactor :math:`\gamma_s` :ref:`(Wang et
+al.) <Wang20152>` along with their associated torques. The rolling and
 twisting components of the relative angular velocities of the two
 atoms are also damped by applying torques with prefactors of
 :math:`\gamma_r` and :math:`\gamma_t`, respectively.
@@ -139,21 +139,23 @@ or :doc:`read_restart <read_restart>` commands:
 * :math:`\gamma_r`      (force*distance/velocity units)
 * :math:`\gamma_t`      (force*distance/velocity units)
 
-However, the *normalize* option will normalize the radial and shear forces
-by :math:`r_0` such that :math:`k_r` and :math:`k_s` are unit less.
+If the *normalize* keyword is set to *yes*, the radial and shear forces
+will be normalized by :math:`r_0` such that :math:`k_r` and :math:`k_s`
+must be given in force units.
 
 By default, pair forces are not calculated between bonded particles.
-Pair forces can alternatively be overlaid on top of bond forces using
-the *overlay/pair* option. These settings require specific
+Pair forces can alternatively be overlaid on top of bond forces by setting
+the *overlay/pair* keyword to *yes*. These settings require specific
 :doc:`special_bonds <special_bonds>` settings described in the
-restrictions.  Further details can be found in the `:doc: how to
-<Howto_BPM>` page on BPMs.
+restrictions.  Further details can be found in the :doc:`how to
+<Howto_bpm>` page on BPMs.
 
 .. versionadded:: 28Mar2023
 
-If the *break* option is used, then LAMMPS assumes bonds should not break
+If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
 during a simulation run. This will prevent some unnecessary calculation.
-However, if a bond does break, it will trigger an error.
+However, if a bond reaches a damage criterion greater than one,
+it will trigger an error.
 
 If the *store/local* keyword is used, an internal fix will track bonds that
 break during the simulation. Whenever a bond breaks, data is processed
@@ -239,9 +241,8 @@ requires setting
 
    special_bonds lj 0 1 1 coul 1 1 1
 
-and :doc:`newton <newton>` must be set to bond off.  If the
-*overlay/pair* option is used, this bond style alternatively requires
-setting
+and :doc:`newton <newton>` must be set to bond off.  If the *overlay/pair*
+keyword is set to *yes*, this bond style alternatively requires setting
 
 .. code-block:: LAMMPS
 
diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst
index d89035dcad..2376b8e077 100644
--- a/doc/src/bond_bpm_spring.rst
+++ b/doc/src/bond_bpm_spring.rst
@@ -10,7 +10,7 @@ Syntax
 
    bond_style bpm/spring keyword value attribute1 attribute2 ...
 
-* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break/no*
+* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
 
   .. parsed-literal::
 
@@ -72,13 +72,13 @@ particles based on a model described by Clemmer and Robbins
 where :math:`k` is a stiffness, :math:`r` is the current distance
 and :math:`r_0` is the initial distance between the two particles, and
 :math:`w` is an optional smoothing factor discussed below. Bonds will
-break at a strain of :math:`\epsilon_c`.  This is done by setting by
-setting its type to 0 such that forces are no longer computed.
+break at a strain of :math:`\epsilon_c`.  This is done by setting
+the bond type to 0 such that forces are no longer computed.
 
 An additional damping force is applied to the bonded
 particles.  This forces is proportional to the difference in the
 normal velocity of particles using a similar construction as
-dissipative particle dynamics (:ref:`(Groot) <Groot4>`):
+dissipative particle dynamics :ref:`(Groot) <Groot4>`:
 
 .. math::
 
@@ -88,9 +88,10 @@ where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
 radial normal vector, and :math:`\vec{v}` is the velocity difference
 between the two particles.
 
-The smoothing factor :math:`w` can be added or removed using the
-*smooth* keyword. It is constructed such that forces smoothly go
-to zero, avoiding discontinuities, as bonds approach the critical strain
+The smoothing factor :math:`w` can be added or removed by setting the
+*smooth* keyword to *yes* or *no*, respectively. It is constructed such
+that forces smoothly go to zero, avoiding discontinuities, as bonds
+approach the critical strain
 
 .. math::
 
@@ -105,21 +106,22 @@ the data file or restart files read by the :doc:`read_data
 * :math:`\epsilon_c`    (unit less)
 * :math:`\gamma`        (force/velocity units)
 
-However, the *normalize* option will normalize the elastic bond force by
-:math:`r_0` such that :math:`k` is unit less.
+If the *normalize* keyword is set to *yes*, the elastic bond force will be
+normalized by :math:`r_0` such that :math:`k` must be given in force units.
 
 By default, pair forces are not calculated between bonded particles.
-Pair forces can alternatively be overlaid on top of bond forces using
-the *overlay/pair* option. These settings require specific
+Pair forces can alternatively be overlaid on top of bond forces by setting
+the *overlay/pair* keyword to *yes*. These settings require specific
 :doc:`special_bonds <special_bonds>` settings described in the
-restrictions.  Further details can be found in the `:doc: how to
-<Howto_BPM>` page on BPMs.
+restrictions.  Further details can be found in the :doc:`how to
+<Howto_bpm>` page on BPMs.
 
 .. versionadded:: 28Mar2023
 
-If the *break* option is used, then LAMMPS assumes bonds should not break
+If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
 during a simulation run. This will prevent some unnecessary calculation.
-However, if a bond does break, it will trigger an error.
+However, if a bond reaches a strain greater than :math:`\epsilon_c`,
+it will trigger an error.
 
 If the *store/local* keyword is used, an internal fix will track bonds that
 break during the simulation. Whenever a bond breaks, data is processed
@@ -196,9 +198,8 @@ requires setting
 
    special_bonds lj 0 1 1 coul 1 1 1
 
-and :doc:`newton <newton>` must be set to bond off.  If the
-*overlay/pair* option is used, this bond style alternatively requires
-setting
+and :doc:`newton <newton>` must be set to bond off.  If the *overlay/pair*
+keyword is set to *yes*, this bond style alternatively requires setting
 
 .. code-block:: LAMMPS
 

From 7551219d81c368e9b1879a3224377693beac306f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 20:16:26 -0400
Subject: [PATCH 209/396] correct multitype unittest for -DLAMMPS_SMALLSMALL

---
 unittest/utils/test_lmptype.cpp | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/unittest/utils/test_lmptype.cpp b/unittest/utils/test_lmptype.cpp
index 6db340fddf..e5dc871953 100644
--- a/unittest/utils/test_lmptype.cpp
+++ b/unittest/utils/test_lmptype.cpp
@@ -41,7 +41,7 @@ TEST(Types, ubuf)
 
 TEST(Types, multitype)
 {
-    multitype m[6];
+    multitype m[7];
     int64_t b1 = (3L << 48) - 1;
     int i1    = 20;
     double d1 = 0.1;
@@ -50,27 +50,22 @@ TEST(Types, multitype)
     m[1] = i1;
     m[2] = d1;
 
-#if !defined(LAMMPS_SMALLSMALL)
-    m[3] = -((1L << 40) + (1L << 50));
-#endif
+    m[3] = (bigint) -((1L << 40) + (1L << 50));
     m[4] = -1023;
     m[5] = -2.225;
 
-#if defined(LAMMPS_SMALLSMALL)
-    EXPECT_EQ(m[0].type, multitype::INT);
-#else
     EXPECT_EQ(m[0].type, multitype::BIGINT);
-#endif
     EXPECT_EQ(m[1].type, multitype::INT);
     EXPECT_EQ(m[2].type, multitype::DOUBLE);
 
 #if defined(LAMMPS_SMALLSMALL)
-    EXPECT_EQ(m[3].type, multitype::NONE);
+    EXPECT_EQ(m[3].type, multitype::INT);
 #else
     EXPECT_EQ(m[3].type, multitype::BIGINT);
 #endif
     EXPECT_EQ(m[4].type, multitype::INT);
     EXPECT_EQ(m[5].type, multitype::DOUBLE);
+    EXPECT_EQ(m[6].type, multitype::NONE);
 
     EXPECT_EQ(m[0].data.b, b1);
     EXPECT_EQ(m[1].data.i, i1);

From dd0bba6ac7a62f4e321f62c6105a7f736d3fd3bb Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Jun 2023 20:37:53 -0400
Subject: [PATCH 210/396] whitespace

---
 src/GRANULAR/gran_sub_mod_normal.h | 6 +++---
 src/library.cpp                    | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/GRANULAR/gran_sub_mod_normal.h b/src/GRANULAR/gran_sub_mod_normal.h
index c1511fdfa5..6f2f3aabbe 100644
--- a/src/GRANULAR/gran_sub_mod_normal.h
+++ b/src/GRANULAR/gran_sub_mod_normal.h
@@ -94,7 +94,7 @@ namespace Granular_NS {
     void coeffs_to_local() override;
     void mix_coeffs(double *, double *) override;
    private:
-    int mixed_coefficients;    
+    int mixed_coefficients;
   };
 
   /* ---------------------------------------------------------------------- */
@@ -110,7 +110,7 @@ namespace Granular_NS {
    protected:
     double k, cohesion;
     double F_pulloff, Fne;
-    int mixed_coefficients;        
+    int mixed_coefficients;
   };
 
   /* ---------------------------------------------------------------------- */
@@ -129,7 +129,7 @@ namespace Granular_NS {
    protected:
     double k, cohesion;
     double Emix, F_pulloff, Fne;
-    int mixed_coefficients;    
+    int mixed_coefficients;
   };
 
 }    // namespace Granular_NS
diff --git a/src/library.cpp b/src/library.cpp
index 6b079b4a93..62d029f625 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -788,7 +788,7 @@ strings. The output depends on the value of the *what* argument string.
      - actual field data for column
      - pointer to either int, int64_t or double cast to void pointer
      - yes
-     
+
 \endverbatim
  *
  * \param  handle   pointer to a previously created LAMMPS instance

From c851c7304c02d8b38424c240e3ee84671a402f7a Mon Sep 17 00:00:00 2001
From: Lars Veldscholte <lars@tuxplace.nl>
Date: Thu, 8 Jun 2023 11:03:21 +0200
Subject: [PATCH 211/396] Update documentation for compute stress/cartesian,

and split the doc page compute_stress_profile into compute_stress_cartesian and compute_stress_curvilinear
---
 doc/src/compute_stress_cartesian.rst          | 118 ++++++++++++++++++
 ...ile.rst => compute_stress_curvilinear.rst} |  48 ++-----
 2 files changed, 125 insertions(+), 41 deletions(-)
 create mode 100644 doc/src/compute_stress_cartesian.rst
 rename doc/src/{compute_stress_profile.rst => compute_stress_curvilinear.rst} (69%)

diff --git a/doc/src/compute_stress_cartesian.rst b/doc/src/compute_stress_cartesian.rst
new file mode 100644
index 0000000000..f52b360aa6
--- /dev/null
+++ b/doc/src/compute_stress_cartesian.rst
@@ -0,0 +1,118 @@
+.. index:: compute stress/cartesian
+
+compute stress/cartesian command
+==================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID stress/cartesian args
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* args = argument specific to the compute style
+
+.. parsed-literal::
+
+  *stress/cartesian* args = dim1 bin_width1 dim2 bin_width2 keyword
+    dim1 = *x* or *y* or *z*
+    bin_width1 = width of the bin
+    dim2 = *x* or *y* or *z* or *NULL*
+    bin_width2 = width of the bin
+    keyword = *ke* or *pair* or *bond*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+   compute 1 all stress/cartesian x 0.1 NULL 0
+   compute 1 all stress/cartesian y 0.1 z 0.1
+   compute 1 all stress/cartesian x 0.1 NULL 0 ke pair
+
+Description
+"""""""""""
+
+Compute *stress/cartesian* defines computations that calculate profiles of the
+diagonal components of the local stress tensor over one or two Cartesian
+dimensions, as described in :ref:`(Ikeshoji)<Ikeshoji2>`. The stress tensor is
+split into a kinetic contribution :math:`P^k` and a virial contribution
+:math:`P^v`. The sum gives the total stress tensor :math:`P = P^k+P^v`.
+This compute obeys momentum balance through fluid interfaces. They use the
+Irving--Kirkwood contour, which is the straight line between particle pairs.
+
+This compute only supports pair and bond (no angle, dihedral, improper,
+or kspace) forces. By default, if no extra keywords are specified, all
+supported contributions to the stress are included (ke, pair, bond). If any
+keywords are specified, then only those components are summed.
+
+Output info
+"""""""""""
+
+The output columns for *stress/cartesian* are the position of the
+center of the local volume in the first and second dimensions, number
+density, :math:`P^k_{xx}`, :math:`P^k_{yy}`, :math:`P^k_{zz}`,
+:math:`P^v_{xx}`, :math:`P^v_{yy}`, and :math:`P^v_{zz}`. There are 8
+columns when one dimension is specified and 9 columns when two
+dimensions are specified. The number of bins (rows) is
+:math:`(L_1/b_1)(L_2/b_2)`, where :math:`L_1` and :math:`L_2` are the lengths
+of the simulation box in the specified dimensions and :math:`b_1` and
+:math:`b_2` are the specified bin widths. When only one dimension is
+specified, the number of bins (rows) is :math:`L_1/b_1`.
+
+This array can be output with :doc:`fix ave/time <fix_ave_time>`,
+
+.. code-block:: LAMMPS
+
+  compute p all stress/cartesian x 0.1
+  fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
+
+The values calculated by this compute are "intensive".  The stress
+values will be in pressure :doc:`units <units>`. The number density
+values are in inverse volume :doc:`units <units>`.
+
+NOTE 1: The local stress does not include any Lennard-Jones tail
+corrections to the stress added by the
+:doc:`pair_modify tail yes <pair_modify>`
+command, since those are contributions to the global system pressure.
+
+NOTE 2: The local stress profiles generated by these computes are
+similar to those obtained by the
+:doc:`method-of-planes (MOP) <compute_stress_mop>`.
+A key difference
+is that compute `stress/mop/profile <compute_stress_mop>`
+considers particles crossing a set of planes, while
+*stress/cartesian* computes averages for a set of small volumes.
+Moreover, this compute computes the diagonal components of the stress
+tensor :math:`P_{xx}`, :math:`P_{yy}`, and :math:`P_{zz}`, while
+`stress/mop/profile <compute_stress_mop>` computes the components
+:math:`P_{ix}`, :math:`P_{iy}`, and :math:`P_{iz}`, where :math:`i` is the
+direction normal to the plane.
+
+More information on the similarities and differences can be found in
+:ref:`(Ikeshoji)<Ikeshoji2>`.
+
+Restrictions
+""""""""""""
+
+These computes calculate the stress tensor contributions for pair and bond
+forces only (no angle, dihedral, improper, or kspace force).
+It requires pairwise force calculations not available for most
+many-body pair styles.
+
+These computes are part of the EXTRA-COMPUTE package.  They are only
+enabled if LAMMPS was built with that package.  See the :doc:`Build
+package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`,
+:doc:`compute stress/mop/profile <compute_stress_mop>`, :doc:`compute stress/spherical <compute_stress_curvilinear>`,
+:doc:`compute stress/cylinder <compute_stress_curvilinear>`
+
+----------
+
+.. _Ikeshoji2:
+
+**(Ikeshoji)** Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
\ No newline at end of file
diff --git a/doc/src/compute_stress_profile.rst b/doc/src/compute_stress_curvilinear.rst
similarity index 69%
rename from doc/src/compute_stress_profile.rst
rename to doc/src/compute_stress_curvilinear.rst
index 7a4b6a38e6..f7cbf5efbe 100644
--- a/doc/src/compute_stress_profile.rst
+++ b/doc/src/compute_stress_curvilinear.rst
@@ -1,11 +1,6 @@
-.. index:: compute stress/cartesian
 .. index:: compute stress/cylinder
 .. index:: compute stress/spherical
 
-
-compute stress/cartesian command
-==================================
-
 compute stress/cylinder command
 =================================
 
@@ -20,15 +15,11 @@ Syntax
    compute ID group-ID style args
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
-* style = stress/cartesian or stress/spherical or stress/cylinder
+* style = stress/spherical or stress/cylinder
 * args = argument specific to the compute style
 
 .. parsed-literal::
 
-  *stress/cartesian* args = dim bin_width
-    dim = *x* or *y* or *z*
-    bin_width = width of the bin
-    one or two dim/bin_width pairs may be appended
   *stress/cylinder* args = zlo zh Rmax bin_width keyword
     zlo = minimum z-boundary for cylinder
     zhi = maximum z-boundary for cylinder
@@ -45,9 +36,6 @@ Examples
 """"""""
 
 .. code-block:: LAMMPS
-
-   compute 1 all stress/cartesian x 0.1
-   compute 1 all stress/cartesian y 0.25 z 0.1
    compute 1 all stress/cylinder -10.0 10.0 15.0 0.25
    compute 1 all stress/cylinder -10.0 10.0 15.0 0.25 ke no
    compute 1 all stress/spherical 0 0 0 0.1 10
@@ -55,21 +43,19 @@ Examples
 Description
 """""""""""
 
-Compute *stress/cartesian*, compute *stress/cylinder*, and compute
+Compute *stress/cylinder*, and compute
 *stress/spherical* define computations that calculate profiles of the
 diagonal components of the local stress tensor in the specified
 coordinate system. The stress tensor is split into a kinetic
 contribution :math:`P^k` and a virial contribution :math:`P^v`. The sum
 gives the total stress tensor :math:`P = P^k+P^v`. These computes can
 for example be used to calculate the diagonal components of the local
-stress tensor of interfaces with flat, cylindrical, or spherical
+stress tensor of surfaces with cylindrical or spherical
 symmetry. These computes obeys momentum balance through fluid
 interfaces. They use the Irving--Kirkwood contour, which is the straight
 line between particle pairs.
 
-The *stress/cartesian* computes the stress profile along one or two
-Cartesian coordinates, as described in :ref:`(Ikeshoji)<Ikeshoji2>`. The
-compute *stress/cylinder* computes the stress profile along the
+The compute *stress/cylinder* computes the stress profile along the
 radial direction in cylindrical coordinates, as described in
 :ref:`(Addington)<Addington1>`. The compute *stress/spherical*
 computes the stress profile along the radial direction in spherical
@@ -79,17 +65,6 @@ coordinates, as described in :ref:`(Ikeshoji)<Ikeshoji2>`.
 Output info
 """""""""""
 
-The output columns for *stress/cartesian* are the position of the
-center of the local volume in the first and second dimensions, number
-density, :math:`P^k_{xx}`, :math:`P^k_{yy}`, :math:`P^k_{zz}`,
-:math:`P^v_{xx}`, :math:`P^v_{yy}`, and :math:`P^v_{zz}`. There are 8
-columns when one dimension is specified and 9 columns when two
-dimensions are specified. The number of bins (rows) is
-:math:`(L_1/b_1)(L_2/b_2)`, where :math:`L_1` and :math:`L_2` are the lengths
-of the simulation box in the specified dimensions and :math:`b_1` and
-:math:`b_2` are the specified bin widths. When only one dimension is
-specified, the number of bins (rows) is :math:`L_1/b_1`.
-
 The default output columns for *stress/cylinder* are the radius to the
 center of the cylindrical shell, number density, :math:`P^k_{rr}`,
 :math:`P^k_{\phi\phi}`, :math:`P^k_{zz}`, :math:`P^v_{rr}`,
@@ -111,7 +86,7 @@ This array can be output with :doc:`fix ave/time <fix_ave_time>`,
 
 .. code-block:: LAMMPS
 
-  compute p all stress/cartesian x 0.1
+  compute 1 all stress/spherical 0 0 0 0.1 10
   fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
 
 The values calculated by this compute are "intensive".  The stress
@@ -123,16 +98,6 @@ corrections to the stress added by the
 :doc:`pair_modify tail yes <pair_modify>`
 command, since those are contributions to the global system pressure.
 
-NOTE 2: The local stress profiles generated by these computes are
-similar to those obtained by the
-:doc:`method-of-planes (MOP) <compute_stress_mop>`.
-A key difference
-is that compute `stress/mop/profile <compute_stress_mop>`
-considers particles crossing a set of planes, while
-*stress/cartesian* computes averages for a set of small volumes.
-More information on the similarities and differences can be found in
-:ref:`(Ikeshoji)<Ikeshoji2>`.
-
 Restrictions
 """"""""""""
 
@@ -150,7 +115,8 @@ package <Build_package>` doc page for more info.
 Related commands
 """"""""""""""""
 
-:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/mop/profile <compute_stress_mop>`
+:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute
+stress/mop/profile <compute_stress_mop>`, :doc:`compute stress/cartesian <compute_stress_cartesian>`
 
 Default
 """""""

From 2272d8dd205c99cf91c202e3961723719b7f673d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 09:45:12 -0400
Subject: [PATCH 212/396] add new library interface function to documentation

---
 doc/src/Library_properties.rst |  6 ++++
 src/library.cpp                | 53 ++++++++++++++++++----------------
 2 files changed, 34 insertions(+), 25 deletions(-)

diff --git a/doc/src/Library_properties.rst b/doc/src/Library_properties.rst
index 21e5609fc0..005bfaeea5 100644
--- a/doc/src/Library_properties.rst
+++ b/doc/src/Library_properties.rst
@@ -5,6 +5,7 @@ This section documents the following functions:
 
 - :cpp:func:`lammps_get_natoms`
 - :cpp:func:`lammps_get_thermo`
+- :cpp:func:`lammps_last_thermo`
 - :cpp:func:`lammps_extract_box`
 - :cpp:func:`lammps_reset_box`
 - :cpp:func:`lammps_memory_usage`
@@ -81,6 +82,11 @@ subdomains and processors.
 
 -----------------------
 
+.. doxygenfunction:: lammps_last_thermo
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_extract_box
    :project: progguide
 
diff --git a/src/library.cpp b/src/library.cpp
index 62d029f625..36d53c3e6c 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -723,10 +723,12 @@ double lammps_get_natoms(void *handle)
  *
 \verbatim embed:rst
 
-This function returns the current value of a :doc:`thermo keyword
-<thermo_style>`.  Unlike :cpp:func:`lammps_extract_global` it does not
-give access to the storage of the desired data but returns its value as
-a ``double``, so it can also return information that is computed on-the-fly.
+This function returns the current value of a :doc:`thermo keyword <thermo_style>`.
+Unlike :cpp:func:`lammps_extract_global` it does not give access to the
+storage of the desired data but returns its value as a ``double``, so it
+can also return information that is computed on-the-fly.
+Use :cpp:func:`lammps_last_thermo` to get access to the cached data from
+the last thermo output.
 
 \endverbatim
  *
@@ -754,49 +756,50 @@ double lammps_get_thermo(void *handle, const char *keyword)
  *
 \verbatim embed:rst
 
-This function provides access to cached data from the last thermo
-output.  This differs from :cpp:func:`lammps_get_thermo` in that it does
-not trigger an evaluation.  It provides direct access to a a read-only
-location of the last thermo output data and the corresponding keyword
-strings. The output depends on the value of the *what* argument string.
+This function provides access to cached data from the last thermo output.
+This differs from :cpp:func:`lammps_get_thermo` in that it does not trigger
+an evaluation.  Instead it provides direct access to a read-only location
+of the last thermo output data and the corresponding keyword strings.
+The how to handle the return value depends on the value of the *what*
+argument string.
 
 .. list-table::
    :header-rows: 1
    :widths: auto
 
-   * - Value of *what
+   * - Value of *what*
      - Description of return value
      - Data type
      - Uses index
    * - step
-     - timestep when the last thermo output was generated or -1 when no data available
-     - pointer to bigint cast to void pointer
+     - timestep when the last thermo output was generated or -1
+     - pointer to bigint
      - no
    * - num
      - number of fields in thermo output
-     - pointer to int cast to void pointer
+     - pointer to int
      - no
    * - keyword
      - column keyword for thermo output
-     - const char pointer cast to void pointer
+     - const char pointer
      - yes
    * - type
-     - data type of thermo output column. LAMMPS_INT, LAMMPS_DOUBLE, or LAMMPS_INT64
-     - const int cast to void pointer
+     - data type of thermo output column; see :cpp:enum:`_LMP_DATATYPE_CONST`
+     - const int
      - yes
    * - data
      - actual field data for column
-     - pointer to either int, int64_t or double cast to void pointer
+     - pointer to either int, int64_t or double
      - yes
 
 \endverbatim
  *
  * \param  handle   pointer to a previously created LAMMPS instance
  * \param  what     string with the kind of data requested
- * \param  idx      integer with index into data arrays, ignored for scalar data
+ * \param  index    integer with index into data arrays, ignored for scalar data
  * \return          pointer to location of requested data cast to void or NULL */
 
-void *lammps_last_thermo(void *handle, const char *what, int idx)
+void *lammps_last_thermo(void *handle, const char *what, int index)
 {
   auto lmp = (LAMMPS *) handle;
   void *val = nullptr;
@@ -813,13 +816,13 @@ void *lammps_last_thermo(void *handle, const char *what, int idx)
       val = (void *) th->get_nfield();
 
     } else if (strcmp(what, "keyword") == 0) {
-      if ((idx < 0) || (idx >= nfield)) return nullptr;
+      if ((index < 0) || (index >= nfield)) return nullptr;
       const auto &keywords = th->get_keywords();
-      val = (void *) keywords[idx].c_str();
+      val = (void *) keywords[index].c_str();
 
     } else if (strcmp(what, "type") == 0) {
-      if ((idx < 0) || (idx >= nfield)) return nullptr;
-      const auto &field = th->get_fields()[idx];
+      if ((index < 0) || (index >= nfield)) return nullptr;
+      const auto &field = th->get_fields()[index];
       if (field.type == multitype::INT) {
         val = (void *) LAMMPS_INT;
       } else if (field.type == multitype::BIGINT) {
@@ -829,8 +832,8 @@ void *lammps_last_thermo(void *handle, const char *what, int idx)
       }
 
     } else if (strcmp(what, "data") == 0) {
-      if ((idx < 0) || (idx >= nfield)) return nullptr;
-      const auto &field = th->get_fields()[idx];
+      if ((index < 0) || (index >= nfield)) return nullptr;
+      const auto &field = th->get_fields()[index];
       if (field.type == multitype::INT) {
         val = (void *) &field.data.i;
       } else if (field.type == multitype::BIGINT) {

From d6ad52ea6604cbf031076dd583c07d154bfdcca7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 09:46:33 -0400
Subject: [PATCH 213/396] allow wildcards with "cutoff" keyword to fix
 reaxff/species

this also switched to using fmtlib for column aligned output formatting
and re-applies clang-format.
---
 doc/src/fix_reaxff_species.rst    |  23 +++++--
 src/REAXFF/fix_reaxff_species.cpp | 106 +++++++++++++++---------------
 src/REAXFF/fix_reaxff_species.h   |   2 -
 3 files changed, 71 insertions(+), 60 deletions(-)

diff --git a/doc/src/fix_reaxff_species.rst b/doc/src/fix_reaxff_species.rst
index f57132f08b..c22c9d7b9f 100644
--- a/doc/src/fix_reaxff_species.rst
+++ b/doc/src/fix_reaxff_species.rst
@@ -25,7 +25,7 @@ Syntax
   .. parsed-literal::
 
        *cutoff* value = I J Cutoff
-         I, J = atom types
+         I, J = atom types (see asterisk form below)
          Cutoff = Bond-order cutoff value for this pair of atom types
        *element* value = Element1, Element2, ...
        *position* value = posfreq filepos
@@ -49,7 +49,7 @@ Examples
 .. code-block:: LAMMPS
 
    fix 1 all reaxff/species 10 10 100 species.out
-   fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
+   fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2*3 0.55
    fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
    fix 1 all reaxff/species 1 100 100 species.out delete species.del masslimit 0 50
 
@@ -88,13 +88,24 @@ If the filename ends with ".gz", the output file is written in gzipped
 format.  A gzipped dump file will be about 3x smaller than the text version,
 but will also take longer to write.
 
+.. versionadded:: TBD
+
+   Support for wildcards added
+
 Optional keyword *cutoff* can be assigned to change the minimum
 bond-order values used in identifying chemical bonds between pairs of
 atoms.  Bond-order cutoffs should be carefully chosen, as bond-order
-cutoffs that are too small may include too many bonds (which will
-result in an error), while cutoffs that are too large will result in
-fragmented molecules.  The default cutoff of 0.3 usually gives good
-results.
+cutoffs that are too small may include too many bonds (which will result
+in an error), while cutoffs that are too large will result in fragmented
+molecules.  The default cutoff of 0.3 usually gives good results.  A
+wildcard asterisk can be used in place of or in conjunction with the I,J
+arguments to set the bond-order cutoff for multiple pairs of atom types.
+This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If :math:`N` is
+the number of atom types, then an asterisk with no numeric values means
+all types from 1 to :math:`N`.  A leading asterisk means all types from
+1 to n (inclusive).  A trailing asterisk means all types from n to
+:math:`N` (inclusive).  A middle asterisk means all types from m to n
+(inclusive).
 
 The optional keyword *element* can be used to specify the chemical
 symbol printed for each LAMMPS atom type. The number of symbols must
diff --git a/src/REAXFF/fix_reaxff_species.cpp b/src/REAXFF/fix_reaxff_species.cpp
index 92bca99ae0..8fa06cafb3 100644
--- a/src/REAXFF/fix_reaxff_species.cpp
+++ b/src/REAXFF/fix_reaxff_species.cpp
@@ -48,15 +48,16 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 
 static const char cite_reaxff_species_delete[] =
-  "fix reaxff/species, 'delete' keyword: https://doi.org/10.1016/j.carbon.2022.11.002\n\n"
-  "@Article{Gissinger23,\n"
-  " author = {J. R. Gissinger, S. R. Zavada, J. G. Smith, J. Kemppainen, I. Gallegos, G. M. Odegard, E. J. Siochi, K. E. Wise},\n"
-  " title = {Predicting char yield of high-temperature resins},\n"
-  " journal = {Carbon},\n"
-  " year =    2023,\n"
-  " volume =  202,\n"
-  " pages =   {336-347}\n"
-  "}\n\n";
+    "fix reaxff/species, 'delete' keyword: https://doi.org/10.1016/j.carbon.2022.11.002\n\n"
+    "@Article{Gissinger23,\n"
+    " author = {J. R. Gissinger, S. R. Zavada, J. G. Smith, J. Kemppainen, I. Gallegos, G. M. "
+    "Odegard, E. J. Siochi, K. E. Wise},\n"
+    " title = {Predicting char yield of high-temperature resins},\n"
+    " journal = {Carbon},\n"
+    " year =    2023,\n"
+    " volume =  202,\n"
+    " pages =   {336-347}\n"
+    "}\n\n";
 
 /* ---------------------------------------------------------------------- */
 
@@ -148,13 +149,11 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
   setupflag = 0;
 
   // set default bond order cutoff
-  int itype, jtype;
-  double bo_cut;
-  bg_cut = 0.30;
+  double bo_cut = 0.30;
   int np1 = ntypes + 1;
   memory->create(BOCut, np1, np1, "reaxff/species:BOCut");
   for (int i = 1; i < np1; i++)
-    for (int j = 1; j < np1; j++) BOCut[i][j] = bg_cut;
+    for (int j = 1; j < np1; j++) BOCut[i][j] = bo_cut;
 
   // optional args
   eletype = nullptr;
@@ -172,16 +171,19 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
     // set BO cutoff
     if (strcmp(arg[iarg], "cutoff") == 0) {
       if (iarg + 4 > narg) utils::missing_cmd_args(FLERR, "fix reaxff/species cutoff", error);
-      itype = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
-      jtype = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
+      int ilo, ihi, jlo, jhi;
+      utils::bounds(FLERR, arg[iarg + 1], 1, atom->ntypes, ilo, ihi, error);
+      utils::bounds(FLERR, arg[iarg + 2], 1, atom->ntypes, jlo, jhi, error);
       bo_cut = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
-      if ((itype <= 0) || (jtype <= 0) || (itype > ntypes) || (jtype > ntypes))
-        error->all(FLERR, "Fix reaxff/species cutoff atom type(s) out of range");
       if ((bo_cut > 1.0) || (bo_cut < 0.0))
         error->all(FLERR, "Fix reaxff/species invalid cutoff value: {}", bo_cut);
 
-      BOCut[itype][jtype] = bo_cut;
-      BOCut[jtype][itype] = bo_cut;
+      for (int i = ilo; i <= ihi; ++i) {
+        for (int j = MAX(jlo, i); j <= jhi; ++j) {
+          BOCut[i][j] = bo_cut;
+          BOCut[j][i] = bo_cut;
+        }
+      }
       iarg += 4;
 
       // modify element type names
@@ -240,17 +242,21 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
         error->all(FLERR, "Unknown fix reaxff/species delete option: {}", arg[iarg]);
       // rate limit when deleting molecules
     } else if (strcmp(arg[iarg], "delete_rate_limit") == 0) {
-      if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "fix reaxff/species delete_rate_limit", error);
+      if (iarg + 3 > narg)
+        utils::missing_cmd_args(FLERR, "fix reaxff/species delete_rate_limit", error);
       delete_Nlimit_varid = -1;
-      if (strncmp(arg[iarg+1],"v_",2) == 0) {
-        delete_Nlimit_varname = &arg[iarg+1][2];
+      if (strncmp(arg[iarg + 1], "v_", 2) == 0) {
+        delete_Nlimit_varname = &arg[iarg + 1][2];
         delete_Nlimit_varid = input->variable->find(delete_Nlimit_varname.c_str());
         if (delete_Nlimit_varid < 0)
-          error->all(FLERR,"Fix reaxff/species: Variable name {} does not exist",delete_Nlimit_varname);
+          error->all(FLERR, "Fix reaxff/species: Variable name {} does not exist",
+                     delete_Nlimit_varname);
         if (!input->variable->equalstyle(delete_Nlimit_varid))
-          error->all(FLERR,"Fix reaxff/species: Variable {} is not equal-style",delete_Nlimit_varname);
-      } else delete_Nlimit = utils::numeric(FLERR, arg[iarg+1], false, lmp);
-      delete_Nsteps = utils::numeric(FLERR, arg[iarg+2], false, lmp);
+          error->all(FLERR, "Fix reaxff/species: Variable {} is not equal-style",
+                     delete_Nlimit_varname);
+      } else
+        delete_Nlimit = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
+      delete_Nsteps = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
       iarg += 3;
       // position of molecules
     } else if (strcmp(arg[iarg], "position") == 0) {
@@ -292,10 +298,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
 
   if (delete_Nsteps > 0) {
     if (lmp->citeme) lmp->citeme->add(cite_reaxff_species_delete);
-    memory->create(delete_Tcount,delete_Nsteps,"reaxff/species:delete_Tcount");
+    memory->create(delete_Tcount, delete_Nsteps, "reaxff/species:delete_Tcount");
 
-    for (int i = 0; i < delete_Nsteps; i++)
-      delete_Tcount[i] = -1;
+    for (int i = 0; i < delete_Nsteps; i++) delete_Tcount[i] = -1;
     delete_Tcount[0] = 0;
   }
 
@@ -393,9 +398,11 @@ void FixReaxFFSpecies::init()
   if (delete_Nsteps > 0) {
     delete_Nlimit_varid = input->variable->find(delete_Nlimit_varname.c_str());
     if (delete_Nlimit_varid < 0)
-      error->all(FLERR,"Fix reaxff/species: Variable name {} does not exist",delete_Nlimit_varname);
+      error->all(FLERR, "Fix reaxff/species: Variable name {} does not exist",
+                 delete_Nlimit_varname);
     if (!input->variable->equalstyle(delete_Nlimit_varid))
-      error->all(FLERR,"Fix reaxff/species: Variable {} is not equal-style",delete_Nlimit_varname);
+      error->all(FLERR, "Fix reaxff/species: Variable {} is not equal-style",
+                 delete_Nlimit_varname);
   }
 }
 
@@ -427,8 +434,7 @@ void FixReaxFFSpecies::Output_ReaxFF_Bonds(bigint ntimestep, FILE * /*fp*/)
   if (ntimestep != nvalid) {
     // push back delete_Tcount on every step
     if (delete_Nsteps > 0)
-      for (int i = delete_Nsteps-1; i > 0; i--)
-        delete_Tcount[i] = delete_Tcount[i-1];
+      for (int i = delete_Nsteps - 1; i > 0; i--) delete_Tcount[i] = delete_Tcount[i - 1];
     return;
   }
 
@@ -732,31 +738,31 @@ void FixReaxFFSpecies::WriteFormulas(int Nmole, int Nspec)
   int i, j, itemp;
   bigint ntimestep = update->ntimestep;
 
-  fprintf(fp, "# Timestep     No_Moles     No_Specs     ");
+  fprintf(fp, "#  Timestep    No_Moles    No_Specs");
 
   Nmoltype = 0;
 
   for (i = 0; i < Nspec; i++) nd[i] = CheckExistence(i, ntypes);
 
   for (i = 0; i < Nmoltype; i++) {
+    std::string molname;
     for (j = 0; j < ntypes; j++) {
       itemp = MolType[ntypes * i + j];
       if (itemp != 0) {
         if (eletype)
-          fprintf(fp, "%s", eletype[j]);
+          molname += eletype[j];
         else
-          fprintf(fp, "%c", ele[j]);
-        if (itemp != 1) fprintf(fp, "%d", itemp);
+          molname += ele[j];
+        if (itemp != 1) molname += std::to_string(itemp);
       }
     }
-    fputs("\t", fp);
+    fmt::print(fp, " {:>11}", molname);
   }
   fputs("\n", fp);
 
-  fmt::print(fp, "{} {:11} {:11}\t", ntimestep, Nmole, Nspec);
-
-  for (i = 0; i < Nmoltype; i++) fprintf(fp, " %d\t", NMol[i]);
-  fprintf(fp, "\n");
+  fmt::print(fp, "{:>11} {:>11} {:>11}", ntimestep, Nmole, Nspec);
+  for (i = 0; i < Nmoltype; i++) fmt::print(fp, " {:>11}", NMol[i]);
+  fputs("\n", fp);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -884,8 +890,8 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
   int ndeletions;
   int headroom = -1;
   if (delete_Nsteps > 0) {
-    if (delete_Tcount[delete_Nsteps-1] == -1) return;
-    ndeletions = delete_Tcount[0] - delete_Tcount[delete_Nsteps-1];
+    if (delete_Tcount[delete_Nsteps - 1] == -1) return;
+    ndeletions = delete_Tcount[0] - delete_Tcount[delete_Nsteps - 1];
     if (delete_Nlimit_varid > -1)
       delete_Nlimit = input->variable->compute_equal(delete_Nlimit_varid);
     headroom = MAX(0, delete_Nlimit - ndeletions);
@@ -925,13 +931,11 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
   std::random_device rnd;
   std::minstd_rand park_rng(rnd());
   int *molrange;
-  memory->create(molrange,Nmole,"reaxff/species:molrange");
-  for (m = 0; m < Nmole; m++)
-    molrange[m] = m + 1;
+  memory->create(molrange, Nmole, "reaxff/species:molrange");
+  for (m = 0; m < Nmole; m++) molrange[m] = m + 1;
   if (delete_Nsteps > 0) {
     // shuffle index when using rate_limit, in case order is biased
-    if (comm->me == 0)
-      std::shuffle(&molrange[0],&molrange[Nmole], park_rng);
+    if (comm->me == 0) std::shuffle(&molrange[0], &molrange[Nmole], park_rng);
     MPI_Bcast(&molrange[0], Nmole, MPI_INT, 0, world);
   }
 
@@ -1060,11 +1064,9 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
     }
   }
 
-
   // push back delete_Tcount on every step
   if (delete_Nsteps > 0) {
-    for (i = delete_Nsteps-1; i > 0; i--)
-      delete_Tcount[i] = delete_Tcount[i-1];
+    for (i = delete_Nsteps - 1; i > 0; i--) delete_Tcount[i] = delete_Tcount[i - 1];
     delete_Tcount[0] += this_delete_Tcount;
   }
 
diff --git a/src/REAXFF/fix_reaxff_species.h b/src/REAXFF/fix_reaxff_species.h
index 27efa0f915..f711cdeb11 100644
--- a/src/REAXFF/fix_reaxff_species.h
+++ b/src/REAXFF/fix_reaxff_species.h
@@ -51,8 +51,6 @@ class FixReaxFFSpecies : public Fix {
   int *Mol2Spec;
   double *clusterID;
   AtomCoord *x0;
-
-  double bg_cut;
   double **BOCut;
 
   std::vector<std::string> del_species;

From 36cac1e83deba7aa03f6122128f6fdf5244ff1bc Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 12:45:41 -0400
Subject: [PATCH 214/396] make sure the field_data vector size always matches
 the size of the keywords vector

---
 src/thermo.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/thermo.cpp b/src/thermo.cpp
index c6e71354ff..6122edec83 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -1068,6 +1068,8 @@ void Thermo::parse_fields(const std::string &str)
       }
     }
   }
+  field_data.clear();
+  field_data.resize(nfield);
 }
 
 /* ----------------------------------------------------------------------

From a2c968386ed31621e288b63b954243d5ae8a9c4e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 12:46:00 -0400
Subject: [PATCH 215/396] include versionadded tag

---
 src/library.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/library.cpp b/src/library.cpp
index 36d53c3e6c..02758abcda 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -756,6 +756,8 @@ double lammps_get_thermo(void *handle, const char *keyword)
  *
 \verbatim embed:rst
 
+.. versionadded:: TBD
+
 This function provides access to cached data from the last thermo output.
 This differs from :cpp:func:`lammps_get_thermo` in that it does not trigger
 an evaluation.  Instead it provides direct access to a read-only location

From 8ddac8cf0229212b046f6eca6b29c4829d319df0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 12:46:41 -0400
Subject: [PATCH 216/396] search through the python folders recursive to detect
 all pending version tags

---
 tools/coding_standard/versiontags.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/coding_standard/versiontags.py b/tools/coding_standard/versiontags.py
index 0b4597046f..ec512a3fad 100644
--- a/tools/coding_standard/versiontags.py
+++ b/tools/coding_standard/versiontags.py
@@ -21,7 +21,7 @@ DEFAULT_CONFIG = """
 recursive: true
 include:
     - doc/src/**
-    - python
+    - python/**
     - src/**
 exclude:
     - src/Make.sh

From 3f6032e80d05039f538aac19f7916102520e08ee Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 13:03:28 -0400
Subject: [PATCH 217/396] add python module interface to lammps_last_thermo,
 small consistency fixes

---
 python/lammps/core.py | 54 +++++++++++++++++++++++++++++++++++++++++++
 src/library.cpp       |  6 ++---
 src/library.h         |  2 +-
 3 files changed, 58 insertions(+), 4 deletions(-)

diff --git a/python/lammps/core.py b/python/lammps/core.py
index 80961186f3..932d4b863c 100644
--- a/python/lammps/core.py
+++ b/python/lammps/core.py
@@ -272,6 +272,9 @@ class lammps(object):
     self.lib.lammps_get_thermo.argtypes = [c_void_p, c_char_p]
     self.lib.lammps_get_thermo.restype = c_double
 
+    self.lib.lammps_last_thermo.argtypes = [c_void_p, c_char_p, c_int]
+    self.lib.lammps_last_thermo.restype = c_void_p
+
     self.lib.lammps_encode_image_flags.restype = self.c_imageint
 
     self.lib.lammps_config_has_package.argtypes = [c_char_p]
@@ -744,6 +747,57 @@ class lammps(object):
 
   # -------------------------------------------------------------------------
 
+  def last_thermo(self):
+    """Get a dictionary of the last thermodynamic output
+
+    This is a wrapper around the :cpp:func:`lammps_last_thermo`
+    function of the C-library interface.  It collects the cached thermo
+    data from the last timestep into a dictionary.  The return value
+    is None, if there has not been any thermo output yet.
+
+    :return: value of thermo keyword
+    :rtype: dict or None
+    """
+
+    rv = dict()
+    with ExceptionCheck(self):
+      ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("step".encode()), 0)
+    mystep = cast(ptr, POINTER(self.c_bigint)).contents.value
+    if mystep < 0:
+      return None
+
+    with ExceptionCheck(self):
+      ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("num".encode()), 0)
+    nfield = cast(ptr, POINTER(c_int)).contents.value
+
+    for i in range(nfield):
+      with ExceptionCheck(self):
+        ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("keyword".encode()), i)
+      kw = cast(ptr, c_char_p).value.decode()
+
+      # temporarily switch return type since this stores an int in a pointer
+      self.lib.lammps_last_thermo.restype = c_int
+      with ExceptionCheck(self):
+        typ = self.lib.lammps_last_thermo(self.lmp, c_char_p("type".encode()), i)
+      self.lib.lammps_last_thermo.restype = c_void_p
+      with ExceptionCheck(self):
+        ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("data".encode()), i)
+
+      if typ == LAMMPS_DOUBLE:
+        val = cast(ptr, POINTER(c_double)).contents.value
+      elif typ == LAMMPS_INT:
+        val = cast(ptr, POINTER(c_int)).contents.value
+      elif typ == LAMMPS_INT64:
+        val = cast(ptr, POINTER(c_int64)).contents.value
+      else:
+        # we should not get here
+        raise TypeError("Unknown LAMMPS data type " + str(typ))
+      rv[kw] = val
+
+    return rv
+
+  # -------------------------------------------------------------------------
+
   def extract_setting(self, name):
     """Query LAMMPS about global settings that can be expressed as an integer.
 
diff --git a/src/library.cpp b/src/library.cpp
index 02758abcda..cf5d131ba6 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -783,15 +783,15 @@ argument string.
      - no
    * - keyword
      - column keyword for thermo output
-     - const char pointer
+     - pointer to 0-terminated const char array
      - yes
    * - type
      - data type of thermo output column; see :cpp:enum:`_LMP_DATATYPE_CONST`
-     - const int
+     - const int (**not** a pointer)
      - yes
    * - data
      - actual field data for column
-     - pointer to either int, int64_t or double
+     - pointer to int, int64_t or double
      - yes
 
 \endverbatim
diff --git a/src/library.h b/src/library.h
index 4c2530210c..5f46e36ccf 100644
--- a/src/library.h
+++ b/src/library.h
@@ -148,7 +148,7 @@ void lammps_commands_string(void *handle, const char *str);
 
 double lammps_get_natoms(void *handle);
 double lammps_get_thermo(void *handle, const char *keyword);
-void *lammps_last_thermo(void *handle, const char *what, int idx);
+void *lammps_last_thermo(void *handle, const char *what, int index);
 
 void lammps_extract_box(void *handle, double *boxlo, double *boxhi, double *xy, double *yz,
                         double *xz, int *pflags, int *boxflag);

From b093f1aac19f056e0decfccef23f95d24cd6d44f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 13:11:19 -0400
Subject: [PATCH 218/396] move versionadded tags to the top, replace some
 missed TBD with version info

---
 python/lammps/core.py          |  71 ++++++++--------
 python/lammps/numpy_wrapper.py |  28 +++----
 src/library.cpp                | 144 +++++++++++++++++----------------
 3 files changed, 125 insertions(+), 118 deletions(-)

diff --git a/python/lammps/core.py b/python/lammps/core.py
index 932d4b863c..b15ddf9302 100644
--- a/python/lammps/core.py
+++ b/python/lammps/core.py
@@ -506,9 +506,9 @@ class lammps(object):
   def error(self, error_type, error_text):
     """Forward error to the LAMMPS Error class.
 
-    This is a wrapper around the :cpp:func:`lammps_error` function of the C-library interface.
+    .. versionadded:: 3Nov2022
 
-    .. versionadded:: TBD
+    This is a wrapper around the :cpp:func:`lammps_error` function of the C-library interface.
 
     :param error_type:
     :type error_type:  int
@@ -1343,6 +1343,8 @@ class lammps(object):
   def gather_bonds(self):
     """Retrieve global list of bonds
 
+    .. versionadded:: 28Jul2021
+
     This is a wrapper around the :cpp:func:`lammps_gather_bonds`
     function of the C-library interface.
 
@@ -1350,8 +1352,6 @@ class lammps(object):
     flat list of ctypes integer values with the bond type, bond atom1,
     bond atom2 for each bond.
 
-    .. versionadded:: 28Jul2021
-
     :return: a tuple with the number of bonds and a list of c_int or c_long
     :rtype: (int, 3*nbonds*c_tagint)
     """
@@ -1366,6 +1366,8 @@ class lammps(object):
   def gather_angles(self):
     """Retrieve global list of angles
 
+    .. versionadded:: 8Feb2023
+
     This is a wrapper around the :cpp:func:`lammps_gather_angles`
     function of the C-library interface.
 
@@ -1373,8 +1375,6 @@ class lammps(object):
     flat list of ctypes integer values with the angle type, angle atom1,
     angle atom2, angle atom3 for each angle.
 
-    .. versionadded:: TBD
-
     :return: a tuple with the number of angles and a list of c_int or c_long
     :rtype: (int, 4*nangles*c_tagint)
     """
@@ -1389,6 +1389,8 @@ class lammps(object):
   def gather_dihedrals(self):
     """Retrieve global list of dihedrals
 
+    .. versionadded:: 8Feb2023
+
     This is a wrapper around the :cpp:func:`lammps_gather_dihedrals`
     function of the C-library interface.
 
@@ -1396,8 +1398,6 @@ class lammps(object):
     flat list of ctypes integer values with the dihedral type, dihedral atom1,
     dihedral atom2, dihedral atom3, dihedral atom4 for each dihedral.
 
-    .. versionadded:: TBD
-
     :return: a tuple with the number of dihedrals and a list of c_int or c_long
     :rtype: (int, 5*ndihedrals*c_tagint)
     """
@@ -1412,6 +1412,8 @@ class lammps(object):
   def gather_impropers(self):
     """Retrieve global list of impropers
 
+    .. versionadded:: 8Feb2023
+
     This is a wrapper around the :cpp:func:`lammps_gather_impropers`
     function of the C-library interface.
 
@@ -1419,8 +1421,6 @@ class lammps(object):
     flat list of ctypes integer values with the improper type, improper atom1,
     improper atom2, improper atom3, improper atom4 for each improper.
 
-    .. versionadded:: TBD
-
     :return: a tuple with the number of impropers and a list of c_int or c_long
     :rtype: (int, 5*nimpropers*c_tagint)
     """
@@ -1659,13 +1659,13 @@ class lammps(object):
   def is_running(self):
     """ Report whether being called from a function during a run or a minimization
 
+    .. versionadded:: 9Oct2020
+
     Various LAMMPS commands must not be called during an ongoing
     run or minimization.  This property allows to check for that.
     This is a wrapper around the :cpp:func:`lammps_is_running`
     function of the library interface.
 
-    .. versionadded:: 9Oct2020
-
     :return: True when called during a run otherwise false
     :rtype: bool
     """
@@ -1676,12 +1676,13 @@ class lammps(object):
   def force_timeout(self):
     """ Trigger an immediate timeout, i.e. a "soft stop" of a run.
 
+    .. versionadded:: 9Oct2020
+
     This function allows to cleanly stop an ongoing run or minimization
     at the next loop iteration.
     This is a wrapper around the :cpp:func:`lammps_force_timeout`
     function of the library interface.
 
-    .. versionadded:: 9Oct2020
     """
     self.lib.lammps_force_timeout(self.lmp)
 
@@ -1764,11 +1765,11 @@ class lammps(object):
   def has_package(self, name):
     """ Report if the named package has been enabled in the LAMMPS shared library.
 
+    .. versionadded:: 3Nov2022
+
     This is a wrapper around the :cpp:func:`lammps_config_has_package`
     function of the library interface.
 
-    .. versionadded:: TBD
-
     :param name: name of the package
     :type  name: string
 
@@ -1908,11 +1909,11 @@ class lammps(object):
   def has_id(self, category, name):
     """Returns whether a given ID name is available in a given category
 
+    .. versionadded:: 9Oct2020
+
     This is a wrapper around the function :cpp:func:`lammps_has_id`
     of the library interface.
 
-    .. versionadded:: 9Oct2020
-
     :param category: name of category
     :type  category: string
     :param name: name of the ID
@@ -1928,11 +1929,11 @@ class lammps(object):
   def available_ids(self, category):
     """Returns a list of IDs available for a given category
 
+    .. versionadded:: 9Oct2020
+
     This is a wrapper around the functions :cpp:func:`lammps_id_count()`
     and :cpp:func:`lammps_id_name()` of the library interface.
 
-    .. versionadded:: 9Oct2020
-
     :param category: name of category
     :type  category: string
 
@@ -1955,11 +1956,11 @@ class lammps(object):
   def available_plugins(self, category):
     """Returns a list of plugins available for a given category
 
+    .. versionadded:: 10Mar2021
+
     This is a wrapper around the functions :cpp:func:`lammps_plugin_count()`
     and :cpp:func:`lammps_plugin_name()` of the library interface.
 
-    .. versionadded:: 10Mar2021
-
     :return: list of style/name pairs of loaded plugins
     :rtype:  list
     """
@@ -2024,11 +2025,11 @@ class lammps(object):
   def fix_external_get_force(self, fix_id):
     """Get access to the array with per-atom forces of a fix external instance with a given fix ID.
 
+    .. versionadded:: 28Jul2021
+
     This is a wrapper around the :cpp:func:`lammps_fix_external_get_force` function
     of the C-library interface.
 
-    .. versionadded:: 28Jul2021
-
     :param fix_id:  Fix-ID of a fix external instance
     :type: string
     :return: requested data
@@ -2043,11 +2044,11 @@ class lammps(object):
   def fix_external_set_energy_global(self, fix_id, eng):
     """Set the global energy contribution for a fix external instance with the given ID.
 
+    .. versionadded:: 28Jul2021
+
     This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_global` function
     of the C-library interface.
 
-    .. versionadded:: 28Jul2021
-
     :param fix_id:  Fix-ID of a fix external instance
     :type: string
     :param eng:     potential energy value to be added by fix external
@@ -2062,11 +2063,11 @@ class lammps(object):
   def fix_external_set_virial_global(self, fix_id, virial):
     """Set the global virial contribution for a fix external instance with the given ID.
 
+    .. versionadded:: 28Jul2021
+
     This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_global` function
     of the C-library interface.
 
-    .. versionadded:: 28Jul2021
-
     :param fix_id:  Fix-ID of a fix external instance
     :type: string
     :param eng:     list of 6 floating point numbers with the virial to be added by fix external
@@ -2082,11 +2083,11 @@ class lammps(object):
   def fix_external_set_energy_peratom(self, fix_id, eatom):
     """Set the per-atom energy contribution for a fix external instance with the given ID.
 
+    .. versionadded:: 28Jul2021
+
     This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_peratom` function
     of the C-library interface.
 
-    .. versionadded:: 28Jul2021
-
     :param fix_id:  Fix-ID of a fix external instance
     :type: string
     :param eatom:   list of potential energy values for local atoms to be added by fix external
@@ -2105,11 +2106,11 @@ class lammps(object):
   def fix_external_set_virial_peratom(self, fix_id, vatom):
     """Set the per-atom virial contribution for a fix external instance with the given ID.
 
+    .. versionadded:: 28Jul2021
+
     This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_peratom` function
     of the C-library interface.
 
-    .. versionadded:: 28Jul2021
-
     :param fix_id:  Fix-ID of a fix external instance
     :type: string
     :param vatom:     list of natoms lists with 6 floating point numbers to be added by fix external
@@ -2137,11 +2138,11 @@ class lammps(object):
   def fix_external_set_vector_length(self, fix_id, length):
     """Set the vector length for a global vector stored with fix external for analysis
 
+    .. versionadded:: 28Jul2021
+
     This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector_length` function
     of the C-library interface.
 
-    .. versionadded:: 28Jul2021
-
     :param fix_id:  Fix-ID of a fix external instance
     :type: string
     :param length:  length of the global vector
@@ -2155,11 +2156,11 @@ class lammps(object):
   def fix_external_set_vector(self, fix_id, idx, val):
     """Store a global vector value for a fix external instance with the given ID.
 
+    .. versionadded:: 28Jul2021
+
     This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector` function
     of the C-library interface.
 
-    .. versionadded:: 28Jul2021
-
     :param fix_id:  Fix-ID of a fix external instance
     :type: string
     :param idx:     1-based index of the value in the global vector
diff --git a/python/lammps/numpy_wrapper.py b/python/lammps/numpy_wrapper.py
index 8286fb9a5c..f3ea0fdf8e 100644
--- a/python/lammps/numpy_wrapper.py
+++ b/python/lammps/numpy_wrapper.py
@@ -262,12 +262,12 @@ class numpy_wrapper:
   def gather_bonds(self):
     """Retrieve global list of bonds as NumPy array
 
+    .. versionadded:: 28Jul2021
+
     This is a wrapper around :py:meth:`lammps.gather_bonds() <lammps.lammps.gather_bonds()>`
     It behaves the same as the original method, but returns a NumPy array instead
     of a ``ctypes`` list.
 
-    .. versionadded:: 28Jul2021
-
     :return: the requested data as a 2d-integer numpy array
     :rtype: numpy.array(nbonds,3)
     """
@@ -280,12 +280,12 @@ class numpy_wrapper:
   def gather_angles(self):
     """ Retrieve global list of angles as NumPy array
 
+    .. versionadded:: 8Feb2023
+
     This is a wrapper around :py:meth:`lammps.gather_angles() <lammps.lammps.gather_angles()>`
     It behaves the same as the original method, but returns a NumPy array instead
     of a ``ctypes`` list.
 
-    .. versionadded:: TBD
-
     :return: the requested data as a 2d-integer numpy array
     :rtype: numpy.array(nangles,4)
     """
@@ -298,12 +298,12 @@ class numpy_wrapper:
   def gather_dihedrals(self):
     """ Retrieve global list of dihedrals as NumPy array
 
+    .. versionadded:: 8Feb2023
+
     This is a wrapper around :py:meth:`lammps.gather_dihedrals() <lammps.lammps.gather_dihedrals()>`
     It behaves the same as the original method, but returns a NumPy array instead
     of a ``ctypes`` list.
 
-    .. versionadded:: TBD
-
     :return: the requested data as a 2d-integer numpy array
     :rtype: numpy.array(ndihedrals,5)
     """
@@ -316,12 +316,12 @@ class numpy_wrapper:
   def gather_impropers(self):
     """ Retrieve global list of impropers as NumPy array
 
+    .. versionadded:: 8Feb2023
+
     This is a wrapper around :py:meth:`lammps.gather_impropers() <lammps.lammps.gather_impropers()>`
     It behaves the same as the original method, but returns a NumPy array instead
     of a ``ctypes`` list.
 
-    .. versionadded:: TBD
-
     :return: the requested data as a 2d-integer numpy array
     :rtype: numpy.array(nimpropers,5)
     """
@@ -334,13 +334,13 @@ class numpy_wrapper:
   def fix_external_get_force(self, fix_id):
     """Get access to the array with per-atom forces of a fix external instance with a given fix ID.
 
+    .. versionchanged:: 28Jul2021
+
     This function is a wrapper around the
     :py:meth:`lammps.fix_external_get_force() <lammps.lammps.fix_external_get_force()>`
     method.  It behaves the same as the original method, but returns a NumPy array instead
     of a ``ctypes`` pointer.
 
-    .. versionchanged:: 28Jul2021
-
     :param fix_id:  Fix-ID of a fix external instance
     :type: string
     :return: requested data
@@ -356,13 +356,13 @@ class numpy_wrapper:
   def fix_external_set_energy_peratom(self, fix_id, eatom):
     """Set the per-atom energy contribution for a fix external instance with the given ID.
 
+    .. versionadded:: 28Jul2021
+
     This function is an alternative to
     :py:meth:`lammps.fix_external_set_energy_peratom() <lammps.lammps.fix_external_set_energy_peratom()>`
     method.  It behaves the same as the original method, but accepts a NumPy array
     instead of a list as argument.
 
-    .. versionadded:: 28Jul2021
-
     :param fix_id:  Fix-ID of a fix external instance
     :type: string
     :param eatom:   per-atom potential energy
@@ -383,13 +383,13 @@ class numpy_wrapper:
   def fix_external_set_virial_peratom(self, fix_id, vatom):
     """Set the per-atom virial contribution for a fix external instance with the given ID.
 
+    .. versionadded:: 28Jul2021
+
     This function is an alternative to
     :py:meth:`lammps.fix_external_set_virial_peratom() <lammps.lammps.fix_external_set_virial_peratom()>`
     method.  It behaves the same as the original method, but accepts a NumPy array
     instead of a list as argument.
 
-    .. versionadded:: 28Jul2021
-
     :param fix_id:  Fix-ID of a fix external instance
     :type: string
     :param eatom:   per-atom potential energy
diff --git a/src/library.cpp b/src/library.cpp
index cf5d131ba6..24a8afa7c7 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -247,6 +247,8 @@ void *lammps_open_no_mpi(int argc, char **argv, void **ptr)
  *
 \verbatim embed:rst
 
+.. versionadded:: 18Sep2020
+
 This function is a version of :cpp:func:`lammps_open`, that uses an
 integer for the MPI communicator as the MPI Fortran interface does.  It
 is used in the :f:func:`lammps` constructor of the LAMMPS Fortran
@@ -257,8 +259,6 @@ communicator with ``MPI_Comm_f2c()`` and then calls
 If for some reason the creation or initialization of the LAMMPS instance
 fails a null pointer is returned.
 
-.. versionadded:: 18Sep2020
-
 *See also*
    :cpp:func:`lammps_open_fortran`, :cpp:func:`lammps_open_no_mpi`
 
@@ -304,13 +304,13 @@ void lammps_close(void *handle)
  *
 \verbatim embed:rst
 
+.. versionadded:: 18Sep2020
+
 The MPI standard requires that any MPI application must call
 ``MPI_Init()`` exactly once before performing any other MPI function
 calls.  This function checks, whether MPI is already initialized and
 calls ``MPI_Init()`` in case it is not.
 
-.. versionadded:: 18Sep2020
-
 \endverbatim */
 
 void lammps_mpi_init()
@@ -333,6 +333,8 @@ void lammps_mpi_init()
  *
 \verbatim embed:rst
 
+.. versionadded:: 18Sep2020
+
 The MPI standard requires that any MPI application calls
 ``MPI_Finalize()`` before exiting.  Even if a calling program does not
 do any MPI calls, MPI is still initialized internally to avoid errors
@@ -341,8 +343,6 @@ before exiting the program to wait until all (parallel) tasks are
 completed and then MPI is cleanly shut down.  After calling this
 function no more MPI calls may be made.
 
-.. versionadded:: 18Sep2020
-
 *See also*
    :cpp:func:`lammps_kokkos_finalize`, :cpp:func:`lammps_python_finalize`
 \endverbatim */
@@ -366,6 +366,8 @@ void lammps_mpi_finalize()
  *
 \verbatim embed:rst
 
+.. versionadded:: 2Jul2021
+
 The Kokkos library may only be initialized once during the execution of
 a process.  This is done automatically the first time Kokkos
 functionality is used.  This requires that the Kokkos environment
@@ -373,8 +375,6 @@ must be explicitly shut down after any LAMMPS instance using it is
 closed (to release associated resources).
 After calling this function no Kokkos functionality may be used.
 
-.. versionadded:: 2Jul2021
-
 *See also*
    :cpp:func:`lammps_mpi_finalize`, :cpp:func:`lammps_python_finalize`
 \endverbatim */
@@ -390,6 +390,8 @@ void lammps_kokkos_finalize()
  *
 \verbatim embed:rst
 
+.. versionadded:: 20Sep2021
+
 This function resets and clears an embedded Python environment
 by calling the `Py_Finalize() function
 <https://docs.python.org/3/c-api/init.html#c.Py_FinalizeEx>`_
@@ -409,8 +411,6 @@ after calling Py_Finalize().
 This function can be called to explicitly clear the Python
 environment in case it is safe to do so.
 
-.. versionadded:: 20Sep2021
-
 *See also*
    :cpp:func:`lammps_mpi_finalize`, :cpp:func:`lammps_kokkos_finalize`
 \endverbatim */
@@ -427,6 +427,8 @@ void lammps_python_finalize()
  *
 \verbatim embed:rst
 
+.. versionadded:: 3Nov2022
+
 This function is a wrapper around functions in the ``Error`` to print an
 error message and then stop LAMMPS.
 
@@ -435,8 +437,6 @@ of constants from :cpp:enum:`_LMP_ERROR_CONST`.  If the value does not
 match any valid combination of constants a warning is printed and the
 function returns.
 
-.. versionadded:: 3Nov2022
-
 \endverbatim
  *
  * \param  handle       pointer to a previously created LAMMPS instance
@@ -979,6 +979,8 @@ void lammps_reset_box(void *handle, double *boxlo, double *boxhi,
  *
 \verbatim embed:rst
 
+.. versionadded:: 18Sep2020
+
 This function will retrieve memory usage information for the current
 LAMMPS instance or process.  The *meminfo* buffer will be filled with
 3 different numbers (if supported by the operating system).  The first
@@ -991,8 +993,6 @@ third number is the maximum amount of RAM (not swap) used by the process
 so far. If any of the two latter parameters is not supported by the operating
 system it will be set to zero.
 
-.. versionadded:: 18Sep2020
-
 \endverbatim
  *
  * \param  handle   pointer to a previously created LAMMPS instance
@@ -1012,6 +1012,8 @@ void lammps_memory_usage(void *handle, double *meminfo)
  *
 \verbatim embed:rst
 
+.. versionadded:: 18Sep2020
+
 This will take the LAMMPS "world" communicator and convert it to an
 integer using ``MPI_Comm_c2f()``, so it is equivalent to the
 corresponding MPI communicator in Fortran. This way it can be safely
@@ -1020,8 +1022,6 @@ to the C language representation use ``MPI_Comm_f2c()``.
 
 If LAMMPS was compiled with MPI_STUBS, this function returns -1.
 
-.. versionadded:: 18Sep2020
-
 *See also*
    :cpp:func:`lammps_open_fortran`
 
@@ -1284,13 +1284,13 @@ int lammps_extract_setting(void *handle, const char *keyword)
  *
 \verbatim embed:rst
 
+.. versionadded:: 18Sep2020
+
 This function returns an integer that encodes the data type of the global
 property with the specified name. See :cpp:enum:`_LMP_DATATYPE_CONST` for valid
 values. Callers of :cpp:func:`lammps_extract_global` can use this information
 to then decide how to cast the ``void *`` pointer and access the data.
 
-.. versionadded:: 18Sep2020
-
 \endverbatim
  *
  * \param  handle   pointer to a previously created LAMMPS instance (unused)
@@ -1773,13 +1773,13 @@ void *lammps_extract_global(void *handle, const char *name)
  *
 \verbatim embed:rst
 
+.. versionadded:: 18Sep2020
+
 This function returns an integer that encodes the data type of the per-atom
 property with the specified name. See :cpp:enum:`_LMP_DATATYPE_CONST` for valid
 values. Callers of :cpp:func:`lammps_extract_atom` can use this information
 to then decide how to cast the ``void *`` pointer and access the data.
 
-.. versionadded:: 18Sep2020
-
 \endverbatim
  *
  * \param  handle  pointer to a previously created LAMMPS instance
@@ -2308,13 +2308,13 @@ void *lammps_extract_variable(void *handle, const char *name, const char *group)
  *
 \verbatim embed:rst
 
+.. versionadded:: 3Nov2022
+
 This function returns an integer that encodes the data type of the variable
 with the specified name. See :cpp:enum:`_LMP_VAR_CONST` for valid values.
 Callers of :cpp:func:`lammps_extract_variable` can use this information to
 decide how to cast the ``void *`` pointer and access the data.
 
-.. versionadded:: 3Nov2022
-
 \endverbatim
  *
  * \param  handle  pointer to a previously created LAMMPS instance
@@ -3166,6 +3166,8 @@ void lammps_scatter_atoms_subset(void *handle, const char *name, int type,
  *
 \verbatim embed:rst
 
+.. versionadded:: 28Jul2021
+
 This function copies the list of all bonds into a buffer provided by
 the calling code. The buffer will be filled with bond type, bond atom 1,
 bond atom 2 for each bond. Thus the buffer has to be allocated to the
@@ -3180,8 +3182,6 @@ When running in parallel, the data buffer must be allocated on **all**
 MPI ranks and will be filled with the information for **all** bonds
 in the system.
 
-.. versionadded:: 28Jul2021
-
 Below is a brief C code demonstrating accessing this collected bond information.
 
 .. code-block:: c
@@ -3277,6 +3277,8 @@ void lammps_gather_bonds(void *handle, void *data)
  *
 \verbatim embed:rst
 
+.. versionadded:: 8Feb2023
+
 This function copies the list of all angles into a buffer provided by
 the calling code. The buffer will be filled with angle type, angle atom 1,
 angle atom 2, angle atom 3 for each angle. Thus the buffer has to be allocated to the
@@ -3291,8 +3293,6 @@ When running in parallel, the data buffer must be allocated on **all**
 MPI ranks and will be filled with the information for **all** angles
 in the system.
 
-.. versionadded:: 8Feb2023
-
 Below is a brief C code demonstrating accessing this collected angle information.
 
 .. code-block:: c
@@ -3388,6 +3388,8 @@ void lammps_gather_angles(void *handle, void *data)
  *
 \verbatim embed:rst
 
+.. versionadded:: 8Feb2023
+
 This function copies the list of all dihedrals into a buffer provided by
 the calling code. The buffer will be filled with dihedral type, dihedral atom 1,
 dihedral atom 2, dihedral atom 3, dihedral atom 4 for each dihedral.
@@ -3403,8 +3405,6 @@ When running in parallel, the data buffer must be allocated on **all**
 MPI ranks and will be filled with the information for **all** dihedrals
 in the system.
 
-.. versionadded:: 8Feb2023
-
 Below is a brief C code demonstrating accessing this collected dihedral information.
 
 .. code-block:: c
@@ -3500,6 +3500,8 @@ void lammps_gather_dihedrals(void *handle, void *data)
  *
 \verbatim embed:rst
 
+.. versionadded:: 8Feb2023
+
 This function copies the list of all impropers into a buffer provided by
 the calling code. The buffer will be filled with improper type, improper atom 1,
 improper atom 2, improper atom 3, improper atom 4 for each improper.
@@ -3515,8 +3517,6 @@ When running in parallel, the data buffer must be allocated on **all**
 MPI ranks and will be filled with the information for **all** impropers
 in the system.
 
-.. versionadded:: 8Feb2023
-
 Below is a brief C code demonstrating accessing this collected improper information.
 
 .. code-block:: c
@@ -5310,6 +5310,8 @@ int lammps_version(void *handle)
  *
 \verbatim embed:rst
 
+.. versionadded:: 9Oct2020
+
 The :cpp:func:`lammps_get_os_info` function can be used to retrieve
 detailed information about the hosting operating system and
 compiler/runtime.
@@ -5318,8 +5320,6 @@ A suitable buffer for a C-style string has to be provided and its length.
 The assembled text will be truncated to not overflow this buffer. The
 string is typically a few hundred bytes long.
 
-.. versionadded:: 9Oct2020
-
 \endverbatim
  *
  * \param  buffer    string buffer to copy the information to
@@ -5548,6 +5548,8 @@ int lammps_config_accelerator(const char *package,
  *
 \verbatim embed:rst
 
+.. versionadded:: 14May2021
+
 The :cpp:func:`lammps_has_gpu_device` function checks at runtime if
 an accelerator device is present that can be used with the
 :doc:`GPU package <Speed_gpu>`. If at least one suitable device is
@@ -5557,8 +5559,6 @@ More detailed information about the available device or devices can
 be obtained by calling the
 :cpp:func:`lammps_get_gpu_device_info` function.
 
-.. versionadded:: 14May2021
-
 \endverbatim
  *
  * \return  1 if viable device is available, 0 if not.  */
@@ -5572,6 +5572,8 @@ int lammps_has_gpu_device()
  *
 \verbatim embed:rst
 
+.. versionadded:: 14May2021
+
 The :cpp:func:`lammps_get_gpu_device_info` function can be used to retrieve
 detailed information about any accelerator devices that are viable for use
 with the :doc:`GPU package <Speed_gpu>`.  It will produce a string that is
@@ -5583,8 +5585,6 @@ A suitable buffer for a C-style string has to be provided and its length.
 The assembled text will be truncated to not overflow this buffer.  This
 string can be several kilobytes long, if multiple devices are present.
 
-.. versionadded:: 14May2021
-
 \endverbatim
  *
  * \param  buffer    string buffer to copy the information to
@@ -5681,12 +5681,13 @@ int lammps_style_name(void *handle, const char *category, int idx,
 /** Check if a specific ID exists in the current LAMMPS instance
  *
 \verbatim embed:rst
+
+.. versionadded:: 9Oct2020
+
 This function checks if the current LAMMPS instance a *category* ID of
 the given *name* exists.  Valid categories are: *compute*\ , *dump*\ ,
 *fix*\ , *group*\ , *molecule*\ , *region*\ , and *variable*\ .
 
-.. versionadded:: 9Oct2020
-
 \endverbatim
  *
  * \param  handle    pointer to a previously created LAMMPS instance cast to ``void *``.
@@ -5720,13 +5721,14 @@ int lammps_has_id(void *handle, const char *category, const char *name) {
 /** Count the number of IDs of a category.
  *
 \verbatim embed:rst
+
+.. versionadded:: 9Oct2020
+
 This function counts how many IDs in the provided *category*
 are defined in the current LAMMPS instance.
 Please see :cpp:func:`lammps_has_id` for a list of valid
 categories.
 
-.. versionadded:: 9Oct2020
-
 \endverbatim
  *
  * \param handle   pointer to a previously created LAMMPS instance cast to ``void *``.
@@ -5758,6 +5760,9 @@ int lammps_id_count(void *handle, const char *category) {
 /** Look up the name of an ID by index in the list of IDs of a given category.
  *
 \verbatim embed:rst
+
+.. versionadded:: 9Oct2020
+
 This function copies the name of the *category* ID with the index
 *idx* into the provided C-style string buffer.  The length of the buffer
 must be provided as *buf_size* argument.  If the name of the style
@@ -5765,8 +5770,6 @@ exceeds the length of the buffer, it will be truncated accordingly.
 If the index is out of range, the function returns 0 and *buffer* is
 set to an empty string, otherwise 1.
 
-.. versionadded:: 9Oct2020
-
 \endverbatim
  *
  * \param handle   pointer to a previously created LAMMPS instance cast to ``void *``.
@@ -5829,10 +5832,11 @@ int lammps_id_name(void *handle, const char *category, int idx, char *buffer, in
 /** Count the number of loaded plugins
  *
 \verbatim embed:rst
-This function counts how many plugins are currently loaded.
 
 .. versionadded:: 10Mar2021
 
+This function counts how many plugins are currently loaded.
+
 \endverbatim
  *
  * \return number of loaded plugins
@@ -5851,6 +5855,9 @@ int lammps_plugin_count()
 /** Look up the info of a loaded plugin by its index in the list of plugins
  *
 \verbatim embed:rst
+
+.. versionadded:: 10Mar2021
+
 This function copies the name of the *style* plugin with the index
 *idx* into the provided C-style string buffer.  The length of the buffer
 must be provided as *buf_size* argument.  If the name of the style
@@ -5858,8 +5865,6 @@ exceeds the length of the buffer, it will be truncated accordingly.
 If the index is out of range, the function returns 0 and *buffer* is
 set to an empty string, otherwise 1.
 
-.. versionadded:: 10Mar2021
-
 \endverbatim
  *
  * \param  idx       index of the plugin in the list all or *style* plugins
@@ -6018,9 +6023,11 @@ void lammps_set_fix_external_callback(void *handle, const char *id, FixExternalF
 
 \verbatim embed:rst
 
-Fix :doc:`external <fix_external>` allows programs that are running LAMMPS through
-its library interface to add or modify certain LAMMPS properties on specific
-timesteps, similar to the way other fixes do.
+.. versionadded:: 28Jul2021
+
+Fix :doc:`external <fix_external>` allows programs that are running
+LAMMPS through its library interface to add or modify certain LAMMPS
+properties on specific timesteps, similar to the way other fixes do.
 
 This function provides access to the per-atom force storage in a fix
 external instance with the given fix-ID to be added to the individual
@@ -6033,12 +6040,12 @@ data structures can change as well as the order of atom as they migrate
 between MPI processes because of the domain decomposition
 parallelization, this function should be always called immediately
 before the forces are going to be set to get an up-to-date pointer.
-You can use, for example, :cpp:func:`lammps_extract_setting` to obtain the
-number of local atoms `nlocal` and then assume the dimensions of the returned
-force array as ``double force[nlocal][3]``.
+You can use, for example, :cpp:func:`lammps_extract_setting` to obtain
+the number of local atoms `nlocal` and then assume the dimensions of
+the returned force array as ``double force[nlocal][3]``.
 
-This is an alternative to the callback mechanism in fix external set up by
-:cpp:func:`lammps_set_fix_external_callback`. The main difference is
+This is an alternative to the callback mechanism in fix external set up
+by :cpp:func:`lammps_set_fix_external_callback`. The main difference is
 that this mechanism can be used when forces are be pre-computed and the
 control alternates between LAMMPS and the external code, while the
 callback mechanism can call the external code to compute the force when
@@ -6048,8 +6055,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
 more information about how to use the fix and how to couple it with an
 external code.
 
-.. versionadded:: 28Jul2021
-
 \endverbatim
  *
  * \param  handle     pointer to a previously created LAMMPS instance cast to ``void *``.
@@ -6080,6 +6085,8 @@ double **lammps_fix_external_get_force(void *handle, const char *id)
 
 \verbatim embed:rst
 
+.. versionadded:: 28Jul2021
+
 This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
 :cpp:func:`lammps_fix_external_get_force` to also set the contribution
 to the global energy from the external code.  The value of the *eng*
@@ -6096,8 +6103,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
 more information about how to use the fix and how to couple it with an
 external code.
 
-.. versionadded:: 28Jul2021
-
 \endverbatim
  *
  * \param  handle   pointer to a previously created LAMMPS instance cast to ``void *``.
@@ -6126,6 +6131,8 @@ void lammps_fix_external_set_energy_global(void *handle, const char *id, double
 
 \verbatim embed:rst
 
+.. versionadded:: 28Jul2021
+
 This is a companion function to :cpp:func:`lammps_set_fix_external_callback`
 and :cpp:func:`lammps_fix_external_get_force` to set the contribution to
 the global virial from the external code.
@@ -6144,8 +6151,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
 more information about how to use the fix and how to couple it with an
 external code.
 
-.. versionadded:: 28Jul2021
-
 \endverbatim
  *
  * \param  handle   pointer to a previously created LAMMPS instance cast to ``void *``.
@@ -6174,6 +6179,8 @@ void lammps_fix_external_set_virial_global(void *handle, const char *id, double
 
 \verbatim embed:rst
 
+.. versionadded:: 28Jul2021
+
 This is a companion function to :cpp:func:`lammps_set_fix_external_callback`
 to set the per-atom energy contribution due to the fix from the external code
 as part of the callback function.  For this to work, the handle to the
@@ -6192,8 +6199,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
 more information about how to use the fix and how to couple it with an
 external code.
 
-.. versionadded:: 28Jul2021
-
 \endverbatim
  *
  * \param  handle   pointer to a previously created LAMMPS instance cast to ``void *``.
@@ -6222,6 +6227,8 @@ void lammps_fix_external_set_energy_peratom(void *handle, const char *id, double
 
 \verbatim embed:rst
 
+.. versionadded:: 28Jul2021
+
 This is a companion function to :cpp:func:`lammps_set_fix_external_callback`
 to set the per-atom virial contribution due to the fix from the external code
 as part of the callback function.  For this to work, the handle to the
@@ -6243,8 +6250,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
 more information about how to use the fix and how to couple it with an
 external code.
 
-.. versionadded:: 28Jul2021
-
 \endverbatim
  *
  * \param  handle   pointer to a previously created LAMMPS instance cast to ``void *``.
@@ -6273,6 +6278,8 @@ void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double
 
 \verbatim embed:rst
 
+.. versionadded:: 28Jul2021
+
 This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
 :cpp:func:`lammps_fix_external_get_force` to set the length of a global vector of
 properties that will be stored with the fix via
@@ -6287,8 +6294,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
 more information about how to use the fix and how to couple it with an
 external code.
 
-.. versionadded:: 28Jul2021
-
 \endverbatim
  *
  * \param  handle   pointer to a previously created LAMMPS instance cast to ``void *``.
@@ -6317,6 +6322,8 @@ void lammps_fix_external_set_vector_length(void *handle, const char *id, int len
 
 \verbatim embed:rst
 
+.. versionadded:: 28Jul2021
+
 This is a companion function to :cpp:func:`lammps_set_fix_external_callback` and
 :cpp:func:`lammps_fix_external_get_force` to set the values of a global vector of
 properties that will be stored with the fix.  And can be accessed from
@@ -6340,8 +6347,6 @@ Please see the documentation for :doc:`fix external <fix_external>` for
 more information about how to use the fix and how to couple it with an
 external code.
 
-.. versionadded:: 28Jul2021
-
 \endverbatim
  *
  * \param  handle   pointer to a previously created LAMMPS instance cast to ``void *``.
@@ -6513,12 +6518,13 @@ int lammps_get_last_error_message(void *handle, char *buffer, int buf_size) {
 /** Return API version of embedded Python interpreter
 
 \verbatim embed:rst
+
+.. versionadded:: 3Nov2022
+
 This function is used by the ML-IAP python code (mliappy) to verify
 the API version of the embedded python interpreter of the PYTHON
 package.  It returns -1 if the PYTHON package is not enabled.
 
-.. versionadded:: 3Nov2022
-
 \endverbatim
  *
  * \return   PYTHON_API_VERSION constant of the python interpreter or -1 */

From 81854cd03e1903e6fc545f1e27028e65d1864385 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 14:55:45 -0400
Subject: [PATCH 219/396] change type keyword to return a pointer to static
 location for better portability

---
 python/lammps/core.py |  7 +++----
 src/library.cpp       | 19 +++++++++++++++----
 2 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/python/lammps/core.py b/python/lammps/core.py
index b15ddf9302..d34d5de4d4 100644
--- a/python/lammps/core.py
+++ b/python/lammps/core.py
@@ -775,11 +775,10 @@ class lammps(object):
         ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("keyword".encode()), i)
       kw = cast(ptr, c_char_p).value.decode()
 
-      # temporarily switch return type since this stores an int in a pointer
-      self.lib.lammps_last_thermo.restype = c_int
       with ExceptionCheck(self):
-        typ = self.lib.lammps_last_thermo(self.lmp, c_char_p("type".encode()), i)
-      self.lib.lammps_last_thermo.restype = c_void_p
+        ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("type".encode()), i)
+      typ = cast(ptr, POINTER(c_int)).contents.value
+
       with ExceptionCheck(self):
         ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("data".encode()), i)
 
diff --git a/src/library.cpp b/src/library.cpp
index 24a8afa7c7..0fcedfc20b 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -765,6 +765,13 @@ of the last thermo output data and the corresponding keyword strings.
 The how to handle the return value depends on the value of the *what*
 argument string.
 
+.. note::
+
+   The *type* property points to a static location that is reassigned
+   with every call, so the returned pointer should be recast,
+   dereferenced, and assigned immediately. Otherwise, its value may be
+   changed with the next invocation of the function.
+
 .. list-table::
    :header-rows: 1
    :widths: auto
@@ -787,7 +794,7 @@ argument string.
      - yes
    * - type
      - data type of thermo output column; see :cpp:enum:`_LMP_DATATYPE_CONST`
-     - const int (**not** a pointer)
+     - pointer to static int
      - yes
    * - data
      - actual field data for column
@@ -808,6 +815,7 @@ void *lammps_last_thermo(void *handle, const char *what, int index)
   Thermo *th = lmp->output->thermo;
   if (!th) return nullptr;
   const int nfield = *th->get_nfield();
+  static int datatype;
 
   BEGIN_CAPTURE
   {
@@ -826,11 +834,14 @@ void *lammps_last_thermo(void *handle, const char *what, int index)
       if ((index < 0) || (index >= nfield)) return nullptr;
       const auto &field = th->get_fields()[index];
       if (field.type == multitype::INT) {
-        val = (void *) LAMMPS_INT;
+        datatype = LAMMPS_INT;
+        val = (void *) &datatype;
       } else if (field.type == multitype::BIGINT) {
-        val = (void *) LAMMPS_INT64;
+        datatype = LAMMPS_INT64;
+        val = (void *) &datatype;
       } else if (field.type == multitype::DOUBLE) {
-        val = (void *) LAMMPS_DOUBLE;
+        datatype = LAMMPS_DOUBLE;
+        val = (void *) &datatype;
       }
 
     } else if (strcmp(what, "data") == 0) {

From 5d4f9abf5b6604414e8f82537e49b21fbbfb65bc Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 15:15:28 -0400
Subject: [PATCH 220/396] add unit tests for c-library interface and plain
 python module

---
 .../c-library/test_library_properties.cpp     | 61 ++++++++++++++++++-
 unittest/python/python-commands.py            | 27 ++++++++
 2 files changed, 86 insertions(+), 2 deletions(-)

diff --git a/unittest/c-library/test_library_properties.cpp b/unittest/c-library/test_library_properties.cpp
index d6dd55f75e..14eab06213 100644
--- a/unittest/c-library/test_library_properties.cpp
+++ b/unittest/c-library/test_library_properties.cpp
@@ -14,6 +14,7 @@
 #define STRINGIFY(val) XSTR(val)
 #define XSTR(val) #val
 
+using ::LAMMPS_NS::bigint;
 using ::LAMMPS_NS::tagint;
 using ::LAMMPS_NS::platform::path_join;
 using ::testing::HasSubstr;
@@ -93,6 +94,9 @@ TEST_F(LibraryProperties, natoms)
 
 TEST_F(LibraryProperties, thermo)
 {
+    bigint bval = *(bigint *)lammps_last_thermo(lmp, "step", 0);
+    EXPECT_EQ(bval, -1);
+
     if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP();
     std::string input = path_join(INPUT_DIR, "in.fourmol");
     ::testing::internal::CaptureStdout();
@@ -105,6 +109,59 @@ TEST_F(LibraryProperties, thermo)
     EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "vol"), 3375.0);
     EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "density"), 0.12211250945013695);
     EXPECT_DOUBLE_EQ(lammps_get_thermo(lmp, "cellalpha"), 90.0);
+
+    bval = *(bigint *)lammps_last_thermo(lmp, "step", 0);
+    EXPECT_EQ(bval, 2);
+    int ival = *(int *)lammps_last_thermo(lmp, "num", 0);
+    EXPECT_EQ(ival, 6);
+
+    const char *key = (const char *)lammps_last_thermo(lmp, "keyword", 0);
+    EXPECT_THAT(key, StrEq("Step"));
+    ival = *(int *)lammps_last_thermo(lmp, "type", 0);
+#if defined(LAMMPS_SMALLSMALL)
+    EXPECT_EQ(ival, LAMMPS_INT);
+    ival = *(int *)lammps_last_thermo(lmp, "data", 0);
+    EXPECT_EQ(ival, 2);
+#else
+    EXPECT_EQ(ival, LAMMPS_INT64);
+    bval = *(bigint *)lammps_last_thermo(lmp, "data", 0);
+    EXPECT_EQ(bval, 2);
+#endif
+
+    key = (const char *)lammps_last_thermo(lmp, "keyword", 1);
+    EXPECT_THAT(key, StrEq("Temp"));
+    ival = *(int *)lammps_last_thermo(lmp, "type", 1);
+    EXPECT_EQ(ival, LAMMPS_DOUBLE);
+    double dval = *(double *)lammps_last_thermo(lmp, "data", 1);
+    EXPECT_DOUBLE_EQ(dval, 28.042780385852982);
+
+    key = (const char *)lammps_last_thermo(lmp, "keyword", 2);
+    EXPECT_THAT(key, StrEq("E_pair"));
+    ival = *(int *)lammps_last_thermo(lmp, "type", 2);
+    EXPECT_EQ(ival, LAMMPS_DOUBLE);
+    dval = *(double *)lammps_last_thermo(lmp, "data", 2);
+    EXPECT_DOUBLE_EQ(dval, 0.0);
+
+    key = (const char *)lammps_last_thermo(lmp, "keyword", 3);
+    EXPECT_THAT(key, StrEq("E_mol"));
+    ival = *(int *)lammps_last_thermo(lmp, "type", 3);
+    EXPECT_EQ(ival, LAMMPS_DOUBLE);
+    dval = *(double *)lammps_last_thermo(lmp, "data", 3);
+    EXPECT_DOUBLE_EQ(dval, 0.0);
+
+    key = (const char *)lammps_last_thermo(lmp, "keyword", 4);
+    EXPECT_THAT(key, StrEq("TotEng"));
+    ival = *(int *)lammps_last_thermo(lmp, "type", 4);
+    EXPECT_EQ(ival, LAMMPS_DOUBLE);
+    dval = *(double *)lammps_last_thermo(lmp, "data", 4);
+    EXPECT_DOUBLE_EQ(dval, 2.3405256449146163);
+
+    key = (const char *)lammps_last_thermo(lmp, "keyword", 5);
+    EXPECT_THAT(key, StrEq("Press"));
+    ival = *(int *)lammps_last_thermo(lmp, "type", 5);
+    EXPECT_EQ(ival, LAMMPS_DOUBLE);
+    dval = *(double *)lammps_last_thermo(lmp, "data", 5);
+    EXPECT_DOUBLE_EQ(dval, 31.700964689115658);
 };
 
 TEST_F(LibraryProperties, box)
@@ -325,8 +382,8 @@ TEST_F(LibraryProperties, global)
 
     EXPECT_EQ(lammps_extract_global_datatype(lmp, "special_lj"), LAMMPS_DOUBLE);
     EXPECT_EQ(lammps_extract_global_datatype(lmp, "special_coul"), LAMMPS_DOUBLE);
-    double *special_lj = (double *)lammps_extract_global(lmp, "special_lj");
-    double *special_coul= (double *)lammps_extract_global(lmp, "special_coul");
+    double *special_lj   = (double *)lammps_extract_global(lmp, "special_lj");
+    double *special_coul = (double *)lammps_extract_global(lmp, "special_coul");
     EXPECT_DOUBLE_EQ(special_lj[0], 1.0);
     EXPECT_DOUBLE_EQ(special_lj[1], 0.0);
     EXPECT_DOUBLE_EQ(special_lj[2], 0.5);
diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py
index 33b19ba4f0..1c25751191 100644
--- a/unittest/python/python-commands.py
+++ b/unittest/python/python-commands.py
@@ -533,6 +533,33 @@ create_atoms 1 single &
             result = self.lmp.get_thermo(key)
             self.assertEqual(value, result, key)
 
+
+    def test_last_thermo(self):
+        self.lmp.command("units lj")
+        self.lmp.command("atom_style atomic")
+        self.lmp.command("atom_modify map array")
+        self.lmp.command("boundary f f f")
+        self.lmp.command("region box block 0 2 0 2 0 2")
+        self.lmp.command("create_box 1 box")
+        self.lmp.command("mass * 1")
+
+        x = [
+          0.5, 0.5, 0.5,
+          1.5, 1.5, 1.5
+        ]
+        types = [1, 1]
+        self.lmp.create_atoms(2, id=None, type=types, x=x)
+
+        self.assertEqual(self.lmp.last_thermo(), None)
+        self.lmp.command("run 2 post no")
+        ref = { "Step" : 2,
+                "Temp" : 0.0,
+                "E_pair" : 0.0,
+                "E_mol" : 0.0,
+                "TotEng" : 0.0,
+                "Press" : 0.0}
+        self.assertDictEqual(self.lmp.last_thermo(), ref)
+
     def test_extract_global(self):
         self.lmp.command("region box block -1 1 -2 2 -3 3")
         self.lmp.command("create_box 1 box")

From 2e1190bfee1bee986abe9e8272e3ab3718815feb Mon Sep 17 00:00:00 2001
From: "W. Michael Brown" <michael.w.brown@intel.com>
Date: Thu, 8 Jun 2023 15:02:17 -0700
Subject: [PATCH 221/396] Fixing issue with when atom styles using torque are
 mixed with intel pair styles not using torque. Generating runtime error for
 mixing intel gayberne style with non-ellipsoid intel pair styles.

---
 src/INTEL/fix_intel.cpp     | 31 +++++++++++++++++++++++++------
 src/INTEL/fix_intel.h       |  2 +-
 src/INTEL/intel_buffers.cpp |  3 ++-
 src/INTEL/intel_buffers.h   |  6 ++++--
 4 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/src/INTEL/fix_intel.cpp b/src/INTEL/fix_intel.cpp
index 2b786b6eed..ef6bfc3408 100644
--- a/src/INTEL/fix_intel.cpp
+++ b/src/INTEL/fix_intel.cpp
@@ -61,6 +61,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) :  Fix(lmp, narg, arg)
   _hybrid_nonpair = 0;
   _print_pkg_info = 1;
   _nthreads = comm->nthreads;
+  _torque_flag = 0;
 
   _precision_mode = PREC_MODE_MIXED;
   _offload_balance = -1.0;
@@ -301,14 +302,29 @@ void FixIntel::init()
   }
   #endif
 
+  _torque_flag = 0;
+  if (force->pair_match("gayberne/intel$", 0)) _torque_flag = 1;
+
   const int nstyles = _pair_intel_count;
   if (force->pair_match("^hybrid", 0) != nullptr) {
     _pair_hybrid_flag = 1;
+
+    // Check if need to handle torque
+    auto hybrid = dynamic_cast<PairHybrid *>(force->pair);
+    for (int i = 0; i < hybrid->nstyles; i++)
+      if (utils::strmatch(hybrid->keywords[i],"/intel$") &&
+          utils::strmatch(hybrid->keywords[i],"gayberne"))
+        _torque_flag = 1;
+
     if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute)
       error->all(FLERR,"INTEL package requires fdotr virial with newton on.");
   } else
     _pair_hybrid_flag = 0;
 
+  if (_torque_flag && nstyles > 1)
+    error->all(FLERR,"gayberne/intel style cannot yet be used with other "
+               "intel pair styles.");
+
   if (nstyles > 1 && _pair_hybrid_flag) _pair_hybrid_flag = 2;
   else if (force->newton_pair == 0) _pair_hybrid_flag = 0;
 
@@ -335,14 +351,17 @@ void FixIntel::init()
   int off_mode = 0;
   if (_offload_balance != 0.0) off_mode = 1;
   if (_precision_mode == PREC_MODE_SINGLE) {
+    _single_buffers->set_torque_flag(_torque_flag);
     _single_buffers->zero_ev();
     _single_buffers->grow_ncache(off_mode, comm->nthreads);
     _single_buffers->free_list_ptrs();
   } else if (_precision_mode == PREC_MODE_MIXED) {
+    _mixed_buffers->set_torque_flag(_torque_flag);
     _mixed_buffers->zero_ev();
     _mixed_buffers->grow_ncache(off_mode, comm->nthreads);
     _mixed_buffers->free_list_ptrs();
   } else {
+    _double_buffers->set_torque_flag(_torque_flag);
     _double_buffers->zero_ev();
     _double_buffers->grow_ncache(off_mode, comm->nthreads);
     _double_buffers->free_list_ptrs();
@@ -620,7 +639,7 @@ void FixIntel::reduce_results(acc_t * _noalias const f_scalar)
     o_range = atom->nlocal + atom->nghost;
   else
     o_range = atom->nlocal;
-  IP_PRE_get_stride(f_stride, o_range, (sizeof(acc_t)*4), lmp->atom->torque);
+  IP_PRE_get_stride(f_stride, o_range, (sizeof(acc_t)*4), _torque_flag);
 
   o_range *= 4;
   const int f_stride4 = f_stride * 4;
@@ -719,7 +738,7 @@ void FixIntel::add_results(const ft * _noalias const f_in,
         add_oresults(f_in, ev_global, eatom, vatom, 0, _offload_nlocal);
         const acc_t * _noalias const enull = 0;
         int offset = _offload_nlocal;
-        if (atom->torque) offset *= 2;
+        if (_torque_flag) offset *= 2;
         add_oresults(f_in + offset, enull, eatom, vatom,
                      _offload_min_ghost, _offload_nghost);
       } else
@@ -730,7 +749,7 @@ void FixIntel::add_results(const ft * _noalias const f_in,
                      _host_min_local, _host_used_local);
         const acc_t * _noalias const enull = 0;
         int offset = _host_used_local;
-        if (atom->torque) offset *= 2;
+        if (_torque_flag) offset *= 2;
         add_oresults(f_in + offset, enull, eatom,
                      vatom, _host_min_ghost, _host_used_ghost);
       } else {
@@ -779,7 +798,7 @@ void FixIntel::add_oresults(const ft * _noalias const f_in,
                             const int eatom, const int /*vatom*/,
                             const int out_offset, const int nall) {
   lmp_ft * _noalias const f = (lmp_ft *) lmp->atom->f[0] + out_offset;
-  if (atom->torque) {
+  if (_torque_flag) {
     if (f_in[1].w)
     {
       if (f_in[1].w == 1)
@@ -803,7 +822,7 @@ void FixIntel::add_oresults(const ft * _noalias const f_in,
     #endif
     int ifrom, ito;
     IP_PRE_omp_range_align(ifrom, ito, tid, nall, packthreads, sizeof(acc_t));
-    if (atom->torque) {
+    if (_torque_flag) {
       int ii = ifrom * 2;
       lmp_ft * _noalias const tor = (lmp_ft *) lmp->atom->torque[0] +
         out_offset;
@@ -927,7 +946,7 @@ void FixIntel::add_off_results(const ft * _noalias const f_in,
       _offload_nlocal;
   }
 
-  if (atom->torque)
+  if (_torque_flag)
     if (f_in[1].w < 0.0)
       error->all(FLERR,"Bad matrix inversion in mldivide3");
   add_results(f_in, ev_global, _off_results_eatom, _off_results_vatom, 1);
diff --git a/src/INTEL/fix_intel.h b/src/INTEL/fix_intel.h
index 050b27c313..08d0a534d9 100644
--- a/src/INTEL/fix_intel.h
+++ b/src/INTEL/fix_intel.h
@@ -116,7 +116,7 @@ class FixIntel : public Fix {
   int _precision_mode, _nthreads, _nbor_pack_width, _three_body_neighbor;
   int _pair_intel_count, _pair_hybrid_flag, _print_pkg_info;
   // These should be removed in subsequent update w/ simpler hybrid arch
-  int _pair_hybrid_zero, _hybrid_nonpair, _zero_master;
+  int _pair_hybrid_zero, _hybrid_nonpair, _zero_master, _torque_flag;
 
  public:
   inline int *get_overflow_flag() { return _overflow_flag; }
diff --git a/src/INTEL/intel_buffers.cpp b/src/INTEL/intel_buffers.cpp
index bb54577097..6d4c9bffcd 100644
--- a/src/INTEL/intel_buffers.cpp
+++ b/src/INTEL/intel_buffers.cpp
@@ -28,6 +28,7 @@ template <class flt_t, class acc_t>
 IntelBuffers<flt_t, acc_t>::IntelBuffers(class LAMMPS *lmp_in) :
     lmp(lmp_in), _x(nullptr), _q(nullptr), _quat(nullptr), _f(nullptr), _off_threads(0),
     _n_list_ptrs(1), _max_list_ptrs(4), _buf_size(0), _buf_local_size(0) {
+  _torque_flag = 0;
   _neigh_list_ptrs = new IntelNeighListPtrs[_max_list_ptrs];
   _neigh_list_ptrs[0].cnumneigh = nullptr;
   _list_alloc_atoms = 0;
@@ -695,7 +696,7 @@ double IntelBuffers<flt_t, acc_t>::memory_usage(const int nthreads)
 {
   double tmem = sizeof(atom_t);
   if (lmp->atom->q) tmem += sizeof(flt_t);
-  if (lmp->atom->torque) tmem += sizeof(quat_t);
+  if (_torque_flag) tmem += sizeof(quat_t);
   #ifdef _LMP_INTEL_OFFLOAD
   if (_separate_buffers) tmem *= 2;
   #endif
diff --git a/src/INTEL/intel_buffers.h b/src/INTEL/intel_buffers.h
index 7422850184..1e9739c3b2 100644
--- a/src/INTEL/intel_buffers.h
+++ b/src/INTEL/intel_buffers.h
@@ -57,7 +57,7 @@ class IntelBuffers {
   inline int get_stride(int nall) {
     int stride;
     IP_PRE_get_stride(stride, nall, sizeof(vec3_acc_t),
-                         lmp->atom->torque);
+                      _torque_flag);
     return stride;
   }
 
@@ -76,6 +76,8 @@ class IntelBuffers {
     _neigh_list_ptrs[0].numneighhalf = atombin;
   }
 
+  inline void set_torque_flag(const int in) { _torque_flag = in; }
+
   inline void grow(const int nall, const int nlocal, const int nthreads,
                    const int offload_end) {
     if (nall >= _buf_size || nlocal >= _buf_local_size)
@@ -329,7 +331,7 @@ class IntelBuffers {
   flt_t *_q;
   quat_t *_quat;
   vec3_acc_t * _f;
-  int _off_threads, _off_map_listlocal;
+  int _torque_flag, _off_threads, _off_map_listlocal;
 
   int _list_alloc_atoms;
   int *_list_alloc, *_cnumneigh, *_atombin, *_binpacked;

From ce38bb988d67f1b82f9093bf1d1563198795cda8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 19:12:59 -0400
Subject: [PATCH 222/396] add lammps_last_thermo support to swig, plugin and
 fortran interface

---
 examples/COUPLE/plugin/liblammpsplugin.c |  1 +
 examples/COUPLE/plugin/liblammpsplugin.h |  1 +
 fortran/lammps.f90                       | 80 +++++++++++++++++++++++-
 tools/swig/lammps.i                      |  2 +
 4 files changed, 83 insertions(+), 1 deletion(-)

diff --git a/examples/COUPLE/plugin/liblammpsplugin.c b/examples/COUPLE/plugin/liblammpsplugin.c
index d446f9cd2f..0cf9bea512 100644
--- a/examples/COUPLE/plugin/liblammpsplugin.c
+++ b/examples/COUPLE/plugin/liblammpsplugin.c
@@ -90,6 +90,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
 
   ADDSYM(get_natoms);
   ADDSYM(get_thermo);
+  ADDSYM(last_thermo);
 
   ADDSYM(extract_box);
   ADDSYM(reset_box);
diff --git a/examples/COUPLE/plugin/liblammpsplugin.h b/examples/COUPLE/plugin/liblammpsplugin.h
index c6ec03e498..40fba6b9e3 100644
--- a/examples/COUPLE/plugin/liblammpsplugin.h
+++ b/examples/COUPLE/plugin/liblammpsplugin.h
@@ -133,6 +133,7 @@ struct _liblammpsplugin {
 
   double (*get_natoms)(void *);
   double (*get_thermo)(void *, const char *);
+  void *(*last_thermo)(void *, const char *, int);
 
   void (*extract_box)(void *, double *, double *,
                       double *, double *, double *, int *, int *);
diff --git a/fortran/lammps.f90 b/fortran/lammps.f90
index cb7adfd34b..f511e6bb60 100644
--- a/fortran/lammps.f90
+++ b/fortran/lammps.f90
@@ -87,10 +87,15 @@ MODULE LIBLAMMPS
     INTEGER(c_int) :: scalar, vector, array
   END TYPE lammps_type
 
+  TYPE lammps_dtype
+    INTEGER(c_int) :: i32, i64, r64, str
+  END TYPE lammps_dtype
+
   TYPE lammps
     TYPE(c_ptr) :: handle = c_null_ptr
     TYPE(lammps_style) :: style
     TYPE(lammps_type) :: type
+    TYPE(lammps_dtype) :: dtype
   CONTAINS
     PROCEDURE :: close                  => lmp_close
     PROCEDURE :: error                  => lmp_error
@@ -100,6 +105,7 @@ MODULE LIBLAMMPS
     PROCEDURE :: commands_string        => lmp_commands_string
     PROCEDURE :: get_natoms             => lmp_get_natoms
     PROCEDURE :: get_thermo             => lmp_get_thermo
+    PROCEDURE :: last_thermo            => lmp_last_thermo
     PROCEDURE :: extract_box            => lmp_extract_box
     PROCEDURE :: reset_box              => lmp_reset_box
     PROCEDURE :: memory_usage           => lmp_memory_usage
@@ -243,7 +249,7 @@ MODULE LIBLAMMPS
   END TYPE lammps_data_baseclass
 
   ! Derived type for receiving LAMMPS data (in lieu of the ability to type cast
-  ! pointers). Used for extract_compute, extract_atom
+  ! pointers). Used for extract_compute, extract_atom, last_thermo
   TYPE, EXTENDS(lammps_data_baseclass) :: lammps_data
     INTEGER(c_int), POINTER :: i32 => NULL()
     INTEGER(c_int), DIMENSION(:), POINTER :: i32_vec => NULL()
@@ -439,6 +445,15 @@ MODULE LIBLAMMPS
       TYPE(c_ptr), INTENT(IN), VALUE :: name
     END FUNCTION lammps_get_thermo
 
+    FUNCTION lammps_last_thermo(handle,what,index) BIND(C)
+      IMPORT :: c_ptr, c_int
+      IMPLICIT NONE
+      TYPE(c_ptr) :: lammps_last_thermo
+      TYPE(c_ptr), INTENT(IN), VALUE :: handle
+      TYPE(c_ptr), INTENT(IN), VALUE :: what
+      INTEGER(c_int), INTENT(IN), VALUE :: index
+    END FUNCTION lammps_last_thermo
+
     SUBROUTINE lammps_extract_box(handle,boxlo,boxhi,xy,yz,xz,pflags, &
         boxflag) BIND(C)
       IMPORT :: c_ptr, c_double, c_int
@@ -995,6 +1010,10 @@ CONTAINS
     lmp_open%type%scalar = LMP_TYPE_SCALAR
     lmp_open%type%vector = LMP_TYPE_VECTOR
     lmp_open%type%array = LMP_TYPE_ARRAY
+    lmp_open%dtype%i32 = LAMMPS_INT
+    lmp_open%dtype%i64 = LAMMPS_INT64
+    lmp_open%dtype%r64 = LAMMPS_DOUBLE
+    lmp_open%dtype%str = LAMMPS_STRING
 
     ! Assign constants for bigint and tagint for use elsewhere
     SIZE_TAGINT = lmp_extract_setting(lmp_open, 'tagint')
@@ -1103,6 +1122,65 @@ CONTAINS
     CALL lammps_free(Cname)
   END FUNCTION lmp_get_thermo
 
+  ! equivalent function to lammps_last_thermo
+  FUNCTION lmp_last_thermo(self,what,index) RESULT(thermo_data)
+    CLASS(lammps), INTENT(IN), TARGET :: self
+    CHARACTER(LEN=*), INTENT(IN) :: what
+    INTEGER(c_int) :: index
+    TYPE(lammps_data) :: thermo_data, type_data
+    INTEGER(c_int) :: datatype
+    TYPE(c_ptr) :: Cname, Cptr
+
+    ! set data type for known cases
+    SELECT CASE (what)
+    CASE ('step')
+        IF (SIZE_BIGINT == 4_c_int) THEN
+            datatype = LAMMPS_INT
+        ELSE
+            datatype = LAMMPS_INT64
+        END IF
+    CASE ('num')
+        datatype = LAMMPS_INT
+    CASE ('type')
+        datatype = LAMMPS_INT
+    CASE ('keyword')
+        datatype = LAMMPS_STRING
+    CASE ('data')
+        Cname = f2c_string('type')
+        Cptr = lammps_last_thermo(self%handle,Cname,index-1)
+        type_data%lammps_instance => self
+        type_data%datatype = DATA_INT
+        CALL C_F_POINTER(Cptr, type_data%i32)
+        datatype = type_data%i32
+        CALL lammps_free(Cname)
+    CASE DEFAULT
+        datatype = -1
+    END SELECT
+
+    Cname = f2c_string(what)
+    Cptr = lammps_last_thermo(self%handle,Cname,index-1)
+    CALL lammps_free(Cname)
+
+    thermo_data%lammps_instance => self
+    SELECT CASE (datatype)
+    CASE (LAMMPS_INT)
+        thermo_data%datatype = DATA_INT
+        CALL C_F_POINTER(Cptr, thermo_data%i32)
+    CASE (LAMMPS_INT64)
+        thermo_data%datatype = DATA_INT64
+        CALL C_F_POINTER(Cptr, thermo_data%i64)
+    CASE (LAMMPS_DOUBLE)
+        thermo_data%datatype = DATA_DOUBLE
+        CALL C_F_POINTER(Cptr, thermo_data%r64)
+    CASE (LAMMPS_STRING)
+        thermo_data%datatype = DATA_STRING
+        thermo_data%str = c2f_string(Cptr)
+    CASE DEFAULT
+        CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
+          'Unknown pointer type in last_thermo')
+    END SELECT
+  END FUNCTION lmp_last_thermo
+
   ! equivalent subroutine to lammps_extract_box
   SUBROUTINE lmp_extract_box(self, boxlo, boxhi, xy, yz, xz, pflags, boxflag)
     CLASS(lammps), INTENT(IN) :: self
diff --git a/tools/swig/lammps.i b/tools/swig/lammps.i
index b7414573ba..c4ef0a7109 100644
--- a/tools/swig/lammps.i
+++ b/tools/swig/lammps.i
@@ -113,6 +113,7 @@ extern void   lammps_commands_string(void *handle, const char *str);
 
 extern double lammps_get_natoms(void *handle);
 extern double lammps_get_thermo(void *handle, const char *keyword);
+extern void  *lammps_last_thermo(void *handle, const char *what, int index);
 extern void   lammps_extract_box(void *handle, double *boxlo, double *boxhi,
                           double *xy, double *yz, double *xz,
                           int *pflags, int *boxflag);
@@ -295,6 +296,7 @@ extern void   lammps_commands_string(void *handle, const char *str);
 
 extern double lammps_get_natoms(void *handle);
 extern double lammps_get_thermo(void *handle, const char *keyword);
+extern void  *lammps_last_thermo(void *handle, const char *what, int index);
 extern void   lammps_extract_box(void *handle, double *boxlo, double *boxhi,
                           double *xy, double *yz, double *xz,
                           int *pflags, int *boxflag);

From 4cad18a057ea81b92ebb119af520fc517dba3fe2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Jun 2023 19:59:47 -0400
Subject: [PATCH 223/396] document Fortran version of lammps_last_thermo

---
 doc/src/Fortran.rst | 191 +++++++++++++++++++++++++++++++++++---------
 1 file changed, 154 insertions(+), 37 deletions(-)

diff --git a/doc/src/Fortran.rst b/doc/src/Fortran.rst
index 92a42997b8..a0e4da56b5 100644
--- a/doc/src/Fortran.rst
+++ b/doc/src/Fortran.rst
@@ -203,40 +203,62 @@ Below is an example demonstrating some of the possible uses.
 
 .. code-block:: fortran
 
-  PROGRAM testprop
-    USE LIBLAMMPS
-    USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t
-    USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
-    TYPE(lammps) :: lmp
-    INTEGER(KIND=c_int64_t), POINTER :: natoms
-    REAL(KIND=c_double), POINTER :: dt
-    INTEGER(KIND=c_int64_t), POINTER :: ntimestep
-    REAL(KIND=c_double) :: pe, ke
+   PROGRAM testprop
+     USE LIBLAMMPS
+     USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
+     USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
+     TYPE(lammps) :: lmp
+     INTEGER(KIND=c_int64_t), POINTER :: natoms, ntimestep, bval
+     REAL(KIND=c_double), POINTER :: dt, dval
+     INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
+     INTEGER(KIND=c_int) :: i
+     CHARACTER(LEN=11) :: key
+     REAL(KIND=c_double) :: pe, ke
 
-    lmp = lammps()
-    CALL lmp%file('in.sysinit')
-    natoms = lmp%extract_global('natoms')
-    WRITE(OUTPUT_UNIT,'(A,I0,A)') 'Running a simulation with ', natoms, ' atoms'
-    WRITE(OUTPUT_UNIT,'(I0,A,I0,A,I0,A)') lmp%extract_setting('nlocal'), &
-        ' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
-        lmp%extract_setting('ntypes'), ' atom types'
+     lmp = lammps()
+     CALL lmp%file('in.sysinit')
+     natoms = lmp%extract_global('natoms')
+     WRITE(OUTPUT_UNIT,'(A,I0,A)') 'Running a simulation with ', natoms, ' atoms'
+     WRITE(OUTPUT_UNIT,'(I0,A,I0,A,I0,A)') lmp%extract_setting('nlocal'), &
+         ' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
+         lmp%extract_setting('ntypes'), ' atom types'
 
-    CALL lmp%command('run 2 post no')
-    dt = lmp%extract_global('dt')
-    ntimestep = lmp%extract_global('ntimestep')
-    WRITE(OUTPUT_UNIT,'(A,I0,A,F4.1,A)') 'At step: ', ntimestep, &
-        '  Changing timestep from', dt, ' to 0.5'
-    dt = 0.5_c_double
-    CALL lmp%command('run 2 post no')
+     CALL lmp%command('run 2 post no')
 
-    WRITE(OUTPUT_UNIT,'(A,I0)') 'At step: ', ntimestep
-    pe = lmp%get_thermo('pe')
-    ke = lmp%get_thermo('ke')
-    PRINT*, 'PE = ', pe
-    PRINT*, 'KE = ', ke
+     ntimestep = lmp%last_thermo('step', 0)
+     nfield = lmp%last_thermo('num', 0)
+     WRITE(OUTPUT_UNIT,'(A,I0,A,I0)') 'Last thermo output on step: ', ntimestep, &
+         ',  number of fields: ', nfield
+     DO i=1, nfield
+         key = lmp%last_thermo('keyword',i)
+         typ = lmp%last_thermo('type',i)
+         IF (typ == lmp%dtype%i32) THEN
+             ival = lmp%last_thermo('data',i)
+             WRITE(OUTPUT_UNIT,*) key, ':', ival
+         ELSE IF (typ == lmp%dtype%i64) THEN
+             bval = lmp%last_thermo('data',i)
+             WRITE(OUTPUT_UNIT,*) key, ':', bval
+         ELSE IF (typ == lmp%dtype%r64) THEN
+             dval = lmp%last_thermo('data',i)
+             WRITE(OUTPUT_UNIT,*) key, ':', dval
+         END IF
+     END DO
 
-    CALL lmp%close(.TRUE.)
-  END PROGRAM testprop
+     dt = lmp%extract_global('dt')
+     ntimestep = lmp%extract_global('ntimestep')
+     WRITE(OUTPUT_UNIT,'(A,I0,A,F4.1,A)') 'At step: ', ntimestep, &
+         '  Changing timestep from', dt, ' to 0.5'
+     dt = 0.5_c_double
+     CALL lmp%command('run 2 post no')
+
+     WRITE(OUTPUT_UNIT,'(A,I0)') 'At step: ', ntimestep
+     pe = lmp%get_thermo('pe')
+     ke = lmp%get_thermo('ke')
+     WRITE(OUTPUT_UNIT,*) 'PE = ', pe
+     WRITE(OUTPUT_UNIT,*) 'KE = ', ke
+
+     CALL lmp%close(.TRUE.)
+   END PROGRAM testprop
 
 ---------------
 
@@ -262,6 +284,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype style: type(lammps_style)
    :f type: derived type to access lammps type constants
    :ftype type: type(lammps_type)
+   :f dtype: derived type to access lammps data type constants
+   :ftype dtype: type(lammps_dtype)
    :f close: :f:subr:`close`
    :ftype close: subroutine
    :f subroutine error: :f:subr:`error`
@@ -278,6 +302,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype get_natoms: function
    :f get_thermo: :f:func:`get_thermo`
    :ftype get_thermo: function
+   :f last_thermo: :f:func:`last_thermo`
+   :ftype last_thermo: function
    :f extract_box: :f:subr:`extract_box`
    :ftype extract_box: subroutine
    :f reset_box: :f:subr:`reset_box`
@@ -587,6 +613,96 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
+.. f:function:: last_thermo(what, index)
+
+   This function will call :cpp:func:`lammps_last_thermo` and returns
+   either a string or a pointer to a cached copy of LAMMPS last thermodynamic
+   output, depending on the data requested through *what*.  Note that *index*
+   uses 1-based indexing to access thermo output columns.
+
+   .. versionadded:: TBD
+
+   Note that this function actually does not return a value, but rather
+   associates the pointer on the left side of the assignment to point to
+   internal LAMMPS data (with the exception of string data, which are
+   copied and returned as ordinary Fortran strings).  Pointers must be
+   of the correct data type to point to said data (typically
+   ``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``).
+   The pointer being associated with LAMMPS data is type-checked at
+   run-time via an overloaded assignment operator.  The pointers
+   returned by this function point to temporary, read-only data that may
+   be overwritten at any time, so their target values need to be copied
+   to local storage if they are supposed to persist.
+
+   For example,
+
+   .. code-block:: fortran
+
+      PROGRAM thermo
+        USE LIBLAMMPS
+        USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
+        TYPE(lammps) :: lmp
+        INTEGER(KIND=c_int64_t), POINTER :: ntimestep, bval
+        REAL(KIND=c_double), POINTER :: dval
+        INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
+        INTEGER(KIND=c_int) :: i
+        CHARACTER(LEN=11) :: key
+
+        lmp = lammps()
+        CALL lmp%file('in.sysinit')
+
+        ntimestep = lmp%last_thermo('step', 0)
+        nfield = lmp%last_thermo('num', 0)
+        PRINT*, 'Last thermo output on step: ', ntimestep, '  Number of fields: ', nfield
+        DO i=1, nfield
+            key = lmp%last_thermo('keyword',i)
+            typ = lmp%last_thermo('type',i)
+            IF (typ == lmp%dtype%i32) THEN
+                ival = lmp%last_thermo('data',i)
+                PRINT*, key, ':', ival
+            ELSE IF (typ == lmp%dtype%i64) THEN
+                bval = lmp%last_thermo('data',i)
+                PRINT*, key, ':', bval
+            ELSE IF (typ == lmp%dtype%r64) THEN
+                dval = lmp%last_thermo('data',i)
+                PRINT*, key, ':', dval
+            END IF
+        END DO
+        CALL lmp%close(.TRUE.)
+      END PROGRAM thermo
+
+   would extract the last timestep where thermo output was done and the number
+   of columns it printed.  Then it loops over the columns to print out column
+   header keywords and the corresponding data.
+
+   .. note::
+
+      If :f:func:`last_thermo` returns a string, the string must have a length
+      greater than or equal to the length of the string (not including the
+      terminal ``NULL`` character) that LAMMPS returns. If the variable's
+      length is too short, the string will be truncated.  As usual in Fortran,
+      strings are padded with spaces at the end.  If you use an allocatable
+      string, the string **must be allocated** prior to calling this function.
+
+   :p character(len=\*) what: string with the name of the thermo keyword
+   :p integer(c_int) index: 1-based column index
+   :to: :cpp:func:`lammps_last_thermo`
+   :r pointer [polymorphic]: pointer to LAMMPS data. The left-hand side of the
+    assignment should be either a string (if expecting string data) or a
+    C-compatible pointer (e.g., ``INTEGER(c_int), POINTER :: nlocal``) to the
+    extracted property.
+
+   .. warning::
+
+       Modifying the data in the location pointed to by the returned pointer
+       may lead to inconsistent internal data and thus may cause failures,
+       crashes, or bogus simulations.  In general, it is much better
+       to use a LAMMPS input command that sets or changes these parameters.
+       Using an input command will take care of all side effects and necessary
+       updates of settings derived from such settings.
+
+--------
+
 .. f:subroutine:: extract_box([boxlo][, boxhi][, xy][, yz][, xz][, pflags][, boxflag])
 
    This subroutine will call :cpp:func:`lammps_extract_box`. All
@@ -764,13 +880,14 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    .. note::
 
-      If :f:func:`extract_global` returns a string, the string must have length
-      greater than or equal to the length of the string (not including the
-      terminal ``NULL`` character) that LAMMPS returns. If the variable's
-      length is too short, the string will be truncated. As usual in Fortran,
-      strings are padded with spaces at the end. If you use an allocatable
-      string, the string **must be allocated** prior to calling this function,
-      but you can automatically reallocate it to the correct length after the
+      If :f:func:`extract_global` returns a string, the string must have
+      a length greater than or equal to the length of the string (not
+      including the terminal ``NULL`` character) that LAMMPS returns. If
+      the variable's length is too short, the string will be
+      truncated. As usual in Fortran, strings are padded with spaces at
+      the end. If you use an allocatable string, the string **must be
+      allocated** prior to calling this function, but you can
+      automatically reallocate it to the correct length after the
       function returns, viz.,
 
       .. code-block :: fortran

From 2cb87bc9a2e3758f342ec6f47b8265d52f05f0bf Mon Sep 17 00:00:00 2001
From: "W. Michael Brown" <michael.w.brown@intel.com>
Date: Thu, 8 Jun 2023 21:47:30 -0700
Subject: [PATCH 224/396] Intel package should not reset atom sort frequency if
 it is 0 (disabled).

---
 src/INTEL/fix_intel.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/INTEL/fix_intel.cpp b/src/INTEL/fix_intel.cpp
index ef6bfc3408..59224cc511 100644
--- a/src/INTEL/fix_intel.cpp
+++ b/src/INTEL/fix_intel.cpp
@@ -411,7 +411,7 @@ bool FixIntel::pair_hybrid_check()
 void FixIntel::pair_init_check(const bool cdmessage)
 {
   #ifdef INTEL_VMASK
-  atom->sortfreq = 1;
+  if (atom->sortfreq) atom->sortfreq = 1;
   #endif
 
   _nbor_pack_width = 1;

From 04a31c33e231bbe2a7151447fa46e4b6b39dc3f7 Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Fri, 9 Jun 2023 09:57:23 -0600
Subject: [PATCH 225/396] Changing output of fforce in pair granular single()

---
 src/GRANULAR/pair_granular.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp
index 0b6bd537e5..390a7581d7 100644
--- a/src/GRANULAR/pair_granular.cpp
+++ b/src/GRANULAR/pair_granular.cpp
@@ -767,10 +767,11 @@ double PairGranular::single(int i, int j, int itype, int jtype,
   model->history = history;
 
   model->calculate_forces();
-  double *forces = model->forces;
 
   // apply forces & torques
-  fforce = MathExtra::len3(forces);
+  // Calculate normal component, normalized by r
+  fforce = MathExtra::dot3(model->forces, model->dx);
+  fforce *= model->rinv * model->rinv;
 
   // set single_extra quantities
   svector[0] = model->fs[0];

From e0cbcff1f9ab272b21c028ca8be1765be37e7178 Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Fri, 9 Jun 2023 10:43:00 -0600
Subject: [PATCH 226/396] Simplying normal force calculation

---
 src/GRANULAR/pair_granular.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp
index 390a7581d7..30f272791e 100644
--- a/src/GRANULAR/pair_granular.cpp
+++ b/src/GRANULAR/pair_granular.cpp
@@ -770,8 +770,7 @@ double PairGranular::single(int i, int j, int itype, int jtype,
 
   // apply forces & torques
   // Calculate normal component, normalized by r
-  fforce = MathExtra::dot3(model->forces, model->dx);
-  fforce *= model->rinv * model->rinv;
+  fforce = model->Fnormal * model->rinv;
 
   // set single_extra quantities
   svector[0] = model->fs[0];

From f6b0981474c0a8ec20c3808efdeae5664280bc49 Mon Sep 17 00:00:00 2001
From: "W. Michael Brown" <michael.w.brown@intel.com>
Date: Fri, 9 Jun 2023 14:05:41 -0700
Subject: [PATCH 227/396] Fixing some issues introduced into
 verlet_lrt_intel.cpp

---
 src/INTEL/verlet_lrt_intel.cpp | 42 +++++++++++++++++++---------------
 1 file changed, 24 insertions(+), 18 deletions(-)

diff --git a/src/INTEL/verlet_lrt_intel.cpp b/src/INTEL/verlet_lrt_intel.cpp
index 42414420b6..9df17d8cef 100644
--- a/src/INTEL/verlet_lrt_intel.cpp
+++ b/src/INTEL/verlet_lrt_intel.cpp
@@ -19,7 +19,6 @@
 #include "atom_vec.h"
 #include "bond.h"
 #include "comm.h"
-#include "compute.h"
 #include "dihedral.h"
 #include "domain.h"
 #include "error.h"
@@ -27,7 +26,6 @@
 #include "force.h"
 #include "improper.h"
 #include "kspace.h"
-#include "memory.h"
 #include "modify.h"
 #include "neighbor.h"
 #include "output.h"
@@ -35,9 +33,7 @@
 #include "timer.h"
 #include "update.h"
 
-#if defined(_OPENMP)
-#include <omp.h>
-#endif
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -67,7 +63,7 @@ void VerletLRTIntel::init()
 {
   Verlet::init();
 
-  _intel_kspace = dynamic_cast<PPPMIntel*>(force->kspace_match("^pppm\\..*intel$", 0));
+  _intel_kspace = dynamic_cast<PPPMIntel*>(force->kspace_match("^pppm/.*intel$", 0));
   // include pppm/electrode/intel
 
   #ifndef LMP_INTEL_USELRT
@@ -95,12 +91,15 @@ void VerletLRTIntel::setup(int flag)
   }
   #endif
 
-  if (comm->me == 0) {
-    fprintf(screen,"Setting up VerletLRTIntel run ...\n");
-    fprintf(screen,"  Unit style    : %s\n", update->unit_style);
-    fmt::print(screen,"  Current step  : {}\n", update->ntimestep);
-    fprintf(screen,"  Time step     : %g\n", update->dt);
-    timer->print_timeout(screen);
+  if (comm->me == 0 && screen) {
+    fputs("Setting up VerletLRTIntel run ...\n",screen);
+    if (flag) {
+      fmt::print(screen,"  Unit style    : {}\n"
+                        "  Current step  : {}\n"
+                        "  Time step     : {}\n",
+                 update->unit_style,update->ntimestep,update->dt);
+      timer->print_timeout(screen);
+    }
   }
 
   #if defined(_LMP_INTEL_LRT_PTHREAD)
@@ -110,8 +109,9 @@ void VerletLRTIntel::setup(int flag)
     sched_getaffinity(0, sizeof(cpuset), &cpuset);
     int my_cpu_count = CPU_COUNT(&cpuset);
     if (my_cpu_count < comm->nthreads + 1) {
-      error->warning(FLERR, "Using {} threads per MPI rank, but only {} core(s) allocated "
-                     "for each MPI rank", comm->nthreads + 1, my_cpu_count);
+      error->warning(FLERR, "Using {} threads per MPI rank, but only {} "
+                     "core(s) allocated for each MPI rank",
+                     comm->nthreads + 1, my_cpu_count);
     }
   }
   #endif
@@ -144,6 +144,7 @@ void VerletLRTIntel::setup(int flag)
   domain->box_too_small_check();
   modify->setup_pre_neighbor();
   neighbor->build(1);
+  modify->setup_post_neighbor();
   neighbor->ncalls = 0;
 
   // compute all forces
@@ -189,11 +190,11 @@ void VerletLRTIntel::setup(int flag)
 
   if (kspace_compute_flag) _intel_kspace->compute_second(eflag,vflag);
 
-  modify->pre_reverse(eflag,vflag);
+  modify->setup_pre_reverse(eflag,vflag);
   if (force->newton) comm->reverse_comm();
 
   modify->setup(vflag);
-  output->setup();
+  output->setup(flag);
   update->setupflag = 0;
 }
 
@@ -214,9 +215,10 @@ void VerletLRTIntel::run(int n)
   int n_post_integrate = modify->n_post_integrate;
   int n_pre_exchange = modify->n_pre_exchange;
   int n_pre_neighbor = modify->n_pre_neighbor;
+  int n_post_neighbor = modify->n_post_neighbor;
   int n_pre_force = modify->n_pre_force;
   int n_pre_reverse = modify->n_pre_reverse;
-  int n_post_force = modify->n_post_force_any;
+  int n_post_force_any = modify->n_post_force_any;
   int n_end_of_step = modify->n_end_of_step;
 
   if (atom->sortfreq > 0) sortflag = 1;
@@ -279,6 +281,10 @@ void VerletLRTIntel::run(int n)
       }
       neighbor->build(1);
       timer->stamp(Timer::NEIGH);
+      if (n_post_neighbor) {
+        modify->post_neighbor();
+        timer->stamp(Timer::MODIFY);
+      }
     }
 
     // force computations
@@ -353,7 +359,7 @@ void VerletLRTIntel::run(int n)
 
     // force modifications, final time integration, diagnostics
 
-    if (n_post_force) modify->post_force(vflag);
+    if (n_post_force_any) modify->post_force(vflag);
     modify->final_integrate();
     if (n_end_of_step) modify->end_of_step();
     timer->stamp(Timer::MODIFY);

From ecf7c24e874cb70c19888811b09838d42cd1912b Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@outlook.com>
Date: Fri, 9 Jun 2023 00:06:00 -0600
Subject: [PATCH 228/396] Avoid static int in lammps_last_thermo

---
 src/library.cpp | 15 ++-------------
 src/lmptype.h   |  3 ++-
 2 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/src/library.cpp b/src/library.cpp
index 0fcedfc20b..a94e385148 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -794,7 +794,7 @@ argument string.
      - yes
    * - type
      - data type of thermo output column; see :cpp:enum:`_LMP_DATATYPE_CONST`
-     - pointer to static int
+     - pointer to int
      - yes
    * - data
      - actual field data for column
@@ -815,7 +815,6 @@ void *lammps_last_thermo(void *handle, const char *what, int index)
   Thermo *th = lmp->output->thermo;
   if (!th) return nullptr;
   const int nfield = *th->get_nfield();
-  static int datatype;
 
   BEGIN_CAPTURE
   {
@@ -833,17 +832,7 @@ void *lammps_last_thermo(void *handle, const char *what, int index)
     } else if (strcmp(what, "type") == 0) {
       if ((index < 0) || (index >= nfield)) return nullptr;
       const auto &field = th->get_fields()[index];
-      if (field.type == multitype::INT) {
-        datatype = LAMMPS_INT;
-        val = (void *) &datatype;
-      } else if (field.type == multitype::BIGINT) {
-        datatype = LAMMPS_INT64;
-        val = (void *) &datatype;
-      } else if (field.type == multitype::DOUBLE) {
-        datatype = LAMMPS_DOUBLE;
-        val = (void *) &datatype;
-      }
-
+      val = (void *) &field.type;
     } else if (strcmp(what, "data") == 0) {
       if ((index < 0) || (index >= nfield)) return nullptr;
       const auto &field = th->get_fields()[index];
diff --git a/src/lmptype.h b/src/lmptype.h
index 6e0b54d988..e559bd9416 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -276,7 +276,8 @@ union ubuf {
 \endverbatim
   */
 struct multitype {
-  enum { NONE, DOUBLE, INT, BIGINT };
+  // same values as LAMMPS_INT, LAMMPS_DOUBLE, and LAMMPS_INT64 in library.h
+  enum { NONE = -1, INT = 0, DOUBLE = 2, BIGINT = 4 };
 
   int type;
   union {

From fe45b766c3067052805548b7ee1a9f5abbcd5f45 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@outlook.com>
Date: Fri, 9 Jun 2023 02:29:30 -0600
Subject: [PATCH 229/396] pylammps: make use of lammps_last_thermo

this now avoids parsing LAMMPS output to extract thermo data, but instead uses
the new lammps_last_thermo library function
---
 python/lammps/core.py     |  9 +++--
 python/lammps/pylammps.py | 75 +++++++++++++--------------------------
 2 files changed, 31 insertions(+), 53 deletions(-)

diff --git a/python/lammps/core.py b/python/lammps/core.py
index d34d5de4d4..cf613fcbf4 100644
--- a/python/lammps/core.py
+++ b/python/lammps/core.py
@@ -746,6 +746,11 @@ class lammps(object):
       return self.lib.lammps_get_thermo(self.lmp,name)
 
   # -------------------------------------------------------------------------
+  @property
+  def last_thermo_step(self):
+    with ExceptionCheck(self):
+      ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("step".encode()), 0)
+    return cast(ptr, POINTER(self.c_bigint)).contents.value
 
   def last_thermo(self):
     """Get a dictionary of the last thermodynamic output
@@ -760,9 +765,7 @@ class lammps(object):
     """
 
     rv = dict()
-    with ExceptionCheck(self):
-      ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("step".encode()), 0)
-    mystep = cast(ptr, POINTER(self.c_bigint)).contents.value
+    mystep = self.last_thermo_step
     if mystep < 0:
       return None
 
diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py
index d0ff7ab1aa..a7349ebd2c 100644
--- a/python/lammps/pylammps.py
+++ b/python/lammps/pylammps.py
@@ -377,55 +377,6 @@ class variable_set:
     def __repr__(self):
         return self.__str__()
 
-# -------------------------------------------------------------------------
-
-def get_thermo_data(output):
-    """ traverse output of runs and extract thermo data columns """
-    if isinstance(output, str):
-        lines = output.splitlines()
-    else:
-        lines = output
-
-    runs = []
-    columns = []
-    in_run = False
-    current_run = {}
-
-    for line in lines:
-        if line.startswith("Per MPI rank memory allocation"):
-            in_run = True
-        elif in_run and len(columns) == 0:
-            # first line after memory usage are column names
-            columns = line.split()
-
-            current_run = {}
-
-            for col in columns:
-                current_run[col] = []
-
-        elif line.startswith("Loop time of "):
-            in_run = False
-            columns = []
-            thermo_data = variable_set('ThermoData', current_run)
-            r = {'thermo' : thermo_data }
-            runs.append(namedtuple('Run', list(r.keys()))(*list(r.values())))
-        elif in_run and len(columns) > 0:
-            items = line.split()
-            # Convert thermo output and store it.
-            # It must have the same number of columns and
-            # all of them must be convertible to floats.
-            # Otherwise we ignore the line
-            if len(items) == len(columns):
-                try:
-                    values = [float(x) for x in items]
-                    for i, col in enumerate(columns):
-                        current_run[col].append(values[i])
-                except ValueError:
-                  # cannot convert. must be a non-thermo output. ignore.
-                  pass
-
-    return runs
-
 # -------------------------------------------------------------------------
 # -------------------------------------------------------------------------
 
@@ -573,6 +524,13 @@ class PyLammps(object):
     if self.enable_cmd_history:
       self._cmd_history.append(cmd)
 
+  def _append_run_thermo(self, thermo):
+    for k, v in thermo.items():
+      if k in self._current_run:
+        self._current_run[k].append(v)
+      else:
+        self._current_run[k] = [v]
+
   def run(self, *args, **kwargs):
     """
     Execute LAMMPS run command with given arguments
@@ -581,8 +539,25 @@ class PyLammps(object):
     :py:attr:`PyLammps.runs`. The latest run can be retrieved by
     :py:attr:`PyLammps.last_run`.
     """
+    self._current_run = {}
+    self._last_thermo_step = -1
+    def end_of_step_callback(lmp):
+      if self.lmp.last_thermo_step == self._last_thermo_step: return
+      thermo = self.lmp.last_thermo()
+      self._append_run_thermo(thermo)
+      self._last_thermo_step = thermo['Step']
+
+    import __main__
+    __main__._PyLammps_end_of_step_callback = end_of_step_callback
+
+    self.fix("__pylammps_internal_run_callback", "all", "python/invoke", "1", "end_of_step", "_PyLammps_end_of_step_callback")
     output = self.__getattr__('run')(*args, **kwargs)
-    self.runs += get_thermo_data(output)
+    self.unfix("__pylammps_internal_run_callback")
+    self._append_run_thermo(self.lmp.last_thermo())
+
+    thermo_data = variable_set('ThermoData', self._current_run)
+    r = {'thermo' : thermo_data }
+    self.runs.append(namedtuple('Run', list(r.keys()))(*list(r.values())))
     return output
 
   @property

From 235e98ee6a2995adf9b431d98fd1550d6b8a2fd4 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@outlook.com>
Date: Fri, 9 Jun 2023 09:49:07 -0600
Subject: [PATCH 230/396] pylammps: only capture all thermo if PYTHON package
 is enabled

---
 python/lammps/pylammps.py          | 18 +++++++++++++++---
 unittest/python/python-pylammps.py | 28 ++++++++++++++++++++--------
 2 files changed, 35 insertions(+), 11 deletions(-)

diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py
index a7349ebd2c..6efc355f5c 100644
--- a/python/lammps/pylammps.py
+++ b/python/lammps/pylammps.py
@@ -434,6 +434,9 @@ class PyLammps(object):
     self._enable_cmd_history = False
     self.runs = []
 
+    if not self.lmp.has_package("PYTHON"):
+      print("WARNING: run thermo data not captured since PYTHON LAMMPS package is not enabled")
+
   def __enter__(self):
     return self
 
@@ -535,9 +538,13 @@ class PyLammps(object):
     """
     Execute LAMMPS run command with given arguments
 
-    All thermo output during the run is captured and saved as new entry in
+    Thermo data of the run is recorded and saved as new entry in
     :py:attr:`PyLammps.runs`. The latest run can be retrieved by
     :py:attr:`PyLammps.last_run`.
+
+    Note, for recording of all thermo steps during a run, the PYTHON package
+    needs to be enabled in LAMMPS. Otherwise, it will only capture the final
+    timestep.
     """
     self._current_run = {}
     self._last_thermo_step = -1
@@ -549,10 +556,15 @@ class PyLammps(object):
 
     import __main__
     __main__._PyLammps_end_of_step_callback = end_of_step_callback
+    capture_thermo = self.lmp.has_package("PYTHON")
+
+    if capture_thermo:
+        self.fix("__pylammps_internal_run_callback", "all", "python/invoke", "1", "end_of_step", "_PyLammps_end_of_step_callback")
 
-    self.fix("__pylammps_internal_run_callback", "all", "python/invoke", "1", "end_of_step", "_PyLammps_end_of_step_callback")
     output = self.__getattr__('run')(*args, **kwargs)
-    self.unfix("__pylammps_internal_run_callback")
+
+    if capture_thermo:
+        self.unfix("__pylammps_internal_run_callback")
     self._append_run_thermo(self.lmp.last_thermo())
 
     thermo_data = variable_set('ThermoData', self._current_run)
diff --git a/unittest/python/python-pylammps.py b/unittest/python/python-pylammps.py
index 2b92f82248..9e691b1b8c 100644
--- a/unittest/python/python-pylammps.py
+++ b/unittest/python/python-pylammps.py
@@ -82,14 +82,26 @@ class PythonPyLammps(unittest.TestCase):
         self.pylmp.variable("fx atom fx")
         self.pylmp.run(10)
 
-        self.assertEqual(len(self.pylmp.runs), 1)
-        self.assertEqual(self.pylmp.last_run, self.pylmp.runs[0])
-        self.assertEqual(len(self.pylmp.last_run.thermo.Step), 2)
-        self.assertEqual(len(self.pylmp.last_run.thermo.Temp), 2)
-        self.assertEqual(len(self.pylmp.last_run.thermo.E_pair), 2)
-        self.assertEqual(len(self.pylmp.last_run.thermo.E_mol), 2)
-        self.assertEqual(len(self.pylmp.last_run.thermo.TotEng), 2)
-        self.assertEqual(len(self.pylmp.last_run.thermo.Press), 2)
+        # thermo data is only captured during a run if PYTHON package is enabled
+        # without it, it will only capture the final thermo at completion
+        if self.pylmp.lmp.has_package("PYTHON"):
+            self.assertEqual(len(self.pylmp.runs), 1)
+            self.assertEqual(self.pylmp.last_run, self.pylmp.runs[0])
+            self.assertEqual(len(self.pylmp.last_run.thermo.Step), 2)
+            self.assertEqual(len(self.pylmp.last_run.thermo.Temp), 2)
+            self.assertEqual(len(self.pylmp.last_run.thermo.E_pair), 2)
+            self.assertEqual(len(self.pylmp.last_run.thermo.E_mol), 2)
+            self.assertEqual(len(self.pylmp.last_run.thermo.TotEng), 2)
+            self.assertEqual(len(self.pylmp.last_run.thermo.Press), 2)
+        else:
+            self.assertEqual(len(self.pylmp.runs), 1)
+            self.assertEqual(self.pylmp.last_run, self.pylmp.runs[0])
+            self.assertEqual(len(self.pylmp.last_run.thermo.Step), 1)
+            self.assertEqual(len(self.pylmp.last_run.thermo.Temp), 1)
+            self.assertEqual(len(self.pylmp.last_run.thermo.E_pair), 1)
+            self.assertEqual(len(self.pylmp.last_run.thermo.E_mol), 1)
+            self.assertEqual(len(self.pylmp.last_run.thermo.TotEng), 1)
+            self.assertEqual(len(self.pylmp.last_run.thermo.Press), 1)
 
     def test_info_queries(self):
         self.pylmp.lattice("fcc", 0.8442),

From 0e7d91b6114d63b49a121e3817318db98c0019c6 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@outlook.com>
Date: Sat, 10 Jun 2023 07:45:52 -0600
Subject: [PATCH 231/396] add missing documentation

---
 doc/src/Python_properties.rst | 5 +++++
 python/lammps/core.py         | 7 ++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/doc/src/Python_properties.rst b/doc/src/Python_properties.rst
index d8e772379c..031461660a 100644
--- a/doc/src/Python_properties.rst
+++ b/doc/src/Python_properties.rst
@@ -53,6 +53,7 @@ against invalid accesses.
 
       * :py:meth:`version() <lammps.lammps.version()>`: return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
       * :py:meth:`get_thermo() <lammps.lammps.get_thermo()>`: return current value of a thermo keyword
+      * :py:meth:`last_thermo() <lammps.lammps.last_thermo()>`: return a dictionary of the last thermodynamic output
       * :py:meth:`get_natoms() <lammps.lammps.get_natoms()>`: total # of atoms as int
       * :py:meth:`reset_box() <lammps.lammps.reset_box()>`: reset the simulation box size
       * :py:meth:`extract_setting() <lammps.lammps.extract_setting()>`: return a global setting
@@ -60,6 +61,10 @@ against invalid accesses.
       * :py:meth:`extract_box() <lammps.lammps.extract_box()>`: extract box info
       * :py:meth:`create_atoms() <lammps.lammps.create_atoms()>`: create N atoms with IDs, types, x, v, and image flags
 
+      **Properties**:
+
+      * :py:attr:`last_thermo_step <lammps.lammps.last_thermo_step>`: the last timestep thermodynamic output was computed
+
    .. tab:: PyLammps/IPyLammps API
 
       In addition to the functions provided by :py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>` objects
diff --git a/python/lammps/core.py b/python/lammps/core.py
index cf613fcbf4..84a80e77a3 100644
--- a/python/lammps/core.py
+++ b/python/lammps/core.py
@@ -748,6 +748,11 @@ class lammps(object):
   # -------------------------------------------------------------------------
   @property
   def last_thermo_step(self):
+    """ Get the last timestep where thermodynamic data was computed
+
+    :return: the timestep or a negative number if there has not been any thermo output yet
+    :rtype: int
+    """
     with ExceptionCheck(self):
       ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("step".encode()), 0)
     return cast(ptr, POINTER(self.c_bigint)).contents.value
@@ -760,7 +765,7 @@ class lammps(object):
     data from the last timestep into a dictionary.  The return value
     is None, if there has not been any thermo output yet.
 
-    :return: value of thermo keyword
+    :return: a dictionary containing the last computed thermo output values
     :rtype: dict or None
     """
 

From acaa2b7f9b3aa8adda8e5d8f228f3799f808259a Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@outlook.com>
Date: Sat, 10 Jun 2023 11:35:36 -0600
Subject: [PATCH 232/396] pylammps: update email

---
 python/lammps/pylammps.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py
index 6efc355f5c..72cfed53f0 100644
--- a/python/lammps/pylammps.py
+++ b/python/lammps/pylammps.py
@@ -13,7 +13,7 @@
 
 ################################################################################
 # Alternative Python Wrapper
-# Written by Richard Berger <richard.berger@temple.edu>
+# Written by Richard Berger <richard.berger@outlook.com>
 ################################################################################
 
 # for python2/3 compatibility

From da9637e94c13c20bbc66c6b83e27f45c1e96ac4f Mon Sep 17 00:00:00 2001
From: "W. Michael Brown" <michael.w.brown@intel.com>
Date: Sat, 10 Jun 2023 13:33:10 -0700
Subject: [PATCH 233/396] Adding std namespace specifier to transcendentals in
 intel pkg

---
 src/INTEL/angle_charmm_intel.cpp              | 10 ++--
 src/INTEL/angle_harmonic_intel.cpp            |  8 +--
 src/INTEL/bond_harmonic_intel.cpp             |  2 +-
 src/INTEL/dihedral_charmm_intel.cpp           |  6 +-
 src/INTEL/dihedral_fourier_intel.cpp          |  4 +-
 src/INTEL/dihedral_harmonic_intel.cpp         |  4 +-
 src/INTEL/dihedral_opls_intel.cpp             | 14 ++---
 src/INTEL/fix_nh_intel.cpp                    | 28 ++++-----
 src/INTEL/improper_cvff_intel.cpp             | 10 ++--
 src/INTEL/improper_harmonic_intel.cpp         | 12 ++--
 src/INTEL/intel_intrinsics.h                  |  2 +-
 src/INTEL/math_extra_intel.h                  | 14 ++---
 src/INTEL/pair_airebo_intel.cpp               |  2 +-
 src/INTEL/pair_buck_coul_cut_intel.cpp        |  2 +-
 src/INTEL/pair_buck_coul_long_intel.cpp       |  2 +-
 src/INTEL/pair_buck_intel.cpp                 |  2 +-
 src/INTEL/pair_dpd_intel.cpp                  |  4 +-
 src/INTEL/pair_eam_intel.cpp                  |  4 +-
 src/INTEL/pair_gayberne_intel.cpp             |  2 +-
 .../pair_lj_charmm_coul_charmm_intel.cpp      |  2 +-
 src/INTEL/pair_lj_charmm_coul_long_intel.cpp  |  6 +-
 src/INTEL/pair_lj_cut_coul_long_intel.cpp     |  2 +-
 src/INTEL/pair_sw_intel.cpp                   |  4 +-
 src/INTEL/pppm_disp_intel.cpp                 | 60 +++++++++----------
 src/INTEL/pppm_intel.cpp                      | 12 ++--
 25 files changed, 109 insertions(+), 109 deletions(-)

diff --git a/src/INTEL/angle_charmm_intel.cpp b/src/INTEL/angle_charmm_intel.cpp
index 1ea9c8348e..e13448e28a 100644
--- a/src/INTEL/angle_charmm_intel.cpp
+++ b/src/INTEL/angle_charmm_intel.cpp
@@ -178,7 +178,7 @@ void AngleCharmmIntel::eval(const int vflag,
       const flt_t delz1 = x[i1].z - x[i2].z;
 
       const flt_t rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
-      flt_t ir12 = (flt_t)1.0/sqrt(rsq1);
+      flt_t ir12 = (flt_t)1.0/std::sqrt(rsq1);
 
       // 2nd bond
 
@@ -187,7 +187,7 @@ void AngleCharmmIntel::eval(const int vflag,
       const flt_t delz2 = x[i3].z - x[i2].z;
 
       const flt_t rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
-      ir12 *= (flt_t)1.0/sqrt(rsq2);
+      ir12 *= (flt_t)1.0/std::sqrt(rsq2);
 
       // Urey-Bradley bond
 
@@ -196,7 +196,7 @@ void AngleCharmmIntel::eval(const int vflag,
       const flt_t delzUB = x[i3].z - x[i1].z;
 
       const flt_t rsqUB = delxUB*delxUB + delyUB*delyUB + delzUB*delzUB;
-      const flt_t irUB = (flt_t)1.0/sqrt(rsqUB);
+      const flt_t irUB = (flt_t)1.0/std::sqrt(rsqUB);
 
       // Urey-Bradley force & energy
 
@@ -219,12 +219,12 @@ void AngleCharmmIntel::eval(const int vflag,
       if (c < (flt_t)-1.0) c = (flt_t)-1.0;
 
       const flt_t sd = (flt_t)1.0 - c * c;
-      flt_t s = (flt_t)1.0 / sqrt(sd);
+      flt_t s = (flt_t)1.0 / std::sqrt(sd);
       if (sd < SMALL2) s = INVSMALL;
 
       // harmonic force & energy
 
-      const flt_t dtheta = acos(c) - fc.fc[type].theta0;
+      const flt_t dtheta = std::acos(c) - fc.fc[type].theta0;
       const flt_t tk = fc.fc[type].k * dtheta;
 
       if (EFLAG) eangle += tk*dtheta;
diff --git a/src/INTEL/angle_harmonic_intel.cpp b/src/INTEL/angle_harmonic_intel.cpp
index 8cdab1d43a..98125b164b 100644
--- a/src/INTEL/angle_harmonic_intel.cpp
+++ b/src/INTEL/angle_harmonic_intel.cpp
@@ -178,7 +178,7 @@ void AngleHarmonicIntel::eval(const int vflag,
       const flt_t delz1 = x[i1].z - x[i2].z;
 
       const flt_t rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
-      const flt_t r1 = (flt_t)1.0/sqrt(rsq1);
+      const flt_t r1 = (flt_t)1.0/std::sqrt(rsq1);
 
       // 2nd bond
 
@@ -187,7 +187,7 @@ void AngleHarmonicIntel::eval(const int vflag,
       const flt_t delz2 = x[i3].z - x[i2].z;
 
       const flt_t rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
-      const flt_t r2 = (flt_t)1.0/sqrt(rsq2);
+      const flt_t r2 = (flt_t)1.0/std::sqrt(rsq2);
 
       // angle (cos and sin)
 
@@ -199,12 +199,12 @@ void AngleHarmonicIntel::eval(const int vflag,
       if (c < (flt_t)-1.0) c = (flt_t)-1.0;
 
       const flt_t sd = (flt_t)1.0 - c * c;
-      flt_t s = (flt_t)1.0/sqrt(sd);
+      flt_t s = (flt_t)1.0/std::sqrt(sd);
       if (sd < SMALL2) s = INVSMALL;
 
       // harmonic force & energy
 
-      const flt_t dtheta = acos(c) - fc.fc[type].theta0;
+      const flt_t dtheta = std::acos(c) - fc.fc[type].theta0;
       const flt_t tk = fc.fc[type].k * dtheta;
 
       flt_t eangle;
diff --git a/src/INTEL/bond_harmonic_intel.cpp b/src/INTEL/bond_harmonic_intel.cpp
index a60050bb6b..ab38cefea4 100644
--- a/src/INTEL/bond_harmonic_intel.cpp
+++ b/src/INTEL/bond_harmonic_intel.cpp
@@ -168,7 +168,7 @@ void BondHarmonicIntel::eval(const int vflag,
       const flt_t delz = x[i1].z - x[i2].z;
 
       const flt_t rsq = delx*delx + dely*dely + delz*delz;
-      const flt_t r = sqrt(rsq);
+      const flt_t r = std::sqrt(rsq);
       const flt_t dr = r - fc.fc[type].r0;
       const flt_t rk = fc.fc[type].k * dr;
 
diff --git a/src/INTEL/dihedral_charmm_intel.cpp b/src/INTEL/dihedral_charmm_intel.cpp
index 6c3ae2c927..a41cfb867c 100644
--- a/src/INTEL/dihedral_charmm_intel.cpp
+++ b/src/INTEL/dihedral_charmm_intel.cpp
@@ -240,14 +240,14 @@ void DihedralCharmmIntel::eval(const int vflag,
       const flt_t rasq = ax*ax + ay*ay + az*az;
       const flt_t rbsq = bx*bx + by*by + bz*bz;
       const flt_t rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
-      const flt_t rg = sqrt(rgsq);
+      const flt_t rg = std::sqrt(rgsq);
 
       flt_t rginv, ra2inv, rb2inv;
       rginv = ra2inv = rb2inv = (flt_t)0.0;
       if (rg > 0) rginv = (flt_t)1.0/rg;
       if (rasq > 0) ra2inv = (flt_t)1.0/rasq;
       if (rbsq > 0) rb2inv = (flt_t)1.0/rbsq;
-      const flt_t rabinv = sqrt(ra2inv*rb2inv);
+      const flt_t rabinv = std::sqrt(ra2inv*rb2inv);
 
       flt_t c = (ax*bx + ay*by + az*bz)*rabinv;
       const flt_t s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
@@ -367,7 +367,7 @@ void DihedralCharmmIntel::eval(const int vflag,
 
       flt_t forcecoul;
       if (implicit) forcecoul = qqrd2e * q[i1]*q[i4]*r2inv;
-      else forcecoul = qqrd2e * q[i1]*q[i4]*sqrt(r2inv);
+      else forcecoul = qqrd2e * q[i1]*q[i4]*std::sqrt(r2inv);
       const flt_t forcelj = r6inv * (fc.ljp[itype][jtype].lj1*r6inv -
                                      fc.ljp[itype][jtype].lj2);
       const flt_t fpair = tweight * (forcelj+forcecoul)*r2inv;
diff --git a/src/INTEL/dihedral_fourier_intel.cpp b/src/INTEL/dihedral_fourier_intel.cpp
index 5448fdae98..595d747839 100644
--- a/src/INTEL/dihedral_fourier_intel.cpp
+++ b/src/INTEL/dihedral_fourier_intel.cpp
@@ -199,14 +199,14 @@ void DihedralFourierIntel::eval(const int vflag,
       const flt_t rasq = ax*ax + ay*ay + az*az;
       const flt_t rbsq = bx*bx + by*by + bz*bz;
       const flt_t rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
-      const flt_t rg = sqrt(rgsq);
+      const flt_t rg = std::sqrt(rgsq);
 
       flt_t rginv, ra2inv, rb2inv;
       rginv = ra2inv = rb2inv = (flt_t)0.0;
       if (rg > 0) rginv = (flt_t)1.0/rg;
       if (rasq > 0) ra2inv = (flt_t)1.0/rasq;
       if (rbsq > 0) rb2inv = (flt_t)1.0/rbsq;
-      const flt_t rabinv = sqrt(ra2inv*rb2inv);
+      const flt_t rabinv = std::sqrt(ra2inv*rb2inv);
 
       flt_t c = (ax*bx + ay*by + az*bz)*rabinv;
       const flt_t s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
diff --git a/src/INTEL/dihedral_harmonic_intel.cpp b/src/INTEL/dihedral_harmonic_intel.cpp
index 8d91a3fd27..138545d94a 100644
--- a/src/INTEL/dihedral_harmonic_intel.cpp
+++ b/src/INTEL/dihedral_harmonic_intel.cpp
@@ -199,14 +199,14 @@ void DihedralHarmonicIntel::eval(const int vflag,
       const flt_t rasq = ax*ax + ay*ay + az*az;
       const flt_t rbsq = bx*bx + by*by + bz*bz;
       const flt_t rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
-      const flt_t rg = sqrt(rgsq);
+      const flt_t rg = std::sqrt(rgsq);
 
       flt_t rginv, ra2inv, rb2inv;
       rginv = ra2inv = rb2inv = (flt_t)0.0;
       if (rg > 0) rginv = (flt_t)1.0/rg;
       if (rasq > 0) ra2inv = (flt_t)1.0/rasq;
       if (rbsq > 0) rb2inv = (flt_t)1.0/rbsq;
-      const flt_t rabinv = sqrt(ra2inv*rb2inv);
+      const flt_t rabinv = std::sqrt(ra2inv*rb2inv);
 
       flt_t c = (ax*bx + ay*by + az*bz)*rabinv;
       const flt_t s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
diff --git a/src/INTEL/dihedral_opls_intel.cpp b/src/INTEL/dihedral_opls_intel.cpp
index 82151a8585..52763e6bd8 100644
--- a/src/INTEL/dihedral_opls_intel.cpp
+++ b/src/INTEL/dihedral_opls_intel.cpp
@@ -195,15 +195,15 @@ void DihedralOPLSIntel::eval(const int vflag,
       // 1st and 2nd angle
 
       const flt_t b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
-      const flt_t rb1 = (flt_t)1.0 / sqrt(b1mag2);
+      const flt_t rb1 = (flt_t)1.0 / std::sqrt(b1mag2);
       const flt_t sb1 = (flt_t)1.0 / b1mag2;
 
       const flt_t b2mag2 = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
-      const flt_t rb2 = (flt_t)1.0 / sqrt(b2mag2);
+      const flt_t rb2 = (flt_t)1.0 / std::sqrt(b2mag2);
       const flt_t sb2 = (flt_t)1.0 / b2mag2;
 
       const flt_t b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
-      const flt_t rb3 = (flt_t)1.0 / sqrt(b3mag2);
+      const flt_t rb3 = (flt_t)1.0 / std::sqrt(b3mag2);
       const flt_t sb3 = (flt_t)1.0 / b3mag2;
 
       const flt_t c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
@@ -219,11 +219,11 @@ void DihedralOPLSIntel::eval(const int vflag,
       // cos and sin of 2 angles and final c
 
       flt_t sin2 = MAX((flt_t)1.0 - c1mag*c1mag,(flt_t)0.0);
-      flt_t sc1 = (flt_t)1.0/sqrt(sin2);
+      flt_t sc1 = (flt_t)1.0/std::sqrt(sin2);
       if (sin2 < SMALL2) sc1 = INVSMALL;
 
       sin2 = MAX((flt_t)1.0 - c2mag*c2mag,(flt_t)0.0);
-      flt_t sc2 = (flt_t)1.0/sqrt(sin2);
+      flt_t sc2 = (flt_t)1.0/std::sqrt(sin2);
       if (sin2 < SMALL2) sc2 = INVSMALL;
 
       const flt_t s1 = sc1 * sc1;
@@ -234,7 +234,7 @@ void DihedralOPLSIntel::eval(const int vflag,
       const flt_t cx = vb1z*vb2ym - vb1y*vb2zm;
       const flt_t cy = vb1x*vb2zm - vb1z*vb2xm;
       const flt_t cz = vb1y*vb2xm - vb1x*vb2ym;
-      const flt_t cmag = (flt_t)1.0/sqrt(cx*cx + cy*cy + cz*cz);
+      const flt_t cmag = (flt_t)1.0/std::sqrt(cx*cx + cy*cy + cz*cz);
       const flt_t dx = (cx*vb3x + cy*vb3y + cz*vb3z)*cmag*rb3;
 
       // error check
@@ -252,7 +252,7 @@ void DihedralOPLSIntel::eval(const int vflag,
 
       const flt_t cossq = c * c;
       const flt_t sinsq = (flt_t)1.0 - cossq;
-      flt_t siinv = (flt_t)1.0/sqrt(sinsq);
+      flt_t siinv = (flt_t)1.0/std::sqrt(sinsq);
       if (sinsq < SMALLER2 ) siinv = INVSMALLER;
       if (dx < (flt_t)0.0) siinv = -siinv;
 
diff --git a/src/INTEL/fix_nh_intel.cpp b/src/INTEL/fix_nh_intel.cpp
index 87ce0dbe43..2c05c3f6fa 100644
--- a/src/INTEL/fix_nh_intel.cpp
+++ b/src/INTEL/fix_nh_intel.cpp
@@ -166,28 +166,28 @@ void FixNHIntel::remap()
   if (pstyle == TRICLINIC) {
 
     if (p_flag[4]) {
-      expfac = exp(dto8*omega_dot[0]);
+      expfac = std::exp(dto8*omega_dot[0]);
       h[4] *= expfac;
       h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
       h[4] *= expfac;
     }
 
     if (p_flag[3]) {
-      expfac = exp(dto4*omega_dot[1]);
+      expfac = std::exp(dto4*omega_dot[1]);
       h[3] *= expfac;
       h[3] += dto2*(omega_dot[3]*h[2]);
       h[3] *= expfac;
     }
 
     if (p_flag[5]) {
-      expfac = exp(dto4*omega_dot[0]);
+      expfac = std::exp(dto4*omega_dot[0]);
       h[5] *= expfac;
       h[5] += dto2*(omega_dot[5]*h[1]);
       h[5] *= expfac;
     }
 
     if (p_flag[4]) {
-      expfac = exp(dto8*omega_dot[0]);
+      expfac = std::exp(dto8*omega_dot[0]);
       h[4] *= expfac;
       h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
       h[4] *= expfac;
@@ -200,7 +200,7 @@ void FixNHIntel::remap()
   if (p_flag[0]) {
     oldlo = domain->boxlo[0];
     oldhi = domain->boxhi[0];
-    expfac = exp(dto*omega_dot[0]);
+    expfac = std::exp(dto*omega_dot[0]);
     domain->boxlo[0] = (oldlo-fixedpoint[0])*expfac + fixedpoint[0];
     domain->boxhi[0] = (oldhi-fixedpoint[0])*expfac + fixedpoint[0];
   }
@@ -208,7 +208,7 @@ void FixNHIntel::remap()
   if (p_flag[1]) {
     oldlo = domain->boxlo[1];
     oldhi = domain->boxhi[1];
-    expfac = exp(dto*omega_dot[1]);
+    expfac = std::exp(dto*omega_dot[1]);
     domain->boxlo[1] = (oldlo-fixedpoint[1])*expfac + fixedpoint[1];
     domain->boxhi[1] = (oldhi-fixedpoint[1])*expfac + fixedpoint[1];
     if (scalexy) h[5] *= expfac;
@@ -217,7 +217,7 @@ void FixNHIntel::remap()
   if (p_flag[2]) {
     oldlo = domain->boxlo[2];
     oldhi = domain->boxhi[2];
-    expfac = exp(dto*omega_dot[2]);
+    expfac = std::exp(dto*omega_dot[2]);
     domain->boxlo[2] = (oldlo-fixedpoint[2])*expfac + fixedpoint[2];
     domain->boxhi[2] = (oldhi-fixedpoint[2])*expfac + fixedpoint[2];
     if (scalexz) h[4] *= expfac;
@@ -229,28 +229,28 @@ void FixNHIntel::remap()
   if (pstyle == TRICLINIC) {
 
     if (p_flag[4]) {
-      expfac = exp(dto8*omega_dot[0]);
+      expfac = std::exp(dto8*omega_dot[0]);
       h[4] *= expfac;
       h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
       h[4] *= expfac;
     }
 
     if (p_flag[3]) {
-      expfac = exp(dto4*omega_dot[1]);
+      expfac = std::exp(dto4*omega_dot[1]);
       h[3] *= expfac;
       h[3] += dto2*(omega_dot[3]*h[2]);
       h[3] *= expfac;
     }
 
     if (p_flag[5]) {
-      expfac = exp(dto4*omega_dot[0]);
+      expfac = std::exp(dto4*omega_dot[0]);
       h[5] *= expfac;
       h[5] += dto2*(omega_dot[5]*h[1]);
       h[5] *= expfac;
     }
 
     if (p_flag[4]) {
-      expfac = exp(dto8*omega_dot[0]);
+      expfac = std::exp(dto8*omega_dot[0]);
       h[4] *= expfac;
       h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
       h[4] *= expfac;
@@ -427,9 +427,9 @@ void FixNHIntel::nh_v_press()
   int nlocal = atom->nlocal;
   if (igroup == atom->firstgroup) nlocal = atom->nfirst;
 
-  double f0 = exp(-dt4*(omega_dot[0]+mtk_term2));
-  double f1 = exp(-dt4*(omega_dot[1]+mtk_term2));
-  double f2 = exp(-dt4*(omega_dot[2]+mtk_term2));
+  double f0 = std::exp(-dt4*(omega_dot[0]+mtk_term2));
+  double f1 = std::exp(-dt4*(omega_dot[1]+mtk_term2));
+  double f2 = std::exp(-dt4*(omega_dot[2]+mtk_term2));
   f0 *= f0;
   f1 *= f1;
   f2 *= f2;
diff --git a/src/INTEL/improper_cvff_intel.cpp b/src/INTEL/improper_cvff_intel.cpp
index 09b2d42167..a503f45541 100644
--- a/src/INTEL/improper_cvff_intel.cpp
+++ b/src/INTEL/improper_cvff_intel.cpp
@@ -191,15 +191,15 @@ void ImproperCvffIntel::eval(const int vflag,
       // 1st and 2nd angle
 
       const flt_t b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
-      const flt_t rb1 = (flt_t)1.0 / sqrt(b1mag2);
+      const flt_t rb1 = (flt_t)1.0 / std::sqrt(b1mag2);
       const flt_t sb1 = (flt_t)1.0 / b1mag2;
 
       const flt_t b2mag2 = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
-      const flt_t rb2 = (flt_t)1.0 / sqrt(b2mag2);
+      const flt_t rb2 = (flt_t)1.0 / std::sqrt(b2mag2);
       const flt_t sb2 = (flt_t)1.0 / b2mag2;
 
       const flt_t b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
-      const flt_t rb3 = (flt_t)1.0 / sqrt(b3mag2);
+      const flt_t rb3 = (flt_t)1.0 / std::sqrt(b3mag2);
       const flt_t sb3 = (flt_t)1.0 / b3mag2;
 
       const flt_t c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3;
@@ -215,11 +215,11 @@ void ImproperCvffIntel::eval(const int vflag,
       // cos and sin of 2 angles and final c
 
       const flt_t sd1 = (flt_t)1.0 - c1mag * c1mag;
-      flt_t sc1 = (flt_t)1.0/sqrt(sd1);
+      flt_t sc1 = (flt_t)1.0/std::sqrt(sd1);
       if (sd1 < SMALL2) sc1 = INVSMALL;
 
       const flt_t sd2 = (flt_t)1.0 - c2mag * c2mag;
-      flt_t sc2 = (flt_t)1.0/sqrt(sd2);
+      flt_t sc2 = (flt_t)1.0/std::sqrt(sd2);
       if (sc2 < SMALL2) sc2 = INVSMALL;
 
       const flt_t s1 = sc1 * sc1;
diff --git a/src/INTEL/improper_harmonic_intel.cpp b/src/INTEL/improper_harmonic_intel.cpp
index a9a152d5f0..869051ab6b 100644
--- a/src/INTEL/improper_harmonic_intel.cpp
+++ b/src/INTEL/improper_harmonic_intel.cpp
@@ -194,9 +194,9 @@ void ImproperHarmonicIntel::eval(const int vflag,
       flt_t ss2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
       flt_t ss3 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
 
-      const flt_t r1 = (flt_t)1.0 / sqrt(ss1);
-      const flt_t r2 = (flt_t)1.0 / sqrt(ss2);
-      const flt_t r3 = (flt_t)1.0 / sqrt(ss3);
+      const flt_t r1 = (flt_t)1.0 / std::sqrt(ss1);
+      const flt_t r2 = (flt_t)1.0 / std::sqrt(ss2);
+      const flt_t r3 = (flt_t)1.0 / std::sqrt(ss3);
 
       ss1 = (flt_t)1.0 / ss1;
       ss2 = (flt_t)1.0 / ss2;
@@ -214,7 +214,7 @@ void ImproperHarmonicIntel::eval(const int vflag,
       flt_t s2 = (flt_t)1.0 - c2*c2;
       if (s2 < SMALL) s2 = SMALL;
 
-      flt_t s12 = (flt_t)1.0 / sqrt(s1*s2);
+      flt_t s12 = (flt_t)1.0 / std::sqrt(s1*s2);
       s1 = (flt_t)1.0 / s1;
       s2 = (flt_t)1.0 / s2;
       flt_t c = (c1*c2 + c0) * s12;
@@ -229,12 +229,12 @@ void ImproperHarmonicIntel::eval(const int vflag,
       if (c < (flt_t)-1.0) c = (flt_t)-1.0;
 
       const flt_t sd = (flt_t)1.0 - c * c;
-      flt_t s = (flt_t)1.0 / sqrt(sd);
+      flt_t s = (flt_t)1.0 / std::sqrt(sd);
       if (sd < SMALL2) s = INVSMALL;
 
       // force & energy
 
-      const flt_t domega = acos(c) - fc.fc[type].chi;
+      const flt_t domega = std::acos(c) - fc.fc[type].chi;
       flt_t a;
       a = fc.fc[type].k * domega;
 
diff --git a/src/INTEL/intel_intrinsics.h b/src/INTEL/intel_intrinsics.h
index 1ff405edd2..c106dfd411 100644
--- a/src/INTEL/intel_intrinsics.h
+++ b/src/INTEL/intel_intrinsics.h
@@ -1764,7 +1764,7 @@ struct vector_ops<flt_t, NONE> {
       return a < b;
     }
     static fvec invsqrt(const fvec &a) {
-      return 1. / sqrt(a);
+      return 1. / std::sqrt(a);
     }
     static fvec sincos(fvec *c, const fvec &a) {
       *c = cos(a);
diff --git a/src/INTEL/math_extra_intel.h b/src/INTEL/math_extra_intel.h
index a8869f7384..556f3f4590 100644
--- a/src/INTEL/math_extra_intel.h
+++ b/src/INTEL/math_extra_intel.h
@@ -100,12 +100,12 @@
    normalize a vector, return in ans
 ------------------------------------------------------------------------- */
 
-#define ME_normalize3(v0, v1, v2, ans)                  \
-{                                                       \
-  flt_t scale = (flt_t)1.0 / sqrt(v0*v0+v1*v1+v2*v2);   \
-  ans##_0 = v0 * scale;                                 \
-  ans##_1 = v1 * scale;                                 \
-  ans##_2 = v2 * scale;                                 \
+#define ME_normalize3(v0, v1, v2, ans)                          \
+{                                                               \
+  flt_t scale = (flt_t)1.0 / std::sqrt(v0*v0+v1*v1+v2*v2);      \
+  ans##_0 = v0 * scale;                                         \
+  ans##_1 = v1 * scale;                                         \
+  ans##_2 = v2 * scale;                                         \
 }
 
 /* ----------------------------------------------------------------------
@@ -359,7 +359,7 @@
 #define ME_qnormalize(q)                                                \
 {                                                                       \
   double norm = 1.0 /                                                   \
-    sqrt(q##_w*q##_w + q##_i*q##_i + q##_j*q##_j + q##_k*q##_k);        \
+    std::sqrt(q##_w*q##_w + q##_i*q##_i + q##_j*q##_j + q##_k*q##_k);   \
   q##_w *= norm;                                                        \
   q##_i *= norm;                                                        \
   q##_j *= norm;                                                        \
diff --git a/src/INTEL/pair_airebo_intel.cpp b/src/INTEL/pair_airebo_intel.cpp
index 0b05447dd7..7bc2b3edb8 100644
--- a/src/INTEL/pair_airebo_intel.cpp
+++ b/src/INTEL/pair_airebo_intel.cpp
@@ -905,7 +905,7 @@ inline flt_t frebo_pij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i, int j,
       flt_t rho_k = ka->params.rho[ktype][1];
       flt_t rho_j = ka->params.rho[jtype][1];
       flt_t lamdajik = 4 * itype * ((rho_k - rikmag) - (rho_j - rijmag));
-      flt_t ex_lam = exp(lamdajik);
+      flt_t ex_lam = overloaded::exp(lamdajik);
       flt_t rcminik = ka->params.rcmin[itype][ktype];
       flt_t rcmaxik = ka->params.rcmax[itype][ktype];
       flt_t dwik;
diff --git a/src/INTEL/pair_buck_coul_cut_intel.cpp b/src/INTEL/pair_buck_coul_cut_intel.cpp
index 01a9f91bcf..424e38c16a 100644
--- a/src/INTEL/pair_buck_coul_cut_intel.cpp
+++ b/src/INTEL/pair_buck_coul_cut_intel.cpp
@@ -267,7 +267,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag,
           const flt_t delz = ztmp - x[j].z;
           const int jtype = IP_PRE_dword_index(x[j].w);
           const flt_t rsq = delx * delx + dely * dely + delz * delz;
-          const flt_t r = sqrt(rsq);
+          const flt_t r = std::sqrt(rsq);
           const flt_t r2inv = (flt_t)1.0 / rsq;
 
           #ifdef INTEL_VMASK
diff --git a/src/INTEL/pair_buck_coul_long_intel.cpp b/src/INTEL/pair_buck_coul_long_intel.cpp
index ff57b571a4..48007c30d9 100644
--- a/src/INTEL/pair_buck_coul_long_intel.cpp
+++ b/src/INTEL/pair_buck_coul_long_intel.cpp
@@ -322,7 +322,7 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag,
           const int jtype = tjtype[jj];
           const flt_t rsq = trsq[jj];
           const flt_t r2inv = (flt_t)1.0 / rsq;
-          const flt_t r = (flt_t)1.0 / sqrt(r2inv);
+          const flt_t r = (flt_t)1.0 / std::sqrt(r2inv);
 
           #ifdef INTEL_ALLOW_TABLE
           if (!ncoultablebits || rsq <= tabinnersq) {
diff --git a/src/INTEL/pair_buck_intel.cpp b/src/INTEL/pair_buck_intel.cpp
index 2461361788..1f2a033784 100644
--- a/src/INTEL/pair_buck_intel.cpp
+++ b/src/INTEL/pair_buck_intel.cpp
@@ -255,7 +255,7 @@ void PairBuckIntel::eval(const int offload, const int vflag,
           const flt_t delz = ztmp - x[j].z;
           const int jtype = IP_PRE_dword_index(x[j].w);
           const flt_t rsq = delx * delx + dely * dely + delz * delz;
-          const flt_t r = sqrt(rsq);
+          const flt_t r = std::sqrt(rsq);
           const flt_t r2inv = (flt_t)1.0 / rsq;
 
           #ifdef INTEL_VMASK
diff --git a/src/INTEL/pair_dpd_intel.cpp b/src/INTEL/pair_dpd_intel.cpp
index 011979223e..7b11053d41 100644
--- a/src/INTEL/pair_dpd_intel.cpp
+++ b/src/INTEL/pair_dpd_intel.cpp
@@ -180,7 +180,7 @@ void PairDPDIntel::eval(const int offload, const int vflag,
   ATOM_T * _noalias const x = buffers->get_x(offload);
   typedef struct { double x, y, z; } lmp_vt;
   auto *v = (lmp_vt *)atom->v[0];
-  const flt_t dtinvsqrt = 1.0/sqrt(update->dt);
+  const flt_t dtinvsqrt = 1.0/std::sqrt(update->dt);
 
   const int * _noalias const ilist = list->ilist;
   const int * _noalias const numneigh = list->numneigh;
@@ -322,7 +322,7 @@ void PairDPDIntel::eval(const int offload, const int vflag,
             icut = parami[jtype].icut;
           }
           const flt_t rsq = delx * delx + dely * dely + delz * delz;
-          const flt_t rinv = (flt_t)1.0/sqrt(rsq);
+          const flt_t rinv = (flt_t)1.0/std::sqrt(rsq);
 
           if (rinv > icut) {
             flt_t factor_dpd, factor_sqrt;
diff --git a/src/INTEL/pair_eam_intel.cpp b/src/INTEL/pair_eam_intel.cpp
index ba5047a15a..9c5d6da5e5 100644
--- a/src/INTEL/pair_eam_intel.cpp
+++ b/src/INTEL/pair_eam_intel.cpp
@@ -340,7 +340,7 @@ void PairEAMIntel::eval(const int offload, const int vflag,
           const int j = tj[jj] & NEIGHMASK;
           if (!ONETYPE) jtype = tjtype[jj];
           const flt_t rsq = trsq[jj];
-          flt_t p = sqrt(rsq)*frdr + (flt_t)1.0;
+          flt_t p = std::sqrt(rsq)*frdr + (flt_t)1.0;
           int m = static_cast<int> (p);
           m = MIN(m,nr-1);
           p -= m;
@@ -546,7 +546,7 @@ void PairEAMIntel::eval(const int offload, const int vflag,
           const int j = tj[jj] & NEIGHMASK;
           if (!ONETYPE) jtype = tjtype[jj];
           const flt_t rsq = trsq[jj];
-          const flt_t r = sqrt(rsq);
+          const flt_t r = std::sqrt(rsq);
           flt_t p = r*frdr + (flt_t)1.0;
           int m = static_cast<int> (p);
           m = MIN(m,nr-1);
diff --git a/src/INTEL/pair_gayberne_intel.cpp b/src/INTEL/pair_gayberne_intel.cpp
index 5609479388..92e074e5e1 100644
--- a/src/INTEL/pair_gayberne_intel.cpp
+++ b/src/INTEL/pair_gayberne_intel.cpp
@@ -492,7 +492,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
 
           flt_t r12hat_0, r12hat_1, r12hat_2;
           ME_normalize3(delx_form[jj], dely_form[jj], delz_form[jj], r12hat);
-          flt_t r = sqrt(rsq_form[jj]);
+          flt_t r = std::sqrt(rsq_form[jj]);
 
           // compute distance of closest approach
 
diff --git a/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp
index e920257ef4..faae6e5cbc 100644
--- a/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp
+++ b/src/INTEL/pair_lj_charmm_coul_charmm_intel.cpp
@@ -306,7 +306,7 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag,
           const int sbindex = tj[jj] >> SBBITS & 3;
           const flt_t rsq = trsq[jj];
           const flt_t r2inv = (flt_t)1.0 / rsq;
-          const flt_t r_inv = (flt_t)1.0 / sqrt(rsq);
+          const flt_t r_inv = (flt_t)1.0 / std::sqrt(rsq);
           forcecoul = qqrd2e * qtmp * q[j] * r_inv;
           if (rsq > cut_coul_innersq) {
             const flt_t ccr = cut_coulsq - rsq;
diff --git a/src/INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/INTEL/pair_lj_charmm_coul_long_intel.cpp
index 0a93621bcd..412af17357 100644
--- a/src/INTEL/pair_lj_charmm_coul_long_intel.cpp
+++ b/src/INTEL/pair_lj_charmm_coul_long_intel.cpp
@@ -339,7 +339,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag,
             const flt_t EWALD_F = 1.12837917;
             const flt_t INV_EWALD_P = 1.0 / 0.3275911;
 
-            const flt_t r = (flt_t)1.0 / sqrt(r2inv);
+            const flt_t r = (flt_t)1.0 / std::sqrt(r2inv);
             const flt_t grij = g_ewald * r;
             const flt_t expm2 = std::exp(-grij * grij);
             const flt_t t = INV_EWALD_P / (INV_EWALD_P + grij);
@@ -591,10 +591,10 @@ void PairLJCharmmCoulLongIntel::pack_force_const(ForceConst<flt_t> &fc,
     for (int j = 1; j < tp1; j++) {
       if (i <= j) {
         fc.lj[i][j].x = epsilon[i][j] * 4.0;
-        fc.lj[i][j].y = pow(sigma[i][j],6.0);
+        fc.lj[i][j].y = std::pow(sigma[i][j],6.0);
       } else {
         fc.lj[i][j].x = epsilon[j][i] * 4.0;
-        fc.lj[i][j].y = pow(sigma[j][i],6.0);
+        fc.lj[i][j].y = std::pow(sigma[j][i],6.0);
       }
       fc.cutsq[i][j] = cutsq[i][j];
     }
diff --git a/src/INTEL/pair_lj_cut_coul_long_intel.cpp b/src/INTEL/pair_lj_cut_coul_long_intel.cpp
index 89e556defa..5eb3cbc1f7 100644
--- a/src/INTEL/pair_lj_cut_coul_long_intel.cpp
+++ b/src/INTEL/pair_lj_cut_coul_long_intel.cpp
@@ -332,7 +332,7 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag,
             const flt_t EWALD_F = 1.12837917;
             const flt_t INV_EWALD_P = 1.0 / 0.3275911;
 
-            const flt_t r = (flt_t)1.0 / sqrt(r2inv);
+            const flt_t r = (flt_t)1.0 / std::sqrt(r2inv);
             const flt_t grij = g_ewald * r;
             const flt_t expm2 = std::exp(-grij * grij);
             const flt_t t = INV_EWALD_P / (INV_EWALD_P + grij);
diff --git a/src/INTEL/pair_sw_intel.cpp b/src/INTEL/pair_sw_intel.cpp
index 07d590ee2c..fa62f499de 100644
--- a/src/INTEL/pair_sw_intel.cpp
+++ b/src/INTEL/pair_sw_intel.cpp
@@ -382,7 +382,7 @@ void PairSWIntel::eval(const int offload, const int vflag,
           const flt_t rsq1 = trsq[jj];
 
           const flt_t rinvsq1 = (flt_t)1.0 / rsq1;
-          const flt_t r1 = (flt_t)1.0/sqrt(rinvsq1);
+          const flt_t r1 = (flt_t)1.0/std::sqrt(rinvsq1);
           if (!ONETYPE) cut = p2f[ijtype].cut;
           const flt_t rainv1 = (flt_t)1.0 / (r1 - cut);
 
@@ -475,7 +475,7 @@ void PairSWIntel::eval(const int offload, const int vflag,
             const flt_t rsq2 = trsq[kk];
 
             const flt_t rinvsq2 = (flt_t)1.0 / rsq2;
-            const flt_t r2 = (flt_t)1.0 / sqrt(rinvsq2);
+            const flt_t r2 = (flt_t)1.0 / std::sqrt(rinvsq2);
             const flt_t rainv2 = (flt_t)1.0 / (r2 - cut);
             const flt_t gsrainv2 = sigma_gamma * rainv2;
             const flt_t gsrainvsq2 = gsrainv2 * rainv2 / r2;
diff --git a/src/INTEL/pppm_disp_intel.cpp b/src/INTEL/pppm_disp_intel.cpp
index fdff23fe5e..e17c077c6e 100644
--- a/src/INTEL/pppm_disp_intel.cpp
+++ b/src/INTEL/pppm_disp_intel.cpp
@@ -662,8 +662,8 @@ void PPPMDispIntel::compute(int eflag, int vflag)
 
     energy_1 -= g_ewald*qsqsum/MY_PIS +
       MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
-    energy_6 += - MY_PI*MY_PIS/(6*volume)*pow(g_ewald_6,3)*csumij +
-      1.0/12.0*pow(g_ewald_6,6)*csum;
+    energy_6 += - MY_PI*MY_PIS/(6*volume)*std::pow(g_ewald_6,3)*csumij +
+      1.0/12.0*std::pow(g_ewald_6,6)*csum;
     energy_1 *= qscale;
   }
 
@@ -676,7 +676,7 @@ void PPPMDispIntel::compute(int eflag, int vflag)
     MPI_Allreduce(virial_6,virial_all,6,MPI_DOUBLE,MPI_SUM,world);
     for (i = 0; i < 6; i++) virial[i] += 0.5*volume*virial_all[i];
     if (function[1]+function[2]+function[3]) {
-      double a =  MY_PI*MY_PIS/(6*volume)*pow(g_ewald_6,3)*csumij;
+      double a =  MY_PI*MY_PIS/(6*volume)*std::pow(g_ewald_6,3)*csumij;
       virial[0] -= a;
       virial[1] -= a;
       virial[2] -= a;
@@ -695,8 +695,8 @@ void PPPMDispIntel::compute(int eflag, int vflag)
       int tmp;
       for (i = 0; i < atom->nlocal; i++) {
         tmp = atom->type[i];
-        eatom[i] += - MY_PI*MY_PIS/(6*volume)*pow(g_ewald_6,3)*csumi[tmp] +
-                      1.0/12.0*pow(g_ewald_6,6)*cii[tmp];
+        eatom[i] += - MY_PI*MY_PIS/(6*volume)*std::pow(g_ewald_6,3)*
+          csumi[tmp] + 1.0/12.0*std::pow(g_ewald_6,6)*cii[tmp];
       }
     }
   }
@@ -708,7 +708,7 @@ void PPPMDispIntel::compute(int eflag, int vflag)
         tmp = atom->type[i];
         //dispersion self virial correction
         for (int n = 0; n < 3; n++) vatom[i][n] -= MY_PI*MY_PIS/(6*volume)*
-                                      pow(g_ewald_6,3)*csumi[tmp];
+                                      std::pow(g_ewald_6,3)*csumi[tmp];
       }
     }
   }
@@ -1788,18 +1788,18 @@ void PPPMDispIntel::fieldforce_c_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
       const flt_t s1 = x[i][0] * hx_inv;
       const flt_t s2 = x[i][1] * hy_inv;
       const flt_t s3 = x[i][2] * hz_inv;
-      flt_t sf = fsf_coeff0 * sin(ftwo_pi * s1);
-      sf += fsf_coeff1 * sin(ffour_pi * s1);
+      flt_t sf = fsf_coeff0 * std::sin(ftwo_pi * s1);
+      sf += fsf_coeff1 * std::sin(ffour_pi * s1);
       sf *= twoqsq;
       f[i][0] += qfactor * particle_ekx[i] - fqqrd2es * sf;
 
-      sf = fsf_coeff2 * sin(ftwo_pi * s2);
-      sf += fsf_coeff3 * sin(ffour_pi * s2);
+      sf = fsf_coeff2 * std::sin(ftwo_pi * s2);
+      sf += fsf_coeff3 * std::sin(ffour_pi * s2);
       sf *= twoqsq;
       f[i][1] += qfactor * particle_eky[i] - fqqrd2es * sf;
 
-      sf = fsf_coeff4 * sin(ftwo_pi * s3);
-      sf += fsf_coeff5 * sin(ffour_pi * s3);
+      sf = fsf_coeff4 * std::sin(ftwo_pi * s3);
+      sf += fsf_coeff5 * std::sin(ffour_pi * s3);
       sf *= twoqsq;
 
       if (slabflag != 2) f[i][2] += qfactor * particle_ekz[i] - fqqrd2es * sf;
@@ -2160,18 +2160,18 @@ void PPPMDispIntel::fieldforce_g_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
       const flt_t s1 = x[i][0] * hx_inv;
       const flt_t s2 = x[i][1] * hy_inv;
       const flt_t s3 = x[i][2] * hz_inv;
-      flt_t sf = fsf_coeff0 * sin(ftwo_pi * s1);
-      sf += fsf_coeff1 * sin(ffour_pi * s1);
+      flt_t sf = fsf_coeff0 * std::sin(ftwo_pi * s1);
+      sf += fsf_coeff1 * std::sin(ffour_pi * s1);
       sf *= twoljsq;
       f[i][0] += lj * particle_ekx[i] - sf;
 
-      sf = fsf_coeff2 * sin(ftwo_pi * s2);
-      sf += fsf_coeff3 * sin(ffour_pi * s2);
+      sf = fsf_coeff2 * std::sin(ftwo_pi * s2);
+      sf += fsf_coeff3 * std::sin(ffour_pi * s2);
       sf *= twoljsq;
       f[i][1] += lj * particle_eky[i] - sf;
 
-      sf = fsf_coeff4 * sin(ftwo_pi * s3);
-      sf += fsf_coeff5 * sin(ffour_pi * s3);
+      sf = fsf_coeff4 * std::sin(ftwo_pi * s3);
+      sf += fsf_coeff5 * std::sin(ffour_pi * s3);
       sf *= twoljsq;
 
       if (slabflag != 2) f[i][2] += lj * particle_ekz[i] -  sf;
@@ -2707,22 +2707,22 @@ void PPPMDispIntel::fieldforce_a_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
       const flt_t s1 = x[i][0] * hx_inv;
       const flt_t s2 = x[i][1] * hy_inv;
       const flt_t s3 = x[i][2] * hz_inv;
-      flt_t sf = fsf_coeff0 * sin(ftwo_pi * s1);
-      sf += fsf_coeff1 * sin(ffour_pi * s1);
+      flt_t sf = fsf_coeff0 * std::sin(ftwo_pi * s1);
+      sf += fsf_coeff1 * std::sin(ffour_pi * s1);
       sf *= 4*lj0*lj6 + 4*lj1*lj5 + 4*lj2*lj4 + 2*lj3*lj3;
       f[i][0] += lj0*particle_ekx0[i] + lj1*particle_ekx1[i] +
         lj2*particle_ekx2[i] + lj3*particle_ekx3[i] + lj4*particle_ekx4[i] +
         lj5*particle_ekx5[i] + lj6*particle_ekx6[i] - sf;
 
-      sf = fsf_coeff2 * sin(ftwo_pi * s2);
-      sf += fsf_coeff3 * sin(ffour_pi * s2);
+      sf = fsf_coeff2 * std::sin(ftwo_pi * s2);
+      sf += fsf_coeff3 * std::sin(ffour_pi * s2);
       sf *= 4*lj0*lj6 + 4*lj1*lj5 + 4*lj2*lj4 + 2*lj3*lj3;
       f[i][1] += lj0*particle_eky0[i] + lj1*particle_eky1[i] +
         lj2*particle_eky2[i] + lj3*particle_eky3[i] + lj4*particle_eky4[i] +
         lj5*particle_eky5[i] + lj6*particle_eky6[i] - sf;
 
-      sf = fsf_coeff4 * sin(ftwo_pi * s3);
-      sf += fsf_coeff5 * sin(ffour_pi * s3);
+      sf = fsf_coeff4 * std::sin(ftwo_pi * s3);
+      sf += fsf_coeff5 * std::sin(ffour_pi * s3);
       sf *= 4*lj0*lj6 + 4*lj1*lj5 + 4*lj2*lj4 + 2*lj3*lj3;
       if (slabflag != 2)
       f[i][2] += lj0*particle_ekz0[i] + lj1*particle_ekz1[i] +
@@ -3106,14 +3106,14 @@ void PPPMDispIntel::fieldforce_none_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
       const flt_t s1 = x[i][0] * hx_inv;
       const flt_t s2 = x[i][1] * hy_inv;
       const flt_t s3 = x[i][2] * hz_inv;
-      flt_t sf1 = fsf_coeff0 * sin(ftwo_pi * s1);
-      sf1 += fsf_coeff1 * sin(ffour_pi * s1);
+      flt_t sf1 = fsf_coeff0 * std::sin(ftwo_pi * s1);
+      sf1 += fsf_coeff1 * std::sin(ffour_pi * s1);
 
-      flt_t sf2 = fsf_coeff2 * sin(ftwo_pi * s2);
-      sf2 += fsf_coeff3 * sin(ffour_pi * s2);
+      flt_t sf2 = fsf_coeff2 * std::sin(ftwo_pi * s2);
+      sf2 += fsf_coeff3 * std::sin(ffour_pi * s2);
 
-      flt_t sf3 = fsf_coeff4 * sin(ftwo_pi * s3);
-      sf3 += fsf_coeff5 * sin(ffour_pi * s3);
+      flt_t sf3 = fsf_coeff4 * std::sin(ftwo_pi * s3);
+      sf3 += fsf_coeff5 * std::sin(ffour_pi * s3);
       for (int k = 0; k < nsplit; k++) {
         const flt_t lj = B[nsplit*type + k];
         const flt_t twoljsq = lj*lj * B[k] * 2;
diff --git a/src/INTEL/pppm_intel.cpp b/src/INTEL/pppm_intel.cpp
index 2ceca54d29..f67b3a89b3 100644
--- a/src/INTEL/pppm_intel.cpp
+++ b/src/INTEL/pppm_intel.cpp
@@ -953,18 +953,18 @@ void PPPMIntel::fieldforce_ad(IntelBuffers<flt_t,acc_t> *buffers)
       const flt_t s1 = x[i].x * hx_inv;
       const flt_t s2 = x[i].y * hy_inv;
       const flt_t s3 = x[i].z * hz_inv;
-      flt_t sf = fsf_coeff0 * sin(ftwo_pi * s1);
-      sf += fsf_coeff1 * sin(ffour_pi * s1);
+      flt_t sf = fsf_coeff0 * std::sin(ftwo_pi * s1);
+      sf += fsf_coeff1 * std::sin(ffour_pi * s1);
       sf *= twoqsq;
       f[i].x += qfactor * particle_ekx[i] - fqqrd2es * sf;
 
-      sf = fsf_coeff2 * sin(ftwo_pi * s2);
-      sf += fsf_coeff3 * sin(ffour_pi * s2);
+      sf = fsf_coeff2 * std::sin(ftwo_pi * s2);
+      sf += fsf_coeff3 * std::sin(ffour_pi * s2);
       sf *= twoqsq;
       f[i].y += qfactor * particle_eky[i] - fqqrd2es * sf;
 
-      sf = fsf_coeff4 * sin(ftwo_pi * s3);
-      sf += fsf_coeff5 * sin(ffour_pi * s3);
+      sf = fsf_coeff4 * std::sin(ftwo_pi * s3);
+      sf += fsf_coeff5 * std::sin(ffour_pi * s3);
       sf *= twoqsq;
 
       if (slabflag != 2) f[i].z += qfactor * particle_ekz[i] - fqqrd2es * sf;

From 0dab1910db6c6e8fb945567131f7da287f6b5e44 Mon Sep 17 00:00:00 2001
From: "W. Michael Brown" <michael.w.brown@intel.com>
Date: Sat, 10 Jun 2023 13:34:16 -0700
Subject: [PATCH 234/396] Small updates to benchmark script in INTEL/TEST

---
 src/INTEL/TEST/run_benchmarks.sh | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

diff --git a/src/INTEL/TEST/run_benchmarks.sh b/src/INTEL/TEST/run_benchmarks.sh
index 01ddfbebf3..82eb51c928 100755
--- a/src/INTEL/TEST/run_benchmarks.sh
+++ b/src/INTEL/TEST/run_benchmarks.sh
@@ -7,12 +7,10 @@
 # --------------------- MPI Launch Command
 
 export MPI="mpirun"
-#export MPI="numactl -p 1 mpirun"    # -- Systems w/ MCDRAM in flat mode
 
 # ------------- Name and location of the LAMMPS binary
 
 export LMP_BIN=../../lmp_intel_cpu_intelmpi
-#export LMP_BIN=../../lmp_knl
 
 # ------------- Directory containing the LAMMPS installation
 
@@ -20,21 +18,18 @@ export LMP_ROOT=../../../
 
 # ------------- Number of physical cores (not HW threads)
 
-export LMP_CORES=36            # -- For Intel Xeon E5-2697v4 SKU
-#export LMP_CORES=68           # -- For Intel Xeon Phi x200 7250 SKU
+export LMP_CORES=36
+# Set automatically with lscpu
+export LMP_CORES=`lscpu | awk '$1=="Core(s)"{t=NF; cores=$t}$1=="Socket(s):"{t=NF; sockets=$t}END{print cores*sockets}'`
 
 # ------------- Number of HW threads to use in tests
 
-export LMP_THREAD_LIST="2"     # -- For 2 threads per core w/ HT enabled
-#export LMP_THREAD_LIST="2 4"   # -- For 2 threads per core w/ HT enabled
+export LMP_THREAD_LIST="1 2"   # -- Also test 2 threads per core w/ HT enabled
 
 # ------------- MPI Tuning Parameters
 
-#export I_MPI_SHM_LMT=shm      # -- Uncomment for Xeon Phi x200 series
-
-# ------------- Library locations for build
-
-#source /opt/intel/parallel_studio_xe_2017.2.050/psxevars.sh
+export I_MPI_FABRICS=shm
+export I_MPI_PIN_DOMAIN=core
 
 #########################################################################
 # End settings for your system
@@ -50,8 +45,6 @@ export DATE_STRING=`date +%s`
 export LOG_DIR=$LOG_DIR_HOST"_"$LOG_DIR_HEADER"_"$DATE_STRING
 mkdir $LOG_DIR
 
-export I_MPI_PIN_DOMAIN=core
-#export I_MPI_FABRICS=shm
 export KMP_BLOCKTIME=0
 
 echo -n "Creating restart file...."
@@ -73,6 +66,9 @@ do
       export LOGFILE=$LOG_DIR/$workload"_lrt".$LMP_CORES"c"$threads"t".log
       cmd="$MPI -np $LMP_CORES $LMP_BIN -in in.intel.$workload -log $LOGFILE $RLMP_ARGS";
       rthreads=$((threads-1))
+      if [ $rthreads -lt 1 ]; then
+          rthreads=1
+      fi
       export KMP_AFFINITY=none
       export OMP_NUM_THREADS=$rthreads
       echo "  $cmd" >> $LOG_DIR/commands.info
@@ -82,4 +78,5 @@ do
 done
 
 # Performance reported by LAMMPS (Timesteps/second ignoring warm-up run)
-grep Perf $LOG_DIR/*.log | awk 'BEGIN{n=1}n%2==0{print $0}{n++}' | sed 's/\/day//g' | sed 's/steps\/s/steps_s/g' | sed 's/hours\/ns//g' | sed 's/.*\///g' | sed 's/\.log:Performance://g' | awk '{c=NF-1; print $1,$c}'
+grep Perf $LOG_DIR/*.log | awk 'n%2==1{c=NF-3; print $1,$c}{n++}' | sed -e 's/.*\///g' -e 's/:.*://g'
+

From 62b388b48fd34e1d5e2bfbd4af221ad062f4847e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 10 Jun 2023 19:23:11 -0400
Subject: [PATCH 235/396] consolidate LAMMPS data type constants and enums and
 use the same names

---
 examples/COUPLE/plugin/liblammpsplugin.h |  5 +++--
 fortran/lammps.f90                       |  3 ++-
 python/lammps/constants.py               |  8 ++++++--
 src/EXTRA-DUMP/dump_yaml.cpp             |  6 +++---
 src/NETCDF/dump_netcdf.cpp               | 12 ++++++------
 src/NETCDF/dump_netcdf_mpiio.cpp         | 12 ++++++------
 src/library.cpp                          |  6 +++---
 src/library.h                            |  3 ++-
 src/lmptype.h                            | 25 ++++++++++++++++++------
 tools/swig/lammps.i                      |  3 ++-
 unittest/utils/test_lmptype.cpp          | 16 +++++++--------
 11 files changed, 60 insertions(+), 39 deletions(-)

diff --git a/examples/COUPLE/plugin/liblammpsplugin.h b/examples/COUPLE/plugin/liblammpsplugin.h
index 40fba6b9e3..1520ef638d 100644
--- a/examples/COUPLE/plugin/liblammpsplugin.h
+++ b/examples/COUPLE/plugin/liblammpsplugin.h
@@ -37,12 +37,13 @@
 #endif
 
 /* The following enums must be kept in sync with the equivalent enums
- * or constants in python/lammps/constants.py, fortran/lammps.f90,
- * tools/swig/lammps.i, and examples/COUPLE/plugin/liblammpsplugin.h */
+ * or constants in src/library.h, src/lmptype.h, python/lammps/constants.py,
+ * fortran/lammps.f90, and tools/swig/lammps.i */
 
 /* Data type constants for extracting data from atoms, computes and fixes */
 
 enum _LMP_DATATYPE_CONST {
+  LAMMPS_NONE = -1,     /*!< no data type assigned (yet) */
   LAMMPS_INT = 0,       /*!< 32-bit integer (array) */
   LAMMPS_INT_2D = 1,    /*!< two-dimensional 32-bit integer array */
   LAMMPS_DOUBLE = 2,    /*!< 64-bit double (array) */
diff --git a/fortran/lammps.f90 b/fortran/lammps.f90
index f511e6bb60..669e9c700d 100644
--- a/fortran/lammps.f90
+++ b/fortran/lammps.f90
@@ -44,11 +44,12 @@ MODULE LIBLAMMPS
   ! Data type constants for extracting data from global, atom, compute, and fix
   !
   ! Must be kept in sync with the equivalent declarations in
-  ! src/library.h, python/lammps/constants.py, tools/swig/lammps.i,
+  ! src/library.h, src/lmptype.h, python/lammps/constants.py, tools/swig/lammps.i,
   ! and examples/COUPLE/plugin/liblammpsplugin.h
   !
   ! These are NOT part of the API (the part the user sees)
   INTEGER(c_int), PARAMETER :: &
+    LAMMPS_NONE = -1, &       ! no data type assigned (yet)
     LAMMPS_INT = 0, &         ! 32-bit integer (or array)
     LAMMPS_INT_2D = 1, &      ! two-dimensional 32-bit integer array
     LAMMPS_DOUBLE = 2, &      ! 64-bit double (or array)
diff --git a/python/lammps/constants.py b/python/lammps/constants.py
index 8fd6a9eaf5..1d0d8adb78 100644
--- a/python/lammps/constants.py
+++ b/python/lammps/constants.py
@@ -13,7 +13,13 @@
 
 # various symbolic constants to be used
 # in certain calls to select data formats
+
+# these must be kept in sync with the enums in src/library.h, src/lmptype.h,
+# tools/swig/lammps.i, examples/COUPLE/plugin/liblammpsplugin.h,
+# and the constants in fortran/lammps.f90
+
 LAMMPS_AUTODETECT  = None
+LAMMPS_NONE        = -1
 LAMMPS_INT         = 0
 LAMMPS_INT_2D      = 1
 LAMMPS_DOUBLE      = 2
@@ -22,8 +28,6 @@ LAMMPS_INT64       = 4
 LAMMPS_INT64_2D    = 5
 LAMMPS_STRING      = 6
 
-# these must be kept in sync with the enums in src/library.h, tools/swig/lammps.i,
-# examples/COUPLE/plugin/liblammpsplugin.h, and the constants in fortran/lammps.f90
 LMP_STYLE_GLOBAL   = 0
 LMP_STYLE_ATOM     = 1
 LMP_STYLE_LOCAL    = 2
diff --git a/src/EXTRA-DUMP/dump_yaml.cpp b/src/EXTRA-DUMP/dump_yaml.cpp
index 47cab1ee02..3ca5c59edf 100644
--- a/src/EXTRA-DUMP/dump_yaml.cpp
+++ b/src/EXTRA-DUMP/dump_yaml.cpp
@@ -71,11 +71,11 @@ void DumpYAML::write_header(bigint ndump)
       thermo_data += "]\n  - data: [ ";
 
       for (int i = 0; i < nfield; ++i) {
-        if (fields[i].type == multitype::DOUBLE)
+        if (fields[i].type == multitype::LAMMPS_DOUBLE)
           thermo_data += fmt::format("{}, ", fields[i].data.d);
-        else if (fields[i].type == multitype::INT)
+        else if (fields[i].type == multitype::LAMMPS_INT)
           thermo_data += fmt::format("{}, ", fields[i].data.i);
-        else if (fields[i].type == multitype::BIGINT)
+        else if (fields[i].type == multitype::LAMMPS_INT64)
           thermo_data += fmt::format("{}, ", fields[i].data.b);
         else
           thermo_data += ", ";
diff --git a/src/NETCDF/dump_netcdf.cpp b/src/NETCDF/dump_netcdf.cpp
index 0115c0bbe9..a4699897a3 100644
--- a/src/NETCDF/dump_netcdf.cpp
+++ b/src/NETCDF/dump_netcdf.cpp
@@ -442,11 +442,11 @@ void DumpNetCDF::openfile()
         const int nfield = *th->get_nfield();
 
         for (int i = 0; i < nfield; i++) {
-          if (fields[i].type == multitype::DOUBLE) {
+          if (fields[i].type == multitype::LAMMPS_DOUBLE) {
             NCERRX( nc_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
-          } else if (fields[i].type == multitype::INT) {
+          } else if (fields[i].type == multitype::LAMMPS_INT) {
             NCERRX( nc_def_var(ncid, keywords[i].c_str(), NC_INT, 1, dims, &thermovar[i]), keywords[i].c_str() );
-          } else if (fields[i].type == multitype::BIGINT) {
+          } else if (fields[i].type == multitype::LAMMPS_INT64) {
             NCERRX( nc_def_var(ncid, keywords[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), keywords[i].c_str() );
           }
         }
@@ -624,11 +624,11 @@ void DumpNetCDF::write()
     int nfield = *th->get_nfield();
     for (int i = 0; i < nfield; i++) {
       if (filewriter) {
-        if (fields[i].type == multitype::DOUBLE) {
+        if (fields[i].type == multitype::LAMMPS_DOUBLE) {
           NCERRX( nc_put_var1_double(ncid, thermovar[i], start, &fields[i].data.d), keywords[i].c_str() );
-        } else if (fields[i].type == multitype::INT) {
+        } else if (fields[i].type == multitype::LAMMPS_INT) {
           NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &fields[i].data.i), keywords[i].c_str() );
-        } else if (fields[i].type == multitype::BIGINT) {
+        } else if (fields[i].type == multitype::LAMMPS_INT64) {
           NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &fields[i].data.b), keywords[i].c_str() );
         }
       }
diff --git a/src/NETCDF/dump_netcdf_mpiio.cpp b/src/NETCDF/dump_netcdf_mpiio.cpp
index f9382dacef..2407678386 100644
--- a/src/NETCDF/dump_netcdf_mpiio.cpp
+++ b/src/NETCDF/dump_netcdf_mpiio.cpp
@@ -432,11 +432,11 @@ void DumpNetCDFMPIIO::openfile()
       const int nfield = *th->get_nfield();
 
       for (int i = 0; i < nfield; i++) {
-        if (fields[i].type == multitype::DOUBLE) {
+        if (fields[i].type == multitype::LAMMPS_DOUBLE) {
           NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
-        } else if (fields[i].type == multitype::INT) {
+        } else if (fields[i].type == multitype::LAMMPS_INT) {
           NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), NC_INT, 1, dims, &thermovar[i]), keywords[i].c_str() );
-        } else if (fields[i].type == multitype::BIGINT) {
+        } else if (fields[i].type == multitype::LAMMPS_INT64) {
           NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), keywords[i].c_str() );
         }
       }
@@ -617,11 +617,11 @@ void DumpNetCDFMPIIO::write()
     int nfield = *th->get_nfield();
     for (int i = 0; i < nfield; i++) {
       if (filewriter) {
-        if (fields[i].type == multitype::DOUBLE) {
+        if (fields[i].type == multitype::LAMMPS_DOUBLE) {
           NCERRX( ncmpi_put_var1_double(ncid, thermovar[i], start, &fields[i].data.d), keywords[i].c_str() );
-        } else if (fields[i].type == multitype::INT) {
+        } else if (fields[i].type == multitype::LAMMPS_INT) {
           NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &fields[i].data.i), keywords[i].c_str() );
-        } else if (fields[i].type == multitype::BIGINT) {
+        } else if (fields[i].type == multitype::LAMMPS_INT64) {
           NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &fields[i].data.b), keywords[i].c_str() );
         }
       }
diff --git a/src/library.cpp b/src/library.cpp
index a94e385148..96af7cbf43 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -836,11 +836,11 @@ void *lammps_last_thermo(void *handle, const char *what, int index)
     } else if (strcmp(what, "data") == 0) {
       if ((index < 0) || (index >= nfield)) return nullptr;
       const auto &field = th->get_fields()[index];
-      if (field.type == multitype::INT) {
+      if (field.type == multitype::LAMMPS_INT) {
         val = (void *) &field.data.i;
-      } else if (field.type == multitype::BIGINT) {
+      } else if (field.type == multitype::LAMMPS_INT64) {
         val = (void *) &field.data.b;
-      } else if (field.type == multitype::DOUBLE) {
+      } else if (field.type == multitype::LAMMPS_DOUBLE) {
         val = (void *) &field.data.d;
       }
 
diff --git a/src/library.h b/src/library.h
index 5f46e36ccf..30a12ebdef 100644
--- a/src/library.h
+++ b/src/library.h
@@ -41,10 +41,11 @@
 /** Data type constants for extracting data from atoms, computes and fixes
  *
  * Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``,
- * ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and
+ * ``fortran/lammps.f90``, ``tools/swig/lammps.i``, ``src/lmptype.h``, and
  *``examples/COUPLE/plugin/liblammpsplugin.h`` */
 
 enum _LMP_DATATYPE_CONST {
+  LAMMPS_NONE = -1,     /*!< no data type assigned (yet) */
   LAMMPS_INT = 0,       /*!< 32-bit integer (array) */
   LAMMPS_INT_2D = 1,    /*!< two-dimensional 32-bit integer array */
   LAMMPS_DOUBLE = 2,    /*!< 64-bit double (array) */
diff --git a/src/lmptype.h b/src/lmptype.h
index e559bd9416..2089350f48 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -276,8 +276,21 @@ union ubuf {
 \endverbatim
   */
 struct multitype {
-  // same values as LAMMPS_INT, LAMMPS_DOUBLE, and LAMMPS_INT64 in library.h
-  enum { NONE = -1, INT = 0, DOUBLE = 2, BIGINT = 4 };
+  /** Data type constants for extracting data from atoms, computes and fixes
+   *
+   * This enum must be kept in sync with the corresponding enum or constants
+   * in ``python/lammps/constants.py``, ``fortran/lammps.f90``, ``tools/swig/lammps.i``,
+   * ``src/library.h``, and ``examples/COUPLE/plugin/liblammpsplugin.h`` */
+  enum _LMP_DATATYPE_CONST {
+    LAMMPS_NONE = -1,     /*!< no data type assigned (yet) */
+    LAMMPS_INT = 0,       /*!< 32-bit integer (array) */
+    LAMMPS_INT_2D = 1,    /*!< two-dimensional 32-bit integer array */
+    LAMMPS_DOUBLE = 2,    /*!< 64-bit double (array) */
+    LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
+    LAMMPS_INT64 = 4,     /*!< 64-bit integer (array) */
+    LAMMPS_INT64_2D = 5,  /*!< two-dimensional 64-bit integer array */
+    LAMMPS_STRING = 6     /*!< C-String */
+  };
 
   int type;
   union {
@@ -286,26 +299,26 @@ struct multitype {
     int64_t b;
   } data;
 
-  multitype() : type(NONE) { data.d = 0.0; }
+  multitype() : type(LAMMPS_NONE) { data.d = 0.0; }
   multitype(const multitype &) = default;
   multitype(multitype &&) = default;
   ~multitype() = default;
 
   multitype &operator=(const double &_d)
   {
-    type = DOUBLE;
+    type = LAMMPS_DOUBLE;
     data.d = _d;
     return *this;
   }
   multitype &operator=(const int &_i)
   {
-    type = INT;
+    type = LAMMPS_INT;
     data.i = _i;
     return *this;
   }
   multitype &operator=(const int64_t &_b)
   {
-    type = BIGINT;
+    type = LAMMPS_INT64;
     data.b = _b;
     return *this;
   }
diff --git a/tools/swig/lammps.i b/tools/swig/lammps.i
index c4ef0a7109..91a6866107 100644
--- a/tools/swig/lammps.i
+++ b/tools/swig/lammps.i
@@ -28,9 +28,10 @@
  *
  * Must be kept in sync with the equivalent constants in ``src/library.h``,
  * ``python/lammps/constants.py``, ``examples/COUPLE/plugin/liblammpsplugin.h``,
- * and ``fortran/lammps.f90`` */
+ * ``src/lmptype.h``, and ``fortran/lammps.f90`` */
 
 enum _LMP_DATATYPE_CONST {
+  LAMMPS_NONE      =-1,     /*!< no data type assigned (yet) */
   LAMMPS_INT       = 0,     /*!< 32-bit integer (array) */
   LAMMPS_INT_2D    = 1,     /*!< two-dimensional 32-bit integer array */
   LAMMPS_DOUBLE    = 2,     /*!< 64-bit double (array) */
diff --git a/unittest/utils/test_lmptype.cpp b/unittest/utils/test_lmptype.cpp
index e5dc871953..383c9d4b2c 100644
--- a/unittest/utils/test_lmptype.cpp
+++ b/unittest/utils/test_lmptype.cpp
@@ -54,18 +54,18 @@ TEST(Types, multitype)
     m[4] = -1023;
     m[5] = -2.225;
 
-    EXPECT_EQ(m[0].type, multitype::BIGINT);
-    EXPECT_EQ(m[1].type, multitype::INT);
-    EXPECT_EQ(m[2].type, multitype::DOUBLE);
+    EXPECT_EQ(m[0].type, multitype::LAMMPS_INT64);
+    EXPECT_EQ(m[1].type, multitype::LAMMPS_INT);
+    EXPECT_EQ(m[2].type, multitype::LAMMPS_DOUBLE);
 
 #if defined(LAMMPS_SMALLSMALL)
-    EXPECT_EQ(m[3].type, multitype::INT);
+    EXPECT_EQ(m[3].type, multitype::LAMMPS_INT);
 #else
-    EXPECT_EQ(m[3].type, multitype::BIGINT);
+    EXPECT_EQ(m[3].type, multitype::LAMMPS_INT64);
 #endif
-    EXPECT_EQ(m[4].type, multitype::INT);
-    EXPECT_EQ(m[5].type, multitype::DOUBLE);
-    EXPECT_EQ(m[6].type, multitype::NONE);
+    EXPECT_EQ(m[4].type, multitype::LAMMPS_INT);
+    EXPECT_EQ(m[5].type, multitype::LAMMPS_DOUBLE);
+    EXPECT_EQ(m[6].type, multitype::LAMMPS_NONE);
 
     EXPECT_EQ(m[0].data.b, b1);
     EXPECT_EQ(m[1].data.i, i1);

From 92e069b19deaf39ea79cadd36b5bce53c18e4988 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 10 Jun 2023 21:36:56 -0400
Subject: [PATCH 236/396] add fortran unit tests for lammps_last_thermo

---
 fortran/lammps.f90                           |   8 +-
 unittest/fortran/test_fortran_get_thermo.f90 | 108 +++++++++++++++++++
 unittest/fortran/wrap_get_thermo.cpp         |  41 +++++++
 3 files changed, 154 insertions(+), 3 deletions(-)

diff --git a/fortran/lammps.f90 b/fortran/lammps.f90
index 669e9c700d..ba3997ac8e 100644
--- a/fortran/lammps.f90
+++ b/fortran/lammps.f90
@@ -1127,11 +1127,13 @@ CONTAINS
   FUNCTION lmp_last_thermo(self,what,index) RESULT(thermo_data)
     CLASS(lammps), INTENT(IN), TARGET :: self
     CHARACTER(LEN=*), INTENT(IN) :: what
-    INTEGER(c_int) :: index
+    INTEGER :: index
+    INTEGER(c_int) :: idx
     TYPE(lammps_data) :: thermo_data, type_data
     INTEGER(c_int) :: datatype
     TYPE(c_ptr) :: Cname, Cptr
 
+    idx = index - 1
     ! set data type for known cases
     SELECT CASE (what)
     CASE ('step')
@@ -1148,7 +1150,7 @@ CONTAINS
         datatype = LAMMPS_STRING
     CASE ('data')
         Cname = f2c_string('type')
-        Cptr = lammps_last_thermo(self%handle,Cname,index-1)
+        Cptr = lammps_last_thermo(self%handle,Cname,idx)
         type_data%lammps_instance => self
         type_data%datatype = DATA_INT
         CALL C_F_POINTER(Cptr, type_data%i32)
@@ -1159,7 +1161,7 @@ CONTAINS
     END SELECT
 
     Cname = f2c_string(what)
-    Cptr = lammps_last_thermo(self%handle,Cname,index-1)
+    Cptr = lammps_last_thermo(self%handle,Cname,idx)
     CALL lammps_free(Cname)
 
     thermo_data%lammps_instance => self
diff --git a/unittest/fortran/test_fortran_get_thermo.f90 b/unittest/fortran/test_fortran_get_thermo.f90
index 7911ab07d5..965e6d58f7 100644
--- a/unittest/fortran/test_fortran_get_thermo.f90
+++ b/unittest/fortran/test_fortran_get_thermo.f90
@@ -152,3 +152,111 @@ FUNCTION f_lammps_get_thermo_zhi() BIND(C)
 
    f_lammps_get_thermo_zhi = lmp%get_thermo('zhi')
 END FUNCTION f_lammps_get_thermo_zhi
+
+SUBROUTINE f_lammps_last_thermo_setup() BIND(C)
+  USE liblammps
+  USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input
+  IMPLICIT NONE
+
+  CALL lmp%commands_list(big_input)
+  CALL lmp%commands_list(cont_input)
+  CALL lmp%commands_list(pair_input)
+  CALL lmp%command('thermo 10')
+  CALL lmp%command('run 15 post no')
+END SUBROUTINE f_lammps_last_thermo_setup
+
+FUNCTION f_lammps_last_thermo_step() BIND(C)
+  USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int, c_int64_t
+  USE liblammps
+  USE keepstuff, ONLY : lmp
+  IMPLICIT NONE
+  INTEGER(c_int) :: f_lammps_last_thermo_step
+  INTEGER :: size_bigint
+  INTEGER(c_int), POINTER :: ival
+  INTEGER(c_int64_t), POINTER :: bval
+
+  size_bigint = lmp%extract_setting('bigint')
+  IF (size_bigint == 4) THEN
+      ival = lmp%last_thermo('step',1)
+      f_lammps_last_thermo_step = INT(ival)
+  ELSE
+      bval = lmp%last_thermo('step',1)
+      f_lammps_last_thermo_step = INT(bval)
+  END IF
+END FUNCTION f_lammps_last_thermo_step
+
+FUNCTION f_lammps_last_thermo_num() BIND(C)
+  USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int
+  USE liblammps
+  USE keepstuff, ONLY : lmp
+  IMPLICIT NONE
+  INTEGER(c_int) :: f_lammps_last_thermo_num
+  INTEGER(c_int), POINTER :: ival
+
+  ival = lmp%last_thermo('num',1)
+  f_lammps_last_thermo_num = ival
+END FUNCTION f_lammps_last_thermo_num
+
+FUNCTION f_lammps_last_thermo_type(idx) BIND(C)
+  USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int
+  USE liblammps
+  USE keepstuff, ONLY : lmp
+  IMPLICIT NONE
+  INTEGER(c_int), VALUE :: idx
+  INTEGER(c_int) :: f_lammps_last_thermo_type
+  INTEGER(c_int), POINTER :: ival
+
+  ival = lmp%last_thermo('type',idx)
+  f_lammps_last_thermo_type = ival
+END FUNCTION f_lammps_last_thermo_type
+
+FUNCTION f_lammps_last_thermo_string(idx) BIND(C)
+  USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int, c_ptr, c_null_ptr
+  USE liblammps
+  USE keepstuff, ONLY : lmp, f2c_string
+  IMPLICIT NONE
+  INTEGER(c_int), VALUE :: idx
+  TYPE(c_ptr) :: f_lammps_last_thermo_string
+  CHARACTER(LEN=12) :: buffer
+
+  buffer = lmp%last_thermo('keyword',idx)
+  IF (LEN_TRIM(buffer) > 0) THEN
+      f_lammps_last_thermo_string = f2c_string(buffer)
+  ELSE
+      f_lammps_last_thermo_string = c_null_ptr
+  END IF
+END FUNCTION f_lammps_last_thermo_string
+
+FUNCTION f_lammps_last_thermo_int(idx) BIND(C)
+  USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int, c_int64_t
+  USE liblammps
+  USE keepstuff, ONLY : lmp
+  IMPLICIT NONE
+  INTEGER(c_int), VALUE :: idx
+  INTEGER(c_int), POINTER :: ival
+  INTEGER(c_int64_t), POINTER :: bval
+  INTEGER(c_int) :: f_lammps_last_thermo_int
+  INTEGER :: size_bigint
+
+  size_bigint = lmp%extract_setting('bigint')
+  IF (size_bigint == 4) THEN
+      ival = lmp%last_thermo('data',idx)
+      f_lammps_last_thermo_int = INT(ival)
+  ELSE
+      bval = lmp%last_thermo('data',idx)
+      f_lammps_last_thermo_int = INT(bval)
+  END IF
+END FUNCTION f_lammps_last_thermo_int
+
+FUNCTION f_lammps_last_thermo_double(idx) BIND(C)
+  USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int, c_double
+  USE liblammps
+  USE keepstuff, ONLY : lmp
+  IMPLICIT NONE
+  INTEGER(c_int), VALUE :: idx
+  REAL(c_double), POINTER :: dval
+  REAL(c_double) :: f_lammps_last_thermo_double
+
+  dval = lmp%last_thermo('data',idx)
+  f_lammps_last_thermo_double = dval
+END FUNCTION f_lammps_last_thermo_double
diff --git a/unittest/fortran/wrap_get_thermo.cpp b/unittest/fortran/wrap_get_thermo.cpp
index 71b51609eb..e18697ba9b 100644
--- a/unittest/fortran/wrap_get_thermo.cpp
+++ b/unittest/fortran/wrap_get_thermo.cpp
@@ -1,6 +1,7 @@
 // unit tests for getting thermodynamic output from a LAMMPS instance through the Fortran wrapper
 
 #include "lammps.h"
+#include "lmptype.h"
 #include <mpi.h>
 #include <string>
 
@@ -23,8 +24,18 @@ double f_lammps_get_thermo_ylo();
 double f_lammps_get_thermo_yhi();
 double f_lammps_get_thermo_zlo();
 double f_lammps_get_thermo_zhi();
+
+void f_lammps_last_thermo_setup();
+int f_lammps_last_thermo_step();
+int f_lammps_last_thermo_num();
+int f_lammps_last_thermo_type(int);
+const char *f_lammps_last_thermo_string(int);
+int f_lammps_last_thermo_int(int);
+double f_lammps_last_thermo_double(int);
 }
 
+using LAMMPS_NS::multitype;
+
 class LAMMPS_thermo : public ::testing::Test {
 protected:
     LAMMPS_NS::LAMMPS *lmp;
@@ -65,3 +76,33 @@ TEST_F(LAMMPS_thermo, get_thermo)
     EXPECT_DOUBLE_EQ(f_lammps_get_thermo_zlo(), 0.0);
     EXPECT_DOUBLE_EQ(f_lammps_get_thermo_zhi(), 4.0);
 };
+
+TEST_F(LAMMPS_thermo, last_thermo)
+{
+    EXPECT_EQ(f_lammps_last_thermo_step(), -1);
+    EXPECT_EQ(f_lammps_last_thermo_type(1), multitype::LAMMPS_NONE);
+    EXPECT_EQ(f_lammps_last_thermo_type(2), multitype::LAMMPS_NONE);
+    f_lammps_last_thermo_setup();
+    EXPECT_EQ(f_lammps_last_thermo_step(), 15);
+    EXPECT_EQ(f_lammps_last_thermo_num(), 6);
+    EXPECT_STREQ(f_lammps_last_thermo_string(1), "Step");
+    EXPECT_STREQ(f_lammps_last_thermo_string(2), "Temp");
+    EXPECT_STREQ(f_lammps_last_thermo_string(3), "E_pair");
+    EXPECT_STREQ(f_lammps_last_thermo_string(6), "Press");
+#if defined(LAMMPS_SMALLSMALL)
+    EXPECT_EQ(f_lammps_last_thermo_type(1), multitype::LAMMPS_INT);
+#else
+    EXPECT_EQ(f_lammps_last_thermo_type(1), multitype::LAMMPS_INT64);
+#endif
+    EXPECT_EQ(f_lammps_last_thermo_int(1), 15);
+    EXPECT_EQ(f_lammps_last_thermo_type(2), multitype::LAMMPS_DOUBLE);
+    EXPECT_EQ(f_lammps_last_thermo_type(3), multitype::LAMMPS_DOUBLE);
+    EXPECT_EQ(f_lammps_last_thermo_type(4), multitype::LAMMPS_DOUBLE);
+    EXPECT_EQ(f_lammps_last_thermo_type(5), multitype::LAMMPS_DOUBLE);
+    EXPECT_EQ(f_lammps_last_thermo_type(6), multitype::LAMMPS_DOUBLE);
+    EXPECT_DOUBLE_EQ(f_lammps_last_thermo_double(2), 0.0);
+    EXPECT_DOUBLE_EQ(f_lammps_last_thermo_double(3), -0.13713425198078993);
+    EXPECT_DOUBLE_EQ(f_lammps_last_thermo_double(4), 0.0);
+    EXPECT_DOUBLE_EQ(f_lammps_last_thermo_double(5), -0.13713425198078993);
+    EXPECT_DOUBLE_EQ(f_lammps_last_thermo_double(6), -0.022421073321023492);
+};

From 23552d4b7a93f4a8a5982880173a076c4c15eb61 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Sun, 11 Jun 2023 17:59:16 -0400
Subject: [PATCH 237/396] refactor to carry around extra per-reaction values

---
 src/REACTION/fix_bond_react.cpp | 79 ++++++++++++++++++---------------
 src/REACTION/fix_bond_react.h   |  2 +
 2 files changed, 44 insertions(+), 37 deletions(-)

diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp
index 784c163f70..4d2d4a0680 100644
--- a/src/REACTION/fix_bond_react.cpp
+++ b/src/REACTION/fix_bond_react.cpp
@@ -131,6 +131,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   global_freq = 1;
   extvector = 0;
   rxnID = 0;
+  cuff = 1;
   maxnconstraints = 0;
   narrhenius = 0;
   status = PROCEED;
@@ -388,7 +389,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
         if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
                                       "'rescale_charges' has too few arguments");
         if (strcmp(arg[iarg+1],"no") == 0) rescale_charges_flag[rxn] = 0; //default
-        else if (strcmp(arg[iarg+1],"yes") == 0) rescale_charges_flag[rxn] = 1;
+        else if (strcmp(arg[iarg+1],"yes") == 0) {
+          rescale_charges_flag[rxn] = 1;
+          cuff = 2; // index shift for extra values carried around by mega_gloves
+        }
         else error->one(FLERR,"Bond/react: Illegal option for 'rescale_charges' keyword");
         iarg += 2;
       } else if (strcmp(arg[iarg],"molecule") == 0) {
@@ -1282,9 +1286,9 @@ void FixBondReact::superimpose_algorithm()
   memory->create(restore_pt,MAXGUESS,4,"bond/react:restore_pt");
   memory->create(pioneers,max_natoms,"bond/react:pioneers");
   memory->create(restore,max_natoms,MAXGUESS*4,"bond/react:restore");
-  memory->create(my_mega_glove,max_natoms+1,allnattempt,"bond/react:local_mega_glove");
+  memory->create(my_mega_glove,max_natoms+cuff,allnattempt,"bond/react:my_mega_glove");
 
-  for (int i = 0; i < max_natoms+1; i++)
+  for (int i = 0; i < max_natoms+cuff; i++)
     for (int j = 0; j < allnattempt; j++)
       my_mega_glove[i][j] = 0;
 
@@ -1338,7 +1342,7 @@ void FixBondReact::superimpose_algorithm()
             status = ACCEPT;
             my_mega_glove[0][my_num_mega] = rxnID;
             for (int i = 0; i < onemol->natoms; i++) {
-              my_mega_glove[i+1][my_num_mega] = glove[i][1];
+              my_mega_glove[i+cuff][my_num_mega] = glove[i][1];
             }
             my_num_mega++;
           }
@@ -1386,7 +1390,7 @@ void FixBondReact::superimpose_algorithm()
           else {
             my_mega_glove[0][my_num_mega] = rxnID;
             for (int i = 0; i < onemol->natoms; i++) {
-              my_mega_glove[i+1][my_num_mega] = glove[i][1];
+              my_mega_glove[i+cuff][my_num_mega] = glove[i][1];
             }
             my_num_mega++;
           }
@@ -1405,10 +1409,10 @@ void FixBondReact::superimpose_algorithm()
 
   global_megasize = 0;
 
-  memory->create(local_mega_glove,max_natoms+1,my_num_mega,"bond/react:local_mega_glove");
-  memory->create(ghostly_mega_glove,max_natoms+1,my_num_mega,"bond/react:ghostly_mega_glove");
+  memory->create(local_mega_glove,max_natoms+cuff,my_num_mega,"bond/react:local_mega_glove");
+  memory->create(ghostly_mega_glove,max_natoms+cuff,my_num_mega,"bond/react:ghostly_mega_glove");
 
-  for (int i = 0; i < max_natoms+1; i++) {
+  for (int i = 0; i < max_natoms+cuff; i++) {
     for (int j = 0; j < my_num_mega; j++) {
       local_mega_glove[i][j] = 0;
       ghostly_mega_glove[i][j] = 0;
@@ -2674,17 +2678,17 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
   }
 
   tagint **dedup_glove;
-  memory->create(dedup_glove,max_natoms+1,dedup_size,"bond/react:dedup_glove");
+  memory->create(dedup_glove,max_natoms+cuff,dedup_size,"bond/react:dedup_glove");
 
   if (dedup_mode == LOCAL) {
     for (int i = 0; i < dedup_size; i++) {
-      for (int j = 0; j < max_natoms+1; j++) {
+      for (int j = 0; j < max_natoms+cuff; j++) {
         dedup_glove[j][i] = my_mega_glove[j][i];
       }
     }
   } else if (dedup_mode == GLOBAL) {
     for (int i = 0; i < dedup_size; i++) {
-      for (int j = 0; j < max_natoms+1; j++) {
+      for (int j = 0; j < max_natoms+cuff; j++) {
         dedup_glove[j][i] = global_mega_glove[j][i];
       }
     }
@@ -2700,16 +2704,16 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
   // let's randomly mix up our reaction instances first
   // then we can feel okay about ignoring ones we've already deleted (or accepted)
   // based off std::shuffle
-  int *temp_rxn = new int[max_natoms+1];
+  int *temp_rxn = new int[max_natoms+cuff];
   for (int i = dedup_size-1; i > 0; --i) { //dedup_size
     // choose random entry to swap current one with
     int k = floor(random[0]->uniform()*(i+1));
 
     // swap entries
-    for (int j = 0; j < max_natoms+1; j++)
+    for (int j = 0; j < max_natoms+cuff; j++)
       temp_rxn[j] = dedup_glove[j][i];
 
-    for (int j = 0; j < max_natoms+1; j++) {
+    for (int j = 0; j < max_natoms+cuff; j++) {
       dedup_glove[j][i] = dedup_glove[j][k];
       dedup_glove[j][k] = temp_rxn[j];
     }
@@ -2721,13 +2725,13 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
       int myrxnid1 = dedup_glove[0][i];
       onemol = atom->molecules[unreacted_mol[myrxnid1]];
       for (int j = 0; j < onemol->natoms; j++) {
-        int check1 = dedup_glove[j+1][i];
+        int check1 = dedup_glove[j+cuff][i];
         for (int ii = i + 1; ii < dedup_size; ii++) {
           if (dedup_mask[ii] == 0) {
             int myrxnid2 = dedup_glove[0][ii];
             twomol = atom->molecules[unreacted_mol[myrxnid2]];
             for (int jj = 0; jj < twomol->natoms; jj++) {
-              int check2 = dedup_glove[jj+1][ii];
+              int check2 = dedup_glove[jj+cuff][ii];
               if (check2 == check1) {
                 dedup_mask[ii] = 1;
                 break;
@@ -2745,7 +2749,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
     int my_new_megasize = 0;
     for (int i = 0; i < my_num_mega; i++) {
       if (dedup_mask[i] == 0) {
-        for (int j = 0; j < max_natoms+1; j++) {
+        for (int j = 0; j < max_natoms+cuff; j++) {
           my_mega_glove[j][my_new_megasize] = dedup_glove[j][i];
         }
         my_new_megasize++;
@@ -2761,7 +2765,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
     for (int i = 0; i < global_megasize; i++) {
       if (dedup_mask[i] == 0) {
         ghostly_rxn_count[dedup_glove[0][i]]++;
-        for (int j = 0; j < max_natoms + 1; j++) {
+        for (int j = 0; j < max_natoms + cuff; j++) {
           global_mega_glove[j][new_global_megasize] = dedup_glove[j][i];
         }
         new_global_megasize++;
@@ -2839,7 +2843,7 @@ void FixBondReact::glove_ghostcheck()
         ghostly = 1;
       } else {
         for (int j = 0; j < onemol->natoms; j++) {
-          int ilocal = atom->map(my_mega_glove[j+1][i]);
+          int ilocal = atom->map(my_mega_glove[j+cuff][i]);
           if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
             ghostly = 1;
             break;
@@ -2852,15 +2856,13 @@ void FixBondReact::glove_ghostcheck()
   #endif
 
     if (ghostly == 1) {
-      ghostly_mega_glove[0][ghostly_num_mega] = rxnID;
-      for (int j = 0; j < onemol->natoms+1; j++) {
+      for (int j = 0; j < onemol->natoms+cuff; j++) {
         ghostly_mega_glove[j][ghostly_num_mega] = my_mega_glove[j][i];
       }
       ghostly_num_mega++;
     } else {
-      local_mega_glove[0][local_num_mega] = rxnID;
       local_rxn_count[rxnID]++;
-      for (int j = 0; j < onemol->natoms+1; j++) {
+      for (int j = 0; j < onemol->natoms+cuff; j++) {
         local_mega_glove[j][local_num_mega] = my_mega_glove[j][i];
       }
       local_num_mega++;
@@ -2899,8 +2901,8 @@ void FixBondReact::ghost_glovecast()
   }
   MPI_Allgather(&start, 1, MPI_INT, allstarts, 1, MPI_INT, world);
   MPI_Datatype columnunsized, column;
-  int sizes[2]    = {max_natoms+1, global_megasize};
-  int subsizes[2] = {max_natoms+1, 1};
+  int sizes[2]    = {max_natoms+cuff, global_megasize};
+  int subsizes[2] = {max_natoms+cuff, 1};
   int starts[2]   = {0,0};
   MPI_Type_create_subarray (2, sizes, subsizes, starts, MPI_ORDER_C,
                             MPI_LMP_TAGINT, &columnunsized);
@@ -2908,14 +2910,14 @@ void FixBondReact::ghost_glovecast()
   MPI_Type_commit(&column);
 
   memory->destroy(global_mega_glove);
-  memory->create(global_mega_glove,max_natoms+1,global_megasize,"bond/react:global_mega_glove");
+  memory->create(global_mega_glove,max_natoms+cuff,global_megasize,"bond/react:global_mega_glove");
 
-  for (int i = 0; i < max_natoms+1; i++)
+  for (int i = 0; i < max_natoms+cuff; i++)
     for (int j = 0; j < global_megasize; j++)
       global_mega_glove[i][j] = 0;
 
   if (ghostly_num_mega > 0) {
-    for (int i = 0; i < max_natoms+1; i++) {
+    for (int i = 0; i < max_natoms+cuff; i++) {
       for (int j = 0; j < ghostly_num_mega; j++) {
         global_mega_glove[i][j+start] = ghostly_mega_glove[i][j];
       }
@@ -3006,6 +3008,7 @@ void FixBondReact::update_everything()
 
   int update_num_mega;
   tagint **update_mega_glove;
+  // for now, keeping rxnID in update_mega_glove, but not rest of cuff
   memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove");
 
   for (int pass = 0; pass < 2; pass++) {
@@ -3030,8 +3033,9 @@ void FixBondReact::update_everything()
           }
         }
 
-        for (int j = 0; j < max_natoms+1; j++)
-          update_mega_glove[j][update_num_mega] = local_mega_glove[j][i];
+        update_mega_glove[0][update_num_mega] = local_mega_glove[0][i];
+        for (int j = 0; j < max_natoms; j++)
+          update_mega_glove[j+1][update_num_mega] = local_mega_glove[j+cuff][i];
         update_num_mega++;
       }
     } else if (pass == 1) {
@@ -3054,8 +3058,9 @@ void FixBondReact::update_everything()
           }
         }
 
-        for (int j = 0; j < max_natoms+1; j++)
-          update_mega_glove[j][update_num_mega] = global_mega_glove[j][i];
+        update_mega_glove[0][update_num_mega] = global_mega_glove[0][i];
+        for (int j = 0; j < max_natoms; j++)
+          update_mega_glove[j+1][update_num_mega] = global_mega_glove[j+cuff][i];
         update_num_mega++;
       }
     }
@@ -3692,7 +3697,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
       n2superpose++;
   }
 
-  int ifit = atom->map(my_mega_glove[ibonding[rxnID]+1][iupdate]); // use this local ID to find fitting proc
+  int ifit = atom->map(my_mega_glove[ibonding[rxnID]+cuff][iupdate]); // use this local ID to find fitting proc
   Superpose3D<double, double **> superposer(n2superpose);
   int fitroot = 0;
   if (ifit >= 0 && ifit < atom->nlocal) {
@@ -3713,12 +3718,12 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
         if (!twomol->fragmentmask[modify_create_fragid[rxnID]][j]) continue;
       int ipre = equivalences[j][1][rxnID]-1; // equiv pre-reaction template index
       if (!create_atoms[j][rxnID] && !delete_atoms[ipre][rxnID]) {
-        if (atom->map(my_mega_glove[ipre+1][iupdate]) < 0) {
+        if (atom->map(my_mega_glove[ipre+cuff][iupdate]) < 0) {
           error->warning(FLERR," eligible atoms skipped for created-atoms fit on rank {}\n",
                          comm->me);
           continue;
         }
-        iatom = atom->map(my_mega_glove[ipre+1][iupdate]);
+        iatom = atom->map(my_mega_glove[ipre+cuff][iupdate]);
         if (iref == -1) iref = iatom;
         iatom = domain->closest_image(iref,iatom);
         for (int k = 0; k < 3; k++) {
@@ -3838,7 +3843,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
         atom->tag[n] = maxtag_all + add_count;
 
         // locally update mega_glove
-        my_mega_glove[preID][iupdate] = atom->tag[n];
+        my_mega_glove[preID+cuff-1][iupdate] = atom->tag[n];
 
         if (atom->molecule_flag) {
           if (twomol->moleculeflag) {
@@ -3866,7 +3871,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
       }
       // globally update mega_glove and equivalences
       MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world);
-      MPI_Bcast(&my_mega_glove[preID][iupdate],1,MPI_LMP_TAGINT,root,world);
+      MPI_Bcast(&my_mega_glove[preID+cuff-1][iupdate],1,MPI_LMP_TAGINT,root,world);
       equivalences[m][0][rxnID] = m+1;
       equivalences[m][1][rxnID] = preID;
       reverse_equiv[preID-1][0][rxnID] = preID;
diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h
index 66a5e4d6a0..5e7ffb733a 100644
--- a/src/REACTION/fix_bond_react.h
+++ b/src/REACTION/fix_bond_react.h
@@ -156,6 +156,8 @@ class FixBondReact : public Fix {
   int lcl_inst;              // reaction instance
   tagint **glove;            // 1st colmn: pre-reacted template, 2nd colmn: global IDs
   // for all mega_gloves: first row is the ID of bond/react
+  // 'cuff' leaves room for additional values carried around
+  int cuff;                       // default = 1, w/ rescale_charges_flag = 2
   tagint **my_mega_glove;         // local + ghostly reaction instances
   tagint **local_mega_glove;      // consolidation of local reaction instances
   tagint **ghostly_mega_glove;    // consolidation of nonlocal reaction instances

From c214f654b6c5206fa40e7fcd96cf623c31ebfb00 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Sun, 11 Jun 2023 19:27:58 -0400
Subject: [PATCH 238/396] update communicated rxn instances to doubles

---
 src/REACTION/fix_bond_react.cpp | 60 ++++++++++++++++++---------------
 src/REACTION/fix_bond_react.h   |  8 ++---
 2 files changed, 36 insertions(+), 32 deletions(-)

diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp
index 4d2d4a0680..5a2f274d91 100644
--- a/src/REACTION/fix_bond_react.cpp
+++ b/src/REACTION/fix_bond_react.cpp
@@ -1340,9 +1340,9 @@ void FixBondReact::superimpose_algorithm()
             status = REJECT;
           } else {
             status = ACCEPT;
-            my_mega_glove[0][my_num_mega] = rxnID;
+            my_mega_glove[0][my_num_mega] = (double) rxnID;
             for (int i = 0; i < onemol->natoms; i++) {
-              my_mega_glove[i+cuff][my_num_mega] = glove[i][1];
+              my_mega_glove[i+cuff][my_num_mega] = (double) glove[i][1];
             }
             my_num_mega++;
           }
@@ -1388,9 +1388,9 @@ void FixBondReact::superimpose_algorithm()
           if (fraction[rxnID] < 1.0 &&
               random[rxnID]->uniform() >= fraction[rxnID]) status = REJECT;
           else {
-            my_mega_glove[0][my_num_mega] = rxnID;
+            my_mega_glove[0][my_num_mega] = (double) rxnID;
             for (int i = 0; i < onemol->natoms; i++) {
-              my_mega_glove[i+cuff][my_num_mega] = glove[i][1];
+              my_mega_glove[i+cuff][my_num_mega] = (double) glove[i][1];
             }
             my_num_mega++;
           }
@@ -2677,7 +2677,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
     dedup_size = global_megasize;
   }
 
-  tagint **dedup_glove;
+  double **dedup_glove;
   memory->create(dedup_glove,max_natoms+cuff,dedup_size,"bond/react:dedup_glove");
 
   if (dedup_mode == LOCAL) {
@@ -2704,7 +2704,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
   // let's randomly mix up our reaction instances first
   // then we can feel okay about ignoring ones we've already deleted (or accepted)
   // based off std::shuffle
-  int *temp_rxn = new int[max_natoms+cuff];
+  double *temp_rxn = new double[max_natoms+cuff];
   for (int i = dedup_size-1; i > 0; --i) { //dedup_size
     // choose random entry to swap current one with
     int k = floor(random[0]->uniform()*(i+1));
@@ -2764,7 +2764,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
     int new_global_megasize = 0;
     for (int i = 0; i < global_megasize; i++) {
       if (dedup_mask[i] == 0) {
-        ghostly_rxn_count[dedup_glove[0][i]]++;
+        ghostly_rxn_count[(int) dedup_glove[0][i]]++;
         for (int j = 0; j < max_natoms + cuff; j++) {
           global_mega_glove[j][new_global_megasize] = dedup_glove[j][i];
         }
@@ -2834,7 +2834,7 @@ void FixBondReact::glove_ghostcheck()
     local_rxn_count[i] = 0;
 
   for (int i = 0; i < my_num_mega; i++) {
-    rxnID = my_mega_glove[0][i];
+    rxnID = (int) my_mega_glove[0][i];
     onemol = atom->molecules[unreacted_mol[rxnID]];
     int ghostly = 0;
   #if !defined(MPI_STUBS)
@@ -2843,7 +2843,7 @@ void FixBondReact::glove_ghostcheck()
         ghostly = 1;
       } else {
         for (int j = 0; j < onemol->natoms; j++) {
-          int ilocal = atom->map(my_mega_glove[j+cuff][i]);
+          int ilocal = atom->map((tagint) my_mega_glove[j+cuff][i]);
           if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
             ghostly = 1;
             break;
@@ -2905,8 +2905,8 @@ void FixBondReact::ghost_glovecast()
   int subsizes[2] = {max_natoms+cuff, 1};
   int starts[2]   = {0,0};
   MPI_Type_create_subarray (2, sizes, subsizes, starts, MPI_ORDER_C,
-                            MPI_LMP_TAGINT, &columnunsized);
-  MPI_Type_create_resized (columnunsized, 0, sizeof(tagint), &column);
+                            MPI_DOUBLE, &columnunsized);
+  MPI_Type_create_resized (columnunsized, 0, sizeof(double), &column);
   MPI_Type_commit(&column);
 
   memory->destroy(global_mega_glove);
@@ -3017,15 +3017,20 @@ void FixBondReact::update_everything()
     for (int i = 0; i < nreacts; i++) iskip[i] = 0;
     if (pass == 0) {
       for (int i = 0; i < local_num_mega; i++) {
-        rxnID = local_mega_glove[0][i];
+        rxnID = (int) local_mega_glove[0][i];
         // reactions already shuffled from dedup procedure, so can skip first N
         if (iskip[rxnID]++ < nlocalskips[rxnID]) continue;
 
+        // this will be overwritten if reaction skipped by create_atoms below
+        update_mega_glove[0][update_num_mega] = (tagint) local_mega_glove[0][i];
+        for (int j = 0; j < max_natoms; j++)
+          update_mega_glove[j+1][update_num_mega] = (tagint) local_mega_glove[j+cuff][i];
+
         // atoms inserted here for serial MPI_STUBS build only
         if (create_atoms_flag[rxnID] == 1) {
           onemol = atom->molecules[unreacted_mol[rxnID]];
           twomol = atom->molecules[reacted_mol[rxnID]];
-          if (insert_atoms(local_mega_glove,i)) {
+          if (insert_atoms(update_mega_glove,update_num_mega)) {
             inserted_atoms_flag = 1;
           } else { // create aborted
             reaction_count_total[rxnID]--;
@@ -3033,24 +3038,26 @@ void FixBondReact::update_everything()
           }
         }
 
-        update_mega_glove[0][update_num_mega] = local_mega_glove[0][i];
-        for (int j = 0; j < max_natoms; j++)
-          update_mega_glove[j+1][update_num_mega] = local_mega_glove[j+cuff][i];
         update_num_mega++;
       }
     } else if (pass == 1) {
       for (int i = 0; i < global_megasize; i++) {
-        rxnID = global_mega_glove[0][i];
+        rxnID = (int) global_mega_glove[0][i];
         // reactions already shuffled from dedup procedure, so can skip first N
         if (iskip[rxnID]++ < nghostlyskips[rxnID]) continue;
 
+        // this will be overwritten if reaction skipped by create_atoms below
+        update_mega_glove[0][update_num_mega] = (tagint) global_mega_glove[0][i];
+        for (int j = 0; j < max_natoms; j++)
+          update_mega_glove[j+1][update_num_mega] = (tagint) global_mega_glove[j+cuff][i];
+
         // we can insert atoms here, now that reactions are finalized
         // can't do it any earlier, due to skipped reactions (max_rxn)
         // for MPI build, reactions that create atoms are always treated as 'global'
         if (create_atoms_flag[rxnID] == 1) {
           onemol = atom->molecules[unreacted_mol[rxnID]];
           twomol = atom->molecules[reacted_mol[rxnID]];
-          if (insert_atoms(global_mega_glove,i)) {
+          if (insert_atoms(update_mega_glove,update_num_mega)) {
             inserted_atoms_flag = 1;
           } else { // create aborted
             reaction_count_total[rxnID]--;
@@ -3058,9 +3065,6 @@ void FixBondReact::update_everything()
           }
         }
 
-        update_mega_glove[0][update_num_mega] = global_mega_glove[0][i];
-        for (int j = 0; j < max_natoms; j++)
-          update_mega_glove[j+1][update_num_mega] = global_mega_glove[j+cuff][i];
         update_num_mega++;
       }
     }
@@ -3648,7 +3652,7 @@ void FixBondReact::update_everything()
 insert created atoms
 ------------------------------------------------------------------------- */
 
-int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
+int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
 {
   // inserting atoms based off fix_deposit->pre_exchange
   int flag;
@@ -3697,14 +3701,14 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
       n2superpose++;
   }
 
-  int ifit = atom->map(my_mega_glove[ibonding[rxnID]+cuff][iupdate]); // use this local ID to find fitting proc
+  int ifit = atom->map(my_update_mega_glove[ibonding[rxnID]+1][iupdate]); // use this local ID to find fitting proc
   Superpose3D<double, double **> superposer(n2superpose);
   int fitroot = 0;
   if (ifit >= 0 && ifit < atom->nlocal) {
     fitroot = comm->me;
 
     // get 'temperatere' averaged over site, used for created atoms' vels
-    t = get_temperature(my_mega_glove,1,iupdate);
+    t = get_temperature(my_update_mega_glove,1,iupdate);
 
     double **xfrozen; // coordinates for the "frozen" target molecule
     double **xmobile; // coordinates for the "mobile" molecule
@@ -3718,12 +3722,12 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
         if (!twomol->fragmentmask[modify_create_fragid[rxnID]][j]) continue;
       int ipre = equivalences[j][1][rxnID]-1; // equiv pre-reaction template index
       if (!create_atoms[j][rxnID] && !delete_atoms[ipre][rxnID]) {
-        if (atom->map(my_mega_glove[ipre+cuff][iupdate]) < 0) {
+        if (atom->map(my_update_mega_glove[ipre+1][iupdate]) < 0) {
           error->warning(FLERR," eligible atoms skipped for created-atoms fit on rank {}\n",
                          comm->me);
           continue;
         }
-        iatom = atom->map(my_mega_glove[ipre+cuff][iupdate]);
+        iatom = atom->map(my_update_mega_glove[ipre+1][iupdate]);
         if (iref == -1) iref = iatom;
         iatom = domain->closest_image(iref,iatom);
         for (int k = 0; k < 3; k++) {
@@ -3843,7 +3847,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
         atom->tag[n] = maxtag_all + add_count;
 
         // locally update mega_glove
-        my_mega_glove[preID+cuff-1][iupdate] = atom->tag[n];
+        my_update_mega_glove[preID][iupdate] = atom->tag[n];
 
         if (atom->molecule_flag) {
           if (twomol->moleculeflag) {
@@ -3871,7 +3875,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
       }
       // globally update mega_glove and equivalences
       MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world);
-      MPI_Bcast(&my_mega_glove[preID+cuff-1][iupdate],1,MPI_LMP_TAGINT,root,world);
+      MPI_Bcast(&my_update_mega_glove[preID][iupdate],1,MPI_LMP_TAGINT,root,world);
       equivalences[m][0][rxnID] = m+1;
       equivalences[m][1][rxnID] = preID;
       reverse_equiv[preID-1][0][rxnID] = preID;
diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h
index 5e7ffb733a..a028e4b5dc 100644
--- a/src/REACTION/fix_bond_react.h
+++ b/src/REACTION/fix_bond_react.h
@@ -158,10 +158,10 @@ class FixBondReact : public Fix {
   // for all mega_gloves: first row is the ID of bond/react
   // 'cuff' leaves room for additional values carried around
   int cuff;                       // default = 1, w/ rescale_charges_flag = 2
-  tagint **my_mega_glove;         // local + ghostly reaction instances
-  tagint **local_mega_glove;      // consolidation of local reaction instances
-  tagint **ghostly_mega_glove;    // consolidation of nonlocal reaction instances
-  tagint **global_mega_glove;     // consolidation (inter-processor) of gloves
+  double **my_mega_glove;         // local + ghostly reaction instances
+  double **local_mega_glove;      // consolidation of local reaction instances
+  double **ghostly_mega_glove;    // consolidation of nonlocal reaction instances
+  double **global_mega_glove;     // consolidation (inter-processor) of gloves
                                   // containing nonlocal atoms
 
   int *localsendlist;      // indicates ghosts of other procs

From 68a73f1c339188beb831d62f9bd20712ea37e29b Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@outlook.com>
Date: Sun, 11 Jun 2023 17:46:58 -0600
Subject: [PATCH 239/396] library: return atom and force styles via
 extract_global

---
 src/library.cpp | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/src/library.cpp b/src/library.cpp
index a94e385148..4022a6ba7b 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -1340,6 +1340,13 @@ int lammps_extract_global_datatype(void * /*handle*/, const char *name)
   if (strcmp(name,"q_flag") == 0) return LAMMPS_INT;
 
   if (strcmp(name,"units") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"atom_style") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"pair_style") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"bond_style") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"angle_style") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"dihedral_style") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"improper_style") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"kspace_style") == 0) return LAMMPS_STRING;
   if (strcmp(name,"boltz") == 0) return LAMMPS_DOUBLE;
   if (strcmp(name,"hplanck") == 0) return LAMMPS_DOUBLE;
   if (strcmp(name,"mvv2e") == 0) return LAMMPS_DOUBLE;
@@ -1586,6 +1593,34 @@ report the "native" data type.  The following tables are provided:
      - int
      - 1
      - **deprecated**. Use :cpp:func:`lammps_extract_setting` instead.
+   * - atom_style
+     - char \*
+     - 1
+     - string with the current atom style.
+   * - pair_style
+     - char \*
+     - 1
+     - string with the current pair style.
+   * - bond_style
+     - char \*
+     - 1
+     - string with the current bond style.
+   * - angle_style
+     - char \*
+     - 1
+     - string with the current angle style.
+   * - dihedral_style
+     - char \*
+     - 1
+     - string with the current dihedral style.
+   * - improper_style
+     - char \*
+     - 1
+     - string with the current improper style.
+   * - kspace_style
+     - char \*
+     - 1
+     - string with the current KSpace style.
 
 .. _extract_unit_settings:
 
@@ -1692,6 +1727,13 @@ void *lammps_extract_global(void *handle, const char *name)
   auto lmp = (LAMMPS *) handle;
 
   if (strcmp(name,"units") == 0) return (void *) lmp->update->unit_style;
+  if (strcmp(name,"atom_style") == 0) return (void *) lmp->atom->atom_style;
+  if (strcmp(name,"pair_style") == 0) return (void *) lmp->force->pair_style;
+  if (strcmp(name,"bond_style") == 0) return (void *) lmp->force->bond_style;
+  if (strcmp(name,"angle_style") == 0) return (void *) lmp->force->angle_style;
+  if (strcmp(name,"dihedral_style") == 0) return (void *) lmp->force->dihedral_style;
+  if (strcmp(name,"improper_style") == 0) return (void *) lmp->force->improper_style;
+  if (strcmp(name,"kspace_style") == 0) return (void *) lmp->force->kspace_style;
   if (strcmp(name,"dt") == 0) return (void *) &lmp->update->dt;
   if (strcmp(name,"ntimestep") == 0) return (void *) &lmp->update->ntimestep;
   // update->atime can be referenced as a pointer

From 82cea7a546aadd72079a74b87e8807f21df06731 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 12 Jun 2023 15:31:03 -0400
Subject: [PATCH 240/396] small doc updates for added pppm_table keyword

---
 doc/src/package.rst | 81 +++++++++++++++++++++++----------------------
 1 file changed, 42 insertions(+), 39 deletions(-)

diff --git a/doc/src/package.rst b/doc/src/package.rst
index ce45a1eb79..1988e78245 100644
--- a/doc/src/package.rst
+++ b/doc/src/package.rst
@@ -49,7 +49,7 @@ Syntax
        *intel* args = NPhi keyword value ...
          Nphi = # of co-processors per node
          zero or more keyword/value pairs may be appended
-         keywords = *mode* or *omp* or *lrt* or *balance* or *ghost* or *tpc* or *tptask* or *no_affinity*
+         keywords = *mode* or *omp* or *lrt* or *balance* or *ghost* or *tpc* or *tptask* or *pppm_table* or *no_affinity*
            *mode* value = *single* or *mixed* or *double*
              single = perform force calculations in single precision
              mixed = perform force calculations in mixed precision
@@ -395,13 +395,13 @@ is identical to the default *verlet* style aside from supporting the
 LRT feature. This feature requires setting the pre-processor flag
 -DLMP_INTEL_USELRT in the makefile when compiling LAMMPS.
 
-The *balance* keyword sets the fraction of :doc:`pair style <pair_style>` work offloaded to the co-processor for split
-values between 0.0 and 1.0 inclusive.  While this fraction of work is
-running on the co-processor, other calculations will run on the host,
-including neighbor and pair calculations that are not offloaded, as
-well as angle, bond, dihedral, kspace, and some MPI communications.
-If *split* is set to -1, the fraction of work is dynamically adjusted
-automatically throughout the run.  This typically give performance
+The *balance* keyword sets the fraction of :doc:`pair style <pair_style>` work
+offloaded to the co-processor for split values between 0.0 and 1.0 inclusive.
+While this fraction of work is running on the co-processor, other calculations
+will run on the host, including neighbor and pair calculations that are not
+offloaded, as well as angle, bond, dihedral, kspace, and some MPI
+communications.  If *split* is set to -1, the fraction of work is dynamically
+adjusted automatically throughout the run.  This typically give performance
 within 5 to 10 percent of the optimal fixed fraction.
 
 The *ghost* keyword determines whether or not ghost atoms, i.e. atoms
@@ -433,6 +433,11 @@ with 16 threads, for a total of 128.
 Note that the default settings for *tpc* and *tptask* are fine for
 most problems, regardless of how many MPI tasks you assign to a Phi.
 
+The *pppm_table* keyword with the argument yes allows to use a
+pre-computed table to efficiently spread the charge to the PPPM grid.
+This feature is enabled by default but can be turned off using the
+keyword with the argument *no*.
+
 The *no_affinity* keyword will turn off automatic setting of core
 affinity for MPI tasks and OpenMP threads on the host when using
 offload to a co-processor. Affinity settings are used when possible
@@ -702,39 +707,37 @@ Related commands
 Default
 """""""
 
-For the GPU package, the default is Ngpu = 0 and the option defaults
-are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
-to Ngpu-1, tpa = 1, omp = 0, and platform=-1.  These settings are made
-automatically if the "-sf gpu" :doc:`command-line switch <Run_options>`
-is used.  If it is not used, you must invoke the package gpu command
-in your input script or via the "-pk gpu" :doc:`command-line switch <Run_options>`.
+For the GPU package, the default is Ngpu = 0 and the option defaults are neigh
+= yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0 to Ngpu-1, tpa = 1,
+omp = 0, and platform=-1.  These settings are made automatically if the "-sf
+gpu" :doc:`command-line switch <Run_options>` is used.  If it is not used, you
+must invoke the package gpu command in your input script or via the "-pk gpu"
+:doc:`command-line switch <Run_options>`.
 
-For the INTEL package, the default is Nphi = 1 and the option
-defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4,
-tptask = 240, pppm_table = yes.  The default ghost option is determined
-by the pair style being used.  This value is output to the screen in
-the offload report at the end of each run.  Note that all of these
-settings, except "omp" and "mode", are ignored if LAMMPS was not built
-with Xeon Phi co-processor support.  These settings are made
-automatically if the "-sf intel" :doc:`command-line switch <Run_options>`
-is used.  If it is not used, you must invoke the package intel command
-in your input script or via the "-pk intel" :doc:`command-line switch <Run_options>`.
+For the INTEL package, the default is Nphi = 1 and the option defaults are omp
+= 0, mode = mixed, lrt = no, balance = -1, tpc = 4, tptask = 240, pppm_table =
+yes.  The default ghost option is determined by the pair style being used.
+This value is output to the screen in the offload report at the end of each
+run.  Note that all of these settings, except "omp" and "mode", are ignored if
+LAMMPS was not built with Xeon Phi co-processor support.  These settings are
+made automatically if the "-sf intel" :doc:`command-line switch <Run_options>`
+is used.  If it is not used, you must invoke the package intel command in your
+input script or via the "-pk intel" :doc:`command-line switch <Run_options>`.
 
 For the KOKKOS package, the option defaults for GPUs are neigh = full,
-neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default
-value, comm = device, sort = device, neigh/transpose = off, gpu/aware =
-on. When LAMMPS can safely detect that GPU-aware MPI is not available,
-the default value of gpu/aware becomes "off". For CPUs or Xeon Phis, the
-option defaults are neigh = half, neigh/qeq = half, newton = on, binsize
-= 0.0, comm = no, and sort = no.  The option neigh/thread = on when
-there are 16K atoms or less on an MPI rank, otherwise it is "off". These
-settings are made automatically by the required "-k on"
-:doc:`command-line switch <Run_options>`. You can change them by using
-the package kokkos command in your input script or via the :doc:`-pk
+neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default value,
+comm = device, sort = device, neigh/transpose = off, gpu/aware = on. When
+LAMMPS can safely detect that GPU-aware MPI is not available, the default value
+of gpu/aware becomes "off". For CPUs or Xeon Phis, the option defaults are
+neigh = half, neigh/qeq = half, newton = on, binsize = 0.0, comm = no, and sort
+= no.  The option neigh/thread = on when there are 16K atoms or less on an MPI
+rank, otherwise it is "off". These settings are made automatically by the
+required "-k on" :doc:`command-line switch <Run_options>`. You can change them
+by using the package kokkos command in your input script or via the :doc:`-pk
 kokkos command-line switch <Run_options>`.
 
-For the OMP package, the default is Nthreads = 0 and the option
-defaults are neigh = yes.  These settings are made automatically if
-the "-sf omp" :doc:`command-line switch <Run_options>` is used.  If it
-is not used, you must invoke the package omp command in your input
-script or via the "-pk omp" :doc:`command-line switch <Run_options>`.
+For the OMP package, the default is Nthreads = 0 and the option defaults are
+neigh = yes.  These settings are made automatically if the "-sf omp"
+:doc:`command-line switch <Run_options>` is used.  If it is not used, you must
+invoke the package omp command in your input script or via the "-pk omp"
+:doc:`command-line switch <Run_options>`.

From 2ba83a4d8f3ef0451b9de2bcd2a1360b1b21a76a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 12 Jun 2023 15:31:37 -0400
Subject: [PATCH 241/396] add versionadded keyword

---
 doc/src/package.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/src/package.rst b/doc/src/package.rst
index 1988e78245..b0549ba7d9 100644
--- a/doc/src/package.rst
+++ b/doc/src/package.rst
@@ -433,6 +433,8 @@ with 16 threads, for a total of 128.
 Note that the default settings for *tpc* and *tptask* are fine for
 most problems, regardless of how many MPI tasks you assign to a Phi.
 
+.. versionadded:: TBD
+
 The *pppm_table* keyword with the argument yes allows to use a
 pre-computed table to efficiently spread the charge to the PPPM grid.
 This feature is enabled by default but can be turned off using the

From 603e397919bc9bd5d7898436411229896a9faf8c Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Mon, 12 Jun 2023 20:20:45 -0400
Subject: [PATCH 242/396] get_totalcharge routine

---
 src/REACTION/fix_bond_react.cpp | 49 +++++++++++++++++++++++++++------
 src/REACTION/fix_bond_react.h   |  2 ++
 2 files changed, 42 insertions(+), 9 deletions(-)

diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp
index 5a2f274d91..8e4202cad0 100644
--- a/src/REACTION/fix_bond_react.cpp
+++ b/src/REACTION/fix_bond_react.cpp
@@ -251,8 +251,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   memory->create(ghostly_rxn_count,nreacts,"bond/react:ghostly_rxn_count");
   memory->create(reaction_count_total,nreacts,"bond/react:reaction_count_total");
 
+  rescale_charges_anyflag = 0;
   for (int i = 0; i < nreacts; i++) {
-    fraction[i] = 1;
+    fraction[i] = 1.0;
     seed[i] = 12345;
     max_rxn[i] = INT_MAX;
     for (int j = 0; j < 3; j++)
@@ -262,7 +263,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
     rescale_charges_flag[i] = 0;
     create_atoms_flag[i] = 0;
     modify_create_fragid[i] = -1;
-    overlapsq[i] = 0;
+    overlapsq[i] = 0.0;
     molecule_keyword[i] = OFF;
     nconstraints[i] = 0;
     // set default limit duration to 60 timesteps
@@ -390,7 +391,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
                                       "'rescale_charges' has too few arguments");
         if (strcmp(arg[iarg+1],"no") == 0) rescale_charges_flag[rxn] = 0; //default
         else if (strcmp(arg[iarg+1],"yes") == 0) {
+          if (!atom->q_flag) error->all(FLERR,"Illegal fix bond/react command: "
+                                      "cannot use 'rescale_charges' without atomic charges enabled");
           rescale_charges_flag[rxn] = 1;
+          rescale_charges_anyflag = 1;
           cuff = 2; // index shift for extra values carried around by mega_gloves
         }
         else error->one(FLERR,"Bond/react: Illegal option for 'rescale_charges' keyword");
@@ -1290,7 +1294,7 @@ void FixBondReact::superimpose_algorithm()
 
   for (int i = 0; i < max_natoms+cuff; i++)
     for (int j = 0; j < allnattempt; j++)
-      my_mega_glove[i][j] = 0;
+      my_mega_glove[i][j] = 0.0;
 
   attempted_rxn = 1;
 
@@ -1341,6 +1345,7 @@ void FixBondReact::superimpose_algorithm()
           } else {
             status = ACCEPT;
             my_mega_glove[0][my_num_mega] = (double) rxnID;
+            if (rescale_charges_flag[rxnID]) my_mega_glove[1][my_num_mega] = get_totalcharge();
             for (int i = 0; i < onemol->natoms; i++) {
               my_mega_glove[i+cuff][my_num_mega] = (double) glove[i][1];
             }
@@ -1389,6 +1394,7 @@ void FixBondReact::superimpose_algorithm()
               random[rxnID]->uniform() >= fraction[rxnID]) status = REJECT;
           else {
             my_mega_glove[0][my_num_mega] = (double) rxnID;
+            if (rescale_charges_flag[rxnID]) my_mega_glove[1][my_num_mega] = get_totalcharge();
             for (int i = 0; i < onemol->natoms; i++) {
               my_mega_glove[i+cuff][my_num_mega] = (double) glove[i][1];
             }
@@ -1414,8 +1420,8 @@ void FixBondReact::superimpose_algorithm()
 
   for (int i = 0; i < max_natoms+cuff; i++) {
     for (int j = 0; j < my_num_mega; j++) {
-      local_mega_glove[i][j] = 0;
-      ghostly_mega_glove[i][j] = 0;
+      local_mega_glove[i][j] = 0.0;
+      ghostly_mega_glove[i][j] = 0.0;
     }
   }
 
@@ -2190,6 +2196,24 @@ double FixBondReact::get_temperature(tagint **myglove, int row_offset, int col)
   return t;
 }
 
+/* ----------------------------------------------------------------------
+compute sum of partial charges in rxn site, for updated atoms
+note: currently uses global rxnID and onemol variables
+------------------------------------------------------------------------- */
+
+double FixBondReact::get_totalcharge()
+{
+  int j,jj,ilocal;
+  double *q = atom->q;
+  double sim_total_charge = 0.0;
+  for (j = 0; j < onemol->natoms; j++) {
+    jj = equivalences[j][1][rxnID]-1;
+    if (custom_charges[jj][rxnID] == 1)
+      sim_total_charge += q[atom->map(glove[jj][1])];
+  }
+  return sim_total_charge;
+}
+
 /* ----------------------------------------------------------------------
 get per-atom variable names used by custom constraint
 ------------------------------------------------------------------------- */
@@ -3008,8 +3032,12 @@ void FixBondReact::update_everything()
 
   int update_num_mega;
   tagint **update_mega_glove;
-  // for now, keeping rxnID in update_mega_glove, but not rest of cuff
-  memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove");
+  // for now, keeping rxnID in update_mega_glove, but not rest of cuff in update_mega_glove
+  int maxmega = MAX(local_num_mega,global_megasize);
+  memory->create(update_mega_glove,max_natoms+1,maxmega,"bond/react:update_mega_glove");
+
+  double *sim_total_charges;
+  if (rescale_charges_anyflag) memory->create(sim_total_charges,maxmega,"bond/react:sim_total_charges");
 
   for (int pass = 0; pass < 2; pass++) {
     update_num_mega = 0;
@@ -3038,6 +3066,7 @@ void FixBondReact::update_everything()
           }
         }
 
+        if (rescale_charges_flag[rxnID]) sim_total_charges[update_num_mega] = local_mega_glove[1][i];
         update_num_mega++;
       }
     } else if (pass == 1) {
@@ -3065,6 +3094,7 @@ void FixBondReact::update_everything()
           }
         }
 
+        if (rescale_charges_flag[rxnID]) sim_total_charges[update_num_mega] = global_mega_glove[1][i];
         update_num_mega++;
       }
     }
@@ -3112,8 +3142,6 @@ void FixBondReact::update_everything()
           int jj = equivalences[j][1][rxnID]-1;
           if (atom->map(update_mega_glove[jj+1][i]) >= 0 &&
               atom->map(update_mega_glove[jj+1][i]) < nlocal) {
-            if (landlocked_atoms[j][rxnID] == 1)
-              type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j];
             if (twomol->qflag && atom->q_flag && custom_charges[jj][rxnID] == 1) {
               double *q = atom->q;
               sim_total_charge += q[atom->map(update_mega_glove[jj+1][i])];
@@ -3122,6 +3150,7 @@ void FixBondReact::update_everything()
             }
           }
         }
+        printf("check1 %g %g\n",sim_total_charge,sim_total_charges[i]);
       }
       charge_rescale_addend = (sim_total_charge-mol_total_charge)/n_custom_charge;
     }
@@ -3564,6 +3593,7 @@ void FixBondReact::update_everything()
   }
 
   memory->destroy(update_mega_glove);
+  if (rescale_charges_anyflag) memory->destroy(sim_total_charges);
 
   // delete atoms. taken from fix_evaporate. but don't think it needs to be in pre_exchange
   // loop in reverse order to avoid copying marked atoms
@@ -3708,6 +3738,7 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
     fitroot = comm->me;
 
     // get 'temperatere' averaged over site, used for created atoms' vels
+    // note: row_offset for my_update_mega_glove is unity, not 'cuff'
     t = get_temperature(my_update_mega_glove,1,iupdate);
 
     double **xfrozen; // coordinates for the "frozen" target molecule
diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h
index a028e4b5dc..d8c6c45494 100644
--- a/src/REACTION/fix_bond_react.h
+++ b/src/REACTION/fix_bond_react.h
@@ -72,6 +72,7 @@ class FixBondReact : public Fix {
   int *stabilize_steps_flag;
   int *custom_charges_fragid;
   int *rescale_charges_flag;
+  int rescale_charges_anyflag;
   int *create_atoms_flag;
   int *modify_create_fragid;
   double *overlapsq;
@@ -193,6 +194,7 @@ class FixBondReact : public Fix {
   int check_constraints();
   void get_IDcoords(int, int, double *);
   double get_temperature(tagint **, int, int);
+  double get_totalcharge();
   void customvarnames();    // get per-atom variables names used by custom constraint
   void get_customvars();    // evaluate local values for variables names used by custom constraint
   double custom_constraint(const std::string &);    // evaulate expression for custom constraint

From 53f90fff3de67475dfb98b31162343e0577fc4b7 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Mon, 12 Jun 2023 21:28:51 -0400
Subject: [PATCH 243/396] final touch

---
 src/REACTION/fix_bond_react.cpp | 56 ++++++++++++++++-----------------
 src/REACTION/fix_bond_react.h   |  5 +--
 2 files changed, 30 insertions(+), 31 deletions(-)

diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp
index 8e4202cad0..8315fde557 100644
--- a/src/REACTION/fix_bond_react.cpp
+++ b/src/REACTION/fix_bond_react.cpp
@@ -393,11 +393,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
         else if (strcmp(arg[iarg+1],"yes") == 0) {
           if (!atom->q_flag) error->all(FLERR,"Illegal fix bond/react command: "
                                       "cannot use 'rescale_charges' without atomic charges enabled");
-          rescale_charges_flag[rxn] = 1;
+          rescale_charges_flag[rxn] = 1; // overloaded below to also indicate number of atoms to update
           rescale_charges_anyflag = 1;
           cuff = 2; // index shift for extra values carried around by mega_gloves
-        }
-        else error->one(FLERR,"Bond/react: Illegal option for 'rescale_charges' keyword");
+        } else error->one(FLERR,"Bond/react: Illegal option for 'rescale_charges' keyword");
         iarg += 2;
       } else if (strcmp(arg[iarg],"molecule") == 0) {
         if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
@@ -450,8 +449,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms");
   memory->create(create_atoms,max_natoms,nreacts,"bond/react:create_atoms");
   memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms");
+  memory->create(mol_total_charge,nreacts,"bond/react:mol_total_charge");
 
   for (int j = 0; j < nreacts; j++) {
+    mol_total_charge[j] = 0.0;
     for (int i = 0; i < max_natoms; i++) {
       edge[i][j] = 0;
       custom_charges[i][j] = 1; // update all partial charges by default
@@ -491,6 +492,21 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
     if (custom_charges_fragid[i] >= 0) CustomCharges(custom_charges_fragid[i],i);
   }
 
+  // charge rescaling values must be calculated after calling CustomCharges
+  for (int myrxn = 0; myrxn < nreacts; myrxn++) {
+    if (rescale_charges_flag[myrxn]) {
+      rescale_charges_flag[myrxn] = 0; // will now store number of updated atoms
+      twomol = atom->molecules[reacted_mol[myrxn]];
+      for (int j = 0; j < twomol->natoms; j++) {
+        int jj = equivalences[j][1][myrxn]-1;
+        if (twomol->qflag && custom_charges[jj][myrxn] == 1) {
+          mol_total_charge[myrxn] += twomol->q[j];
+          rescale_charges_flag[myrxn]++;
+        }
+      }
+    }
+  }
+
   // get the names of per-atom variables needed by 'rxn' functions of custom constraint
   customvarnames();
 
@@ -613,6 +629,7 @@ FixBondReact::~FixBondReact()
   memory->destroy(delete_atoms);
   memory->destroy(create_atoms);
   memory->destroy(chiral_atoms);
+  memory->destroy(mol_total_charge);
   if (vvec != nullptr) memory->destroy(vvec);
 
   memory->destroy(rxn_name);
@@ -3129,37 +3146,18 @@ void FixBondReact::update_everything()
       }
     }
 
-    // get charge rescale delta
-    double charge_rescale_addend = 0;
-    if (rescale_charges_flag[rxnID] == 1) {
-      double sim_total_charge = 0;
-      double mol_total_charge = 0;
-      int n_custom_charge = 0;
-      for (int i = 0; i < update_num_mega; i++) {
-        rxnID = update_mega_glove[0][i];
-        twomol = atom->molecules[reacted_mol[rxnID]];
-        for (int j = 0; j < twomol->natoms; j++) {
-          int jj = equivalences[j][1][rxnID]-1;
-          if (atom->map(update_mega_glove[jj+1][i]) >= 0 &&
-              atom->map(update_mega_glove[jj+1][i]) < nlocal) {
-            if (twomol->qflag && atom->q_flag && custom_charges[jj][rxnID] == 1) {
-              double *q = atom->q;
-              sim_total_charge += q[atom->map(update_mega_glove[jj+1][i])];
-              mol_total_charge += twomol->q[j];
-              n_custom_charge++;
-            }
-          }
-        }
-        printf("check1 %g %g\n",sim_total_charge,sim_total_charges[i]);
-      }
-      charge_rescale_addend = (sim_total_charge-mol_total_charge)/n_custom_charge;
-    }
-
     // update charges and types of landlocked atoms
     // also keep track of 'stabilization' groups here
+    int n_custom_charge;
+    double charge_rescale_addend;
     for (int i = 0; i < update_num_mega; i++) {
+      charge_rescale_addend = 0;
       rxnID = update_mega_glove[0][i];
       twomol = atom->molecules[reacted_mol[rxnID]];
+      if (rescale_charges_flag[rxnID]) {
+        n_custom_charge = rescale_charges_flag[rxnID];
+        charge_rescale_addend = (sim_total_charges[i]-mol_total_charge[rxnID])/n_custom_charge;
+      }
       for (int j = 0; j < twomol->natoms; j++) {
         int jj = equivalences[j][1][rxnID]-1;
         int ilocal = atom->map(update_mega_glove[jj+1][i]);
diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h
index d8c6c45494..534261e11d 100644
--- a/src/REACTION/fix_bond_react.h
+++ b/src/REACTION/fix_bond_react.h
@@ -71,8 +71,9 @@ class FixBondReact : public Fix {
   int **store_rxn_count;
   int *stabilize_steps_flag;
   int *custom_charges_fragid;
-  int *rescale_charges_flag;
-  int rescale_charges_anyflag;
+  int *rescale_charges_flag;   // if nonzero, indicates number of atoms whose charges are updated
+  int rescale_charges_anyflag; // indicates if any reactions do charge rescaling
+  double *mol_total_charge;    // sum of charges of post-reaction atoms whose charges are updated
   int *create_atoms_flag;
   int *modify_create_fragid;
   double *overlapsq;

From 2f7c3bf959b8ebd11e9001b2e610f39acebbdc1b Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@outlook.com>
Date: Sun, 11 Jun 2023 18:02:11 -0600
Subject: [PATCH 244/396] pylammps: reduce dependency to info command output

---
 python/lammps/pylammps.py | 85 ++++++++++++++++-----------------------
 1 file changed, 35 insertions(+), 50 deletions(-)

diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py
index 72cfed53f0..d3c65f783c 100644
--- a/python/lammps/pylammps.py
+++ b/python/lammps/pylammps.py
@@ -707,66 +707,55 @@ class PyLammps(object):
 
   def _parse_info_system(self, output):
     system = {}
+    system['dimensions'] = self.lmp.extract_setting("dimension")
+    system['xlo'] = self.lmp.extract_global("boxxlo")
+    system['ylo'] = self.lmp.extract_global("boxylo")
+    system['zlo'] = self.lmp.extract_global("boxzlo")
+    system['xhi'] = self.lmp.extract_global("boxxhi")
+    system['yhi'] = self.lmp.extract_global("boxyhi")
+    system['zhi'] = self.lmp.extract_global("boxzhi")
+    xprd = system["xhi"] - system["xlo"]
+    yprd = system["yhi"] - system["ylo"]
+    zprd = system["zhi"] - system["zlo"]
+    if self.lmp.extract_setting("triclinic") == 1:
+      system['triclinic_box'] = (xprd, yprd, zprd)
+    else:
+      system['orthogonal_box'] = (xprd, yprd, zprd)
+    system['nangles'] = self.lmp.extract_global("nbonds")
+    system['nangletypes'] = self.lmp.extract_setting("nbondtypes")
+    system['angle_style'] = self.lmp.extract_global("angle_style")
+    system['nbonds'] = self.lmp.extract_global("nbonds")
+    system['nbondtypes'] = self.lmp.extract_setting("nbondtypes")
+    system['bond_style'] = self.lmp.extract_global("bond_style")
+    system['ndihedrals'] = self.lmp.extract_global("ndihedrals")
+    system['ndihedraltypes'] = self.lmp.extract_setting("ndihedraltypes")
+    system['dihedral_style'] = self.lmp.extract_global("dihedral_style")
+    system['nimpropers'] = self.lmp.extract_global("nimpropers")
+    system['nimpropertypes'] = self.lmp.extract_setting("nimpropertypes")
+    system['improper_style'] = self.lmp.extract_global("improper_style")
+    system['kspace_style'] = self.lmp.extract_global("kspace_style")
+    system['natoms'] = self.lmp.extract_global("natoms")
+    system['ntypes'] = self.lmp.extract_global("ntypes")
+    system['pair_style'] = self.lmp.extract_global("pair_style")
+    system['atom_style'] = self.lmp.extract_global("atom_style")
+    system['units'] = self.lmp.extract_global("units")
 
     for line in output:
-      if line.startswith("Units"):
-        system['units'] = self._get_pair(line)[1]
-      elif line.startswith("Atom style"):
-        system['atom_style'] = self._get_pair(line)[1]
-      elif line.startswith("Atom map"):
+      if line.startswith("Atom map"):
         system['atom_map'] = self._get_pair(line)[1]
       elif line.startswith("Atoms"):
         parts = self._split_values(line)
-        system['natoms'] = int(self._get_pair(parts[0])[1])
-        system['ntypes'] = int(self._get_pair(parts[1])[1])
-        system['style'] = self._get_pair(parts[2])[1]
-      elif line.startswith("Kspace style"):
-        system['kspace_style'] = self._get_pair(line)[1]
-      elif line.startswith("Dimensions"):
-        system['dimensions'] = int(self._get_pair(line)[1])
-      elif line.startswith("Orthogonal box"):
-        system['orthogonal_box'] = [float(x) for x in self._get_pair(line)[1].split('x')]
       elif line.startswith("Boundaries"):
         system['boundaries'] = self._get_pair(line)[1]
-      elif line.startswith("xlo"):
-        keys, values = [self._split_values(x) for x in self._get_pair(line)]
-        for key, value in zip(keys, values):
-          system[key] = float(value)
-      elif line.startswith("ylo"):
-        keys, values = [self._split_values(x) for x in self._get_pair(line)]
-        for key, value in zip(keys, values):
-          system[key] = float(value)
-      elif line.startswith("zlo"):
-        keys, values = [self._split_values(x) for x in self._get_pair(line)]
-        for key, value in zip(keys, values):
-          system[key] = float(value)
       elif line.startswith("Molecule type"):
         system['molecule_type'] = self._get_pair(line)[1]
-      elif line.startswith("Bonds"):
-        parts = self._split_values(line)
-        system['nbonds'] = int(self._get_pair(parts[0])[1])
-        system['nbondtypes'] = int(self._get_pair(parts[1])[1])
-        system['bond_style'] = self._get_pair(parts[2])[1]
-      elif line.startswith("Angles"):
-        parts = self._split_values(line)
-        system['nangles'] = int(self._get_pair(parts[0])[1])
-        system['nangletypes'] = int(self._get_pair(parts[1])[1])
-        system['angle_style'] = self._get_pair(parts[2])[1]
-      elif line.startswith("Dihedrals"):
-        parts = self._split_values(line)
-        system['ndihedrals'] = int(self._get_pair(parts[0])[1])
-        system['ndihedraltypes'] = int(self._get_pair(parts[1])[1])
-        system['dihedral_style'] = self._get_pair(parts[2])[1]
-      elif line.startswith("Impropers"):
-        parts = self._split_values(line)
-        system['nimpropers'] = int(self._get_pair(parts[0])[1])
-        system['nimpropertypes'] = int(self._get_pair(parts[1])[1])
-        system['improper_style'] = self._get_pair(parts[2])[1]
 
     return system
 
   def _parse_info_communication(self, output):
     comm = {}
+    comm['nprocs'] = self.lmp.extract_setting("world_size")
+    comm['nthreads'] = self.lmp.extract_setting("nthreads")
 
     for line in output:
       if line.startswith("MPI library"):
@@ -779,10 +768,6 @@ class PyLammps(object):
         comm['proc_grid'] = [int(x) for x in self._get_pair(line)[1].split('x')]
       elif line.startswith("Communicate velocities for ghost atoms"):
         comm['ghost_velocity'] = (self._get_pair(line)[1] == "yes")
-      elif line.startswith("Nprocs"):
-        parts = self._split_values(line)
-        comm['nprocs'] = int(self._get_pair(parts[0])[1])
-        comm['nthreads'] = int(self._get_pair(parts[1])[1])
     return comm
 
   def _parse_element_list(self, output):

From d7ecf41ff6acba213e5c2c55725d873342739ad7 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@outlook.com>
Date: Sun, 11 Jun 2023 23:11:28 -0600
Subject: [PATCH 245/396] pylammps: use library API for variable access

---
 python/lammps/pylammps.py | 48 +++++++++++++++++++++++++++------------
 1 file changed, 34 insertions(+), 14 deletions(-)

diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py
index d3c65f783c..7acdff658a 100644
--- a/python/lammps/pylammps.py
+++ b/python/lammps/pylammps.py
@@ -28,6 +28,7 @@ import tempfile
 from collections import namedtuple
 
 from .core import lammps
+from .constants import *                # lgtm [py/polluting-import]
 
 # -------------------------------------------------------------------------
 
@@ -65,22 +66,43 @@ class OutputCapture(object):
 # -------------------------------------------------------------------------
 
 class Variable(object):
-  def __init__(self, pylammps_instance, name, style, definition):
+  def __init__(self, pylammps_instance, name):
     self._pylmp = pylammps_instance
     self.name = name
-    self.style = style
-    self.definition = definition.split()
+
+  @property
+  def style(self):
+    vartype = self._pylmp.lmp.lib.lammps_extract_variable_datatype(self._pylmp.lmp.lmp, self.name.encode())
+    if vartype == LMP_VAR_EQUAL:
+      return "equal"
+    elif vartype == LMP_VAR_ATOM:
+      return "atom"
+    elif vartype == LMP_VAR_VECTOR:
+      return "vector"
+    elif vartype == LMP_VAR_STRING:
+      return "string"
+    return None
 
   @property
   def value(self):
-    if self.style == 'atom':
-      return list(self._pylmp.lmp.extract_variable(self.name, "all", 1))
+    return self._pylmp.lmp.extract_variable(self.name)
+
+  @value.setter
+  def value(self, newvalue):
+    style = self.style
+    if style == "equal" or style == "string":
+      self._pylmp.variable("{} {} {}".format(self.name, style, newvalue))
     else:
-      value = self._pylmp.lmp_print('"${%s}"' % self.name).strip()
-      try:
-        return float(value)
-      except ValueError:
-        return value
+      raise Exception("Setter not implemented for {} style variables.".format(style))
+
+  def __str__(self):
+    value = self.value
+    if isinstance(value, str):
+      value = "\"{}\"".format(value)
+    return "Variable(name=\"{}\", value={})".format(self.name, value)
+
+  def __repr__(self):
+    return self.__str__()
 
 # -------------------------------------------------------------------------
 
@@ -676,11 +698,9 @@ class PyLammps(object):
     :getter: Returns a dictionary of all variables that are defined in this LAMMPS instance
     :type: dict
     """
-    output = self.lmp_info("variables")
-    output = output[output.index("Variable information:")+1:]
     variables = {}
-    for v in self._parse_element_list(output):
-      variables[v['name']] = Variable(self, v['name'], v['style'], v['def'])
+    for name in self.lmp.available_ids("variable"):
+      variables[name] = Variable(self, name)
     return variables
 
   def eval(self, expr):

From 64508e08aac5d6c73c0511fab4903603cd6d8da0 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@outlook.com>
Date: Sun, 11 Jun 2023 23:19:20 -0600
Subject: [PATCH 246/396] pylammps: use library API to return available groups

---
 python/lammps/pylammps.py | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py
index 7acdff658a..bdbed3e971 100644
--- a/python/lammps/pylammps.py
+++ b/python/lammps/pylammps.py
@@ -686,9 +686,7 @@ class PyLammps(object):
     :getter: Returns a list of atom groups that are currently active in this LAMMPS instance
     :type: list
     """
-    output = self.lmp_info("groups")
-    output = output[output.index("Group information:")+1:]
-    return self._parse_groups(output)
+    return self.lmp.available_ids("group")
 
   @property
   def variables(self):
@@ -802,16 +800,6 @@ class PyLammps(object):
       elements.append(element)
     return elements
 
-  def _parse_groups(self, output):
-    groups = []
-    group_pattern = re.compile(r"(?P<name>.+) \((?P<type>.+)\)")
-
-    for line in output:
-      m = group_pattern.match(line.split(':')[1].strip())
-      group = {'name': m.group('name'), 'type': m.group('type')}
-      groups.append(group)
-    return groups
-
   def lmp_print(self, s):
     """ needed for Python2 compatibility, since print is a reserved keyword """
     return self.__getattr__("print")(s)

From f128de7dd0ef6cdd83297399910b287a87ab909b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 13 Jun 2023 15:13:16 -0400
Subject: [PATCH 247/396] Bugfix from @ndtrung81 for indexing bug when tallying
 per-atom Coulomb energy

---
 lib/gpu/lal_answer.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/gpu/lal_answer.cpp b/lib/gpu/lal_answer.cpp
index 1911be8431..fc8e2cfe7a 100644
--- a/lib/gpu/lal_answer.cpp
+++ b/lib/gpu/lal_answer.cpp
@@ -260,10 +260,10 @@ double AnswerT::energy_virial(double *eatom, double **vatom,
     ecoul+=ecv;
     if (_ef_atom) {
       if (_ilist==nullptr) {
-        for (int i=0; i<_ev_stride; i++)
-          eatom[i]+=engv[i];
-        for (int i=_ev_stride; i<iend; i++)
-          eatom[i]+=engv[i];
+        for (int i=0, ii=0; i<_ev_stride; i++)
+          eatom[ii++]+=engv[i];
+        for (int i=_ev_stride, ii=0; i<iend; i++)
+          eatom[ii++]+=engv[i];
       } else {
         for (int i=0, ii=0; i<_ev_stride; i++)
           eatom[_ilist[ii++]]+=engv[i];

From 105ef5f103fd667dc88c83e11f73d6dff3312438 Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndactrung@gmail.com>
Date: Tue, 13 Jun 2023 14:24:12 -0500
Subject: [PATCH 248/396] Rescaled EPSILON with a length scale (rounded radii)
 for contact detection

---
 src/BODY/fix_wall_body_polygon.cpp        |  2 +-
 src/BODY/fix_wall_body_polyhedron.cpp     |  2 +-
 src/BODY/pair_body_rounded_polygon.cpp    | 22 +++++++++++++-------
 src/BODY/pair_body_rounded_polyhedron.cpp | 25 +++++++++++++++++------
 4 files changed, 36 insertions(+), 15 deletions(-)

diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp
index 4d0517e527..6f0622cbf6 100644
--- a/src/BODY/fix_wall_body_polygon.cpp
+++ b/src/BODY/fix_wall_body_polygon.cpp
@@ -44,7 +44,7 @@ enum {FAR=0,XLO,XHI,YLO,YHI};
 
 //#define _POLYGON_DEBUG
 #define DELTA 10000
-#define EPSILON 1e-2
+#define EPSILON 1e-2    // dimensionless threshold (dot products, end point checks, contact checks)
 #define BIG 1.0e20
 #define MAX_CONTACTS 4  // maximum number of contacts for 2D models
 #define EFF_CONTACTS 2  // effective contacts for 2D models
diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp
index 212830eb81..546ef1f0d4 100644
--- a/src/BODY/fix_wall_body_polyhedron.cpp
+++ b/src/BODY/fix_wall_body_polyhedron.cpp
@@ -42,7 +42,7 @@ enum {FAR=0,XLO,XHI,YLO,YHI,ZLO,ZHI};
 
 //#define _POLYHEDRON_DEBUG
 #define DELTA 10000
-#define EPSILON 1e-2
+#define EPSILON 1e-3    // dimensionless threshold (dot products, end point checks)
 #define BIG 1.0e20
 #define MAX_CONTACTS 4  // maximum number of contacts for 2D models
 #define EFF_CONTACTS 2  // effective contacts for 2D models
diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp
index 0e83b63f99..24f38a6a0a 100644
--- a/src/BODY/pair_body_rounded_polygon.cpp
+++ b/src/BODY/pair_body_rounded_polygon.cpp
@@ -40,7 +40,7 @@
 using namespace LAMMPS_NS;
 
 #define DELTA 10000
-#define EPSILON 1e-3
+#define EPSILON 1e-3    // dimensionless threshold (dot products, end point checks, contact checks)
 #define MAX_CONTACTS 4  // maximum number of contacts for 2D models
 #define EFF_CONTACTS 2  // effective contacts for 2D models
 
@@ -624,7 +624,8 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j,
   fy = dely*fpair/rij;
   fz = delz*fpair/rij;
 
-  if (R <= EPSILON) { // in contact
+  double rmin = MIN(rradi, rradj);
+  if (R <= EPSILON*rmin) { // in contact
 
     // relative translational velocity
 
@@ -1019,6 +1020,7 @@ int PairBodyRoundedPolygon::compute_distance_to_vertex(int ibody,
   double xi1[3],xi2[3],u[3],v[3],uij[3];
   double udotv, magv, magucostheta;
   double delx,dely,delz;
+  double rmin = MIN(rounded_radius, x0_rounded_radius);
 
   ifirst = dfirst[ibody];
   iefirst = edfirst[ibody];
@@ -1105,17 +1107,17 @@ int PairBodyRoundedPolygon::compute_distance_to_vertex(int ibody,
       // x0 and xmi are on the different sides
       // t is the ratio to detect if x0 is closer to the vertices xi or xj
 
-      if (fabs(xi2[0] - xi1[0]) > EPSILON)
+      if (fabs(xi2[0] - xi1[0]) > EPSILON*rmin)
         t = (hi[0] - xi1[0]) / (xi2[0] - xi1[0]);
-      else if (fabs(xi2[1] - xi1[1]) > EPSILON)
+      else if (fabs(xi2[1] - xi1[1]) > EPSILON*rmin)
         t = (hi[1] - xi1[1]) / (xi2[1] - xi1[1]);
-      else if (fabs(xi2[2] - xi1[2]) > EPSILON)
+      else if (fabs(xi2[2] - xi1[2]) > EPSILON*rmin)
         t = (hi[2] - xi1[2]) / (xi2[2] - xi1[2]);
 
       double contact_dist = rounded_radius + x0_rounded_radius;
       if (t >= 0 && t <= 1) {
         mode = EDGE;
-        if (d < contact_dist + EPSILON)
+        if (d < contact_dist + EPSILON*rmin)
           contact = 1;
 
       } else { // t < 0 || t > 1: closer to either vertices of the edge
@@ -1293,8 +1295,14 @@ double PairBodyRoundedPolygon::contact_separation(const Contact& c1,
   double x3 = c2.xv[0];
   double y3 = c2.xv[1];
 
+  int ibody = c1.ibody;
+  int jbody = c1.ibody;
+  double rradi = rounded_radius[ibody];
+  double rradj = rounded_radius[jbody];
+  double rmin = MIN(rradi, rradj);
+
   double delta_a = 0.0;
-  if (fabs(x2 - x1) > EPSILON) {
+  if (fabs(x2 - x1) > EPSILON*rmin) {
     double A = (y2 - y1) / (x2 - x1);
     delta_a = fabs(y1 - A * x1 - y3 + A * x3) / sqrt(1 + A * A);
   } else {
diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp
index 2c23199e33..d9a79abad0 100644
--- a/src/BODY/pair_body_rounded_polyhedron.cpp
+++ b/src/BODY/pair_body_rounded_polyhedron.cpp
@@ -44,7 +44,7 @@ using namespace LAMMPS_NS;
 using namespace MathConst;
 
 #define DELTA 10000
-#define EPSILON 1e-3
+#define EPSILON 1e-3     // dimensionless threshold (dot products, end point checks, contact checks)
 #define MAX_FACE_SIZE 4  // maximum number of vertices per face (same as BodyRoundedPolyhedron)
 #define MAX_CONTACTS 32  // for 3D models (including duplicated counts)
 
@@ -1186,7 +1186,13 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody,
 
   // singularity case, ignore interactions
 
-  if (r < EPSILON) return interact;
+  double rmin = MIN(rounded_radius_i, rounded_radius_j);
+  if (r < EPSILON*rmin) {
+    #ifdef _POLYHEDRON_DEBUG
+    printf("ignore interaction: r = %0.16f\n", r);
+    #endif
+    return interact;
+  }
 
   // include the vertices for interactions
 
@@ -1898,10 +1904,12 @@ void PairBodyRoundedPolyhedron::inside_polygon(int ibody, int face_index,
 
 {
   int i,n,ifirst,iffirst,npi1,npi2;
-  double xi1[3],xi2[3],u[3],v[3],costheta,anglesum1,anglesum2,magu,magv;
+  double xi1[3],xi2[3],u[3],v[3],costheta,anglesum1,anglesum2,magu,magv,rradi;
 
   ifirst = dfirst[ibody];
   iffirst = facfirst[ibody];
+  rradi = rounded_radius[ibody];
+  double rradsq = rradi*rradi;
   anglesum1 = anglesum2 = 0;;
   for (i = 0; i < MAX_FACE_SIZE; i++) {
     npi1 = static_cast<int>(face[iffirst+face_index][i]);
@@ -1929,7 +1937,7 @@ void PairBodyRoundedPolyhedron::inside_polygon(int ibody, int face_index,
 
     // the point is at either vertices
 
-    if (magu * magv < EPSILON) inside1 = 1;
+    if (magu * magv < EPSILON*rradsq) inside1 = 1;
     else {
       costheta = MathExtra::dot3(u,v)/(magu*magv);
       anglesum1 += acos(costheta);
@@ -1940,7 +1948,7 @@ void PairBodyRoundedPolyhedron::inside_polygon(int ibody, int face_index,
       MathExtra::sub3(xi2,q2,v);
       magu = MathExtra::len3(u);
       magv = MathExtra::len3(v);
-      if (magu * magv < EPSILON) inside2 = 1;
+      if (magu * magv < EPSILON*rradsq) inside2 = 1;
       else {
         costheta = MathExtra::dot3(u,v)/(magu*magv);
         anglesum2 += acos(costheta);
@@ -2338,7 +2346,12 @@ void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list,
     for (int j = i + 1; j < n; j++) {
       if (contact_list[i].unique == 0) continue;
       double d = contact_separation(contact_list[i], contact_list[j]);
-      if (d < EPSILON) contact_list[j].unique = 0;
+      int ibody = contact_list[i].ibody;
+      int jbody = contact_list[i].jbody;
+      double rradi = rounded_radius[ibody];
+      double rradj = rounded_radius[jbody];
+      double rmin = MIN(rradi, rradj);
+      if (d < EPSILON*rmin) contact_list[j].unique = 0;
     }
   }
 }

From 14a27e98c9e9e2db7b1fc88ebe36a397a2825c05 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Tue, 13 Jun 2023 21:09:29 -0400
Subject: [PATCH 249/396] fix for when deleting atoms

---
 src/REACTION/fix_bond_react.cpp | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp
index 8315fde557..7e5da4a3ca 100644
--- a/src/REACTION/fix_bond_react.cpp
+++ b/src/REACTION/fix_bond_react.cpp
@@ -497,11 +497,13 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
     if (rescale_charges_flag[myrxn]) {
       rescale_charges_flag[myrxn] = 0; // will now store number of updated atoms
       twomol = atom->molecules[reacted_mol[myrxn]];
-      for (int j = 0; j < twomol->natoms; j++) {
-        int jj = equivalences[j][1][myrxn]-1;
-        if (twomol->qflag && custom_charges[jj][myrxn] == 1) {
-          mol_total_charge[myrxn] += twomol->q[j];
-          rescale_charges_flag[myrxn]++;
+      if (twomol->qflag) {
+        for (int j = 0; j < twomol->natoms; j++) {
+          int jj = equivalences[j][1][myrxn]-1;
+          if (custom_charges[jj][myrxn] == 1 && delete_atoms[jj][myrxn] == 0) {
+            mol_total_charge[myrxn] += twomol->q[j];
+            rescale_charges_flag[myrxn]++;
+          }
         }
       }
     }

From 03b25dcbaaab70ac46cec5e323dd577cf84470a2 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Tue, 13 Jun 2023 21:25:58 -0400
Subject: [PATCH 250/396] update error checks

---
 src/REACTION/fix_bond_react.cpp | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp
index 7e5da4a3ca..83442ecb25 100644
--- a/src/REACTION/fix_bond_react.cpp
+++ b/src/REACTION/fix_bond_react.cpp
@@ -391,8 +391,11 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
                                       "'rescale_charges' has too few arguments");
         if (strcmp(arg[iarg+1],"no") == 0) rescale_charges_flag[rxn] = 0; //default
         else if (strcmp(arg[iarg+1],"yes") == 0) {
-          if (!atom->q_flag) error->all(FLERR,"Illegal fix bond/react command: "
-                                      "cannot use 'rescale_charges' without atomic charges enabled");
+          if (!atom->q_flag) error->all(FLERR,"Illegal fix bond/react command: cannot use "
+                                      "'rescale_charges' without atomic charges enabled");
+          twomol = atom->molecules[reacted_mol[rxn]];
+          if (!twomol->qflag) error->all(FLERR,"Illegal fix bond/react command: cannot use "
+                                      "'rescale_charges' without Charges section in post-reaction template");
           rescale_charges_flag[rxn] = 1; // overloaded below to also indicate number of atoms to update
           rescale_charges_anyflag = 1;
           cuff = 2; // index shift for extra values carried around by mega_gloves
@@ -497,13 +500,11 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
     if (rescale_charges_flag[myrxn]) {
       rescale_charges_flag[myrxn] = 0; // will now store number of updated atoms
       twomol = atom->molecules[reacted_mol[myrxn]];
-      if (twomol->qflag) {
-        for (int j = 0; j < twomol->natoms; j++) {
-          int jj = equivalences[j][1][myrxn]-1;
-          if (custom_charges[jj][myrxn] == 1 && delete_atoms[jj][myrxn] == 0) {
-            mol_total_charge[myrxn] += twomol->q[j];
-            rescale_charges_flag[myrxn]++;
-          }
+      for (int j = 0; j < twomol->natoms; j++) {
+        int jj = equivalences[j][1][myrxn]-1;
+        if (custom_charges[jj][myrxn] == 1 && delete_atoms[jj][myrxn] == 0) {
+          mol_total_charge[myrxn] += twomol->q[j];
+          rescale_charges_flag[myrxn]++;
         }
       }
     }

From 233fb67eaa7b6e82ec22a74886288660267567a3 Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndactrung@gmail.com>
Date: Wed, 14 Jun 2023 00:28:24 -0500
Subject: [PATCH 251/396] Reverted the zero net induced charge constraint,
 updated the fix polarize doc page for q_scaled and q

---
 doc/src/fix_polarize.rst                   | 15 +++++++++++++-
 src/DIELECTRIC/fix_polarize_bem_gmres.cpp  | 24 ----------------------
 src/DIELECTRIC/fix_polarize_bem_icc.cpp    | 24 ----------------------
 src/DIELECTRIC/fix_polarize_functional.cpp | 13 +-----------
 4 files changed, 15 insertions(+), 61 deletions(-)

diff --git a/doc/src/fix_polarize.rst b/doc/src/fix_polarize.rst
index dd8a0c7d75..f35e34bc67 100644
--- a/doc/src/fix_polarize.rst
+++ b/doc/src/fix_polarize.rst
@@ -130,10 +130,23 @@ Fix *polarize/functional* employs the energy functional variation
 approach as described in :ref:`(Jadhao) <Jadhao>` to solve
 :math:`\sigma_b`.
 
+The induced charges computed by these fixes are stored in the *q_scaled* field,
+and can be accessed as in the following example:
+
+.. code-block:: LAMMPS
+
+  compute qs all property/atom q_scaled
+  dump 1 all custom 1000 all.txt id type q x y z c_qs
+
+Note that the *q* field is the regular atom charges, which do not change
+during the simulation. For interface particles, *q_scaled* is the sum
+of the real charge, divided by the local dielectric constant *epsilon*,
+and their induced charges. For non-interface particles, *q_scaled* is
+the real charge, divided by the local dielectric constant *epsilon*.
+
 More details on the implementation of these fixes and their recommended
 use are described in :ref:`(NguyenTD) <NguyenTD>`.
 
-
 Restart, fix_modify, output, run start/stop, minimize info
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
diff --git a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp
index b11ac7e482..3945b76641 100644
--- a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp
+++ b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp
@@ -445,31 +445,7 @@ void FixPolarizeBEMGMRES::compute_induced_charges()
 
   comm->forward_comm(this);
 
-  // compute the total induced charges of the interface particles
-  // for interface particles: set the charge to be the sum of unscaled (free) charges and induced charges
-
-  double tmp = 0;
-  for (int i = 0; i < nlocal; i++) {
-    if (!(mask[i] & groupbit)) continue;
-
-    double q_bound = q_scaled[i] - q[i];
-    tmp += q_bound;
-    q[i] = q_scaled[i];
-  }
-
   if (first) first = 0;
-
-  // ensure sum of all induced charges being zero
-
-  int ncount = group->count(igroup);
-  double sum = 0;
-  MPI_Allreduce(&tmp, &sum, 1, MPI_DOUBLE, MPI_SUM, world);
-  double qboundave = sum / (double) ncount;
-
-  for (int i = 0; i < nlocal; i++) {
-    if (!(mask[i] & groupbit)) continue;
-    q[i] -= qboundave;
-  }
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/DIELECTRIC/fix_polarize_bem_icc.cpp b/src/DIELECTRIC/fix_polarize_bem_icc.cpp
index 697d45f416..2b5664e4f5 100644
--- a/src/DIELECTRIC/fix_polarize_bem_icc.cpp
+++ b/src/DIELECTRIC/fix_polarize_bem_icc.cpp
@@ -361,30 +361,6 @@ void FixPolarizeBEMICC::compute_induced_charges()
   }
 
   iterations = itr;
-
-  // compute the total induced charges of the interface particles
-  // for interface particles: set the charge to be the sum of unscaled (free) charges and induced charges
-
-  double tmp = 0;
-  for (int i = 0; i < nlocal; i++) {
-    if (!(mask[i] & groupbit)) continue;
-
-    double q_bound = q_scaled[i] - q[i];
-    tmp += q_bound;
-    q[i] = q_scaled[i];
-  }
-
-  // ensure sum of all induced charges being zero
-
-  int ncount = group->count(igroup);
-  double sum = 0;
-  MPI_Allreduce(&tmp, &sum, 1, MPI_DOUBLE, MPI_SUM, world);
-  double qboundave = sum / (double) ncount;
-
-  for (int i = 0; i < nlocal; i++) {
-    if (!(mask[i] & groupbit)) continue;
-    q[i] -= qboundave;
-  }
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/DIELECTRIC/fix_polarize_functional.cpp b/src/DIELECTRIC/fix_polarize_functional.cpp
index a0dc034818..ab039f9c48 100644
--- a/src/DIELECTRIC/fix_polarize_functional.cpp
+++ b/src/DIELECTRIC/fix_polarize_functional.cpp
@@ -386,18 +386,7 @@ void FixPolarizeFunctional::update_induced_charges()
   for (int i = 0; i < nlocal; i++) {
     if (induced_charge_idx[i] < 0) continue;
     int idx = induced_charge_idx[i];
-    q[i] = -induced_charges[idx] / (4 * MY_PI);
-    q_scaled[i] = q[i] / epsilon[i];
-    tmp += q_scaled[i];
-  }
-
-  double sum = 0;
-  MPI_Allreduce(&tmp, &sum, 1, MPI_DOUBLE, MPI_SUM, world);
-  double qboundave = sum/(double)num_induced_charges;
-
-  for (int i = 0; i < nlocal; i++) {
-    if (induced_charge_idx[i] < 0) continue;
-    q_scaled[i] -=  qboundave;
+    q_scaled[i] = -induced_charges[idx] / (4 * MY_PI);
   }
 
   // revert to scaled charges to calculate forces

From 8984b89feb469b35acec18757f21fc30c202cfcf Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 03:18:17 -0400
Subject: [PATCH 252/396] use consistent comments, apply clang-format

---
 src/REPLICA/fix_pimd_langevin.h | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.h b/src/REPLICA/fix_pimd_langevin.h
index dc48832855..d3b9d5b77e 100644
--- a/src/REPLICA/fix_pimd_langevin.h
+++ b/src/REPLICA/fix_pimd_langevin.h
@@ -41,7 +41,7 @@ class FixPIMDLangevin : public Fix {
   double compute_vector(int) override;
 
  protected:
-  /* System setting variables */
+  // System setting variables
   int method;                              // PIMD or NMPIMD or CMD
   int fmmode;                              // physical or normal
   int np;                                  // number of beads
@@ -51,7 +51,7 @@ class FixPIMDLangevin : public Fix {
   double lj_epsilon, lj_sigma, lj_mass;    // LJ unit energy, length, and mass scales
   double other_planck;
   double other_mvv2e;
-  double kt;              // k_B * temp
+  double kt;               // k_B * temp
   double beta, beta_np;    // beta = 1./kBT beta_np = 1./kBT/np
   int thermostat;          // NHC or PILE_L
   int barostat;            // BZP
@@ -62,15 +62,16 @@ class FixPIMDLangevin : public Fix {
   double masstotal;
 
   double fixedpoint[3];    // location of dilation fixed-point
-  /* ring-polymer model */
+
+  // ring-polymer model
 
   double omega_np, fbond, spring_energy, sp;
 
-  /* fictitious mass */
+  // fictitious mass
 
   double fmass, *mass;
 
-  /* inter-partition communication */
+  // inter-partition communication
 
   MPI_Comm rootworld;
   int me, nprocs, ireplica, nreplica, nprocs_universe;
@@ -117,7 +118,8 @@ class FixPIMDLangevin : public Fix {
   int tstat_flag;    // tstat_flat = 1 if thermostat if used
   void langevin_init();
   void b_step();    // integrate for dt/2 according to B part (v <- v + f * dt/2)
-  void a_step();    // integrate for dt/2 according to A part (non-centroid mode, harmonic force between replicas)
+  void
+  a_step();    // integrate for dt/2 according to A part (non-centroid mode, harmonic force between replicas)
   void qc_step();    // integrate for dt/2 for the centroid mode (x <- x + v * dt/2)
   void o_step();     // integrate for dt according to O part (O-U process, for thermostating)
 

From 6f69e5ae02a8cacead4f5b76d930d2d7a4d76593 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 03:18:37 -0400
Subject: [PATCH 253/396] initialized all pointers to null in initializer list

---
 src/REPLICA/fix_pimd_langevin.cpp | 39 ++++++++++++-------------------
 1 file changed, 15 insertions(+), 24 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 0af08b43b3..e4e60520d1 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -64,31 +64,23 @@ enum { SINGLE_PROC, MULTI_PROC };
 /* ---------------------------------------------------------------------- */
 
 FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
-    Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr)
+    Fix(lmp, narg, arg), mass(nullptr), plansend(nullptr), planrecv(nullptr), tagsend(nullptr),
+    tagrecv(nullptr), bufsend(nullptr), bufrecv(nullptr), bufbeads(nullptr), bufsorted(nullptr),
+    bufsortedall(nullptr), outsorted(nullptr), buftransall(nullptr), bufsendall(nullptr),
+    bufrecvall(nullptr), tagsendall(nullptr), tagrecvall(nullptr), counts(nullptr),
+    displacements(nullptr), lam(nullptr), M_x2xp(nullptr), M_xp2x(nullptr), M_f2fp(nullptr),
+    M_fp2f(nullptr), modeindex(nullptr), tau_k(nullptr), c1_k(nullptr), c2_k(nullptr),
+    _omega_k(nullptr), Lan_s(nullptr), Lan_c(nullptr), , random(nullptr), xc(nullptr),
+    xcall(nullptr), x_unwrap(nullptr), id_pe(nullptr), id_press(nullptr), c_pe(nullptr),
+    c_press(nullptr)
 {
   restart_global = 1;
   time_integrate = 1;
-  tagsend = tagrecv = nullptr;
-  bufsend = bufrecv = nullptr;
-  bufsendall = bufrecvall = nullptr;
-  bufsorted = bufsortedall = nullptr;
-  outsorted = buftransall = nullptr;
 
   ntotal = 0;
   maxlocal = maxunwrap = maxxc = 0;
-  bufbeads = nullptr;
-  x_unwrap = xc = nullptr;
-  xcall = nullptr;
-  counts = nullptr;
 
   sizeplan = 0;
-  plansend = planrecv = nullptr;
-
-  M_x2xp = M_xp2x = M_f2fp = M_fp2f = nullptr;
-  lam = nullptr;
-  modeindex = nullptr;
-
-  mass = nullptr;
 
   method = NMPIMD;
   ensemble = NVT;
@@ -97,6 +89,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   barostat = BZP;
   fmass = 1.0;
   np = universe->nworlds;
+  inverse_np = 1.0 / np;
   sp = 1.0;
   temp = 298.15;
   Lan_temp = 298.15;
@@ -155,8 +148,8 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         pstat_flag = 1;
       } else
         error->universe_all(FLERR,
-                            "Unknown ensemble parameter for fix pimd/langevin. Only nve, nvt, nph, and npt "
-                            "ensembles are supported!");
+                            "Unknown ensemble parameter for fix pimd/langevin. Only nve, nvt, nph, "
+                            "and npt ensembles are supported!");
     } else if (strcmp(arg[i], "fmass") == 0) {
       fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (fmass < 0.0 || fmass > np)
@@ -170,10 +163,9 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
       else if (strcmp(arg[i + 1], "normal") == 0)
         fmmode = NORMAL;
       else
-        error->universe_all(
-            FLERR,
-            "Unknown fictitious mass mode for fix pimd/langevin. Only physical mass and "
-            "normal mode mass are supported!");
+        error->universe_all(FLERR,
+                            "Unknown fictitious mass mode for fix pimd/langevin. Only physical "
+                            "mass and normal mode mass are supported!");
     } else if (strcmp(arg[i], "scale") == 0) {
       pilescale = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (pilescale < 0.0)
@@ -409,7 +401,6 @@ void FixPIMDLangevin::init()
   // prepare the constants
 
   masstotal = group->mass(igroup);
-  inverse_np = 1.0 / np;
 
   double planck;
   if (strcmp(update->unit_style, "lj") == 0) {

From 494341ba48df6284d86df1000d1517e828a584df Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 03:39:52 -0400
Subject: [PATCH 254/396] error out when using barostat without pressure couple
 or vice versa

---
 src/REPLICA/fix_pimd_langevin.cpp | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index e4e60520d1..58b9ec6726 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -56,11 +56,12 @@ enum { BAOAB, OBABO };
 enum { ISO, ANISO, TRICLINIC };
 enum { PILE_L };
 enum { MTTK, BZP };
-
-static std::map<int, std::string> Barostats{{MTTK, "MTTK"}, {BZP, "BZP"}};
 enum { NVE, NVT, NPH, NPT };
 enum { SINGLE_PROC, MULTI_PROC };
 
+static std::map<int, std::string> Barostats{{MTTK, "MTTK"}, {BZP, "BZP"}};
+static std::map<int, std::string> Ensembles{{NVE, "NVE"}, {NVT, "NVT"}, {NPH, "NPH"}, {NPT, "NPT"}};
+
 /* ---------------------------------------------------------------------- */
 
 FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
@@ -235,13 +236,20 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
     }
   }
 
+  if (pstat_flag && !pdim)
+    error->universe_all(
+        FLERR, fmt::format("Must use pressure coupling with {} ensemble", Ensembles[ensemble]));
+  if (!pstat_flag && pdim)
+    error->universe_all(
+        FLERR, fmt::format("Must not use pressure coupling with {} ensemble", Ensembles[ensemble]));
+
   /* Initiation */
 
   global_freq = 1;
   vector_flag = 1;
-  if (!pstat_flag)
+  if (!pstat_flag) {
     size_vector = 10;
-  else if (pstat_flag) {
+  } else if (pstat_flag) {
     if (pstyle == ISO) {
       size_vector = 15;
     } else if (pstyle == ANISO) {
@@ -250,7 +258,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   }
   extvector = 1;
   kt = force->boltz * temp;
-  if (pstat_flag) baro_init();
+  if (pstat_flag) FixPIMDLangevin::baro_init();
 
   // some initilizations
 

From dfd384eeffa9e78df315a7b9a58070070a2754c0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 03:40:38 -0400
Subject: [PATCH 255/396] some more formatting and programming style
 improvements

---
 src/REPLICA/fix_pimd_langevin.cpp | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 58b9ec6726..75280fd3d5 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -67,13 +67,12 @@ static std::map<int, std::string> Ensembles{{NVE, "NVE"}, {NVT, "NVT"}, {NPH, "N
 FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
     Fix(lmp, narg, arg), mass(nullptr), plansend(nullptr), planrecv(nullptr), tagsend(nullptr),
     tagrecv(nullptr), bufsend(nullptr), bufrecv(nullptr), bufbeads(nullptr), bufsorted(nullptr),
-    bufsortedall(nullptr), outsorted(nullptr), buftransall(nullptr), bufsendall(nullptr),
-    bufrecvall(nullptr), tagsendall(nullptr), tagrecvall(nullptr), counts(nullptr),
+    bufsortedall(nullptr), outsorted(nullptr), buftransall(nullptr), tagsendall(nullptr),
+    tagrecvall(nullptr), bufsendall(nullptr), bufrecvall(nullptr), counts(nullptr),
     displacements(nullptr), lam(nullptr), M_x2xp(nullptr), M_xp2x(nullptr), M_f2fp(nullptr),
     M_fp2f(nullptr), modeindex(nullptr), tau_k(nullptr), c1_k(nullptr), c2_k(nullptr),
-    _omega_k(nullptr), Lan_s(nullptr), Lan_c(nullptr), , random(nullptr), xc(nullptr),
-    xcall(nullptr), x_unwrap(nullptr), id_pe(nullptr), id_press(nullptr), c_pe(nullptr),
-    c_press(nullptr)
+    _omega_k(nullptr), Lan_s(nullptr), Lan_c(nullptr), random(nullptr), xc(nullptr), xcall(nullptr),
+    x_unwrap(nullptr), id_pe(nullptr), id_press(nullptr), c_pe(nullptr), c_press(nullptr)
 {
   restart_global = 1;
   time_integrate = 1;
@@ -126,10 +125,9 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
       else if (strcmp(arg[i + 1], "baoab") == 0)
         integrator = BAOAB;
       else
-        error->universe_all(
-            FLERR,
-            "Unknown integrator parameter for fix pimd/langevin. Only obabo and baoab "
-            "integrators are supported!");
+        error->universe_all(FLERR,
+                            "Unknown integrator parameter for fix pimd/langevin. Only obabo and "
+                            "baoab integrators are supported!");
     } else if (strcmp(arg[i], "ensemble") == 0) {
       if (strcmp(arg[i + 1], "nve") == 0) {
         ensemble = NVE;
@@ -273,7 +271,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
   fixedpoint[0] = 0.5 * (domain->boxlo[0] + domain->boxhi[0]);
   fixedpoint[1] = 0.5 * (domain->boxlo[1] + domain->boxhi[1]);
   fixedpoint[2] = 0.5 * (domain->boxlo[2] + domain->boxhi[2]);
-  if (pstat_flag) { p_hydro = (p_target[0] + p_target[1] + p_target[2]) / pdim; }
+  if (pstat_flag) p_hydro = (p_target[0] + p_target[1] + p_target[2]) / pdim;
 
   // initialize Marsaglia RNG with processor-unique seed
 

From 2afa07655f810bea8649a20f8fa998296c67446e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 03:44:11 -0400
Subject: [PATCH 256/396] set code owner for fix pimd/langevin

---
 .github/CODEOWNERS | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 2686011281..f99a336dbb 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -67,6 +67,7 @@ src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
 src/MISC/*_tracker.*                @jtclemm
 src/MC/fix_gcmc.*                   @athomps
 src/MC/fix_sgcmc.*                  @athomps
+src/REPLICA/fix_pimd_langevin.*     @Yi-FanLi
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp

From beabb4effec6bdf62cbd3d29fa01e0021280df6c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 03:48:59 -0400
Subject: [PATCH 257/396] remove dead code

---
 src/npair_skip_size_off2on_oneside.cpp | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp
index eecf293755..3300ef1526 100644
--- a/src/npair_skip_size_off2on_oneside.cpp
+++ b/src/npair_skip_size_off2on_oneside.cpp
@@ -36,7 +36,7 @@ NPairSkipSizeOff2onOneside::NPairSkipSizeOff2onOneside(LAMMPS *lmp) :
 
 void NPairSkipSizeOff2onOneside::build(NeighList *list)
 {
-  int i,j,ii,jj,n,itype,jnum,joriginal,flip,tmp;
+  int i,j,ii,jj,itype,jnum,joriginal,flip,tmp;
   int *surf,*jlist;
 
   int *type = atom->type;
@@ -76,8 +76,6 @@ void NPairSkipSizeOff2onOneside::build(NeighList *list)
     itype = type[i];
     if (iskip[itype]) continue;
 
-    n = 0;
-
     // loop over parent non-skip size list
 
     jlist = firstneigh_skip[i];
@@ -108,8 +106,7 @@ void NPairSkipSizeOff2onOneside::build(NeighList *list)
 
   for (i = 0; i < nlocal; i++) {
     if (numneigh[i] == 0) continue;
-    n = numneigh[i];
-    firstneigh[i] = ipage->get(n);
+    firstneigh[i] = ipage->get(numneigh[i]);
     if (ipage->status())
       error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }

From bc52d863b46876c85f67e76be572d9ce5df72e1d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 08:48:01 -0400
Subject: [PATCH 258/396] cosmetic

---
 src/MC/fix_gcmc.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index 634b512936..5d1e318db2 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -2328,8 +2328,7 @@ double FixGCMC::energy_full()
       }
       if (overlaptest) break;
     }
-    MPI_Allreduce(&overlaptest, &overlaptestall, 1,
-                  MPI_INT, MPI_MAX, world);
+    MPI_Allreduce(&overlaptest, &overlaptestall, 1, MPI_INT, MPI_MAX, world);
     if (overlaptestall) return MAXENERGYSIGNAL;
   }
 

From 8aeb059ce867b279f1b30fe359475b6fc1b3b243 Mon Sep 17 00:00:00 2001
From: Lars Veldscholte <lars@tuxplace.nl>
Date: Wed, 14 Jun 2023 15:03:35 +0200
Subject: [PATCH 259/396] Update doc/src/compute_stress_cartesian.rst

Co-authored-by: Axel Kohlmeyer <akohlmey@gmail.com>
---
 doc/src/compute_stress_cartesian.rst | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/doc/src/compute_stress_cartesian.rst b/doc/src/compute_stress_cartesian.rst
index f52b360aa6..b9f090ef58 100644
--- a/doc/src/compute_stress_cartesian.rst
+++ b/doc/src/compute_stress_cartesian.rst
@@ -41,6 +41,10 @@ split into a kinetic contribution :math:`P^k` and a virial contribution
 This compute obeys momentum balance through fluid interfaces. They use the
 Irving--Kirkwood contour, which is the straight line between particle pairs.
 
+.. versionadded:: TBD
+
+   Added support for bond styles
+
 This compute only supports pair and bond (no angle, dihedral, improper,
 or kspace) forces. By default, if no extra keywords are specified, all
 supported contributions to the stress are included (ke, pair, bond). If any

From e6cd79e0e928071fbff2617ac9fd172657acc5d3 Mon Sep 17 00:00:00 2001
From: Lars Veldscholte <lars@tuxplace.nl>
Date: Wed, 14 Jun 2023 15:04:35 +0200
Subject: [PATCH 260/396] Fix doc links

---
 doc/src/Commands_compute.rst           |  6 +++---
 doc/src/compute.rst                    |  6 +++---
 doc/src/compute_stress_cartesian.rst   |  6 +++---
 doc/src/compute_stress_curvilinear.rst |  4 ++--
 doc/src/compute_stress_mop.rst         | 22 +++++++++++++++-------
 5 files changed, 26 insertions(+), 18 deletions(-)

diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
index 755000c976..9066531459 100644
--- a/doc/src/Commands_compute.rst
+++ b/doc/src/Commands_compute.rst
@@ -153,11 +153,11 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`sph/t/atom <compute_sph_t_atom>`
    * :doc:`spin <compute_spin>`
    * :doc:`stress/atom <compute_stress_atom>`
-   * :doc:`stress/cartesian <compute_stress_profile>`
-   * :doc:`stress/cylinder <compute_stress_profile>`
+   * :doc:`stress/cartesian <compute_stress_cartesian>`
+   * :doc:`stress/cylinder <compute_stress_curvilinear>`
    * :doc:`stress/mop <compute_stress_mop>`
    * :doc:`stress/mop/profile <compute_stress_mop>`
-   * :doc:`stress/spherical <compute_stress_profile>`
+   * :doc:`stress/spherical <compute_stress_curvilinear>`
    * :doc:`stress/tally <compute_tally>`
    * :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
    * :doc:`temp (k) <compute_temp>`
diff --git a/doc/src/compute.rst b/doc/src/compute.rst
index 950487cb72..4e5d8e6cb4 100644
--- a/doc/src/compute.rst
+++ b/doc/src/compute.rst
@@ -307,11 +307,11 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`sph/t/atom <compute_sph_t_atom>` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
 * :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
 * :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
-* :doc:`stress/cartesian <compute_stress_profile>` - stress tensor in cartesian coordinates
-* :doc:`stress/cylinder <compute_stress_profile>` - stress tensor in cylindrical coordinates
+* :doc:`stress/cartesian <compute_stress_cartesian>` - stress tensor in cartesian coordinates
+* :doc:`stress/cylinder <compute_stress_curvilinear>` - stress tensor in cylindrical coordinates
 * :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
 * :doc:`stress/mop/profile <compute_stress_mop>` - profile of the normal components of the local stress tensor using the method of planes
-* :doc:`stress/spherical <compute_stress_profile>` - stress tensor in spherical coordinates
+* :doc:`stress/spherical <compute_stress_curvilinear>` - stress tensor in spherical coordinates
 * :doc:`stress/tally <compute_tally>` - stress between two groups of atoms via the tally callback mechanism
 * :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` - per-atom chemical concentration of a specified species for each tDPD particle
 * :doc:`temp <compute_temp>` - temperature of group of atoms
diff --git a/doc/src/compute_stress_cartesian.rst b/doc/src/compute_stress_cartesian.rst
index b9f090ef58..3e1e9d9a8a 100644
--- a/doc/src/compute_stress_cartesian.rst
+++ b/doc/src/compute_stress_cartesian.rst
@@ -83,13 +83,13 @@ command, since those are contributions to the global system pressure.
 NOTE 2: The local stress profiles generated by these computes are
 similar to those obtained by the
 :doc:`method-of-planes (MOP) <compute_stress_mop>`.
-A key difference
-is that compute `stress/mop/profile <compute_stress_mop>`
+A key difference is that compute
+:doc:`stress/mop/profile <compute_stress_mop>`
 considers particles crossing a set of planes, while
 *stress/cartesian* computes averages for a set of small volumes.
 Moreover, this compute computes the diagonal components of the stress
 tensor :math:`P_{xx}`, :math:`P_{yy}`, and :math:`P_{zz}`, while
-`stress/mop/profile <compute_stress_mop>` computes the components
+*stress/mop/profile* computes the components
 :math:`P_{ix}`, :math:`P_{iy}`, and :math:`P_{iz}`, where :math:`i` is the
 direction normal to the plane.
 
diff --git a/doc/src/compute_stress_curvilinear.rst b/doc/src/compute_stress_curvilinear.rst
index f7cbf5efbe..edd1df9217 100644
--- a/doc/src/compute_stress_curvilinear.rst
+++ b/doc/src/compute_stress_curvilinear.rst
@@ -115,8 +115,8 @@ package <Build_package>` doc page for more info.
 Related commands
 """"""""""""""""
 
-:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute
-stress/mop/profile <compute_stress_mop>`, :doc:`compute stress/cartesian <compute_stress_cartesian>`
+:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`,
+:doc:`compute stress/mop/profile <compute_stress_mop>`, :doc:`compute stress/cartesian <compute_stress_cartesian>`
 
 Default
 """""""
diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst
index 4ad2261bb0..0b31805fbf 100644
--- a/doc/src/compute_stress_mop.rst
+++ b/doc/src/compute_stress_mop.rst
@@ -76,12 +76,16 @@ command, since those are contributions to the global system pressure.
 
 NOTE 3: The local stress profile generated by compute *stress/mop/profile*
 is similar to that obtained by compute
-:doc:`stress/cartesian <compute_stress_profile>`.
-A key difference is that compute *stress/mop/profile* considers particles
-crossing a set of planes, while compute *stress/cartesian* computes averages
-for a set of small volumes.  More information
-on the similarities and differences can be found in
-:ref:`(Ikeshoji)<Ikeshoji2>`.
+:doc:`stress/cartesian <compute_stress_cartesian>`.
+A key difference is that compute *stress/mop/profile*
+considers particles crossing a set of planes, while
+*stress/cartesian* computes averages for a set
+of small volumes.
+Moreover, *stress/cartesian* compute computes the diagonal components of the stress
+tensor :math:`P_{xx}`, :math:`P_{yy}`, and :math:`P_{zz}`, while
+*stress/mop/profile* computes the components
+:math:`P_{ix}`, :math:`P_{iy}`, and :math:`P_{iz}`, where :math:`i` is the
+direction normal to the plane.
 
 Output info
 """""""""""
@@ -123,7 +127,11 @@ intra-molecular interactions, and long range (kspace) interactions.
 Related commands
 """"""""""""""""
 
-:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_profile>`, :doc:`compute stress/cylinder <compute_stress_profile>`, :doc:`compute stress/spherical <compute_stress_profile>`
+:doc:`compute stress/atom <compute_stress_atom>`,
+:doc:`compute pressure <compute_pressure>`,
+:doc:`compute stress/cartesian <compute_stress_cartesian>`,
+:doc:`compute stress/cylinder <compute_stress_curvilinear>`,
+:doc:`compute stress/spherical <compute_stress_curvilinear>`
 
 Default
 """""""

From 3b37c92b87df94a3087cbb038ec4bcc0d8328be0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 10:06:01 -0400
Subject: [PATCH 261/396] consistently print error when box has changed to
 triclinic without redefining kspace style

---
 src/INTEL/pppm_disp_intel.cpp | 15 ++++-------
 src/KOKKOS/pppm_kokkos.cpp    |  6 ++++-
 src/KSPACE/pppm_disp.cpp      | 47 +++++++++++++++++++----------------
 3 files changed, 35 insertions(+), 33 deletions(-)

diff --git a/src/INTEL/pppm_disp_intel.cpp b/src/INTEL/pppm_disp_intel.cpp
index fdff23fe5e..319d070e66 100644
--- a/src/INTEL/pppm_disp_intel.cpp
+++ b/src/INTEL/pppm_disp_intel.cpp
@@ -124,8 +124,7 @@ void PPPMDispIntel::init()
 
   _use_lrt = fix->lrt();
   if (_use_lrt)
-    error->all(FLERR,
-               "LRT mode is currently not supported for pppm/disp/intel");
+    error->all(FLERR, "LRT mode is currently not supported for pppm/disp/intel");
 
 
   // For vectorization, we need some padding in the end
@@ -142,19 +141,15 @@ void PPPMDispIntel::init()
   if (_use_table) {
     rho_points = 5000;
     memory->destroy(rho_lookup);
-    memory->create(rho_lookup, rho_points, INTEL_P3M_ALIGNED_MAXORDER,
-                   "pppmdispintel:rho_lookup");
+    memory->create(rho_lookup, rho_points, INTEL_P3M_ALIGNED_MAXORDER,"pppmdispintel:rho_lookup");
     memory->destroy(rho6_lookup);
-    memory->create(rho6_lookup, rho_points, INTEL_P3M_ALIGNED_MAXORDER,
-                   "pppmdispintel:rho6_lookup");
+    memory->create(rho6_lookup, rho_points, INTEL_P3M_ALIGNED_MAXORDER,"pppmdispintel:rho6_lookup");
 
     if (differentiation_flag == 1) {
       memory->destroy(drho_lookup);
-      memory->create(drho_lookup, rho_points, INTEL_P3M_ALIGNED_MAXORDER,
-                     "pppmdispintel:drho_lookup");
+      memory->create(drho_lookup, rho_points, INTEL_P3M_ALIGNED_MAXORDER,"pppmdispintel:drho_lookup");
       memory->destroy(drho6_lookup);
-      memory->create(drho6_lookup, rho_points, INTEL_P3M_ALIGNED_MAXORDER,
-                     "pppmdispintel:drho6_lookup");
+      memory->create(drho6_lookup, rho_points, INTEL_P3M_ALIGNED_MAXORDER,"pppmdispintel:drho6_lookup");
     }
     precompute_rho();
   }
diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp
index f76cab6f0f..912ae36f6f 100644
--- a/src/KOKKOS/pppm_kokkos.cpp
+++ b/src/KOKKOS/pppm_kokkos.cpp
@@ -138,7 +138,7 @@ PPPMKokkos<DeviceType>::~PPPMKokkos()
 template<class DeviceType>
 void PPPMKokkos<DeviceType>::init()
 {
-  if (me == 0) utils::logmesg(lmp,"PPPM initialization ...\n");
+  if (me == 0) utils::logmesg(lmp,"PPPM Kokkos initialization ...\n");
 
   // error check
 
@@ -146,6 +146,10 @@ void PPPMKokkos<DeviceType>::init()
     error->all(FLERR,"Cannot (yet) use PPPM Kokkos with 'kspace_modify diff ad'");
 
   triclinic_check();
+
+  if (triclinic != domain->triclinic)
+    error->all(FLERR,"Must redefine kspace_style after changing to triclinic box");
+
   if (domain->triclinic && slabflag)
     error->all(FLERR,"Cannot (yet) use PPPM with triclinic box and slab correction");
   if (domain->dimension == 2)
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index 84a21b46e6..ffa34a7e14 100644
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -242,12 +242,12 @@ void PPPMDisp::settings(int narg, char **arg)
 
 PPPMDisp::~PPPMDisp()
 {
-  delete [] factors;
-  delete [] B;
+  delete[] factors;
+  delete[] B;
   B = nullptr;
-  delete [] cii;
+  delete[] cii;
   cii = nullptr;
-  delete [] csumi;
+  delete[] csumi;
   csumi = nullptr;
   PPPMDisp::deallocate();
   PPPMDisp::deallocate_peratom();
@@ -268,6 +268,9 @@ void PPPMDisp::init()
 
   triclinic_check();
 
+  if (triclinic != domain->triclinic)
+    error->all(FLERR,"Must redefine kspace_style after changing to triclinic box");
+
   if (domain->dimension == 2)
     error->all(FLERR,"Cannot use PPPMDisp with 2d simulation");
   if (comm->style != Comm::BRICK)
@@ -1277,7 +1280,7 @@ void PPPMDisp::init_coeffs()
   int n = atom->ntypes;
   int converged;
 
-  delete [] B;
+  delete[] B;
   B = nullptr;
 
   // no mixing rule or arithmetic
@@ -3352,10 +3355,10 @@ void PPPMDisp::calc_csum()
   int ntypes = atom->ntypes;
   int i,j,k;
 
-  delete [] cii;
+  delete[] cii;
   cii = new double[ntypes+1];
   for (i = 0; i<=ntypes; i++) cii[i] = 0.0;
-  delete [] csumi;
+  delete[] csumi;
   csumi = new double[ntypes+1];
   for (i = 0; i<=ntypes; i++) csumi[i] = 0.0;
   int *neach = new int[ntypes+1];
@@ -3447,8 +3450,8 @@ void PPPMDisp::calc_csum()
     }
   }
 
-  delete [] neach;
-  delete [] neach_all;
+  delete[] neach;
+  delete[] neach_all;
 }
 
 /* ----------------------------------------------------------------------
@@ -6538,9 +6541,9 @@ void PPPMDisp::fieldforce_none_ik()
     }
   }
 
-  delete [] ekx;
-  delete [] eky;
-  delete [] ekz;
+  delete[] ekx;
+  delete[] eky;
+  delete[] ekz;
 }
 
 /* ----------------------------------------------------------------------
@@ -6660,9 +6663,9 @@ void PPPMDisp::fieldforce_none_ad()
     }
   }
 
-  delete [] ekx;
-  delete [] eky;
-  delete [] ekz;
+  delete[] ekx;
+  delete[] eky;
+  delete[] ekz;
 }
 
 /* ----------------------------------------------------------------------
@@ -6756,13 +6759,13 @@ void PPPMDisp::fieldforce_none_peratom()
     }
   }
 
-  delete [] u_pa;
-  delete [] v0;
-  delete [] v1;
-  delete [] v2;
-  delete [] v3;
-  delete [] v4;
-  delete [] v5;
+  delete[] u_pa;
+  delete[] v0;
+  delete[] v1;
+  delete[] v2;
+  delete[] v3;
+  delete[] v4;
+  delete[] v5;
 }
 
 /* ----------------------------------------------------------------------

From 0314c9892cee6410349f7ae147b669384e1de937 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 10:26:38 -0400
Subject: [PATCH 262/396] silence compiler warnings

---
 .../fortran/test_fortran_gather_scatter.f90    | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/unittest/fortran/test_fortran_gather_scatter.f90 b/unittest/fortran/test_fortran_gather_scatter.f90
index 1f8d4f0905..8741bba485 100644
--- a/unittest/fortran/test_fortran_gather_scatter.f90
+++ b/unittest/fortran/test_fortran_gather_scatter.f90
@@ -207,7 +207,7 @@ END SUBROUTINE f_lammps_scatter_atoms_subset_mask
 
 SUBROUTINE f_lammps_setup_gather_topology() BIND(C)
   USE LIBLAMMPS
-  USE keepstuff, ONLY : lmp, cont_input, more_input, pair_input
+  USE keepstuff, ONLY : lmp
   IMPLICIT NONE
 
   CALL lmp%command('include ${input_dir}/in.fourmol')
@@ -232,7 +232,7 @@ FUNCTION f_lammps_test_gather_bonds_small() BIND(C) RESULT(count)
       nbonds = nbonds_small
   ELSE
       nbonds_big = lmp%extract_global('nbonds')
-      nbonds = nbonds_big
+      nbonds = INT(nbonds_big)
   END IF
 
   CALL lmp%gather_bonds(bonds)
@@ -280,7 +280,7 @@ FUNCTION f_lammps_test_gather_bonds_big() BIND(C) RESULT(count)
   INTEGER(c_int64_t), POINTER :: nbonds_big
 
   nbonds_big = lmp%extract_global('nbonds')
-  nbonds = nbonds_big
+  nbonds = INT(nbonds_big)
   CALL lmp%gather_bonds(bonds)
   bonds_array(1:3,1:SIZE(bonds)/3) => bonds
   count = 0
@@ -332,7 +332,7 @@ FUNCTION f_lammps_test_gather_angles_small() BIND(C) RESULT(count)
       nangles = nangles_small
   ELSE
       nangles_big = lmp%extract_global('nangles')
-      nangles = nangles_big
+      nangles = INT(nangles_big)
   END IF
 
   CALL lmp%gather_angles(angles)
@@ -380,7 +380,7 @@ FUNCTION f_lammps_test_gather_angles_big() BIND(C) RESULT(count)
   INTEGER(c_int64_t), POINTER :: nangles_big
 
   nangles_big = lmp%extract_global('nangles')
-  nangles = nangles_big
+  nangles = INT(nangles_big)
   CALL lmp%gather_angles(angles)
   angles_array(1:4,1:SIZE(angles)/4) => angles
   count = 0
@@ -432,7 +432,7 @@ FUNCTION f_lammps_test_gather_dihedrals_small() BIND(C) RESULT(count)
       ndihedrals = ndihedrals_small
   ELSE
       ndihedrals_big = lmp%extract_global('ndihedrals')
-      ndihedrals = ndihedrals_big
+      ndihedrals = INT(ndihedrals_big)
   END IF
 
   CALL lmp%gather_dihedrals(dihedrals)
@@ -478,7 +478,7 @@ FUNCTION f_lammps_test_gather_dihedrals_big() BIND(C) RESULT(count)
   INTEGER(c_int64_t), POINTER :: ndihedrals_big
 
   ndihedrals_big = lmp%extract_global('ndihedrals')
-  ndihedrals = ndihedrals_big
+  ndihedrals = INT(ndihedrals_big)
   CALL lmp%gather_dihedrals(dihedrals)
   dihedrals_array(1:5,1:SIZE(dihedrals)/5) => dihedrals
   count = 0
@@ -528,7 +528,7 @@ FUNCTION f_lammps_test_gather_impropers_small() BIND(C) RESULT(count)
       nimpropers = nimpropers_small
   ELSE
       nimpropers_big = lmp%extract_global('nimpropers')
-      nimpropers = nimpropers_big
+      nimpropers = INT(nimpropers_big)
   END IF
 
   CALL lmp%gather_impropers(impropers)
@@ -566,7 +566,7 @@ FUNCTION f_lammps_test_gather_impropers_big() BIND(C) RESULT(count)
   INTEGER(c_int64_t), POINTER :: nimpropers_big
 
   nimpropers_big = lmp%extract_global('nimpropers')
-  nimpropers = nimpropers_big
+  nimpropers = INT(nimpropers_big)
   CALL lmp%gather_impropers(impropers)
   impropers_array(1:5,1:SIZE(impropers)/5) => impropers
   count = 0

From b225c94f5964f51e7220f8542666a8d8e8146718 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 12:12:04 -0400
Subject: [PATCH 263/396] remove variable shadowing instance in base class

---
 src/KOKKOS/pppm_kokkos.h | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h
index 50b5ac0f35..2c6dcc4e15 100644
--- a/src/KOKKOS/pppm_kokkos.h
+++ b/src/KOKKOS/pppm_kokkos.h
@@ -430,7 +430,6 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT {
 
   // triclinic
 
-  int triclinic;               // domain settings, orthog or triclinic
   void setup_triclinic();
   void compute_gf_ik_triclinic();
   void poisson_ik_triclinic();

From 8a738fabcb073ab9a0a7a0709be91079bb983e9d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 12:12:18 -0400
Subject: [PATCH 264/396] must initialized triclinic variable in constructor

---
 src/KSPACE/pppm_disp.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index ffa34a7e14..78ebad512a 100644
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -110,6 +110,7 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp) : KSpace(lmp),
 {
   triclinic_support = 0;
   pppmflag = dispersionflag = 1;
+  triclinic = domain->triclinic;
 
   nfactors = 3;
   factors = new int[nfactors];

From 0cd566a4179d123a98b288ec3c270725fc87477c Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Wed, 14 Jun 2023 10:43:30 -0600
Subject: [PATCH 265/396] Fix compile error for HIP

---
 src/KOKKOS/pair_eam_alloy_kokkos.cpp | 53 +++++++++++++++-------------
 src/KOKKOS/pair_eam_alloy_kokkos.h   |  4 +--
 src/KOKKOS/pair_eam_fs_kokkos.cpp    | 51 ++++++++++++++------------
 src/KOKKOS/pair_eam_fs_kokkos.h      |  4 +--
 src/KOKKOS/pair_eam_kokkos.cpp       | 51 ++++++++++++++------------
 src/KOKKOS/pair_eam_kokkos.h         |  4 +--
 6 files changed, 91 insertions(+), 76 deletions(-)

diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index f97af7bce2..2b81e21e2b 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -193,7 +193,7 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
              *this,ev);
     else
       Kokkos::parallel_for(
-            policyInstance<TagPairEAMAlloyKernelAB<0>>(inum),
+            policyInstance<TagPairEAMAlloyKernelAB<0>>::get(inum),
             *this);
   }
 
@@ -246,31 +246,31 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     if (neighflag == HALF) {
       if (newton_pair) {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMAlloyKernelC<HALF,1,0>>(inum),
+              policyInstance<TagPairEAMAlloyKernelC<HALF,1,0>>::get(inum),
               *this);
       } else {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMAlloyKernelC<HALF,0,0>>(inum),
+              policyInstance<TagPairEAMAlloyKernelC<HALF,0,0>>::get(inum),
               *this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMAlloyKernelC<HALFTHREAD,1,0>>(inum),
+              policyInstance<TagPairEAMAlloyKernelC<HALFTHREAD,1,0>>::get(inum),
               *this);
       } else {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMAlloyKernelC<HALFTHREAD,0,0>>(inum),
+              policyInstance<TagPairEAMAlloyKernelC<HALFTHREAD,0,0>>::get(inum),
               *this);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMAlloyKernelC<FULL,1,0>>(inum),
+              policyInstance<TagPairEAMAlloyKernelC<FULL,1,0>>::get(inum),
               *this);
       } else {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMAlloyKernelC<FULL,0,0>>(inum),
+              policyInstance<TagPairEAMAlloyKernelC<FULL,0,0>>::get(inum),
               *this);
       }
     }
@@ -655,7 +655,7 @@ void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelB<EFLAG>, c
 ////Specialisation for Neighborlist types Half, HalfThread, Full
 template<class DeviceType>
 template<int EFLAG>
-
+KOKKOS_INLINE_FUNCTION
 void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelAB<EFLAG>, const int &ii, EV_FLOAT& ev) const {
 
   // rho = density at each atom
@@ -1474,27 +1474,32 @@ void PairEAMAlloyKokkos<DeviceType>::file2array_alloy()
 
 /* ---------------------------------------------------------------------- */
 
-template<class DeviceType>
-template<class tag>
-auto PairEAMAlloyKokkos<DeviceType>::policyInstance(int inum) {
-  #ifdef KOKKOS_ENABLE_HIP
-    if (execution_space != Host) {
+template<typename DeviceType>
+template<class TAG>
+struct PairEAMAlloyKokkos<DeviceType>::policyInstance {
+  KOKKOS_INLINE_FUNCTION
+  static auto get(int inum) {
+    auto policy = Kokkos::RangePolicy<DeviceType, TAG>(0,inum);
+    return policy;
+  }
+};
+
+#ifdef KOKKOS_ENABLE_HIP
+template<>
+template<class TAG>
+struct PairEAMAlloyKokkos<Kokkos::Experimental::HIP>::policyInstance {
+  KOKKOS_INLINE_FUNCTION
+  static auto get(int inum) {
     static_assert(t_ffloat_2d_n7::static_extent(2) == 7,
                   "Breaking assumption of spline dim for KernelAB and KernelC scratch caching");
 
-    auto policy = Kokkos::TeamPolicy<DeviceType,tag>((inum+1023)/1024, 1024)
+    auto policy = Kokkos::TeamPolicy<Kokkos::Experimental::HIP,TAG>((inum+1023)/1024, 1024)
                            .set_scratch_size(0,
-                                Kokkos::PerTeam(MAX_CACHE_ROWS*t_ffloat_2d_n7::static_extent(2)*sizeof(double)));
+                                Kokkos::PerTeam(MAX_CACHE_ROWS*7*sizeof(double)));
     return policy;
-    } else {
-      auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
-      return policy;
-    }
-  #else
-    auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
-    return policy;
-  #endif
-}
+  }
+};
+#endif
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h
index f9703ef473..2eb40189ac 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.h
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.h
@@ -183,8 +183,8 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
   void array2spline() override;
   void read_file(char *) override;
 
-  template<class tag>
-  auto policyInstance(int inum);
+  template<class TAG>
+  struct policyInstance;
 
   typename AT::t_neighbors_2d d_neighbors;
   typename AT::t_int_1d d_ilist;
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index a437527584..4572d14e48 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -193,7 +193,7 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
              *this,ev);
     else
       Kokkos::parallel_for(
-            policyInstance<TagPairEAMFSKernelAB<0>>(inum),
+            policyInstance<TagPairEAMFSKernelAB<0>>::get(inum),
             *this);
   }
 
@@ -246,31 +246,31 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     if (neighflag == HALF) {
       if (newton_pair) {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMFSKernelC<HALF,1,0>>(inum),
+              policyInstance<TagPairEAMFSKernelC<HALF,1,0>>::get(inum),
               *this);
       } else {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMFSKernelC<HALF,0,0>>(inum),
+              policyInstance<TagPairEAMFSKernelC<HALF,0,0>>::get(inum),
               *this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMFSKernelC<HALFTHREAD,1,0>>(inum),
+              policyInstance<TagPairEAMFSKernelC<HALFTHREAD,1,0>>::get(inum),
               *this);
       } else {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMFSKernelC<HALFTHREAD,0,0>>(inum),
+              policyInstance<TagPairEAMFSKernelC<HALFTHREAD,0,0>>::get(inum),
               *this);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMFSKernelC<FULL,1,0>>(inum),
+              policyInstance<TagPairEAMFSKernelC<FULL,1,0>>::get(inum),
               *this);
       } else {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMFSKernelC<FULL,0,0>>(inum),
+              policyInstance<TagPairEAMFSKernelC<FULL,0,0>>::get(inum),
               *this);
       }
     }
@@ -1484,27 +1484,32 @@ void PairEAMFSKokkos<DeviceType>::file2array_fs()
 
 /* ---------------------------------------------------------------------- */
 
-template<class DeviceType>
-template<class tag>
-auto PairEAMFSKokkos<DeviceType>::policyInstance(int inum) {
-  #ifdef KOKKOS_ENABLE_HIP
-    if (execution_space != Host) {
+template<typename DeviceType>
+template<class TAG>
+struct PairEAMFSKokkos<DeviceType>::policyInstance {
+  KOKKOS_INLINE_FUNCTION
+  static auto get(int inum) {
+    auto policy = Kokkos::RangePolicy<DeviceType, TAG>(0,inum);
+    return policy;
+  }
+};
+
+#ifdef KOKKOS_ENABLE_HIP
+template<>
+template<class TAG>
+struct PairEAMFSKokkos<Kokkos::Experimental::HIP>::policyInstance {
+  KOKKOS_INLINE_FUNCTION
+  static auto get(int inum) {
     static_assert(t_ffloat_2d_n7::static_extent(2) == 7,
                   "Breaking assumption of spline dim for KernelAB and KernelC scratch caching");
 
-    auto policy = Kokkos::TeamPolicy<DeviceType,tag>((inum+1023)/1024, 1024)
+    auto policy = Kokkos::TeamPolicy<Kokkos::Experimental::HIP,TAG>((inum+1023)/1024, 1024)
                            .set_scratch_size(0,
-                                Kokkos::PerTeam(MAX_CACHE_ROWS*t_ffloat_2d_n7::static_extent(2)*sizeof(double)));
+                                Kokkos::PerTeam(MAX_CACHE_ROWS*7*sizeof(double)));
     return policy;
-    } else {
-      auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
-      return policy;
-    }
-  #else
-    auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
-    return policy;
-  #endif
-}
+  }
+};
+#endif
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h
index f7513b3008..bd03ab0015 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.h
+++ b/src/KOKKOS/pair_eam_fs_kokkos.h
@@ -183,8 +183,8 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
   void array2spline() override;
   void read_file(char *) override;
 
-  template<class tag>
-  auto policyInstance(int inum);
+  template<class TAG>
+  struct policyInstance;
 
   typename AT::t_neighbors_2d d_neighbors;
   typename AT::t_int_1d d_ilist;
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 5e2ea4357f..de6d3646bf 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -188,7 +188,7 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
              *this,ev);
     else
       Kokkos::parallel_for(
-            policyInstance<TagPairEAMKernelAB<0>>(inum),
+            policyInstance<TagPairEAMKernelAB<0>>::get(inum),
             *this);
   }
 
@@ -241,31 +241,31 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
     if (neighflag == HALF) {
       if (newton_pair) {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMKernelC<HALF,1,0>>(inum),
+              policyInstance<TagPairEAMKernelC<HALF,1,0>>::get(inum),
               *this);
       } else {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMKernelC<HALF,0,0>>(inum),
+              policyInstance<TagPairEAMKernelC<HALF,0,0>>::get(inum),
               *this);
       }
     } else if (neighflag == HALFTHREAD) {
       if (newton_pair) {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMKernelC<HALFTHREAD,1,0>>(inum),
+              policyInstance<TagPairEAMKernelC<HALFTHREAD,1,0>>::get(inum),
               *this);
       } else {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMKernelC<HALFTHREAD,0,0>>(inum),
+              policyInstance<TagPairEAMKernelC<HALFTHREAD,0,0>>::get(inum),
               *this);
       }
     } else if (neighflag == FULL) {
       if (newton_pair) {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMKernelC<FULL,1,0>>(inum),
+              policyInstance<TagPairEAMKernelC<FULL,1,0>>::get(inum),
               *this);
       } else {
         Kokkos::parallel_for(
-              policyInstance<TagPairEAMKernelC<FULL,0,0>>(inum),
+              policyInstance<TagPairEAMKernelC<FULL,0,0>>::get(inum),
               *this);
       }
     }
@@ -1159,27 +1159,32 @@ void PairEAMKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &
 
 /* ---------------------------------------------------------------------- */
 
-template<class DeviceType>
-template<class tag>
-auto PairEAMKokkos<DeviceType>::policyInstance(int inum) {
-  #ifdef KOKKOS_ENABLE_HIP
-    if (execution_space != Host) {
+template<typename DeviceType>
+template<class TAG>
+struct PairEAMKokkos<DeviceType>::policyInstance {
+  KOKKOS_INLINE_FUNCTION
+  static auto get(int inum) {
+    auto policy = Kokkos::RangePolicy<DeviceType, TAG>(0,inum);
+    return policy;
+  }
+};
+
+#ifdef KOKKOS_ENABLE_HIP
+template<>
+template<class TAG>
+struct PairEAMKokkos<Kokkos::Experimental::HIP>::policyInstance {
+  KOKKOS_INLINE_FUNCTION
+  static auto get(int inum) {
     static_assert(t_ffloat_2d_n7::static_extent(2) == 7,
                   "Breaking assumption of spline dim for KernelAB and KernelC scratch caching");
 
-    auto policy = Kokkos::TeamPolicy<DeviceType,tag>((inum+1023)/1024, 1024)
+    auto policy = Kokkos::TeamPolicy<Kokkos::Experimental::HIP,TAG>((inum+1023)/1024, 1024)
                            .set_scratch_size(0,
-                                Kokkos::PerTeam(MAX_CACHE_ROWS*t_ffloat_2d_n7::static_extent(2)*sizeof(double)));
+                                Kokkos::PerTeam(MAX_CACHE_ROWS*7*sizeof(double)));
     return policy;
-    } else {
-      auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
-      return policy;
-    }
-  #else
-    auto policy = Kokkos::RangePolicy<DeviceType, tag>(0,inum);
-    return policy;
-  #endif
-}
+  }
+};
+#endif
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index 41e02e68cc..d9765b37c0 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -179,8 +179,8 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
   void file2array() override;
   void array2spline() override;
 
-  template<class tag>
-  auto policyInstance(int inum);
+  template<class TAG>
+  struct policyInstance;
 
   typename AT::t_neighbors_2d d_neighbors;
   typename AT::t_int_1d d_ilist;

From 0564d795700e92d527d3ce034c09071d19a57320 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Wed, 14 Jun 2023 10:52:47 -0600
Subject: [PATCH 266/396] Fix SYCL compile error with GNU make, see
 https://github.com/kokkos/kokkos/pull/6218

---
 lib/kokkos/Makefile.kokkos | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos
index 361995d847..adcee303ba 100644
--- a/lib/kokkos/Makefile.kokkos
+++ b/lib/kokkos/Makefile.kokkos
@@ -1376,6 +1376,7 @@ ifneq ($(KOKKOS_INTERNAL_NEW_CONFIG), 0)
   ifeq ($(KOKKOS_INTERNAL_USE_SYCL), 1)
     tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_SYCL.hpp>","KokkosCore_Config_FwdBackend.hpp")
     tmp := $(call kokkos_append_config_header,"$H""include <decl/Kokkos_Declare_SYCL.hpp>","KokkosCore_Config_DeclareBackend.hpp")
+    tmp := $(call kokkos_append_config_header,"$H""include <setup/Kokkos_Setup_SYCL.hpp>","KokkosCore_Config_SetupBackend.hpp")
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
     tmp := $(call kokkos_append_config_header,"$H""include <fwd/Kokkos_Fwd_HIP.hpp>","KokkosCore_Config_FwdBackend.hpp")

From c83dc1ff305f950cbc60c72c89b3cc6c85a5fd9f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 13:52:54 -0400
Subject: [PATCH 267/396] fix STORE global -> fix STORE/GLOBAL

---
 src/EXTRA-FIX/fix_npt_cauchy.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/EXTRA-FIX/fix_npt_cauchy.cpp b/src/EXTRA-FIX/fix_npt_cauchy.cpp
index 380964f058..feb5a95c6f 100644
--- a/src/EXTRA-FIX/fix_npt_cauchy.cpp
+++ b/src/EXTRA-FIX/fix_npt_cauchy.cpp
@@ -2461,7 +2461,7 @@ void FixNPTCauchy::CauchyStat_init()
 
   if (!init_store)
     init_store = dynamic_cast<FixStoreGlobal *>(
-      modify->add_fix(std::string(id_store) + " all STORE global 1 6"));
+      modify->add_fix(std::string(id_store) + " all STORE/GLOBAL 1 6"));
 
   initRUN = 0;
   initPK = 1;

From 27908139aeb0509550cbc84b47913524bff7135e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 14:14:47 -0400
Subject: [PATCH 268/396] whitespace

---
 src/KOKKOS/pair_eam_kokkos.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index d9765b37c0..9d066d40a0 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -59,7 +59,7 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
   ~PairEAMKokkos() override;
   void compute(int, int) override;
   void init_style() override;
-  
+
 
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMPackForwardComm, const int&) const;

From 82f664acd4613e2b103eb0c648eb48391233bdc7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 14:43:29 -0400
Subject: [PATCH 269/396] update log files for BODY package styles

---
 examples/body/log.14Jun23.body.g++.1          | 180 ++++++++++++++
 examples/body/log.14Jun23.body.g++.4          | 180 ++++++++++++++
 ...18.cubes.g++.1 => log.14Jun23.cubes.g++.1} |  70 +++---
 ...18.cubes.g++.4 => log.14Jun23.cubes.g++.4} |  72 +++---
 examples/body/log.14Jun23.pour3d.g++.1        | 148 +++++++++++
 examples/body/log.14Jun23.pour3d.g++.4        | 148 +++++++++++
 examples/body/log.14Jun23.squares.g++.1       | 226 +++++++++++++++++
 examples/body/log.14Jun23.squares.g++.4       | 226 +++++++++++++++++
 examples/body/log.14Jun23.wall2d.g++.1        | 229 ++++++++++++++++++
 examples/body/log.14Jun23.wall2d.g++.4        | 229 ++++++++++++++++++
 examples/body/log.27Nov18.body.g++.1          | 177 --------------
 examples/body/log.27Nov18.body.g++.4          | 177 --------------
 examples/body/log.27Nov18.pour3d.g++.1        |  74 ------
 examples/body/log.27Nov18.pour3d.g++.4        |  74 ------
 examples/body/log.27Nov18.squares.g++.1       | 222 -----------------
 examples/body/log.27Nov18.squares.g++.4       | 222 -----------------
 examples/body/log.27Nov18.wall2d.g++.1        | 224 -----------------
 examples/body/log.27Nov18.wall2d.g++.4        | 224 -----------------
 18 files changed, 1641 insertions(+), 1461 deletions(-)
 create mode 100644 examples/body/log.14Jun23.body.g++.1
 create mode 100644 examples/body/log.14Jun23.body.g++.4
 rename examples/body/{log.27Nov18.cubes.g++.1 => log.14Jun23.cubes.g++.1} (52%)
 rename examples/body/{log.27Nov18.cubes.g++.4 => log.14Jun23.cubes.g++.4} (50%)
 create mode 100644 examples/body/log.14Jun23.pour3d.g++.1
 create mode 100644 examples/body/log.14Jun23.pour3d.g++.4
 create mode 100644 examples/body/log.14Jun23.squares.g++.1
 create mode 100644 examples/body/log.14Jun23.squares.g++.4
 create mode 100644 examples/body/log.14Jun23.wall2d.g++.1
 create mode 100644 examples/body/log.14Jun23.wall2d.g++.4
 delete mode 100644 examples/body/log.27Nov18.body.g++.1
 delete mode 100644 examples/body/log.27Nov18.body.g++.4
 delete mode 100644 examples/body/log.27Nov18.pour3d.g++.1
 delete mode 100644 examples/body/log.27Nov18.pour3d.g++.4
 delete mode 100644 examples/body/log.27Nov18.squares.g++.1
 delete mode 100644 examples/body/log.27Nov18.squares.g++.4
 delete mode 100644 examples/body/log.27Nov18.wall2d.g++.1
 delete mode 100644 examples/body/log.27Nov18.wall2d.g++.4

diff --git a/examples/body/log.14Jun23.body.g++.1 b/examples/body/log.14Jun23.body.g++.1
new file mode 100644
index 0000000000..e016e88b0b
--- /dev/null
+++ b/examples/body/log.14Jun23.body.g++.1
@@ -0,0 +1,180 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+# 2d polygon nparticle bodies
+
+units		lj
+dimension       2
+atom_style	body nparticle 2 6
+
+read_data       data.body
+Reading data file ...
+  orthogonal box = (-15.532225 -15.532225 -0.5) to (15.532225 15.532225 0.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  100 atoms
+  100 bodies
+  read_data CPU = 0.002 seconds
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	body/nparticle 5.0
+pair_coeff	* * 1.0 1.0
+
+neighbor	0.5 bin
+neigh_modify    every 1 delay 0 check yes
+
+fix		1 all nve/body
+#fix		1 all nvt/body temp 1.44 1.44 1.0
+fix		2 all enforce2d
+
+#compute         1 all body/local type 1 2 3
+#dump            1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
+
+#dump		2 all image 1000 image.*.jpg type type #		zoom 1.6 adiam 1.5 body type 1.0 0
+#dump_modify    2 pad 5
+
+thermo          100
+run		10000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.5
+  ghost atom cutoff = 5.5
+  binsize = 2.75, bins = 12 12 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair body/nparticle, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.279 | 5.279 | 5.279 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.44          -0.63799525     0              0.78760475    -0.15028724   
+       100   1.6423694     -1.0001516      0              0.62579417     0.16116443   
+       200   1.4802187     -1.2479519      0              0.21746458     0.35445329   
+       300   1.4734223     -1.3213583      0              0.1373298      0.45266192   
+       400   1.5118818     -1.5924889      0             -0.095725867    0.13296961   
+       500   1.5471951     -1.630886       0             -0.099162814    0.12439793   
+       600   1.6264248     -1.6468162      0             -0.03665568     0.43392484   
+       700   1.597475      -1.6539821      0             -0.072481849    0.13128147   
+       800   1.6841531     -1.775776       0             -0.10846445    -0.032960346  
+       900   1.556262      -1.6750139      0             -0.1343146      0.53484605   
+      1000   1.6272373     -1.7572956      0             -0.14633067     0.18431831   
+      1100   1.6448235     -1.7176556      0             -0.089280316    0.25900065   
+      1200   1.5486928     -1.6481004      0             -0.11489454     0.036934194  
+      1300   1.7449183     -1.6039068      0              0.12356231    -0.071099427  
+      1400   1.668581      -1.5939776      0              0.057917584    0.02239666   
+      1500   1.6514223     -1.7086624      0             -0.073754397    0.39021328   
+      1600   1.8367415     -1.808017       0              0.010357066    0.1405097    
+      1700   1.6439993     -1.7711084      0             -0.14354908     0.37488252   
+      1800   1.8105437     -1.7312044      0              0.061233893    0.033817829  
+      1900   1.7745557     -1.7184539      0              0.038356243    0.26826112   
+      2000   1.4919032     -1.7635799      0             -0.28659575     0.32901186   
+      2100   1.5086111     -1.5151192      0             -0.021594146    0.37082072   
+      2200   1.4464813     -1.5702682      0             -0.13825163    -0.043079808  
+      2300   1.398236      -1.5359564      0             -0.15170277     0.14467017   
+      2400   1.5050139     -1.6002694      0             -0.11030569     0.30358205   
+      2500   1.5549789     -1.652805       0             -0.11337589     0.2916046    
+      2600   1.4774593     -1.5406116      0             -0.077926888    0.020921323  
+      2700   1.3700851     -1.5855698      0             -0.22918557     0.22226615   
+      2800   1.4656869     -1.629742       0             -0.17871195    -0.0090503155 
+      2900   1.4355808     -1.6486992      0             -0.22747424     0.12741636   
+      3000   1.5859288     -1.5467092      0              0.023360382    0.23081334   
+      3100   1.6099287     -1.4917881      0              0.10204129     0.22085916   
+      3200   1.6814814     -1.554998       0              0.10966853     0.10312492   
+      3300   1.5319494     -1.4723195      0              0.044310484    0.18583117   
+      3400   1.5124418     -1.499312       0             -0.0019945387   0.15564425   
+      3500   1.6106798     -1.5568215      0              0.037751529    0.27433785   
+      3600   1.460087      -1.5530078      0             -0.10752165     0.0073889211 
+      3700   1.5744452     -1.5720821      0             -0.013381308    0.27735962   
+      3800   1.7290106     -1.6504739      0              0.061246632    0.48173619   
+      3900   1.611197      -1.6452216      0             -0.05013663     0.4286963    
+      4000   1.6715425     -1.6409258      0              0.013901267    0.017020657  
+      4100   1.6913694     -1.5885259      0              0.085929717    0.13679669   
+      4200   1.5347633     -1.6316222      0             -0.11220653     0.024396005  
+      4300   1.5221369     -1.5924627      0             -0.085547139    0.29634927   
+      4400   1.7020273     -1.7069204      0             -0.021913362    0.12700619   
+      4500   1.7176336     -1.7439335      0             -0.043476251    0.14745343   
+      4600   1.4409943     -1.6121558      0             -0.18557152     0.018887675  
+      4700   1.7868207     -1.6707762      0              0.098176247    0.20004565   
+      4800   1.8720226     -1.7000206      0              0.15328178     0.25661867   
+      4900   1.7128343     -1.7289913      0             -0.033285317    0.24698662   
+      5000   1.7242114     -1.6662075      0              0.040761785    0.18935677   
+      5100   1.7589418     -1.7267393      0              0.014613086    0.40918365   
+      5200   1.7138074     -1.778402       0             -0.081732715    0.39679805   
+      5300   1.8149032     -1.7708654      0              0.025888786    0.29874434   
+      5400   1.7140097     -1.6444743      0              0.052395323    0.62588743   
+      5500   1.8076873     -1.7276245      0              0.061985946    0.25434646   
+      5600   1.7137948     -1.678778       0              0.017878859    0.21062182   
+      5700   1.8625614     -1.7114074      0              0.1325284      0.14365823   
+      5800   1.667941      -1.6462142      0              0.0050473638   0.36134037   
+      5900   1.7080521     -1.6919526      0             -0.00098107526  0.27472252   
+      6000   1.7180315     -1.6677683      0              0.033082909    0.29905397   
+      6100   1.8264687     -1.6837934      0              0.12441065     0.033504487  
+      6200   1.757998      -1.634503       0              0.10591508     0.14360478   
+      6300   1.6444838     -1.5734502      0              0.05458881     0.50314779   
+      6400   1.7213235     -1.705482       0             -0.0013717454  -0.063375271  
+      6500   1.5454026     -1.7236013      0             -0.19365272     0.21355367   
+      6600   1.7550617     -1.7304462      0              0.0070648556   0.1782743    
+      6700   1.6931304     -1.7005361      0             -0.024337029    0.31165135   
+      6800   1.7953505     -1.7377126      0              0.039684354    0.27052592   
+      6900   1.6547086     -1.6971987      0             -0.059037125    0.26390513   
+      7000   1.678321      -1.6343689      0              0.027168906    0.23632145   
+      7100   1.6389472     -1.690589       0             -0.068031265    0.26471258   
+      7200   1.6772509     -1.7305397      0             -0.070061301    0.16013956   
+      7300   1.7401473     -1.7461921      0             -0.023446315    0.14462402   
+      7400   1.7381776     -1.6586839      0              0.06211186     0.47746891   
+      7500   1.7184021     -1.8309755      0             -0.1297574      0.27706616   
+      7600   1.8404039     -1.7957552      0              0.026244663    0.12898128   
+      7700   1.8474196     -1.7118818      0              0.11706359     0.1959609    
+      7800   1.7635506     -1.6119363      0              0.1339788      0.086260229  
+      7900   1.5873929     -1.5651473      0              0.0063716922   0.0010935251 
+      8000   1.6394989     -1.5900851      0              0.033018817    0.41301427   
+      8100   1.6731865     -1.6981463      0             -0.041691712    0.46624156   
+      8200   1.7728067     -1.7515658      0              0.0035128109   0.16520115   
+      8300   1.6142221     -1.8030321      0             -0.20495225     0.039485737  
+      8400   1.6775678     -1.8266472      0             -0.16585509     0.074514313  
+      8500   1.8399403     -1.8100014      0              0.011539538    0.38126754   
+      8600   1.8259529     -1.6641902      0              0.14350318     0.80219793   
+      8700   1.8454807     -1.68448        0              0.14254593     0.18855669   
+      8800   1.7017088     -1.7219601      0             -0.037268433    0.36465692   
+      8900   1.612135      -1.5813013      0              0.014712431    0.21657263   
+      9000   1.5992353     -1.7093785      0             -0.12613559     0.038933966  
+      9100   1.7486466     -1.7024749      0              0.028685202    0.28688996   
+      9200   1.546781      -1.6512407      0             -0.1199275      0.16188207   
+      9300   1.8424683     -1.7304781      0              0.093565478    0.35295164   
+      9400   1.7646311     -1.7795324      0             -0.032547636    0.39114207   
+      9500   1.8061763     -1.8458669      0             -0.057752329    0.18930255   
+      9600   1.6953348     -1.7144901      0             -0.036108734    0.18392219   
+      9700   1.693168      -1.5860306      0              0.090205689    0.18749665   
+      9800   1.6057784     -1.6478049      0             -0.05808426     0.28339031   
+      9900   1.712654      -1.6566387      0              0.038888773    0.52108885   
+     10000   1.7102385     -1.6670768      0              0.026059337    0.073458218  
+Loop time of 1.09582 on 1 procs for 10000 steps with 100 atoms
+
+Performance: 3942257.351 tau/day, 9125.596 timesteps/s, 912.560 katom-step/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.95651    | 0.95651    | 0.95651    |   0.0 | 87.29
+Neigh   | 0.0064365  | 0.0064365  | 0.0064365  |   0.0 |  0.59
+Comm    | 0.015238   | 0.015238   | 0.015238   |   0.0 |  1.39
+Output  | 0.00059554 | 0.00059554 | 0.00059554 |   0.0 |  0.05
+Modify  | 0.10993    | 0.10993    | 0.10993    |   0.0 | 10.03
+Other   |            | 0.007113   |            |       |  0.65
+
+Nlocal:            100 ave         100 max         100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             80 ave          80 max          80 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            448 ave         448 max         448 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 448
+Ave neighs/atom = 4.48
+Neighbor list builds = 463
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/body/log.14Jun23.body.g++.4 b/examples/body/log.14Jun23.body.g++.4
new file mode 100644
index 0000000000..54ae630872
--- /dev/null
+++ b/examples/body/log.14Jun23.body.g++.4
@@ -0,0 +1,180 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+# 2d polygon nparticle bodies
+
+units		lj
+dimension       2
+atom_style	body nparticle 2 6
+
+read_data       data.body
+Reading data file ...
+  orthogonal box = (-15.532225 -15.532225 -0.5) to (15.532225 15.532225 0.5)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  100 atoms
+  100 bodies
+  read_data CPU = 0.001 seconds
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	body/nparticle 5.0
+pair_coeff	* * 1.0 1.0
+
+neighbor	0.5 bin
+neigh_modify    every 1 delay 0 check yes
+
+fix		1 all nve/body
+#fix		1 all nvt/body temp 1.44 1.44 1.0
+fix		2 all enforce2d
+
+#compute         1 all body/local type 1 2 3
+#dump            1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
+
+#dump		2 all image 1000 image.*.jpg type type #		zoom 1.6 adiam 1.5 body type 1.0 0
+#dump_modify    2 pad 5
+
+thermo          100
+run		10000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.5
+  ghost atom cutoff = 5.5
+  binsize = 2.75, bins = 12 12 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair body/nparticle, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.268 | 5.268 | 5.268 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   1.44          -0.63799525     0              0.78760475    -0.15028724   
+       100   1.6423663     -1.000111       0              0.62583161     0.16116978   
+       200   1.4802732     -1.2478364      0              0.21763407     0.35464152   
+       300   1.4735433     -1.3211072      0              0.13770068     0.45307413   
+       400   1.5119491     -1.5930779      0             -0.096248286    0.13119532   
+       500   1.5449834     -1.6300143      0             -0.10048065     0.12635421   
+       600   1.621105      -1.6459036      0             -0.041009639    0.43837884   
+       700   1.5959719     -1.6348501      0             -0.054837867    0.13233006   
+       800   1.6862723     -1.6902254      0             -0.020815854    0.20072937   
+       900   1.6771131     -1.6544493      0              0.0058926625   0.34898089   
+      1000   1.5867        -1.6797024      0             -0.10886943     0.33511593   
+      1100   1.7842277     -1.6814985      0              0.084886913    0.23634574   
+      1200   1.7089241     -1.6766866      0              0.015148192    0.40440454   
+      1300   1.6195529     -1.6078381      0             -0.004480726    0.12193834   
+      1400   1.5967912     -1.563198       0              0.017625291    0.2233618    
+      1500   1.6131091     -1.5731367      0              0.023841282    0.13856054   
+      1600   1.6096972     -1.5741595      0              0.01944073     0.096081201  
+      1700   1.6099281     -1.5875363      0              0.0062924683   0.28628509   
+      1800   1.7328539     -1.5696894      0              0.14583598     0.2202503    
+      1900   1.6433157     -1.6659757      0             -0.039093124    0.12006746   
+      2000   1.8262234     -1.778379       0              0.029582122    0.17815935   
+      2100   1.7441298     -1.704871       0              0.021817442    0.30772022   
+      2200   1.7933363     -1.7246149      0              0.050788098    0.11323852   
+      2300   1.7458809     -1.7186101      0              0.0098120012   0.0034260299 
+      2400   1.8202324     -1.7777769      0              0.024253178    0.089077551  
+      2500   1.691512      -1.6976236      0             -0.023026761    0.23901369   
+      2600   1.6221153     -1.639172       0             -0.033277785    0.36881214   
+      2700   1.5532388     -1.7286197      0             -0.19091334     0.1714534    
+      2800   1.6648128     -1.7298542      0             -0.081689467    0.0077427265 
+      2900   1.6548465     -1.7126766      0             -0.074378524    0.096972027  
+      3000   1.604345      -1.7210036      0             -0.13270205     0.25227471   
+      3100   1.67823       -1.6537385      0              0.0077092269   0.13198555   
+      3200   1.4695581     -1.5609142      0             -0.10605159     0.28909806   
+      3300   1.6778332     -1.7396206      0             -0.078565681    0.25069132   
+      3400   1.7588934     -1.680043       0              0.061261505    0.28609454   
+      3500   1.6699117     -1.7762865      0             -0.12307397     0.2584648    
+      3600   1.5951406     -1.6611845      0             -0.081995282    0.35801267   
+      3700   1.5267137     -1.6371603      0             -0.12571366     0.6116418    
+      3800   1.6792717     -1.638182       0              0.024296953    0.43447072   
+      3900   1.5857658     -1.6607833      0             -0.09087513     0.19479457   
+      4000   1.6062152     -1.5436014      0              0.046551586    0.55118141   
+      4100   1.5505892     -1.5259333      0              0.0091500726   0.49075107   
+      4200   1.6933        -1.6314975      0              0.044869524    0.032970187  
+      4300   1.6498743     -1.7298746      0             -0.096499053    0.14837573   
+      4400   1.6535324     -1.7095911      0             -0.072593998    0.24207879   
+      4500   1.835466      -1.7677327      0              0.049378652    0.18168744   
+      4600   1.7346556     -1.6379956      0              0.07931344     0.49973778   
+      4700   1.8050359     -1.8354358      0             -0.048450223   -0.037354111  
+      4800   1.6361661     -1.7741414      0             -0.15433697     0.36409064   
+      4900   1.6511224     -1.7703808      0             -0.13576956     0.23794467   
+      5000   1.6249047     -1.6516641      0             -0.043008453    0.15155643   
+      5100   1.6842561     -1.7128485      0             -0.045434914    0.30999124   
+      5200   1.6153583     -1.630441       0             -0.031236245   -0.0083460068 
+      5300   1.6806066     -1.6907533      0             -0.026952801    0.16886559   
+      5400   1.7541932     -1.7161908      0              0.020460503    0.16560614   
+      5500   1.8643473     -1.7810235      0              0.064680293    0.061200837  
+      5600   1.5963536     -1.6145484      0             -0.034158307    0.47888104   
+      5700   1.7385482     -1.7214092      0             -0.00024648083  0.22078849   
+      5800   1.6726308     -1.6987799      0             -0.042875376    0.46131938   
+      5900   1.7830081     -1.7766484      0             -0.011470422    0.12597212   
+      6000   1.9057941     -1.719849       0              0.16688715     0.37367068   
+      6100   1.6882353     -1.6888488      0             -0.0174959      0.33635307   
+      6200   1.8644261     -1.7435021      0              0.10227973     0.54157135   
+      6300   1.8043895     -1.8169618      0             -0.030616242    0.20596562   
+      6400   1.8745855     -1.7752732      0              0.080566434    0.18365661   
+      6500   1.8330698     -1.6984304      0              0.11630864     0.058109254  
+      6600   1.8006644     -1.7398524      0              0.042805376    0.17509961   
+      6700   1.7471279     -1.7009995      0              0.0286571      0.13439557   
+      6800   1.7077006     -1.7462928      0             -0.055669263    0.16474264   
+      6900   1.7602738     -1.8336138      0             -0.090942793    0.37533762   
+      7000   1.6962037     -1.7746381      0             -0.095396485    0.28764793   
+      7100   1.6040275     -1.652448       0             -0.064460796    0.47621288   
+      7200   1.7595892     -1.6260406      0              0.11595278     0.55174207   
+      7300   1.8031743     -1.7436876      0              0.041454978    0.35699364   
+      7400   1.6575485     -1.5994276      0              0.041545422    0.38389368   
+      7500   1.8539985     -1.6888181      0              0.14664046     0.25524239   
+      7600   1.6721617     -1.6819419      0             -0.026501825    0.18077253   
+      7700   1.4696976     -1.5368001      0             -0.081799475    0.37392274   
+      7800   1.6532125     -1.6604679      0             -0.023787555    0.25683053   
+      7900   1.5890818     -1.711541       0             -0.13834993     0.28943398   
+      8000   1.6729844     -1.674981       0             -0.01872644     0.1725141    
+      8100   1.6041427     -1.7188678      0             -0.13076654     0.22948004   
+      8200   1.7000012     -1.5584259      0              0.12457532     0.82913741   
+      8300   1.6662649     -1.8411986      0             -0.19159634     0.40893581   
+      8400   1.6031593     -1.8225478      0             -0.23542004     0.21287004   
+      8500   1.6615542     -1.685667       0             -0.040728376    0.40063656   
+      8600   1.6094262     -1.7942547      0             -0.20092282     0.28738874   
+      8700   1.6040855     -1.6483081      0             -0.060263486    0.22614876   
+      8800   1.6658931     -1.6751256      0             -0.025891437    0.027723314  
+      8900   1.7989105     -1.7318497      0              0.049071648    0.27645866   
+      9000   1.8242262     -1.6879124      0              0.11807158     0.21701732   
+      9100   1.6795701     -1.6926952      0             -0.029920813    0.28702517   
+      9200   1.8093352     -1.8430841      0             -0.051842329    0.04182244   
+      9300   1.7654746     -1.7580453      0             -0.010225436    0.41460279   
+      9400   1.9494599     -1.7162713      0              0.21369396     0.22445951   
+      9500   1.8650839     -1.6517629      0              0.19467014     0.34042974   
+      9600   1.8080088     -1.651068       0              0.13886064     0.38597156   
+      9700   1.757349      -1.6397227      0              0.10005277     0.12075072   
+      9800   1.8111959     -1.7155458      0              0.077538075    0.023545696  
+      9900   1.7255423     -1.7364511      0             -0.02816423     0.24284116   
+     10000   1.794001      -1.7545014      0              0.021559597    0.15092078   
+Loop time of 0.461554 on 4 procs for 10000 steps with 100 atoms
+
+Performance: 9359693.727 tau/day, 21665.958 timesteps/s, 2.167 Matom-step/s
+93.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.21335    | 0.24947    | 0.30554    |   7.2 | 54.05
+Neigh   | 0.0016861  | 0.0018238  | 0.0019357  |   0.2 |  0.40
+Comm    | 0.078727   | 0.14542    | 0.19247    |  10.9 | 31.51
+Output  | 0.00086191 | 0.0026451  | 0.0079866  |   6.0 |  0.57
+Modify  | 0.028228   | 0.029642   | 0.030811   |   0.5 |  6.42
+Other   |            | 0.03255    |            |       |  7.05
+
+Nlocal:             25 ave          28 max          21 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost:           47.5 ave          50 max          46 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Neighs:         117.25 ave         144 max          91 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 469
+Ave neighs/atom = 4.69
+Neighbor list builds = 494
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/body/log.27Nov18.cubes.g++.1 b/examples/body/log.14Jun23.cubes.g++.1
similarity index 52%
rename from examples/body/log.27Nov18.cubes.g++.1
rename to examples/body/log.14Jun23.cubes.g++.1
index 588f95f69d..4010d1013b 100644
--- a/examples/body/log.27Nov18.cubes.g++.1
+++ b/examples/body/log.14Jun23.cubes.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (28 Mar 2023 - Development)
   using 1 OpenMP thread(s) per MPI task
 # 3d rounded cubes
 
@@ -11,20 +11,23 @@ dimension   3
 atom_style  body rounded/polyhedron 1 10
 
 read_data   data.cubes
+Reading data file ...
   orthogonal box = (0 0 0) to (6 6 6)
   1 by 1 by 1 MPI processor grid
   reading atoms ...
   2 atoms
   2 bodies
+  read_data CPU = 0.001 seconds
 
 replicate   $r $r $r
 replicate   3 $r $r
 replicate   3 3 $r
 replicate   3 3 3
+Replication is creating a 3x3x3 = 27 times larger system...
   orthogonal box = (0 0 0) to (18 18 18)
   1 by 1 by 1 MPI processor grid
   54 atoms
-  Time spent = 0.000426769 secs
+  replicate CPU = 0.001 seconds
 
 velocity    all create 1.2 187287 dist gaussian mom yes rot yes
 
@@ -71,56 +74,57 @@ thermo       1000
 
 run          ${steps}
 run          10000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 3.9641
-  ghost atom cutoff = 3.9641
-  binsize = 1.98205, bins = 10 10 10
+  master list distance cutoff = 3.9641016
+  ghost atom cutoff = 3.9641016
+  binsize = 1.9820508, bins = 10 10 10
   1 neighbor lists, perpetual/occasional/extra = 1 0 0
   (1) pair body/rounded/polyhedron, perpetual
       attributes: half, newton on
       pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
+      stencil: half/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.953 | 4.953 | 4.953 Mbytes
-Step KinEng PotEng TotEng c_p2 c_1_temp 
-       0    1.7666667            0    1.7666667   0.01090535   0.59439252 
-    1000    3.1462962   0.17392649    3.3202227   0.02361912    1.1654694 
-    2000    2.9311648   0.13836102    3.0695258  0.021748224    1.1950624 
-    3000     3.090491   0.16511199     3.255603  0.018691142      1.23672 
-    4000    2.7401565   0.17792155    2.9180781  0.015093853    1.1180839 
-    5000    3.0880849   0.17587085    3.2639557  0.030563042    1.2831154 
-    6000    3.2180776   0.19732251    3.4154001  0.028338151     1.258839 
-    7000    2.9514882   0.25088882     3.202377  0.025296925    1.1746326 
-    8000    3.0101226   0.28825968    3.2983823  0.027273454    1.2138056 
-    9000    3.0164253    0.1901733    3.2065986  0.033228915    1.3095914 
-   10000    2.3780401   0.34082434    2.7188644  0.031838531    1.0208679 
-Loop time of 51.5779 on 1 procs for 10000 steps with 54 atoms
+Per MPI rank memory allocation (min/avg/max) = 5.973 | 5.973 | 5.973 Mbytes
+   Step         KinEng         PotEng         TotEng          c_p2         c_1_temp   
+         0   1.7666667      0              1.7666667      0.01090535     0.59439252   
+      1000   3.1462962      0.17392649     3.3202227      0.02361912     1.1654694    
+      2000   2.9311648      0.13836102     3.0695258      0.021748224    1.1950624    
+      3000   3.090491       0.16511199     3.255603       0.018691142    1.23672      
+      4000   2.7401565      0.17792155     2.9180781      0.015093853    1.1180839    
+      5000   3.0880849      0.17587085     3.2639557      0.030563042    1.2831154    
+      6000   3.2180776      0.19732251     3.4154001      0.028338151    1.258839     
+      7000   2.9514882      0.25088882     3.202377       0.025296925    1.1746326    
+      8000   3.0101226      0.28825968     3.2983823      0.027273454    1.2138056    
+      9000   3.0164253      0.1901733      3.2065986      0.033228915    1.3095914    
+     10000   2.3780401      0.34082434     2.7188644      0.031838531    1.0208679    
+Loop time of 33.0201 on 1 procs for 10000 steps with 54 atoms
 
-Performance: 16751.376 tau/day, 193.882 timesteps/s
+Performance: 26165.890 tau/day, 302.846 timesteps/s, 16.354 katom-step/s
 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 51.377     | 51.377     | 51.377     |   0.0 | 99.61
-Neigh   | 0.0063686  | 0.0063686  | 0.0063686  |   0.0 |  0.01
-Comm    | 0.072127   | 0.072127   | 0.072127   |   0.0 |  0.14
-Output  | 0.0002768  | 0.0002768  | 0.0002768  |   0.0 |  0.00
-Modify  | 0.10849    | 0.10849    | 0.10849    |   0.0 |  0.21
-Other   |            | 0.01404    |            |       |  0.03
+Pair    | 32.897     | 32.897     | 32.897     |   0.0 | 99.63
+Neigh   | 0.0028124  | 0.0028124  | 0.0028124  |   0.0 |  0.01
+Comm    | 0.034404   | 0.034404   | 0.034404   |   0.0 |  0.10
+Output  | 0.00017643 | 0.00017643 | 0.00017643 |   0.0 |  0.00
+Modify  | 0.078202   | 0.078202   | 0.078202   |   0.0 |  0.24
+Other   |            | 0.00767    |            |       |  0.02
 
-Nlocal:    54 ave 54 max 54 min
+Nlocal:             54 ave          54 max          54 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    96 ave 96 max 96 min
+Nghost:             96 ave          96 max          96 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    100 ave 100 max 100 min
+Neighs:            100 ave         100 max         100 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 100
-Ave neighs/atom = 1.85185
+Ave neighs/atom = 1.8518519
 Neighbor list builds = 268
 Dangerous builds = 0
 
-Total wall time: 0:00:51
+Total wall time: 0:00:33
diff --git a/examples/body/log.27Nov18.cubes.g++.4 b/examples/body/log.14Jun23.cubes.g++.4
similarity index 50%
rename from examples/body/log.27Nov18.cubes.g++.4
rename to examples/body/log.14Jun23.cubes.g++.4
index f10a4c8a0a..1439af95a0 100644
--- a/examples/body/log.27Nov18.cubes.g++.4
+++ b/examples/body/log.14Jun23.cubes.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (28 Mar 2023 - Development)
   using 1 OpenMP thread(s) per MPI task
 # 3d rounded cubes
 
@@ -11,20 +11,23 @@ dimension   3
 atom_style  body rounded/polyhedron 1 10
 
 read_data   data.cubes
+Reading data file ...
   orthogonal box = (0 0 0) to (6 6 6)
   1 by 2 by 2 MPI processor grid
   reading atoms ...
   2 atoms
   2 bodies
+  read_data CPU = 0.001 seconds
 
 replicate   $r $r $r
 replicate   3 $r $r
 replicate   3 3 $r
 replicate   3 3 3
+Replication is creating a 3x3x3 = 27 times larger system...
   orthogonal box = (0 0 0) to (18 18 18)
   1 by 2 by 2 MPI processor grid
   54 atoms
-  Time spent = 0.000776052 secs
+  replicate CPU = 0.001 seconds
 
 velocity    all create 1.2 187287 dist gaussian mom yes rot yes
 
@@ -71,56 +74,57 @@ thermo       1000
 
 run          ${steps}
 run          10000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
+  update: every = 1 steps, delay = 0 steps, check = yes
   max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 3.9641
-  ghost atom cutoff = 3.9641
-  binsize = 1.98205, bins = 10 10 10
+  master list distance cutoff = 3.9641016
+  ghost atom cutoff = 3.9641016
+  binsize = 1.9820508, bins = 10 10 10
   1 neighbor lists, perpetual/occasional/extra = 1 0 0
   (1) pair body/rounded/polyhedron, perpetual
       attributes: half, newton on
       pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
+      stencil: half/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.879 | 5.068 | 5.256 Mbytes
-Step KinEng PotEng TotEng c_p2 c_1_temp 
-       0    1.7666667            0    1.7666667   0.01090535   0.59439252 
-    1000    3.1462962   0.17392649    3.3202227   0.02361912    1.1654694 
-    2000    2.9311648   0.13836102    3.0695258  0.021748224    1.1950624 
-    3000     3.090491   0.16511199     3.255603  0.018691142      1.23672 
-    4000    2.7401565   0.17792155    2.9180781  0.015093853    1.1180839 
-    5000    3.0880849   0.17587085    3.2639557  0.030563042    1.2831154 
-    6000    3.2180776   0.19732251    3.4154001  0.028338151     1.258839 
-    7000    2.9514882   0.25088882     3.202377  0.025296925    1.1746326 
-    8000    3.0101226   0.28825968    3.2983823  0.027273454    1.2138056 
-    9000    3.0164253    0.1901733    3.2065986  0.033228915    1.3095914 
-   10000    2.3780401   0.34082434    2.7188644  0.031838531    1.0208679 
-Loop time of 25.5798 on 4 procs for 10000 steps with 54 atoms
+Per MPI rank memory allocation (min/avg/max) = 5.901 | 5.902 | 5.904 Mbytes
+   Step         KinEng         PotEng         TotEng          c_p2         c_1_temp   
+         0   1.7666667      0              1.7666667      0.01090535     0.59439252   
+      1000   3.1462962      0.17392649     3.3202227      0.02361912     1.1654694    
+      2000   2.9311648      0.13836102     3.0695258      0.021748224    1.1950624    
+      3000   3.090491       0.16511199     3.255603       0.018691142    1.23672      
+      4000   2.7401565      0.17792155     2.9180781      0.015093853    1.1180839    
+      5000   3.0880849      0.17587085     3.2639557      0.030563042    1.2831154    
+      6000   3.2180776      0.19732251     3.4154001      0.028338151    1.258839     
+      7000   2.9514882      0.25088882     3.202377       0.025296925    1.1746326    
+      8000   3.0101226      0.28825968     3.2983823      0.027273454    1.2138056    
+      9000   3.0164253      0.1901733      3.2065986      0.033228915    1.3095914    
+     10000   2.3780401      0.34082434     2.7188644      0.031838531    1.0208679    
+Loop time of 16.4904 on 4 procs for 10000 steps with 54 atoms
 
-Performance: 33776.718 tau/day, 390.934 timesteps/s
-97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 52394.037 tau/day, 606.412 timesteps/s, 32.746 katom-step/s
+95.4% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 9.256      | 13.423     | 24.653     | 177.1 | 52.47
-Neigh   | 0.0021949  | 0.0024942  | 0.0031152  |   0.7 |  0.01
-Comm    | 0.73678    | 11.948     | 16.096     | 187.4 | 46.71
-Output  | 0.00023246 | 0.00041932 | 0.0009768  |   0.0 |  0.00
-Modify  | 0.12505    | 0.15661    | 0.18165    |   6.0 |  0.61
-Other   |            | 0.04968    |            |       |  0.19
+Pair    | 5.8583     | 8.5985     | 15.966     | 145.2 | 52.14
+Neigh   | 0.00098311 | 0.0011219  | 0.0014163  |   0.5 |  0.01
+Comm    | 0.39088    | 7.7607     | 10.504     | 152.9 | 47.06
+Output  | 0.00016175 | 0.00044056 | 0.0012766  |   0.0 |  0.00
+Modify  | 0.084729   | 0.094756   | 0.10558    |   2.8 |  0.57
+Other   |            | 0.0349     |            |       |  0.21
 
-Nlocal:    13.5 ave 17 max 9 min
+Nlocal:           13.5 ave          17 max           9 min
 Histogram: 1 0 0 1 0 0 0 0 1 1
-Nghost:    63.5 ave 68 max 58 min
+Nghost:           63.5 ave          68 max          58 min
 Histogram: 1 0 0 1 0 0 0 0 0 2
-Neighs:    25 ave 38 max 6 min
+Neighs:             25 ave          38 max           6 min
 Histogram: 1 0 0 0 0 1 0 0 1 1
 
 Total # of neighbors = 100
-Ave neighs/atom = 1.85185
+Ave neighs/atom = 1.8518519
 Neighbor list builds = 268
 Dangerous builds = 0
 
-Total wall time: 0:00:25
+Total wall time: 0:00:16
diff --git a/examples/body/log.14Jun23.pour3d.g++.1 b/examples/body/log.14Jun23.pour3d.g++.1
new file mode 100644
index 0000000000..3bca25ee6b
--- /dev/null
+++ b/examples/body/log.14Jun23.pour3d.g++.1
@@ -0,0 +1,148 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+# pouring 3d rounded polyhedron bodies
+
+variable    steps index 6000
+
+units       lj
+boundary    p p fm
+comm_modify vel yes
+
+atom_style  body rounded/polyhedron 1 8
+atom_modify map array
+
+region		reg block 0 50 0 50 0 50 units box
+create_box	4 reg
+Created orthogonal box = (0 0 0) to (50 50 50)
+  1 by 1 by 1 MPI processor grid
+
+variable cut_inner  equal 0.5
+variable k_n        equal 100
+variable k_na       equal 5
+variable c_n        equal 20
+variable c_t        equal 5
+variable mu         equal 0
+variable A_ua       equal 1
+
+pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
+pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
+pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
+pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
+pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
+pair_style body/rounded/polyhedron 20 5 0 1 0.5
+pair_coeff * * ${k_n} ${k_na}
+pair_coeff * * 100 ${k_na}
+pair_coeff * * 100 5
+
+neighbor     0.5 bin
+neigh_modify every 1 delay 0 check yes
+
+timestep     0.001
+
+fix          1 all nve/body
+fix          2 all gravity 1.0 spherical 0.0 -180.0
+
+molecule     object molecule.cube molecule.tetra toff 1              molecule.rod3d toff 2 molecule.point3d toff 3
+Read molecule template object:
+  1 molecules
+  0 fragments
+  1 atoms with max type 1
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+Read molecule template object:
+  1 molecules
+  0 fragments
+  1 atoms with max type 2
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+Read molecule template object:
+  1 molecules
+  0 fragments
+  1 atoms with max type 3
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+Read molecule template object:
+  1 molecules
+  0 fragments
+  1 atoms with max type 4
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+
+region       slab block 5 45 5 45 25 35 units box
+fix          ins all pour 500 0 4767548 vol 0.4 10 region slab mol object              molfrac 0.25 0.25 0.25 0.25
+Particle insertion: 134 every 4472 steps, 500 by step 13417
+
+fix          4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL
+
+#compute      1 all body/local type 1 2 3
+#dump         1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4]
+#dump         10 all custom 1000 tmp.dump id type x y z radius
+
+thermo_style custom step atoms ke pe etotal press
+
+thermo       1000
+
+#dump	     2 all image 500 image.*.jpg type type #	     zoom 1.5 adiam 1.5 body type 0 0 view 75 15
+#dump_modify  2 pad 6
+
+run	     ${steps}
+run	     6000
+Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5
+  ghost atom cutoff = 5
+  binsize = 2.5, bins = 20 20 20
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair body/rounded/polyhedron, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.508 | 0.508 | 0.508 Mbytes
+   Step        Atoms        KinEng         PotEng         TotEng         Press     
+         0           0  -0              0              0              0            
+      1000         134  -0              0.0038737172   0.0038737172  -3.395325e-06 
+      2000         134  -0             -0.0009235483  -0.0009235483  -6.5977025e-07
+      3000         134  -0              0.004338364    0.004338364   -1.4565607e-05
+      4000         134  -0              0.0028464278   0.0028464278  -7.6723299e-06
+      5000         268  -0              0.017425002    0.017425002    0.000175191  
+      6000         268  -0              0.035730061    0.035730061    0.00019697961
+Loop time of 0.432886 on 1 procs for 6000 steps with 268 atoms
+
+Performance: 1197543.331 tau/day, 13860.455 timesteps/s, 3.715 Matom-step/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.29261    | 0.29261    | 0.29261    |   0.0 | 67.59
+Neigh   | 0.0040123  | 0.0040123  | 0.0040123  |   0.0 |  0.93
+Comm    | 0.0019937  | 0.0019937  | 0.0019937  |   0.0 |  0.46
+Output  | 5.8179e-05 | 5.8179e-05 | 5.8179e-05 |   0.0 |  0.01
+Modify  | 0.12864    | 0.12864    | 0.12864    |   0.0 | 29.72
+Other   |            | 0.005574   |            |       |  1.29
+
+Nlocal:            268 ave         268 max         268 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              2 ave           2 max           2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:             95 ave          95 max          95 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 95
+Ave neighs/atom = 0.35447761
+Neighbor list builds = 167
+Dangerous builds = 0
+
+
+Total wall time: 0:00:00
diff --git a/examples/body/log.14Jun23.pour3d.g++.4 b/examples/body/log.14Jun23.pour3d.g++.4
new file mode 100644
index 0000000000..5a8206b95a
--- /dev/null
+++ b/examples/body/log.14Jun23.pour3d.g++.4
@@ -0,0 +1,148 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+# pouring 3d rounded polyhedron bodies
+
+variable    steps index 6000
+
+units       lj
+boundary    p p fm
+comm_modify vel yes
+
+atom_style  body rounded/polyhedron 1 8
+atom_modify map array
+
+region		reg block 0 50 0 50 0 50 units box
+create_box	4 reg
+Created orthogonal box = (0 0 0) to (50 50 50)
+  1 by 2 by 2 MPI processor grid
+
+variable cut_inner  equal 0.5
+variable k_n        equal 100
+variable k_na       equal 5
+variable c_n        equal 20
+variable c_t        equal 5
+variable mu         equal 0
+variable A_ua       equal 1
+
+pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
+pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
+pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
+pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
+pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
+pair_style body/rounded/polyhedron 20 5 0 1 0.5
+pair_coeff * * ${k_n} ${k_na}
+pair_coeff * * 100 ${k_na}
+pair_coeff * * 100 5
+
+neighbor     0.5 bin
+neigh_modify every 1 delay 0 check yes
+
+timestep     0.001
+
+fix          1 all nve/body
+fix          2 all gravity 1.0 spherical 0.0 -180.0
+
+molecule     object molecule.cube molecule.tetra toff 1              molecule.rod3d toff 2 molecule.point3d toff 3
+Read molecule template object:
+  1 molecules
+  0 fragments
+  1 atoms with max type 1
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+Read molecule template object:
+  1 molecules
+  0 fragments
+  1 atoms with max type 2
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+Read molecule template object:
+  1 molecules
+  0 fragments
+  1 atoms with max type 3
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+Read molecule template object:
+  1 molecules
+  0 fragments
+  1 atoms with max type 4
+  0 bonds with max type 0
+  0 angles with max type 0
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+
+region       slab block 5 45 5 45 25 35 units box
+fix          ins all pour 500 0 4767548 vol 0.4 10 region slab mol object              molfrac 0.25 0.25 0.25 0.25
+Particle insertion: 134 every 4472 steps, 500 by step 13417
+
+fix          4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL
+
+#compute      1 all body/local type 1 2 3
+#dump         1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4]
+#dump         10 all custom 1000 tmp.dump id type x y z radius
+
+thermo_style custom step atoms ke pe etotal press
+
+thermo       1000
+
+#dump	     2 all image 500 image.*.jpg type type #	     zoom 1.5 adiam 1.5 body type 0 0 view 75 15
+#dump_modify  2 pad 6
+
+run	     ${steps}
+run	     6000
+Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5
+  ghost atom cutoff = 5
+  binsize = 2.5, bins = 20 20 20
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair body/rounded/polyhedron, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 0.4666 | 0.4666 | 0.4666 Mbytes
+   Step        Atoms        KinEng         PotEng         TotEng         Press     
+         0           0  -0              0              0              0            
+      1000         134  -0              0.0038737172   0.0038737172  -3.395325e-06 
+      2000         134  -0             -0.0009235483  -0.0009235483  -6.5977025e-07
+      3000         134  -0              0.004338364    0.004338364   -1.4565607e-05
+      4000         134  -0              0.0028464278   0.0028464278  -7.6723299e-06
+      5000         268  -0              0.017425002    0.017425002    0.000175191  
+      6000         268  -0              0.035730061    0.035730061    0.00019697961
+Loop time of 0.266391 on 4 procs for 6000 steps with 268 atoms
+
+Performance: 1946012.521 tau/day, 22523.293 timesteps/s, 6.036 Matom-step/s
+92.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.024599   | 0.072944   | 0.14627    |  18.6 | 27.38
+Neigh   | 0.0011942  | 0.0013474  | 0.0014323  |   0.3 |  0.51
+Comm    | 0.047438   | 0.11992    | 0.17106    |  14.8 | 45.02
+Output  | 7.6297e-05 | 0.00017637 | 0.00044875 |   0.0 |  0.07
+Modify  | 0.029377   | 0.035972   | 0.040396   |   2.4 | 13.50
+Other   |            | 0.03603    |            |       | 13.52
+
+Nlocal:             67 ave          89 max          43 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:             38 ave          53 max          25 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Neighs:          23.75 ave          42 max           7 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+
+Total # of neighbors = 95
+Ave neighs/atom = 0.35447761
+Neighbor list builds = 167
+Dangerous builds = 0
+
+
+Total wall time: 0:00:00
diff --git a/examples/body/log.14Jun23.squares.g++.1 b/examples/body/log.14Jun23.squares.g++.1
new file mode 100644
index 0000000000..4588481dc6
--- /dev/null
+++ b/examples/body/log.14Jun23.squares.g++.1
@@ -0,0 +1,226 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+# 2d rounded polygon bodies
+
+variable    r     index 4
+variable    steps index 100000
+variable    T     index 0.5
+variable    P     index 0.1
+variable    seed  index 980411
+
+units       lj
+dimension   2
+
+atom_style  body rounded/polygon 1 6
+atom_modify map array
+read_data   data.squares
+Reading data file ...
+  orthogonal box = (0 0 -0.5) to (12 12 0.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2 atoms
+  2 bodies
+  read_data CPU = 0.001 seconds
+
+replicate   $r $r 1
+replicate   4 $r 1
+replicate   4 4 1
+Replication is creating a 4x4x1 = 16 times larger system...
+  orthogonal box = (0 0 -0.5) to (48 48 0.5)
+  1 by 1 by 1 MPI processor grid
+  32 atoms
+  replicate CPU = 0.001 seconds
+
+velocity    all create $T ${seed} dist gaussian mom yes rot yes
+velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
+velocity    all create 0.5 980411 dist gaussian mom yes rot yes
+
+variable cut_inner  equal 0.5
+variable k_n        equal 100
+variable k_na       equal 2
+variable c_n        equal 1
+variable c_t        equal 1
+variable mu         equal 0.1
+variable delta_ua   equal 0.5
+
+pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
+pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
+pair_coeff * * ${k_n} ${k_na}
+pair_coeff * * 100 ${k_na}
+pair_coeff * * 100 2
+
+comm_modify vel yes
+
+neighbor     0.5 bin
+neigh_modify every 1 delay 0 check yes
+
+timestep     0.001
+
+#fix         1 all nve/body
+#fix         1 all nvt/body temp $T $T 1.0
+fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
+
+fix          2 all enforce2d
+
+#compute      1 all body/local id 1 2 3
+#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
+
+thermo_style custom step ke pe etotal press
+thermo       1000
+
+#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
+#dump_modify  2 pad 6
+
+run          ${steps}
+run          100000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1568542
+  ghost atom cutoff = 6.1568542
+  binsize = 3.0784271, bins = 16 16 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair body/rounded/polygon, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.386 | 5.386 | 5.386 Mbytes
+   Step         KinEng         PotEng         TotEng         Press     
+         0   0.484375       0.25           0.734375       0.0067274306 
+      1000   0.39720235     0.0015845731   0.39878692     0.00223489   
+      2000   0.42893425     0.011718891    0.44065314     0.0027413224 
+      3000   0.57823511     0.012407489    0.5906426      0.0025306081 
+      4000   0.71610647     0.028149437    0.74425591     0.0016504948 
+      5000   0.84027279     0.018917017    0.8591898      0.0037451875 
+      6000   0.72410001     0.073495378    0.79759539     0.00018672875
+      7000   0.53886484     0.077723366    0.61658821     0.004729216  
+      8000   0.66196054     0.05502242     0.71698296     0.0054997323 
+      9000   0.93104065     0.071628784    1.0026694      0.011330629  
+     10000   0.75494389     0.15204106     0.90698495     0.021702117  
+     11000   0.72349154     0.11102332     0.83451486     0.019264158  
+     12000   0.56216531     0.117059       0.67922431    -0.028295891  
+     13000   0.63793498     0.11701868     0.75495366     0.029470631  
+     14000   0.62996509     0.020871971    0.65083706     0.0086224023 
+     15000   0.6403927      0.0091092209   0.64950192     0.016897685  
+     16000   0.70288045     0.046856749    0.7497372      0.02312871   
+     17000   0.6820593      0.038994474    0.72105377     0.0068705173 
+     18000   0.75623543     0.0069908315   0.76322626     0.025170959  
+     19000   0.85962145     0.059005169    0.91862661     0.012725758  
+     20000   0.73334823     0.033043489    0.76639172     0.023661433  
+     21000   0.60850654     0.081277767    0.68978431     0.021031136  
+     22000   0.38251144     0.27624263     0.65875407     0.047336318  
+     23000   0.4288127      0.30632792     0.73514062     0.034108416  
+     24000   0.4452138      0.13179024     0.57700404     0.010303821  
+     25000   0.48091107     0.1816109      0.66252197     0.021201342  
+     26000   0.67970784     0.088616708    0.76832455     0.034997245  
+     27000   0.8223642      0.08699442     0.90935862     0.023508839  
+     28000   0.60062179     0.1119578      0.71257959    -0.0010008016 
+     29000   0.54629437     0.1202995      0.66659387     0.040613547  
+     30000   0.28102412     0.38657163     0.66759575    -0.0086538064 
+     31000   0.12433474     0.18824131     0.31257605     0.049899211  
+     32000   0.089510322    0.20890679     0.29841711     0.045555094  
+     33000   0.12657665     0.17720119     0.30377784     0.028306214  
+     34000   0.18400652     0.17677189     0.36077841     0.034628531  
+     35000   0.24048631     0.11010844     0.35059475     0.029848365  
+     36000   0.33435006     0.077341882    0.41169194     0.055963098  
+     37000   0.46088842     0.1210638      0.58195222     0.072006022  
+     38000   0.76551752     0.07037755     0.83589507     0.018204686  
+     39000   0.89388464     0.080990198    0.97487484     0.038361105  
+     40000   0.65618718     0.078644754    0.73483193     0.040567246  
+     41000   0.47284043     0.16391389     0.63675432     0.027523843  
+     42000   0.52454668     0.057988616    0.58253529     0.03122996   
+     43000   0.78769394     0.08405077     0.87174471     0.044743697  
+     44000   0.92932837     0.093922981    1.0232514      0.042510479  
+     45000   0.5722596      0.17607834     0.74833794     0.034646914  
+     46000   0.54352389     0.085652886    0.62917677     0.033203865  
+     47000   0.45608912     0.25183842     0.70792754     0.08370224   
+     48000   0.47530886     0.10106466     0.57637352     0.046113986  
+     49000   0.67945305     0.0065249477   0.68597799     0.054743491  
+     50000   0.49661922     0.097381596    0.59400082     0.006998965  
+     51000   0.60992235     0.059017331    0.66893968     0.09445106   
+     52000   0.69563455     0.18702969     0.88266424     0.034154598  
+     53000   0.87598532     0.18260917     1.0585945      0.065734536  
+     54000   0.58822846     0.27562038     0.86384884     0.0764045    
+     55000   0.43454899     0.17174441     0.6062934      0.026434052  
+     56000   0.4004495      0.12778644     0.52823594     0.065986005  
+     57000   0.36272102     0.09849578     0.4612168      0.064217596  
+     58000   0.40987214     0.21777618     0.62764832     0.058625636  
+     59000   0.64813089     0.1479689      0.79609979     0.033378701  
+     60000   0.90328265     0.11049926     1.0137819      0.055828397  
+     61000   0.82921839     0.074638688    0.90385707     0.062488824  
+     62000   0.63223087     0.094386302    0.72661718     0.054784559  
+     63000   0.62946839     0.087807829    0.71727622     0.058398323  
+     64000   0.79784108     0.094756776    0.89259786     0.065765914  
+     65000   0.87500942     0.13514078     1.0101502      0.068123475  
+     66000   0.66961949     0.19942965     0.86904914     0.065587832  
+     67000   0.61612396     0.11436282     0.73048678     0.061233427  
+     68000   0.74149449     0.03129016     0.77278465     0.072517897  
+     69000   0.84060202     0.027261803    0.86786382     0.063374451  
+     70000   0.78182528     0.023528774    0.80535405     0.07431822   
+     71000   0.71611101     0.023512727    0.73962374     0.069575276  
+     72000   0.68437263     0.023941199    0.70831382     0.069821154  
+     73000   0.75652323     0.023580324    0.78010355     0.075046425  
+     74000   0.92077658     0.023272419    0.944049       0.070992373  
+     75000   0.75277766     0.023186631    0.77596429     0.074859227  
+     76000   0.59333539     0.024276648    0.61761204     0.076132037  
+     77000   0.68243436     0.024600726    0.70703508     0.075525977  
+     78000   0.79699751     0.024238959    0.82123647     0.078255526  
+     79000   0.77318109     0.024249895    0.79743099     0.078223339  
+     80000   0.72004911     0.024522473    0.74457159     0.079009398  
+     81000   0.71732947     0.024702988    0.74203245     0.080902007  
+     82000   0.73395391     0.024817681    0.75877159     0.081203115  
+     83000   0.74389794     0.02487774     0.76877568     0.082273058  
+     84000   0.73219737     0.024967311    0.75716468     0.08359401   
+     85000   0.66523255     0.025299293    0.69053184     0.084260931  
+     86000   0.67031201     0.02564609     0.6959581      0.085495986  
+     87000   0.81345283     0.025297963    0.8387508      0.086292085  
+     88000   0.85008513     0.024879647    0.87496478     0.087116741  
+     89000   0.62893149     0.025674927    0.65460642     0.088514693  
+     90000   0.58336052     0.026632218    0.60999274     0.089459637  
+     91000   0.72615388     0.026181899    0.75233578     0.090289473  
+     92000   0.76593408     0.025893082    0.79182717     0.091294308  
+     93000   0.73475998     0.026113022    0.76087301     0.092256366  
+     94000   0.68995562     0.026409704    0.71636532     0.093332419  
+     95000   0.69491284     0.026726159    0.721639       0.094314615  
+     96000   0.83274635     0.026420125    0.85916648     0.09513317   
+     97000   0.85486073     0.025941089    0.88080181     0.096122793  
+     98000   0.63095894     0.027021709    0.65798064     0.097348373  
+     99000   0.60847495     0.027908563    0.63638351     0.098362493  
+    100000   0.75867487     0.027331375    0.78600625     0.099184572  
+Loop time of 3.87848 on 1 procs for 100000 steps with 32 atoms
+
+Performance: 2227674.150 tau/day, 25783.266 timesteps/s, 825.065 katom-step/s
+97.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.9048     | 2.9048     | 2.9048     |   0.0 | 74.90
+Neigh   | 0.0027304  | 0.0027304  | 0.0027304  |   0.0 |  0.07
+Comm    | 0.071653   | 0.071653   | 0.071653   |   0.0 |  1.85
+Output  | 0.00069287 | 0.00069287 | 0.00069287 |   0.0 |  0.02
+Modify  | 0.85771    | 0.85771    | 0.85771    |   0.0 | 22.11
+Other   |            | 0.04088    |            |       |  1.05
+
+Nlocal:             32 ave          32 max          32 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             32 ave          32 max          32 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:             57 ave          57 max          57 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 57
+Ave neighs/atom = 1.78125
+Neighbor list builds = 1379
+Dangerous builds = 0
+Total wall time: 0:00:03
diff --git a/examples/body/log.14Jun23.squares.g++.4 b/examples/body/log.14Jun23.squares.g++.4
new file mode 100644
index 0000000000..51f1a0c7e9
--- /dev/null
+++ b/examples/body/log.14Jun23.squares.g++.4
@@ -0,0 +1,226 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+# 2d rounded polygon bodies
+
+variable    r     index 4
+variable    steps index 100000
+variable    T     index 0.5
+variable    P     index 0.1
+variable    seed  index 980411
+
+units       lj
+dimension   2
+
+atom_style  body rounded/polygon 1 6
+atom_modify map array
+read_data   data.squares
+Reading data file ...
+  orthogonal box = (0 0 -0.5) to (12 12 0.5)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  2 atoms
+  2 bodies
+  read_data CPU = 0.001 seconds
+
+replicate   $r $r 1
+replicate   4 $r 1
+replicate   4 4 1
+Replication is creating a 4x4x1 = 16 times larger system...
+  orthogonal box = (0 0 -0.5) to (48 48 0.5)
+  2 by 2 by 1 MPI processor grid
+  32 atoms
+  replicate CPU = 0.001 seconds
+
+velocity    all create $T ${seed} dist gaussian mom yes rot yes
+velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
+velocity    all create 0.5 980411 dist gaussian mom yes rot yes
+
+variable cut_inner  equal 0.5
+variable k_n        equal 100
+variable k_na       equal 2
+variable c_n        equal 1
+variable c_t        equal 1
+variable mu         equal 0.1
+variable delta_ua   equal 0.5
+
+pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
+pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
+pair_coeff * * ${k_n} ${k_na}
+pair_coeff * * 100 ${k_na}
+pair_coeff * * 100 2
+
+comm_modify vel yes
+
+neighbor     0.5 bin
+neigh_modify every 1 delay 0 check yes
+
+timestep     0.001
+
+#fix         1 all nve/body
+#fix         1 all nvt/body temp $T $T 1.0
+fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
+
+fix          2 all enforce2d
+
+#compute      1 all body/local id 1 2 3
+#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
+
+thermo_style custom step ke pe etotal press
+thermo       1000
+
+#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
+#dump_modify  2 pad 6
+
+run          ${steps}
+run          100000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1568542
+  ghost atom cutoff = 6.1568542
+  binsize = 3.0784271, bins = 16 16 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair body/rounded/polygon, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.379 | 5.379 Mbytes
+   Step         KinEng         PotEng         TotEng         Press     
+         0   0.484375       0.25           0.734375       0.0067274306 
+      1000   0.39720235     0.0015845731   0.39878692     0.00223489   
+      2000   0.42893425     0.011718891    0.44065314     0.0027413224 
+      3000   0.57823511     0.012407489    0.5906426      0.0025306081 
+      4000   0.71610647     0.028149437    0.74425591     0.0016504948 
+      5000   0.84027279     0.018917017    0.8591898      0.0037451875 
+      6000   0.72410001     0.073495378    0.79759539     0.00018672875
+      7000   0.53886484     0.077723366    0.61658821     0.004729216  
+      8000   0.66196054     0.05502242     0.71698296     0.0054997327 
+      9000   0.93104065     0.071628784    1.0026694      0.011330629  
+     10000   0.75494389     0.15204106     0.90698496     0.021702127  
+     11000   0.72349155     0.11102332     0.83451487     0.019264192  
+     12000   0.56216536     0.11705898     0.67922434    -0.028296196  
+     13000   0.63793556     0.11701866     0.75495421     0.029469295  
+     14000   0.62999448     0.020866813    0.65086129     0.008609569  
+     15000   0.6404504      0.0090011224   0.64945152     0.01706906   
+     16000   0.70195749     0.044735201    0.74669269     0.0179597    
+     17000   0.69097976     0.03894214     0.72992191     0.015704476  
+     18000   0.75303457     0.0019263825   0.75496095     0.021536711  
+     19000   0.6459718      0.10419136     0.75016317     0.033861092  
+     20000   0.73026363     0.13023974     0.86050337     0.022207497  
+     21000   0.77107035     0.30464112     1.0757115      0.013967631  
+     22000   0.44134768     0.22883887     0.67018655     0.014202518  
+     23000   0.53410601     0.16702381     0.70112983     0.009305779  
+     24000   0.5144312      0.19041122     0.70484242    -0.0059836303 
+     25000   0.60922681     0.15475207     0.76397888     0.016370526  
+     26000   0.70922367     0.25374443     0.9629681      0.027301754  
+     27000   0.67289133     0.39287626     1.0657676      0.025562031  
+     28000   0.62112601     0.017177715    0.63830372     0.018556767  
+     29000   0.56492546     0.087573524    0.65249898     0.025132036  
+     30000   0.62612507    -0.01835118     0.60777389     0.050139664  
+     31000   0.69157641     0.064849873    0.75642628     0.033954585  
+     32000   0.72648211     0.08597545     0.81245756     0.038082388  
+     33000   0.58608821     0.13013111     0.71621932     0.054766043  
+     34000   0.49330983     0.080490598    0.57380043     0.034154681  
+     35000   0.54570666     0.075020466    0.62072713     0.03879264   
+     36000   0.60305736     0.10717781     0.71023516     0.030701059  
+     37000   0.52801767     0.12516316     0.65318083     0.007411688  
+     38000   0.5838277      0.12569072     0.70951842     0.03272916   
+     39000   0.53999819     0.043261294    0.58325949     0.084115917  
+     40000   0.64957099     0.040023268    0.68959426     0.027021958  
+     41000   0.59235949     0.10449793     0.69685742     0.045773377  
+     42000   0.71752786     0.043289363    0.76081722     0.040926021  
+     43000   0.78581005     0.024363927    0.81017398     0.034694164  
+     44000   0.6396541      0.06004252     0.69969662     0.037227348  
+     45000   0.35753293     0.11456039     0.47209332     0.033569048  
+     46000   0.11031158     0.11831834     0.22862991     0.076545681  
+     47000   0.11720754     0.035471414    0.15267896     0.022093929  
+     48000   0.13370328     0.031802339    0.16550562     0.053298269  
+     49000   0.2700883      0.15584422     0.42593252     0.057108168  
+     50000   0.53837779     0.13398219     0.67235998     0.047704986  
+     51000   0.38133073     0.011372933    0.39270366     0.04696367   
+     52000   0.32448241     0.009137008    0.33361942     0.033573259  
+     53000   0.25798301    -0.016530605    0.2414524      0.04623663   
+     54000   0.2842707      0.054504088    0.33877479     0.03751156   
+     55000   0.28895106     0.025307766    0.31425882     0.03935955   
+     56000   0.19130753     0.099678989    0.29098652     0.051888728  
+     57000   0.12237303     0.057536458    0.17990949     0.09984021   
+     58000   0.17962003     0.012450682    0.19207072     0.028644351  
+     59000   0.21667262    -0.013693164    0.20297945     0.048086277  
+     60000   0.4298123     -0.012970819    0.41684148     0.019347498  
+     61000   0.69591654    -0.027048452    0.66886809     0.069793861  
+     62000   1.0040382     -0.044228622    0.95980957     0.056563167  
+     63000   0.78189663    -0.053045577    0.72885106     0.059491526  
+     64000   0.57051419    -0.050757181    0.51975701     0.061863162  
+     65000   0.62584243    -0.050616328    0.5752261      0.068924362  
+     66000   0.85558894    -0.051396155    0.80419278     0.059309337  
+     67000   0.86314978    -0.052635701    0.81051408     0.071855924  
+     68000   0.65427495    -0.05147951     0.60279544     0.064001735  
+     69000   0.60658011    -0.050623824    0.55595629     0.0715805    
+     70000   0.76353932    -0.050863795    0.71267553     0.06771349   
+     71000   0.87559332    -0.051720153    0.82387317     0.071884106  
+     72000   0.71924774    -0.051167456    0.66808029     0.071010747  
+     73000   0.6100998     -0.050025233    0.56007457     0.073319802  
+     74000   0.71838075    -0.049907287    0.66847346     0.07314982   
+     75000   0.91863251    -0.051069435    0.86756308     0.07493433   
+     76000   0.78459189    -0.050803207    0.73378868     0.075397431  
+     77000   0.70827012    -0.049701237    0.65856888     0.076901086  
+     78000   0.72333497    -0.04940986     0.67392511     0.077456938  
+     79000   0.76543474    -0.049588137    0.7158466      0.078792278  
+     80000   0.77759003    -0.049596899    0.72799313     0.079470668  
+     81000   0.67474562    -0.048929658    0.62581596     0.080740407  
+     82000   0.60162355    -0.047698966    0.55392459     0.081758686  
+     83000   0.7602675     -0.047827179    0.71244032     0.082547083  
+     84000   0.9061851     -0.049481366    0.85670374     0.083443845  
+     85000   0.74071256    -0.048645397    0.69206717     0.084605474  
+     86000   0.67634638    -0.046894309    0.62945207     0.085608904  
+     87000   0.71669859    -0.046524067    0.67017453     0.086561551  
+     88000   0.77025498    -0.047090994    0.72316398     0.087515495  
+     89000   0.76590655    -0.047083362    0.71882319     0.088522842  
+     90000   0.61372503    -0.045529779    0.56819526     0.08963777   
+     91000   0.58583927    -0.043777544    0.54206173     0.093090208  
+     92000   0.80507421    -0.04423346     0.76084075     0.093861418  
+     93000   0.84631942    -0.046878171    0.79944125     0.093279847  
+     94000   0.70915593    -0.04570489     0.66345104     0.092425564  
+     95000   0.66813988    -0.043460537    0.62467934     0.093467021  
+     96000   0.71739316    -0.042402374    0.67499079     0.095183179  
+     97000   0.74132854    -0.042457291    0.69887124     0.096665917  
+     98000   0.74033914    -0.042269007    0.69807013     0.097869908  
+     99000   0.72447372    -0.041519159    0.68295457     0.098825459  
+    100000   0.6968193     -0.040321034    0.65649827     0.099797629  
+Loop time of 2.55809 on 4 procs for 100000 steps with 32 atoms
+
+Performance: 3377521.712 tau/day, 39091.686 timesteps/s, 1.251 Matom-step/s
+91.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.53547    | 0.78258    | 1.0169     |  21.0 | 30.59
+Neigh   | 0.0010868  | 0.0011973  | 0.0013608  |   0.3 |  0.05
+Comm    | 0.57019    | 0.78963    | 1.0091     |  19.2 | 30.87
+Output  | 0.00075581 | 0.0030547  | 0.0098741  |   7.1 |  0.12
+Modify  | 0.80723    | 0.81855    | 0.83849    |   1.3 | 32.00
+Other   |            | 0.1631     |            |       |  6.37
+
+Nlocal:              8 ave          12 max           2 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost:          15.25 ave          19 max          13 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+Neighs:             12 ave          18 max           1 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 48
+Ave neighs/atom = 1.5
+Neighbor list builds = 1420
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/body/log.14Jun23.wall2d.g++.1 b/examples/body/log.14Jun23.wall2d.g++.1
new file mode 100644
index 0000000000..dd54f37c03
--- /dev/null
+++ b/examples/body/log.14Jun23.wall2d.g++.1
@@ -0,0 +1,229 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+# 2d rounded polygon bodies
+
+variable    r     index 4
+variable    steps index 100000
+variable    T     index 0.5
+variable    P     index 0.1
+variable    seed  index 980411
+
+units       lj
+dimension   2
+
+atom_style  body rounded/polygon 1 6
+atom_modify map array
+read_data   data.squares
+Reading data file ...
+  orthogonal box = (0 0 -0.5) to (12 12 0.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2 atoms
+  2 bodies
+  read_data CPU = 0.001 seconds
+
+replicate   $r $r 1
+replicate   4 $r 1
+replicate   4 4 1
+Replication is creating a 4x4x1 = 16 times larger system...
+  orthogonal box = (0 0 -0.5) to (48 48 0.5)
+  1 by 1 by 1 MPI processor grid
+  32 atoms
+  replicate CPU = 0.001 seconds
+
+velocity    all create $T ${seed} dist gaussian mom yes rot yes
+velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
+velocity    all create 0.5 980411 dist gaussian mom yes rot yes
+
+change_box  all boundary p f p
+Changing box ...
+
+variable cut_inner  equal 0.5
+variable k_n        equal 100
+variable k_na       equal 2
+variable c_n        equal 0.1
+variable c_t        equal 0.1
+variable mu         equal 0.1
+variable delta_ua   equal 0.5
+
+pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
+pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
+pair_coeff * * ${k_n} ${k_na}
+pair_coeff * * 100 ${k_na}
+pair_coeff * * 100 2
+
+comm_modify vel yes
+
+neighbor     0.5 bin
+neigh_modify every 1 delay 0 check yes
+
+timestep     0.001
+
+#fix         1 all nve/body
+#fix         1 all nvt/body temp $T $T 1.0
+fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
+
+fix          2 all enforce2d
+fix          3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
+
+#compute      1 all body/local id 1 2 3
+#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
+
+thermo_style custom step ke pe etotal press
+thermo       1000
+
+#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
+#dump_modify  2 pad 6
+
+run          ${steps}
+run          100000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1568542
+  ghost atom cutoff = 6.1568542
+  binsize = 3.0784271, bins = 16 16 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair body/rounded/polygon, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.376 | 5.376 | 5.376 Mbytes
+   Step         KinEng         PotEng         TotEng         Press     
+         0   0.484375       0.25           0.734375       0.0067274306 
+      1000   0.51464289     0.00099012638  0.51563301     0.013444625  
+      2000   0.55653313     0.0040982283   0.56063136     0.0034505512 
+      3000   0.75323998     0.023578898    0.77681887     0.0036652891 
+      4000   0.70044978     0.092406287    0.79285607     0.0089262842 
+      5000   0.54548803     0.096501313    0.64198934     0.0051379523 
+      6000   0.48208829     0.097798861    0.57988715     0.015298049  
+      7000   0.68219182     0.038843941    0.72103576     0.016842202  
+      8000   0.53792445     0.012983807    0.55090825     0.0066797902 
+      9000   0.49980359     0.029397948    0.52920154     0.0046731993 
+     10000   0.48705779     0.10138799     0.58844578    -1.9696743e-05
+     11000   0.52151792     0.065893508    0.58741142     0.0049365175 
+     12000   0.59066419     0.039261015    0.62992521     0.001420608  
+     13000   0.46059009     0.07386532     0.53445541     0.005654565  
+     14000   0.37899234     0.13421331     0.51320565     0.0097199047 
+     15000   0.49566894     0.052006844    0.54767578     0.00053157628
+     16000   0.59294062     0.028393451    0.62133407     0.0057809461 
+     17000   0.51260882     0.1266054      0.63921422     0.0021637817 
+     18000   0.45603179     0.15710959     0.61314138     0.017707488  
+     19000   0.52137969     0.1123825      0.63376219     0.015894031  
+     20000   0.64553686     0.11579772     0.76133459     0.013239309  
+     21000   0.38581837     0.17867419     0.56449256     0.0048572535 
+     22000   0.42776514     0.12979071     0.55755585     0.008093469  
+     23000   0.490055       0.14197765     0.63203265    -0.003575896  
+     24000   0.57689881     0.10164831     0.67854712     0.022418321  
+     25000   0.45630031     0.057905852    0.51420616     0.007959034  
+     26000   0.59497685     0.193113       0.78808985     0.0076331679 
+     27000   0.40943362     0.098595954    0.50802958     0.0016863757 
+     28000   0.34512273     0.15696637     0.50208909     0.037435926  
+     29000   0.59187862     0.1845377      0.77641632     0.014563665  
+     30000   0.69204623     0.16392147     0.8559677      0.031708423  
+     31000   0.40436029     0.34429435     0.74865464     0.073818847  
+     32000   0.47580383     0.22708448     0.70288831     0.015795198  
+     33000   0.48923447     0.23636413     0.72559861     0.025932606  
+     34000   0.51960128     0.15145893     0.67106021    -0.00079607564
+     35000   0.44792834     0.19927109     0.64719943    -0.0063461505 
+     36000   0.54265821     0.17924788     0.72190609     0.017916439  
+     37000   0.56020344     0.24977507     0.80997851     0.057844411  
+     38000   0.28874871     0.21399353     0.50274224     0.022675277  
+     39000   0.39030236     0.30170176     0.69200411     0.037482614  
+     40000   0.4699469      0.20663643     0.67658333    -0.014082215  
+     41000   0.50202447     0.21510708     0.71713155    -0.0063284222 
+     42000   0.43029593     0.23511818     0.6654141      0.046478372  
+     43000   0.41628842     0.21031596     0.62660438    -0.0053073644 
+     44000   0.51101573     0.15862165     0.66963738     0.010251868  
+     45000   0.56984114     0.18071709     0.75055823     0.021333409  
+     46000   0.45510513     0.15385488     0.60896001     0.048441048  
+     47000   0.41229547     0.20577222     0.61806769     0.027485704  
+     48000   0.64114797     0.33672519     0.97787315     0.13522091   
+     49000   0.44298056     0.27708867     0.72006923     0.026660315  
+     50000   0.43250082     0.17778506     0.61028588     0.02714938   
+     51000   0.59697891     0.25460003     0.85157894     0.026959715  
+     52000   0.63110331     0.21528376     0.84638707     0.023157155  
+     53000   0.46085491     0.25375607     0.71461099     0.024933391  
+     54000   0.50772891     0.29280628     0.80053519     0.010621547  
+     55000   0.67213557     0.2071375      0.87927307     0.061770903  
+     56000   0.61184167     0.34686662     0.95870829     0.095262009  
+     57000   0.42364554     0.29899934     0.72264488    -0.0080865129 
+     58000   0.5033641      0.39810693     0.90147103     0.081474225  
+     59000   0.61363438     0.25296035     0.86659472     0.041921315  
+     60000   0.64600872     0.36997737     1.0159861      0.053833686  
+     61000   0.43392277     0.29276613     0.7266889      0.054911225  
+     62000   0.38910577     0.27714798     0.66625375    -0.0141031    
+     63000   0.42343097     0.21637816     0.63980913    -1.6862315e-05
+     64000   0.52512516     0.38797726     0.91310242     0.03170217   
+     65000   0.48930994     0.4863269      0.97563684     0.025108671  
+     66000   0.68354817     0.3629732      1.0465214      0.066714362  
+     67000   0.5361863      0.44003399     0.97622029     0.1063525    
+     68000   0.3605148      0.40138904     0.76190383     0.03287684   
+     69000   0.62747502     0.49229352     1.1197685      0.053648724  
+     70000   0.51326037     0.36561885     0.87887922     0.070871008  
+     71000   0.45429341     0.38458357     0.83887698     0.010485881  
+     72000   0.55377877     0.36434231     0.91812107     0.10507819   
+     73000   0.6857324      0.45242968     1.1381621      0.022470322  
+     74000   0.46349397     0.39082798     0.85432196     0.067650912  
+     75000   0.59216869     0.32893138     0.92110008     0.0196582    
+     76000   0.42985327     0.40674342     0.83659669     0.025700762  
+     77000   0.54319568     0.55627833     1.099474       0.067233159  
+     78000   0.59244798     0.5121155      1.1045635      0.12063624   
+     79000   0.61140864     0.45505083     1.0664595      0.088578795  
+     80000   0.64308346     0.4143502      1.0574337      0.038537249  
+     81000   0.55053046     0.43357659     0.98410705     0.053930256  
+     82000   0.54049882     0.41354335     0.95404217    -0.036458392  
+     83000   0.47517728     0.30128468     0.77646196     0.0019488841 
+     84000   0.57452781     0.1949493      0.76947711     0.039244382  
+     85000   0.7907368      0.51406164     1.3047984      0.12766082   
+     86000   0.59488507     0.50084726     1.0957323      0.080232158  
+     87000   0.43071262     0.4682738      0.89898642     0.1266876    
+     88000   0.53305256     0.55941308     1.0924656      0.17062068   
+     89000   0.60672487     0.64951209     1.256237       0.17194524   
+     90000   0.7134227      0.57323404     1.2866567      0.074617282  
+     91000   0.65670871     0.58567381     1.2423825      0.025281565  
+     92000   0.72364891     0.59755693     1.3212058      0.092201188  
+     93000   0.69254418     0.75766186     1.450206       0.16036111   
+     94000   0.56326058     0.6398442      1.2031048      0.26280736   
+     95000   0.47480145     0.57734551     1.052147       0.039940021  
+     96000   0.56909151     0.73081903     1.2999105      0.030223516  
+     97000   0.53198039     0.71808155     1.2500619      0.033191485  
+     98000   0.63572731     0.86931519     1.5050425      0.20901135   
+     99000   0.64477038     0.76771721     1.4124876      0.059732095  
+    100000   0.71275398     0.66613673     1.3788907      0.020038364  
+Loop time of 2.21223 on 1 procs for 100000 steps with 32 atoms
+
+Performance: 3905566.671 tau/day, 45203.318 timesteps/s, 1.447 Matom-step/s
+96.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.1162     | 1.1162     | 1.1162     |   0.0 | 50.45
+Neigh   | 0.0049629  | 0.0049629  | 0.0049629  |   0.0 |  0.22
+Comm    | 0.045069   | 0.045069   | 0.045069   |   0.0 |  2.04
+Output  | 0.00060169 | 0.00060169 | 0.00060169 |   0.0 |  0.03
+Modify  | 1.0017     | 1.0017     | 1.0017     |   0.0 | 45.28
+Other   |            | 0.04368    |            |       |  1.97
+
+Nlocal:             32 ave          32 max          32 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             19 ave          19 max          19 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:             59 ave          59 max          59 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 59
+Ave neighs/atom = 1.84375
+Neighbor list builds = 3214
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/body/log.14Jun23.wall2d.g++.4 b/examples/body/log.14Jun23.wall2d.g++.4
new file mode 100644
index 0000000000..0d0005c6ef
--- /dev/null
+++ b/examples/body/log.14Jun23.wall2d.g++.4
@@ -0,0 +1,229 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+# 2d rounded polygon bodies
+
+variable    r     index 4
+variable    steps index 100000
+variable    T     index 0.5
+variable    P     index 0.1
+variable    seed  index 980411
+
+units       lj
+dimension   2
+
+atom_style  body rounded/polygon 1 6
+atom_modify map array
+read_data   data.squares
+Reading data file ...
+  orthogonal box = (0 0 -0.5) to (12 12 0.5)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  2 atoms
+  2 bodies
+  read_data CPU = 0.001 seconds
+
+replicate   $r $r 1
+replicate   4 $r 1
+replicate   4 4 1
+Replication is creating a 4x4x1 = 16 times larger system...
+  orthogonal box = (0 0 -0.5) to (48 48 0.5)
+  2 by 2 by 1 MPI processor grid
+  32 atoms
+  replicate CPU = 0.001 seconds
+
+velocity    all create $T ${seed} dist gaussian mom yes rot yes
+velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
+velocity    all create 0.5 980411 dist gaussian mom yes rot yes
+
+change_box  all boundary p f p
+Changing box ...
+
+variable cut_inner  equal 0.5
+variable k_n        equal 100
+variable k_na       equal 2
+variable c_n        equal 0.1
+variable c_t        equal 0.1
+variable mu         equal 0.1
+variable delta_ua   equal 0.5
+
+pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
+pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
+pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
+pair_coeff * * ${k_n} ${k_na}
+pair_coeff * * 100 ${k_na}
+pair_coeff * * 100 2
+
+comm_modify vel yes
+
+neighbor     0.5 bin
+neigh_modify every 1 delay 0 check yes
+
+timestep     0.001
+
+#fix         1 all nve/body
+#fix         1 all nvt/body temp $T $T 1.0
+fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
+fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
+
+fix          2 all enforce2d
+fix          3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
+
+#compute      1 all body/local id 1 2 3
+#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
+
+thermo_style custom step ke pe etotal press
+thermo       1000
+
+#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
+#dump_modify  2 pad 6
+
+run          ${steps}
+run          100000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1568542
+  ghost atom cutoff = 6.1568542
+  binsize = 3.0784271, bins = 16 16 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair body/rounded/polygon, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.378 | 5.378 | 5.379 Mbytes
+   Step         KinEng         PotEng         TotEng         Press     
+         0   0.484375       0.25           0.734375       0.0067274306 
+      1000   0.51464289     0.00099012638  0.51563301     0.013444625  
+      2000   0.55653313     0.0040982283   0.56063136     0.0034505512 
+      3000   0.75323998     0.023578898    0.77681887     0.0036652891 
+      4000   0.70044978     0.092406287    0.79285607     0.0089262842 
+      5000   0.54548803     0.096501313    0.64198934     0.0051379522 
+      6000   0.48208828     0.097798868    0.57988715     0.01529805   
+      7000   0.68219182     0.038843949    0.72103577     0.016842202  
+      8000   0.53792445     0.01298383     0.55090828     0.0066797984 
+      9000   0.49980358     0.029397965    0.52920155     0.0046731992 
+     10000   0.48705755     0.10138831     0.58844586    -1.9690665e-05
+     11000   0.52151879     0.065897951    0.58741674     0.0049324908 
+     12000   0.59065198     0.03929683     0.62994881     0.0014198454 
+     13000   0.46076897     0.073363984    0.53413295     0.0057849056 
+     14000   0.38058168     0.16336914     0.54395082     0.0099910111 
+     15000   0.58924494     0.13219579     0.72144074     0.012781632  
+     16000   0.65163924     0.10979538     0.76143462     0.015088945  
+     17000   0.51431594     0.036344433    0.55066037     0.001446035  
+     18000   0.42677394     0.093297234    0.52007117     0.00093775852
+     19000   0.62399853     0.13309136     0.75708989     0.0095351169 
+     20000   0.52835966     0.085936455    0.61429611     0.013158115  
+     21000   0.42999051     0.12857394     0.55856445     0.024369485  
+     22000   0.56770038     0.19738636     0.76508675     0.024211788  
+     23000   0.55137392     0.18212359     0.7334975      0.024095463  
+     24000   0.6225794      0.13091248     0.75349189     0.032707954  
+     25000   0.47106345     0.10241626     0.57347971     0.0059731265 
+     26000   0.60567231     0.055894222    0.66156653     0.010614697  
+     27000   0.49075416     0.13914345     0.62989761     0.00048442735
+     28000   0.48902573     0.21423204     0.70325777     0.021295043  
+     29000   0.42728391     0.24136135     0.66864527     0.031633766  
+     30000   0.64658635     0.15368867     0.80027502     0.0084616839 
+     31000   0.71370199     0.18014549     0.89384748     0.02367184   
+     32000   0.40141173     0.1833294      0.58474113     0.034918949  
+     33000   0.55780706     0.14130843     0.69911549     0.012266172  
+     34000   0.36544303     0.15788143     0.52332446     0.0084938225 
+     35000   0.56844142     0.17507842     0.74351984     0.061506713  
+     36000   0.5048707      0.15834563     0.66321633     0.0286909    
+     37000   0.4371274      0.087735559    0.52486296    -0.0016289252 
+     38000   0.49941117     0.22576207     0.72517324     0.059233327  
+     39000   0.69480051     0.15465372     0.84945423     0.039061293  
+     40000   0.52881719     0.29110071     0.8199179      0.032439208  
+     41000   0.56931201     0.38596881     0.95528082     0.045284803  
+     42000   0.46759969     0.21337568     0.68097537     0.086759715  
+     43000   0.63416318     0.44687151     1.0810347      0.072272415  
+     44000   0.43914666     0.20832735     0.64747401     0.026280272  
+     45000   0.38329718     0.25407815     0.63737533     0.017356403  
+     46000   0.59511045     0.32148788     0.91659833    -0.0076184601 
+     47000   0.50635988     0.37243112     0.878791       0.025435347  
+     48000   0.42316224     0.29368731     0.71684954     0.00067040329
+     49000   0.40194259     0.26659105     0.66853364     0.069225504  
+     50000   0.4740342      0.305674       0.77970819     0.014813566  
+     51000   0.57279011     0.32080139     0.8935915      0.0091332017 
+     52000   0.54543481     0.34482955     0.89026435    -0.021131696  
+     53000   0.39241519     0.36432403     0.75673922     0.0077163816 
+     54000   0.62021406     0.32010094     0.940315       0.044477965  
+     55000   0.45160485     0.29442122     0.74602607     0.02563201   
+     56000   0.41737028     0.31207675     0.72944704     0.050342936  
+     57000   0.53454189     0.29192181     0.8264637      0.068452573  
+     58000   0.65449932     0.33567481     0.99017413     0.055352019  
+     59000   0.58742699     0.37317432     0.96060131     0.012805462  
+     60000   0.42430458     0.33744246     0.76174704     0.018744436  
+     61000   0.65433333     0.40723506     1.0615684      0.019757611  
+     62000   0.64472397     0.34658649     0.99131047     0.090688735  
+     63000   0.65381774     0.47452792     1.1283457      0.2090513    
+     64000   0.44107995     0.60507044     1.0461504      0.03144844   
+     65000   0.38159186     0.45527276     0.83686462     0.090856608  
+     66000   0.48842595     0.49445721     0.98288316     0.08753844   
+     67000   0.65088575     0.4611542      1.11204        0.066602605  
+     68000   0.5155131      0.38693864     0.90245174     0.0062596909 
+     69000   0.41477899     0.45120406     0.86598306     0.037396561  
+     70000   0.60305022     0.47624271     1.0792929      0.040607751  
+     71000   0.67077877     0.51044906     1.1812278      0.029084971  
+     72000   0.50912034     0.34340114     0.85252148     0.055767674  
+     73000   0.55167778     0.43795801     0.98963579     0.083371911  
+     74000   0.53603549     0.37357862     0.90961411     0.058762722  
+     75000   0.47521522     0.529749       1.0049642      0.12419171   
+     76000   0.48952134     0.63953611     1.1290574      0.09709472   
+     77000   0.63445283     0.57542295     1.2098758      0.11868116   
+     78000   0.62184463     0.60025138     1.222096       0.079417229  
+     79000   0.52715665     0.54847579     1.0756324      0.033981154  
+     80000   0.6264593      0.39323366     1.019693       0.05627332   
+     81000   0.78582235     0.47541992     1.2612423      0.031287815  
+     82000   0.69665491     0.58355423     1.2802091     -0.04433392   
+     83000   0.4994351      0.40089694     0.90033204    -0.0019687817 
+     84000   0.50932093     0.62716285     1.1364838      0.095177695  
+     85000   0.56251638     0.56010929     1.1226257      0.013989132  
+     86000   0.67155822     0.51326814     1.1848264      0.10616402   
+     87000   0.61317511     0.52704394     1.140219       0.076578899  
+     88000   0.57436568     0.60641096     1.1807766      0.042050421  
+     89000   0.62350614     0.65896923     1.2824754      0.15949038   
+     90000   0.57445242     0.65085438     1.2253068      0.034123951  
+     91000   0.50043488     0.69213026     1.1925651     -0.076403957  
+     92000   0.57345231     0.74801993     1.3214722      0.033715387  
+     93000   0.63056204     0.64474627     1.2753083      0.051205732  
+     94000   0.70948937     0.61081243     1.3203018     -0.0069457836 
+     95000   0.66048722     0.61001641     1.2705036      0.16072266   
+     96000   0.48720026     0.64888522     1.1360855      0.12573765   
+     97000   0.41570988     0.68810987     1.1038198     -0.033070846  
+     98000   0.53689925     0.83787736     1.3747766      0.098173219  
+     99000   0.5147061      0.92360546     1.4383116      0.12155736   
+    100000   0.5793939      0.63393822     1.2133321      0.090967465  
+Loop time of 2.08698 on 4 procs for 100000 steps with 32 atoms
+
+Performance: 4139957.491 tau/day, 47916.175 timesteps/s, 1.533 Matom-step/s
+92.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.31       | 0.33594    | 0.35254    |   2.8 | 16.10
+Neigh   | 0.001991   | 0.0021241  | 0.0022581  |   0.2 |  0.10
+Comm    | 0.40717    | 0.43106    | 0.46731    |   3.4 | 20.65
+Output  | 0.00076842 | 0.002908   | 0.0092082  |   6.7 |  0.14
+Modify  | 1.1389     | 1.1624     | 1.1753     |   1.3 | 55.70
+Other   |            | 0.1525     |            |       |  7.31
+
+Nlocal:              8 ave           9 max           7 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:             14 ave          16 max          12 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs:          13.25 ave          17 max          11 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 53
+Ave neighs/atom = 1.65625
+Neighbor list builds = 3000
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/body/log.27Nov18.body.g++.1 b/examples/body/log.27Nov18.body.g++.1
deleted file mode 100644
index adb2c5dd6f..0000000000
--- a/examples/body/log.27Nov18.body.g++.1
+++ /dev/null
@@ -1,177 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d polygon nparticle bodies
-
-units		lj
-dimension       2
-atom_style	body nparticle 2 6
-
-read_data       data.body
-  orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  100 atoms
-  100 bodies
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	body/nparticle 5.0
-pair_coeff	* * 1.0 1.0
-
-neighbor	0.5 bin
-neigh_modify    every 1 delay 0 check yes
-
-fix		1 all nve/body
-#fix		1 all nvt/body temp 1.44 1.44 1.0
-fix		2 all enforce2d
-
-#compute         1 all body/local type 1 2 3
-#dump            1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
-
-#dump		2 all image 1000 image.*.jpg type type #		zoom 1.6 adiam 1.5 body type 1.0 0
-#dump_modify    2 pad 5
-
-thermo          100
-run		10000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.5
-  ghost atom cutoff = 5.5
-  binsize = 2.75, bins = 12 12 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair body/nparticle, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.772 | 4.772 | 4.772 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44  -0.63799525            0   0.78760475  -0.15028724 
-     100     1.642337   -1.0003869            0   0.62552682   0.16140818 
-     200     1.470473   -1.2465469            0   0.20922135   0.35146925 
-     300    1.4834687   -1.3464946            0   0.12213946   0.40783535 
-     400    1.5075814   -1.6170041            0  -0.12449852   0.11302717 
-     500    1.5681124   -1.6060641            0 -0.053632801   0.23819933 
-     600    1.7129405   -1.6939468            0 0.0018642497   0.46490776 
-     700    1.5803869   -1.6182998            0 -0.053716823   0.36807869 
-     800    1.6454324   -1.6537709            0 -0.024792836   0.21305673 
-     900    1.5454528   -1.6310447            0  -0.10104644   0.22323772 
-    1000    1.7596217   -1.7290976            0  0.012927885   0.12600944 
-    1100    1.3845533    -1.635035            0  -0.26432721   0.31778997 
-    1200    1.6448321   -1.6985254            0 -0.070141617   0.14347958 
-    1300    1.6158541    -1.581817            0  0.017878542   0.16186588 
-    1400    1.4702758   -1.5210898            0 -0.065516797   0.35241206 
-    1500    1.5746718   -1.5427933            0  0.016131764   0.21832857 
-    1600    1.5276572   -1.6755951            0  -0.16321447 -0.046196207 
-    1700    1.8182153   -1.7471337            0  0.052899504   0.14576284 
-    1800    1.8054446   -1.8814075            0 -0.094017352   0.11678153 
-    1900    1.6318148    -1.636557            0 -0.021060353   0.29300401 
-    2000    1.6187604   -1.5563087            0  0.046264125   0.35910875 
-    2100    1.8270056   -1.9189599            0  -0.11022441 -0.031374982 
-    2200    1.8203075   -1.8672658            0 -0.065161309   0.38667462 
-    2300    2.1336292   -1.8962621            0    0.2160309   0.13286893 
-    2400      1.79223   -1.7128682            0  0.061439536   0.30570635 
-    2500    1.7208941   -1.6955053            0 0.0081798834   0.24562038 
-    2600    1.7755824   -1.7744614            0 -0.016634836   0.11148721 
-    2700    1.7308273    -1.744062            0 -0.030542972   0.17938105 
-    2800    1.7059134   -1.6131603            0  0.075694024   0.06746694 
-    2900    1.7152544    -1.665102            0  0.032999854   0.14918116 
-    3000    1.7917767   -1.6654545            0   0.10840436   0.22990289 
-    3100    1.7153899   -1.8140872            0  -0.11585128    0.1070804 
-    3200    1.5704305   -1.5645642            0 -0.0098380461   0.30331339 
-    3300    1.6707504   -1.6224865            0   0.03155641   0.21402203 
-    3400    1.7390711   -1.6969145            0  0.024765924   0.25633302 
-    3500    1.7601895   -1.7159833            0  0.026604288   0.10350991 
-    3600    1.7796243   -1.6848496            0  0.076978483   0.24287746 
-    3700    1.8883198   -1.7216992            0   0.14773748  0.071179538 
-    3800    1.5757461   -1.6445584            0 -0.084569808   0.23580968 
-    3900    1.5509957   -1.6221122            0 -0.086626425    0.2208604 
-    4000    1.7403415   -1.6515882            0  0.071349901     0.171317 
-    4100    1.6394046     -1.69549            0 -0.072479406   0.18077211 
-    4200     1.788413   -1.6410039            0   0.12952501   0.41737981 
-    4300    1.7211754   -1.6535323            0  0.050431306    0.1688929 
-    4400    1.6034779   -1.7771275            0  -0.18968442  0.091947982 
-    4500    1.5692666   -1.6176359            0 -0.064061965   0.31716418 
-    4600    1.6454802   -1.5764942            0  0.052531194  0.021026463 
-    4700    1.4715049    -1.582096            0  -0.12530612   0.17687943 
-    4800    1.5615071   -1.6276031            0 -0.081711137  0.077798682 
-    4900    1.6407636    -1.622773            0 0.0015829265   0.28751203 
-    5000    1.6390013   -1.7257036            0  -0.10309236   0.35133795 
-    5100    1.6540912   -1.7056399            0 -0.068089648   0.52254354 
-    5200    1.6438013   -1.7568895            0  -0.12952624   0.16423828 
-    5300    1.6791806    -1.756297            0 -0.093908192    0.3151943 
-    5400    1.7527095    -1.729977            0 0.0052053655   0.29874227 
-    5500    1.7604924   -1.6920395            0  0.050847912    0.2062502 
-    5600    1.8225025   -1.6746221            0   0.12965535   0.29423091 
-    5700    1.6896356   -1.6591445            0  0.013594822   0.41582329 
-    5800     1.575776   -1.6605307            0  -0.10051246   0.17434812 
-    5900    1.6893771   -1.6046258            0  0.067857462     0.188486 
-    6000    1.6506959   -1.6295482            0 0.0046407782   0.18737656 
-    6100    1.8137143   -1.6634096            0   0.13216758   0.22425414 
-    6200    1.6337368   -1.6016206            0  0.015778794   0.17026591 
-    6300    1.6232904   -1.7102709            0  -0.10321339   0.22621086 
-    6400    1.8146767   -1.7354533            0  0.061076657   0.25907309 
-    6500    1.5565608   -1.8652953            0  -0.32430015  0.096916202 
-    6600    1.6366532     -1.65732            0 -0.037033272   0.30276466 
-    6700    1.6612051   -1.6621545            0 -0.017561423   0.16685109 
-    6800    1.5574268   -1.6082827            0 -0.066430166   0.37630931 
-    6900    1.6556225   -1.6744213            0 -0.035355078   0.11599545 
-    7000    1.5078585   -1.6049482            0  -0.11216833   0.37716682 
-    7100    1.6147622   -1.7044793            0  -0.10586467   0.48915924 
-    7200    1.8022216   -1.7117836            0  0.072415791   0.24007939 
-    7300    1.6302834   -1.8522784            0  -0.23829784   0.19326557 
-    7400    1.7108472   -1.8993043            0  -0.20556558   0.34554364 
-    7500    1.8570536   -1.7135598            0   0.12492326   0.53728185 
-    7600    1.7812105   -1.7239897            0  0.039408716   0.44348124 
-    7700    1.8724942   -1.7871204            0  0.066648837    0.2529344 
-    7800    1.8237412   -1.6467621            0   0.15874169    0.2354529 
-    7900    1.7222899   -1.7254585            0  -0.02039155   0.13271481 
-    8000       1.6839   -1.5913695            0  0.075691547  0.011932379 
-    8100     1.599835    -1.672507            0 -0.088670351   0.11203274 
-    8200    1.8369376   -1.7464532            0  0.072115105   0.21380276 
-    8300    1.9603301   -1.9121791            0   0.02854768   0.18178367 
-    8400    1.7903688   -1.8798475            0  -0.10738231   0.37173469 
-    8500     1.687183    -1.760587            0 -0.090275846   0.23751647 
-    8600    1.6515772   -1.7918091            0  -0.15674775  0.099895142 
-    8700    1.7083909   -1.7297068            0 -0.038399775   0.57093506 
-    8800    1.6150569   -1.6976608            0 -0.098754502   0.15348519 
-    8900    1.5452011   -1.7517421            0  -0.22199306   0.22143091 
-    9000    1.7498686   -1.8569695            0  -0.12459962    0.1989093 
-    9100    1.6287336   -1.7505293            0  -0.13808305   0.23881397 
-    9200    1.5431194   -1.6845999            0  -0.15691169   0.10646288 
-    9300    1.4900229   -1.5671955            0 -0.092072887   0.31588548 
-    9400     1.523362   -1.5531592            0 -0.045030785   0.21546483 
-    9500    1.5783775     -1.65292            0 -0.090326215   0.25980559 
-    9600    1.9192786   -1.9303222            0 -0.030236392 -0.0046632743 
-    9700     1.747544   -1.7886479            0 -0.058579385   0.38543046 
-    9800    1.6713187   -1.6842507            0 -0.029645137   0.17982115 
-    9900    1.7707351   -1.6638268            0  0.089200949    0.2983883 
-   10000    1.6466807    -1.592436            0  0.037777866   0.12761693 
-Loop time of 1.76365 on 1 procs for 10000 steps with 100 atoms
-
-Performance: 2449465.017 tau/day, 5670.058 timesteps/s
-98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.5533     | 1.5533     | 1.5533     |   0.0 | 88.08
-Neigh   | 0.01155    | 0.01155    | 0.01155    |   0.0 |  0.65
-Comm    | 0.042146   | 0.042146   | 0.042146   |   0.0 |  2.39
-Output  | 0.00089574 | 0.00089574 | 0.00089574 |   0.0 |  0.05
-Modify  | 0.14124    | 0.14124    | 0.14124    |   0.0 |  8.01
-Other   |            | 0.01448    |            |       |  0.82
-
-Nlocal:    100 ave 100 max 100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    82 ave 82 max 82 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    467 ave 467 max 467 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 467
-Ave neighs/atom = 4.67
-Neighbor list builds = 468
-Dangerous builds = 0
-Total wall time: 0:00:01
diff --git a/examples/body/log.27Nov18.body.g++.4 b/examples/body/log.27Nov18.body.g++.4
deleted file mode 100644
index 24ed0a5436..0000000000
--- a/examples/body/log.27Nov18.body.g++.4
+++ /dev/null
@@ -1,177 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d polygon nparticle bodies
-
-units		lj
-dimension       2
-atom_style	body nparticle 2 6
-
-read_data       data.body
-  orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  100 atoms
-  100 bodies
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	body/nparticle 5.0
-pair_coeff	* * 1.0 1.0
-
-neighbor	0.5 bin
-neigh_modify    every 1 delay 0 check yes
-
-fix		1 all nve/body
-#fix		1 all nvt/body temp 1.44 1.44 1.0
-fix		2 all enforce2d
-
-#compute         1 all body/local type 1 2 3
-#dump            1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
-
-#dump		2 all image 1000 image.*.jpg type type #		zoom 1.6 adiam 1.5 body type 1.0 0
-#dump_modify    2 pad 5
-
-thermo          100
-run		10000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.5
-  ghost atom cutoff = 5.5
-  binsize = 2.75, bins = 12 12 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair body/nparticle, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.759 | 4.759 | 4.759 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1.44  -0.63799525            0   0.78760475  -0.15028724 
-     100     1.642337   -1.0003869            0   0.62552682   0.16140818 
-     200     1.470473   -1.2465469            0   0.20922135   0.35146925 
-     300    1.4834687   -1.3464946            0   0.12213946   0.40783535 
-     400    1.5075814   -1.6170041            0  -0.12449852   0.11302717 
-     500    1.5681124   -1.6060641            0 -0.053632801   0.23819933 
-     600    1.7129405   -1.6939468            0 0.0018642497   0.46490776 
-     700    1.5803869   -1.6182998            0 -0.053716823   0.36807869 
-     800    1.6454324   -1.6537709            0 -0.024792836   0.21305673 
-     900    1.5454528   -1.6310447            0  -0.10104644   0.22323772 
-    1000    1.7596217   -1.7290976            0  0.012927885   0.12600944 
-    1100    1.3845533    -1.635035            0  -0.26432721   0.31778997 
-    1200    1.6448321   -1.6985254            0 -0.070141617   0.14347958 
-    1300    1.6158541    -1.581817            0  0.017878542   0.16186588 
-    1400    1.4702758   -1.5210898            0 -0.065516796   0.35241206 
-    1500    1.5746718   -1.5427933            0  0.016131765   0.21832856 
-    1600    1.5276572   -1.6755951            0  -0.16321446 -0.046196204 
-    1700    1.8182153   -1.7471336            0  0.052899516   0.14576285 
-    1800    1.8054446   -1.8814074            0 -0.094017286   0.11678173 
-    1900    1.6318146    -1.636557            0 -0.021060549    0.2930043 
-    2000    1.6187614   -1.5563095            0  0.046264283    0.3591072 
-    2100    1.8270046   -1.9189568            0  -0.11022215 -0.031366859 
-    2200    1.8203171   -1.8672823            0 -0.065168391   0.38665482 
-    2300    2.1336582   -1.8962717            0   0.21604988   0.13283887 
-    2400    1.7923604   -1.7129915            0  0.061445317   0.30554793 
-    2500    1.7207328    -1.694912            0  0.008613452   0.24608272 
-    2600    1.7761079   -1.7743463            0 -0.015999568   0.11128836 
-    2700    1.7327782   -1.7433093            0 -0.027858862   0.17923355 
-    2800    1.6869096   -1.6050313            0  0.065009255  0.082020625 
-    2900     1.723365   -1.6453122            0   0.06081914   0.11381101 
-    3000     1.759037   -1.7499957            0 -0.008549105   0.12711249 
-    3100    1.7608876   -1.8502753            0  -0.10699653   0.10597269 
-    3200    1.6030658   -1.6772861            0 -0.090250949   0.16058698 
-    3300    1.6136204   -1.6247049            0 -0.027220627   0.27194341 
-    3400    1.7126562   -1.6002267            0  0.095302885  0.034174254 
-    3500    1.5286242   -1.5693205            0 -0.055982557 -0.028526272 
-    3600    1.5529814   -1.6309948            0 -0.093543248   0.25627254 
-    3700    1.4066962   -1.4583439            0  -0.06571463   0.36890582 
-    3800    1.5736098   -1.5849626            0 -0.027088852   0.19376983 
-    3900    1.5819362   -1.6452885            0  -0.07917158   0.17494451 
-    4000     1.806905   -1.7114262            0  0.077409698  0.059568431 
-    4100    1.7116803   -1.7160461            0  -0.02148265   0.12178783 
-    4200    1.8262315   -1.6682893            0   0.13967987   0.25082769 
-    4300    1.7548351   -1.6835554            0  0.053731392   0.39252317 
-    4400    1.7564816   -1.8020325            0 -0.063115749   0.18973764 
-    4500     1.727529    -1.771176            0  -0.06092227   0.51752631 
-    4600     1.633861   -1.7554104            0  -0.13788808   0.43310585 
-    4700    1.6678523   -1.8066719            0  -0.15549814 -0.086702533 
-    4800    1.5903598   -1.7410621            0   -0.1666059  0.064914366 
-    4900    1.4894085   -1.5982645            0  -0.12375007   0.23124626 
-    5000    1.5422574   -1.6830449            0  -0.15621011   0.12943511 
-    5100    1.6123243   -1.6577202            0 -0.061519159   0.26031057 
-    5200    1.6815554   -1.6889534            0 -0.024213484    0.1747903 
-    5300    1.6502994   -1.5929462            0  0.040850243   0.25623758 
-    5400    1.5900521   -1.8240806            0  -0.24992903   0.17822148 
-    5500    1.6976803   -1.8370034            0  -0.15629992   0.30793026 
-    5600     1.737085   -1.6873775            0  0.032336607   0.32235718 
-    5700    1.6995769   -1.6328398            0   0.04974131   0.22932613 
-    5800    1.6299367   -1.6582188            0 -0.044581533   0.33036589 
-    5900    1.6232041   -1.6456588            0 -0.038686805   0.20701623 
-    6000    1.6912228   -1.6401907            0  0.034119867  0.091519693 
-    6100    1.6314651   -1.6045998            0  0.010550658   0.32331621 
-    6200    1.7575091   -1.7271281            0  0.012805903   0.14214943 
-    6300    1.6830653   -1.7955472            0  -0.12931258   0.38730996 
-    6400    1.6323392   -1.7470603            0  -0.13104448   0.16724215 
-    6500     1.537874   -1.7277794            0  -0.20528423   0.28976791 
-    6600    1.8375539   -1.8388229            0 -0.019644528   0.31704541 
-    6700    1.7519102   -1.7739002            0 -0.039509043   0.19065098 
-    6800    1.4602447   -1.6902787            0  -0.24463645   0.20244553 
-    6900    1.6734836     -1.72224            0 -0.065491224   0.27092829 
-    7000    1.8166001   -1.7288037            0  0.069630392   0.43514063 
-    7100    1.9080746   -1.7849767            0   0.10401717  0.086258744 
-    7200    1.6346559    -1.602179            0  0.016130393   0.37208486 
-    7300     1.669382    -1.594527            0  0.058161153   0.12543161 
-    7400    1.5858819    -1.447937            0   0.12208615   0.42666321 
-    7500    1.6947983    -1.637715            0  0.040135322 -0.020875259 
-    7600    1.7085903   -1.6810854            0  0.010419044    0.1341074 
-    7700    1.5780919   -1.6213683            0 -0.059057356    0.3826822 
-    7800    1.8079476    -1.761193            0  0.028675183  0.034143718 
-    7900     1.836977   -1.8401332            0 -0.021525986   0.21458105 
-    8000    1.9135057   -1.8302694            0  0.064101272   0.23217665 
-    8100    1.8606829   -1.6984146            0   0.14366143   0.18168582 
-    8200    1.7474236   -1.7574166            0 -0.027467252   0.26529178 
-    8300    1.7637155   -1.7861969            0 -0.040118627   0.12298468 
-    8400    1.6564242    -1.477104            0   0.16275596   0.14143164 
-    8500    1.5868929   -1.6520125            0 -0.080988476   0.22461508 
-    8600    1.7556628   -1.7647169            0 -0.026610688   0.19913257 
-    8700     1.804704   -1.7892113            0 -0.0025543811    0.2825016 
-    8800    1.6511248   -1.8632147            0  -0.22860119  0.041019097 
-    8900    1.8323591   -1.7923506            0  0.021684941   0.21335945 
-    9000    1.9100569    -1.955559            0 -0.064602644     0.158775 
-    9100    1.7562572   -1.8720716            0  -0.13337695   0.19662119 
-    9200    1.6566561   -1.9406507            0  -0.30056122   0.12296597 
-    9300    1.8367792   -1.9060138            0 -0.087602325   0.19447518 
-    9400    1.8420592   -1.6318148            0   0.19182383   0.50726082 
-    9500    1.7773475   -1.6973532            0  0.062220818    0.2487172 
-    9600    1.6545313    -1.701977            0 -0.063991036   0.20549434 
-    9700    1.7463358   -1.8329845            0  -0.10411212   0.15498427 
-    9800    1.7799071   -1.7889616            0 -0.026853542    0.3169291 
-    9900    1.5838158    -1.718909            0  -0.15093133   0.46050618 
-   10000    1.6100625   -1.7018091            0  -0.10784725   0.10312591 
-Loop time of 0.715445 on 4 procs for 10000 steps with 100 atoms
-
-Performance: 6038199.147 tau/day, 13977.313 timesteps/s
-95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.35395    | 0.40307    | 0.45588    |   5.9 | 56.34
-Neigh   | 0.0033705  | 0.0036112  | 0.0039394  |   0.4 |  0.50
-Comm    | 0.17564    | 0.22399    | 0.26912    |   7.8 | 31.31
-Output  | 0.0014601  | 0.0024824  | 0.0054784  |   3.5 |  0.35
-Modify  | 0.038037   | 0.039219   | 0.04163    |   0.7 |  5.48
-Other   |            | 0.04308    |            |       |  6.02
-
-Nlocal:    25 ave 28 max 23 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-Nghost:    47.25 ave 49 max 42 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Neighs:    113.25 ave 132 max 104 min
-Histogram: 2 0 1 0 0 0 0 0 0 1
-
-Total # of neighbors = 453
-Ave neighs/atom = 4.53
-Neighbor list builds = 483
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/body/log.27Nov18.pour3d.g++.1 b/examples/body/log.27Nov18.pour3d.g++.1
deleted file mode 100644
index 10a4999d14..0000000000
--- a/examples/body/log.27Nov18.pour3d.g++.1
+++ /dev/null
@@ -1,74 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# pouring 3d rounded polyhedron bodies
-
-variable    steps index 6000
-
-units       lj
-boundary    p p fm
-comm_modify vel yes
-
-atom_style  body rounded/polyhedron 1 8
-atom_modify map array
-
-region		reg block 0 50 0 50 0 50 units box
-create_box	4 reg
-Created orthogonal box = (0 0 0) to (50 50 50)
-  1 by 1 by 1 MPI processor grid
-
-variable cut_inner  equal 0.5
-variable k_n        equal 100
-variable k_na       equal 5
-variable c_n        equal 20
-variable c_t        equal 5
-variable mu         equal 0
-variable A_ua       equal 1
-
-pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
-pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
-pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
-pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
-pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
-pair_style body/rounded/polyhedron 20 5 0 1 0.5
-pair_coeff * * ${k_n} ${k_na}
-pair_coeff * * 100 ${k_na}
-pair_coeff * * 100 5
-
-neighbor     0.5 bin
-neigh_modify every 1 delay 0 check yes
-
-timestep     0.001
-
-fix          1 all nve/body
-fix          2 all gravity 1.0 spherical 0.0 -180.0
-
-molecule     object molecule.cube molecule.tetra toff 1              molecule.rod3d toff 2 molecule.point3d toff 3
-Read molecule object:
-  1 atoms with max type 1
-  0 bonds with max type 0
-  0 angles with max type 0
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-Read molecule object:
-  1 atoms with max type 2
-  0 bonds with max type 0
-  0 angles with max type 0
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-Read molecule object:
-  1 atoms with max type 3
-  0 bonds with max type 0
-  0 angles with max type 0
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-Read molecule object:
-  1 atoms with max type 4
-  0 bonds with max type 0
-  0 angles with max type 0
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-
-region       slab block 5 45 5 45 25 35 units box
-fix          ins all pour 500 0 4767548 vol 0.4 10 region slab mol object              molfrac 0.25 0.25 0.25 0.25
-ERROR: Unknown fix style pour (src/modify.cpp:898)
-Last command: fix          ins all pour 500 0 4767548 vol 0.4 10 region slab mol object              molfrac 0.25 0.25 0.25 0.25
diff --git a/examples/body/log.27Nov18.pour3d.g++.4 b/examples/body/log.27Nov18.pour3d.g++.4
deleted file mode 100644
index eb65f99bc2..0000000000
--- a/examples/body/log.27Nov18.pour3d.g++.4
+++ /dev/null
@@ -1,74 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# pouring 3d rounded polyhedron bodies
-
-variable    steps index 6000
-
-units       lj
-boundary    p p fm
-comm_modify vel yes
-
-atom_style  body rounded/polyhedron 1 8
-atom_modify map array
-
-region		reg block 0 50 0 50 0 50 units box
-create_box	4 reg
-Created orthogonal box = (0 0 0) to (50 50 50)
-  1 by 2 by 2 MPI processor grid
-
-variable cut_inner  equal 0.5
-variable k_n        equal 100
-variable k_na       equal 5
-variable c_n        equal 20
-variable c_t        equal 5
-variable mu         equal 0
-variable A_ua       equal 1
-
-pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
-pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
-pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
-pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
-pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
-pair_style body/rounded/polyhedron 20 5 0 1 0.5
-pair_coeff * * ${k_n} ${k_na}
-pair_coeff * * 100 ${k_na}
-pair_coeff * * 100 5
-
-neighbor     0.5 bin
-neigh_modify every 1 delay 0 check yes
-
-timestep     0.001
-
-fix          1 all nve/body
-fix          2 all gravity 1.0 spherical 0.0 -180.0
-
-molecule     object molecule.cube molecule.tetra toff 1              molecule.rod3d toff 2 molecule.point3d toff 3
-Read molecule object:
-  1 atoms with max type 1
-  0 bonds with max type 0
-  0 angles with max type 0
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-Read molecule object:
-  1 atoms with max type 2
-  0 bonds with max type 0
-  0 angles with max type 0
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-Read molecule object:
-  1 atoms with max type 3
-  0 bonds with max type 0
-  0 angles with max type 0
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-Read molecule object:
-  1 atoms with max type 4
-  0 bonds with max type 0
-  0 angles with max type 0
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-
-region       slab block 5 45 5 45 25 35 units box
-fix          ins all pour 500 0 4767548 vol 0.4 10 region slab mol object              molfrac 0.25 0.25 0.25 0.25
-ERROR: Unknown fix style pour (src/modify.cpp:898)
-Last command: fix          ins all pour 500 0 4767548 vol 0.4 10 region slab mol object              molfrac 0.25 0.25 0.25 0.25
diff --git a/examples/body/log.27Nov18.squares.g++.1 b/examples/body/log.27Nov18.squares.g++.1
deleted file mode 100644
index cc334b416c..0000000000
--- a/examples/body/log.27Nov18.squares.g++.1
+++ /dev/null
@@ -1,222 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d rounded polygon bodies
-
-variable    r     index 4
-variable    steps index 100000
-variable    T     index 0.5
-variable    P     index 0.1
-variable    seed  index 980411
-
-units       lj
-dimension   2
-
-atom_style  body rounded/polygon 1 6
-atom_modify map array
-read_data   data.squares
-  orthogonal box = (0 0 -0.5) to (12 12 0.5)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  2 atoms
-  2 bodies
-
-replicate   $r $r 1
-replicate   4 $r 1
-replicate   4 4 1
-  orthogonal box = (0 0 -0.5) to (48 48 0.5)
-  1 by 1 by 1 MPI processor grid
-  32 atoms
-  Time spent = 0.000279665 secs
-
-velocity    all create $T ${seed} dist gaussian mom yes rot yes
-velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
-velocity    all create 0.5 980411 dist gaussian mom yes rot yes
-
-variable cut_inner  equal 0.5
-variable k_n        equal 100
-variable k_na       equal 2
-variable c_n        equal 1
-variable c_t        equal 1
-variable mu         equal 0.1
-variable delta_ua   equal 0.5
-
-pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
-pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
-pair_coeff * * ${k_n} ${k_na}
-pair_coeff * * 100 ${k_na}
-pair_coeff * * 100 2
-
-comm_modify vel yes
-
-neighbor     0.5 bin
-neigh_modify every 1 delay 0 check yes
-
-timestep     0.001
-
-#fix         1 all nve/body
-#fix         1 all nvt/body temp $T $T 1.0
-fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
-
-fix          2 all enforce2d
-
-#compute      1 all body/local id 1 2 3
-#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
-
-thermo_style custom step ke pe etotal press
-thermo       1000
-
-#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
-#dump_modify  2 pad 6
-
-run          ${steps}
-run          100000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.15685
-  ghost atom cutoff = 6.15685
-  binsize = 3.07843, bins = 16 16 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair body/rounded/polygon, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.781 | 4.781 | 4.781 Mbytes
-Step KinEng PotEng TotEng Press 
-       0     0.484375         0.25     0.734375 0.0067274306 
-    1000   0.38428256 0.0014168922   0.38569945 0.0020468171 
-    2000   0.41372193  0.015263236   0.42898517 0.0029343462 
-    3000   0.54844547  0.014870378   0.56331585  0.001978353 
-    4000   0.73816048  0.031668204   0.76982869 0.0025939718 
-    5000   0.84536165  0.011504649    0.8568663 0.0037990517 
-    6000   0.73776478   0.14445932    0.8822241 0.0086538113 
-    7000   0.52022565  0.069507637   0.58973329 0.0072098694 
-    8000   0.72653213   0.12783368   0.85436581  0.023907183 
-    9000   0.87685727    0.1239819    1.0008392 0.0064590959 
-   10000    0.7250918  0.097243508   0.82233531 0.0012448267 
-   11000   0.62302234   0.05597557   0.67899791 0.00080239872 
-   12000   0.57159363   0.18199602   0.75358965   0.01033626 
-   13000    0.7505295  0.071545266   0.82207477  0.011480236 
-   14000   0.84703598   0.15914379    1.0061798  0.032814039 
-   15000   0.41905013  0.090552572    0.5096027  0.015717153 
-   16000   0.41805189  0.042916881   0.46096877  0.020702707 
-   17000   0.59966233   0.05285043   0.65251275  0.016526024 
-   18000   0.54282285   0.20835047   0.75117332  0.036414059 
-   19000     0.777922  0.034754101    0.8126761  0.036467537 
-   20000   0.54703924   0.14633506    0.6933743  0.012917248 
-   21000   0.49337931    0.1858754   0.67925471  0.037890735 
-   22000   0.64916623   0.19281344   0.84197967  0.011996773 
-   23000   0.66958738   0.20459682    0.8741842  0.023639466 
-   24000   0.63729755    0.1111959   0.74849345  0.025049919 
-   25000   0.60094316   0.13375799   0.73470115  0.035286376 
-   26000   0.35419589   0.22049451    0.5746904 0.0024215291 
-   27000   0.33789786   0.18494942   0.52284728 0.0066457643 
-   28000   0.32376056   0.13151726   0.45527782  0.010773856 
-   29000   0.36198203   0.11044834   0.47243037  0.063012638 
-   30000   0.22624436   0.19690087   0.42314523  0.037422734 
-   31000   0.32284312  0.059623656   0.38246677    0.0287682 
-   32000    0.4457193  0.042396136   0.48811544  0.022025252 
-   33000   0.61078662  0.059447221   0.67023384  0.030335089 
-   34000   0.63157762  0.062056279    0.6936339  0.044624352 
-   35000   0.69577644  0.086216204   0.78199264    0.0319995 
-   36000   0.76814336  0.062105963   0.83024933  0.044316891 
-   37000   0.58641664  0.095034548   0.68145119   0.03234133 
-   38000   0.48772813   0.12911854   0.61684667  0.038732146 
-   39000   0.74957742   0.09823432   0.84781174  0.053181162 
-   40000   0.57881374    0.2932491   0.87206284  0.065740126 
-   41000    0.4415176   0.22899179   0.67050939  0.026159841 
-   42000    0.5260339    0.2048105    0.7308444  0.046294432 
-   43000   0.33493572   0.32500572   0.65994144  -0.01250241 
-   44000   0.46467243   0.07907132   0.54374375   0.13386238 
-   45000   0.48135518    0.2618908   0.74324598 -0.016767159 
-   46000   0.27223209   0.24562643   0.51785852  0.052118439 
-   47000   0.26402739    0.1838767   0.44790409 -0.0015878764 
-   48000   0.10229166   0.25519169   0.35748335 -0.033927088 
-   49000   0.24313495   0.16578185   0.40891679   0.12414926 
-   50000   0.27400066   0.27688032   0.55088098   0.10421157 
-   51000   0.43081855   0.18111733   0.61193587   0.16373371 
-   52000   0.81969298  0.060995894   0.88068887  0.057285357 
-   53000   0.99936159  0.029137886    1.0284995   0.19425015 
-   54000   0.69750047  0.038079774   0.73558024 -0.089236384 
-   55000   0.54823746  0.056369886   0.60460734 -0.021320579 
-   56000    0.6752322  0.050322917   0.72555512   0.25303548 
-   57000   0.90328009  0.061107142   0.96438723   -0.1962713 
-   58000   0.81463148  0.050387847   0.86501933   0.35952157 
-   59000   0.61636455  0.064910223   0.68127478  -0.27208497 
-   60000   0.62573918  0.052264617   0.67800379    0.4493407 
-   61000   0.81065726  0.071269668   0.88192693  -0.34643283 
-   62000   0.86420318  0.052799365   0.91700254   0.48308047 
-   63000   0.67848508  0.069087342   0.74757242  -0.31814526 
-   64000   0.61430417  0.052109373   0.66641354   0.38336646 
-   65000   0.75782937  0.063488206   0.82131757  -0.19113322 
-   66000   0.88735857  0.051779306   0.93913787   0.29410996 
-   67000   0.70684373  0.061786313   0.76863005  -0.16503578 
-   68000   0.58571951  0.052402151   0.63812166   0.30173228 
-   69000   0.64997491  0.064435462   0.71441037   -0.1920633 
-   70000   0.75071821  0.053416991    0.8041352    0.3846747 
-   71000    0.8124718   0.06877986   0.88125166  -0.26852566 
-   72000   0.71352066   0.05358784    0.7671085   0.41321806 
-   73000   0.55151827  0.066470642   0.61798891   -0.2211738 
-   74000   0.65473635  0.061946814   0.71668316   0.29536873 
-   75000   0.88704613  0.059476353   0.94652248   -0.0312656 
-   76000   0.76899803  0.057351665    0.8263497  0.017885214 
-   77000   0.65149455   0.05407174   0.70556629   0.25192449 
-   78000   0.68614394  0.074251169   0.76039511  -0.19369404 
-   79000   0.97451567   0.06262739    1.0371431    0.4217182 
-   80000   0.88207775  0.070157004   0.95223476  -0.27318477 
-   81000   0.69294455  0.062623957   0.75556851   0.40150141 
-   82000   0.70748016  0.073924331   0.78140449  -0.17128794 
-   83000   0.78180774  0.063513978   0.84532172   0.22033652 
-   84000   0.80170993  0.065812223   0.86752216  0.083202913 
-   85000   0.64788122  0.070348079    0.7182293 -0.066913668 
-   86000   0.56575431  0.064865112   0.63061942   0.33905786 
-   87000   0.78205358   0.07983702    0.8618906  -0.22844912 
-   88000   0.87426443  0.065703482   0.93996791     0.448573 
-   89000   0.73269893  0.079827385   0.81252632  -0.24183162 
-   90000   0.66703106  0.065630146   0.73266121   0.35410109 
-   91000   0.73107154   0.07402702   0.80509856 -0.085492997 
-   92000     1.043635  0.067156523    1.1107915   0.14311135 
-   93000   0.86063344  0.065607238   0.92624068   0.20750649 
-   94000   0.68304235  0.075962239   0.75900459  -0.14594625 
-   95000    0.7069191  0.067125732   0.77404483   0.39459759 
-   96000   0.79860046  0.090957588   0.88955805  -0.24202125 
-   97000   0.81366777  0.071387081   0.88505485   0.32217266 
-   98000   0.61885746  0.041524228   0.66038169   0.31635364 
-   99000   0.57007759  0.055438456   0.62551604  -0.21172902 
-  100000   0.80462394  0.045542313   0.85016626  0.099207503 
-Loop time of 6.34495 on 1 procs for 100000 steps with 32 atoms
-
-Performance: 1361713.788 tau/day, 15760.576 timesteps/s
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 5.0158     | 5.0158     | 5.0158     |   0.0 | 79.05
-Neigh   | 0.0072868  | 0.0072868  | 0.0072868  |   0.0 |  0.11
-Comm    | 0.18669    | 0.18669    | 0.18669    |   0.0 |  2.94
-Output  | 0.00098681 | 0.00098681 | 0.00098681 |   0.0 |  0.02
-Modify  | 1.0417     | 1.0417     | 1.0417     |   0.0 | 16.42
-Other   |            | 0.09245    |            |       |  1.46
-
-Nlocal:    32 ave 32 max 32 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    35 ave 35 max 35 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    61 ave 61 max 61 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 61
-Ave neighs/atom = 1.90625
-Neighbor list builds = 1545
-Dangerous builds = 0
-Total wall time: 0:00:06
diff --git a/examples/body/log.27Nov18.squares.g++.4 b/examples/body/log.27Nov18.squares.g++.4
deleted file mode 100644
index 62c6206677..0000000000
--- a/examples/body/log.27Nov18.squares.g++.4
+++ /dev/null
@@ -1,222 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d rounded polygon bodies
-
-variable    r     index 4
-variable    steps index 100000
-variable    T     index 0.5
-variable    P     index 0.1
-variable    seed  index 980411
-
-units       lj
-dimension   2
-
-atom_style  body rounded/polygon 1 6
-atom_modify map array
-read_data   data.squares
-  orthogonal box = (0 0 -0.5) to (12 12 0.5)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  2 atoms
-  2 bodies
-
-replicate   $r $r 1
-replicate   4 $r 1
-replicate   4 4 1
-  orthogonal box = (0 0 -0.5) to (48 48 0.5)
-  2 by 2 by 1 MPI processor grid
-  32 atoms
-  Time spent = 0.000400782 secs
-
-velocity    all create $T ${seed} dist gaussian mom yes rot yes
-velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
-velocity    all create 0.5 980411 dist gaussian mom yes rot yes
-
-variable cut_inner  equal 0.5
-variable k_n        equal 100
-variable k_na       equal 2
-variable c_n        equal 1
-variable c_t        equal 1
-variable mu         equal 0.1
-variable delta_ua   equal 0.5
-
-pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
-pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
-pair_coeff * * ${k_n} ${k_na}
-pair_coeff * * 100 ${k_na}
-pair_coeff * * 100 2
-
-comm_modify vel yes
-
-neighbor     0.5 bin
-neigh_modify every 1 delay 0 check yes
-
-timestep     0.001
-
-#fix         1 all nve/body
-#fix         1 all nvt/body temp $T $T 1.0
-fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
-
-fix          2 all enforce2d
-
-#compute      1 all body/local id 1 2 3
-#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
-
-thermo_style custom step ke pe etotal press
-thermo       1000
-
-#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
-#dump_modify  2 pad 6
-
-run          ${steps}
-run          100000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.15685
-  ghost atom cutoff = 6.15685
-  binsize = 3.07843, bins = 16 16 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair body/rounded/polygon, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 Mbytes
-Step KinEng PotEng TotEng Press 
-       0     0.484375         0.25     0.734375 0.0067274306 
-    1000   0.38428256 0.0014168922   0.38569945 0.0020468171 
-    2000   0.41372193  0.015263236   0.42898517 0.0029343462 
-    3000   0.54844547  0.014870378   0.56331585  0.001978353 
-    4000   0.73816048  0.031668204   0.76982869 0.0025939718 
-    5000   0.84536165  0.011504649    0.8568663 0.0037990517 
-    6000   0.73776478   0.14445932    0.8822241 0.0086538113 
-    7000   0.52022565  0.069507637   0.58973329 0.0072098694 
-    8000   0.72653213   0.12783367   0.85436581  0.023907185 
-    9000   0.87685728   0.12398193    1.0008392 0.0064591005 
-   10000   0.72509641  0.097241969   0.82233837 0.0012418726 
-   11000   0.62314955  0.056042914   0.67919247 0.0018880786 
-   12000   0.57157436   0.18187429   0.75344865 0.0096135623 
-   13000    0.7489742   0.08262775   0.83160195  0.009183917 
-   14000   0.78835138   0.18761048   0.97596186  0.023684357 
-   15000   0.40408761  0.079431327   0.48351893  0.025285348 
-   16000    0.4071013   0.13207058   0.53917188   0.02015488 
-   17000   0.48417067   0.16699781   0.65116848  0.059188189 
-   18000   0.60038567   0.18317457   0.78356024 -0.046456387 
-   19000   0.73796958  0.064271521    0.8022411  0.090257204 
-   20000   0.62508659   0.14486336   0.76994994   0.04948543 
-   21000    0.5596837   0.10018831   0.65987201  0.044961962 
-   22000   0.30731517    0.1386103   0.44592547  0.015096596 
-   23000   0.34371843    0.1486761   0.49239453  0.026100892 
-   24000   0.33484204   0.25428479   0.58912683   0.01974393 
-   25000   0.48714744   0.32743616    0.8145836  0.037925893 
-   26000   0.33255994   0.29851422   0.63107417  0.049419529 
-   27000   0.21735889   0.18816203   0.40552093  0.050622152 
-   28000   0.31911317   0.12559898   0.44471215 -0.0036236361 
-   29000   0.53280161  0.055185441   0.58798705  0.083856225 
-   30000   0.52916941   0.28697284   0.81614225  0.055873213 
-   31000   0.47861645   0.21932568   0.69794214   0.02762301 
-   32000   0.46786314  0.041856438   0.50971958  0.029923804 
-   33000   0.69944716  0.039356744    0.7388039  0.028174645 
-   34000   0.39964317    0.1027175   0.50236068  0.039495865 
-   35000   0.70199237   0.10421859   0.80621095  0.015943417 
-   36000   0.45053533  0.078626602   0.52916193 0.0073950287 
-   37000   0.41587918  0.056551665   0.47243084  0.034091318 
-   38000   0.58663473  0.039228671    0.6258634  0.033093641 
-   39000   0.72480658   0.14792564   0.87273222  0.030903741 
-   40000   0.51163285   0.13445292   0.64608577  -0.03114559 
-   41000   0.56273761   0.16720374   0.72994135  0.027968528 
-   42000   0.61850184   0.10584389   0.72434573 -0.036301799 
-   43000   0.60039772   0.11984289   0.72024062  0.080894236 
-   44000   0.57499839  0.068211092   0.64320948  0.049726122 
-   45000   0.69937239   0.16287141    0.8622438  0.044921114 
-   46000   0.23303785    0.2391726   0.47221045  0.021668935 
-   47000   0.27051781   0.10690378   0.37742159   0.11963476 
-   48000     0.408895  0.079919688   0.48881469  0.087484004 
-   49000   0.74363181  0.040819422   0.78445123  0.011937456 
-   50000   0.84482316   0.10205256   0.94687572  0.064133262 
-   51000   0.84923574  0.089882984   0.93911872  0.062696388 
-   52000   0.66278324    0.0331554   0.69593864  0.035150337 
-   53000   0.64737251  0.039608076   0.68698058  0.057687461 
-   54000   0.68931435  0.042661403   0.73197576  0.069664795 
-   55000   0.84523308   0.10293275   0.94816583  0.047343755 
-   56000   0.80033937    0.1534797   0.95381907  0.070206074 
-   57000    0.6214799    0.1174575    0.7389374  0.078530452 
-   58000   0.64228495  0.088089896   0.73037485  0.060245994 
-   59000   0.89376363  0.065171887   0.95893552  0.071658895 
-   60000   0.90162992  0.016564761   0.91819468  0.089245946 
-   61000   0.72439995 0.0076508835   0.73205083  0.031430213 
-   62000   0.71590702 0.0046728326   0.72057986   0.10153514 
-   63000   0.74491219 0.0046757926   0.74958798  0.077145851 
-   64000   0.77173614  0.008265632   0.78000178 -0.049932265 
-   65000   0.72789092 0.0053605745   0.73325149   0.27060389 
-   66000   0.63001101  0.013871945   0.64388296  -0.17766692 
-   67000   0.65887071 0.0069105692   0.66578128   0.31632918 
-   68000   0.89042862 0.0026334652   0.89306209 -0.050495873 
-   69000   0.83442374 0.0059232957   0.84034703  -0.21871692 
-   70000   0.65149642  0.004885383   0.65638181   0.50428108 
-   71000   0.66888808   0.01125057   0.68013865  -0.29575772 
-   72000   0.74941609 0.0026616299   0.75207772   0.34800716 
-   73000    0.7898844 0.0048982026    0.7947826 -0.096872644 
-   74000   0.68823538 0.0021467794   0.69038216   0.12272852 
-   75000    0.5238808 0.0046112795   0.52849208   0.25760316 
-   76000   0.65512889  0.014567969   0.66969686  -0.24622674 
-   77000   0.82292373 0.0092471048   0.83217083    0.4002304 
-   78000   0.76305221   0.01101937   0.77407158  -0.10704945 
-   79000   0.66279814 0.0090486405   0.67184678  0.037466134 
-   80000   0.65808885  0.010000569   0.66808942   0.31742291 
-   81000   0.91357798  0.046226814   0.95980479  -0.20945693 
-   82000   0.87611859 -0.016794871   0.85932372   0.31759733 
-   83000   0.66285455 -0.017921021   0.64493353   0.27065273 
-   84000   0.67460715 -0.0076174891   0.66698966 -0.024772659 
-   85000   0.77786135 0.0014316505     0.779293  -0.21635327 
-   86000   0.83246393  0.087489797   0.91995372  -0.13431455 
-   87000   0.62935573  0.045088823   0.67444455  0.037766395 
-   88000   0.55264538 -0.024625272   0.52802011   0.18121213 
-   89000   0.74171392 -0.012629926     0.729084  -0.27666424 
-   90000   0.82542165  -0.02296567   0.80245598  -0.30497174 
-   91000   0.72958657 -0.026275093   0.70331147  -0.27624518 
-   92000    0.6319558  0.022568297   0.65452409  -0.33539318 
-   93000   0.66685301  0.021889807   0.68874282  -0.39890762 
-   94000   0.91243243 0.0078218509   0.92025428  -0.27213648 
-   95000   0.81125179 -0.0096756295   0.80157616 -0.099802335 
-   96000   0.63354907 -0.018329423   0.61521965   0.18199604 
-   97000   0.66812347 -0.016650228   0.65147324   0.49878257 
-   98000   0.81490013 -0.0049164866   0.80998365  -0.13473106 
-   99000   0.82131147 0.0043198846   0.82563136   -0.3083957 
-  100000   0.50880983 -0.010467027    0.4983428  0.060606332 
-Loop time of 4.3169 on 4 procs for 100000 steps with 32 atoms
-
-Performance: 2001435.573 tau/day, 23164.764 timesteps/s
-95.1% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.2078     | 1.3972     | 1.6653     |  15.1 | 32.36
-Neigh   | 0.0030954  | 0.003284   | 0.0034814  |   0.3 |  0.08
-Comm    | 1.074      | 1.3595     | 1.6003     |  16.2 | 31.49
-Output  | 0.001703   | 0.0030067  | 0.0068843  |   4.1 |  0.07
-Modify  | 1.2071     | 1.2647     | 1.3062     |   3.6 | 29.30
-Other   |            | 0.2893     |            |       |  6.70
-
-Nlocal:    8 ave 9 max 6 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:    17.75 ave 20 max 16 min
-Histogram: 1 0 1 0 0 1 0 0 0 1
-Neighs:    14 ave 18 max 7 min
-Histogram: 1 0 0 0 0 0 0 1 1 1
-
-Total # of neighbors = 56
-Ave neighs/atom = 1.75
-Neighbor list builds = 1566
-Dangerous builds = 0
-Total wall time: 0:00:04
diff --git a/examples/body/log.27Nov18.wall2d.g++.1 b/examples/body/log.27Nov18.wall2d.g++.1
deleted file mode 100644
index 1987280bee..0000000000
--- a/examples/body/log.27Nov18.wall2d.g++.1
+++ /dev/null
@@ -1,224 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d rounded polygon bodies
-
-variable    r     index 4
-variable    steps index 100000
-variable    T     index 0.5
-variable    P     index 0.1
-variable    seed  index 980411
-
-units       lj
-dimension   2
-
-atom_style  body rounded/polygon 1 6
-atom_modify map array
-read_data   data.squares
-  orthogonal box = (0 0 -0.5) to (12 12 0.5)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  2 atoms
-  2 bodies
-
-replicate   $r $r 1
-replicate   4 $r 1
-replicate   4 4 1
-  orthogonal box = (0 0 -0.5) to (48 48 0.5)
-  1 by 1 by 1 MPI processor grid
-  32 atoms
-  Time spent = 0.000318766 secs
-
-velocity    all create $T ${seed} dist gaussian mom yes rot yes
-velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
-velocity    all create 0.5 980411 dist gaussian mom yes rot yes
-
-change_box  all boundary p f p
-
-variable cut_inner  equal 0.5
-variable k_n        equal 100
-variable k_na       equal 2
-variable c_n        equal 0.1
-variable c_t        equal 0.1
-variable mu         equal 0.1
-variable delta_ua   equal 0.5
-
-pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
-pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
-pair_coeff * * ${k_n} ${k_na}
-pair_coeff * * 100 ${k_na}
-pair_coeff * * 100 2
-
-comm_modify vel yes
-
-neighbor     0.5 bin
-neigh_modify every 1 delay 0 check yes
-
-timestep     0.001
-
-#fix         1 all nve/body
-#fix         1 all nvt/body temp $T $T 1.0
-fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
-
-fix          2 all enforce2d
-fix          3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
-
-#compute      1 all body/local id 1 2 3
-#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
-
-thermo_style custom step ke pe etotal press
-thermo       1000
-
-#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
-#dump_modify  2 pad 6
-
-run          ${steps}
-run          100000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.15685
-  ghost atom cutoff = 6.15685
-  binsize = 3.07843, bins = 16 16 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair body/rounded/polygon, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.771 | 4.771 | 4.771 Mbytes
-Step KinEng PotEng TotEng Press 
-       0     0.484375         0.25     0.734375 0.0067274306 
-    1000   0.51467204 0.00099202506   0.51566407  0.013452386 
-    2000   0.55674899 0.0040762275   0.56082522 0.0034529066 
-    3000    0.7546177   0.02259362   0.77721132  0.003650781 
-    4000   0.72710218   0.10284108   0.82994326 0.0059629371 
-    5000    0.5771012  0.069052145   0.64615335 0.00053937622 
-    6000   0.53848154  0.041891239   0.58037277 0.0018693312 
-    7000   0.61777556  0.033379829   0.65115538 0.0027584418 
-    8000   0.47427227  0.059558934    0.5338312  0.017087187 
-    9000   0.46822364  0.064382578   0.53260622  0.023258465 
-   10000   0.46511051  0.027799371   0.49290988  0.015319493 
-   11000   0.58686703  0.088016891   0.67488392 0.0088428936 
-   12000   0.49962603   0.09879099   0.59841702 0.00074311497 
-   13000   0.53160049  0.069625775   0.60122626  0.017019775 
-   14000   0.49574902  0.041214164   0.53696318 0.0060355978 
-   15000   0.56620415   0.13621516   0.70241931  0.045583297 
-   16000   0.40942564   0.11469877   0.52412441  0.029905784 
-   17000     0.608066  0.096938921   0.70500493  0.018509814 
-   18000   0.45622168  0.057018077   0.51323975 0.0034035281 
-   19000   0.48763322  0.057832224   0.54546545 0.0022972169 
-   20000   0.41577025   0.14480819   0.56057844  0.023882542 
-   21000   0.58565738    0.1601676   0.74582498   0.01702799 
-   22000   0.60430354   0.16740706    0.7717106 -0.0047632836 
-   23000   0.45659601   0.13740896   0.59400497    0.0191143 
-   24000   0.42741367   0.25490516   0.68231884  0.051459175 
-   25000   0.40851048  0.077823072   0.48633355  0.024392284 
-   26000   0.53392894   0.14504323   0.67897217  0.028964572 
-   27000   0.39775205   0.13101153   0.52876358 0.0080564916 
-   28000   0.63138106   0.17706612   0.80844718  0.017594524 
-   29000   0.57897788   0.26855503   0.84753292  0.019310624 
-   30000   0.37401002    0.2274666   0.60147663 0.0044804008 
-   31000   0.60924323   0.23142663   0.84066986  0.088271242 
-   32000   0.60310397   0.35719837   0.96030234 0.0096762289 
-   33000   0.47468105   0.17727177   0.65195282 0.0078486602 
-   34000   0.42270829   0.20131235   0.62402064  0.090216203 
-   35000   0.49578606    0.1697981   0.66558416  0.079099134 
-   36000   0.50744538   0.29600416   0.80344954  0.018819487 
-   37000   0.66728184   0.28166655   0.94894838  -0.01679437 
-   38000   0.38972905   0.25798163   0.64771068  0.040442456 
-   39000   0.38292839   0.21774389   0.60067228  0.016754932 
-   40000   0.61770336   0.34202184    0.9597252   0.10986262 
-   41000   0.42252651   0.13424708    0.5567736  0.040987711 
-   42000   0.67513868   0.29515562    0.9702943 0.0013757417 
-   43000   0.36768915   0.20349753   0.57118668  0.031443504 
-   44000   0.49371025  0.095615653    0.5893259  0.032289477 
-   45000   0.42144079   0.28894639   0.71038718  0.040302569 
-   46000   0.36360136   0.33117431   0.69477567  0.010881881 
-   47000    0.4206309   0.19557595   0.61620685  0.051137535 
-   48000    0.4131465   0.37027912   0.78342561   0.11903042 
-   49000     0.544703   0.38013565   0.92483865  0.054939742 
-   50000   0.47394272   0.32384493   0.79778764  0.088363602 
-   51000   0.55377533   0.38103395   0.93480927  0.097981664 
-   52000   0.60648433   0.30877364   0.91525797  0.088877781 
-   53000   0.62933509   0.33187159   0.96120668   0.10275954 
-   54000   0.55077522   0.39050008   0.94127529  0.066721412 
-   55000   0.41646397   0.34545572   0.76191969  0.011056796 
-   56000   0.44244954   0.39274744   0.83519698  0.039963853 
-   57000   0.41963092   0.33483982   0.75447073  0.032555938 
-   58000   0.37941475   0.36905323   0.74846798  0.043952263 
-   59000   0.53008564   0.32843795   0.85852359  0.080787301 
-   60000   0.43408908   0.19840268   0.63249176   0.06421165 
-   61000   0.56287814   0.31500577   0.87788391   0.12031895 
-   62000    0.5185192   0.18275672   0.70127592 -0.0086212356 
-   63000   0.57275413   0.45147395    1.0242281  0.054617465 
-   64000   0.28322907   0.33687722   0.62010629   0.07268947 
-   65000   0.40230876   0.37989067   0.78219943 -0.029604066 
-   66000   0.58601209   0.52721274    1.1132248 -0.00037054404 
-   67000   0.52669356   0.44276199   0.96945554   0.18969356 
-   68000   0.41566831   0.47320489    0.8888732  0.040635264 
-   69000   0.52140574    0.4261935   0.94759923  0.016566201 
-   70000   0.42034133   0.55867009   0.97901142  0.047465899 
-   71000   0.48720036   0.43749264     0.924693   0.15984789 
-   72000    0.5244238   0.55854139    1.0829652   0.10155994 
-   73000   0.69990219   0.57313852    1.2730407   0.11108648 
-   74000   0.38274347   0.23359664   0.61634011  0.027968087 
-   75000   0.47493369   0.49472607   0.96965976   0.10961568 
-   76000   0.57064727   0.37996383    0.9506111  0.034746271 
-   77000   0.50401727   0.34437588   0.84839315  0.015116686 
-   78000   0.59504118   0.44154772    1.0365889  0.059341875 
-   79000    0.4920801   0.58935767    1.0814378   0.12139906 
-   80000   0.56992818   0.38916606   0.95909424  0.073618074 
-   81000   0.38446945   0.77314417    1.1576136   0.12173381 
-   82000   0.48734531   0.56198203    1.0493273    0.1080115 
-   83000    0.5516933   0.56743096    1.1191243   0.13936805 
-   84000   0.53336893   0.62914863    1.1625176 0.0084970895 
-   85000   0.46456977   0.77446084    1.2390306   0.18024688 
-   86000   0.58067599   0.53109608    1.1117721  0.012492021 
-   87000   0.55096446   0.61715622    1.1681207   0.13264723 
-   88000   0.56548774   0.74463701    1.3101247   0.14491188 
-   89000   0.52492634   0.58482194    1.1097483   0.21155245 
-   90000   0.64973565   0.85514474    1.5048804  0.036911953 
-   91000   0.55367722   0.74046971    1.2941469   0.23918851 
-   92000   0.44863249   0.56773761    1.0163701 0.00042860088 
-   93000   0.64728356   0.66594086    1.3132244 0.0022850006 
-   94000   0.65255497   0.82136644    1.4739214   0.10037643 
-   95000   0.62266654   0.82642147     1.449088   0.11964602 
-   96000   0.50656004   0.83312844    1.3396885  0.078491084 
-   97000   0.47126712   0.70469684     1.175964   0.12956056 
-   98000   0.48661103    1.0121726    1.4987837  0.043537851 
-   99000   0.48379797    0.9520931    1.4358911  0.082047522 
-  100000   0.54266361    1.0959698    1.6386334  -0.13092175 
-Loop time of 3.8532 on 1 procs for 100000 steps with 32 atoms
-
-Performance: 2242290.202 tau/day, 25952.433 timesteps/s
-98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.3917     | 2.3917     | 2.3917     |   0.0 | 62.07
-Neigh   | 0.012386   | 0.012386   | 0.012386   |   0.0 |  0.32
-Comm    | 0.11307    | 0.11307    | 0.11307    |   0.0 |  2.93
-Output  | 0.0010369  | 0.0010369  | 0.0010369  |   0.0 |  0.03
-Modify  | 1.246      | 1.246      | 1.246      |   0.0 | 32.34
-Other   |            | 0.08895    |            |       |  2.31
-
-Nlocal:    32 ave 32 max 32 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    21 ave 21 max 21 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    55 ave 55 max 55 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 55
-Ave neighs/atom = 1.71875
-Neighbor list builds = 2886
-Dangerous builds = 0
-Total wall time: 0:00:03
diff --git a/examples/body/log.27Nov18.wall2d.g++.4 b/examples/body/log.27Nov18.wall2d.g++.4
deleted file mode 100644
index d9a27cb1e4..0000000000
--- a/examples/body/log.27Nov18.wall2d.g++.4
+++ /dev/null
@@ -1,224 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d rounded polygon bodies
-
-variable    r     index 4
-variable    steps index 100000
-variable    T     index 0.5
-variable    P     index 0.1
-variable    seed  index 980411
-
-units       lj
-dimension   2
-
-atom_style  body rounded/polygon 1 6
-atom_modify map array
-read_data   data.squares
-  orthogonal box = (0 0 -0.5) to (12 12 0.5)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  2 atoms
-  2 bodies
-
-replicate   $r $r 1
-replicate   4 $r 1
-replicate   4 4 1
-  orthogonal box = (0 0 -0.5) to (48 48 0.5)
-  2 by 2 by 1 MPI processor grid
-  32 atoms
-  Time spent = 0.000329733 secs
-
-velocity    all create $T ${seed} dist gaussian mom yes rot yes
-velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
-velocity    all create 0.5 980411 dist gaussian mom yes rot yes
-
-change_box  all boundary p f p
-
-variable cut_inner  equal 0.5
-variable k_n        equal 100
-variable k_na       equal 2
-variable c_n        equal 0.1
-variable c_t        equal 0.1
-variable mu         equal 0.1
-variable delta_ua   equal 0.5
-
-pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
-pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
-pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
-pair_coeff * * ${k_n} ${k_na}
-pair_coeff * * 100 ${k_na}
-pair_coeff * * 100 2
-
-comm_modify vel yes
-
-neighbor     0.5 bin
-neigh_modify every 1 delay 0 check yes
-
-timestep     0.001
-
-#fix         1 all nve/body
-#fix         1 all nvt/body temp $T $T 1.0
-fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
-fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
-
-fix          2 all enforce2d
-fix          3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
-
-#compute      1 all body/local id 1 2 3
-#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
-
-thermo_style custom step ke pe etotal press
-thermo       1000
-
-#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
-#dump_modify  2 pad 6
-
-run          ${steps}
-run          100000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.15685
-  ghost atom cutoff = 6.15685
-  binsize = 3.07843, bins = 16 16 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair body/rounded/polygon, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.773 | 4.773 | 4.773 Mbytes
-Step KinEng PotEng TotEng Press 
-       0     0.484375         0.25     0.734375 0.0067274306 
-    1000   0.51467204 0.00099202506   0.51566407  0.013452386 
-    2000   0.55674899 0.0040762275   0.56082522 0.0034529066 
-    3000    0.7546177   0.02259362   0.77721132  0.003650781 
-    4000   0.72710218   0.10284108   0.82994326 0.0059629371 
-    5000   0.57710119  0.069052154   0.64615335 0.00053937664 
-    6000   0.53848104  0.041891152   0.58037219 0.0018693259 
-    7000   0.61777485  0.033380825   0.65115568 0.0027584782 
-    8000   0.47427732  0.059553658   0.53383098  0.017087698 
-    9000   0.46820943  0.064379697   0.53258913   0.02325702 
-   10000   0.46605511   0.02332689     0.489382  0.013699209 
-   11000   0.57547516  0.090133398   0.66560855 0.0083913962 
-   12000     0.465348  0.084853345   0.55020135  0.006231552 
-   13000   0.55340889   0.07116165   0.62457054  0.030622563 
-   14000   0.58866362  0.052281859   0.64094548 0.0079106838 
-   15000   0.51757672   0.12255618    0.6401329  0.014005369 
-   16000   0.42696011  0.086987541   0.51394765 -0.0017128649 
-   17000   0.37612579   0.13054778   0.50667357 0.0046284992 
-   18000   0.47659682   0.14670523   0.62330205   0.02206928 
-   19000   0.47897909   0.15540332   0.63438241   0.02544138 
-   20000   0.59377323   0.15357757    0.7473508  0.030262926 
-   21000   0.52781204   0.22074491   0.74855695 -0.0022170167 
-   22000   0.44843285   0.12779345    0.5762263 0.0097268482 
-   23000   0.60400735   0.18098124   0.78498858   0.05778325 
-   24000   0.58254338    0.1570243   0.73956769  0.022530491 
-   25000   0.60524318   0.23660272    0.8418459  0.062530421 
-   26000   0.45892702   0.34294121   0.80186823  0.038657393 
-   27000   0.58418023   0.19551937    0.7796996 -0.0055396645 
-   28000   0.45655369   0.26718934   0.72374303  0.006593108 
-   29000   0.50277299    0.1747088   0.67748179  0.016059369 
-   30000   0.38640717    0.1631573   0.54956447  0.036055723 
-   31000   0.46944541   0.22076826   0.69021367  0.014334038 
-   32000   0.53862858   0.26867594   0.80730452  0.057406282 
-   33000   0.45666352   0.21796554   0.67462906  0.056555205 
-   34000   0.51644038   0.21866786   0.73510824     0.015713 
-   35000   0.50489584    0.1596236   0.66451945  0.040400644 
-   36000   0.41723489   0.16227853   0.57951342   0.02863261 
-   37000     0.481638   0.28830624   0.76994424  0.038381986 
-   38000    0.6036094   0.33479287   0.93840227 0.0032059452 
-   39000   0.47822122   0.18876355   0.66698476  0.029252649 
-   40000   0.54949607   0.35011086   0.89960693  0.093909148 
-   41000   0.54876522   0.27501735   0.82378257 -0.0084167014 
-   42000   0.67801592   0.18102522   0.85904114 -0.0058395209 
-   43000   0.54342066   0.34322081   0.88664146   0.12263806 
-   44000   0.46672513   0.29749157   0.76421671  0.051073701 
-   45000    0.4679867   0.25820875   0.72619545  0.069790993 
-   46000   0.59598501   0.22285276   0.81883777  0.050578807 
-   47000   0.48858341   0.29811577   0.78669917  0.080971431 
-   48000   0.41238073   0.29362937    0.7060101  0.031893588 
-   49000   0.61516435   0.33082609   0.94599044 -0.010710982 
-   50000   0.57576635   0.37137185   0.94713819  0.062160249 
-   51000   0.54614001   0.36960628   0.91574629 -0.0083424769 
-   52000   0.42232354   0.25214442   0.67446796  0.028666126 
-   53000   0.43025129   0.24479385   0.67504514  0.030342054 
-   54000   0.54614922   0.29602426   0.84217348  0.083070642 
-   55000   0.60719748    0.3577285   0.96492598  0.053799744 
-   56000   0.47073149   0.31070429   0.78143579  0.083895368 
-   57000   0.56861582   0.33249784   0.90111366  0.032324233 
-   58000   0.75061035   0.33313728    1.0837476  0.031039937 
-   59000   0.59473893   0.48870773    1.0834467  0.039503585 
-   60000   0.55252481   0.38350562   0.93603043 0.0027643882 
-   61000   0.45010855   0.43945065    0.8895592  0.028168222 
-   62000   0.63942467   0.53372899    1.1731537   0.13790959 
-   63000   0.69407873   0.37980402    1.0738828  0.035919608 
-   64000   0.54898275   0.39910419   0.94808693 0.0015016851 
-   65000   0.58229838   0.42300361     1.005302  0.089787193 
-   66000   0.53443537    0.5597136     1.094149 -0.015781756 
-   67000   0.59212426   0.56172146    1.1538457  0.030464683 
-   68000   0.68164926   0.48724393    1.1688932  0.071465948 
-   69000   0.59721737   0.49476309    1.0919805   0.07575647 
-   70000   0.52314551   0.31950477   0.84265028   0.11206672 
-   71000   0.53230509   0.53846575    1.0707708 0.0047204701 
-   72000   0.71341933    0.4924749    1.2058942     0.116568 
-   73000   0.70498496   0.54121008     1.246195   0.11210249 
-   74000   0.54188682   0.61729607    1.1591829  0.044083048 
-   75000   0.44073609   0.42072284   0.86145893 -0.041508511 
-   76000   0.51225567   0.36848317   0.88073884 -0.028636748 
-   77000    0.6517329    0.5503086    1.2020415  0.049605026 
-   78000   0.60053898   0.52760266    1.1281416  0.094361256 
-   79000   0.51560788   0.46563043   0.98123832  -0.03336136 
-   80000   0.53357884   0.60743981    1.1410186  0.027259883 
-   81000    0.6256228   0.40412923     1.029752  0.083274981 
-   82000    0.6903519   0.69599412     1.386346     0.168747 
-   83000   0.62621394   0.50082841    1.1270424   0.12294403 
-   84000    0.5682146   0.73827702    1.3064916  0.085884707 
-   85000   0.48179077   0.73669563    1.2184864  0.065002035 
-   86000   0.61101399   0.80673836    1.4177523  0.037555163 
-   87000   0.52278725   0.71608722    1.2388745  0.020943688 
-   88000   0.53318823   0.50916748    1.0423557  -0.01946691 
-   89000   0.56428713   0.56042234    1.1247095  0.040998134 
-   90000   0.58720508   0.66023073    1.2474358  0.040313529 
-   91000   0.61509407   0.86254343    1.4776375   0.15215034 
-   92000    0.5640475   0.57694543    1.1409929   0.10238679 
-   93000   0.60586378   0.67978456    1.2856483 -0.043948113 
-   94000   0.75406595   0.74795347    1.5020194  0.015341415 
-   95000    0.4974314   0.60192267    1.0993541 -0.018173218 
-   96000   0.50048302   0.82845218    1.3289352  0.045394283 
-   97000   0.65335222    0.6470855    1.3004377  0.011624967 
-   98000   0.65693072   0.45222133     1.109152   0.13763684 
-   99000   0.60573344   0.50284289    1.1085763   0.12853674 
-  100000   0.50677068   0.58143063    1.0882013   0.11351254 
-Loop time of 3.24642 on 4 procs for 100000 steps with 32 atoms
-
-Performance: 2661396.711 tau/day, 30803.203 timesteps/s
-94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.64148    | 0.70244    | 0.76391    |   6.5 | 21.64
-Neigh   | 0.0049012  | 0.0050417  | 0.0052478  |   0.2 |  0.16
-Comm    | 0.79447    | 0.88412    | 0.97443    |   8.1 | 27.23
-Output  | 0.001776   | 0.0031438  | 0.0072262  |   4.2 |  0.10
-Modify  | 1.325      | 1.3684     | 1.4049     |   2.4 | 42.15
-Other   |            | 0.2833     |            |       |  8.73
-
-Nlocal:    8 ave 9 max 7 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Nghost:    14 ave 15 max 13 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs:    13.25 ave 16 max 11 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-
-Total # of neighbors = 53
-Ave neighs/atom = 1.65625
-Neighbor list builds = 2654
-Dangerous builds = 0
-Total wall time: 0:00:03

From 4faebaf4ed32aae48f5a4f531821362913b91118 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 14:53:06 -0400
Subject: [PATCH 270/396] add log files for fix pimd/langevin

---
 .../data.metalnpt01                           |   0
 .../data.metalnpt02                           |   0
 .../data.metalnpt03                           |   0
 .../data.metalnpt04                           |   0
 .../pimd/{lj => langevin_metal_units}/in.lmp  |   6 +-
 .../log.14Jun23.langevin.metal.g++            |   2 +
 .../log.14Jun23.langevin.metal.g++.0          | 106 ++++++++++++++++++
 .../log.14Jun23.langevin.metal.g++.1          | 106 ++++++++++++++++++
 .../log.14Jun23.langevin.metal.g++.2          | 106 ++++++++++++++++++
 .../log.14Jun23.langevin.metal.g++.3          | 106 ++++++++++++++++++
 .../pimd/{lj => langevin_metal_units}/run.sh  |   0
 .../data.lj01                                 |   0
 .../data.lj02                                 |   0
 .../in.lmp                                    |   6 +-
 .../log.14Jun23.langevin.reduced.g++          |   2 +
 .../log.14Jun23.langevin.reduced.g++.0        |  97 ++++++++++++++++
 .../log.14Jun23.langevin.reduced.g++.1        |  97 ++++++++++++++++
 .../run.sh                                    |   0
 18 files changed, 628 insertions(+), 6 deletions(-)
 rename examples/PACKAGES/pimd/{lj => langevin_metal_units}/data.metalnpt01 (100%)
 rename examples/PACKAGES/pimd/{lj => langevin_metal_units}/data.metalnpt02 (100%)
 rename examples/PACKAGES/pimd/{lj => langevin_metal_units}/data.metalnpt03 (100%)
 rename examples/PACKAGES/pimd/{lj => langevin_metal_units}/data.metalnpt04 (100%)
 rename examples/PACKAGES/pimd/{lj => langevin_metal_units}/in.lmp (56%)
 create mode 100644 examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++
 create mode 100644 examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.0
 create mode 100644 examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.1
 create mode 100644 examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.2
 create mode 100644 examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.3
 rename examples/PACKAGES/pimd/{lj => langevin_metal_units}/run.sh (100%)
 rename examples/PACKAGES/pimd/{lj_reduced_units => langevin_reduced_units}/data.lj01 (100%)
 rename examples/PACKAGES/pimd/{lj_reduced_units => langevin_reduced_units}/data.lj02 (100%)
 rename examples/PACKAGES/pimd/{lj_reduced_units => langevin_reduced_units}/in.lmp (56%)
 create mode 100644 examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++
 create mode 100644 examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.0
 create mode 100644 examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.1
 rename examples/PACKAGES/pimd/{lj_reduced_units => langevin_reduced_units}/run.sh (100%)

diff --git a/examples/PACKAGES/pimd/lj/data.metalnpt01 b/examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt01
similarity index 100%
rename from examples/PACKAGES/pimd/lj/data.metalnpt01
rename to examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt01
diff --git a/examples/PACKAGES/pimd/lj/data.metalnpt02 b/examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt02
similarity index 100%
rename from examples/PACKAGES/pimd/lj/data.metalnpt02
rename to examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt02
diff --git a/examples/PACKAGES/pimd/lj/data.metalnpt03 b/examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt03
similarity index 100%
rename from examples/PACKAGES/pimd/lj/data.metalnpt03
rename to examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt03
diff --git a/examples/PACKAGES/pimd/lj/data.metalnpt04 b/examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt04
similarity index 100%
rename from examples/PACKAGES/pimd/lj/data.metalnpt04
rename to examples/PACKAGES/pimd/langevin_metal_units/data.metalnpt04
diff --git a/examples/PACKAGES/pimd/lj/in.lmp b/examples/PACKAGES/pimd/langevin_metal_units/in.lmp
similarity index 56%
rename from examples/PACKAGES/pimd/lj/in.lmp
rename to examples/PACKAGES/pimd/langevin_metal_units/in.lmp
index 9670225958..124063df99 100644
--- a/examples/PACKAGES/pimd/lj/in.lmp
+++ b/examples/PACKAGES/pimd/langevin_metal_units/in.lmp
@@ -20,9 +20,9 @@ fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau
 
 thermo_style custom step temp f_1[*] vol press
 thermo 100
-thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
+thermo_modify norm no
 
-dump dcd all custom 100 ${ibead}.xyz id type xu yu zu vx vy vz ix iy iz fx fy fz
-dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
+# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
 
 run 1000
diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++ b/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++
new file mode 100644
index 0000000000..fa22106766
--- /dev/null
+++ b/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++
@@ -0,0 +1,2 @@
+LAMMPS (28 Mar 2023)
+Running on 4 partitions of processors
diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.0 b/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.0
new file mode 100644
index 0000000000..00787df8ba
--- /dev/null
+++ b/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.0
@@ -0,0 +1,106 @@
+LAMMPS (28 Mar 2023)
+Processor partition = 0
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+read_data data.metalnpt01
+Reading data file ...
+  orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  reading velocities ...
+  200 velocities
+  read_data CPU = 0.001 seconds
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+velocity all create 0.0 01
+
+fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+
+Initializing PIMD BZP barostat...
+The barostat mass is W = 2.3401256650800001e+01
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
+# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+
+Initializing PI Langevin equation thermostat...
+Bead ID    |    omega    |    tau    |    c1    |    c2
+    0     0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
+    1     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
+    2     1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
+    3     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
+PILE_L thermostat successfully initialized!
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.5251
+  ghost atom cutoff = 11.5251
+  binsize = 5.76255, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
+   Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]        f_1[11]        f_1[12]        f_1[13]        f_1[14]        f_1[15]         Volume         Press     
+         0   0              0              0             -7.3046601      4.3005229     -21.877018     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -164.47373    
+       100   149.95804      3.8573359      0             -7.7921375      42.886648     -23.396327     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861     -101.30374    
+       200   245.00113      6.3021074      0             -8.2639651      41.690123     -22.521598     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      112.22426    
+       300   300.57486      7.7316177      0             -8.2986331      43.180131     -21.755813     -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        814.45889    
+       400   368.08438      9.4681493      0             -8.4800193      49.109699     -24.824142      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1202.0398    
+       500   419.32066      10.786088      0             -8.640773       45.427771     -22.825143      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      952.59748    
+       600   385.4127       9.9138817      0             -8.4356035      47.783726     -22.456104      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      676.62913    
+       700   360.14242      9.2638601      0             -8.2900275      42.626187     -20.571698     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      456.91446    
+       800   346.92167      8.923786       0             -8.0694169      45.160336     -21.885719     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      454.60123    
+       900   364.39442      9.3732334      0             -8.0415668      45.604542     -21.816625      5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      499.75868    
+      1000   390.77042      10.051697      0             -8.1948009      45.264242     -22.833545      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      572.98799    
+Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.14541    | 0.14541    | 0.14541    |   0.0 | 58.59
+Neigh   | 0.00099082 | 0.00099082 | 0.00099082 |   0.0 |  0.40
+Comm    | 0.0039966  | 0.0039966  | 0.0039966  |   0.0 |  1.61
+Output  | 0.00016346 | 0.00016346 | 0.00016346 |   0.0 |  0.07
+Modify  | 0.096205   | 0.096205   | 0.096205   |   0.0 | 38.76
+Other   |            | 0.001425   |            |       |  0.57
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1342 ave        1342 max        1342 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          10325 ave       10325 max       10325 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 10325
+Ave neighs/atom = 51.625
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.1 b/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.1
new file mode 100644
index 0000000000..83821cafb7
--- /dev/null
+++ b/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.1
@@ -0,0 +1,106 @@
+LAMMPS (28 Mar 2023)
+Processor partition = 1
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+read_data data.metalnpt02
+Reading data file ...
+  orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  reading velocities ...
+  200 velocities
+  read_data CPU = 0.001 seconds
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+velocity all create 0.0 02
+
+fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+
+Initializing PIMD BZP barostat...
+The barostat mass is W = 2.3401256650800001e+01
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
+# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+
+Initializing PI Langevin equation thermostat...
+Bead ID    |    omega    |    tau    |    c1    |    c2
+    0     0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
+    1     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
+    2     1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
+    3     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
+PILE_L thermostat successfully initialized!
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.5251
+  ghost atom cutoff = 11.5251
+  binsize = 5.76255, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
+   Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]        f_1[11]        f_1[12]        f_1[13]        f_1[14]        f_1[15]         Volume         Press     
+         0   0              0              11.920908     -7.3063682      4.3005229     -21.877018     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -167.65544    
+       100   483.61933      12.440028      11.405863     -7.7749671      42.886648     -23.396327     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861      606.14668    
+       200   452.03836      11.627678      11.47094      -8.2534927      41.690123     -22.521598     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      583.5476     
+       300   470.25997      12.096389      11.739306     -8.3750153      43.180131     -21.755813     -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        1152.6851    
+       400   459.46597      11.818737      12.502421     -8.5240576      49.109699     -24.824142      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1381.0251    
+       500   442.73121      11.388273      11.19396      -8.6488583      45.427771     -22.825143      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      1000.6119    
+       600   493.47034      12.693424      11.91335      -8.4625706      47.783726     -22.456104      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      904.52944    
+       700   470.04548      12.090871      10.348757     -8.278182       42.626187     -20.571698     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      715.22796    
+       800   458.04928      11.782296      11.152029     -8.0926613      45.160336     -21.885719     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      678.21261    
+       900   468.60547      12.05383       10.937315     -8.0319335      45.604542     -21.816625      5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      735.24377    
+      1000   427.44192      10.99499       11.916587     -8.2229199      45.264242     -22.833545      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      637.98311    
+Loop time of 0.248186 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 348.126 ns/day, 0.069 hours/ns, 4029.238 timesteps/s, 805.848 katom-step/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.14654    | 0.14654    | 0.14654    |   0.0 | 59.04
+Neigh   | 0.00099986 | 0.00099986 | 0.00099986 |   0.0 |  0.40
+Comm    | 0.0041628  | 0.0041628  | 0.0041628  |   0.0 |  1.68
+Output  | 0.00018019 | 0.00018019 | 0.00018019 |   0.0 |  0.07
+Modify  | 0.094878   | 0.094878   | 0.094878   |   0.0 | 38.23
+Other   |            | 0.001424   |            |       |  0.57
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1346 ave        1346 max        1346 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          10328 ave       10328 max       10328 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 10328
+Ave neighs/atom = 51.64
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.2 b/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.2
new file mode 100644
index 0000000000..fd8dd409ae
--- /dev/null
+++ b/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.2
@@ -0,0 +1,106 @@
+LAMMPS (28 Mar 2023)
+Processor partition = 2
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+read_data data.metalnpt03
+Reading data file ...
+  orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  reading velocities ...
+  200 velocities
+  read_data CPU = 0.001 seconds
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+velocity all create 0.0 03
+
+fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+
+Initializing PIMD BZP barostat...
+The barostat mass is W = 2.3401256650800001e+01
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
+# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+
+Initializing PI Langevin equation thermostat...
+Bead ID    |    omega    |    tau    |    c1    |    c2
+    0     0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
+    1     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
+    2     1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
+    3     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
+PILE_L thermostat successfully initialized!
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.5251
+  ghost atom cutoff = 11.5251
+  binsize = 5.76255, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
+   Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]        f_1[11]        f_1[12]        f_1[13]        f_1[14]        f_1[15]         Volume         Press     
+         0   0              0              10.862314     -7.320388       4.3005229     -21.877018     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -175.34503    
+       100   455.18121      11.708521      11.48472      -7.8033686      42.886648     -23.396327     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861      526.41632    
+       200   460.81997      11.853566      10.817157     -8.2276485      41.690123     -22.521598     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      615.80924    
+       300   481.48652      12.385166      10.035423     -8.3866916      43.180131     -21.755813     -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        1169.2917    
+       400   487.3584       12.536208      11.766522     -8.3643382      49.109699     -24.824142      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1574.1427    
+       500   446.36019      11.48162       12.144202     -8.680266       45.427771     -22.825143      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      979.68395    
+       600   500.3783       12.871115      11.075008     -8.47833        47.783726     -22.456104      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      912.39361    
+       700   435.40634      11.199857      10.923558     -8.3090105      42.626187     -20.571698     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      617.20857    
+       800   446.82793      11.493652      11.599712     -8.0900498      45.160336     -21.885719     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      652.13243    
+       900   448.28506      11.531133      12.130739     -8.0810557      45.604542     -21.816625      5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      674.68073    
+      1000   440.94913      11.342433      10.765654     -8.1419484      45.264242     -22.833545      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      730.67128    
+Loop time of 0.248185 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 348.128 ns/day, 0.069 hours/ns, 4029.259 timesteps/s, 805.852 katom-step/s
+97.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.14702    | 0.14702    | 0.14702    |   0.0 | 59.24
+Neigh   | 0.0010003  | 0.0010003  | 0.0010003  |   0.0 |  0.40
+Comm    | 0.0039821  | 0.0039821  | 0.0039821  |   0.0 |  1.60
+Output  | 0.00023527 | 0.00023527 | 0.00023527 |   0.0 |  0.09
+Modify  | 0.094519   | 0.094519   | 0.094519   |   0.0 | 38.08
+Other   |            | 0.001427   |            |       |  0.58
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1346 ave        1346 max        1346 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          10313 ave       10313 max       10313 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 10313
+Ave neighs/atom = 51.565
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.3 b/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.3
new file mode 100644
index 0000000000..423ebb7d63
--- /dev/null
+++ b/examples/PACKAGES/pimd/langevin_metal_units/log.14Jun23.langevin.metal.g++.3
@@ -0,0 +1,106 @@
+LAMMPS (28 Mar 2023)
+Processor partition = 3
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+read_data data.metalnpt04
+Reading data file ...
+  orthogonal box = (-11.876697 -11.876697 -11.876697) to (11.876697 11.876697 11.876697)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  reading velocities ...
+  200 velocities
+  read_data CPU = 0.001 seconds
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+velocity all create 0.0 04
+
+fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+
+Initializing PIMD BZP barostat...
+The barostat mass is W = 2.3401256650800001e+01
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+# dump dcd all custom 100 ${ibead}.dcd id type xu yu zu vx vy vz ix iy iz fx fy fz
+# dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+
+Initializing PI Langevin equation thermostat...
+Bead ID    |    omega    |    tau    |    c1    |    c2
+    0     0.00000000e+00 1.00000000e+00 9.99500125e-01 3.16148726e-02
+    1     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
+    2     1.18509233e+02 4.21908054e-03 8.88243614e-01 4.59372705e-01
+    3     8.37986825e+01 5.96668092e-03 9.19616372e-01 3.92817678e-01
+PILE_L thermostat successfully initialized!
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.5251
+  ghost atom cutoff = 11.5251
+  binsize = 5.76255, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.121 | 3.121 | 3.121 Mbytes
+   Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]        f_1[11]        f_1[12]        f_1[13]        f_1[14]        f_1[15]         Volume         Press     
+         0   0              0              10.794425     -7.3457072      4.3005229     -21.877018     -8.7249482      2.9571502     -1743.5332     -698.49808     -172.07477      0              0              0.033460054   -0.37064378     4.216227       13402.228     -191.02389    
+       100   426.01705      10.958338      12.206372     -7.8040582      42.886648     -23.396327     -1.980193       2.954003      -1888.0547     -1648.7118     -332.0298      -0.099139345    0.11500091     0.033044702   -0.3701566      42.83112       13235.861      464.39271    
+       200   414.52703      10.662783      11.934129     -8.2331312      41.690123     -22.521598     -4.273021       2.9600599     -1906.2904     -1609.02       -265.94404     -0.20527926     0.49305948     0.031504957   -0.36829556     41.729191      12619.125      502.87052    
+       300   424.85622      10.928478      11.681713     -8.357621       43.180131     -21.755813     -7.7032433      2.9714114     -1968.7685      290.49656      251.72564     -0.21935745     0.56300721     0.029467915   -0.36568855     43.236828      11803.2        1058.1162    
+       400   485.80103      12.496148      12.255827     -8.3658975      49.109699     -24.824142      2.9744597      2.9794185     -2335.993       1368.7398      570.03286     -0.028366234    0.0094148316   0.028338146   -0.36416383     49.028096      11350.678      1570.2486    
+       500   462.99006      11.909386      11.187609     -8.6934698      45.427771     -22.825143      16.22356       2.9684828     -2113.91       -272.84753      185.53392      0.091614289    0.098205455    0.028793585   -0.36478567     45.368325      11533.101      1014.2134    
+       600   465.24407      11.967366      11.168375     -8.4422887      47.783726     -22.456104      6.837575       2.967236      -2023.8117     -918.27943     -2.4106994      0.093360761    0.10198539     0.029589188   -0.36584873     47.725157      11851.775      864.12413    
+       700   426.16111      10.962044      11.000011     -8.2855512      42.626187     -20.571698     -5.7252564      2.9560528     -1806.9448     -1418.2247     -148.41657      0.075011202    0.065835696    0.030359455   -0.36685105     42.558523      12160.301      614.76939    
+       800   454.53159      11.691811      10.834606     -8.0654281      45.160336     -21.885719     -6.7745694      2.9575472     -1894.3641     -1329.3179     -136.42193      0.011114896    0.0014455064   0.030808183   -0.3674233      45.076543      12340.037      684.85907    
+       900   441.72064      11.362278      10.4492       -8.0786302      45.604542     -21.816625      5.586068       2.9578604     -1890.4653     -1271.1107     -111.89061     -0.020285587    0.0048148677   0.030774258   -0.36738033     45.521594      12326.448      659.68525    
+      1000   429.90929      11.058457      11.851933     -8.1578394      45.264242     -22.833545      6.9260573      2.960122      -2007.6188     -1179.7125     -70.907567     -0.062733519    0.046047757    0.030329191   -0.36681215     45.191633      12148.179      698.73278    
+Loop time of 0.248175 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 348.141 ns/day, 0.069 hours/ns, 4029.409 timesteps/s, 805.882 katom-step/s
+98.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.14919    | 0.14919    | 0.14919    |   0.0 | 60.12
+Neigh   | 0.00099112 | 0.00099112 | 0.00099112 |   0.0 |  0.40
+Comm    | 0.0040992  | 0.0040992  | 0.0040992  |   0.0 |  1.65
+Output  | 0.0001723  | 0.0001723  | 0.0001723  |   0.0 |  0.07
+Modify  | 0.092299   | 0.092299   | 0.092299   |   0.0 | 37.19
+Other   |            | 0.00142    |            |       |  0.57
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1346 ave        1346 max        1346 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          10332 ave       10332 max       10332 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 10332
+Ave neighs/atom = 51.66
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/PACKAGES/pimd/lj/run.sh b/examples/PACKAGES/pimd/langevin_metal_units/run.sh
similarity index 100%
rename from examples/PACKAGES/pimd/lj/run.sh
rename to examples/PACKAGES/pimd/langevin_metal_units/run.sh
diff --git a/examples/PACKAGES/pimd/lj_reduced_units/data.lj01 b/examples/PACKAGES/pimd/langevin_reduced_units/data.lj01
similarity index 100%
rename from examples/PACKAGES/pimd/lj_reduced_units/data.lj01
rename to examples/PACKAGES/pimd/langevin_reduced_units/data.lj01
diff --git a/examples/PACKAGES/pimd/lj_reduced_units/data.lj02 b/examples/PACKAGES/pimd/langevin_reduced_units/data.lj02
similarity index 100%
rename from examples/PACKAGES/pimd/lj_reduced_units/data.lj02
rename to examples/PACKAGES/pimd/langevin_reduced_units/data.lj02
diff --git a/examples/PACKAGES/pimd/lj_reduced_units/in.lmp b/examples/PACKAGES/pimd/langevin_reduced_units/in.lmp
similarity index 56%
rename from examples/PACKAGES/pimd/lj_reduced_units/in.lmp
rename to examples/PACKAGES/pimd/langevin_reduced_units/in.lmp
index 012214c4b2..80bfbe4956 100644
--- a/examples/PACKAGES/pimd/lj_reduced_units/in.lmp
+++ b/examples/PACKAGES/pimd/langevin_reduced_units/in.lmp
@@ -18,9 +18,9 @@ fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188
 
 thermo_style custom step temp f_1[*] vol press
 thermo 100
-thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
+thermo_modify norm no
 
-dump dcd all custom 1 ${ibead}.xyz id type x y z vx vy vz ix iy iz fx fy fz
-dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+#dump dcd all custom 1 ${ibead}.lammpstrj id type x y z vx vy vz ix iy iz fx fy fz
+#dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
 
 run 1000
diff --git a/examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++ b/examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++
new file mode 100644
index 0000000000..4ed421dddb
--- /dev/null
+++ b/examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++
@@ -0,0 +1,2 @@
+LAMMPS (28 Mar 2023)
+Running on 2 partitions of processors
diff --git a/examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.0 b/examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.0
new file mode 100644
index 0000000000..d219e20845
--- /dev/null
+++ b/examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.0
@@ -0,0 +1,97 @@
+LAMMPS (28 Mar 2023)
+Processor partition = 0
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 32 pad
+
+units lj
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 2.8015
+read_data data.lj${ibead}
+read_data data.lj01
+Reading data file ...
+  orthogonal box = (-3.4945131 -3.4945131 -3.4945131) to (3.4945131 3.4945131 3.4945131)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  read_data CPU = 0.001 seconds
+
+pair_coeff    * * 1.0 1.0
+pair_modify shift yes
+
+mass 1 1.0
+
+timestep 0.00044905847
+
+fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L ${ibead}
+fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L 01
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+#dump dcd all custom 1 ${ibead}.lammpstrj id type x y z vx vy vz ix iy iz fx fy fz
+#dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+
+Initializing PI Langevin equation thermostat...
+Bead ID    |    omega    |    tau    |    c1    |    c2
+    0     0.00000000e+00 1.00000000e+00 9.99775496e-01 2.11886210e-02
+    1     1.31777963e+02 3.79426112e-03 9.42540858e-01 3.34090903e-01
+PILE_L thermostat successfully initialized!
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.1015
+  ghost atom cutoff = 3.1015
+  binsize = 1.55075, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.117 | 3.117 | 3.117 Mbytes
+   Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]         Volume         Press     
+         0   0              0              0             -875.67022      841866.06     -843041.14      253.30998      382.47517     -1646.2945     -1.9663356     -0.82731217     341.38937     -1.3810467    
+       100   14.815998      4422.5753      0             -534.91485      5336.9805     -409.03828      7790.9787      306.80845     -0.79877176     13.250868      8.3263811      341.38937      12.561531    
+       200   13.762526      4108.114       0             -535.07896      4177.1707      63.548813     -8225.489       308.68383      0.1240984      12.723365      8.0800159      341.38937      12.1757      
+       300   12.566448      3751.0847      0             -493.13907      3999.3337     -31.433066      8675.7059      309.21599     -0.061382631    14.105486      8.6052841      341.38937      12.245009    
+       400   11.843976      3535.4267      0             -515.14836      3784.077      -23.971605     -81.467506      309.02093     -0.046811856    13.638064      8.2470184      341.38937      11.61585     
+       500   11.100239      3313.4214      0             -521.49831      3555.6926     -56.076799      648.94757      309.45936     -0.10950702     12.805213      7.7261445      341.38937      10.991018    
+       600   9.9616183      2973.5431      0             -462.72888      3219.061       41.992567      3171.6576      309.48724      0.082003271    13.759365      8.0375919      341.38937      11.071546    
+       700   9.3388468      2787.6458      0             -501.33865      2901.4483      81.033913      2000.5159      309.02619      0.15824338     12.744135      7.4580508      341.38937      10.129991    
+       800   8.9069211      2658.716       0             -523.1858       2864.6773     -29.435005      2329.1521      308.67617     -0.057480808    11.604242      6.8135454      341.38937      9.3513467    
+       900   8.5046965      2538.6519      0             -543.75602      2597.5491      50.752591      601.47078      308.62547      0.099109884    10.497389      6.2142574      341.38937      8.6389792    
+      1000   8.0725601      2409.6592      0             -571.72872      2533.47       -23.431499     -1267.4683      308.58765     -0.045757135    9.421094       5.5928021      341.38937      7.8375753    
+Loop time of 0.201181 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 192854.150 tau/day, 4970.640 timesteps/s, 994.128 katom-step/s
+98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.11949    | 0.11949    | 0.11949    |   0.0 | 59.39
+Neigh   | 0.011868   | 0.011868   | 0.011868   |   0.0 |  5.90
+Comm    | 0.0041169  | 0.0041169  | 0.0041169  |   0.0 |  2.05
+Output  | 0.00011916 | 0.00011916 | 0.00011916 |   0.0 |  0.06
+Modify  | 0.064249   | 0.064249   | 0.064249   |   0.0 | 31.94
+Other   |            | 0.00134    |            |       |  0.67
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1117 ave        1117 max        1117 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           7492 ave        7492 max        7492 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7492
+Ave neighs/atom = 37.46
+Neighbor list builds = 55
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.1 b/examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.1
new file mode 100644
index 0000000000..0804a3488a
--- /dev/null
+++ b/examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.1
@@ -0,0 +1,97 @@
+LAMMPS (28 Mar 2023)
+Processor partition = 1
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 32 pad
+
+units lj
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 2.8015
+read_data data.lj${ibead}
+read_data data.lj02
+Reading data file ...
+  orthogonal box = (-3.4945131 -3.4945131 -3.4945131) to (3.4945131 3.4945131 3.4945131)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  200 atoms
+  read_data CPU = 0.001 seconds
+
+pair_coeff    * * 1.0 1.0
+pair_modify shift yes
+
+mass 1 1.0
+
+timestep 0.00044905847
+
+fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L ${ibead}
+fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L 02
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no
+
+#dump dcd all custom 1 ${ibead}.lammpstrj id type x y z vx vy vz ix iy iz fx fy fz
+#dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+
+Initializing PI Langevin equation thermostat...
+Bead ID    |    omega    |    tau    |    c1    |    c2
+    0     0.00000000e+00 1.00000000e+00 9.99775496e-01 2.11886210e-02
+    1     1.31777963e+02 3.79426112e-03 9.42540858e-01 3.34090903e-01
+PILE_L thermostat successfully initialized!
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.1015
+  ghost atom cutoff = 3.1015
+  binsize = 1.55075, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.117 | 3.117 | 3.117 Mbytes
+   Step          Temp          f_1[1]         f_1[2]         f_1[3]         f_1[4]         f_1[5]         f_1[6]         f_1[7]         f_1[8]         f_1[9]        f_1[10]         Volume         Press     
+         0   0              0              843646.47     -904.74343      841866.06     -843041.14      253.30998      382.47517     -1646.2945     -1.9663356     -0.82731217     341.38937     -0.58528882   
+       100   3.1994696      955.04167      1014.3663     -520.08788      5336.9805     -409.03828      7790.9787      306.80845     -0.79877176     13.250868      8.3263811      341.38937      5.9400539    
+       200   2.0518234      612.46927      541.77919     -550.11284      4177.1707      63.548813     -8225.489       308.68383      0.1240984      12.723365      8.0800159      341.38937      5.1568532    
+       300   2.0005565      597.16612      636.76107     -492.53916      3999.3337     -31.433066      8675.7059      309.21599     -0.061382631    14.105486      8.6052841      341.38937      6.1061183    
+       400   2.1301774      635.85796      629.2996      -501.35894      3784.077      -23.971605     -81.467506      309.02093     -0.046811856    13.638064      8.2470184      341.38937      6.0950651    
+       500   2.1090509      629.55171      661.4048      -527.18699      3555.6926     -56.076799      648.94757      309.45936     -0.10950702     12.805213      7.7261445      341.38937      5.6641225    
+       600   2.1073653      629.04855      563.33543     -484.13719      3219.061       41.992567      3171.6576      309.48724      0.082003271    13.759365      8.0375919      341.38937      6.2053973    
+       700   1.9719777      588.63535      524.29409     -497.78822      2901.4483      81.033913      2000.5159      309.02619      0.15824338     12.744135      7.4580508      341.38937      5.9107525    
+       800   2.0469949      611.02799      634.76301     -516.64387      2864.6773     -29.435005      2329.1521      308.67617     -0.057480808    11.604242      6.8135454      341.38937      5.445481     
+       900   1.9587942      584.70008      554.57541     -536.62232      2597.5491      50.752591      601.47078      308.62547      0.099109884    10.497389      6.2142574      341.38937      4.9080572    
+      1000   2.0978185      626.19882      628.7595      -559.41879      2533.47       -23.431499     -1267.4683      308.58765     -0.045757135    9.421094       5.5928021      341.38937      4.5477372    
+Loop time of 0.20118 on 1 procs for 1000 steps with 200 atoms
+
+Performance: 192855.450 tau/day, 4970.674 timesteps/s, 994.135 katom-step/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.12009    | 0.12009    | 0.12009    |   0.0 | 59.69
+Neigh   | 0.012807   | 0.012807   | 0.012807   |   0.0 |  6.37
+Comm    | 0.0040331  | 0.0040331  | 0.0040331  |   0.0 |  2.00
+Output  | 0.00012271 | 0.00012271 | 0.00012271 |   0.0 |  0.06
+Modify  | 0.062764   | 0.062764   | 0.062764   |   0.0 | 31.20
+Other   |            | 0.001361   |            |       |  0.68
+
+Nlocal:            200 ave         200 max         200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1117 ave        1117 max        1117 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           7460 ave        7460 max        7460 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7460
+Ave neighs/atom = 37.3
+Neighbor list builds = 57
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/PACKAGES/pimd/lj_reduced_units/run.sh b/examples/PACKAGES/pimd/langevin_reduced_units/run.sh
similarity index 100%
rename from examples/PACKAGES/pimd/lj_reduced_units/run.sh
rename to examples/PACKAGES/pimd/langevin_reduced_units/run.sh

From 77898e4a86f82d9c231fe743f07662671351ceed Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 18:28:51 -0400
Subject: [PATCH 271/396] update log files for fix widom

---
 examples/mc/log.14Jun23.widom.lj.g++.1   |  91 +++++++++++++++
 examples/mc/log.14Jun23.widom.lj.g++.4   |  91 +++++++++++++++
 examples/mc/log.14Jun23.widom.spce.g++.1 | 139 +++++++++++++++++++++++
 examples/mc/log.30Jun20.widom.lj.g++.1   |  89 ---------------
 examples/mc/log.30Jun20.widom.lj.g++.4   |  89 ---------------
 examples/mc/log.30Jun20.widom.spce.g++.1 | 133 ----------------------
 6 files changed, 321 insertions(+), 311 deletions(-)
 create mode 100644 examples/mc/log.14Jun23.widom.lj.g++.1
 create mode 100644 examples/mc/log.14Jun23.widom.lj.g++.4
 create mode 100644 examples/mc/log.14Jun23.widom.spce.g++.1
 delete mode 100644 examples/mc/log.30Jun20.widom.lj.g++.1
 delete mode 100644 examples/mc/log.30Jun20.widom.lj.g++.4
 delete mode 100644 examples/mc/log.30Jun20.widom.spce.g++.1

diff --git a/examples/mc/log.14Jun23.widom.lj.g++.1 b/examples/mc/log.14Jun23.widom.lj.g++.1
new file mode 100644
index 0000000000..6cbbae89ed
--- /dev/null
+++ b/examples/mc/log.14Jun23.widom.lj.g++.1
@@ -0,0 +1,91 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
+
+units           lj
+atom_style      atomic
+
+pair_style      lj/cut 2.5
+pair_modify     shift yes
+
+read_data       data.widom.lj
+Reading data file ...
+  orthogonal box = (0 0 0) to (9.4 9.4 9.4)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1000 atoms
+  reading velocities ...
+  1000 velocities
+  read_data CPU = 0.006 seconds
+
+pair_coeff      1 1 1.0 1.0 2.5
+pair_coeff      1 2 1.5 0.8 2.0
+pair_coeff      2 2 0.5 0.88 2.2
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 5 check yes
+
+fix             mywidom all widom 10 100000 2 29494 0.75
+
+fix             1 all langevin 0.75 0.75 0.1 48279 zero yes
+fix             2 all nve
+
+timestep        0.002
+
+thermo_style    custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
+thermo          10
+
+run             100
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 5 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.181 | 3.181 | 3.181 Mbytes
+   Step          Temp          PotEng         TotEng         Press          Volume        Density      f_mywidom[1]   f_mywidom[2]   f_mywidom[3] 
+         0   0.75021245    -6.4204308     -5.2962374      7.2962696      830.584        1.2039721      0              0              830.584      
+        10   0.7358936     -6.4405082     -5.3377717      7.1699962      830.584        1.2039721     -3.8577501      171.3429       830.584      
+        20   0.75426414    -6.4267946     -5.2965298      7.2833985      830.584        1.2039721     -4.0708206      227.63895      830.584      
+        30   0.72947489    -6.4064078     -5.3132896      7.3872583      830.584        1.2039721     -4.4304803      367.7146       830.584      
+        40   0.73504751    -6.4248725     -5.3234038      7.2927069      830.584        1.2039721     -4.1904189      266.99373      830.584      
+        50   0.76497439    -6.4352472     -5.2889331      7.3046861      830.584        1.2039721     -3.8628472      172.51133      830.584      
+        60   0.75752861    -6.4147051     -5.2795485      7.4416         830.584        1.2039721     -3.5355467      111.5042       830.584      
+        70   0.77775078    -6.4210798     -5.2556202      7.4473703      830.584        1.2039721     -3.4754802      102.92223      830.584      
+        80   0.80937104    -6.4320008     -5.2191583      7.4121087      830.584        1.2039721     -3.9287513      188.35625      830.584      
+        90   0.76321255    -6.4203633     -5.2766893      7.4307727      830.584        1.2039721     -4.2257529      279.87337      830.584      
+       100   0.74561743    -6.4010576     -5.2837499      7.52907        830.584        1.2039721     -3.6817835      135.5099       830.584      
+Loop time of 10.2362 on 1 procs for 100 steps with 1000 atoms
+
+Performance: 1688.128 tau/day, 9.769 timesteps/s, 9.769 katom-step/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.058411   | 0.058411   | 0.058411   |   0.0 |  0.57
+Neigh   | 0.017611   | 0.017611   | 0.017611   |   0.0 |  0.17
+Comm    | 0.001774   | 0.001774   | 0.001774   |   0.0 |  0.02
+Output  | 0.00029892 | 0.00029892 | 0.00029892 |   0.0 |  0.00
+Modify  | 10.158     | 10.158     | 10.158     |   0.0 | 99.23
+Other   |            | 0.0003838  |            |       |  0.00
+
+Nlocal:           1000 ave        1000 max        1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           3049 ave        3049 max        3049 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          46176 ave       46176 max       46176 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 46176
+Ave neighs/atom = 46.176
+Neighbor list builds = 10
+Dangerous builds = 0
+Total wall time: 0:00:10
diff --git a/examples/mc/log.14Jun23.widom.lj.g++.4 b/examples/mc/log.14Jun23.widom.lj.g++.4
new file mode 100644
index 0000000000..7a1171f1b8
--- /dev/null
+++ b/examples/mc/log.14Jun23.widom.lj.g++.4
@@ -0,0 +1,91 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
+
+units           lj
+atom_style      atomic
+
+pair_style      lj/cut 2.5
+pair_modify     shift yes
+
+read_data       data.widom.lj
+Reading data file ...
+  orthogonal box = (0 0 0) to (9.4 9.4 9.4)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  1000 atoms
+  reading velocities ...
+  1000 velocities
+  read_data CPU = 0.009 seconds
+
+pair_coeff      1 1 1.0 1.0 2.5
+pair_coeff      1 2 1.5 0.8 2.0
+pair_coeff      2 2 0.5 0.88 2.2
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 5 check yes
+
+fix             mywidom all widom 10 100000 2 29494 0.75
+
+fix             1 all langevin 0.75 0.75 0.1 48279 zero yes
+fix             2 all nve
+
+timestep        0.002
+
+thermo_style    custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
+thermo          10
+
+run             100
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 5 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.13 | 3.131 Mbytes
+   Step          Temp          PotEng         TotEng         Press          Volume        Density      f_mywidom[1]   f_mywidom[2]   f_mywidom[3] 
+         0   0.75021245    -6.4204308     -5.2962374      7.2962696      830.584        1.2039721      0              0              830.584      
+        10   0.74279259    -6.4332442     -5.3201696      7.2071344      830.584        1.2039721     -3.4462258      98.984938      830.584      
+        20   0.73016272    -6.4222911     -5.3281423      7.2714238      830.584        1.2039721     -4.4887329      397.41346      830.584      
+        30   0.74416342    -6.429139      -5.3140101      7.2713375      830.584        1.2039721     -4.3313574      322.19056      830.584      
+        40   0.73295457    -6.4370942     -5.3387618      7.227091       830.584        1.2039721     -4.7419281      557.00309      830.584      
+        50   0.76914235    -6.4473959     -5.2948361      7.2179148      830.584        1.2039721     -3.1794069      69.352982      830.584      
+        60   0.74099083    -6.4433012     -5.3329265      7.204973       830.584        1.2039721     -3.5231065      109.66994      830.584      
+        70   0.74514671    -6.4288463     -5.312244       7.2771269      830.584        1.2039721     -1.0154832      3.8727995      830.584      
+        80   0.72787097    -6.4457574     -5.3550427      7.1130709      830.584        1.2039721     -3.6691709      133.2501       830.584      
+        90   0.78452846    -6.5034376     -5.3278217      6.8238659      830.584        1.2039721     -2.0798339      16.008373      830.584      
+       100   0.77188499    -6.487313      -5.3306433      6.9133194      830.584        1.2039721     -2.066579       15.727938      830.584      
+Loop time of 1.59209 on 4 procs for 100 steps with 1000 atoms
+
+Performance: 10853.637 tau/day, 62.810 timesteps/s, 62.810 katom-step/s
+96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.014713   | 0.015481   | 0.016154   |   0.4 |  0.97
+Neigh   | 0.0045952  | 0.0047537  | 0.0048917  |   0.2 |  0.30
+Comm    | 0.026382   | 0.086811   | 0.14145    |  13.9 |  5.45
+Output  | 0.00022704 | 0.0002596  | 0.00035704 |   0.0 |  0.02
+Modify  | 1.4299     | 1.4845     | 1.5447     |   3.4 | 93.24
+Other   |            | 0.0003365  |            |       |  0.02
+
+Nlocal:            250 ave         256 max         242 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost:           1666 ave        1670 max        1659 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Neighs:          11538 ave       11832 max       11091 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 46152
+Ave neighs/atom = 46.152
+Neighbor list builds = 10
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/mc/log.14Jun23.widom.spce.g++.1 b/examples/mc/log.14Jun23.widom.spce.g++.1
new file mode 100644
index 0000000000..712566985d
--- /dev/null
+++ b/examples/mc/log.14Jun23.widom.spce.g++.1
@@ -0,0 +1,139 @@
+LAMMPS (28 Mar 2023 - Development)
+  using 1 OpenMP thread(s) per MPI task
+units           real
+dimension       3
+boundary        p p p
+atom_style      full
+
+pair_style      lj/cut/coul/long 10.0
+bond_style      harmonic
+angle_style     harmonic
+
+read_data       data.spce
+Reading data file ...
+  orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8640 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  5760 bonds
+  reading angles ...
+  2880 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.002 seconds
+  read_data CPU = 0.048 seconds
+
+molecule        h2omol H2O.txt
+Read molecule template h2omol:
+  1 molecules
+  0 fragments
+  3 atoms with max type 2
+  2 bonds with max type 1
+  1 angles with max type 1
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+
+### Flexible SPC/E Potential Parameters ###
+### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
+pair_coeff 1 1 0.1502629 3.1169
+pair_coeff 1 2 0.0341116368 2.04845
+pair_coeff 2 2 0.00774378 0.98
+
+bond_coeff  1 176.864 0.9611
+angle_coeff 1 42.1845 109.4712
+kspace_style pppm 1.0e-4
+
+fix mywidom all widom 10 20 0 29494 298 mol h2omol
+
+fix 2 all nvt temp 298.0 298.0 100.0
+
+neighbor 2.0 bin
+neigh_modify delay 10 every 2 check yes
+
+
+#run variables
+timestep        0.5
+
+thermo          10
+thermo_style    custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
+
+run             100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.2690183
+  grid = 24 24 24
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.024843102
+  estimated relative force accuracy = 7.4814263e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 29791 13824
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Fix widom using full_energy option (src/MC/fix_widom.cpp:320)
+0 atoms in group FixWidom:widom_exclusion_group:mywidom
+0 atoms in group FixWidom:rotation_gas_atoms:mywidom
+WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:654)
+Neighbor list info ...
+  update: every = 2 steps, delay = 10 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 29.66 | 29.66 | 29.66 Mbytes
+   Step         TotEng         PotEng          Temp          Press          Volume        Density      f_mywidom[1]   f_mywidom[2]   f_mywidom[3] 
+         0  -29703.973     -29703.973      0             -4764.5901      82468.116      1.0447118      0              0              82468.116    
+        10  -29718         -32598.944      111.87604     -498.88935      82468.116      1.0447118      200.15526      1.6274344e-147  82468.116    
+        20  -29698.227     -32625.357      113.6696      -3120.7115      82468.116      1.0447118     -1.0295764      5.6893637      82468.116    
+        30  -29668.463     -33188.922      136.71037     -8129.0179      82468.116      1.0447118      5.5971294      7.856256e-05   82468.116    
+        40  -29654.066     -34017.797      169.45726     -5730.6427      82468.116      1.0447118      128.14313      1.0550462e-94  82468.116    
+        50  -29627.714     -33214.549      139.28799     -3954.0179      82468.116      1.0447118      122.28545      2.0851209e-90  82468.116    
+        60  -29602.616     -32995.039      131.73836     -8099.2136      82468.116      1.0447118     -1.4752191      12.07497       82468.116    
+        70  -29591.096     -33872.451      166.25834     -7065.2821      82468.116      1.0447118      17.210054      2.3911575e-13  82468.116    
+        80  -29553.631     -32971.209      132.7152      -3535.4257      82468.116      1.0447118      11.148921      6.6631697e-09  82468.116    
+        90  -29530.109     -33346.146      148.18857     -5312.6414      82468.116      1.0447118      51.783293      1.055658e-38   82468.116    
+       100  -29505.327     -34074.801      177.4469      -5991.0034      82468.116      1.0447118      32.415523      1.6878187e-24  82468.116    
+Loop time of 55.4401 on 1 procs for 100 steps with 8640 atoms
+
+Performance: 0.078 ns/day, 308.000 hours/ns, 1.804 timesteps/s, 15.584 katom-step/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.4117     | 5.4117     | 5.4117     |   0.0 |  9.76
+Bond    | 0.029451   | 0.029451   | 0.029451   |   0.0 |  0.05
+Kspace  | 0.73758    | 0.73758    | 0.73758    |   0.0 |  1.33
+Neigh   | 1.4296     | 1.4296     | 1.4296     |   0.0 |  2.58
+Comm    | 0.018593   | 0.018593   | 0.018593   |   0.0 |  0.03
+Output  | 0.00069303 | 0.00069303 | 0.00069303 |   0.0 |  0.00
+Modify  | 47.81      | 47.81      | 47.81      |   0.0 | 86.24
+Other   |            | 0.002525   |            |       |  0.00
+
+Nlocal:           8640 ave        8640 max        8640 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          23534 ave       23534 max       23534 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3.27356e+06 ave 3.27356e+06 max 3.27356e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3273560
+Ave neighs/atom = 378.88426
+Ave special neighs/atom = 2
+Neighbor list builds = 220
+Dangerous builds = 0
+Total wall time: 0:00:55
diff --git a/examples/mc/log.30Jun20.widom.lj.g++.1 b/examples/mc/log.30Jun20.widom.lj.g++.1
deleted file mode 100644
index 71621f9b4e..0000000000
--- a/examples/mc/log.30Jun20.widom.lj.g++.1
+++ /dev/null
@@ -1,89 +0,0 @@
-LAMMPS (30 Jun 2020)
-  using 1 OpenMP thread(s) per MPI task
-# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
-
-units           lj
-atom_style      atomic
-
-pair_style      lj/cut 2.5
-pair_modify     shift yes
-
-read_data       data.widom.lj
-  orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1000 atoms
-  reading velocities ...
-  1000 velocities
-  read_data CPU = 0.003 seconds
-
-pair_coeff      1 1 1.0 1.0 2.5
-pair_coeff      1 2 1.5 0.8 2.0
-pair_coeff      2 2 0.5 0.88 2.2
-
-neighbor        0.3 bin
-neigh_modify    delay 0 every 5 check yes
-
-fix             mywidom all widom 10 100000 2 29494 0.75
-
-fix             1 all langevin 0.75 0.75 0.1 48279 zero yes
-fix             2 all nve
-
-timestep        0.002
-
-thermo_style    custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
-thermo          10
-
-run             100
-Neighbor list info ...
-  update every 5 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4, bins = 7 7 7
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.181 | 3.181 | 3.181 Mbytes
-Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3] 
-       0   0.75021245   -6.4204308   -5.2962374    7.2962696      830.584    1.2039721            0            0      830.584 
-      10    0.7358936   -6.4405082   -5.3377717    7.1699962      830.584    1.2039721   -3.8577501     171.3429      830.584 
-      20   0.75426414   -6.4267946   -5.2965298    7.2833985      830.584    1.2039721   -4.0708206    227.63895      830.584 
-      30   0.72947489   -6.4064078   -5.3132896    7.3872583      830.584    1.2039721   -4.4304803     367.7146      830.584 
-      40   0.73504751   -6.4248725   -5.3234038    7.2927069      830.584    1.2039721   -4.1904189    266.99373      830.584 
-      50   0.76497439   -6.4352472   -5.2889331    7.3046861      830.584    1.2039721   -3.8628472    172.51133      830.584 
-      60   0.75752861   -6.4147051   -5.2795485       7.4416      830.584    1.2039721   -3.5355467     111.5042      830.584 
-      70   0.77775078   -6.4210798   -5.2556202    7.4473703      830.584    1.2039721   -3.4754802    102.92223      830.584 
-      80   0.80937104   -6.4320008   -5.2191583    7.4121087      830.584    1.2039721   -3.9287513    188.35625      830.584 
-      90   0.76321255   -6.4203633   -5.2766893    7.4307727      830.584    1.2039721   -4.2257529    279.87337      830.584 
-     100   0.74561743   -6.4010576   -5.2837499      7.52907      830.584    1.2039721   -3.6817835     135.5099      830.584 
-Loop time of 25.8264 on 1 procs for 100 steps with 1000 atoms
-
-Performance: 669.082 tau/day, 3.872 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.08186    | 0.08186    | 0.08186    |   0.0 |  0.32
-Neigh   | 0.023613   | 0.023613   | 0.023613   |   0.0 |  0.09
-Comm    | 0.0053532  | 0.0053532  | 0.0053532  |   0.0 |  0.02
-Output  | 0.00037837 | 0.00037837 | 0.00037837 |   0.0 |  0.00
-Modify  | 25.715     | 25.715     | 25.715     |   0.0 | 99.57
-Other   |            | 0.0005643  |            |       |  0.00
-
-Nlocal:        1000.00 ave        1000 max        1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:        3049.00 ave        3049 max        3049 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:        46176.0 ave       46176 max       46176 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 46176
-Ave neighs/atom = 46.176000
-Neighbor list builds = 10
-Dangerous builds = 0
-Total wall time: 0:00:25
diff --git a/examples/mc/log.30Jun20.widom.lj.g++.4 b/examples/mc/log.30Jun20.widom.lj.g++.4
deleted file mode 100644
index f726faed66..0000000000
--- a/examples/mc/log.30Jun20.widom.lj.g++.4
+++ /dev/null
@@ -1,89 +0,0 @@
-LAMMPS (30 Jun 2020)
-  using 1 OpenMP thread(s) per MPI task
-# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
-
-units           lj
-atom_style      atomic
-
-pair_style      lj/cut 2.5
-pair_modify     shift yes
-
-read_data       data.widom.lj
-  orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  1000 atoms
-  reading velocities ...
-  1000 velocities
-  read_data CPU = 0.002 seconds
-
-pair_coeff      1 1 1.0 1.0 2.5
-pair_coeff      1 2 1.5 0.8 2.0
-pair_coeff      2 2 0.5 0.88 2.2
-
-neighbor        0.3 bin
-neigh_modify    delay 0 every 5 check yes
-
-fix             mywidom all widom 10 100000 2 29494 0.75
-
-fix             1 all langevin 0.75 0.75 0.1 48279 zero yes
-fix             2 all nve
-
-timestep        0.002
-
-thermo_style    custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
-thermo          10
-
-run             100
-Neighbor list info ...
-  update every 5 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4, bins = 7 7 7
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.13 | 3.131 Mbytes
-Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3] 
-       0   0.75021245   -6.4204308   -5.2962374    7.2962696      830.584    1.2039721            0            0      830.584 
-      10   0.74279259   -6.4332442   -5.3201696    7.2071344      830.584    1.2039721   -3.4462258    98.984938      830.584 
-      20   0.73016272   -6.4222911   -5.3281423    7.2714238      830.584    1.2039721   -4.4887329    397.41346      830.584 
-      30   0.74416342    -6.429139   -5.3140101    7.2713375      830.584    1.2039721   -4.3313574    322.19056      830.584 
-      40   0.73295457   -6.4370942   -5.3387618     7.227091      830.584    1.2039721   -4.7419281    557.00309      830.584 
-      50   0.76914235   -6.4473959   -5.2948361    7.2179148      830.584    1.2039721   -3.1794069    69.352982      830.584 
-      60   0.74099083   -6.4433012   -5.3329265     7.204973      830.584    1.2039721   -3.5231065    109.66994      830.584 
-      70   0.74514671   -6.4288463    -5.312244    7.2771269      830.584    1.2039721   -1.0154832    3.8727995      830.584 
-      80   0.72787097   -6.4457574   -5.3550427    7.1130709      830.584    1.2039721   -3.6691709     133.2501      830.584 
-      90   0.78452846   -6.5034376   -5.3278217    6.8238659      830.584    1.2039721   -2.0798339    16.008373      830.584 
-     100   0.77188499    -6.487313   -5.3306433    6.9133194      830.584    1.2039721    -2.066579    15.727938      830.584 
-Loop time of 3.37748 on 4 procs for 100 steps with 1000 atoms
-
-Performance: 5116.239 tau/day, 29.608 timesteps/s
-98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.02025    | 0.020952   | 0.021322   |   0.3 |  0.62
-Neigh   | 0.0059071  | 0.0060568  | 0.0061543  |   0.1 |  0.18
-Comm    | 0.016558   | 0.059554   | 0.094282   |  12.2 |  1.76
-Output  | 0.00022173 | 0.00042927 | 0.0010471  |   0.0 |  0.01
-Modify  | 3.2552     | 3.2902     | 3.3335     |   1.7 | 97.42
-Other   |            | 0.0003003  |            |       |  0.01
-
-Nlocal:        250.000 ave         256 max         242 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-Nghost:        1666.00 ave        1670 max        1659 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Neighs:        11538.0 ave       11832 max       11091 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 46152
-Ave neighs/atom = 46.152000
-Neighbor list builds = 10
-Dangerous builds = 0
-Total wall time: 0:00:03
diff --git a/examples/mc/log.30Jun20.widom.spce.g++.1 b/examples/mc/log.30Jun20.widom.spce.g++.1
deleted file mode 100644
index 25aecc685d..0000000000
--- a/examples/mc/log.30Jun20.widom.spce.g++.1
+++ /dev/null
@@ -1,133 +0,0 @@
-LAMMPS (30 Jun 2020)
-  using 1 OpenMP thread(s) per MPI task
-units           real
-dimension       3
-boundary        p p p
-atom_style      full
-
-pair_style      lj/cut/coul/long 10.0
-bond_style      harmonic
-angle_style     harmonic
-
-read_data       data.spce
-  orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  8640 atoms
-  scanning bonds ...
-  2 = max bonds/atom
-  scanning angles ...
-  1 = max angles/atom
-  reading bonds ...
-  5760 bonds
-  reading angles ...
-  2880 angles
-     2 = max # of 1-2 neighbors
-     1 = max # of 1-3 neighbors
-     1 = max # of 1-4 neighbors
-     2 = max # of special neighbors
-  special bonds CPU = 0.008 seconds
-  read_data CPU = 0.028 seconds
-
-molecule        h2omol H2O.txt
-Read molecule template h2omol:
-  1 molecules
-  3 atoms with max type 2
-  2 bonds with max type 1
-  1 angles with max type 1
-  0 dihedrals with max type 0
-  0 impropers with max type 0
-
-### Flexible SPC/E Potential Parameters ###
-### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
-pair_coeff 1 1 0.1502629 3.1169
-pair_coeff 1 2 0.0341116368 2.04845
-pair_coeff 2 2 0.00774378 0.98
-
-bond_coeff  1 176.864 0.9611
-angle_coeff 1 42.1845 109.4712
-kspace_style pppm 1.0e-4
-
-fix mywidom all widom 10 20 0 29494 298 mol h2omol
-
-fix 2 all nvt temp 298.0 298.0 100.0
-
-neighbor 2.0 bin
-neigh_modify delay 10 every 2 check yes
-
-
-#run variables
-timestep        0.5
-
-thermo          10
-thermo_style    custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
-
-run             100
-PPPM initialization ...
-  using 12-bit tables for long-range coulomb (src/kspace.cpp:330)
-  G vector (1/distance) = 0.2690183
-  grid = 24 24 24
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.024843102
-  estimated relative force accuracy = 7.4814263e-05
-  using double precision FFTW3
-  3d grid and FFT values/proc = 29791 13824
-WARNING: Fix Widom using full_energy option (src/MC/fix_widom.cpp:297)
-0 atoms in group FixWidom:widom_exclusion_group:mywidom
-0 atoms in group FixWidom:rotation_gas_atoms:mywidom
-WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:487)
-Neighbor list info ...
-  update every 2 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 8 8 8
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 29.66 | 29.66 | 29.66 Mbytes
-Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3] 
-       0   -29703.973   -29703.973            0   -4764.5901    82468.116    1.9140713            0            0    82468.116 
-      10   -29712.131   -31110.041    54.285179   -3154.4423    82468.116    1.9140713    241.93348 3.7366217e-178    82468.116 
-      20   -29711.939   -32614.429    112.71273   -4216.1592    82468.116    1.9140713    16.095006 1.5716469e-12    82468.116 
-      30   -29688.142   -32368.506    104.08688   -4093.6515    82468.116    1.9140713    5.7862327 5.7086352e-05    82468.116 
-      40   -29662.343   -32252.144    100.57005   -1458.5339    82468.116    1.9140713    126.68071 1.2467216e-93    82468.116 
-      50    -29646.78   -32837.635    123.91081   -4607.1155    82468.116    1.9140713    74.622397 1.8790479e-55    82468.116 
-      60   -29628.968   -33001.229     130.9554   -4589.5296    82468.116    1.9140713    3.6575433 0.0020780497    82468.116 
-      70    -29602.78    -32816.28    124.79023   -3082.1133    82468.116    1.9140713    13.983097 5.561247e-11    82468.116 
-      80   -29577.552   -33141.454    138.39742   -6332.8138    82468.116    1.9140713     41.98931 1.6075608e-31    82468.116 
-      90   -29550.865   -33792.115    164.70094   -4607.6419    82468.116    1.9140713    68.690681 4.2082269e-51    82468.116 
-     100   -29515.107   -34052.782    176.21207   -3609.5709    82468.116    1.9140713    41.090597 7.3326206e-31    82468.116 
-Loop time of 163.407 on 1 procs for 100 steps with 8640 atoms
-
-Performance: 0.026 ns/day, 907.819 hours/ns, 0.612 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 8.5495     | 8.5495     | 8.5495     |   0.0 |  5.23
-Bond    | 0.031981   | 0.031981   | 0.031981   |   0.0 |  0.02
-Kspace  | 2.3995     | 2.3995     | 2.3995     |   0.0 |  1.47
-Neigh   | 5.0542     | 5.0542     | 5.0542     |   0.0 |  3.09
-Comm    | 0.051965   | 0.051965   | 0.051965   |   0.0 |  0.03
-Output  | 0.0018802  | 0.0018802  | 0.0018802  |   0.0 |  0.00
-Modify  | 147.31     | 147.31     | 147.31     |   0.0 | 90.15
-Other   |            | 0.003614   |            |       |  0.00
-
-Nlocal:        8640.00 ave        8640 max        8640 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:        23499.0 ave       23499 max       23499 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    3.27380e+06 ave  3.2738e+06 max  3.2738e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3273800
-Ave neighs/atom = 378.91204
-Ave special neighs/atom = 2.0000000
-Neighbor list builds = 220
-Dangerous builds = 0
-Total wall time: 0:02:44

From 4d02c6f26f391f9703b49ba7a79af890c5a147b3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 21:50:27 -0400
Subject: [PATCH 272/396] update version strings for upcoming release

---
 doc/lammps.1                         | 4 ++--
 doc/src/Commands_removed.rst         | 2 +-
 doc/src/Fortran.rst                  | 2 +-
 doc/src/compute_count_type.rst       | 2 +-
 doc/src/compute_stress_cartesian.rst | 4 ++--
 doc/src/compute_stress_mop.rst       | 2 +-
 doc/src/fix_dpd_source.rst           | 2 +-
 doc/src/fix_efield.rst               | 2 +-
 doc/src/fix_print.rst                | 2 +-
 doc/src/fix_reaxff_species.rst       | 2 +-
 doc/src/package.rst                  | 2 +-
 doc/src/pair_aip_water_2dm.rst       | 2 +-
 doc/src/pair_lepton.rst              | 6 ++++--
 doc/src/pair_lj_cut_sphere.rst       | 2 +-
 doc/src/pair_lj_expand_sphere.rst    | 2 +-
 doc/src/print.rst                    | 2 +-
 doc/src/variable.rst                 | 4 ++--
 src/library.cpp                      | 2 +-
 src/version.h                        | 3 +--
 19 files changed, 25 insertions(+), 24 deletions(-)

diff --git a/doc/lammps.1 b/doc/lammps.1
index b1be867e60..9bc107624f 100644
--- a/doc/lammps.1
+++ b/doc/lammps.1
@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "28 March 2023" "2023-03-28"
+.TH LAMMPS "1" "15 June 2023" "2023-06-15"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 28 March 2023
+\- Molecular Dynamics Simulator.  Version 15 June 2023
 
 .SH SYNOPSIS
 .B lmp
diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst
index d50eab3a41..1848a28024 100644
--- a/doc/src/Commands_removed.rst
+++ b/doc/src/Commands_removed.rst
@@ -41,7 +41,7 @@ warning.
 LATTE package
 -------------
 
-.. deprecated:: TBD
+.. deprecated:: 15Jun2023
 
 The LATTE package with the fix latte command was removed from LAMMPS.
 This functionality has been superseded by :doc:`fix mdi/qm <fix_mdi_qm>`
diff --git a/doc/src/Fortran.rst b/doc/src/Fortran.rst
index a0e4da56b5..7e9f16fa70 100644
--- a/doc/src/Fortran.rst
+++ b/doc/src/Fortran.rst
@@ -620,7 +620,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    output, depending on the data requested through *what*.  Note that *index*
    uses 1-based indexing to access thermo output columns.
 
-   .. versionadded:: TBD
+   .. versionadded:: 15Jun2023
 
    Note that this function actually does not return a value, but rather
    associates the pointer on the left side of the assignment to point to
diff --git a/doc/src/compute_count_type.rst b/doc/src/compute_count_type.rst
index 81fffb4f28..ca3b02ecdb 100644
--- a/doc/src/compute_count_type.rst
+++ b/doc/src/compute_count_type.rst
@@ -25,7 +25,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
 Define a computation that counts the current number of atoms for each
 atom type.  Or the number of bonds (angles, dihedrals, impropers) for
diff --git a/doc/src/compute_stress_cartesian.rst b/doc/src/compute_stress_cartesian.rst
index 3e1e9d9a8a..46785149f8 100644
--- a/doc/src/compute_stress_cartesian.rst
+++ b/doc/src/compute_stress_cartesian.rst
@@ -41,7 +41,7 @@ split into a kinetic contribution :math:`P^k` and a virial contribution
 This compute obeys momentum balance through fluid interfaces. They use the
 Irving--Kirkwood contour, which is the straight line between particle pairs.
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
    Added support for bond styles
 
@@ -119,4 +119,4 @@ Related commands
 
 .. _Ikeshoji2:
 
-**(Ikeshoji)** Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
\ No newline at end of file
+**(Ikeshoji)** Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst
index ec654dc61c..21c2963545 100644
--- a/doc/src/compute_stress_mop.rst
+++ b/doc/src/compute_stress_mop.rst
@@ -66,7 +66,7 @@ that atoms have crossed the plane if their positions at times
 and uses the velocity at time :math:`t-\Delta t/2` given by the velocity
 Verlet algorithm.
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
    contributions from bond and angle potentials
 
diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst
index ade9659d00..71894161f1 100644
--- a/doc/src/fix_dpd_source.rst
+++ b/doc/src/fix_dpd_source.rst
@@ -61,7 +61,7 @@ heat conduction with a source term (see Fig.12 in :ref:`(Li2014) <Li2014b>`)
 or diffusion with a source term (see Fig.1 in :ref:`(Li2015) <Li2015b>`), as
 an analog of a periodic Poiseuille flow problem.
 
-.. deprecated:: TBD
+.. deprecated:: 15Jun2023
 
    The *sphere* and *cuboid* keywords will be removed in a future version
    of LAMMPS.  The same functionality and more can be achieved with a region.
diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst
index 4cf92cf946..e38e1e6894 100644
--- a/doc/src/fix_efield.rst
+++ b/doc/src/fix_efield.rst
@@ -136,7 +136,7 @@ due to the electric field were a spring-like F = kx, then the energy
 formula should be E = -0.5kx\^2.  If you don't do this correctly, the
 minimization will not converge properly.
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
 The *potential* keyword can be used as an alternative to the *energy* keyword
 to specify the name of an atom-style variable, which is used to compute the
diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst
index 938b40d1f9..05abbe3c98 100644
--- a/doc/src/fix_print.rst
+++ b/doc/src/fix_print.rst
@@ -44,7 +44,7 @@ one word.  If it contains variables it must be enclosed in double
 quotes to ensure they are not evaluated when the input script line is
 read, but will instead be evaluated each time the string is printed.
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
    support for vector style variables
 
diff --git a/doc/src/fix_reaxff_species.rst b/doc/src/fix_reaxff_species.rst
index c22c9d7b9f..6a171ede5e 100644
--- a/doc/src/fix_reaxff_species.rst
+++ b/doc/src/fix_reaxff_species.rst
@@ -88,7 +88,7 @@ If the filename ends with ".gz", the output file is written in gzipped
 format.  A gzipped dump file will be about 3x smaller than the text version,
 but will also take longer to write.
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
    Support for wildcards added
 
diff --git a/doc/src/package.rst b/doc/src/package.rst
index b0549ba7d9..0f28598029 100644
--- a/doc/src/package.rst
+++ b/doc/src/package.rst
@@ -433,7 +433,7 @@ with 16 threads, for a total of 128.
 Note that the default settings for *tpc* and *tptask* are fine for
 most problems, regardless of how many MPI tasks you assign to a Phi.
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
 The *pppm_table* keyword with the argument yes allows to use a
 pre-computed table to efficiently spread the charge to the PPPM grid.
diff --git a/doc/src/pair_aip_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst
index 532ee8f8f6..5cee40edda 100644
--- a/doc/src/pair_aip_water_2dm.rst
+++ b/doc/src/pair_aip_water_2dm.rst
@@ -33,7 +33,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
 The *aip/water/2dm* style computes the anisotropic interfacial potential
 (AIP) potential for interfaces of water with two-dimensional (2D)
diff --git a/doc/src/pair_lepton.rst b/doc/src/pair_lepton.rst
index 608265ecbd..21e619a3d9 100644
--- a/doc/src/pair_lepton.rst
+++ b/doc/src/pair_lepton.rst
@@ -61,9 +61,11 @@ Description
 
 .. versionadded:: 8Feb2023
 
-.. versionchanged:: TBD
+   added pair styles *lepton* and *lepton/coul*
 
-   added pair style lepton/sphere
+.. versionchanged:: 15Jun2023
+
+   added pair style *lepton/sphere*
 
 Pair styles *lepton*, *lepton/coul*, *lepton/sphere* compute pairwise
 interactions between particles which depend on the distance and have a
diff --git a/doc/src/pair_lj_cut_sphere.rst b/doc/src/pair_lj_cut_sphere.rst
index 428047d5df..31f84bc40e 100644
--- a/doc/src/pair_lj_cut_sphere.rst
+++ b/doc/src/pair_lj_cut_sphere.rst
@@ -33,7 +33,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
 The *lj/cut/sphere* style compute the standard 12/6 Lennard-Jones potential,
 given by
diff --git a/doc/src/pair_lj_expand_sphere.rst b/doc/src/pair_lj_expand_sphere.rst
index c60cf160f0..2c01624251 100644
--- a/doc/src/pair_lj_expand_sphere.rst
+++ b/doc/src/pair_lj_expand_sphere.rst
@@ -33,7 +33,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
 The *lj/expand/sphere* style compute a 12/6 Lennard-Jones potential with
 a distance shifted by :math:`\Delta = \frac{1}{2} (d_i + d_j)`, the
diff --git a/doc/src/print.rst b/doc/src/print.rst
index f5a872e768..a221ed04b6 100644
--- a/doc/src/print.rst
+++ b/doc/src/print.rst
@@ -46,7 +46,7 @@ lines of output, the string can be enclosed in triple quotes, as in
 the last example above.  If the text string contains variables, they
 will be evaluated and their current values printed.
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
    support for vector style variables
 
diff --git a/doc/src/variable.rst b/doc/src/variable.rst
index 1b1acba92d..67600af62d 100644
--- a/doc/src/variable.rst
+++ b/doc/src/variable.rst
@@ -1001,7 +1001,7 @@ map kind (atom, bond, angle, dihedral, or improper) and the second
 argument is the label.  The function returns the corresponding numeric
 type or triggers an error if the queried label does not exist.
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
 The is_typelabel(kind,label) function has the same arguments as
 label2type(), but returns 1 if the type label has been assigned,
@@ -1320,7 +1320,7 @@ Vectors" discussion above.
 Vector Initialization
 ---------------------
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
 *Vector*-style variables only can be initialized with a special
 syntax, instead of using a formula.  The syntax is a bracketed,
diff --git a/src/library.cpp b/src/library.cpp
index 1996ebbcb4..872b59693f 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -756,7 +756,7 @@ double lammps_get_thermo(void *handle, const char *keyword)
  *
 \verbatim embed:rst
 
-.. versionadded:: TBD
+.. versionadded:: 15Jun2023
 
 This function provides access to cached data from the last thermo output.
 This differs from :cpp:func:`lammps_get_thermo` in that it does not trigger
diff --git a/src/version.h b/src/version.h
index 2d0eb0480e..63547c4a01 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1,2 +1 @@
-#define LAMMPS_VERSION "28 Mar 2023"
-#define LAMMPS_UPDATE "Development"
+#define LAMMPS_VERSION "15 Jun 2023"

From b8dda7ebfe9c3b04b9ca46e375714a139a9ac24b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 22:08:30 -0400
Subject: [PATCH 273/396] documentation formatting and spelling fixes

---
 doc/src/compute_stress_cartesian.rst        | 3 ++-
 doc/src/compute_stress_curvilinear.rst      | 5 +++--
 doc/utils/sphinx-config/false_positives.txt | 1 +
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/doc/src/compute_stress_cartesian.rst b/doc/src/compute_stress_cartesian.rst
index 3e1e9d9a8a..d2c2aa9ba9 100644
--- a/doc/src/compute_stress_cartesian.rst
+++ b/doc/src/compute_stress_cartesian.rst
@@ -26,6 +26,7 @@ Examples
 """"""""
 
 .. code-block:: LAMMPS
+
    compute 1 all stress/cartesian x 0.1 NULL 0
    compute 1 all stress/cartesian y 0.1 z 0.1
    compute 1 all stress/cartesian x 0.1 NULL 0 ke pair
@@ -119,4 +120,4 @@ Related commands
 
 .. _Ikeshoji2:
 
-**(Ikeshoji)** Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
\ No newline at end of file
+**(Ikeshoji)** Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
diff --git a/doc/src/compute_stress_curvilinear.rst b/doc/src/compute_stress_curvilinear.rst
index edd1df9217..022a87058f 100644
--- a/doc/src/compute_stress_curvilinear.rst
+++ b/doc/src/compute_stress_curvilinear.rst
@@ -36,6 +36,7 @@ Examples
 """"""""
 
 .. code-block:: LAMMPS
+
    compute 1 all stress/cylinder -10.0 10.0 15.0 0.25
    compute 1 all stress/cylinder -10.0 10.0 15.0 0.25 ke no
    compute 1 all stress/spherical 0 0 0 0.1 10
@@ -59,7 +60,7 @@ The compute *stress/cylinder* computes the stress profile along the
 radial direction in cylindrical coordinates, as described in
 :ref:`(Addington)<Addington1>`. The compute *stress/spherical*
 computes the stress profile along the radial direction in spherical
-coordinates, as described in :ref:`(Ikeshoji)<Ikeshoji2>`.
+coordinates, as described in :ref:`(Ikeshoji)<Ikeshoji4>`.
 
 
 Output info
@@ -125,7 +126,7 @@ The keyword default for ke in style *stress/cylinder* is yes.
 
 ----------
 
-.. _Ikeshoji2:
+.. _Ikeshoji4:
 
 **(Ikeshoji)** Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
 
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 867a0e0631..5791288a06 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -552,6 +552,7 @@ conformational
 Connor
 conp
 conq
+const
 ConstMatrix
 Contrib
 cooperativity

From 4eb602e0d47530b05baff96df6b625e282a8eae3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Jun 2023 22:18:08 -0400
Subject: [PATCH 274/396] improve error messages and apply clang-format

---
 src/EXTRA-COMPUTE/compute_stress_cartesian.cpp | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
index 3835b8bea9..0380acbb82 100644
--- a/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_cartesian.cpp
@@ -62,7 +62,7 @@ ComputeStressCartesian::ComputeStressCartesian(LAMMPS *lmp, int narg, char **arg
 {
   if (lmp->citeme) lmp->citeme->add(cite_compute_stress_cartesian);
 
-  if (narg < 7) error->all(FLERR, "Illegal compute stress/cartesian command: illegal number of arguments.");
+  if (narg < 7) utils::missing_cmd_args(FLERR, "compute stress/cartesian", error);
 
   // no triclinic boxes
   if (domain->triclinic) error->all(FLERR, "Compute stress/cartesian requires an orthogonal box");
@@ -158,10 +158,14 @@ ComputeStressCartesian::ComputeStressCartesian(LAMMPS *lmp, int narg, char **arg
     compute_bond = false;
     int iarg = 7;
     while (iarg < narg) {
-      if (strcmp(arg[iarg], "ke") == 0)        compute_ke = true;
-      else if (strcmp(arg[iarg], "pair") == 0) compute_pair = true;
-      else if (strcmp(arg[iarg], "bond") == 0) compute_bond = true;
-      else error->all(FLERR, "Illegal compute stress/atom command");
+      if (strcmp(arg[iarg], "ke") == 0)
+        compute_ke = true;
+      else if (strcmp(arg[iarg], "pair") == 0)
+        compute_pair = true;
+      else if (strcmp(arg[iarg], "bond") == 0)
+        compute_bond = true;
+      else
+        error->all(FLERR, "Unknown compute stress/cartesian keyword: {}", arg[iarg]);
       iarg++;
     }
   }
@@ -371,7 +375,7 @@ void ComputeStressCartesian::compute_array()
       // i == atom1, j == atom2
       int i = neighbor->bondlist[i_bond][0];
       int j = neighbor->bondlist[i_bond][1];
-      int btype  = neighbor->bondlist[i_bond][2];
+      int btype = neighbor->bondlist[i_bond][2];
 
       // Skip if one of both atoms is not in group
       if (!(mask[i] & groupbit)) continue;
@@ -389,7 +393,7 @@ void ComputeStressCartesian::compute_array()
       double dx = x[j][0] - x[i][0];
       double dy = x[j][1] - x[i][1];
       double dz = x[j][2] - x[i][2];
-      double rsq = dx*dx + dy*dy + dz*dz;
+      double rsq = dx * dx + dy * dy + dz * dz;
       double xi = x[i][dir1] - boxlo[dir1];
       double yi = x[i][dir2] - boxlo[dir2];
 

From e01bde5be518853f14ee2b72481b51168a090d8a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 15 Jun 2023 01:50:07 -0400
Subject: [PATCH 275/396] avoid null pointer dereference

---
 src/INTEL/fix_intel.cpp | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/INTEL/fix_intel.cpp b/src/INTEL/fix_intel.cpp
index 59224cc511..4c46608677 100644
--- a/src/INTEL/fix_intel.cpp
+++ b/src/INTEL/fix_intel.cpp
@@ -306,16 +306,17 @@ void FixIntel::init()
   if (force->pair_match("gayberne/intel$", 0)) _torque_flag = 1;
 
   const int nstyles = _pair_intel_count;
-  if (force->pair_match("^hybrid", 0) != nullptr) {
+  if (force->pair_match("^hybrid", 0)) {
     _pair_hybrid_flag = 1;
 
     // Check if need to handle torque
     auto hybrid = dynamic_cast<PairHybrid *>(force->pair);
-    for (int i = 0; i < hybrid->nstyles; i++)
-      if (utils::strmatch(hybrid->keywords[i],"/intel$") &&
-          utils::strmatch(hybrid->keywords[i],"gayberne"))
-        _torque_flag = 1;
-
+    if (hybrid) {
+      for (int i = 0; i < hybrid->nstyles; i++)
+        if (utils::strmatch(hybrid->keywords[i],"/intel$") &&
+            utils::strmatch(hybrid->keywords[i],"gayberne"))
+          _torque_flag = 1;
+    }
     if (force->newton_pair != 0 && force->pair->no_virial_fdotr_compute)
       error->all(FLERR,"INTEL package requires fdotr virial with newton on.");
   } else

From 55d767e41609cbbd0016e9cff0f6279ed59621c8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 15 Jun 2023 01:51:12 -0400
Subject: [PATCH 276/396] make sure intermediate results are 64-bit compatible,
 so the won't overflow

---
 src/INTEL/npair_full_bin_ghost_intel.cpp | 2 +-
 src/INTEL/npair_intel.cpp                | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/INTEL/npair_full_bin_ghost_intel.cpp b/src/INTEL/npair_full_bin_ghost_intel.cpp
index 381db62c08..920c0c559a 100644
--- a/src/INTEL/npair_full_bin_ghost_intel.cpp
+++ b/src/INTEL/npair_full_bin_ghost_intel.cpp
@@ -559,7 +559,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
         if (ct + obound > list_size) {
           if (i < ito - 1) {
             *overflow = 1;
-            ct = (ifrom + tid * 2) * maxnbors;
+            ct = (bigint)(ifrom + tid * 2) * (bigint)maxnbors;
           }
         }
       }
diff --git a/src/INTEL/npair_intel.cpp b/src/INTEL/npair_intel.cpp
index 8b05aa38aa..600109d7ae 100644
--- a/src/INTEL/npair_intel.cpp
+++ b/src/INTEL/npair_intel.cpp
@@ -723,7 +723,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
             if (ct + obound > list_size) {
               if (i < ito - 1) {
                 *overflow = 1;
-                ct = (ifrom + tid * 2) * maxnbors;
+                ct = (bigint)(ifrom + tid * 2) * (bigint)maxnbors;
               }
             }
           }
@@ -737,7 +737,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
           if (ct + obound > list_size) {
             if (i < ito - 1) {
               *overflow = 1;
-              ct = (ifrom + tid * 2) * maxnbors;
+              ct = (bigint)(ifrom + tid * 2) * (bigint)maxnbors;
             }
           }
         }

From 0df1542be10815a6d735779fecd7ffce4f5835e5 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Thu, 15 Jun 2023 10:22:35 -0600
Subject: [PATCH 277/396] Pair SNAP tuning for Kokkos SYCL

---
 src/KOKKOS/kokkos_type.h      |  8 ++++++--
 src/KOKKOS/pair_snap_kokkos.h | 11 +++++++++++
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h
index 3c9886905e..fac75221bc 100644
--- a/src/KOKKOS/kokkos_type.h
+++ b/src/KOKKOS/kokkos_type.h
@@ -1310,9 +1310,13 @@ struct alignas(4 * sizeof(int)) reax_int4 {
 #define SNAP_KOKKOS_HOST_VECLEN 1
 
 #ifdef LMP_KOKKOS_GPU
-#define SNAP_KOKKOS_DEVICE_VECLEN 32
+  #if defined(KOKKOS_ENABLE_SYCL)
+    #define SNAP_KOKKOS_DEVICE_VECLEN 16
+  #else
+    #define SNAP_KOKKOS_DEVICE_VECLEN 32
+  #endif
 #else
-#define SNAP_KOKKOS_DEVICE_VECLEN 1
+  #define SNAP_KOKKOS_DEVICE_VECLEN 1
 #endif
 
 
diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h
index fba95a679e..0df02e0bc7 100644
--- a/src/KOKKOS/pair_snap_kokkos.h
+++ b/src/KOKKOS/pair_snap_kokkos.h
@@ -97,6 +97,17 @@ class PairSNAPKokkos : public PairSNAP {
   static constexpr int tile_size_transform_bi = 2;
   static constexpr int tile_size_compute_yi = 2;
   static constexpr int team_size_compute_fused_deidrj = 2;
+#elif defined(KOKKOS_ENABLE_SYCL)
+  static constexpr int team_size_compute_neigh = 4;
+  static constexpr int tile_size_compute_ck = 4;
+  static constexpr int tile_size_pre_ui = 4;
+  static constexpr int team_size_compute_ui = 4;
+  static constexpr int tile_size_transform_ui = 4;
+  static constexpr int tile_size_compute_zi = 4;
+  static constexpr int tile_size_compute_bi = 4;
+  static constexpr int tile_size_transform_bi = 4;
+  static constexpr int tile_size_compute_yi = 8;
+  static constexpr int team_size_compute_fused_deidrj = 4;
 #else
   static constexpr int team_size_compute_neigh = 4;
   static constexpr int tile_size_compute_ck = 4;

From 74c4eb10636e3fe6656c3bebd070b443a0445e3e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 16 Jun 2023 12:12:12 -0400
Subject: [PATCH 278/396] indicate that LAMMPS was built from a development
 version

---
 src/version.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/version.h b/src/version.h
index 63547c4a01..2a1c8a9a37 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1,2 @@
 #define LAMMPS_VERSION "15 Jun 2023"
+#define LAMMPS_UPDATE "Development"

From 59c5ed63e375ff1b66ee9d27468d9874b579a597 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 16 Jun 2023 12:12:23 -0400
Subject: [PATCH 279/396] programming style

---
 src/dump_image.cpp | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index ff1c540d3f..0d54c60595 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -201,7 +201,7 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
 
       if (iflag == ArgInfo::COMPUTE) id_grid_compute = utils::strdup(id);
       else if (iflag == ArgInfo::FIX) id_grid_fix = utils::strdup(id);
-      delete [] id;
+      delete[] id;
       grid_igrid = igrid;
       grid_idata = idata;
       grid_index = index;
@@ -461,18 +461,18 @@ DumpImage::~DumpImage()
 {
   delete image;
 
-  delete [] diamtype;
-  delete [] diamelement;
-  delete [] colortype;
-  delete [] colorelement;
-  delete [] bdiamtype;
-  delete [] bcolortype;
+  delete[] diamtype;
+  delete[] diamelement;
+  delete[] colortype;
+  delete[] colorelement;
+  delete[] bdiamtype;
+  delete[] bcolortype;
   memory->destroy(chooseghost);
   memory->destroy(bufcopy);
   memory->destroy(gbuf);
 
-  delete [] id_grid_compute;
-  delete [] id_grid_fix;
+  delete[] id_grid_compute;
+  delete[] id_grid_fix;
 }
 
 /* ---------------------------------------------------------------------- */

From a20ed8e5e4bc40ebc65e0ba0954a4c091e8d76f2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 16 Jun 2023 12:13:22 -0400
Subject: [PATCH 280/396] improve error messages for dump style custom

---
 src/dump_custom.cpp | 75 +++++++++++++++++++++++----------------------
 1 file changed, 38 insertions(+), 37 deletions(-)

diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 517956caf1..33cfba2cef 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -61,12 +61,12 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
   fix(nullptr), id_variable(nullptr), variable(nullptr), vbuf(nullptr), id_custom(nullptr),
   custom(nullptr), custom_flag(nullptr), typenames(nullptr), pack_choice(nullptr)
 {
-  if (narg == 5) error->all(FLERR,"No dump custom arguments specified");
+  if (narg == 5) error->all(FLERR,"No dump {} arguments specified", style);
 
   clearstep = 1;
 
   nevery = utils::inumeric(FLERR,arg[3],false,lmp);
-  if (nevery <= 0) error->all(FLERR,"Illegal dump custom command");
+  if (nevery <= 0) error->all(FLERR,"Illegal dump {} command: output frequency must be > 0", style);
 
   // expand args if any have wildcard character "*"
   // ok to include trailing optional args,
@@ -141,7 +141,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
     else if (vtype[i] == Dump::BIGINT) cols += BIGINT_FORMAT " ";
     vformat[i] = nullptr;
   }
-  cols.resize(cols.size()-1);
+  if (nfield > 0) cols.resize(cols.size()-1);
   format_default = utils::strdup(cols);
 
   format_column_user = new char*[nfield];
@@ -309,20 +309,20 @@ void DumpCustom::init_style()
 
   for (i = 0; i < ncompute; i++) {
     compute[i] = modify->get_compute_by_id(id_compute[i]);
-    if (!compute[i]) error->all(FLERR,"Could not find dump custom compute ID {}",id_compute[i]);
+    if (!compute[i]) error->all(FLERR,"Could not find dump {} compute ID {}",style,id_compute[i]);
   }
 
   for (i = 0; i < nfix; i++) {
     fix[i] = modify->get_fix_by_id(id_fix[i]);
-    if (!fix[i]) error->all(FLERR,"Could not find dump custom fix ID {}", id_fix[i]);
+    if (!fix[i]) error->all(FLERR,"Could not find dump {} fix ID {}", style, id_fix[i]);
     if (nevery % fix[i]->peratom_freq)
-      error->all(FLERR,"Dump custom and fix not computed at compatible times");
+      error->all(FLERR,"Dump {} and fix not computed at compatible times", style);
   }
 
   for (i = 0; i < nvariable; i++) {
     int ivariable = input->variable->find(id_variable[i]);
     if (ivariable < 0)
-      error->all(FLERR,"Could not find dump custom variable name {}", id_variable[i]);
+      error->all(FLERR,"Could not find dump {} variable name {}", style, id_variable[i]);
     variable[i] = ivariable;
   }
 
@@ -330,7 +330,7 @@ void DumpCustom::init_style()
   for (int i = 0; i < ncustom; i++) {
     icustom = atom->find_custom(id_custom[i],flag,cols);
     if (icustom < 0)
-      error->all(FLERR,"Could not find dump custom atom property name");
+      error->all(FLERR,"Could not find dump {} atom property name", style);
     custom[i] = icustom;
     if (!flag && !cols) custom_flag[i] = IVEC;
     else if (flag && !cols) custom_flag[i] = DVEC;
@@ -341,7 +341,7 @@ void DumpCustom::init_style()
   // check validity of region
 
   if (idregion && !domain->get_region_by_id(idregion))
-    error->all(FLERR,"Region {} for dump custom does not exist", idregion);
+    error->all(FLERR,"Region {} for dump {} does not exist", idregion, style);
 
   // open single file, one time only
 
@@ -1461,7 +1461,8 @@ int DumpCustom::parse_fields(int narg, char **arg)
       switch (argi.get_type()) {
 
       case ArgInfo::UNKNOWN:
-        error->all(FLERR,"Invalid attribute in dump custom command");
+      case ArgInfo::NONE:
+        error->all(FLERR,"Invalid attribute {} in dump {} command",arg[iarg],style);
         break;
 
       // compute value = c_ID
@@ -1472,15 +1473,15 @@ int DumpCustom::parse_fields(int narg, char **arg)
         vtype[iarg] = Dump::DOUBLE;
 
         icompute = modify->get_compute_by_id(name);
-        if (!icompute) error->all(FLERR,"Could not find dump custom compute ID: {}",name);
+        if (!icompute) error->all(FLERR,"Could not find dump {} compute ID: {}", style, name);
         if (icompute->peratom_flag == 0)
-          error->all(FLERR,"Dump custom compute {} does not compute per-atom info",name);
+          error->all(FLERR,"Dump {} compute {} does not compute per-atom info", style, name);
         if (argi.get_dim() == 0 && icompute->size_peratom_cols > 0)
-          error->all(FLERR,"Dump custom compute {} does not calculate per-atom vector",name);
+          error->all(FLERR,"Dump {} compute {} does not calculate per-atom vector", style, name);
         if (argi.get_dim() > 0 && icompute->size_peratom_cols == 0)
-          error->all(FLERR,"Dump custom compute {} does not calculate per-atom array",name);
+          error->all(FLERR,"Dump {} compute {} does not calculate per-atom array", style, name);
         if (argi.get_dim() > 0 && argi.get_index1() > icompute->size_peratom_cols)
-          error->all(FLERR,"Dump custom compute {} vector is accessed out-of-range",name);
+          error->all(FLERR,"Dump {} compute {} vector is accessed out-of-range", style, name);
 
         field2index[iarg] = add_compute(name);
         break;
@@ -1493,15 +1494,15 @@ int DumpCustom::parse_fields(int narg, char **arg)
         vtype[iarg] = Dump::DOUBLE;
 
         ifix = modify->get_fix_by_id(name);
-        if (!ifix) error->all(FLERR,"Could not find dump custom fix ID: {}",name);
+        if (!ifix) error->all(FLERR,"Could not find dump {} fix ID: {}", style, name);
         if (ifix->peratom_flag == 0)
-          error->all(FLERR,"Dump custom fix {} does not compute per-atom info",name);
+          error->all(FLERR,"Dump {} fix {} does not compute per-atom info", style, name);
         if (argi.get_dim() == 0 && ifix->size_peratom_cols > 0)
-          error->all(FLERR,"Dump custom fix {} does not compute per-atom vector",name);
+          error->all(FLERR,"Dump {} fix {} does not compute per-atom vector", style, name);
         if (argi.get_dim() > 0 && ifix->size_peratom_cols == 0)
-          error->all(FLERR,"Dump custom fix {} does not compute per-atom array",name);
+          error->all(FLERR,"Dump {} fix {} does not compute per-atom array", style, name);
         if (argi.get_dim() > 0 && argi.get_index1() > ifix->size_peratom_cols)
-          error->all(FLERR,"Dump custom fix {} vector is accessed out-of-range",name);
+          error->all(FLERR,"Dump {} fix {} vector is accessed out-of-range", style, name);
 
         field2index[iarg] = add_fix(name);
         break;
@@ -1513,9 +1514,9 @@ int DumpCustom::parse_fields(int narg, char **arg)
         vtype[iarg] = Dump::DOUBLE;
 
         n = input->variable->find(name);
-        if (n < 0) error->all(FLERR,"Could not find dump custom variable name {}",name);
+        if (n < 0) error->all(FLERR,"Could not find dump {} variable name {}", style, name);
         if (input->variable->atomstyle(n) == 0)
-          error->all(FLERR,"Dump custom variable {} is not atom-style variable",name);
+          error->all(FLERR,"Dump {} variable {} is not atom-style variable", style, name);
 
         field2index[iarg] = add_variable(name);
         break;
@@ -1532,12 +1533,12 @@ int DumpCustom::parse_fields(int narg, char **arg)
           error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
         if (argindex[iarg] == 0) {
           if (!flag || cols)
-            error->all(FLERR,"Property double vector {} for dump custom does not exist",name);
+            error->all(FLERR,"Property double vector {} for dump {} does not exist", name, style);
         } else {
           if (!flag || !cols)
-            error->all(FLERR,"Property double array {} for dump custom does not exist",name);
+            error->all(FLERR,"Property double array {} for dump {} does not exist", name, style);
           if (argindex[iarg] > atom->dcols[n])
-            error->all(FLERR,"Dump custom property array {} is accessed out-of-range",name);
+            error->all(FLERR,"Dump {} property array {} is accessed out-of-range", style, name);
         }
 
         field2index[iarg] = add_custom(name,1);
@@ -1555,12 +1556,12 @@ int DumpCustom::parse_fields(int narg, char **arg)
           error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
         if (argindex[iarg] == 0) {
           if (flag || cols)
-            error->all(FLERR,"Property integer vector {} for dump custom does not exist",name);
+            error->all(FLERR,"Property integer vector {} for dump {} does not exist", name, style);
         } else {
           if (flag || !cols)
-            error->all(FLERR,"Property integer array {} for dump custom does not exist",name);
+            error->all(FLERR,"Property integer array {} for dump {} does not exist", name, style);
           if (argindex[iarg] > atom->icols[n])
-            error->all(FLERR,"Dump custom property array {} is accessed out-of-range",name);
+            error->all(FLERR,"Dump {} property array {} is accessed out-of-range", style, name);
         }
 
         field2index[iarg] = add_custom(name,0);
@@ -1945,9 +1946,9 @@ int DumpCustom::modify_param(int narg, char **arg)
       case ArgInfo::VARIABLE:
         thresh_array[nthresh] = VARIABLE;
         n = input->variable->find(name);
-        if (n < 0) error->all(FLERR,"Could not find dump modify variable name: {}",name);
+        if (n < 0) error->all(FLERR,"Could not find dump modify variable name: {}", name);
         if (input->variable->atomstyle(n) == 0)
-          error->all(FLERR,"Dump modify variable {} is not atom-style variable",name);
+          error->all(FLERR,"Dump modify variable {} is not atom-style variable", name);
 
         field2index[nfield+nthresh] = add_variable(name);
         break;
@@ -1961,13 +1962,13 @@ int DumpCustom::modify_param(int narg, char **arg)
           error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
         if (argindex[nfield+nthresh] == 0) {
           if (!flag || cols)
-            error->all(FLERR,"Property double vector for dump custom does not exist");
+            error->all(FLERR,"Property double vector {} for dump {} does not exist", name, style);
           thresh_array[nthresh] = DVEC;
         } else {
           if (!flag || !cols)
-            error->all(FLERR,"Property double array for dump custom does not exist");
+            error->all(FLERR,"Property double array {} for dump {} does not exist", name, style);
           if (argindex[nfield+nthresh] > atom->dcols[n])
-            error->all(FLERR,"Dump custom property array is accessed out-of-range");
+            error->all(FLERR,"Dump {} property array {} is accessed out-of-range", style, name);
           thresh_array[nthresh] = DARRAY;
         }
 
@@ -1983,13 +1984,13 @@ int DumpCustom::modify_param(int narg, char **arg)
           error->all(FLERR,"Could not find custom per-atom property ID: {}", name);
         if (argindex[nfield+nthresh] == 0) {
           if (flag || cols)
-            error->all(FLERR,"Property integer vector for dump custom does not exist");
+            error->all(FLERR,"Property integer vector {} for dump {} does not exist", name, style);
           thresh_array[nthresh] = IVEC;
         } else {
           if (flag || !cols)
-            error->all(FLERR,"Property integer array for dump custom does not exist");
+            error->all(FLERR,"Property integer array {} for dump {} does not exist", name, style);
           if (argindex[nfield+nthresh] > atom->icols[n])
-            error->all(FLERR,"Dump custom property array is accessed out-of-range");
+            error->all(FLERR,"Dump {} property array {} is accessed out-of-range", style, name);
           thresh_array[nthresh] = IARRAY;
         }
 
@@ -1999,7 +2000,7 @@ int DumpCustom::modify_param(int narg, char **arg)
       // no match
 
       default:
-        error->all(FLERR,"Invalid dump_modify thresh attribute: {}",name);
+        error->all(FLERR,"Invalid dump_modify thresh attribute: {}", name);
         break;
       }
     }

From bb9dc960b76ebb92841352f6b00fbc88dd90c9e9 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Fri, 16 Jun 2023 10:26:01 -0600
Subject: [PATCH 281/396] Use updated values from @cjknight

---
 src/KOKKOS/pair_snap_kokkos.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h
index 0df02e0bc7..ca1884bfd2 100644
--- a/src/KOKKOS/pair_snap_kokkos.h
+++ b/src/KOKKOS/pair_snap_kokkos.h
@@ -100,9 +100,9 @@ class PairSNAPKokkos : public PairSNAP {
 #elif defined(KOKKOS_ENABLE_SYCL)
   static constexpr int team_size_compute_neigh = 4;
   static constexpr int tile_size_compute_ck = 4;
-  static constexpr int tile_size_pre_ui = 4;
-  static constexpr int team_size_compute_ui = 4;
-  static constexpr int tile_size_transform_ui = 4;
+  static constexpr int tile_size_pre_ui = 8;
+  static constexpr int team_size_compute_ui = 8;
+  static constexpr int tile_size_transform_ui = 8;
   static constexpr int tile_size_compute_zi = 4;
   static constexpr int tile_size_compute_bi = 4;
   static constexpr int tile_size_transform_bi = 4;

From 2d3bbd2e725a00e2af227862ea86d9de2f9422d9 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Fri, 16 Jun 2023 10:52:21 -0600
Subject: [PATCH 282/396] Temporarily disable team policy for ghost neigh list
 build due to known bug

---
 src/KOKKOS/npair_kokkos.cpp | 33 ++++++++++++++++++---------------
 1 file changed, 18 insertions(+), 15 deletions(-)

diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp
index 852a4a9280..06567cbeb6 100644
--- a/src/KOKKOS/npair_kokkos.cpp
+++ b/src/KOKKOS/npair_kokkos.cpp
@@ -240,22 +240,25 @@ void NPairKokkos<DeviceType,HALF,NEWTON,GHOST,TRI,SIZE>::build(NeighList *list_)
       // assumes newton off
 
       NPairKokkosBuildFunctorGhost<DeviceType,HALF> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
-#ifdef LMP_KOKKOS_GPU
-      if (ExecutionSpaceFromDevice<DeviceType>::space == Device) {
-        int team_size = atoms_per_bin*factor;
-        int team_size_max = Kokkos::TeamPolicy<DeviceType>(team_size,Kokkos::AUTO).team_size_max(f,Kokkos::ParallelForTag());
-        if (team_size <= team_size_max) {
-          Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,team_size);
-          Kokkos::parallel_for(config, f);
-        } else { // fall back to flat method
-          f.sharedsize = 0;
-          Kokkos::parallel_for(nall, f);
-        }
-      } else
-        Kokkos::parallel_for(nall, f);
-#else
+
+// temporarily disable team policy for ghost due to known bug
+
+//#ifdef LMP_KOKKOS_GPU
+//      if (ExecutionSpaceFromDevice<DeviceType>::space == Device) {
+//        int team_size = atoms_per_bin*factor;
+//        int team_size_max = Kokkos::TeamPolicy<DeviceType>(team_size,Kokkos::AUTO).team_size_max(f,Kokkos::ParallelForTag());
+//        if (team_size <= team_size_max) {
+//          Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,team_size);
+//          Kokkos::parallel_for(config, f);
+//        } else { // fall back to flat method
+//          f.sharedsize = 0;
+//          Kokkos::parallel_for(nall, f);
+//        }
+//      } else
+//        Kokkos::parallel_for(nall, f);
+//#else
       Kokkos::parallel_for(nall, f);
-#endif
+//#endif
     } else {
       if (SIZE) {
         NPairKokkosBuildFunctorSize<DeviceType,HALF,NEWTON,TRI> f(data,atoms_per_bin * 6 * sizeof(X_FLOAT) * factor);

From 6f5e5746b356e15f2a18a60c4e67de73f946182d Mon Sep 17 00:00:00 2001
From: ilia-nikiforov-umn
 <78983960+ilia-nikiforov-umn@users.noreply.github.com>
Date: Fri, 16 Jun 2023 12:21:42 -0500
Subject: [PATCH 283/396] Update lib/kim/README

Fix some typos and update to non-deprecated form of kim commands
---
 lib/kim/README | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/kim/README b/lib/kim/README
index 3cba4a4597..b4cba92fb5 100644
--- a/lib/kim/README
+++ b/lib/kim/README
@@ -1,6 +1,6 @@
 This directory contains build settings for the KIM API library which is
-required to use the KIM package and its kim_init, kim_interactions, kim_query,
-and pair_kim commands in a LAMMPS input script.
+required to use the KIM package and its kim init, kim interactions and kim query 
+commands in a LAMMPS input script.
 
 Information about the KIM project can be found at https://openkim.org.
 The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn).
@@ -13,7 +13,7 @@ do the same thing by typing "python Install.py" from within this
 directory, or you can do it manually by following the instructions
 below.
 
-Use of the kim_query command requires that the CURL library (libcurl)
+Use of the kim query command requires that the CURL library (libcurl)
 development package and its configuration query tool, curl-config, are
 installed. The provided Makefile.lammps is set up to automatically detect this.
 
@@ -29,7 +29,7 @@ $ printf "${PWD}/installed-kim-api-X-X.Y.Z" > ./kim-prefix.txt
 2. Download and unpack the kim-api
 
 $ wget http://s3.openkim.org/kim-api/kim-api-X.Y.Z.txz
-$ tar zxvf kim-api-X.Y.Z.txz
+$ tar xvf kim-api-X.Y.Z.txz
 
 # configure the kim-api
 $ cd kim-api-X.Y.Z
@@ -50,7 +50,7 @@ $ rm -rf kim-api-X.Y.Z.txz
 5. To add items do the following (replace the kim item name with your
    desired value)
 
-$ source ${PWD}/kim-api-X.Y.Z/bin/kim-api-activate
+$ source ${PWD}/installed-kim-api-X.Y.Z/bin/kim-api-activate
 $ kim-api-collections-management install system EAM_ErcolessiAdams_1994_Al__MO_324507536345_002
 
 
@@ -59,7 +59,7 @@ $ kim-api-collections-management install system EAM_ErcolessiAdams_1994_Al__MO_3
 When these steps are complete you can build LAMMPS with the KIM
 package installed:
 
-$ cd lammpos/src
+$ cd lammps/src
 $ make yes-kim
 $ make g++ (or whatever target you wish)
 

From ce75691eaed0c71c5eb8d258c534dd97d96297a5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 00:35:05 -0400
Subject: [PATCH 284/396] address issues flagged by coverity scan

---
 src/DPD-REACT/fix_eos_table_rx.cpp          | 10 ++++------
 src/DPD-REACT/fix_rx.cpp                    | 15 +++++----------
 src/YAFF/pair_lj_switch3_coulgauss_long.cpp |  2 --
 3 files changed, 9 insertions(+), 18 deletions(-)

diff --git a/src/DPD-REACT/fix_eos_table_rx.cpp b/src/DPD-REACT/fix_eos_table_rx.cpp
index 2687a11658..f7afddc64f 100644
--- a/src/DPD-REACT/fix_eos_table_rx.cpp
+++ b/src/DPD-REACT/fix_eos_table_rx.cpp
@@ -476,16 +476,14 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword)
     utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
 
     nwords = utils::count_words(utils::trim_comment(line));
-    if (nwords != nspecies+2) {
-      printf("nwords=%d  nspecies=%d\n",nwords,nspecies);
-      error->all(FLERR,"Illegal fix eos/table/rx command");
-    }
-    nwords = 0;
+    if (nwords != nspecies+2)
+      error->all(FLERR,"Illegal fix eos/table/rx command: nwords={} nspecies={}", nwords, nspecies);
+
     word = strtok(line," \t\n\r\f");
     word = strtok(nullptr," \t\n\r\f");
     rtmp = atof(word);
 
-    for (int icolumn=0;icolumn<ncolumn;icolumn++) {
+    for (int icolumn=0; icolumn < ncolumn; icolumn++) {
       ispecies = eosSpecies[icolumn];
 
       Table *tbl = &tables[ispecies];
diff --git a/src/DPD-REACT/fix_rx.cpp b/src/DPD-REACT/fix_rx.cpp
index 96eb9d4572..cce88cf465 100644
--- a/src/DPD-REACT/fix_rx.cpp
+++ b/src/DPD-REACT/fix_rx.cpp
@@ -249,7 +249,7 @@ void FixRX::post_constructor()
 
   // Assign species names to tmpspecies array and determine the number of unique species
 
-  int n,nwords;
+  int n;
   char line[MAXLINE],*ptr;
   int eof = 0;
   char * word;
@@ -270,12 +270,10 @@ void FixRX::post_constructor()
     // strip comment, skip line if blank
 
     if ((ptr = strchr(line,'#'))) *ptr = '\0';
-    nwords = utils::count_words(line);
-    if (nwords == 0) continue;
+    if (utils::count_words(line) == 0) continue;
 
     // words = ptrs to all words in line
 
-    nwords = 0;
     word = strtok(line," \t\n\r\f");
     while (word != nullptr) {
       word = strtok(nullptr, " \t\n\r\f");
@@ -785,7 +783,7 @@ void FixRX::read_file(char *file)
 
   // Count the number of reactions from kinetics file
 
-  int n,nwords,ispecies;
+  int n,ispecies;
   char line[MAXLINE],*ptr;
   int eof = 0;
 
@@ -805,8 +803,7 @@ void FixRX::read_file(char *file)
     // strip comment, skip line if blank
 
     if ((ptr = strchr(line,'#'))) *ptr = '\0';
-    nwords = utils::count_words(line);
-    if (nwords == 0) continue;
+    if (utils::count_words(line) == 0) continue;
 
     nreactions++;
   }
@@ -859,12 +856,10 @@ void FixRX::read_file(char *file)
     // strip comment, skip line if blank
 
     if ((ptr = strchr(line,'#'))) *ptr = '\0';
-    nwords = utils::count_words(line);
-    if (nwords == 0) continue;
+    if (utils::count_words(line) == 0) continue;
 
     // words = ptrs to all words in line
 
-    nwords = 0;
     word = strtok(line," \t\n\r\f");
     while (word != nullptr) {
       tmpStoich = atof(word);
diff --git a/src/YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/YAFF/pair_lj_switch3_coulgauss_long.cpp
index 5266901318..dbbab7e5fe 100644
--- a/src/YAFF/pair_lj_switch3_coulgauss_long.cpp
+++ b/src/YAFF/pair_lj_switch3_coulgauss_long.cpp
@@ -165,7 +165,6 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
           // Correction for Gaussian radii
           if (lj2[itype][jtype]==0.0) {
             // This means a point charge is considered, so the correction is zero
-            expn2 = 0.0;
             erfc2 = 0.0;
             forcecoul2 = 0.0;
             prefactor2 = 0.0;
@@ -616,7 +615,6 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype,
     r6inv = r2inv*r2inv*r2inv;
     forcelj = r6inv*(12.0*lj3[itype][jtype]*r6inv-6.0*lj4[itype][jtype]);
     if (lj2[itype][jtype] == 0.0) {
-      expn2 = 0.0;
       erfc2 = 0.0;
       forcecoul2 = 0.0;
       prefactor2 = 0.0;

From 60d060eeb1f825bc2719b0339af990d52a72fa15 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 14:38:49 -0400
Subject: [PATCH 285/396] fix logic bug

---
 src/ELECTRODE/fix_electrode_conp.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp
index 1547fa6b97..dafd3c8fec 100644
--- a/src/ELECTRODE/fix_electrode_conp.cpp
+++ b/src/ELECTRODE/fix_electrode_conp.cpp
@@ -1209,8 +1209,8 @@ FixElectrodeConp::~FixElectrodeConp()
     } catch (std::exception &) {
     }
   }
-  if (!modify->get_fix_by_id(id))             // avoid segfault if derived fixes' ctor throws err
-    atom->delete_callback(id, Atom::GROW);    // atomvec track local electrode atoms
+
+  if (modify->get_fix_by_id(id)) atom->delete_callback(id, Atom::GROW);
 
   delete[] recvcounts;
   delete[] displs;

From 37ca3f9af83e7e99614eff5c281e4a5925c5aa53 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 14:38:59 -0400
Subject: [PATCH 286/396] apply clang-format

---
 src/ELECTRODE/fix_electrode_conp.cpp | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/ELECTRODE/fix_electrode_conp.cpp b/src/ELECTRODE/fix_electrode_conp.cpp
index dafd3c8fec..85f59127f1 100644
--- a/src/ELECTRODE/fix_electrode_conp.cpp
+++ b/src/ELECTRODE/fix_electrode_conp.cpp
@@ -859,7 +859,7 @@ void FixElectrodeConp::update_charges()
 
 std::vector<double> FixElectrodeConp::ele_ele_interaction(const std::vector<double> &q_local)
 {
-  assert((int)q_local.size() == nlocalele);
+  assert((int) q_local.size() == nlocalele);
   assert(algo == Algo::CG || algo == Algo::MATRIX_CG);
   if (algo == Algo::CG) {
     set_charges(q_local);
@@ -873,7 +873,7 @@ std::vector<double> FixElectrodeConp::ele_ele_interaction(const std::vector<doub
 
 void FixElectrodeConp::set_charges(std::vector<double> q_local)
 {
-  assert((int)q_local.size() == nlocalele);
+  assert((int) q_local.size() == nlocalele);
   double *q = atom->q;
   for (int i = 0; i < nlocalele; i++) q[atom->map(taglist_local[i])] = q_local[i];
   comm->forward_comm(this);
@@ -942,7 +942,7 @@ std::vector<double> FixElectrodeConp::scale_vector(double alpha, std::vector<dou
 
 std::vector<double> FixElectrodeConp::add_nlocalele(std::vector<double> a, std::vector<double> b)
 {
-  assert(((int)a.size() == nlocalele) && ((int)b.size() == nlocalele));
+  assert(((int) a.size() == nlocalele) && ((int) b.size() == nlocalele));
   for (int i = 0; i < nlocalele; i++) a[i] += b[i];
   return a;
 }
@@ -951,7 +951,7 @@ std::vector<double> FixElectrodeConp::add_nlocalele(std::vector<double> a, std::
 
 double FixElectrodeConp::dot_nlocalele(std::vector<double> a, std::vector<double> b)
 {
-  assert(((int)a.size() == nlocalele) && ((int)b.size() == nlocalele));
+  assert(((int) a.size() == nlocalele) && ((int) b.size() == nlocalele));
   double out = 0.;
   for (int i = 0; i < nlocalele; i++) out += a[i] * b[i];
   MPI_Allreduce(MPI_IN_PLACE, &out, 1, MPI_DOUBLE, MPI_SUM, world);
@@ -962,7 +962,7 @@ double FixElectrodeConp::dot_nlocalele(std::vector<double> a, std::vector<double
 
 std::vector<double> FixElectrodeConp::times_elastance(std::vector<double> x)
 {
-  assert((int)x.size() == ngroup);
+  assert((int) x.size() == ngroup);
   auto out = std::vector<double>(nlocalele, 0.);
   for (int i = 0; i < nlocalele; i++) {
     double *_noalias row = elastance[list_iele[i]];
@@ -1412,7 +1412,7 @@ void FixElectrodeConp::gather_list_iele()
     }
   }
   nlocalele = static_cast<int>(taglist_local.size());    // just for safety
-  assert((int)iele_to_group_local.size() == nlocalele);
+  assert((int) iele_to_group_local.size() == nlocalele);
 
   if (matrix_algo) {
     MPI_Allgather(&nlocalele, 1, MPI_INT, recvcounts, 1, MPI_INT, world);

From 9231ec6dbe6978c79dd81f60ee7c1739a25665bc Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 14:39:32 -0400
Subject: [PATCH 287/396] avoid segfault on deleting callback when there is an
 error in the constructor or a derived class

---
 src/QEQ/fix_qeq.cpp           | 3 ++-
 src/RIGID/fix_rigid_small.cpp | 2 +-
 src/RIGID/fix_shake.cpp       | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index c8112ca24d..394ce69d22 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -143,7 +143,8 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) :
 FixQEq::~FixQEq()
 {
   // unregister callbacks to this fix from Atom class
-  atom->delete_callback(id,Atom::GROW);
+
+  if (modify->get_fix_by_id(id)) atom->delete_callback(id,Atom::GROW);
 
   memory->destroy(s_hist);
   memory->destroy(t_hist);
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index 089c644f1e..c579e362c7 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -481,7 +481,7 @@ FixRigidSmall::~FixRigidSmall()
 {
   // unregister callbacks to this fix from Atom class
 
-  atom->delete_callback(id,Atom::GROW);
+  if (modify->get_fix_by_id(id)) atom->delete_callback(id,Atom::GROW);
 
   // delete locally stored arrays
 
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 6cd624c755..94c7668453 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -255,7 +255,7 @@ FixShake::~FixShake()
 
   // unregister callbacks to this fix from Atom class
 
-  atom->delete_callback(id,Atom::GROW);
+  if (modify->get_fix_by_id(id)) atom->delete_callback(id,Atom::GROW);
 
   // set bond_type and angle_type back to positive for SHAKE clusters
   // must set for all SHAKE bonds and angles stored by each atom

From a3de790a0da60c1ff13a39e0617bc75f45bdb9b1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 15:01:17 -0400
Subject: [PATCH 288/396] include git descriptor info when compiling develop or
 maintenance version

---
 src/lammps.cpp          | 8 +++++++-
 unittest/CMakeLists.txt | 2 +-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/lammps.cpp b/src/lammps.cpp
index 1c7d12f79c..956793c20a 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -132,6 +132,12 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
   num_ver = utils::date2num(version);
   restart_ver = -1;
 
+  // append git descriptor info to update string when compiling development or maintenance version
+
+  std::string update_string = UPDATE_STRING;
+  if (has_git_info() && (update_string == " - Development") || (update_string == " - Maintenance"))
+    update_string += fmt::format(" - {}", git_descriptor());
+
   external_comm = 0;
   mdicomm = nullptr;
 
@@ -524,7 +530,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
       if (infile == nullptr)
         error->one(FLERR,"Cannot open input script {}: {}", arg[inflag], utils::getsyserror());
       if (!helpflag)
-        utils::logmesg(this,fmt::format("LAMMPS ({}{})\n",version,UPDATE_STRING));
+        utils::logmesg(this,fmt::format("LAMMPS ({}{})\n", version, update_string));
 
      // warn against using I/O redirection in parallel runs
       if ((inflag == 0) && (universe->nprocs > 1))
diff --git a/unittest/CMakeLists.txt b/unittest/CMakeLists.txt
index f41e8a2878..f7be54f9ae 100644
--- a/unittest/CMakeLists.txt
+++ b/unittest/CMakeLists.txt
@@ -54,7 +54,7 @@ add_test(NAME RunLammps
          COMMAND $<TARGET_FILE:lmp> -log none -echo none -in in.empty)
 set_tests_properties(RunLammps PROPERTIES
         ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;HWLOC_HIDE_ERRORS=2"
-        PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?( - Development)?( - Maintenance)?\\)")
+        PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?( - Development.*)?( - Maintenance.*)?\\)")
 
 # check if the compiled executable will print the help message
 add_test(NAME HelpMessage

From 058d817335db93ed263cb9aa16770af20761a408 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 17:45:16 -0400
Subject: [PATCH 289/396] whitespace

---
 src/RIGID/fix_rigid_small.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index c579e362c7..bf0a847d48 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -259,7 +259,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
         utils::numeric(FLERR,arg[iarg+3],false,lmp);
       p_flag[0] = p_flag[1] = p_flag[2] = 1;
       if (domain->dimension == 2) {
-              p_start[2] = p_stop[2] = p_period[2] = 0.0;
+        p_start[2] = p_stop[2] = p_period[2] = 0.0;
         p_flag[2] = 0;
       }
       iarg += 4;
@@ -275,7 +275,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       p_flag[0] = p_flag[1] = p_flag[2] = 1;
       if (domain->dimension == 2) {
         p_start[2] = p_stop[2] = p_period[2] = 0.0;
-              p_flag[2] = 0;
+        p_flag[2] = 0;
       }
       iarg += 4;
 

From f193a87426b0a4bb32abd8fb22369869aa15f25c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 18:04:38 -0400
Subject: [PATCH 290/396] correct CMake syntax

---
 unittest/c-library/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/unittest/c-library/CMakeLists.txt b/unittest/c-library/CMakeLists.txt
index 21b00b5c03..496cbb5055 100644
--- a/unittest/c-library/CMakeLists.txt
+++ b/unittest/c-library/CMakeLists.txt
@@ -88,7 +88,7 @@ if(BUILD_MPI)
   add_test(NAME RunCoupleSimpleCC
     COMMAND $<TARGET_FILE:simpleCC> 1 ${LAMMPS_DIR}/examples/COUPLE/simple/in.lj)
 
-  if($<TARGET_EXISTS:simpleF90>)
+  if(TARGET simpleF90)
     add_test(NAME RunCoupleSimpleF90
       COMMAND $<TARGET_FILE:simpleF90> 1 ${LAMMPS_DIR}/examples/COUPLE/simple/in.lj)
     set_tests_properties(RunCoupleSimpleF90 PROPERTIES

From 5eba9d7ee3de42cc5fbc20c1bdfa45e614f013cd Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 18:04:54 -0400
Subject: [PATCH 291/396] update regex for change to version output

---
 unittest/c-library/CMakeLists.txt | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/unittest/c-library/CMakeLists.txt b/unittest/c-library/CMakeLists.txt
index 496cbb5055..3e5b7a8cc0 100644
--- a/unittest/c-library/CMakeLists.txt
+++ b/unittest/c-library/CMakeLists.txt
@@ -80,7 +80,7 @@ if(BUILD_MPI)
       COMMAND $<TARGET_FILE:simple-plugin> 1 ${LAMMPS_DIR}/examples/COUPLE/plugin/in.lj $<TARGET_FILE:lammps>)
     set_tests_properties(RunCoupleSimplePlugin PROPERTIES
       ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;HWLOC_HIDE_ERRORS=2"
-      PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?( - Development)?( - Maintenance)?\\)")
+      PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?( - Development.*)?( - Maintenance.*)?\\)")
   endif()
   add_subdirectory(${LAMMPS_DIR}/examples/COUPLE/simple ${CMAKE_BINARY_DIR}/build-simple)
   add_test(NAME RunCoupleSimpleC
@@ -93,10 +93,10 @@ if(BUILD_MPI)
       COMMAND $<TARGET_FILE:simpleF90> 1 ${LAMMPS_DIR}/examples/COUPLE/simple/in.lj)
     set_tests_properties(RunCoupleSimpleF90 PROPERTIES
       ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;HWLOC_HIDE_ERRORS=2"
-      PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?( - Development)?( - Maintenance)?\\)")
+      PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?( - Development.*)?( - Maintenance.*)?\\)")
   endif()
 
   set_tests_properties(RunCoupleSimpleC RunCoupleSimpleCC PROPERTIES
     ENVIRONMENT "TSAN_OPTIONS=ignore_noninstrumented_modules=1;HWLOC_HIDE_ERRORS=2"
-    PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?( - Development)?( - Maintenance)?\\)")
+    PASS_REGULAR_EXPRESSION "LAMMPS \\([0-9]+ [A-Za-z]+ 2[0-9][0-9][0-9]( - Update [0-9]+)?( - Development.*)?( - Maintenance.*)?\\)")
 endif()

From 753a0bd386162925b4d93c48bd4bcda06df308fe Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 18:22:53 -0400
Subject: [PATCH 292/396] remove obsolete Fortran interfaces from
 examples/COUPLE folder

---
 doc/src/Fortran.rst                           |   11 -
 examples/COUPLE/README                        |   13 +-
 examples/COUPLE/fortran2/.gitignore           |    1 -
 examples/COUPLE/fortran2/LAMMPS-wrapper.cpp   |   96 -
 examples/COUPLE/fortran2/LAMMPS-wrapper.h     |   41 -
 examples/COUPLE/fortran2/LAMMPS.F90           | 1788 -----------------
 examples/COUPLE/fortran2/Makefile             |   41 -
 examples/COUPLE/fortran2/README               |  273 ---
 examples/COUPLE/fortran2/in.simple            |   16 -
 examples/COUPLE/fortran2/simple.f90           |  112 --
 .../COUPLE/fortran_dftb/LAMMPS-wrapper.cpp    |   96 -
 examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h |   40 -
 .../COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp   |   80 -
 .../COUPLE/fortran_dftb/LAMMPS-wrapper2.h     |   37 -
 examples/COUPLE/fortran_dftb/LAMMPS.F90       |  982 ---------
 examples/COUPLE/fortran_dftb/README           |   37 -
 examples/COUPLE/fortran_dftb/data.diamond     |  148 --
 examples/COUPLE/fortran_dftb/dftb_in.hsd      |   40 -
 examples/COUPLE/fortran_dftb/dftb_pin.hsd     |  129 --
 examples/COUPLE/fortran_dftb/in.simple        |   16 -
 examples/COUPLE/fortran_dftb/log.simple       |   71 -
 examples/COUPLE/fortran_dftb/makefile         |   45 -
 examples/COUPLE/fortran_dftb/simple.f90       |  110 -
 23 files changed, 4 insertions(+), 4219 deletions(-)
 delete mode 100644 examples/COUPLE/fortran2/.gitignore
 delete mode 100644 examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
 delete mode 100644 examples/COUPLE/fortran2/LAMMPS-wrapper.h
 delete mode 100644 examples/COUPLE/fortran2/LAMMPS.F90
 delete mode 100644 examples/COUPLE/fortran2/Makefile
 delete mode 100644 examples/COUPLE/fortran2/README
 delete mode 100644 examples/COUPLE/fortran2/in.simple
 delete mode 100644 examples/COUPLE/fortran2/simple.f90
 delete mode 100644 examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
 delete mode 100644 examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h
 delete mode 100644 examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
 delete mode 100644 examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h
 delete mode 100644 examples/COUPLE/fortran_dftb/LAMMPS.F90
 delete mode 100644 examples/COUPLE/fortran_dftb/README
 delete mode 100644 examples/COUPLE/fortran_dftb/data.diamond
 delete mode 100644 examples/COUPLE/fortran_dftb/dftb_in.hsd
 delete mode 100644 examples/COUPLE/fortran_dftb/dftb_pin.hsd
 delete mode 100644 examples/COUPLE/fortran_dftb/in.simple
 delete mode 100644 examples/COUPLE/fortran_dftb/log.simple
 delete mode 100644 examples/COUPLE/fortran_dftb/makefile
 delete mode 100644 examples/COUPLE/fortran_dftb/simple.f90

diff --git a/doc/src/Fortran.rst b/doc/src/Fortran.rst
index 7e9f16fa70..3b9ad9d1ff 100644
--- a/doc/src/Fortran.rst
+++ b/doc/src/Fortran.rst
@@ -56,17 +56,6 @@ C++ in the ``examples/COUPLE/simple`` folder of the LAMMPS distribution.
    and Ubuntu 18.04 LTS and not compatible.  Either newer compilers
    need to be installed or the Linux updated.
 
-.. versionchanged:: 8Feb2023
-
-.. note::
-
-   A contributed Fortran interface is available in the
-   ``examples/COUPLE/fortran2`` folder.  However, since the completion
-   of the :f:mod:`LIBLAMMPS` module, this interface is now deprecated,
-   no longer actively maintained and will likely be removed in the
-   future.  Please see the ``README`` file in that folder for more
-   information about it and how to contact its author and maintainer.
-
 ----------
 
 Creating or deleting a LAMMPS object
diff --git a/examples/COUPLE/README b/examples/COUPLE/README
index adf46d027d..13e593d55d 100644
--- a/examples/COUPLE/README
+++ b/examples/COUPLE/README
@@ -19,12 +19,12 @@ See these sections of the LAMMPS manual for details:
 Build LAMMPS as a library (doc/html/Build_basics.html)
 Link LAMMPS as a library to another code (doc/html/Build_link.html)
 Coupling LAMMPS to other codes (doc/html/Howto_couple.html)
-Using LAMMPS in client/server mode (doc/html/Howto_client_server.html)
 Library interface to LAMMPS (doc/html/Howto_library.html)
+Detailed documentation of the LAMMPS interfaces (doc/html/Library.html)
 
-The library interface to LAMMPS is in src/library.cpp.  Routines can
-be easily added to this file so an external program can perform the
-LAMMPS tasks desired.
+The core library interface to LAMMPS is in src/library.cpp.  Routines
+can be easily added to this file so an external program can perform
+the LAMMPS tasks desired.
 
 -------------------------------------------------------------------
 
@@ -36,10 +36,5 @@ plugin              example for loading LAMMPS at runtime from a shared library
 lammps_spparks      grain-growth Monte Carlo with strain via MD,
                     coupling to SPPARKS kinetic MC code
 library             collection of useful inter-code communication routines
-fortran2            a more sophisticated wrapper on the LAMMPS library API that
-                      can be called from Fortran
-fortran_dftb        wrapper written by Nir Goldman (LLNL), as an
-                      extension to fortran2, used for calling LAMMPS
-                      from Fortran DFTB+ tight-binding code
 
 Each sub-directory has its own README with more details.
diff --git a/examples/COUPLE/fortran2/.gitignore b/examples/COUPLE/fortran2/.gitignore
deleted file mode 100644
index 63a7748cf4..0000000000
--- a/examples/COUPLE/fortran2/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-*.mod
diff --git a/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp b/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
deleted file mode 100644
index 4774cb6b49..0000000000
--- a/examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
+++ /dev/null
@@ -1,96 +0,0 @@
-/* -----------------------------------------------------------------------
-    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/, Sandia National Laboratories
-    LAMMPS development team: developers@lammps.org
- 
-    Copyright (2003) Sandia Corporation.  Under the terms of Contract
-    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-    certain rights in this software.  This software is distributed under 
-    the GNU General Public License.
- 
-    See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-                          University of Missouri (USA), 2012
-------------------------------------------------------------------------- */
-
-/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
-   provides a (I hope) robust Fortran interface to library.cpp and
-   library.h.  All functions herein COULD be added to library.cpp instead of
-   including this as a separate file. See the README for instructions. */
-
-#include <mpi.h>
-#include "LAMMPS-wrapper.h"
-#define LAMMPS_LIB_MPI 1
-#include <library.h>
-#include <lammps.h>
-#include <atom.h>
-#include <fix.h>
-#include <compute.h>
-#include <modify.h>
-#include <error.h>
-#include <cstdlib>
-
-using namespace LAMMPS_NS;
-
-void lammps_open_fortran_wrapper (int argc, char **argv,
-      MPI_Fint communicator, void **ptr)
-{
-   MPI_Comm C_communicator = MPI_Comm_f2c (communicator);
-   lammps_open (argc, argv, C_communicator, ptr);
-}
-
-int lammps_get_ntypes (void *ptr)
-{
-  class LAMMPS *lmp = (class LAMMPS *) ptr;
-  int ntypes = lmp->atom->ntypes;
-  return ntypes;
-}
-
-void lammps_error_all (void *ptr, const char *file, int line, const char *str)
-{
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
-   lmp->error->all (file, line, str);
-}
-
-int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
-{
-   int *size;
-   size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR);
-   if (size) return *size;
-   return 0;
-}
-
-void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
-      int *nrows, int *ncols)
-{
-   int *tmp;
-   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS);
-   if (tmp) *nrows = *tmp;
-   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS);
-   if (tmp) *ncols = *tmp;
-   return;
-}
-
-int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
-{
-   int *size;
-   size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0);
-   if (size) return *size;
-   return 0;
-}
-
-void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
-      int *nrows, int *ncols)
-{
-   int *tmp;
-   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0);
-   if (tmp) *nrows = *tmp;
-   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0);
-   if (tmp) *ncols = *tmp;
-   return;
-}
-
-/* vim: set ts=3 sts=3 expandtab: */
diff --git a/examples/COUPLE/fortran2/LAMMPS-wrapper.h b/examples/COUPLE/fortran2/LAMMPS-wrapper.h
deleted file mode 100644
index 02e1a651a9..0000000000
--- a/examples/COUPLE/fortran2/LAMMPS-wrapper.h
+++ /dev/null
@@ -1,41 +0,0 @@
-/* -----------------------------------------------------------------------
-    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/, Sandia National Laboratories
-    LAMMPS development team: developers@lammps.org
- 
-    Copyright (2003) Sandia Corporation.  Under the terms of Contract
-    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-    certain rights in this software.  This software is distributed under 
-    the GNU General Public License.
- 
-    See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-                          University of Missouri (USA), 2012
-------------------------------------------------------------------------- */
-
-/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
-   provides a (I hope) robust Fortran interface to library.cpp and
-   library.h.  All prototypes herein COULD be added to library.h instead of
-   including this as a separate file. See the README for instructions. */
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/* Prototypes for auxiliary functions */
-void lammps_open_fortran_wrapper (int, char**, MPI_Fint, void**);
-int lammps_get_ntypes (void*);
-int lammps_extract_compute_vectorsize (void*, char*, int);
-void lammps_extract_compute_arraysize (void*, char*, int, int*, int*);
-int lammps_extract_fix_vectorsize (void*, char*, int);
-void lammps_extract_fix_arraysize (void*, char*, int, int*, int*);
-void lammps_error_all (void*, const char*, int, const char*);
-
-#ifdef __cplusplus
-}
-#endif
-
-/* vim: set ts=3 sts=3 expandtab: */
diff --git a/examples/COUPLE/fortran2/LAMMPS.F90 b/examples/COUPLE/fortran2/LAMMPS.F90
deleted file mode 100644
index 2f4ae2c95e..0000000000
--- a/examples/COUPLE/fortran2/LAMMPS.F90
+++ /dev/null
@@ -1,1788 +0,0 @@
-!! -----------------------------------------------------------------------
-!   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-!   https://www.lammps.org/ Sandia National Laboratories
-!   LAMMPS Development team: developers@lammps.org
-!
-!   Copyright (2003) Sandia Corporation.  Under the terms of Contract
-!   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-!   certain rights in this software.  This software is distributed under 
-!   the GNU General Public License.
-!
-!   See the README file in the top-level LAMMPS directory.
-!--------------------------------------------------------------------------
-
-!! ------------------------------------------------------------------------
-!   Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-!                         University of Tennessee, Knoxville (USA), 2012
-!   Updated October 2020 by the author (now at the University of Missouri).
-!--------------------------------------------------------------------------
-
-!! NOTE -------------------------------------------------------------------
-!  This interface is obsolete and may be removed in a future release of
-!  LAMMPS. The interface in fortran/lammps.f90 replaces this one. That API
-!  is maintained by the LAMMPS developers and has documentation written for
-!  it; it is based loosely on this one, but binds all procedures to a lammps
-!  derived type. That interface was written in large
-!  part by the same author, but is also supported by other developers.
-!--------------------------------------------------------------------------
-
-!! LAMMPS, a Fortran 2003 module containing an interface between Fortran
-!! programs and the C-style functions in library.cpp that ship with LAMMPS.
-!! This file should be accompanied by LAMMPS-wrapper.cpp and LAMMPS-wrapper.h,
-!! which define wrapper functions that ease portability and enforce array
-!! dimensions.
-!!
-!! Everything in this module should be 100% portable by way of Fortran 2003's
-!! ISO_C_BINDING intrinsic module.  See the README for instructions for
-!! compilation and use.
-!!
-!! Here are the PUBLIC functions and subroutines included in this module.
-!!    subroutine lammps_open (command_line, communicator, ptr)
-!!    subroutine lammps_open_no_mpi (command_line, ptr)
-!!    subroutine lammps_close (ptr)
-!!    integer (kind=C_int) lammps_version (ptr)
-!!    subroutine lammps_file (ptr, str)
-!!    subroutine lammps_command (ptr, str)
-!!    subroutine lammps_commands_list (ptr, cmds)
-!!    subroutine lammps_commands_string (ptr, str)
-!!    subroutine lammps_free (ptr)
-!!    integer function lammps_extract_setting (ptr, name)
-!!    subroutine lammps_extract_global (global, ptr, name)
-!!    subroutine lammps_extract_box (ptr, boxlo, boxhi, xy, yz, xz, &
-!!       periodicity, box_change)
-!!    subroutine lammps_extract_atom (atom, ptr, name)
-!!    subroutine lammps_extract_compute (compute, ptr, id, style, type)
-!!    subroutine lammps_extract_fix (fix, ptr, id, style, type, i, j)
-!!    subroutine lammps_extract_variable (variable, ptr, name, group)
-!!    double precision function lammps_get_thermo (ptr, name)
-!!    double precision function lammps_get_natoms (ptr)
-!!    subroutine lammps_set_variable (ptr, name, str, [err])
-!!    subroutine lammps_reset_box (ptr, boxlo, boxhi, xy, yz, xz)
-!!    subroutine lammps_gather_atoms (ptr, name, count, data)
-!!    subroutine lammps_gather_atoms_concat (ptr, name, count, data)
-!!    subroutine lammps_gather_atoms_subset (ptr, name, count, ids, data)
-!!    subroutine lammps_scatter_atoms (ptr, name, data)
-!!    subroutine lammps_scatter_atoms_subset (ptr, name, ids, data)
-!!    logical function lammps_config_has_package (package_name)
-!!    integer function lammps_config_package_count ()
-!!    logical function lammps_config_package_name (index, buffer)
-!!    logical function lammps_config_has_gzip_support ()
-!!    logical function lammps_config_has_png_support ()
-!!    logical function lammps_config_has_jpeg_support ()
-!!    logical function lammps_config_has_ffmpeg_support ()
-!!    logical function lammps_config_has_exceptions ()
-!!    integer function lammps_find_pair_neighlist (ptr, style, exact, nsub,
-!!       request)
-!!    integer function lammps_find_fix_neighlist (ptr, id, request)
-!!    integer function lammps_find_compute_neighlist (ptr, id, request)
-!!    integer function lammps_neighlist_num_elements (ptr, idx)
-!!    subroutine lammps_neighlist_element_neighbors (ptr, idx, element, iatom,
-!!       numneigh, neighbors)
-!!    subroutine lammps_create_atoms (ptr, n, id, type, x, v, image,
-!1       shrinkexceed)
-!!
-!! The following are also available if compiled with -DLAMMPS_EXCEPTIONS
-!!    function lammps_has_error (ptr)
-!!    function lammps_get_last_error_message (ptr, buffer)
-!!
-!! Note that the following function is not implemented from this interface:
-!!    lammps_set_fix_external_callback
-
-#define FLERR __FILE__,__LINE__
-! The above line allows for similar error checking as is done with standard
-! LAMMPS files.
-
-! This should (?) allow this module to work with settings in lmptype.h
-#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
-#define LAMMPS_SMALLBIG
-#endif
-
-#ifdef LAMMPS_SMALLBIG
-#define C_smallint C_int
-#define C_imageint C_int
-#define C_tagint C_int
-#define C_bigint C_int64_t
-#endif
-
-#ifdef LAMMPS_BIGBIG
-#define C_smallint C_int
-#define C_imageint C_int64_t
-#define C_tagint C_int64_t
-#define C_bigint C_int64_t
-#endif
-
-#ifdef LAMMPS_SMALLSMALL
-#define C_smallint C_int
-#define C_imageint C_int
-#define C_tagint C_int
-#define C_bigint C_int
-#endif
-
-module LAMMPS
-
-   use, intrinsic :: ISO_C_binding, only : C_double, C_int, C_ptr, C_char, &
-      C_NULL_CHAR, C_NULL_PTR, C_loc, C_F_pointer, C_int64_t, &
-      lammps_instance => C_ptr
-   implicit none
-   private
-
-   ! We inherit some ISO_C_BINDING entities for ease of use
-   public :: lammps_instance, C_ptr, C_double, C_int
-   ! Only the following functions may be called by the user:
-   public :: lammps_open, lammps_open_no_mpi, lammps_close, &
-      lammps_version, lammps_file, lammps_command, lammps_commands_list, &
-      lammps_commands_string, lammps_free, lammps_extract_setting, &
-      lammps_extract_global, lammps_extract_box, lammps_extract_atom, &
-      lammps_extract_compute, lammps_extract_fix, lammps_extract_variable, &
-      lammps_get_thermo, lammps_get_natoms, lammps_set_variable, &
-      lammps_reset_box, lammps_gather_atoms, lammps_gather_atoms_concat, &
-      lammps_gather_atoms_subset, lammps_scatter_atoms, &
-      lammps_scatter_atoms_subset, lammps_config_has_package, &
-      lammps_config_package_count, lammps_config_package_name, &
-      lammps_config_has_gzip_support, lammps_config_has_png_support, &
-      lammps_config_has_jpeg_support, lammps_config_has_ffmpeg_support, &
-      lammps_config_has_exceptions, lammps_find_pair_neighlist, &
-      lammps_find_fix_neighlist, lammps_find_compute_neighlist, &
-      lammps_neighlist_num_elements, lammps_neighlist_element_neighbors, &
-      lammps_create_atoms
-
-#ifdef LAMMPS_EXCEPTIONS
-   public :: lammps_has_error, lammps_get_last_error_message
-#endif
-
-   !! constants for extracting data from computes and fixes
-   !! and data types
-
-   INTEGER, PARAMETER :: LMP_STYLE_GLOBAL = 0, LMP_STYLE_ATOM = 1, &
-       LMP_STYLE_LOCAL = 2, LMP_TYPE_SCALAR = 0, LMP_TYPE_VECTOR = 1, &
-       LMP_TYPE_ARRAY = 2, LMP_SIZE_VECTOR = 3, LMP_SIZE_ROWS = 4, &
-       LMP_SIZE_COLS = 5, LAMMPS_INT = 0, LAMMPS_INT_2D = 1, &
-       LAMMPS_DOUBLE = 2, LAMMPS_DOUBLE_2D = 3, LAMMPS_INT64 = 4, &
-       LAMMPS_INT64_2D = 5, LAMMPS_STRING = 6
-
-   PUBLIC :: LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, LMP_STYLE_LOCAL, &
-       LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, &
-       LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS,  LAMMPS_INT, &
-       LAMMPS_INT_2D, LAMMPS_DOUBLE, LAMMPS_DOUBLE_2D, LAMMPS_INT64, &
-       LAMMPS_INT64_2D, LAMMPS_STRING 
-
-   !! Functions supplemental to the prototypes in library.h. {{{1
-   !! The function definitions (in C++) are contained in LAMMPS-wrapper.cpp.
-   !! I would have written the first in Fortran, but the MPI libraries (which
-   !! were written in C) have C-based functions to convert from Fortran MPI
-   !! handles to C MPI handles, and there is no Fortran equivalent for those
-   !! functions.
-   interface
-      subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
-      bind (C, name='lammps_open_fortran_wrapper')
-         import :: C_int, C_ptr
-         integer (C_int), value :: argc
-         type (C_ptr), dimension(*) :: argv
-         integer, value :: communicator
-         type (C_ptr) :: ptr
-      end subroutine lammps_open_wrapper
-      subroutine lammps_actual_error_all (ptr, file, line, str) &
-      bind (C, name='lammps_error_all')
-         import :: C_int, C_char, C_ptr
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: file, str
-         integer (C_int), value :: line
-      end subroutine lammps_actual_error_all
-      function lammps_get_ntypes (ptr) result (ntypes) &
-      bind (C, name='lammps_get_ntypes')
-         import :: C_int, C_ptr
-         type (C_ptr), value :: ptr
-         integer (C_int) :: ntypes
-      end function lammps_get_ntypes
-      function lammps_actual_extract_compute_vectorsize (ptr, id, style) &
-      result (vectorsize) bind (C, name='lammps_extract_compute_vectorsize')
-         import :: C_int, C_char, C_ptr
-         integer (C_int) :: vectorsize
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style
-      end function lammps_actual_extract_compute_vectorsize
-      subroutine lammps_actual_extract_compute_arraysize (ptr, id, style, &
-            nrows, ncols) bind (C, name='lammps_extract_compute_arraysize')
-         import :: C_int, C_char, C_ptr
-         integer (C_int) :: arraysize
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style
-         integer (C_int) :: nrows, ncols
-      end subroutine lammps_actual_extract_compute_arraysize
-      function lammps_actual_extract_fix_vectorsize (ptr, id, style) &
-      result (vectorsize) bind (C, name='lammps_extract_fix_vectorsize')
-         import :: C_int, C_char, C_ptr
-         integer (C_int) :: vectorsize
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style
-      end function lammps_actual_extract_fix_vectorsize
-      subroutine lammps_actual_extract_fix_arraysize (ptr, id, style, &
-            nrows, ncols) bind (C, name='lammps_extract_fix_arraysize')
-         import :: C_int, C_char, C_ptr
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style
-         integer (C_int) :: nrows, ncols
-      end subroutine lammps_actual_extract_fix_arraysize
-   end interface
-
-   !! Functions/subroutines defined in library.h and library.cpp {{{1
-   interface
-      subroutine lammps_actual_open_no_mpi (argc, argv, ptr) &
-      bind (C, name='lammps_open_no_mpi')
-         import :: C_int, C_ptr
-         integer (C_int), value :: argc
-         type (C_ptr), dimension(*) :: argv
-         type (C_ptr) :: ptr
-      end subroutine lammps_actual_open_no_mpi
-
-      subroutine lammps_close (ptr) bind (C, name='lammps_close')
-         import :: C_ptr
-         type (C_ptr), value :: ptr
-      end subroutine lammps_close
-
-      function lammps_version (ptr) result (version) &
-      bind (C, name='lammps_version')
-         import :: C_ptr, C_int
-         type (C_ptr), value :: ptr
-         integer (kind=C_int) :: version
-      end function lammps_version
-
-      subroutine lammps_actual_file (ptr, str) bind (C, name='lammps_file')
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: str
-      end subroutine lammps_actual_file
-
-      function lammps_actual_command (ptr, str) result (command) &
-      bind (C, name='lammps_command')
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: str
-         type (C_ptr) :: command
-      end function lammps_actual_command
-
-      subroutine lammps_actual_commands_list (ptr, ncmd, cmds) &
-      bind (C, name='lammps_commands_list')
-         import :: C_ptr, C_int
-         type (C_ptr), value :: ptr
-         type (C_ptr), dimension(*) :: cmds
-         integer (C_int), value :: ncmd
-      end subroutine lammps_actual_commands_list
-
-      subroutine lammps_actual_commands_string (ptr, str) &
-      bind (C, name='lammps_commands_string')
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: str
-      end subroutine lammps_actual_commands_string
-
-      subroutine lammps_free (ptr) bind (C, name='lammps_free')
-         import :: C_ptr
-         type (C_ptr), value :: ptr
-      end subroutine lammps_free
-
-      function lammps_actual_extract_setting (ptr, name) result (setting) &
-      bind(C, name='lammps_extract_setting')
-         import :: C_ptr, C_char, C_int
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: name
-         integer (kind=C_int) :: setting
-      end function lammps_actual_extract_setting
-
-      function lammps_actual_extract_global (ptr, name) &
-      bind (C, name='lammps_extract_global') result (global)
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: name
-         type (C_ptr) :: global
-      end function lammps_actual_extract_global
-
-      subroutine lammps_actual_extract_box (ptr, boxlo, boxhi, xy, yz, &
-            xz, periodicity, box_change) bind (C, name='lammps_extract_box')
-         import :: C_ptr, C_double, C_int
-         type (C_ptr), value :: ptr
-         real (C_double) :: boxlo(3), boxhi(3), xy, yz, xz
-         integer (C_int) :: periodicity(3), box_change
-      end subroutine lammps_actual_extract_box
-
-      function lammps_actual_extract_atom (ptr, name) &
-      bind (C, name='lammps_extract_atom') result (atom)
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: name
-         type (C_ptr) :: atom
-      end function lammps_actual_extract_atom
-
-      function lammps_actual_extract_compute (ptr, id, style, type) &
-      result (compute) bind (C, name='lammps_extract_compute')
-         import :: C_ptr, C_char, C_int
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style, type
-         type (C_ptr) :: compute
-      end function lammps_actual_extract_compute
-
-      function lammps_actual_extract_fix (ptr, id, style, type, i, j) &
-      result (fix) bind (C, name='lammps_extract_fix')
-         import :: C_ptr, C_char, C_int
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style, type, i, j
-         type (C_ptr) :: fix
-      end function lammps_actual_extract_fix
-
-      function lammps_actual_extract_variable (ptr, name, group) &
-      result (variable) bind (C, name='lammps_extract_variable')
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: name, group
-         type (C_ptr) :: variable
-      end function lammps_actual_extract_variable
-
-      function lammps_actual_get_thermo (ptr, name) result (dval) &
-      bind (C, name='lammps_get_thermo')
-         import :: C_ptr, C_char, C_double
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: name
-         real (C_double) :: dval
-      end function lammps_actual_get_thermo
-
-      function lammps_get_natoms (ptr) result (natoms) &
-      bind (C, name='lammps_get_natoms')
-         import :: C_ptr, C_double
-         type (C_ptr), value :: ptr
-         real (C_double) :: natoms
-      end function lammps_get_natoms
-
-      function lammps_actual_set_variable (ptr, name, str) result (err) &
-      bind (C, name='lammps_set_variable')
-         import :: C_ptr, C_char, C_int
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: name, str
-         integer (C_int) :: err
-      end function lammps_actual_set_variable
-
-      subroutine lammps_actual_reset_box (ptr, boxlo, boxhi, xy, yz, xz) &
-      bind (C, name='lammps_reset_box')
-         import :: C_ptr, C_double, C_int
-         type (C_ptr), value :: ptr
-         real (C_double) :: boxlo(3), boxhi(3), xy, yz, xz
-      end subroutine lammps_actual_reset_box
-
-      subroutine lammps_actual_gather_atoms (ptr, name, type, count, data) &
-      bind (C, name='lammps_gather_atoms')
-         import :: C_ptr, C_int, C_char
-         type (C_ptr), value :: ptr, data
-         character (kind=C_char), dimension(*) :: name
-         integer (C_int), value :: type, count
-      end subroutine lammps_actual_gather_atoms
-
-      subroutine lammps_actual_gather_atoms_concat (ptr, name, type, count, &
-      data) bind (C, name='lammps_gather_atoms_concat')
-         import :: C_ptr, C_int, C_char
-         type (C_ptr), value :: ptr, data
-         character (kind=C_char), dimension(*) :: name
-         integer (C_int), value :: type, count
-      end subroutine lammps_actual_gather_atoms_concat
-
-      subroutine lammps_actual_gather_atoms_subset (ptr, name, type, count, &
-      ndata, ids, data) bind (C, name='lammps_gather_atoms_subset')
-         import :: C_ptr, C_int, C_char
-         type (C_ptr), value :: ptr, data
-         character (kind=C_char), dimension(*) :: name
-         integer (C_int), value :: type, count, ndata
-         integer (C_int) :: ids(:)
-      end subroutine lammps_actual_gather_atoms_subset
-
-      subroutine lammps_actual_scatter_atoms (ptr, name, type, count, data) &
-      bind (C, name='lammps_scatter_atoms')
-         import :: C_ptr, C_int, C_char
-         type (C_ptr), value :: ptr, data
-         character (kind=C_char), dimension(*) :: name
-         integer (C_int), value :: type, count
-      end subroutine lammps_actual_scatter_atoms
-
-      subroutine lammps_actual_scatter_atoms_subset (ptr, name, type, count, &
-      ndata, ids, data) bind (C, name='lammps_scatter_atoms_subset')
-         import :: C_ptr, C_int, C_char
-         type (C_ptr), value :: ptr, data
-         character (kind=C_char), dimension(*) :: name
-         integer (C_int), value :: type, count, ndata
-         integer (C_int), dimension(*) :: ids
-      end subroutine lammps_actual_scatter_atoms_subset
-
-      function lammps_actual_config_has_package (package_name) &
-      result (has_it) bind (C, name='lammps_config_has_package')
-         import :: C_char, C_int
-         character (len=1, kind=C_char), dimension(*) :: package_name
-         integer (C_int) :: has_it
-      end function lammps_actual_config_has_package
-
-      function lammps_config_package_count () result (count) &
-      bind (C, name='lammps_config_package_count')
-         import :: C_int
-         integer (C_int) :: count
-      end function lammps_config_package_count
-
-      function lammps_actual_config_package_name (index, buffer, max_size) &
-      result (num) bind (C, name='lammps_config_package_name')
-         import :: C_int, C_char
-         integer (C_int), value :: index, max_size
-         character (len=1, kind=C_char), dimension(*) :: buffer
-         integer (C_int) :: num
-      end function lammps_actual_config_package_name
-
-      function lammps_actual_config_has_gzip_support () result (C_has_it) &
-      bind (C, name='lammps_config_has_gzip_support')
-         import :: C_int
-         integer (C_int) :: C_has_it
-      end function lammps_actual_config_has_gzip_support
-
-      function lammps_actual_config_has_png_support () result (C_has_it) &
-      bind (C, name='lammps_config_has_png_support')
-         import :: C_int
-         integer (C_int) :: C_has_it
-      end function lammps_actual_config_has_png_support
-
-      function lammps_actual_config_has_jpeg_support () result (C_has_it) &
-      bind (C, name='lammps_config_has_jpeg_support')
-         import :: C_int
-         integer (C_int) :: C_has_it
-      end function lammps_actual_config_has_jpeg_support
-
-      function lammps_actual_config_has_ffmpeg_support () result (C_has_it) &
-      bind (C, name='lammps_config_has_ffmpeg_support')
-         import :: C_int
-         integer (C_int) :: C_has_it
-      end function lammps_actual_config_has_ffmpeg_support
-
-      function lammps_actual_config_has_exceptions () result (C_has_it) &
-      bind (C, name='lammps_config_has_exceptions')
-         import :: C_int
-         integer (C_int) :: C_has_it
-      end function lammps_actual_config_has_exceptions
-
-      function lammps_actual_find_pair_neighlist (ptr, style, exact, nsub, &
-            request) result (C_neighlist) &
-      bind (C, name='lammps_find_pair_neighlist')
-         import :: C_ptr, C_int, C_char
-         integer (C_int) :: C_neighlist
-         type (C_ptr), value :: ptr
-         character (len=1, kind=C_char), dimension(*) :: style
-         integer (C_int), value :: exact, nsub, request
-      end function lammps_actual_find_pair_neighlist
-
-      function lammps_actual_find_fix_neighlist (ptr, id, request) &
-      result (C_neighlist) bind (C, name='lammps_find_fix_neighlist')
-         import :: C_ptr, C_int, C_char
-         integer (C_int) :: C_neighlist
-         type (C_ptr), value :: ptr
-         character (len=1, kind=C_char), dimension(*) :: id
-         integer (C_int), value :: request
-      end function lammps_actual_find_fix_neighlist
-
-      function lammps_actual_find_compute_neighlist (ptr, id, request) &
-      result (C_neighlist) bind (C, name='lammps_find_compute_neighlist')
-         import :: C_ptr, C_int, C_char
-         integer (C_int) :: C_neighlist
-         type (C_ptr), value :: ptr
-         character (len=1, kind=C_char), dimension(*) :: id
-         integer (C_int), value :: request
-      end function lammps_actual_find_compute_neighlist
-
-      function lammps_actual_neighlist_num_elements (ptr, idx) &
-      result (nelements) bind (C, name='lammps_neighlist_num_elements')
-         import :: C_ptr, C_int
-         integer (C_int) :: nelements
-         type (C_ptr), value :: ptr
-         integer (C_int), value :: idx
-      end function lammps_actual_neighlist_num_elements
-
-      subroutine lammps_actual_neighlist_element_neighbors (ptr, idx, &
-         element, iatom, numneigh, neighbors) &
-      bind (C, name='lammps_neighlist_element_neighbors')
-         import :: C_ptr, C_int
-         type (C_ptr), value :: ptr
-         integer (C_int), value :: idx, element
-         integer (C_int) :: iatom, numneigh
-         type (C_ptr) :: neighbors
-      end subroutine lammps_actual_neighlist_element_neighbors
-
-      subroutine lammps_actual_create_atoms (ptr, n, id, type, x, v, image, &
-      shrinkexceed) bind (C, name='lammps_create_atoms')
-         import :: C_ptr, C_int64_t, C_double, C_int
-         type (C_ptr), value :: ptr
-         integer (C_int), value :: n
-         integer (C_tagint) :: id
-         integer (C_int) :: type
-         real (C_double), dimension(*) :: x, v
-         integer (C_imageint), dimension(*) :: image
-         integer (C_int), value :: shrinkexceed
-      end subroutine lammps_actual_create_atoms
-
-#ifdef LAMMPS_EXCEPTIONS
-
-      function lammps_actual_has_error (ptr) result (C_has_it) &
-      bind (C, name='lammps_has_error')
-         import :: C_int, C_ptr
-         type (C_ptr), value :: ptr
-         integer (C_int) :: C_has_it
-      end function lammps_actual_has_error
-
-      function lammps_actual_get_last_error_message (ptr, buffer, &
-      buffer_size) result (error_type) &
-      bind (C, name='lammps_get_last_error_message')
-         import :: C_ptr, C_char, C_int
-         type (C_ptr), value :: ptr
-         integer (C_int), value :: buffer_size
-         character (len=1, kind=C_char), dimension(*) :: buffer
-         integer (C_int) :: error_type
-      end function lammps_actual_get_last_error_message
-
-#endif
-
-   end interface
-
-   ! Generic functions for the wrappers below {{{1
-
-   interface lammps_extract_global
-      module procedure lammps_extract_global_i, &
-         lammps_extract_global_dp
-   end interface lammps_extract_global
-
-   interface lammps_extract_atom
-      module procedure lammps_extract_atom_ia, &
-         lammps_extract_atom_dpa, &
-         lammps_extract_atom_dp2a
-   end interface lammps_extract_atom
-
-   interface lammps_extract_compute
-      module procedure lammps_extract_compute_dp, &
-         lammps_extract_compute_dpa, &
-         lammps_extract_compute_dp2a
-   end interface lammps_extract_compute
-
-   interface lammps_extract_fix
-      module procedure lammps_extract_fix_dp, &
-         lammps_extract_fix_dpa, &
-         lammps_extract_fix_dp2a
-   end interface lammps_extract_fix
-
-   interface lammps_extract_variable
-      module procedure lammps_extract_variable_dp, &
-         lammps_extract_variable_dpa
-   end interface lammps_extract_variable
-
-   interface lammps_gather_atoms
-      module procedure lammps_gather_atoms_ia, lammps_gather_atoms_dpa
-   end interface lammps_gather_atoms
-
-   interface lammps_gather_atoms_concat
-      module procedure lammps_gather_atoms_concat_ia, &
-         lammps_gather_atoms_concat_dpa
-   end interface lammps_gather_atoms_concat
-
-   interface lammps_gather_atoms_subset
-      module procedure lammps_gather_atoms_subset_ia, &
-         lammps_gather_atoms_subset_dpa
-   end interface lammps_gather_atoms_subset
-
-   interface lammps_scatter_atoms
-      module procedure lammps_scatter_atoms_ia, lammps_scatter_atoms_dpa
-   end interface lammps_scatter_atoms
-
-   interface lammps_scatter_atoms_subset
-      module procedure lammps_scatter_atoms_subset_ia, &
-         lammps_scatter_atoms_subset_dpa
-   end interface lammps_scatter_atoms_subset
-
-contains !! Wrapper functions local to this module {{{1
-
-   subroutine lammps_open (command_line, communicator, ptr)
-      character (len=*), intent(in) :: command_line
-      integer, intent(in) :: communicator
-      type (C_ptr) :: ptr
-      integer (C_int) :: argc
-      type (C_ptr), dimension(:), allocatable :: argv
-      character (kind=C_char), dimension(len_trim(command_line)+1), target :: &
-         c_command_line
-      c_command_line = string2Cstring (command_line)
-      call Cstring2argcargv (c_command_line, argc, argv)
-      call lammps_open_wrapper (argc, argv, communicator, ptr)
-      deallocate (argv)
-   end subroutine lammps_open
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_open_no_mpi (command_line, ptr)
-      character (len=*), intent(in) :: command_line
-      type (C_ptr) :: ptr
-      integer (C_int) :: argc
-      type (C_ptr), dimension(:), allocatable :: argv
-      character (kind=C_char), dimension(len_trim(command_line)+1), target :: &
-         c_command_line
-      c_command_line = string2Cstring (command_line)
-      call Cstring2argcargv (c_command_line, argc, argv)
-      call lammps_actual_open_no_mpi (argc, argv, ptr)
-      deallocate (argv)
-   end subroutine lammps_open_no_mpi
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_file (ptr, str)
-      type (C_ptr) :: ptr
-      character (len=*) :: str
-      character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
-      Cstr = string2Cstring (str)
-      call lammps_actual_file (ptr, Cstr)
-   end subroutine lammps_file
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_command (ptr, str)
-      type (C_ptr) :: ptr
-      character (len=*) :: str
-      character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
-      type (C_ptr) :: dummy
-      Cstr = string2Cstring (str)
-      dummy = lammps_actual_command (ptr, Cstr)
-   end subroutine lammps_command
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_commands_list (ptr, cmds)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), dimension(:) :: cmds
-      integer (C_int) :: ncmd
-!      character (kind=C_char,len=1), dimension(size(cmds)) :: C_cmds
-      type (C_ptr), dimension(:), allocatable :: C_cmds
-      character (len=1, kind=C_char), allocatable, target :: C_strings(:,:)
-      integer :: i, max_len
-      ncmd = size(cmds)
-      allocate (C_cmds(ncmd))
-      max_len = 0
-      do i=1, size(cmds)
-         if ( len(cmds(i)) > max_len ) max_len = len(cmds(i))
-      end do
-      allocate (C_strings(max_len + 1, ncmd))
-      do i=1, size(cmds)
-         C_strings(:,i) = string2Cstring(cmds(i))
-         C_cmds(i) = C_loc(C_strings(1,i))
-      end do
-      call lammps_actual_commands_list (ptr, ncmd, C_cmds)
-      deallocate (C_strings)
-      deallocate (C_cmds)
-   end subroutine lammps_commands_list
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_commands_string (ptr, str)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: str
-      character (kind=C_char), dimension(len_trim(str)+1) :: C_str
-      C_str = string2Cstring (str)
-      call lammps_actual_commands_string (ptr, C_str)
-   end subroutine lammps_commands_string
-
-!-----------------------------------------------------------------------------
-
-   function lammps_extract_setting (ptr, name) result (setting)
-      integer :: setting
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      character (kind=C_char), dimension(len_trim(name)+1) :: C_name
-      C_name = string2Cstring (name)
-      setting = lammps_actual_extract_setting (ptr, C_name)
-   end function lammps_extract_setting
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_global {{{2
-   function lammps_extract_global_Cptr (ptr, name) result (global)
-      type (C_ptr) :: global
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      Cname = string2Cstring (name)
-      global = lammps_actual_extract_global (ptr, Cname)
-   end function lammps_extract_global_Cptr
-   subroutine lammps_extract_global_i (global, ptr, name)
-      integer (C_int), pointer, intent(out) :: global
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      type (C_ptr) :: Cptr
-      Cptr = lammps_extract_global_Cptr (ptr, name)
-      call C_F_pointer (Cptr, global)
-   end subroutine lammps_extract_global_i
-   subroutine lammps_extract_global_dp (global, ptr, name)
-      real (C_double), pointer, intent(out) :: global
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      type (C_ptr) :: Cptr
-      Cptr = lammps_extract_global_Cptr (ptr, name)
-      call C_F_pointer (Cptr, global)
-   end subroutine lammps_extract_global_dp
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_box {{{2
-   subroutine lammps_extract_box (ptr, boxlo, boxhi, xy, yz, xz, &
-         periodicity, box_change)
-      type (C_ptr), intent(in) :: ptr
-      double precision, dimension(3), intent(out) :: boxlo, boxhi
-      double precision, intent(out) :: xy, yz, xz
-      logical, intent(out) :: periodicity(3), box_change
-      integer (kind=C_int) :: C_periodicity(3), C_box_change
-      real (C_double) :: C_boxlo(3), C_boxhi(3), C_xy, C_yz, C_xz
-      call lammps_actual_extract_box (ptr, C_boxlo, C_boxhi, C_xy, C_yz, &
-         C_xz, C_periodicity, C_box_change)
-      boxlo = C_boxlo
-      boxhi = C_boxhi
-      xy = C_xy
-      yz = C_yz
-      xz = C_xz
-      periodicity = (C_periodicity == 1) 
-      box_change = (C_box_change == 1)
-   end subroutine
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_atom {{{2
-   function lammps_extract_atom_Cptr (ptr, name) result (atom)
-      type (C_ptr) :: atom
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      Cname = string2Cstring (name)
-      atom = lammps_actual_extract_atom (ptr, Cname)
-   end function lammps_extract_atom_Cptr
-   subroutine lammps_extract_atom_ia (atom, ptr, name)
-      integer (C_int), dimension(:), pointer, intent(out) :: atom
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      type (C_ptr) :: Cptr
-      integer (C_int), pointer :: nelements
-      call lammps_extract_global_i (nelements, ptr, 'nlocal')
-      Cptr = lammps_extract_atom_Cptr (ptr, name)
-      call C_F_pointer (Cptr, atom, (/nelements/))
-   end subroutine lammps_extract_atom_ia
-   subroutine lammps_extract_atom_dpa (atom, ptr, name)
-      real (C_double), dimension(:), pointer, intent(out) :: atom
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      type (C_ptr) :: Cptr
-      integer (C_int), pointer :: nlocal
-      integer :: nelements
-      real (C_double), dimension(:), pointer :: Fptr
-      if ( name == 'mass' ) then
-         nelements = lammps_get_ntypes (ptr) + 1
-      else if ( name == 'x' .or. name == 'v' .or. name == 'f' .or. &
-                name == 'mu' .or. name == 'omega' .or. name == 'torque' .or. &
-                name == 'angmom' ) then
-         ! We should not be getting a rank-2 array here!
-         call lammps_error_all (ptr, FLERR, 'You cannot extract those atom&
-            & data (' // trim(name) // ') into a rank 1 array.')
-         return
-      else
-         ! Everything else we can get is probably nlocal units long
-         call lammps_extract_global_i (nlocal, ptr, 'nlocal')
-         nelements = nlocal
-      end if
-      Cptr = lammps_extract_atom_Cptr (ptr, name)
-      call C_F_pointer (Cptr, Fptr, (/nelements/))
-      if ( name == 'mass' ) then
-         atom(0:) => Fptr
-      else
-         atom => Fptr
-      end if
-   end subroutine lammps_extract_atom_dpa
-   subroutine lammps_extract_atom_dp2a (atom, ptr, name)
-      real (C_double), dimension(:,:), pointer, intent(out) :: atom
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      type (C_ptr) :: Cptr
-      type (C_ptr), pointer, dimension(:) :: Catom
-      integer (C_int), pointer :: nelements
-      if ( name /= 'x' .and. name /= 'v' .and. name /= 'f' .and. &
-           name /= 'mu' .and. name /= 'omega' .and. name /= 'tandque' .and. &
-           name /= 'angmom' ) then
-         ! We should not be getting a rank-2 array here!
-         call lammps_error_all (ptr, FLERR, 'You cannot extract those atom&
-            & data (' // trim(name) // ') into a rank 2 array.')
-         return
-      end if
-      Cptr = lammps_extract_atom_Cptr (ptr, name)
-      call lammps_extract_global_i (nelements, ptr, 'nlocal')
-      ! Catom will now be the array of void* pointers that the void** pointer
-      ! pointed to.  Catom(1) is now the pointer to the first element.
-      call C_F_pointer (Cptr, Catom, (/nelements/))
-      ! Now get the actual array, which has its shape transposed from what we
-      ! might think of it in C
-      call C_F_pointer (Catom(1), atom, (/3, nelements/))
-   end subroutine lammps_extract_atom_dp2a
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_compute {{{2
-   function lammps_extract_compute_Cptr (ptr, id, style, type) result (compute)
-      type (C_ptr) :: compute
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type
-      integer (kind=C_int) :: Cstyle, Ctype
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      Cid = string2Cstring (id)
-      Cstyle = style
-      Ctype = type
-      compute = lammps_actual_extract_compute (ptr, Cid, Cstyle, Ctype)
-   end function lammps_extract_compute_Cptr
-   subroutine lammps_extract_compute_dp (compute, ptr, id, style, type)
-      real (C_double), pointer, intent(out) :: compute
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type
-      type (C_ptr) :: Cptr
-      ! The only valid values of (style,type) are (0,0) for scalar 'compute'
-      if ( style /= 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot pack per-atom/local&
-            & data into a scalar.')
-         return
-      end if
-      if ( type == 1 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & vector (rank 1) into a scalar.')
-         return
-      else if ( type == 2 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & array (rank 2) into a scalar.')
-         return
-      end if
-      Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
-      call C_F_pointer (Cptr, compute)
-   end subroutine lammps_extract_compute_dp
-   subroutine lammps_extract_compute_dpa (compute, ptr, id, style, type)
-      real (C_double), dimension(:), pointer, intent(out) :: compute
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type
-      type (C_ptr) :: Cptr
-      integer :: nelements
-      ! Check for the correct dimensionality
-      if ( type == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & scalar (rank 0) into a rank 1 variable.')
-         return
-      else if ( type == 2 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & array (rank 2) into a rank 1 variable.')
-         return
-      end if
-      nelements = lammps_extract_compute_vectorsize (ptr, id, style)
-      Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
-      call C_F_pointer (Cptr, compute, (/nelements/))
-   end subroutine lammps_extract_compute_dpa
-   subroutine lammps_extract_compute_dp2a (compute, ptr, id, style, type)
-      real (C_double), dimension(:,:), pointer, intent(out) :: compute
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type
-      type (C_ptr) :: Cptr
-      type (C_ptr), pointer, dimension(:) :: Ccompute
-      integer :: nr, nc
-      ! Check for the correct dimensionality
-      if ( type == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & scalar (rank 0) into a rank 2 variable.')
-         return
-      else if ( type == 1 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & array (rank 1) into a rank 2 variable.')
-         return
-      end if
-      call lammps_extract_compute_arraysize (ptr, id, style, nr, nc)
-      Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
-      call C_F_pointer (Cptr, Ccompute, (/nr/))
-      ! Note that the matrix is transposed, from Fortran's perspective
-      call C_F_pointer (Ccompute(1), compute, (/nc, nr/))
-   end subroutine lammps_extract_compute_dp2a
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_fix {{{2
-   function lammps_extract_fix_Cptr (ptr, id, style, type, i, j) &
-   result (fix)
-      type (C_ptr) :: fix
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type, i, j
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      integer (kind=C_int) :: Cstyle, Ctype, Ci, Cj
-      Cid = string2Cstring (id)
-      Cstyle = style
-      Ctype = type
-      Ci = i - 1  ! This is for consistency with the values from f_ID[i],
-      Cj = j - 1  ! which is different from what library.cpp uses!
-      if ( (type >= 1 .and. Ci < 0) .or. &
-           (type == 2 .and. (Ci < 0 .or. Cj < 0) ) ) then
-         call lammps_error_all (ptr, FLERR, 'Index out of range in&
-            & lammps_extract_fix')
-      end if
-      fix = lammps_actual_extract_fix (ptr, Cid, Cstyle, Ctype, Ci, Cj)
-   end function lammps_extract_fix_Cptr
-   subroutine lammps_extract_fix_dp (fix, ptr, id, style, type, i, j)
-      real (C_double), intent(out) :: fix
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type, i, j
-      type (C_ptr) :: Cptr
-      real (C_double), pointer :: Fptr
-      ! Check for the correct dimensionality
-      if ( style /= 0 ) then
-         select case (type)
-         case (0)
-            call lammps_error_all (ptr, FLERR, 'There is no per-atom or local&
-               & scalar data available from fixes.')
-         case (1)
-            call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s &
-               &per-atom/local vector (rank 1) into a scalar.')
-         case (2)
-            call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s &
-               &per-atom/local array (rank 2) into a scalar.')
-         case default
-            call lammps_error_all (ptr, FLERR, 'Invalid extract_fix style/&
-               &type combination.')
-         end select
-         return
-      end if
-      Cptr = lammps_extract_fix_Cptr (ptr, id, style, type, i, j)
-      call C_F_pointer (Cptr, Fptr)
-      fix = Fptr
-      nullify (Fptr)
-      ! Memory is only allocated for "global" fix variables
-      if ( style == 0 ) call lammps_free (Cptr)
-   end subroutine lammps_extract_fix_dp
-   subroutine lammps_extract_fix_dpa (fix, ptr, id, style, type, i, j)
-      real (C_double), dimension(:), pointer, intent(out) :: fix
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type, i, j
-      type (C_ptr) :: Cptr
-      integer :: fix_len
-      ! Check for the correct dimensionality
-      if ( style == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You can''t extract the&
-            & whole vector from global fix data')
-         return
-      else if ( type == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You can''t extract a fix&
-            & scalar into a rank 1 variable')
-         return
-      else if ( type == 2 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
-            & array into a rank 1 variable.')
-         return
-      else if ( type /= 1 ) then
-         call lammps_error_all (ptr, FLERR, 'Invalid type for fix extraction.')
-         return
-      end if
-      fix_len = lammps_extract_fix_vectorsize (ptr, id, style)
-      call C_F_pointer (Cptr, fix, (/fix_len/))
-      ! Memory is only allocated for "global" fix variables, which we should
-      ! never get here, so no need to call lammps_free!
-   end subroutine lammps_extract_fix_dpa
-   subroutine lammps_extract_fix_dp2a (fix, ptr, id, style, type, i, j)
-      real (C_double), dimension(:,:), pointer, intent(out) :: fix
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type, i, j
-      type (C_ptr) :: Cptr
-      type (C_ptr), pointer, dimension(:) :: Cfix
-      integer :: nr, nc
-      ! Check for the correct dimensionality
-      if ( style == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'It is not possible to extract the&
-            & entire array from global fix data.')
-         return
-      else if ( type == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
-            & scalar (rank 0) into a rank 2 variable.')
-         return
-      else if ( type == 1 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
-            & vector (rank 1) into a rank 2 variable.')
-         return
-      end if
-      call lammps_extract_fix_arraysize (ptr, id, style, nr, nc)
-      ! Extract pointer to first element as Cfix(1)
-      call C_F_pointer (Cptr, Cfix, (/nr/))
-      ! Now extract the array, which is transposed
-      call C_F_pointer (Cfix(1), fix, (/nc, nr/))
-   end subroutine lammps_extract_fix_dp2a
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_variable {{{2
-   function lammps_extract_variable_Cptr (ptr, name, group) result (variable)
-      type (C_ptr) :: ptr, variable
-      character (len=*) :: name
-      character (len=*), optional :: group
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      character (kind=C_char), dimension(:), allocatable :: Cgroup
-      Cname = string2Cstring (name)
-      if ( present(group) ) then
-         allocate (Cgroup(len_trim(group)+1))
-         Cgroup = string2Cstring (group)
-      else
-         allocate (Cgroup(1))
-         Cgroup(1) = C_NULL_CHAR
-      end if
-      variable = lammps_actual_extract_variable (ptr, Cname, Cgroup)
-      deallocate (Cgroup)
-   end function lammps_extract_variable_Cptr
-   subroutine lammps_extract_variable_dp (variable, ptr, name, group)
-      real (C_double), intent(out) :: variable
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      character (len=*), intent(in), optional :: group
-      type (C_ptr) :: Cptr
-      real (C_double), pointer :: Fptr
-      if ( present(group) ) then
-         Cptr = lammps_extract_variable_Cptr (ptr, name, group)
-      else
-         Cptr = lammps_extract_variable_Cptr (ptr, name)
-      end if
-      call C_F_pointer (Cptr, Fptr)
-      variable = Fptr
-      nullify (Fptr)
-      call lammps_free (Cptr)
-   end subroutine lammps_extract_variable_dp
-   subroutine lammps_extract_variable_dpa (variable, ptr, name, group)
-      real (C_double), dimension(:), allocatable, intent(out) :: variable
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      character (len=*), intent(in), optional :: group
-      type (C_ptr) :: Cptr
-      real (C_double), dimension(:), pointer :: Fptr
-      integer :: natoms
-      if ( present(group) ) then
-         Cptr = lammps_extract_variable_Cptr (ptr, name, group)
-      else
-         Cptr = lammps_extract_variable_Cptr (ptr, name)
-      end if
-      natoms = lammps_get_natoms (ptr)
-      allocate (variable(natoms))
-      call C_F_pointer (Cptr, Fptr, (/natoms/))
-      variable = Fptr
-      nullify (Fptr)
-      call lammps_free (Cptr)
-   end subroutine lammps_extract_variable_dpa
-
-!-------------------------------------------------------------------------2}}}
-
-   function lammps_get_thermo (ptr, name) result (dval)
-      double precision :: dval
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      Cname = string2Cstring (name)
-      dval = lammps_actual_get_thermo (ptr, Cname)
-   end function lammps_get_thermo
-
-   subroutine lammps_set_variable (ptr, name, str, err)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name, str
-      integer, optional :: err
-      integer (C_int) :: Cerr
-      character (kind=C_char) :: Cname(len_trim(name)+1), Cstr(len_trim(str)+1)
-      Cname = string2Cstring (name)
-      Cstr = string2Cstring (str)
-      Cerr = lammps_actual_set_variable (ptr, Cname, Cstr)
-      if ( present(err) ) err = Cerr
-   end subroutine lammps_set_variable
-
-   subroutine lammps_reset_box (ptr, boxlo, boxhi, xy, yz, xz)
-      type (C_ptr), intent(in) :: ptr
-      double precision, dimension(3), intent(in) :: boxlo, boxhi
-      double precision, intent(in) :: xy, yz, xz
-      real (C_double) :: C_boxlo(3), C_boxhi(3), C_xy, C_yz, C_xz
-      C_boxlo = boxlo
-      C_boxhi = boxhi
-      C_xy = xy
-      C_xz = xz
-      C_yz = yz
-      call lammps_actual_reset_box (ptr, C_boxlo, C_boxhi, C_xy, C_yz, C_xz)
-   end subroutine lammps_reset_box
-
-! lammps_gather_atoms {{{2
-   subroutine lammps_gather_atoms_ia (ptr, name, count, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, intent(in) :: count
-      integer, dimension(:), allocatable, intent(out) :: data
-      type (C_ptr) :: Cdata
-      integer (C_int), dimension(:), pointer :: Fdata
-      integer (C_int) :: natoms
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), parameter :: Ctype = 0_C_int
-      integer (C_int) :: Ccount
-      natoms = lammps_get_natoms (ptr)
-      Cname = string2Cstring (name)
-      if ( count /= 1 .and. count /= 3 ) then
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
-            & count to be either 1 or 3')
-      else
-         Ccount = count
-      end if
-      allocate ( Fdata(count*natoms) )
-      allocate ( data(count*natoms) )
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
-      data = Fdata
-      deallocate (Fdata)
-   end subroutine lammps_gather_atoms_ia
-   subroutine lammps_gather_atoms_dpa (ptr, name, count, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, intent(in) :: count
-      double precision, dimension(:), allocatable, intent(out) :: data
-      type (C_ptr) :: Cdata
-      real (C_double), dimension(:), pointer :: Fdata
-      integer (C_int) :: natoms
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), parameter :: Ctype = 1_C_int
-      integer (C_int) :: Ccount
-      natoms = lammps_get_natoms (ptr)
-      Cname = string2Cstring (name)
-      if ( count /= 1 .and. count /= 3 ) then
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
-            & count to be either 1 or 3')
-      else
-         Ccount = count
-      end if
-      allocate ( Fdata(count*natoms) )
-      allocate ( data(count*natoms) )
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
-      data = Fdata(:)
-      deallocate (Fdata)
-   end subroutine lammps_gather_atoms_dpa
-
-! lammps_gather_atoms_concat {{{2
-   subroutine lammps_gather_atoms_concat_ia (ptr, name, count, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, intent(in) :: count
-      integer, dimension(:), allocatable, intent(out) :: data
-      type (C_ptr) :: Cdata
-      integer (C_int), dimension(:), pointer :: Fdata
-      integer (C_int) :: natoms
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), parameter :: Ctype = 0_C_int
-      integer (C_int) :: Ccount
-      natoms = lammps_get_natoms (ptr)
-      Cname = string2Cstring (name)
-      if ( count /= 1 .and. count /= 3 ) then
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
-            & count to be either 1 or 3')
-      else
-         Ccount = count
-      end if
-      allocate ( Fdata(count*natoms) )
-      allocate ( data(count*natoms) )
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_gather_atoms_concat (ptr, Cname, Ctype, Ccount, Cdata)
-      data = Fdata
-      deallocate (Fdata)
-   end subroutine lammps_gather_atoms_concat_ia
-   subroutine lammps_gather_atoms_concat_dpa (ptr, name, count, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, intent(in) :: count
-      double precision, dimension(:), allocatable, intent(out) :: data
-      type (C_ptr) :: Cdata
-      real (C_double), dimension(:), pointer :: Fdata
-      integer (C_int) :: natoms
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), parameter :: Ctype = 1_C_int
-      integer (C_int) :: Ccount
-      natoms = lammps_get_natoms (ptr)
-      Cname = string2Cstring (name)
-      if ( count /= 1 .and. count /= 3 ) then
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms_concat&
-            & requires count to be either 1 or 3')
-      else
-         Ccount = count
-      end if
-      allocate ( Fdata(count*natoms) )
-      allocate ( data(count*natoms) )
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_gather_atoms_concat (ptr, Cname, Ctype, Ccount, Cdata)
-      data = Fdata(:)
-      deallocate (Fdata)
-   end subroutine lammps_gather_atoms_concat_dpa
-
-!-----------------------------------------------------------------------------
-
-! lammps_gather_atoms_subset {{{2
-   subroutine lammps_gather_atoms_subset_ia (ptr,name,count,ids,data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, intent(in) :: count, ids(:)
-      integer, dimension(:), allocatable, intent(out) :: data
-      type (C_ptr) :: Cdata
-      integer (C_int), dimension(:), pointer :: Fdata
-      integer (C_int) :: ndata, Cids(size(ids))
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), parameter :: Ctype = 0_C_int
-      integer (C_int) :: Ccount
-      ndata = size(ids)
-      Cname = string2Cstring (name)
-      Cids = ids
-      if ( count /= 1 .and. count /= 3 ) then
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms_subset&
-            & requires count to be either 1 or 3')
-      else
-         Ccount = count
-      end if
-      allocate ( Fdata(count*ndata) )
-      allocate ( data(count*ndata) )
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_gather_atoms_subset (ptr, Cname, Ctype, Ccount, &
-         ndata, Cids, Cdata)
-      data = Fdata
-      deallocate (Fdata)
-   end subroutine lammps_gather_atoms_subset_ia
-   subroutine lammps_gather_atoms_subset_dpa (ptr,name,count,ids,data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, intent(in) :: count, ids(:)
-      double precision, dimension(:), allocatable, intent(out) :: data
-      type (C_ptr) :: Cdata
-      real (C_double), dimension(:), pointer :: Fdata
-      integer (C_int) :: ndata, Cids(size(ids))
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), parameter :: Ctype = 1_C_int
-      integer (C_int) :: Ccount
-      ndata = size(ids)
-      Cname = string2Cstring (name)
-      Cids = ids
-      if ( count /= 1 .and. count /= 3 ) then
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
-            & count to be either 1 or 3')
-      else
-         Ccount = count
-      end if
-      allocate ( Fdata(count*ndata) )
-      allocate ( data(count*ndata) )
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_gather_atoms_subset (ptr, Cname, Ctype, Ccount, &
-         ndata, Cids, Cdata)
-      data = Fdata
-      deallocate (Fdata)
-   end subroutine lammps_gather_atoms_subset_dpa
-
-!-----------------------------------------------------------------------------
-
-! lammps_scatter_atoms {{{2
-   subroutine lammps_scatter_atoms_ia (ptr, name, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, dimension(:), intent(in) :: data
-      integer (kind=C_int) :: natoms, Ccount
-      integer (kind=C_int), parameter :: Ctype = 0_C_int
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), dimension(size(data)), target :: Fdata
-      type (C_ptr) :: Cdata
-      natoms = lammps_get_natoms (ptr)
-      Cname = string2Cstring (name)
-      Ccount = size(data) / natoms
-      if ( Ccount /= 1 .and. Ccount /= 3 ) &
-         call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
-            & count to be either 1 or 3')
-      Fdata = data
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
-   end subroutine lammps_scatter_atoms_ia
-   subroutine lammps_scatter_atoms_dpa (ptr, name, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      double precision, dimension(:), intent(in) :: data
-      integer (kind=C_int) :: natoms, Ccount
-      integer (kind=C_int), parameter :: Ctype = 1_C_int
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      real (C_double), dimension(size(data)), target :: Fdata
-      type (C_ptr) :: Cdata
-      natoms = lammps_get_natoms (ptr)
-      Cname = string2Cstring (name)
-      Ccount = size(data) / natoms
-      if ( Ccount /= 1 .and. Ccount /= 3 ) &
-         call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
-            & count to be either 1 or 3')
-      Fdata = data
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
-   end subroutine lammps_scatter_atoms_dpa
-
-!-----------------------------------------------------------------------------
-
-! lammps_scatter_atoms_subset {{{2
-   subroutine lammps_scatter_atoms_subset_ia (ptr, name, ids, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, dimension(:), intent(in) :: data, ids
-      integer (kind=C_int) :: ndata, Ccount, Cids(size(ids))
-      integer (kind=C_int), parameter :: Ctype = 0_C_int
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), dimension(size(data)), target :: Fdata
-      type (C_ptr) :: Cdata
-      ndata = size(ids)
-      Cname = string2Cstring (name)
-      Ccount = size(data) / ndata
-      if ( Ccount /= 1 .and. Ccount /= 3 ) &
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
-            & count to be either 1 or 3')
-      Fdata = data
-      Cdata = C_loc (Fdata(1))
-      Cids = ids
-      call lammps_actual_scatter_atoms_subset (ptr, Cname, Ctype, Ccount, &
-         ndata, Cids, Cdata)
-   end subroutine lammps_scatter_atoms_subset_ia
-   subroutine lammps_scatter_atoms_subset_dpa (ptr, name, ids, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      double precision, dimension(:), intent(in) :: data, ids
-      integer (kind=C_int) :: ndata, Ccount, Cids(size(ids))
-      integer (kind=C_int), parameter :: Ctype = 1_C_int
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      real (C_double), dimension(size(data)), target :: Fdata
-      type (C_ptr) :: Cdata
-      ndata = size(ids)
-      Cname = string2Cstring (name)
-      Ccount = size(data) / ndata
-      if ( Ccount /= 1 .and. Ccount /= 3 ) &
-         call lammps_error_all (ptr, FLERR, 'lammps_scatter_atoms requires&
-            & count to be either 1 or 3')
-      Fdata = data
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_scatter_atoms_subset (ptr, Cname, Ctype, Ccount, &
-         ndata, Cids, Cdata)
-   end subroutine lammps_scatter_atoms_subset_dpa
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_create_atoms (ptr, id, type, x, v, image, shrinkexceed)
-      type (C_ptr), intent(in) :: ptr
-      integer (kind=C_tagint), dimension(:), optional :: id
-      integer, dimension(:) :: type
-      double precision, dimension(:,:) :: x
-      double precision, dimension(:,:), optional :: v
-      integer (kind=C_imageint), dimension(:), target, optional :: image
-      logical, optional :: shrinkexceed
-      real (C_double), dimension(size(x)) :: C_x, C_v
-      integer (C_int) :: C_shrinkexceed, n
-      integer (kind=C_tagint) :: C_id
-      integer (C_imageint), dimension(size(x)/3) :: C_image
-      integer (C_int) :: C_type
-      if (shrinkexceed) then
-         C_shrinkexceed = 1_C_int
-      else
-         C_shrinkexceed = 0_C_int
-      end if
-      C_x = reshape(transpose(x), shape(C_x))
-      if ( present(v) ) then
-         C_v = reshape(transpose(v), shape(C_v))
-      else
-         C_v = 0.0_C_double
-      end if
-      if ( present(image) ) then
-         C_image = image
-      else
-         C_image = int(0,kind=C_imageint)
-      end if
-      n = size(type)
-      call lammps_actual_create_atoms (ptr, n, C_id, C_type, C_x, C_v, &
-         C_image, C_shrinkexceed)
-   end subroutine lammps_create_atoms
-
-!-----------------------------------------------------------------------------
-
-   function lammps_config_has_package (package_name) result (has_it)
-      character (len=*), intent(in) :: package_name
-      character (len=1, kind=C_char), dimension(len_trim(package_name)+1) :: &
-         C_package_name
-      logical :: has_it
-      integer (C_int) :: C_has_it
-      C_package_name = string2Cstring (package_name)
-      C_has_it = lammps_actual_config_has_package (C_package_name)
-      has_it = (C_has_it == 1)
-   end function lammps_config_has_package
-
-!-----------------------------------------------------------------------------
-
-   function lammps_config_package_name (index, buffer) result (installed)
-      character (len=*), intent(inout) :: buffer
-      integer, intent(in) :: index
-      logical :: installed
-      integer (kind=C_int) :: C_installed, C_index, max_size
-      character (len=1, kind=C_char), dimension(len_trim(buffer)+1) :: C_buffer
-      C_buffer = string2Cstring (buffer)
-      max_size = len(buffer)
-      C_index = index
-      C_installed = lammps_actual_config_package_name (C_index, C_buffer, &
-         max_size)
-      installed = (C_installed == 1_C_int)
-      buffer = Cstring2string (C_buffer)
-   end function lammps_config_package_name
-
-!-----------------------------------------------------------------------------
-
-   logical function lammps_config_has_gzip_support () result (has_it)
-      integer (C_int) :: C_has_it
-      C_has_it = lammps_actual_config_has_gzip_support ()
-      has_it = (C_has_it == 1_C_int)
-   end function lammps_config_has_gzip_support
-
-!-----------------------------------------------------------------------------
-
-   logical function lammps_config_has_png_support () result (has_it)
-      integer (C_int) :: C_has_it
-      C_has_it = lammps_actual_config_has_png_support ()
-      has_it = (C_has_it == 1_C_int)
-   end function lammps_config_has_png_support
-
-!-----------------------------------------------------------------------------
-
-   logical function lammps_config_has_jpeg_support () result (has_it)
-      integer (C_int) :: C_has_it
-      C_has_it = lammps_actual_config_has_jpeg_support ()
-      has_it = (C_has_it == 1_C_int)
-   end function lammps_config_has_jpeg_support
-
-!-----------------------------------------------------------------------------
-
-   logical function lammps_config_has_ffmpeg_support () result (has_it)
-      integer (C_int) :: C_has_it
-      C_has_it = lammps_actual_config_has_ffmpeg_support ()
-      has_it = (C_has_it == 1_C_int)
-   end function lammps_config_has_ffmpeg_support
-
-!-----------------------------------------------------------------------------
-
-   logical function lammps_config_has_exceptions () result (has_it)
-      integer (C_int) :: C_has_it
-      C_has_it = lammps_actual_config_has_exceptions ()
-      has_it = (C_has_it == 1_C_int)
-   end function lammps_config_has_exceptions
-
-!-----------------------------------------------------------------------------
-
-   function lammps_find_pair_neighlist (ptr, style, exact, nsub, request) &
-   result (neighlist)
-      integer :: neighlist
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: style
-      logical, intent(in) :: exact
-      integer, intent(in) :: nsub, request
-      integer (C_int) :: C_exact, C_nsub, C_neighlist, C_request
-      character (kind=C_char), dimension(len_trim(style)+1) :: C_style
-      if (exact) then
-         C_exact = 1_C_int
-      else
-         C_exact = 0_C_int
-      end if
-      C_nsub = nsub
-      C_request = request
-      C_style = string2Cstring (style)
-      C_neighlist = lammps_actual_find_pair_neighlist (ptr, C_style, C_exact, &
-         C_nsub, C_request)
-      neighlist = C_neighlist
-   end function lammps_find_pair_neighlist
-
-!-----------------------------------------------------------------------------
-
-   function lammps_find_fix_neighlist (ptr, id, request) result (neighlist)
-      integer :: neighlist
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: request
-      integer (C_int) :: C_request, C_neighlist
-      character (kind=C_char), dimension(len_trim(id)+1) :: C_id
-      C_id = string2Cstring(id)
-      C_request = request
-      C_neighlist = lammps_actual_find_fix_neighlist (ptr, C_id, C_request)
-      neighlist = C_neighlist
-   end function lammps_find_fix_neighlist
-
-!-----------------------------------------------------------------------------
-
-   function lammps_find_compute_neighlist (ptr, id, request) result (neighlist)
-      integer :: neighlist
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: request
-      integer (C_int) :: C_request
-      character (kind=C_char), dimension(len_trim(id)+1) :: C_id
-      C_id = string2Cstring(id)
-      C_request = request
-      neighlist = lammps_actual_find_compute_neighlist (ptr, C_id, C_request)
-   end function lammps_find_compute_neighlist
-
-!-----------------------------------------------------------------------------
-
-   function lammps_neighlist_num_elements (ptr, idx) result (nelements)
-      integer :: nelements
-      type (C_ptr), intent(in) :: ptr
-      integer, intent(in) :: idx
-      integer (C_int) :: C_idx
-      C_idx = idx
-      nelements = lammps_actual_neighlist_num_elements (ptr, C_idx)
-   end function lammps_neighlist_num_elements
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_neighlist_element_neighbors (ptr, idx, element, iatom, &
-         numneigh, neighbors)
-      type (C_ptr), intent(in) :: ptr
-      integer, intent(in) :: idx, element
-      integer, intent(out) :: iatom, numneigh
-      integer (C_int), dimension(:), pointer, intent(out) :: neighbors
-      integer (C_int) :: C_idx, C_element, C_iatom, C_numneigh
-      type (C_ptr) :: C_neighbors
-      C_idx = idx
-      C_element = element
-      call lammps_actual_neighlist_element_neighbors (ptr, C_idx, C_element, &
-         C_iatom, C_numneigh, C_neighbors)
-      iatom = C_iatom
-      numneigh = C_numneigh
-      call C_F_pointer (C_neighbors, neighbors, [numneigh])
-   end subroutine lammps_neighlist_element_neighbors
-
-!-----------------------------------------------------------------------------
-
-! These are only defined if -DLAMMPS_EXCEPTIONS was issued
-#ifdef LAMMPS_EXCEPTIONS
-   logical function lammps_has_error (ptr) result (has_it)
-      type (C_ptr), intent(in) :: ptr
-      integer (kind=C_int) :: C_has_it
-      C_has_it = lammps_actual_has_error (ptr)
-      has_it = (C_has_it == 1_C_int)
-   end function lammps_has_error
-
-!-----------------------------------------------------------------------------
-
-   function lammps_get_last_error_message (ptr, buffer) result (error_type)
-      integer (C_int) :: error_type
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(out) :: buffer
-      integer (C_int) :: buffer_size
-      character (len=1, kind=C_char), dimension(len(buffer)+1) :: C_buffer
-      buffer_size = len(buffer)
-      error_type = lammps_actual_get_last_error_message (ptr, C_buffer, &
-         buffer_size)
-      buffer = Cstring2string (C_buffer)
-   end function lammps_get_last_error_message
-#endif
-!-------------------------------------------------------------------------2}}}
-
-   function lammps_extract_compute_vectorsize (ptr, id, style) &
-   result (vectorsize)
-      integer :: vectorsize
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style
-      integer (C_int) :: Cvectorsize, Cstyle
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      Cid = string2Cstring (id)
-      Cstyle = int(style, C_int)
-      Cvectorsize = lammps_actual_extract_compute_vectorsize (ptr, Cid, Cstyle)
-      vectorsize = int(Cvectorsize, kind(vectorsize))
-   end function lammps_extract_compute_vectorsize
-
-!-----------------------------------------------------------------------------
-
-   function lammps_extract_fix_vectorsize (ptr, id, style) &
-   result (vectorsize)
-      integer :: vectorsize
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style
-      integer (C_int) :: Cvectorsize, Cstyle
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      Cid = string2Cstring (id)
-      Cstyle = int(style, C_int)
-      Cvectorsize = lammps_actual_extract_fix_vectorsize (ptr, Cid, Cstyle)
-      vectorsize = int(Cvectorsize, kind(vectorsize))
-   end function lammps_extract_fix_vectorsize
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_extract_compute_arraysize (ptr, id, style, nrows, ncols)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style
-      integer, intent(out) :: nrows, ncols
-      integer (C_int) :: Cstyle, Cnrows, Cncols
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      Cid = string2Cstring (id)
-      Cstyle = int (style, C_int)
-      call lammps_actual_extract_compute_arraysize (ptr, Cid, Cstyle, &
-         Cnrows, Cncols)
-      nrows = int (Cnrows, kind(nrows))
-      ncols = int (Cncols, kind(ncols))
-   end subroutine lammps_extract_compute_arraysize
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_extract_fix_arraysize (ptr, id, style, nrows, ncols)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style
-      integer, intent(out) :: nrows, ncols
-      integer (C_int) :: Cstyle, Cnrows, Cncols
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      Cid = string2Cstring (id)
-      Cstyle = int (style, kind(Cstyle))
-      call lammps_actual_extract_fix_arraysize (ptr, Cid, Cstyle, &
-         Cnrows, Cncols)
-      nrows = int (Cnrows, kind(nrows))
-      ncols = int (Cncols, kind(ncols))
-   end subroutine lammps_extract_fix_arraysize
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_error_all (ptr, file, line, str)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: file, str
-      integer, intent(in) :: line
-      character (kind=C_char), dimension(len_trim(file)+1) :: Cfile
-      character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
-      integer (C_int) :: Cline
-      Cline = int(line, kind(Cline))
-      Cfile = string2Cstring (file)
-      Cstr = string2Cstring (str)
-      call lammps_actual_error_all (ptr, Cfile, Cline, Cstr)
-   end subroutine lammps_error_all
-
-!-----------------------------------------------------------------------------
-
-! Locally defined helper functions {{{1
-
-   pure function string2Cstring (string) result (C_string)
-      use, intrinsic :: ISO_C_binding, only : C_char, C_NULL_CHAR
-      character (len=*), intent(in) :: string
-      character (len=1, kind=C_char) :: C_string (len_trim(string)+1)
-      integer :: i, n
-      n = len_trim (string)
-      forall (i = 1:n)
-         C_string(i) = string(i:i)
-      end forall
-      C_string(n+1) = C_NULL_CHAR
-   end function string2Cstring
-
-!-----------------------------------------------------------------------------
-
-   pure function Cstrlen (Cstring) result (n)
-      character (len=1, kind=C_char), dimension(:), intent(in) :: Cstring
-      integer :: n, i
-      n = size(Cstring)
-      do i = 1, size(Cstring)
-         if ( Cstring(i) == C_NULL_CHAR ) then
-            n = i - 1
-            return
-         end if
-      end do
-   end function Cstrlen
-
-!-----------------------------------------------------------------------------
-
-   pure function Cstring2string (Cstring) result (string)
-      !use, intrinsic :: ISO_C_binding, only : C_char, C_NULL_CHAR
-      character (len=1, kind=C_char), intent(in) :: Cstring (:)
-      character (len=Cstrlen(Cstring)) :: string
-      integer :: i, n
-      n = Cstrlen(Cstring)
-      string = ''
-      forall (i = 1:n)
-         string(i:i) = Cstring(i)
-      end forall
-   end function Cstring2string
-
-!-----------------------------------------------------------------------------
-
-   subroutine Cstring2argcargv (Cstring, argc, argv)
-   !! Converts a C-style string to argc and argv, that is, words in Cstring
-   !! become C-style strings in argv.  IMPORTANT:  Cstring is modified by
-   !! this routine!  I would make Cstring local TO this routine and accept
-   !! a Fortran-style string instead, but we run into scoping and
-   !! allocation problems that way.  This routine assumes the string is
-   !! null-terminated, as all C-style strings must be.
-
-      character (kind=C_char), dimension(*), target, intent(inout) :: Cstring
-      integer (C_int), intent(out) :: argc
-      type (C_ptr), dimension(:), allocatable, intent(out) :: argv
-
-      integer :: StringStart, SpaceIndex, strlen, argnum
-
-      argc = 1_C_int
-
-      ! Find the length of the string
-      strlen = 1
-      do while ( Cstring(strlen) /= C_NULL_CHAR )
-         strlen = strlen + 1
-      end do
-
-      ! Find the number of non-escaped spaces
-      SpaceIndex = 2
-      do while ( SpaceIndex < strlen )
-         if ( Cstring(SpaceIndex) == ' ' .and. &
-              Cstring(SpaceIndex-1) /= '\' ) then
-            argc = argc + 1_C_int
-            ! Find the next non-space character
-            do while ( Cstring(SpaceIndex+1) == ' ')
-               SpaceIndex = SpaceIndex + 1
-            end do
-         end if
-         SpaceIndex = SpaceIndex + 1
-      end do
-
-      ! Now allocate memory for argv
-      allocate (argv(argc))
-
-      ! Now find the string starting and ending locations
-      StringStart = 1
-      SpaceIndex = 2
-      argnum = 1
-      do while ( SpaceIndex < strlen )
-         if ( Cstring(SpaceIndex) == ' ' .and. &
-              Cstring(SpaceIndex-1) /= '\' ) then
-            ! Found a real space => split strings and store this one
-            Cstring(Spaceindex) = C_NULL_CHAR ! Replaces space with NULL
-            argv(argnum) = C_loc(Cstring(StringStart))
-            argnum = argnum + 1
-            ! Find the next non-space character
-            do while ( Cstring(SpaceIndex+1) == ' ')
-               SpaceIndex = SpaceIndex + 1
-            end do
-            StringStart = SpaceIndex + 1
-         else if ( Cstring(SpaceIndex) == ' ' .and. &
-              Cstring(SpaceIndex-1) == '\' ) then
-            ! Escaped space => remove backslash and move rest of array
-            Cstring(SpaceIndex-1:strlen-1) = Cstring(SpaceIndex:strlen)
-            strlen = strlen - 1 ! Last character is still C_NULL_CHAR
-         end if
-         SpaceIndex = SpaceIndex + 1
-      end do
-      ! Now handle the last argument
-      argv(argnum) = C_loc(Cstring(StringStart))
-
-   end subroutine Cstring2argcargv
-
-! 1}}}
-
-end module LAMMPS
-
-! vim: foldmethod=marker tabstop=3 softtabstop=3 shiftwidth=3 expandtab
diff --git a/examples/COUPLE/fortran2/Makefile b/examples/COUPLE/fortran2/Makefile
deleted file mode 100644
index 8ac957a4c1..0000000000
--- a/examples/COUPLE/fortran2/Makefile
+++ /dev/null
@@ -1,41 +0,0 @@
-SHELL = /bin/sh
-
-# Path to LAMMPS extraction directory
-LAMMPS_ROOT = ../../..
-LAMMPS_SRC = $(LAMMPS_ROOT)/src
-
-# Uncomment the line below if using the MPI stubs library
-MPI_STUBS = #-I$(LAMMPS_SRC)/STUBS
-
-FC = mpifort         # replace with your Fortran compiler
-CXX = mpicxx         # replace with your C++ compiler
-CXXLIB = -lstdc++    # replace with your C++ runtime libs
-
-# Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
-FFLAGS = -O2 -fPIC
-CXXFLAGS = -O2 -fPIC
-CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
-
-all : liblammps_fortran.a liblammps_fortran.so
-	@echo "WARNING: this Fortran interface is obsolete and is no longer
-maintained. See $(LAMMPS_ROOT)/fortran for the new, maintained interface
-(largely written by the same author). You may continue to use this interface if
-desired, but it may eventually be removed from LAMMPS."
-
-liblammps_fortran.so : LAMMPS.o LAMMPS-wrapper.o
-	$(FC) $(FFLAGS) -shared -o $@ $^ $(CXXLIB)
-
-liblammps_fortran.a : LAMMPS.o LAMMPS-wrapper.o
-	$(AR) rs $@ $^
-
-LAMMPS.o lammps.mod : LAMMPS.F90
-	$(FC) $(CPPFLAGS) $(FFLAGS) -c $<
-
-LAMMPS-wrapper.o : LAMMPS-wrapper.cpp LAMMPS-wrapper.h
-	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -I$(LAMMPS_SRC) $(MPI_STUBS)
-
-clean :
-	$(RM) *.o *.mod liblammps_fortran.a liblammps_fortran.so
-
-dist :
-	tar -czf Fortran-interface.tar.gz LAMMPS-wrapper.h LAMMPS-wrapper.cpp LAMMPS.F90 makefile README
diff --git a/examples/COUPLE/fortran2/README b/examples/COUPLE/fortran2/README
deleted file mode 100644
index b36cb43746..0000000000
--- a/examples/COUPLE/fortran2/README
+++ /dev/null
@@ -1,273 +0,0 @@
-!! NOTE -------------------------------------------------------------------
-!  This interface is obsolete and may be removed in a future release of
-!  LAMMPS. The interface in fortran/lammps.f90 replaces this one. That API
-!  is maintained by the LAMMPS developers and has documentation written for
-!  it; it is based loosely on this one, but binds all procedures to a lammps
-!  derived type. That interface was written in large
-!  part by the same author, but is also supported by other developers.
-!--------------------------------------------------------------------------
-
-LAMMPS.F90 defines a Fortran 2003 module, LAMMPS, which wraps all functions in
-src/library.h so they can be used directly from Fortran-encoded programs.
-
-All functions in src/library.h that use and/or return C-style pointers have
-Fortran wrapper functions that use Fortran-style arrays, pointers, and
-strings; all C-style memory management is handled internally with no user
-intervention.  See --USE-- for notes on how this interface differs from the
-C interface (and the Python interface).
-
-This interface was created by Karl Hammond who you can contact with
-questions:
-
-Karl D. Hammond
-University of Missouri
-hammondkd at missouri.edu
-
--------------------------------------
-
---COMPILATION--
-
-First, be advised that mixed-language programming is not trivial.  It requires
-you to link in the required libraries of all languages you use (in this case,
-those for Fortran, C, and C++), as well as any other libraries required.
-You are also advised to read the --USE-- section below before trying to
-compile.
-
-The following steps will work to compile this module (replace ${LAMMPS_SRC}
-with the path to your LAMMPS source directory).
-
-Steps 3-5 are accomplished, possibly after some modifications to
-the makefile, by make using the attached makefile.  Said makefile also builds
-the dynamically-linkable library (liblammps_fortran.so).
-
-** STATIC LIBRARY INSTRUCTIONS **
- (1) Compile LAMMPS as a static library.
-     Call the resulting file ${LAMMPS_LIB}, which will have an actual name
-     like liblmp_openmpi.a.  If compiling using the MPI stubs in
-     ${LAMMPS_SRC}/STUBS, you will need to know where libmpi_stubs.a
-     is as well (I'll call it ${MPI_STUBS} hereafter)
- (2) Copy said library to your Fortran program's source directory or replace
-     ${LAMMPS_LIB} with its full path in the instructions below.
- (3) Compile (but don't link!) LAMMPS.F90.  Example:
-        mpifort -c LAMMPS.f90
-     OR
-        gfortran -c LAMMPS.F90
-     NOTE:  you may get a warning such as,
-        subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
-        Variable 'communicator' at (1) is a parameter to the BIND(C)
-        procedure 'lammps_open_wrapper' but may not be C interoperable
-     This is normal (see --IMPLEMENTATION NOTES--).
-
- (4) Compile (but don't link) LAMMPS-wrapper.cpp.  You will need its header
-     file as well.  You will have to provide the locations of LAMMPS's
-     header files.  For example,
-        mpicxx -c -I${LAMMPS_SRC} LAMMPS-wrapper.cpp
-     OR
-        g++ -c -I${LAMMPS_SRC} -I${LAMMPS_SRC}/STUBS LAMMPS-wrapper.cpp
-     OR
-        icpc -c -I${LAMMPS_SRC} -I${LAMMPS_SRC}/STUBS LAMMPS-wrapper.cpp
- (5) OPTIONAL:  Make a library from the object files so you can carry around
-     two files instead of three.  Example:
-        ar rs liblammps_fortran.a LAMMPS.o LAMMPS-wrapper.o
-     This will create the file liblammps_fortran.a that you can use in place
-     of "LAMMPS.o LAMMPS-wrapper.o" later.  Note that you will still
-     need to have the .mod file from part (3).
-
-     It is also possible to add LAMMPS.o and LAMMPS-wrapper.o into the
-     LAMMPS library (e.g., liblmp_openmpi.a) instead of creating a separate
-     library, like so:
-        ar rs ${LAMMPS_LIB} LAMMPS.o LAMMPS-wrapper.o
-     In this case, you can now use the Fortran wrapper functions as if they
-     were part of the usual LAMMPS library interface (if you have the module
-     file visible to the compiler, that is).
- (6) Compile (but don't link) your Fortran program.  Example:
-        mpifort -c myfreeformatfile.f90
-        mpifort -c myfixedformatfile.f
-     OR
-        gfortran -c myfreeformatfile.f90
-        gfortran -c myfixedformatfile.f
-     The object files generated by these steps are collectively referred to
-     as ${my_object_files} in the next step(s).
-
-     IMPORTANT:  If the Fortran module from part (3) is not in the current
-     directory or in one searched by the compiler for module files, you will
-     need to include that location via the -I flag to the compiler, like so:
-        mpifort -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
-
- (7) Link everything together, including any libraries needed by LAMMPS (such
-     as the C++ standard library, the C math library, the JPEG library, fftw,
-     etc.)  For example,
-        mpifort LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
-            ${LAMMPS_LIB} -lmpi_cxx -lstdc++ -lm
-     OR
-        gfortran LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
-            ${LAMMPS_LIB} ${MPI_STUBS} -lstdc++ -lm
-     OR
-        ifort LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
-            ${LAMMPS_LIB} ${MPI_STUBS} -cxxlib -lm
-     Any other required libraries (e.g. -ljpeg, -lfftw) should be added to
-     the end of this line.
-
-You should now have a working executable.
-
-** DYNAMIC LIBRARY INSTRUCTIONS **
- (1) Compile LAMMPS as a dynamic library
-     (make makeshlib && make -f Makefile.shlib [targetname]).
- (2) Compile, but don't link, LAMMPS.F90 using the -fPIC flag, such as
-        mpifort -fPIC -c LAMMPS.f90
- (3) Compile, but don't link, LAMMPS-wrapper.cpp in the same manner, e.g.
-        mpicxx -fPIC -c LAMMPS-wrapper.cpp
- (4) Make the dynamic library, like so:
-        mpifort -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
- (5) Compile your program, such as,
-        mpifort -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
-     where ${LAMMPS_SRC}/examples/COUPLE/fortran2 contains the .mod file from
-     step (3)
- (6) Link everything together, such as
-        mpifort ${my_object_files} -L${LAMMPS_SRC} \
-            -L${LAMMPS_SRC}/examples/COUPLE/fortran2 -llammps_fortran \
-            -llammps_openmpi -lmpi_cxx -lstdc++ -lm
-
-If you wish to avoid the -L flags, add the directories containing your
-shared libraries to the LIBRARY_PATH environment variable.  At run time, you
-will have to add these directories to LD_LIBRARY_PATH as well; otherwise,
-your executable will not find the libraries it needs.
-
--------------------------------------
-
---USAGE--
-
-To use this API, your program unit (PROGRAM/SUBROUTINE/FUNCTION/MODULE/etc.)
-should look something like this:
-  program call_lammps
-    use LAMMPS
-    ! Other modules, etc.
-    implicit none
-    type (lammps_instance) :: lmp ! This is a pointer to your LAMMPS instance
-    real (C_double) :: fix
-    real (C_double), dimension(:), pointer :: fix2
-    ! Rest of declarations
-    call lammps_open_no_mpi ('lmp -in /dev/null -screen out.lammps',lmp)
-    ! Set up rest of program here
-    call lammps_file (lmp, 'in.example')
-    call lammps_extract_fix (fix, lmp, '2', 0, 1, 1, 1)
-    call lammps_extract_fix (fix2, lmp, '4', 0, 2, 1, 1)
-    call lammps_close (lmp)
-  end program call_lammps
-
-Important notes:
- * Though I dislike the use of pointers, they are necessary when communicating
-   with C and C++, which do not support Fortran's ALLOCATABLE attribute.
- * There is no need to deallocate C-allocated memory; this is done for you in
-   the cases when it is done (which are all cases when pointers are not
-   accepted, such as global fix data)
- * All arguments which are char* variables in library.cpp are character (len=*)
-   variables here.  For example,
-        call lammps_command (lmp, 'units metal')
-   will work as expected.
- * The public functions (the only ones you can use) have interfaces as
-   described in the comments at the top of LAMMPS.F90.  They are not always
-   the same as those in library.h, since C strings are replaced by Fortran
-   strings and the like.
- * The module attempts to check whether you have done something stupid (such
-   as assign a 2D array to a scalar), but it's not perfect.  For example, the
-   command
-        call lammps_extract_global (nlocal, ptr, 'nlocal')
-   will give nlocal correctly if nlocal is a pointer to type INTEGER, but it
-   will give the wrong answer if nlocal is a pointer to type REAL.  This is a
-   feature of the (void*) type cast in library.cpp.  There is no way I can
-   check this for you!  It WILL catch you if you pass it an allocatable or
-   fixed-size array when it expects a pointer.
- * Arrays constructed from temporary data from LAMMPS are ALLOCATABLE, and
-   represent COPIES of data, not the originals.  Functions like
-   lammps_extract_atom, which return actual LAMMPS data, are pointers.
- * IMPORTANT:  Due to the differences between C and Fortran arrays (C uses
-   row-major vectors, Fortran uses column-major vectors), all arrays returned
-   from LAMMPS have their indices swapped.
- * An example of a complete program, simple.f90, is included with this
-   package.
-
--------------------------------------
-
---TROUBLESHOOTING--
-
-Compile-time errors (when compiling LAMMPS.F90, that is) probably indicate
-that your compiler is not new enough to support Fortran 2003 features.  For
-example, GCC 4.1.2 will not compile this module, but GCC 4.4.0 will.
-
-If your compiler balks at 'use, intrinsic :: ISO_C_binding,' try removing the
-intrinsic part so it looks like an ordinary module.  However, it is likely
-that such a compiler will also have problems with everything else in the
-file as well.
-
-If you get a segfault as soon as the lammps_open call is made, check that you
-compiled your program AND LAMMPS-wrapper.cpp using the same MPI headers.  Using
-the stubs for one and the actual MPI library for the other will cause Bad
-Things to happen.
-
-If you find run-time errors, please pass them along via the LAMMPS Users
-mailing list (please CC me as well; address above).  Please provide a minimal
-working example along with the names and versions of the compilers you are
-using.  Please make sure the error is repeatable and is in MY code, not yours
-(generating a minimal working example will usually ensure this anyway).
-
--------------------------------------
-
---IMPLEMENTATION NOTES--
-
-The Fortran procedures have the same names as the C procedures, and
-their purpose is the same, but they may take different arguments.  Here are
-some of the important differences:
- * lammps_open and lammps_open_no_mpi take a string instead of argc and
-   argv.  This is necessary because C and C++ have a very different way
-   of treating strings than Fortran.  If you want the command line to be
-   passed to lammps_open (as it often would be from C/C++), use the
-   GET_COMMAND intrinsic to obtain it.
- * All C++ functions that accept char* pointers now accept Fortran-style
-   strings within this interface instead.
- * All of the lammps_extract_[something] functions, which return void*
-   C-style pointers, have been replaced by generic subroutines that return
-   Fortran variables (which may be arrays).  The first argument houses the
-   variable/pointer to be returned (pretend it's on the left-hand side); all
-   other arguments are identical except as stipulated above.
-   Note that it is not possible to declare generic functions that are selected
-   based solely on the type/kind/rank (TKR) signature of the return value,
-   only based on the TKR of the arguments.
- * The SHAPE of the first argument to lammps_extract_[something] is checked
-   against the "shape" of the C array (e.g., double vs. double* vs. double**).
-   Calling a subroutine with arguments of inappropriate rank will result in an
-   error at run time.
- * The indices i and j in lammps_extract_fix are used the same way they
-   are in f_ID[i][j] references in LAMMPS (i.e., starting from 1).  This is
-   different than the way library.cpp uses these numbers, but is more
-   consistent with the way arrays are accessed in LAMMPS and in Fortran.
- * The char* pointer normally returned by lammps_command is thrown away
-   in this version; note also that lammps_command is now a subroutine
-   instead of a function.
- * The pointer to LAMMPS itself is of type(lammps_instance), which is itself
-   a synonym for type(C_ptr), part of ISO_C_BINDING.  Type (C_ptr) is
-   C's void* data type.
- * This module will almost certainly generate a compile-time warning,
-   such as,
-         subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
-      Variable 'communicator' at (1) is a parameter to the BIND(C)
-      procedure 'lammps_open_wrapper' but may not be C interoperable
-   This happens because lammps_open_wrapper actually takes a Fortran
-   INTEGER argument, whose type is defined by the MPI library itself.  The
-   Fortran integer is converted to a C integer by the MPI library (if such
-   conversion is actually necessary).
-  * lammps_extract_global returns COPIES of the (scalar) data, as does the
-    C version.
-  * lammps_extract_atom, lammps_extract_compute, and lammps_extract_fix
-        have a first argument that will be associated with ACTUAL LAMMPS DATA.
-        This means the first argument must be:
-          * The right rank (via the DIMENSION modifier)
-          * A C-interoperable POINTER type (i.e., INTEGER (C_int) or
-            REAL (C_double)).
-  * lammps_extract_variable returns COPIES of the data, as the C library
-    interface does.  There is no need to deallocate using lammps_free.
-  * The 'data' argument to lammps_gather_atoms and lammps_scatter atoms must
-    be ALLOCATABLE.  It should be of type INTEGER or DOUBLE PRECISION.  It
-    does NOT need to be C inter-operable (and indeed should not be).
-  * The 'count' argument of lammps_scatter_atoms is unnecessary; the shape of
-    the array determines the number of elements LAMMPS will read.
diff --git a/examples/COUPLE/fortran2/in.simple b/examples/COUPLE/fortran2/in.simple
deleted file mode 100644
index 5982cbaac1..0000000000
--- a/examples/COUPLE/fortran2/in.simple
+++ /dev/null
@@ -1,16 +0,0 @@
-units lj
-atom_modify map array
-lattice bcc 1.0
-region simbox block 0 10 0 10 0 10
-create_box 2 simbox
-create_atoms 1 region simbox
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0
-mass 1 58.2 # These are made-up numbers
-mass 2 28.3
-velocity all create 1200.0 7474848 dist gaussian
-fix 1 all nve
-fix 2 all dt/reset 1 1E-5 1E-3 0.01 units box
-fix 4 all ave/histo 10 5 100 0.5 1.5 50 f_2 file temp.histo ave running
-thermo_style custom step dt temp press etotal f_4[1][1]
-thermo 100
diff --git a/examples/COUPLE/fortran2/simple.f90 b/examples/COUPLE/fortran2/simple.f90
deleted file mode 100644
index 0b84a1ecc1..0000000000
--- a/examples/COUPLE/fortran2/simple.f90
+++ /dev/null
@@ -1,112 +0,0 @@
-program simple
-
-   use MPI
-   use LAMMPS
-
-   ! The following line is unnecessary, as I have included these three entities
-   ! with the LAMMPS module, but I leave them in anyway to remind people where
-   ! they came from
-   use, intrinsic :: ISO_C_binding, only : C_double, C_ptr, C_int
-
-   implicit none
-
-   ! Notes:
-   !  * If LAMMPS returns a scalar that is allocated by the library interface
-   !     (see library.cpp), then that memory is deallocated automatically and
-   !     the argument to lammps_extract_fix must be a SCALAR.
-   !  * If LAMMPS returns a pointer to an array, consisting of internal LAMMPS
-   !     data, then the argument must be an interoperable Fortran pointer.
-   !     Interoperable means it is of type INTEGER (C_INT) or of type
-   !     REAL (C_DOUBLE) in this context.
-   !  * Pointers should NEVER be deallocated, as that would deallocate internal
-   !     LAMMPS data!
-   !  * Note that just because you can read the values of, say, a compute at
-   !     any time does not mean those values represent the "correct" values.
-   !     LAMMPS will abort you if you try to grab a pointer to a non-current
-   !     entity, but once it's bound, it's your responsibility to check that
-   !     it's current before evaluating.
-   !  * IMPORTANT:  Two-dimensional arrays (such as 'x' from extract_atom)
-   !     will be transposed from what they might look like in C++.  This is
-   !     because of different bookkeeping conventions between Fortran and C
-   !     that date back to about 1970 or so (when C was written).
-   !  * Arrays start from 1, EXCEPT for mass from extract_atom, which
-   !     starts from 0.  This is because the C array actually has a blank
-   !     first element (and thus mass[1] corresponds to the mass of type 1)
-
-   type (C_ptr) :: lmp
-   real (C_double), pointer :: compute => NULL()
-   real (C_double) :: fix, fix2
-   real (C_double), dimension(:), pointer :: compute_v => NULL()
-   real (C_double), dimension(:,:), pointer :: x => NULL()
-   real (C_double), dimension(:), pointer :: mass => NULL()
-   integer, dimension(:), allocatable :: types
-   double precision, dimension(:), allocatable :: r
-   integer :: error, narg, me, nprocs
-   character (len=1024) :: command_line
-
-   call MPI_Init (error)
-   call MPI_Comm_rank (MPI_COMM_WORLD, me, error)
-   call MPI_Comm_size (MPI_COMM_WORLD, nprocs, error)
-
-   ! You are free to pass any string you like to lammps_open or
-   ! lammps_open_no_mpi; here is how you pass it the command line
-   !call get_command (command_line)
-   !call lammps_open (command_line, MPI_COMM_WORLD, lmp)
-
-   ! And here's how to to it with a string constant of your choice
-   call lammps_open_no_mpi ('lmp -log log.simple', lmp)
-
-   call lammps_file (lmp, 'in.simple')
-   call lammps_command (lmp, 'run 500')
-
-   ! This extracts f_2 as a scalar (the last two arguments can be arbitrary)
-   call lammps_extract_fix (fix, lmp, '2', LMP_STYLE_GLOBAL, LMP_TYPE_SCALAR, 1, 1)
-   print *, 'Fix is ', fix
-
-   ! This extracts f_4[1][1] as a scalar
-   call lammps_extract_fix (fix2, lmp, '4', LMP_STYLE_GLOBAL, LMP_TYPE_ARRAY, 1, 1)
-   print *, 'Fix 2 is ', fix2
-
-   ! This extracts the scalar compute of compute thermo_temp
-   call lammps_extract_compute (compute, lmp, 'thermo_temp', LMP_STYLE_GLOBAL, LMP_TYPE_SCALAR)
-   print *, 'Compute is ', compute
-
-   ! This extracts the vector compute of compute thermo_temp
-   call lammps_extract_compute (compute_v, lmp, 'thermo_temp', LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR)
-   print *, 'Vector is ', compute_v
-
-   ! This extracts the masses
-   call lammps_extract_atom (mass, lmp, 'mass')
-   print *, 'Mass is ', mass(1:)
-
-   ! Extracts a pointer to the arrays of positions for all atoms
-   call lammps_extract_atom (x, lmp, 'x')
-   if ( .not. associated (x) ) print *, 'x is not associated'
-   print *, 'x is ', x(:,1)  ! Prints x, y, z for atom 1
-
-   ! Extracts pointer to atom types
-   call lammps_gather_atoms (lmp, 'type', 1, types)
-   print *, 'types is ', types(1:3)
-
-   ! Allocates an array and assigns all positions to it
-   call lammps_gather_atoms (lmp, 'x', 3, r)
-   print *, 'natoms = ', int(lammps_get_natoms(lmp))
-   print *, 'size(r) = ', size(r)
-   print *, 'r is ', r(1:6)
-
-   ! Puts those position data back
-   call lammps_scatter_atoms (lmp, 'x', r)
-
-   call lammps_command (lmp, 'run 1')
-   print *, 'x is ', x(:,1)  ! Note that the position updates!
-   print *, 'Compute is ', compute  ! This did only because "temp" is part of
-                                    ! the thermo output; the vector part did
-                                    ! not, and won't until we give LAMMPS a
-                                    ! thermo output or other command that
-                                    ! requires its value
-
-   call lammps_close (lmp)
-
-   call MPI_Finalize (error)
-
-end program simple
diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
deleted file mode 100644
index 4774cb6b49..0000000000
--- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
+++ /dev/null
@@ -1,96 +0,0 @@
-/* -----------------------------------------------------------------------
-    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/, Sandia National Laboratories
-    LAMMPS development team: developers@lammps.org
- 
-    Copyright (2003) Sandia Corporation.  Under the terms of Contract
-    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-    certain rights in this software.  This software is distributed under 
-    the GNU General Public License.
- 
-    See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-                          University of Missouri (USA), 2012
-------------------------------------------------------------------------- */
-
-/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
-   provides a (I hope) robust Fortran interface to library.cpp and
-   library.h.  All functions herein COULD be added to library.cpp instead of
-   including this as a separate file. See the README for instructions. */
-
-#include <mpi.h>
-#include "LAMMPS-wrapper.h"
-#define LAMMPS_LIB_MPI 1
-#include <library.h>
-#include <lammps.h>
-#include <atom.h>
-#include <fix.h>
-#include <compute.h>
-#include <modify.h>
-#include <error.h>
-#include <cstdlib>
-
-using namespace LAMMPS_NS;
-
-void lammps_open_fortran_wrapper (int argc, char **argv,
-      MPI_Fint communicator, void **ptr)
-{
-   MPI_Comm C_communicator = MPI_Comm_f2c (communicator);
-   lammps_open (argc, argv, C_communicator, ptr);
-}
-
-int lammps_get_ntypes (void *ptr)
-{
-  class LAMMPS *lmp = (class LAMMPS *) ptr;
-  int ntypes = lmp->atom->ntypes;
-  return ntypes;
-}
-
-void lammps_error_all (void *ptr, const char *file, int line, const char *str)
-{
-   class LAMMPS *lmp = (class LAMMPS *) ptr;
-   lmp->error->all (file, line, str);
-}
-
-int lammps_extract_compute_vectorsize (void *ptr, char *id, int style)
-{
-   int *size;
-   size = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_VECTOR);
-   if (size) return *size;
-   return 0;
-}
-
-void lammps_extract_compute_arraysize (void *ptr, char *id, int style,
-      int *nrows, int *ncols)
-{
-   int *tmp;
-   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_ROWS);
-   if (tmp) *nrows = *tmp;
-   tmp = (int *) lammps_extract_compute(ptr, id, style, LMP_SIZE_COLS);
-   if (tmp) *ncols = *tmp;
-   return;
-}
-
-int lammps_extract_fix_vectorsize (void *ptr, char *id, int style)
-{
-   int *size;
-   size = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_VECTOR, 0, 0);
-   if (size) return *size;
-   return 0;
-}
-
-void lammps_extract_fix_arraysize (void *ptr, char *id, int style,
-      int *nrows, int *ncols)
-{
-   int *tmp;
-   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_ROWS, 0, 0);
-   if (tmp) *nrows = *tmp;
-   tmp = (int *) lammps_extract_fix(ptr, id, style, LMP_SIZE_COLS, 0, 0);
-   if (tmp) *ncols = *tmp;
-   return;
-}
-
-/* vim: set ts=3 sts=3 expandtab: */
diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h
deleted file mode 100644
index e1eec9fc72..0000000000
--- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/* -----------------------------------------------------------------------
-    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/, Sandia National Laboratories
-    LAMMPS development team: developers@lammps.org
- 
-    Copyright (2003) Sandia Corporation.  Under the terms of Contract
-    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-    certain rights in this software.  This software is distributed under 
-    the GNU General Public License.
- 
-    See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ------------------------------------------------------------------------
-    Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-                          University of Missouri (USA), 2012
-------------------------------------------------------------------------- */
-
-/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
-   provides a (I hope) robust Fortran interface to library.cpp and
-   library.h.  All prototypes herein COULD be added to library.h instead of
-   including this as a separate file. See the README for instructions. */
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/* Prototypes for auxiliary functions */
-void lammps_open_fortran_wrapper (int, char**, MPI_Fint, void**);
-int lammps_get_ntypes (void*);
-int lammps_extract_compute_vectorsize (void*, char*, int);
-void lammps_extract_compute_arraysize (void*, char*, int, int*, int*);
-int lammps_extract_fix_vectorsize (void*, char*, int);
-void lammps_extract_fix_arraysize (void*, char*, int, int*, int*);
-void lammps_error_all (void*, const char*, int, const char*);
-
-#ifdef __cplusplus
-}
-#endif
-
-/* vim: set ts=3 sts=3 expandtab: */
diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
deleted file mode 100644
index 83d594df60..0000000000
--- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
+++ /dev/null
@@ -1,80 +0,0 @@
-/* -----------------------------------------------------------------------
-    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/, Sandia National Laboratories
-    LAMMPS development team: developers@lammps.org
- 
-    Copyright (2003) Sandia Corporation.  Under the terms of Contract
-    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-    certain rights in this software.  This software is distributed under 
-    the GNU General Public License.
- 
-    See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ------------------------------------------------------------------------
-    Contributing author:  Nir Goldman, LLNL <ngoldman@llnl.gov>, 2016
-------------------------------------------------------------------------- */
-
-/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
-   provides a (I hope) robust Fortran interface to library.cpp and
-   library.h.  All functions herein COULD be added to library.cpp instead of
-   including this as a separate file. See the README for instructions. */
-
-#include <mpi.h>
-#include "LAMMPS-wrapper2.h"
-#include <library.h>
-#include <lammps.h>
-#include <atom.h>
-#include <input.h>
-#include <modify.h>
-#include <fix.h>
-#include <fix_external.h>
-#include <compute.h>
-#include <modify.h>
-#include <error.h>
-#include <cstdlib>
-
-using namespace LAMMPS_NS;
-
-extern "C" void f_callback(void *, bigint, int, tagint *, double **, double **);
-
-void lammps_set_callback (void *ptr) {
-  class LAMMPS *lmp = (class LAMMPS *) ptr;
-  int ifix = lmp->modify->find_fix_by_style("external");
-  FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
-  fix->set_callback(f_callback, ptr);
-  return;
-}
-
-void lammps_set_external_vector_length (void *ptr, int n) {
-  class LAMMPS *lmp = (class LAMMPS *) ptr;
-  int ifix = lmp->modify->find_fix_by_style("external");
-  FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
-  fix->set_vector_length(n);
-  return;
-}
-
-void lammps_set_external_vector (void *ptr, int n, double val) {
-  class LAMMPS *lmp = (class LAMMPS *) ptr;
-  int ifix = lmp->modify->find_fix_by_style("external");
-  FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
-  fix->set_vector (n, val);
-  return;
-}
-
-void lammps_set_user_energy (void *ptr, double energy) {
-  class LAMMPS *lmp = (class LAMMPS *) ptr;
-  int ifix = lmp->modify->find_fix_by_style("external");
-  FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
-  fix->set_energy_global(energy);
-  return;
-}
-
-void lammps_set_user_virial (void *ptr, double *virial) {
-  class LAMMPS *lmp = (class LAMMPS *) ptr;
-  int ifix = lmp->modify->find_fix_by_style("external");
-  FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
-  fix->set_virial_global(virial);
-  return;
-}
-
diff --git a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h
deleted file mode 100644
index 45c41b569a..0000000000
--- a/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h
+++ /dev/null
@@ -1,37 +0,0 @@
-/* -----------------------------------------------------------------------
-    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/, Sandia National Laboratories
-    LAMMPS development team: developers@lammps.org
- 
-    Copyright (2003) Sandia Corporation.  Under the terms of Contract
-    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-    certain rights in this software.  This software is distributed under 
-    the GNU General Public License.
- 
-    See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ------------------------------------------------------------------------
-    Contributing author:  Nir Goldman, LLNL <ngoldman@llnl.gov>, 2016
-------------------------------------------------------------------------- */
-
-/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself
-   provides a (I hope) robust Fortran interface to library.cpp and
-   library.h.  All prototypes herein COULD be added to library.h instead of
-   including this as a separate file. See the README for instructions. */
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/* Prototypes for auxiliary functions */
-void lammps_set_callback (void *); 
-void lammps_set_user_energy (void*, double); 
-void lammps_set_user_virial (void*, double*); 
-void lammps_set_external_vector_length (void*, int); 
-void lammps_set_external_vector (void*, int, double); 
-
-#ifdef __cplusplus
-}
-#endif
-
-/* vim: set ts=3 sts=3 expandtab: */
diff --git a/examples/COUPLE/fortran_dftb/LAMMPS.F90 b/examples/COUPLE/fortran_dftb/LAMMPS.F90
deleted file mode 100644
index 188fff9d60..0000000000
--- a/examples/COUPLE/fortran_dftb/LAMMPS.F90
+++ /dev/null
@@ -1,982 +0,0 @@
-!! -----------------------------------------------------------------------
-!   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-!   www.cs.sandia.gov/~sjplimp/lammps.html
-!   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
-!
-!   Copyright (2003) Sandia Corporation.  Under the terms of Contract
-!   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-!   certain rights in this software.  This software is distributed under 
-!   the GNU General Public License.
-!
-!   See the README file in the top-level LAMMPS directory.
-!--------------------------------------------------------------------------
-
-!! ------------------------------------------------------------------------
-!   Contributing author:  Karl D. Hammond <hammondkd@missouri.edu>
-!                         University of Missouri (USA), 2012
-!--------------------------------------------------------------------------
-
-!! LAMMPS, a Fortran 2003 module containing an interface between Fortran
-!! programs and the C-style functions in library.cpp that ship with LAMMPS.
-!! This file should be accompanied by LAMMPS-wrapper.cpp and LAMMPS-wrapper.h,
-!! which define wrapper functions that ease portability and enforce array
-!! dimensions.
-!!
-!! Everything in this module should be 100% portable by way of Fortran 2003's
-!! ISO_C_BINDING intrinsic module.  See the README for instructions for
-!! compilation and use.
-!!
-!! Here are the PUBLIC functions and subroutines included in this module.
-!!    subroutine lammps_open (command_line, communicator, ptr)
-!!    subroutine lammps_open_no_mpi (command_line, ptr)
-!!    subroutine lammps_close (ptr)
-!!    subroutine lammps_file (ptr, str)
-!!    subroutine lammps_command (ptr, str)
-!!    subroutine lammps_free (ptr)
-!!    subroutine lammps_extract_global (global, ptr, name)
-!!    subroutine lammps_extract_atom (atom, ptr, name)
-!!    subroutine lammps_extract_fix (fix, ptr, id, style, type, i, j)
-!!    subroutine lammps_extract_compute (compute, ptr, id, style, type)
-!!    subroutine lammps_extract_variable (variable, ptr, name, group)
-!!    function lammps_get_natoms (ptr)
-!!    subroutine lammps_gather_atoms (ptr, name, count, data)
-!!    subroutine lammps_scatter_atoms (ptr, name, data)
-
-#define FLERR __FILE__,__LINE__
-! The above line allows for similar error checking as is done with standard
-! LAMMPS files.
-
-module LAMMPS
-
-   use, intrinsic :: ISO_C_binding, only : C_double, C_int, C_ptr, C_char, &
-      C_NULL_CHAR, C_loc, C_F_pointer, lammps_instance => C_ptr
-   implicit none
-   private
-   public :: lammps_set_user_virial
-   public :: lammps_set_external_vector_length
-   public :: lammps_set_external_vector
-   public :: lammps_set_user_energy
-   public :: lammps_open, lammps_open_no_mpi, lammps_close, lammps_file, &
-      lammps_command, lammps_free, lammps_extract_global, &
-      lammps_extract_atom, lammps_extract_compute, lammps_extract_fix, &
-      lammps_extract_variable, lammps_get_natoms, lammps_gather_atoms, &
-      lammps_set_callback
-   public :: lammps_scatter_atoms, lammps_instance, C_ptr, C_double, C_int
-
-   !! Functions supplemental to the prototypes in library.h. {{{1
-   !! The function definitions (in C++) are contained in LAMMPS-wrapper.cpp.
-   !! I would have written the first in Fortran, but the MPI libraries (which
-   !! were written in C) have C-based functions to convert from Fortran MPI
-   !! handles to C MPI handles, and there is no Fortran equivalent for those
-   !! functions.
-   interface
-      subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
-      bind (C, name='lammps_open_fortran_wrapper')
-         import :: C_int, C_ptr
-         integer (C_int), value :: argc
-         type (C_ptr), dimension(*) :: argv
-         integer, value :: communicator
-         type (C_ptr) :: ptr
-      end subroutine lammps_open_wrapper
-      subroutine lammps_actual_error_all (ptr, file, line, str) &
-      bind (C, name='lammps_error_all')
-         import :: C_int, C_char, C_ptr
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*), intent(in) :: file, str
-         integer (C_int), value :: line
-      end subroutine lammps_actual_error_all
-      function lammps_get_ntypes (ptr) result (ntypes) &
-      bind (C, name='lammps_get_ntypes')
-         import :: C_int, C_ptr
-         type (C_ptr), value :: ptr
-         integer (C_int) :: ntypes
-      end function lammps_get_ntypes
-      function lammps_actual_extract_compute_vectorsize (ptr, id, style) &
-      result (vectorsize) bind (C, name='lammps_extract_compute_vectorsize')
-         import :: C_int, C_char, C_ptr
-         integer (C_int) :: vectorsize
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style
-      end function lammps_actual_extract_compute_vectorsize
-      subroutine lammps_actual_extract_compute_arraysize (ptr, id, style, &
-            nrows, ncols) bind (C, name='lammps_extract_compute_arraysize')
-         import :: C_int, C_char, C_ptr
-         integer (C_int) :: arraysize
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style
-         integer (C_int) :: nrows, ncols
-      end subroutine lammps_actual_extract_compute_arraysize
-      function lammps_actual_extract_fix_vectorsize (ptr, id, style) &
-      result (vectorsize) bind (C, name='lammps_extract_fix_vectorsize')
-         import :: C_int, C_char, C_ptr
-         integer (C_int) :: vectorsize
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style
-      end function lammps_actual_extract_fix_vectorsize
-      subroutine lammps_actual_extract_fix_arraysize (ptr, id, style, &
-            nrows, ncols) bind (C, name='lammps_extract_fix_arraysize')
-         import :: C_int, C_char, C_ptr
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style
-         integer (C_int) :: nrows, ncols
-      end subroutine lammps_actual_extract_fix_arraysize
-   end interface
-
-   !! Functions/subroutines defined in library.h and library.cpp {{{1
-   interface
-      subroutine lammps_actual_open_no_mpi (argc, argv, ptr) &
-      bind (C, name='lammps_open_no_mpi')
-         import :: C_int, C_ptr
-         integer (C_int), value :: argc
-         type (C_ptr), dimension(*) :: argv
-         type (C_ptr) :: ptr
-      end subroutine lammps_actual_open_no_mpi
-
-      subroutine lammps_close (ptr) bind (C, name='lammps_close')
-         import :: C_ptr
-         type (C_ptr), value :: ptr
-      end subroutine lammps_close
-
-      subroutine lammps_actual_file (ptr, str) bind (C, name='lammps_file')
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: str
-      end subroutine lammps_actual_file
-
-      function lammps_actual_command (ptr, str) result (command) &
-      bind (C, name='lammps_command')
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: str
-         type (C_ptr) :: command
-      end function lammps_actual_command
-
-      subroutine lammps_free (ptr) bind (C, name='lammps_free')
-         import :: C_ptr
-         type (C_ptr), value :: ptr
-      end subroutine lammps_free
-
-      function lammps_actual_extract_global (ptr, name) &
-      bind (C, name='lammps_extract_global') result (global)
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: name
-         type (C_ptr) :: global
-      end function lammps_actual_extract_global
-
-      function lammps_actual_extract_atom (ptr, name) &
-      bind (C, name='lammps_extract_atom') result (atom)
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: name
-         type (C_ptr) :: atom
-      end function lammps_actual_extract_atom
-
-      function lammps_actual_extract_compute (ptr, id, style, type) &
-      result (compute) bind (C, name='lammps_extract_compute')
-         import :: C_ptr, C_char, C_int
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style, type
-         type (C_ptr) :: compute
-      end function lammps_actual_extract_compute
-
-      function lammps_actual_extract_fix (ptr, id, style, type, i, j) &
-      result (fix) bind (C, name='lammps_extract_fix')
-         import :: C_ptr, C_char, C_int
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: id
-         integer (C_int), value :: style, type, i, j
-         type (C_ptr) :: fix
-      end function lammps_actual_extract_fix
-
-      function lammps_actual_extract_variable (ptr, name, group) &
-      result (variable) bind (C, name='lammps_extract_variable')
-         import :: C_ptr, C_char
-         type (C_ptr), value :: ptr
-         character (kind=C_char), dimension(*) :: name, group
-         type (C_ptr) :: variable
-      end function lammps_actual_extract_variable
-
-      function lammps_get_natoms (ptr) result (natoms) &
-      bind (C, name='lammps_get_natoms')
-         import :: C_ptr, C_int
-         type (C_ptr), value :: ptr
-         integer (C_int) :: natoms
-      end function lammps_get_natoms
- 
-      subroutine lammps_set_callback (ptr) &
-      bind (C, name='lammps_set_callback')
-        import :: C_ptr
-        type (C_ptr), value :: ptr
-      end subroutine lammps_set_callback
-
-      subroutine lammps_set_user_energy (ptr, energy) &
-      bind (C, name='lammps_set_user_energy')
-        import :: C_ptr, C_double 
-        type (C_ptr), value :: ptr
-        real(C_double), value :: energy
-      end subroutine lammps_set_user_energy 
-
-      subroutine lammps_set_user_virial (ptr, virial) &
-      bind (C, name='lammps_set_user_virial')
-        import :: C_ptr, C_double 
-        type (C_ptr), value :: ptr
-        real(C_double) :: virial(6)
-      end subroutine lammps_set_user_virial
-
-      subroutine lammps_set_external_vector_length (ptr, n) &
-      bind (C, name='lammps_set_external_vector_length')
-        import :: C_ptr, C_double, C_int 
-        type(C_ptr), value :: ptr
-        integer (C_int), value ::  n
-      end subroutine lammps_set_external_vector_length
-
-      subroutine lammps_set_external_vector (ptr, n, val) &
-      bind (C, name='lammps_set_external_vector')
-        import :: C_ptr, C_int, C_double 
-        type (C_ptr), value :: ptr
-        integer (C_int), value ::  n
-        real(C_double), value :: val
-      end subroutine lammps_set_external_vector
-
-      subroutine lammps_actual_gather_atoms (ptr, name, type, count, data) &
-      bind (C, name='lammps_gather_atoms')
-         import :: C_ptr, C_int, C_char
-         type (C_ptr), value :: ptr, data
-         character (kind=C_char), dimension(*) :: name
-         integer (C_int), value :: type, count
-      end subroutine lammps_actual_gather_atoms
-
-      subroutine lammps_actual_scatter_atoms (ptr, name, type, count, data) &
-      bind (C, name='lammps_scatter_atoms')
-         import :: C_ptr, C_int, C_char
-         type (C_ptr), value :: ptr, data
-         character (kind=C_char), dimension(*) :: name
-         integer (C_int), value :: type, count
-      end subroutine lammps_actual_scatter_atoms
-   end interface
-
-   ! Generic functions for the wrappers below {{{1
-
-   interface lammps_extract_global
-      module procedure lammps_extract_global_i, &
-         lammps_extract_global_dp
-   end interface lammps_extract_global
-
-   interface lammps_extract_atom
-      module procedure lammps_extract_atom_ia, &
-         lammps_extract_atom_dpa, &
-         lammps_extract_atom_dp2a
-   end interface lammps_extract_atom
-
-   interface lammps_extract_compute
-      module procedure lammps_extract_compute_dp, &
-         lammps_extract_compute_dpa, &
-         lammps_extract_compute_dp2a
-   end interface lammps_extract_compute
-
-   interface lammps_extract_fix
-      module procedure lammps_extract_fix_dp, &
-         lammps_extract_fix_dpa, &
-         lammps_extract_fix_dp2a
-   end interface lammps_extract_fix
-
-   interface lammps_extract_variable
-      module procedure lammps_extract_variable_dp, &
-         lammps_extract_variable_dpa
-   end interface lammps_extract_variable
-
-   interface lammps_gather_atoms
-      module procedure lammps_gather_atoms_ia, lammps_gather_atoms_dpa
-   end interface lammps_gather_atoms
-
-   interface lammps_scatter_atoms
-      module procedure lammps_scatter_atoms_ia, lammps_scatter_atoms_dpa
-   end interface lammps_scatter_atoms
-
-contains !! Wrapper functions local to this module {{{1
-
-   subroutine lammps_open (command_line, communicator, ptr)
-      character (len=*), intent(in) :: command_line
-      integer, intent(in) :: communicator
-      type (C_ptr) :: ptr
-      integer (C_int) :: argc
-      type (C_ptr), dimension(:), allocatable :: argv
-      character (kind=C_char), dimension(len_trim(command_line)+1), target :: &
-         c_command_line
-      c_command_line = string2Cstring (command_line)
-      call Cstring2argcargv (c_command_line, argc, argv)
-      call lammps_open_wrapper (argc, argv, communicator, ptr)
-      deallocate (argv)
-   end subroutine lammps_open
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_open_no_mpi (command_line, ptr)
-      character (len=*), intent(in) :: command_line
-      type (C_ptr) :: ptr
-      integer (C_int) :: argc
-      type (C_ptr), dimension(:), allocatable :: argv
-      character (kind=C_char), dimension(len_trim(command_line)+1), target :: &
-         c_command_line
-      c_command_line = string2Cstring (command_line)
-      call Cstring2argcargv (c_command_line, argc, argv)
-      call lammps_actual_open_no_mpi (argc, argv, ptr)
-      deallocate (argv)
-   end subroutine lammps_open_no_mpi
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_file (ptr, str)
-      type (C_ptr) :: ptr
-      character (len=*) :: str
-      character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
-      Cstr = string2Cstring (str)
-      call lammps_actual_file (ptr, Cstr)
-   end subroutine lammps_file
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_command (ptr, str)
-      type (C_ptr) :: ptr
-      character (len=*) :: str
-      character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
-      type (C_ptr) :: dummy
-      Cstr = string2Cstring (str)
-      dummy = lammps_actual_command (ptr, Cstr)
-   end subroutine lammps_command
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_global {{{2
-   function lammps_extract_global_Cptr (ptr, name) result (global)
-      type (C_ptr) :: global
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      Cname = string2Cstring (name)
-      global = lammps_actual_extract_global (ptr, Cname)
-   end function lammps_extract_global_Cptr
-   subroutine lammps_extract_global_i (global, ptr, name)
-      integer (C_int), pointer, intent(out) :: global
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      type (C_ptr) :: Cptr
-      Cptr = lammps_extract_global_Cptr (ptr, name)
-      call C_F_pointer (Cptr, global)
-   end subroutine lammps_extract_global_i
-   subroutine lammps_extract_global_dp (global, ptr, name)
-      real (C_double), pointer, intent(out) :: global
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      type (C_ptr) :: Cptr
-      Cptr = lammps_extract_global_Cptr (ptr, name)
-      call C_F_pointer (Cptr, global)
-   end subroutine lammps_extract_global_dp
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_atom {{{2
-   function lammps_extract_atom_Cptr (ptr, name) result (atom)
-      type (C_ptr) :: atom
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      Cname = string2Cstring (name)
-      atom = lammps_actual_extract_atom (ptr, Cname)
-   end function lammps_extract_atom_Cptr
-   subroutine lammps_extract_atom_ia (atom, ptr, name)
-      integer (C_int), dimension(:), pointer, intent(out) :: atom
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      type (C_ptr) :: Cptr
-      integer (C_int), pointer :: nelements
-      call lammps_extract_global_i (nelements, ptr, 'nlocal')
-      Cptr = lammps_extract_atom_Cptr (ptr, name)
-      call C_F_pointer (Cptr, atom, (/nelements/))
-   end subroutine lammps_extract_atom_ia
-   subroutine lammps_extract_atom_dpa (atom, ptr, name)
-      real (C_double), dimension(:), pointer, intent(out) :: atom
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      type (C_ptr) :: Cptr
-      integer (C_int), pointer :: nlocal
-      integer :: nelements
-      real (C_double), dimension(:), pointer :: Fptr
-      if ( name == 'mass' ) then
-         nelements = lammps_get_ntypes (ptr) + 1
-      else if ( name == 'x' .or. name == 'v' .or. name == 'f' .or. &
-                name == 'mu' .or. name == 'omega' .or. name == 'torque' .or. &
-                name == 'angmom' ) then
-         ! We should not be getting a rank-2 array here!
-         call lammps_error_all (ptr, FLERR, 'You cannot extract those atom&
-            & data (' // trim(name) // ') into a rank 1 array.')
-         return
-      else
-         ! Everything else we can get is probably nlocal units long
-         call lammps_extract_global_i (nlocal, ptr, 'nlocal')
-         nelements = nlocal
-      end if
-      Cptr = lammps_extract_atom_Cptr (ptr, name)
-      call C_F_pointer (Cptr, Fptr, (/nelements/))
-      if ( name == 'mass' ) then
-         !atom(0:) => Fptr
-         atom => Fptr
-      else
-         atom => Fptr
-      end if
-   end subroutine lammps_extract_atom_dpa
-   subroutine lammps_extract_atom_dp2a (atom, ptr, name)
-      real (C_double), dimension(:,:), pointer, intent(out) :: atom
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      type (C_ptr) :: Cptr
-      type (C_ptr), pointer, dimension(:) :: Catom
-      integer (C_int), pointer :: nelements
-      if ( name /= 'x' .and. name /= 'v' .and. name /= 'f' .and. &
-           name /= 'mu' .and. name /= 'omega' .and. name /= 'tandque' .and. &
-           name /= 'angmom' .and. name /= 'fexternal' ) then
-         ! We should not be getting a rank-2 array here!
-         call lammps_error_all (ptr, FLERR, 'You cannot extract those atom&
-            & data (' // trim(name) // ') into a rank 2 array.')
-         return
-      end if
-      Cptr = lammps_extract_atom_Cptr (ptr, name)
-      call lammps_extract_global_i (nelements, ptr, 'nlocal')
-      ! Catom will now be the array of void* pointers that the void** pointer
-      ! pointed to.  Catom(1) is now the pointer to the first element.
-      call C_F_pointer (Cptr, Catom, (/nelements/))
-      ! Now get the actual array, which has its shape transposed from what we
-      ! might think of it in C
-      call C_F_pointer (Catom(1), atom, (/3, nelements/))
-   end subroutine lammps_extract_atom_dp2a
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_compute {{{2
-   function lammps_extract_compute_Cptr (ptr, id, style, type) result (compute)
-      type (C_ptr) :: compute
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type
-      integer (kind=C_int) :: Cstyle, Ctype
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      Cid = string2Cstring (id)
-      Cstyle = style
-      Ctype = type
-      compute = lammps_actual_extract_compute (ptr, Cid, Cstyle, Ctype)
-   end function lammps_extract_compute_Cptr
-   subroutine lammps_extract_compute_dp (compute, ptr, id, style, type)
-      real (C_double), pointer, intent(out) :: compute
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type
-      type (C_ptr) :: Cptr
-      ! The only valid values of (style,type) are (0,0) for scalar 'compute'
-      if ( style /= 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot pack per-atom/local&
-            & data into a scalar.')
-         return
-      end if
-      if ( type == 1 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & vector (rank 1) into a scalar.')
-         return
-      else if ( type == 2 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & array (rank 2) into a scalar.')
-         return
-      end if
-      Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
-      call C_F_pointer (Cptr, compute)
-   end subroutine lammps_extract_compute_dp
-   subroutine lammps_extract_compute_dpa (compute, ptr, id, style, type)
-      real (C_double), dimension(:), pointer, intent(out) :: compute
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type
-      type (C_ptr) :: Cptr
-      integer :: nelements
-      ! Check for the correct dimensionality
-      if ( type == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & scalar (rank 0) into a rank 1 variable.')
-         return
-      else if ( type == 2 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & array (rank 2) into a rank 1 variable.')
-         return
-      end if
-      nelements = lammps_extract_compute_vectorsize (ptr, id, style)
-      Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
-      call C_F_pointer (Cptr, compute, (/nelements/))
-   end subroutine lammps_extract_compute_dpa
-   subroutine lammps_extract_compute_dp2a (compute, ptr, id, style, type)
-      real (C_double), dimension(:,:), pointer, intent(out) :: compute
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type
-      type (C_ptr) :: Cptr
-      type (C_ptr), pointer, dimension(:) :: Ccompute
-      integer :: nr, nc
-      ! Check for the correct dimensionality
-      if ( type == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & scalar (rank 0) into a rank 2 variable.')
-         return
-      else if ( type == 1 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a compute&
-            & array (rank 1) into a rank 2 variable.')
-         return
-      end if
-      call lammps_extract_compute_arraysize (ptr, id, style, nr, nc)
-      Cptr = lammps_extract_compute_Cptr (ptr, id, style, type)
-      call C_F_pointer (Cptr, Ccompute, (/nr/))
-      ! Note that the matrix is transposed, from Fortran's perspective
-      call C_F_pointer (Ccompute(1), compute, (/nc, nr/))
-   end subroutine lammps_extract_compute_dp2a
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_fix {{{2
-   function lammps_extract_fix_Cptr (ptr, id, style, type, i, j) &
-   result (fix)
-      type (C_ptr) :: fix
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type, i, j
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      integer (kind=C_int) :: Cstyle, Ctype, Ci, Cj
-      Cid = string2Cstring (id)
-      Cstyle = style
-      Ctype = type
-      Ci = i - 1  ! This is for consistency with the values from f_ID[i],
-      Cj = j - 1  ! which is different from what library.cpp uses!
-      if ( (type >= 1 .and. Ci < 0) .or. &
-           (type == 2 .and. (Ci < 0 .or. Cj < 0) ) ) then
-         call lammps_error_all (ptr, FLERR, 'Index out of range in&
-            & lammps_extract_fix')
-      end if
-      fix = lammps_actual_extract_fix (ptr, Cid, Cstyle, Ctype, Ci, Cj)
-   end function lammps_extract_fix_Cptr
-   subroutine lammps_extract_fix_dp (fix, ptr, id, style, type, i, j)
-      real (C_double), intent(out) :: fix
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type, i, j
-      type (C_ptr) :: Cptr
-      real (C_double), pointer :: Fptr
-      ! Check for the correct dimensionality
-      if ( style /= 0 ) then
-         select case (type)
-         case (0)
-            call lammps_error_all (ptr, FLERR, 'There is no per-atom or local&
-               & scalar data available from fixes.')
-         case (1)
-            call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s &
-               &per-atom/local vector (rank 1) into a scalar.')
-         case (2)
-            call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s &
-               &per-atom/local array (rank 2) into a scalar.')
-         case default
-            call lammps_error_all (ptr, FLERR, 'Invalid extract_fix style/&
-               &type combination.')
-         end select
-         return
-      end if
-      Cptr = lammps_extract_fix_Cptr (ptr, id, style, type, i, j)
-      call C_F_pointer (Cptr, Fptr)
-      fix = Fptr
-      nullify (Fptr)
-      ! Memory is only allocated for "global" fix variables
-      if ( style == 0 ) call lammps_free (Cptr)
-   end subroutine lammps_extract_fix_dp
-   subroutine lammps_extract_fix_dpa (fix, ptr, id, style, type, i, j)
-      real (C_double), dimension(:), pointer, intent(out) :: fix
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type, i, j
-      type (C_ptr) :: Cptr
-      integer :: fix_len
-      ! Check for the correct dimensionality
-      if ( style == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You can''t extract the&
-            & whole vector from global fix data')
-         return
-      else if ( type == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You can''t extract a fix&
-            & scalar into a rank 1 variable')
-         return
-      else if ( type == 2 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
-            & array into a rank 1 variable.')
-         return
-      else if ( type /= 1 ) then
-         call lammps_error_all (ptr, FLERR, 'Invalid type for fix extraction.')
-         return
-      end if
-      fix_len = lammps_extract_fix_vectorsize (ptr, id, style)
-      call C_F_pointer (Cptr, fix, (/fix_len/))
-      ! Memory is only allocated for "global" fix variables, which we should
-      ! never get here, so no need to call lammps_free!
-   end subroutine lammps_extract_fix_dpa
-   subroutine lammps_extract_fix_dp2a (fix, ptr, id, style, type, i, j)
-      real (C_double), dimension(:,:), pointer, intent(out) :: fix
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style, type, i, j
-      type (C_ptr) :: Cptr
-      type (C_ptr), pointer, dimension(:) :: Cfix
-      integer :: nr, nc
-      ! Check for the correct dimensionality
-      if ( style == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'It is not possible to extract the&
-            & entire array from global fix data.')
-         return
-      else if ( type == 0 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
-            & scalar (rank 0) into a rank 2 variable.')
-         return
-      else if ( type == 1 ) then
-         call lammps_error_all (ptr, FLERR, 'You cannot extract a fix&
-            & vector (rank 1) into a rank 2 variable.')
-         return
-      end if
-      call lammps_extract_fix_arraysize (ptr, id, style, nr, nc)
-      ! Extract pointer to first element as Cfix(1)
-      call C_F_pointer (Cptr, Cfix, (/nr/))
-      ! Now extract the array, which is transposed
-      call C_F_pointer (Cfix(1), fix, (/nc, nr/))
-   end subroutine lammps_extract_fix_dp2a
-
-!-----------------------------------------------------------------------------
-
-! lammps_extract_variable {{{2
-   function lammps_extract_variable_Cptr (ptr, name, group) result (variable)
-      type (C_ptr) :: ptr, variable
-      character (len=*) :: name
-      character (len=*), optional :: group
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      character (kind=C_char), dimension(:), allocatable :: Cgroup
-      Cname = string2Cstring (name)
-      if ( present(group) ) then
-         allocate (Cgroup(len_trim(group)+1))
-         Cgroup = string2Cstring (group)
-      else
-         allocate (Cgroup(1))
-         Cgroup(1) = C_NULL_CHAR
-      end if
-      variable = lammps_actual_extract_variable (ptr, Cname, Cgroup)
-      deallocate (Cgroup)
-   end function lammps_extract_variable_Cptr
-   subroutine lammps_extract_variable_dp (variable, ptr, name, group)
-      real (C_double), intent(out) :: variable
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      character (len=*), intent(in), optional :: group
-      type (C_ptr) :: Cptr
-      real (C_double), pointer :: Fptr
-      if ( present(group) ) then
-         Cptr = lammps_extract_variable_Cptr (ptr, name, group)
-      else
-         Cptr = lammps_extract_variable_Cptr (ptr, name)
-      end if
-      call C_F_pointer (Cptr, Fptr)
-      variable = Fptr
-      nullify (Fptr)
-      call lammps_free (Cptr)
-   end subroutine lammps_extract_variable_dp
-   subroutine lammps_extract_variable_dpa (variable, ptr, name, group)
-      real (C_double), dimension(:), allocatable, intent(out) :: variable
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      character (len=*), intent(in), optional :: group
-      type (C_ptr) :: Cptr
-      real (C_double), dimension(:), pointer :: Fptr
-      integer :: natoms
-      if ( present(group) ) then
-         Cptr = lammps_extract_variable_Cptr (ptr, name, group)
-      else
-         Cptr = lammps_extract_variable_Cptr (ptr, name)
-      end if
-      natoms = lammps_get_natoms (ptr)
-      allocate (variable(natoms))
-      call C_F_pointer (Cptr, Fptr, (/natoms/))
-      variable = Fptr
-      nullify (Fptr)
-      call lammps_free (Cptr)
-   end subroutine lammps_extract_variable_dpa
-
-!-------------------------------------------------------------------------2}}}
-
-   subroutine lammps_gather_atoms_ia (ptr, name, count, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, intent(in) :: count
-      integer, dimension(:), allocatable, intent(out) :: data
-      type (C_ptr) :: Cdata
-      integer (C_int), dimension(:), pointer :: Fdata
-      integer (C_int) :: natoms
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), parameter :: Ctype = 0_C_int
-      integer (C_int) :: Ccount
-      natoms = lammps_get_natoms (ptr)
-      Cname = string2Cstring (name)
-      if ( count /= 1 .and. count /= 3 ) then
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
-            & count to be either 1 or 3')
-      else
-         Ccount = count
-      end if
-      allocate ( Fdata(count*natoms) )
-      allocate ( data(count*natoms) )
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
-      data = Fdata
-      deallocate (Fdata)
-   end subroutine lammps_gather_atoms_ia
-   subroutine lammps_gather_atoms_dpa (ptr, name, count, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, intent(in) :: count
-      double precision, dimension(:), allocatable, intent(out) :: data
-      type (C_ptr) :: Cdata
-      real (C_double), dimension(:), pointer :: Fdata
-      integer (C_int) :: natoms
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), parameter :: Ctype = 1_C_int
-      integer (C_int) :: Ccount
-      natoms = lammps_get_natoms (ptr)
-      Cname = string2Cstring (name)
-      if ( count /= 1 .and. count /= 3 ) then
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
-            & count to be either 1 or 3')
-      else
-         Ccount = count
-      end if
-      allocate ( Fdata(count*natoms) )
-      allocate ( data(count*natoms) )
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata)
-      data = Fdata(:)
-      deallocate (Fdata)
-   end subroutine lammps_gather_atoms_dpa
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_scatter_atoms_ia (ptr, name, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      integer, dimension(:), intent(in) :: data
-      integer (kind=C_int) :: natoms, Ccount
-      integer (kind=C_int), parameter :: Ctype = 0_C_int
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      integer (C_int), dimension(size(data)), target :: Fdata
-      type (C_ptr) :: Cdata
-      natoms = lammps_get_natoms (ptr)
-      Cname = string2Cstring (name)
-      Ccount = size(data) / natoms
-      if ( Ccount /= 1 .and. Ccount /= 3 ) &
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
-            & count to be either 1 or 3')
-      Fdata = data
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
-   end subroutine lammps_scatter_atoms_ia
-   subroutine lammps_scatter_atoms_dpa (ptr, name, data)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: name
-      double precision, dimension(:), intent(in) :: data
-      integer (kind=C_int) :: natoms, Ccount
-      integer (kind=C_int), parameter :: Ctype = 1_C_int
-      character (kind=C_char), dimension(len_trim(name)+1) :: Cname
-      real (C_double), dimension(size(data)), target :: Fdata
-      type (C_ptr) :: Cdata
-      natoms = lammps_get_natoms (ptr)
-      Cname = string2Cstring (name)
-      Ccount = size(data) / natoms
-      if ( Ccount /= 1 .and. Ccount /= 3 ) &
-         call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires&
-            & count to be either 1 or 3')
-      Fdata = data
-      Cdata = C_loc (Fdata(1))
-      call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata)
-   end subroutine lammps_scatter_atoms_dpa
-
-!-----------------------------------------------------------------------------
-
-   function lammps_extract_compute_vectorsize (ptr, id, style) &
-   result (vectorsize)
-      integer :: vectorsize
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style
-      integer (C_int) :: Cvectorsize, Cstyle
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      Cid = string2Cstring (id)
-      Cstyle = int(style, C_int)
-      Cvectorsize = lammps_actual_extract_compute_vectorsize (ptr, Cid, Cstyle)
-      vectorsize = int(Cvectorsize, kind(vectorsize))
-   end function lammps_extract_compute_vectorsize
-
-!-----------------------------------------------------------------------------
-
-   function lammps_extract_fix_vectorsize (ptr, id, style) &
-   result (vectorsize)
-      integer :: vectorsize
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style
-      integer (C_int) :: Cvectorsize, Cstyle
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      Cid = string2Cstring (id)
-      Cstyle = int(style, C_int)
-      Cvectorsize = lammps_actual_extract_fix_vectorsize (ptr, Cid, Cstyle)
-      vectorsize = int(Cvectorsize, kind(vectorsize))
-   end function lammps_extract_fix_vectorsize
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_extract_compute_arraysize (ptr, id, style, nrows, ncols)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style
-      integer, intent(out) :: nrows, ncols
-      integer (C_int) :: Cstyle, Cnrows, Cncols
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      Cid = string2Cstring (id)
-      Cstyle = int (style, C_int)
-      call lammps_actual_extract_compute_arraysize (ptr, Cid, Cstyle, &
-         Cnrows, Cncols)
-      nrows = int (Cnrows, kind(nrows))
-      ncols = int (Cncols, kind(ncols))
-   end subroutine lammps_extract_compute_arraysize
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_extract_fix_arraysize (ptr, id, style, nrows, ncols)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: id
-      integer, intent(in) :: style
-      integer, intent(out) :: nrows, ncols
-      integer (C_int) :: Cstyle, Cnrows, Cncols
-      character (kind=C_char), dimension(len_trim(id)+1) :: Cid
-      Cid = string2Cstring (id)
-      Cstyle = int (style, kind(Cstyle))
-      call lammps_actual_extract_fix_arraysize (ptr, Cid, Cstyle, &
-         Cnrows, Cncols)
-      nrows = int (Cnrows, kind(nrows))
-      ncols = int (Cncols, kind(ncols))
-   end subroutine lammps_extract_fix_arraysize
-
-!-----------------------------------------------------------------------------
-
-   subroutine lammps_error_all (ptr, file, line, str)
-      type (C_ptr), intent(in) :: ptr
-      character (len=*), intent(in) :: file, str
-      integer, intent(in) :: line
-      character (kind=C_char), dimension(len_trim(file)+1) :: Cfile
-      character (kind=C_char), dimension(len_trim(str)+1) :: Cstr
-      integer (C_int) :: Cline
-      Cline = int(line, kind(Cline))
-      Cfile = string2Cstring (file)
-      Cstr = string2Cstring (str)
-      call lammps_actual_error_all (ptr, Cfile, Cline, Cstr)
-   end subroutine lammps_error_all
-
-!-----------------------------------------------------------------------------
-
-! Locally defined helper functions {{{1
-
-   pure function string2Cstring (string) result (C_string)
-      use, intrinsic :: ISO_C_binding, only : C_char, C_NULL_CHAR
-      character (len=*), intent(in) :: string
-      character (len=1, kind=C_char) :: C_string (len_trim(string)+1)
-      integer :: i, n
-      n = len_trim (string)
-      forall (i = 1:n)
-         C_string(i) = string(i:i)
-      end forall
-      C_string(n+1) = C_NULL_CHAR
-   end function string2Cstring
-
-!-----------------------------------------------------------------------------
-
-   subroutine Cstring2argcargv (Cstring, argc, argv)
-   !! Converts a C-style string to argc and argv, that is, words in Cstring
-   !! become C-style strings in argv.  IMPORTANT:  Cstring is modified by
-   !! this routine!  I would make Cstring local TO this routine and accept
-   !! a Fortran-style string instead, but we run into scoping and
-   !! allocation problems that way.  This routine assumes the string is
-   !! null-terminated, as all C-style strings must be.
-
-      character (kind=C_char), dimension(*), target, intent(inout) :: Cstring
-      integer (C_int), intent(out) :: argc
-      type (C_ptr), dimension(:), allocatable, intent(out) :: argv
-
-      integer :: StringStart, SpaceIndex, strlen, argnum
-
-      argc = 1_C_int
-
-      ! Find the length of the string
-      strlen = 1
-      do while ( Cstring(strlen) /= C_NULL_CHAR )
-         strlen = strlen + 1
-      end do
-
-      ! Find the number of non-escaped spaces
-      SpaceIndex = 2
-      do while ( SpaceIndex < strlen )
-         if ( Cstring(SpaceIndex) == ' ' .and. &
-              Cstring(SpaceIndex-1) /= '\' ) then
-            argc = argc + 1_C_int
-            ! Find the next non-space character
-            do while ( Cstring(SpaceIndex+1) == ' ')
-               SpaceIndex = SpaceIndex + 1
-            end do
-         end if
-         SpaceIndex = SpaceIndex + 1
-      end do
-
-      ! Now allocate memory for argv
-      allocate (argv(argc))
-
-      ! Now find the string starting and ending locations
-      StringStart = 1
-      SpaceIndex = 2
-      argnum = 1
-      do while ( SpaceIndex < strlen )
-         if ( Cstring(SpaceIndex) == ' ' .and. &
-              Cstring(SpaceIndex-1) /= '\' ) then
-            ! Found a real space => split strings and store this one
-            Cstring(Spaceindex) = C_NULL_CHAR ! Replaces space with NULL
-            argv(argnum) = C_loc(Cstring(StringStart))
-            argnum = argnum + 1
-            ! Find the next non-space character
-            do while ( Cstring(SpaceIndex+1) == ' ')
-               SpaceIndex = SpaceIndex + 1
-            end do
-            StringStart = SpaceIndex + 1
-         else if ( Cstring(SpaceIndex) == ' ' .and. &
-              Cstring(SpaceIndex-1) == '\' ) then
-            ! Escaped space => remove backslash and move rest of array
-            Cstring(SpaceIndex-1:strlen-1) = Cstring(SpaceIndex:strlen)
-            strlen = strlen - 1 ! Last character is still C_NULL_CHAR
-         end if
-         SpaceIndex = SpaceIndex + 1
-      end do
-      ! Now handle the last argument
-      argv(argnum) = C_loc(Cstring(StringStart))
-
-   end subroutine Cstring2argcargv
-
-! 1}}}
-
-end module LAMMPS
-
-! vim: foldmethod=marker tabstop=3 softtabstop=3 shiftwidth=3 expandtab
diff --git a/examples/COUPLE/fortran_dftb/README b/examples/COUPLE/fortran_dftb/README
deleted file mode 100644
index 39a2f18169..0000000000
--- a/examples/COUPLE/fortran_dftb/README
+++ /dev/null
@@ -1,37 +0,0 @@
-This directory has an example of using a callback function to obtain
-forces from a fortran code for a LAMMPS simulation.  The reader should
-refer to the README file in COUPLE/fortran2 before proceeding. Here,
-the LAMMPS.F90 file has been modified slightly and additional files
-named LAMMPS-wrapper2.h and LAMMPS-wrapper2.cpp have been included in
-order to supply wrapper functions to set the LAMMPS callback function,
-total energy, virial, and electronic entropy contribution (needed for 
-MSST simulations with a quantum code).
-
-In this example, the callback function is set to run the
-semi-empirical quantum code DFTB+ in serial and then read in the total
-energy, forces, and stress tensor from file.  In this case, nlocal =
-the total number of atoms in the system, so particle positions can be
-read from the pos array directly, and DFTB+ forces can simply be
-included via the fext array. The user should take care in the case of
-a parallel calculation, where LAMMPS can assign different particules
-to each processor. For example, the user should use functions such as
-lammps_gather_atoms() and lammps_scatter_atoms() in the case where the
-fortran force calculating code requires the positions of all atoms,
-etc.
-
-A few more important notes: 
-
--Calling the subroutine lammps_set_callback() is required in order to set
-       a pointer to the callback function in LAMMPS.
--The subroutine lammps_set_user_energy() passes in the potential energy
-       from DFTB+ to LAMMPS. Similarly, lammps_set_user_virial passes the stress tensor.
-
--The electronic entropy contribution is set via lammps_set_external_vector(). Their needs
-	to be a call to lammps_set_external_vector_length() before this value can be
-	passed to LAMMPS.
-
-This example was created by Nir Goldman, whom you can contact with
-questions:
-
-Nir Goldman, LLNL
-ngoldman@llnl.gov
diff --git a/examples/COUPLE/fortran_dftb/data.diamond b/examples/COUPLE/fortran_dftb/data.diamond
deleted file mode 100644
index b3dd599cf4..0000000000
--- a/examples/COUPLE/fortran_dftb/data.diamond
+++ /dev/null
@@ -1,148 +0,0 @@
-# Position data file
-
-64 atoms
-1 atom types
-
-0 7.134 xlo xhi
-0 7.134 ylo yhi
-0 7.134 zlo zhi
-
-0.00000000 0.00000000 0.00000000 xy xz yz
-
-Masses
-
-1 12.010000
-
-Atoms
-
-     1 1 0     0 0 0
-     2 1 0     0.89175 0.89175 0.89175
-     3 1 0     1.7835 1.7835 0
-     4 1 0     2.67525 2.67525 0.89175
-     5 1 0     0 1.7835 1.7835
-     6 1 0     0.89175 2.67525 2.67525
-     7 1 0     1.7835 0 1.7835
-     8 1 0     2.67525 0.89175 2.67525
-     9 1 0     0 0 3.567
-     10 1 0     0.89175 0.89175 4.45875
-     11 1 0     1.7835 1.7835 3.567
-     12 1 0     2.67525 2.67525 4.45875
-     13 1 0     0 1.7835 5.3505
-     14 1 0     0.89175 2.67525 6.24225
-     15 1 0     1.7835 0 5.3505
-     16 1 0     2.67525 0.89175 6.24225
-     17 1 0     0 3.567 0
-     18 1 0     0.89175 4.45875 0.89175
-     19 1 0     1.7835 5.3505 0
-     20 1 0     2.67525 6.24225 0.89175
-     21 1 0     0 5.3505 1.7835
-     22 1 0     0.89175 6.24225 2.67525
-     23 1 0     1.7835 3.567 1.7835
-     24 1 0     2.67525 4.45875 2.67525
-     25 1 0     0 3.567 3.567
-     26 1 0     0.89175 4.45875 4.45875
-     27 1 0     1.7835 5.3505 3.567
-     28 1 0     2.67525 6.24225 4.45875
-     29 1 0     0 5.3505 5.3505
-     30 1 0     0.89175 6.24225 6.24225
-     31 1 0     1.7835 3.567 5.3505
-     32 1 0     2.67525 4.45875 6.24225
-     33 1 0     3.567 0 0
-     34 1 0     4.45875 0.89175 0.89175
-     35 1 0     5.3505 1.7835 0
-     36 1 0     6.24225 2.67525 0.89175
-     37 1 0     3.567 1.7835 1.7835
-     38 1 0     4.45875 2.67525 2.67525
-     39 1 0     5.3505 0 1.7835
-     40 1 0     6.24225 0.89175 2.67525
-     41 1 0     3.567 0 3.567
-     42 1 0     4.45875 0.89175 4.45875
-     43 1 0     5.3505 1.7835 3.567
-     44 1 0     6.24225 2.67525 4.45875
-     45 1 0     3.567 1.7835 5.3505
-     46 1 0     4.45875 2.67525 6.24225
-     47 1 0     5.3505 0 5.3505
-     48 1 0     6.24225 0.89175 6.24225
-     49 1 0     3.567 3.567 0
-     50 1 0     4.45875 4.45875 0.89175
-     51 1 0     5.3505 5.3505 0
-     52 1 0     6.24225 6.24225 0.89175
-     53 1 0     3.567 5.3505 1.7835
-     54 1 0     4.45875 6.24225 2.67525
-     55 1 0     5.3505 3.567 1.7835
-     56 1 0     6.24225 4.45875 2.67525
-     57 1 0     3.567 3.567 3.567
-     58 1 0     4.45875 4.45875 4.45875
-     59 1 0     5.3505 5.3505 3.567
-     60 1 0     6.24225 6.24225 4.45875
-     61 1 0     3.567 5.3505 5.3505
-     62 1 0     4.45875 6.24225 6.24225
-     63 1 0     5.3505 3.567 5.3505
-     64 1 0     6.24225 4.45875 6.24225
-
-Velocities
-
-1 -0.00733742 -0.0040297 -0.00315229 
-2 -0.00788609 -0.00567535 -0.00199152 
-3 -0.00239042 0.00710139 -0.00335049 
-4 0.00678551 0.0019976 0.00219289 
-5 0.00413717 0.00275709 0.000937637 
-6 -0.00126313 0.00485636 0.00727862 
-7 0.00337547 -0.00234623 -0.000922223 
-8 -0.00792183 -0.00509186 -0.00104168 
-9 0.00414091 0.00390285 0.000845961 
-10 -0.000284543 0.0010771 -0.00458404 
-11 -0.00394968 -0.00446363 -0.00361688 
-12 0.00067088 -0.00655175 -0.00752464 
-13 0.00306632 -0.00245545 -0.00183867 
-14 -0.0082145 -0.00564127 0.000281191 
-15 0.00504454 0.0045835 0.000495763 
-16 0.0035767 0.00320441 -0.00486426 
-17 0.00420597 0.00262005 -0.0049459 
-18 0.00440579 -1.76783e-05 0.00449311 
-19 -0.00406463 0.00613304 0.00285599 
-20 0.00171215 -0.00517887 0.00124326 
-21 0.0011118 0.00334129 -0.0015222 
-22 -0.00838394 -0.00112906 -0.00353379 
-23 -0.00578527 -0.00415501 0.00297043 
-24 -0.00211466 0.000964108 -0.00716523 
-25 -0.000204107 -0.00380986 0.00681648 
-26 0.00677838 0.00540935 0.0044354 
-27 -0.00266809 -0.00358382 -0.00241889 
-28 -0.0003973 0.00236566 0.00558871 
-29 0.000754103 0.00457797 0.000105531 
-30 -0.00246049 0.00110428 0.00511088 
-31 0.00248891 0.00623314 0.00461597 
-32 -0.00509423 0.000570503 0.00720856 
-33 -0.00244427 -0.00374384 0.00618767 
-34 -0.000360752 -8.10558e-05 0.00314052 
-35 0.00435313 -0.00630587 -0.0070309 
-36 0.00651087 -0.00389833 3.72525e-05 
-37 0.00631828 -0.00316064 0.00231522 
-38 -0.00579624 -0.00345068 -0.000277486 
-39 0.00483974 0.000715028 0.000206355 
-40 -0.00388164 -0.00189242 -0.00554862 
-41 0.00398115 0.00152915 0.00756919 
-42 -0.000552263 0.00352025 -0.000246143 
-43 -0.00800284 0.00555703 0.00425716 
-44 -0.00734405 -0.00752512 0.00667173 
-45 -0.00545636 0.00421035 0.00399552 
-46 0.00480246 0.00621147 -0.00492715 
-47 -0.00424168 0.00621818 -9.37733e-05 
-48 -0.00649561 0.00612908 -0.0020753 
-49 -0.0075007 -0.00384737 -0.00687913 
-50 -0.00203903 -0.00764372 0.0023883 
-51 0.00442642 0.00744072 -0.0049344 
-52 -0.00280486 -0.00509128 -0.00678045 
-53 0.00679491 0.00583493 0.00333875 
-54 0.00574665 -0.00521074 0.00523475 
-55 0.00305618 -0.00320094 0.00341297 
-56 0.004304 0.000615544 -0.00668787 
-57 0.00564532 0.00327373 0.00388611 
-58 0.000676899 0.00210326 0.00495295 
-59 0.000160781 -0.00744313 -0.00279828 
-60 0.00623521 0.00371301 0.00178015 
-61 0.00520759 0.000642669 0.00207913 
-62 0.00398042 0.0046438 -0.00359978 
-63 -0.00478071 -0.00304932 -0.00765125 
-64 0.00282671 -0.00548392 -0.00692691 
diff --git a/examples/COUPLE/fortran_dftb/dftb_in.hsd b/examples/COUPLE/fortran_dftb/dftb_in.hsd
deleted file mode 100644
index 104a4c04ce..0000000000
--- a/examples/COUPLE/fortran_dftb/dftb_in.hsd
+++ /dev/null
@@ -1,40 +0,0 @@
-#sample DFTB+  script to run this test code
-Geometry = GenFormat {
-<<< "lammps.gen"
-}
-
-Driver = {
-}
-
-Hamiltonian = DFTB {
-  LAMMPS = Yes # keyword to print energy, forces, and stress tensor to file(results.out)
-  SCC = No
-  MaxAngularMomentum = {
-    C = "p"
-  }
-  Charge = 0.0
-  Eigensolver = Standard {}
-  Filling = Fermi {
-    Temperature [Kelvin] = 298.0
-  }
-  SlaterKosterFiles = Type2FileNames {
-    Prefix = "~/slako/mio-1-1/" # the user must define the location of the skf files
-    Separator = "-"
-    Suffix = ".skf"
-    LowerCaseTypeName = No
-  }
-  KPointsAndWeights = {
-    0.0000000000000 0.0000000000000 0.0000000000000 1.00000000000000
-  }
-}
-
-Options = {
-  CalculateForces = Yes
-  WriteDetailedOut = No
-  WriteBandOut = No
-  RandomSeed = 12345
-}
-
-ParserOptions = {
-  ParserVersion = 3
-}
diff --git a/examples/COUPLE/fortran_dftb/dftb_pin.hsd b/examples/COUPLE/fortran_dftb/dftb_pin.hsd
deleted file mode 100644
index 6d9dea4a15..0000000000
--- a/examples/COUPLE/fortran_dftb/dftb_pin.hsd
+++ /dev/null
@@ -1,129 +0,0 @@
-Geometry = GenFormat {
-64 S
-C
-1           1       7.099007       7.117657       7.119139
-2           1       0.858709       0.867233       0.882294
-3           1       1.772527       1.811776       7.120239
-4           1       2.702145       2.681271       0.901362
-5           1       0.017539       1.794455       1.788454
-6           1       0.885593       2.694118       2.707994
-7           1       1.795055       7.120787       1.777896
-8           1       2.642849       0.868278       2.670699
-9           1       0.016060       0.017156       3.568644
-10           1       0.891891       0.896406       4.439286
-11           1       1.766086       1.764402       3.550134
-12           1       2.677349       2.648926       4.427174
-13           1       0.010133       1.771283       5.342173
-14           1       0.858153       2.653565       6.241596
-15           1       1.804087       0.020636       5.353268
-16           1       2.689680       0.907188       6.224575
-17           1       0.017845       3.577563       7.113016
-18           1       0.910027       4.459286       0.910286
-19           1       1.766394       5.376046       0.015526
-20           1       2.683727       6.220728       0.898553
-21           1       0.003357       5.363423       1.774139
-22           1       0.856735       6.238324       2.660213
-23           1       1.761079       3.549776       1.797054
-24           1       2.667227       4.463441       2.646074
-25           1       7.132499       3.551558       3.599764
-26           1       0.920387       4.482191       4.479257
-27           1       1.772194       5.337132       3.555569
-28           1       2.675010       6.251629       4.483124
-29           1       0.005702       5.371095       5.351147
-30           1       0.880807       6.249819       6.264231
-31           1       1.793177       3.592396       5.369939
-32           1       2.653179       4.463595       6.274044
-33           1       3.557243       7.118913       0.026006
-34           1       4.458971       0.889331       0.904950
-35           1       5.367903       1.759757       7.104941
-36           1       6.271565       2.658454       0.890168
-37           1       3.591915       1.768681       1.793880
-38           1       4.435612       2.662184       2.676722
-39           1       5.371040       0.000196       1.783464
-40           1       6.226453       0.886640       2.653384
-41           1       3.583339       0.005449       3.600177
-42           1       4.453692       0.909417       4.459713
-43           1       5.314554       1.805409       3.584215
-44           1       6.210181       2.642660       4.486206
-45           1       3.545704       1.802745       5.365369
-46           1       4.476660       2.701226       6.220451
-47           1       5.332820       0.029557       5.347965
-48           1       6.215725       0.915081       6.230289
-49           1       3.536446       3.551469       7.106600
-50           1       4.451181       4.426439       0.900180
-51           1       5.368735       5.377996       7.109524
-52           1       6.230666       6.220985       0.862175
-53           1       3.596626       5.372822       1.797613
-54           1       4.485613       6.221252       2.699652
-55           1       5.364421       3.549838       1.796281
-56           1       6.261739       4.459046       2.648152
-57           1       3.588752       3.581054       3.581755
-58           1       4.462342       4.467270       4.478800
-59           1       5.355202       5.318323       3.556531
-60           1       6.268570       6.259831       4.465795
-61           1       3.588636       5.354278       5.362327
-62           1       4.475747       6.263866       6.227803
-63           1       5.331158       3.554349       5.318368
-64           1       6.254581       4.436344       6.209681
-0.0 0.0 0.0
-7.13400000000000                0           0
-0   7.13400000000000                0
-0           0   7.13400000000000
-}
-Driver = {}
-Hamiltonian = DFTB {
-  LAMMPS = Yes
-  SCC = No
-  MaxAngularMomentum = {
-    C = "p"
-  }
-  Charge = 0.0
-  Eigensolver = Standard {}
-  Filling = Fermi {
-    Temperature [Kelvin] = 298.0
-    IndependentKFilling = No
-  }
-  SlaterKosterFiles = Type2FileNames {
-    Prefix = "~/slako/mio-1-1/"
-    Separator = "-"
-    Suffix = ".skf"
-    LowerCaseTypeName = No
-  }
-  KPointsAndWeights = {
-0.0000000000000 0.0000000000000 0.0000000000000 1.00000000000000
-  }
-  PolynomialRepulsive = {}
-  OldRepulsiveSum = No
-  OrbitalResolvedSCC = No
-  OldSKInterpolation = No
-  NoErep = No
-  Dispersion = {}
-  ThirdOrder = No
-  ThirdOrderFull = No
-}
-Options = {
-  CalculateForces = Yes
-  WriteDetailedOut = No
-  WriteBandOut = No
-  RandomSeed = 12345
-  MullikenAnalysis = No
-  WriteEigenvectors = No
-  WriteAutotestTag = No
-  WriteDetailedXML = No
-  WriteResultsTag = No
-  AtomResolvedEnergies = No
-  WriteHS = No
-  WriteRealHS = No
-  MinimiseMemoryUsage = No
-  ShowFoldedCoords = No
-}
-ParserOptions = {
-  ParserVersion = 3
-  WriteHSDInput = Yes
-  WriteXMLInput = No
-  StopAfterParsing = No
-  IgnoreUnprocessedNodes = No
-}
-Analysis = {
-  ProjectStates = {}
-}
diff --git a/examples/COUPLE/fortran_dftb/in.simple b/examples/COUPLE/fortran_dftb/in.simple
deleted file mode 100644
index 894a490cf8..0000000000
--- a/examples/COUPLE/fortran_dftb/in.simple
+++ /dev/null
@@ -1,16 +0,0 @@
-units real
-atom_style	charge
-atom_modify map array
-atom_modify sort 0 0.0
-read_data data.diamond
-neighbor        1.0 bin
-neigh_modify    delay 0 every 5 check no
-fix 1 all nve
-fix 2 all external pf/callback 1 1
-
-fix_modify 2 energy yes 
-thermo_style custom step temp etotal ke pe lx ly lz pxx pyy pzz press 
-
-thermo          1
-timestep        0.5
-
diff --git a/examples/COUPLE/fortran_dftb/log.simple b/examples/COUPLE/fortran_dftb/log.simple
deleted file mode 100644
index 3496e94ebe..0000000000
--- a/examples/COUPLE/fortran_dftb/log.simple
+++ /dev/null
@@ -1,71 +0,0 @@
-LAMMPS (6 Jul 2017)
-units real
-atom_style	charge
-atom_modify map array
-atom_modify sort 0 0.0
-read_data data.diamond
-  triclinic box = (0 0 0) to (7.134 7.134 7.134) with tilt (0 0 0)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  64 atoms
-  reading velocities ...
-  64 velocities
-neighbor        1.0 bin
-neigh_modify    delay 0 every 5 check no
-fix 1 all nve
-fix 2 all external pf/callback 1 1
-
-fix_modify 2 energy yes
-thermo_style custom step temp etotal ke pe lx ly lz pxx pyy pzz press
-
-thermo          1
-timestep        0.5
-
-run 10
-Neighbor list info ...
-  update every 5 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 0
-  ghost atom cutoff = 0
-  binsize = 7.134, bins = 1 1 1
-  0 neighbor lists, perpetual/occasional/extra = 0 0 0
-Per MPI rank memory allocation (min/avg/max) = 2.3 | 2.3 | 2.3 Mbytes
-Step Temp TotEng KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Press 
-       0    298.24835   -69593.587    56.008365   -69649.595        7.134        7.134        7.134    -19980.19   -21024.038   -21097.458   -20700.562 
-       1    295.24358   -69593.585    55.444098   -69649.029        7.134        7.134        7.134   -19778.833   -20799.657   -20854.156   -20477.549 
-       2    286.37211    -69593.58    53.778115   -69647.358        7.134        7.134        7.134    -19227.52    -20177.28    -20176.12   -19860.306 
-       3      272.062   -69593.572    51.090804   -69644.663        7.134        7.134        7.134   -18360.869   -19189.684   -19100.021   -18883.525 
-       4    253.01834   -69593.561    47.514575   -69641.075        7.134        7.134        7.134   -17198.143    -17855.03   -17652.036   -17568.403 
-       5    230.19242   -69593.547    43.228073   -69636.775        7.134        7.134        7.134   -15750.247   -16183.764   -15854.145   -15929.386 
-       6    204.71787   -69593.533     38.44418   -69631.977        7.134        7.134        7.134   -14083.498   -14247.434   -13789.835   -14040.256 
-       7    177.82397   -69593.518    33.393748   -69626.911        7.134        7.134        7.134   -12340.963   -12202.878   -11623.171   -12055.671 
-       8    150.76736   -69593.503    28.312758   -69621.816        7.134        7.134        7.134   -10637.824   -10180.827   -9495.0496   -10104.567 
-       9     124.7737    -69593.49    23.431383   -69616.921        7.134        7.134        7.134   -9113.3842   -8339.0492   -7572.8076    -8341.747 
-      10    100.98183   -69593.478    18.963481   -69612.442        7.134        7.134        7.134   -7833.9349   -6756.9749   -5945.8968   -6845.6022 
-Loop time of 2.20497 on 1 procs for 10 steps with 64 atoms
-
-Performance: 0.196 ns/day, 122.499 hours/ns, 4.535 timesteps/s
-0.2% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 1.4305e-06 | 1.4305e-06 | 1.4305e-06 |   0.0 |  0.00
-Comm    | 4.22e-05   | 4.22e-05   | 4.22e-05   |   0.0 |  0.00
-Output  | 0.00067687 | 0.00067687 | 0.00067687 |   0.0 |  0.03
-Modify  | 2.2042     | 2.2042     | 2.2042     |   0.0 | 99.96
-Other   |            | 6.533e-05  |            |       |  0.00
-
-Nlocal:    64 ave 64 max 64 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 0
-Ave neighs/atom = 0
-Neighbor list builds = 2
-Dangerous builds not checked
-Total wall time: 0:00:02
diff --git a/examples/COUPLE/fortran_dftb/makefile b/examples/COUPLE/fortran_dftb/makefile
deleted file mode 100644
index 225bd0025a..0000000000
--- a/examples/COUPLE/fortran_dftb/makefile
+++ /dev/null
@@ -1,45 +0,0 @@
-SHELL = /bin/sh
-
-# Path to LAMMPS extraction directory
-LAMMPS_ROOT = ../../..
-LAMMPS_SRC = $(LAMMPS_ROOT)/src
-
-# Uncomment the line below if using the MPI stubs library
-MPI_STUBS = #-I$(LAMMPS_SRC)/STUBS
-
-FC = mpif90 # replace with your Fortran compiler
-CXX = mpicc # replace with your C++ compiler
-
-# Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
-FFLAGS = -O2 -fPIC 
-CXXFLAGS = -O2 -fPIC
-CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
-
-all : liblammps_fortran.a liblammps_fortran.so simpleF.x
-
-liblammps_fortran.so : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
-	$(FC) $(FFLAGS) -shared -o $@ $^
-
-simpleF.x: simple.o LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
-	$(FC) $(FFLAGS) simple.o -o simpleF.x liblammps_fortran.a $(LAMMPS_SRC)/liblammps_mvapich.a -lstdc++ /usr/lib64/libfftw3.a 
-
-liblammps_fortran.a : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
-	$(AR) rs $@ $^
-
-LAMMPS.o lammps.mod : LAMMPS.F90
-	$(FC) $(CPPFLAGS) $(FFLAGS) -c $<
-
-simple.o : simple.f90
-	$(FC) $(FFLAGS) -c $<
-
-LAMMPS-wrapper.o : LAMMPS-wrapper.cpp LAMMPS-wrapper.h
-	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -I$(LAMMPS_SRC) $(MPI_STUBS)
-
-LAMMPS-wrapper2.o : LAMMPS-wrapper2.cpp LAMMPS-wrapper2.h
-	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -I$(LAMMPS_SRC) $(MPI_STUBS)
-
-clean :
-	$(RM) *.o *.mod liblammps_fortran.a liblammps_fortran.so
-
-dist :
-	tar -czvf fortran-interface-callback.tar.gz LAMMPS-wrapper.h LAMMPS-wrapper.cpp LAMMPS-wrapper2.h LAMMPS-wrapper2.cpp LAMMPS.F90 makefile README simple.f90
diff --git a/examples/COUPLE/fortran_dftb/simple.f90 b/examples/COUPLE/fortran_dftb/simple.f90
deleted file mode 100644
index 4604b4e4a9..0000000000
--- a/examples/COUPLE/fortran_dftb/simple.f90
+++ /dev/null
@@ -1,110 +0,0 @@
-   module callback
-     implicit none
-     contains
-       subroutine fortran_callback(lmp, timestep, nlocal, ids, c_pos, c_fext) & 
-     & bind(C, name='f_callback')
-       use, intrinsic :: ISO_C_binding
-       use LAMMPS
-       implicit none
-       type (C_ptr), value :: lmp
-       integer(C_int64_t), intent(in), value :: timestep
-       integer(C_int), intent(in), value :: nlocal
-       real (C_double), dimension(:,:), pointer :: x
-       type(c_ptr) :: c_pos, c_fext, c_ids
-       double precision, pointer :: fext(:,:), pos(:,:)
-       integer, intent(in) :: ids(nlocal)
-       real(C_double) :: virial(6)
-       real (C_double) :: etot
-       real(C_double), pointer :: ts_lmp
-       double precision :: stress(3,3), ts_dftb
-       integer :: natom , i
-       real (C_double), parameter :: econv = 627.4947284155114 ! converts from Ha to
-       double precision, parameter :: fconv = 1185.793095983065 ! converts from Ha/bohr to
-       double precision, parameter :: autoatm = 2.9037166638E8
-       double precision lx, ly, lz
-       real (C_double), pointer :: boxxlo, boxxhi
-       real (C_double), pointer :: boxylo, boxyhi
-       real (C_double), pointer :: boxzlo, boxzhi
-       double precision, parameter :: nktv2p = 68568.4149999999935972
-       double precision :: volume
-       type (C_ptr) :: Cptr
-       type (C_ptr), pointer, dimension(:) :: Catom
-
-       call c_f_pointer(c_pos, pos, [3,nlocal])
-       call c_f_pointer(c_fext, fext, [3,nlocal])
-       call lammps_extract_global(boxxlo, lmp, 'boxxlo')
-       call lammps_extract_global(boxxhi, lmp, 'boxxhi')
-       call lammps_extract_global(boxylo, lmp, 'boxylo')
-       call lammps_extract_global(boxyhi, lmp, 'boxyhi')
-       call lammps_extract_global(boxzlo, lmp, 'boxzlo')
-       call lammps_extract_global(boxzhi, lmp, 'boxzhi')
-       lx = boxxhi - boxxlo
-       ly = boxyhi - boxylo
-       lz = boxzhi - boxzlo
-       volume = lx*ly*lz
-       open (unit = 10, status = 'replace', action = 'write', file='lammps.gen')
-       write(10,*)nlocal,"S"
-       write(10,*) "C"
-       do i = 1, nlocal
-         write(10,'(2I,3F15.6)')i,1,pos(:,ids(i))
-       enddo
-       write(10,*)"0.0 0.0 0.0"
-       write(10,*)lx,0,0
-       write(10,*)0,ly,0
-       write(10,*)0,0,lz
-       close(10)
-       call system("./dftb+ > dftb.out")
-       open (unit = 10, status = 'old', file = 'results.out')
-       read(10,*)etot
-       read(10,*)ts_dftb
-       do i = 1, 3
-         read(10,*)stress(i,:)
-       enddo
-       stress (:,:) = stress(:,:)*autoatm
-       virial(1) = stress(1,1)/(nktv2p/volume)
-       virial(2) = stress(2,2)/(nktv2p/volume)
-       virial(3) = stress(3,3)/(nktv2p/volume)
-       virial(4) = stress(1,2)/(nktv2p/volume)
-       virial(5) = stress(1,3)/(nktv2p/volume)
-       virial(6) = stress(2,3)/(nktv2p/volume)
-       etot = etot*econv
-       call lammps_set_external_vector(lmp,1,ts_dftb*econv)
-       do i = 1, nlocal
-         read(10,*)fext(:,ids(i))
-         fext(:,ids(i)) = fext(:,ids(i))*fconv
-       enddo
-       close(10)
-       call lammps_set_user_energy (lmp, etot)
-       call lammps_set_user_virial (lmp, virial)
-
-       end  subroutine
-    end module callback
-
-
-program simple_fortran_callback
-
-   use MPI
-   use LAMMPS
-   use callback
-   use, intrinsic :: ISO_C_binding, only : C_double, C_ptr, C_int, C_FUNPTR
-   implicit none
-   type (C_ptr) :: lmp
-   integer :: error, narg, me, nprocs
-
-   call MPI_Init (error)
-   call MPI_Comm_rank (MPI_COMM_WORLD, me, error)
-   call MPI_Comm_size (MPI_COMM_WORLD, nprocs, error)
-
-   call lammps_open_no_mpi ('lmp -log log.simple', lmp)
-   call lammps_file (lmp, 'in.simple')
-   call lammps_set_callback(lmp)
-   call lammps_set_external_vector_length(lmp,2)
-
-   call lammps_command (lmp, 'run 10')
-   call lammps_close (lmp)
-   call MPI_Finalize (error)
-
-
-end program simple_fortran_callback
-
-

From e2e9170dfa8ddcd9bce8f3376619b8993537c46c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 18:52:57 -0400
Subject: [PATCH 293/396] protect a couple more fixes from segfaults from
 errors in derived classes

---
 src/RIGID/fix_rigid.cpp | 2 +-
 src/fix_langevin.cpp    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index df49d84439..44427d2914 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -610,7 +610,7 @@ FixRigid::~FixRigid()
 {
   // unregister callbacks to this fix from Atom class
 
-  atom->delete_callback(id,Atom::GROW);
+  if (modify->get_fix_by_id(id)) atom->delete_callback(id,Atom::GROW);
 
   delete random;
   delete[] inpfile;
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index 0e083ce012..35bffb24fa 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -203,7 +203,7 @@ FixLangevin::~FixLangevin()
   if (gjfflag) {
     memory->destroy(franprev);
     memory->destroy(lv);
-    atom->delete_callback(id, Atom::GROW);
+    if (modify->get_fix_by_id(id)) atom->delete_callback(id, Atom::GROW);
   }
 }
 

From 70823cac50a1bfecce5ed484adc6c7010bba8056 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 17 Jun 2023 23:30:36 -0400
Subject: [PATCH 294/396] remove dead code

---
 python/lammps/pylammps.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py
index bdbed3e971..c693b7d565 100644
--- a/python/lammps/pylammps.py
+++ b/python/lammps/pylammps.py
@@ -761,8 +761,6 @@ class PyLammps(object):
     for line in output:
       if line.startswith("Atom map"):
         system['atom_map'] = self._get_pair(line)[1]
-      elif line.startswith("Atoms"):
-        parts = self._split_values(line)
       elif line.startswith("Boundaries"):
         system['boundaries'] = self._get_pair(line)[1]
       elif line.startswith("Molecule type"):

From 5196e4422be2059a68081c1197729fe0759660d2 Mon Sep 17 00:00:00 2001
From: Shern Tee <shernren@gmail.com>
Date: Sun, 18 Jun 2023 17:51:15 +1000
Subject: [PATCH 295/396] debug fix_modify press for press/berendsen

---
 src/fix_press_berendsen.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp
index da49b3dbdb..e27a4560f0 100644
--- a/src/fix_press_berendsen.cpp
+++ b/src/fix_press_berendsen.cpp
@@ -491,7 +491,7 @@ int FixPressBerendsen::modify_param(int narg, char **arg)
     id_press = utils::strdup(arg[1]);
 
     pressure = modify->get_compute_by_id(arg[1]);
-    if (pressure) error->all(FLERR,"Could not find fix_modify pressure compute ID: {}", arg[1]);
+    if (!pressure) error->all(FLERR,"Could not find fix_modify pressure compute ID: {}", arg[1]);
     if (pressure->pressflag == 0)
       error->all(FLERR,"Fix_modify pressure compute {} does not compute pressure", arg[1]);
     return 2;

From 2cea819e7fe05e1ee97e152a29eecd0701a20f5e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 18 Jun 2023 07:24:42 -0400
Subject: [PATCH 296/396] cosmetic

---
 potentials/BNC.tersoff | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/potentials/BNC.tersoff b/potentials/BNC.tersoff
index 046566dd99..a072aa05b3 100644
--- a/potentials/BNC.tersoff
+++ b/potentials/BNC.tersoff
@@ -1,4 +1,4 @@
-# DATE: 2013-03-21 UNITS: metal CONTRIBUTOR: Cem Sevik CITATION: Kinaci, Haskins, Sevik and Cagin,  Phys Rev B, 86, 115410 (2012) 
+# DATE: 2013-03-21 UNITS: metal CONTRIBUTOR: Cem Sevik CITATION: Kinaci, Haskins, Sevik and Cagin,  Phys Rev B, 86, 115410 (2012)
 # Tersoff parameters for B, C, and BN-C hybrid based graphene like nano structures
 # multiple entries can be added to this file, LAMMPS reads the ones it needs
 
@@ -7,11 +7,11 @@
 #   other quantities are unitless
 
 # Cem Sevik (csevik at anadolu.edu.tr) takes full blame for this
-# file.  It specifies B-N, B-C, and N-C interaction parameters 
-# generated and published by the reseacrh group of Prof. Tahir Cagin.
+# file.  It specifies B-N, B-C, and N-C interaction parameters
+# generated and published by the research group of Prof. Tahir Cagin.
 
 # 1. Physical Review B 84, 085409 2011
-#    Characterization of thermal transport in low-dimensional boron nitride nanostructures, 
+#    Characterization of thermal transport in low-dimensional boron nitride nanostructures,
 #
 
 # 2. Physical Review B 86, 075403 2012
@@ -22,14 +22,14 @@
 #    Thermal conductivity of BN-C nanostructures
 #
 
-# The file also specifies C-C, interaction parameters 
+# The file also specifies C-C, interaction parameters
 # generated and published by the research group of Dr. D. A. Broido
 # Physical Review B 81, 205441 2010
-# Optimized Tersoff and Brenner empirical potential parameters for 
+# Optimized Tersoff and Brenner empirical potential parameters for
 # lattice dynamics and phonon thermal transport in carbon nanotubes and graphene
 
 # Users in referring the full parameters can cite the full parameter paper (3) as:
-#      A. Kinaci, J. B. Haskins, C. Sevik, T. Cagin,  Physical Review B 86, 115410 (2012) 
+#      A. Kinaci, J. B. Haskins, C. Sevik, T. Cagin,  Physical Review B 86, 115410 (2012)
 #      Thermal conductivity of BN-C nanostructures
 #
 
@@ -38,11 +38,11 @@
 #   m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
 
 N      B       B         3.0 1.0 0.0 25000    4.3484 -0.89000 0.72751   1.25724e-7      2.199        340.00          1.95    0.05    3.568       1380.0
-N      B       N         3.0 1.0 0.0 25000    4.3484 -0.89000 0.72751   1.25724e-7      2.199        340.00          1.95    0.05    3.568       1380.0    
+N      B       N         3.0 1.0 0.0 25000    4.3484 -0.89000 0.72751   1.25724e-7      2.199        340.00          1.95    0.05    3.568       1380.0
 N      B       C         3.0 1.0 0.0 25000    4.3484 -0.89000 0.72751   1.25724e-7      2.199        340.00          1.95    0.05    3.568       1380.0
 
 B      N       B         3.0 1.0 0.0 25000    4.3484 -0.89000 0.72751   1.25724e-7      2.199        340.00          1.95    0.05    3.568       1380.0
-B      N       N         3.0 1.0 0.0 25000    4.3484 -0.89000 0.72751   1.25724e-7      2.199        340.00          1.95    0.05    3.568       1380.0    
+B      N       N         3.0 1.0 0.0 25000    4.3484 -0.89000 0.72751   1.25724e-7      2.199        340.00          1.95    0.05    3.568       1380.0
 B      N       C         3.0 1.0 0.0 25000    4.3484 -0.89000 0.72751   1.25724e-7      2.199        340.00          1.95    0.05    3.568       1380.0
 
 N      N       B         3.0 1.0 0.0 17.7959  5.9484  0.00000 0.6184432 0.019251        2.6272721    138.77866       2.0     0.1     2.8293093    128.86866

From 21fb50f37b264c7ec33cb34be97b76fbd0169578 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 18 Jun 2023 07:40:04 -0400
Subject: [PATCH 297/396] correct logic bug

---
 src/compute_chunk_spread_atom.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp
index 933cf0af0c..53b8517c22 100644
--- a/src/compute_chunk_spread_atom.cpp
+++ b/src/compute_chunk_spread_atom.cpp
@@ -106,7 +106,7 @@ ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) :
 
     } else if (val.which == ArgInfo::FIX) {
       auto ifix = modify->get_fix_by_id(val.id);
-      if (ifix)
+      if (!ifix)
         error->all(FLERR,"Fix ID {} for compute chunk/spread/atom does not exist", val.id);
       if (val.argindex == 0) {
         if (!ifix->vector_flag)

From 6ccf5f107c3767b0f1e42b4ced7cee141aaebff5 Mon Sep 17 00:00:00 2001
From: John Lucas <jklucas25@gmail.com>
Date: Sun, 18 Jun 2023 20:39:18 -0500
Subject: [PATCH 298/396] fix a bug in fix pair

---
 src/fix_pair.cpp | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/fix_pair.cpp b/src/fix_pair.cpp
index 81e62ba966..66212684a8 100644
--- a/src/fix_pair.cpp
+++ b/src/fix_pair.cpp
@@ -283,11 +283,14 @@ void FixPair::post_force(int /*vflag*/)
 
     } else {
       double **parray = (double **) pvoid;
-      for (int i = 0; i < nlocal; i++)
+      int icoltmp = icol;
+      for (int i = 0; i < nlocal; i++) {
+        icol = icoltmp;
         for (int m = 0; m < columns; m++) {
           array[i][icol] = parray[i][m];
           icol++;
         }
+      }
     }
   }
 

From 542aa203dad3b18602b8b4ff58a1292ba4bb7f71 Mon Sep 17 00:00:00 2001
From: John Lucas <jklucas25@gmail.com>
Date: Sun, 18 Jun 2023 20:42:45 -0500
Subject: [PATCH 299/396] correct typo in fix pair documentation

---
 doc/src/fix_pair.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/fix_pair.rst b/doc/src/fix_pair.rst
index 44c91f18ee..07e934d1c0 100644
--- a/doc/src/fix_pair.rst
+++ b/doc/src/fix_pair.rst
@@ -85,7 +85,7 @@ columns 4-6 will store the "uinp" values.
 .. code-block:: LAMMPS
 
    pair_style amoeba
-   fix ex all pair amoeba 10 uind 0 uinp 0
+   fix ex all pair 10 amoeba uind 0 uinp 0
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""

From 838be24af426e9769adde43ce7fdac1684b71bbe Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Mon, 19 Jun 2023 10:15:06 -0600
Subject: [PATCH 300/396] Fixing argument parsing increment

---
 src/BPM/bond_bpm.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp
index da189ccaf5..d965a19067 100644
--- a/src/BPM/bond_bpm.cpp
+++ b/src/BPM/bond_bpm.cpp
@@ -189,11 +189,11 @@ void BondBPM::settings(int narg, char **arg)
     } else if (strcmp(arg[iarg], "overlay/pair") == 0) {
       if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for overlay/pair");
       overlay_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
-      iarg++;
+      iarg += 2;
     } else if (strcmp(arg[iarg], "break") == 0) {
       if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for break");
       break_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
-      iarg++;
+      iarg += 2;
     } else {
       leftover_iarg.push_back(iarg);
       iarg++;

From af3d97102383772d3f96743d8afec8e93e54dfa4 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 19 Jun 2023 15:28:27 -0400
Subject: [PATCH 301/396] allow longer argument strings to avoid failues with
 unit tests

---
 examples/COUPLE/simple/simple.f90 | 2 +-
 fortran/lammps.f90                | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/COUPLE/simple/simple.f90 b/examples/COUPLE/simple/simple.f90
index 3aafbee01b..d9505fff4d 100644
--- a/examples/COUPLE/simple/simple.f90
+++ b/examples/COUPLE/simple/simple.f90
@@ -30,7 +30,7 @@ PROGRAM f_driver
   REAL (kind=8), ALLOCATABLE :: x(:)
   REAL (kind=8), PARAMETER   :: epsilon=0.1
 
-  CHARACTER (len=64)   :: arg
+  CHARACTER (len=1024) :: arg
   CHARACTER (len=1024) :: line
 
   ! setup MPI and various communicators
diff --git a/fortran/lammps.f90 b/fortran/lammps.f90
index ba3997ac8e..28e40bca44 100644
--- a/fortran/lammps.f90
+++ b/fortran/lammps.f90
@@ -20,7 +20,7 @@
 !   University of Missouri, 2012-2020
 !
 ! Contributing authors:
-!  - Axel Kohlmeyer <akohlmey@gmail.com>, Temple University, 2020-2022
+!  - Axel Kohlmeyer <akohlmey@gmail.com>, Temple University, 2020-2023
 !  - Karl D. Hammond <hammondkd@missouri.edu>, University of Missouri, 2022
 !
 ! The Fortran module tries to follow the API of the C library interface

From 6791651b62b047da4d69889fc8343b47f6120f7e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 20 Jun 2023 09:41:55 -0400
Subject: [PATCH 302/396] add else branch to make coverity scan happy

---
 src/REPLICA/fix_pimd_langevin.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp
index 75280fd3d5..7ba502d2e6 100644
--- a/src/REPLICA/fix_pimd_langevin.cpp
+++ b/src/REPLICA/fix_pimd_langevin.cpp
@@ -906,7 +906,10 @@ void FixPIMDLangevin::langevin_init()
       Lan_c[i] = cos(_omega_np_dt_half);
       Lan_s[i] = sin(_omega_np_dt_half);
     }
+  } else {
+    error->universe_all(FLERR, "Unknown fmmode setting; only physical and normal are supported!");
   }
+
   if (tau > 0)
     gamma = 1.0 / tau;
   else

From fcc3c99e2bf402abf683e9d4518d5732f5917348 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 20 Jun 2023 13:31:16 -0400
Subject: [PATCH 303/396] avoid segfaults if a dump is created and followed by
 run pre no

---
 src/MPIIO/dump_atom_mpiio.cpp   |  2 ++
 src/MPIIO/dump_custom_mpiio.cpp |  2 ++
 src/dump.cpp                    | 39 ++++++++++-----------------------
 src/dump_atom.cpp               |  9 ++++++--
 src/dump_custom.cpp             | 18 ++++++++-------
 src/dump_grid.cpp               |  2 ++
 src/dump_xyz.cpp                |  7 +++---
 7 files changed, 39 insertions(+), 40 deletions(-)

diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp
index 4e0fd47a29..844d1a46e4 100644
--- a/src/MPIIO/dump_atom_mpiio.cpp
+++ b/src/MPIIO/dump_atom_mpiio.cpp
@@ -283,6 +283,8 @@ void DumpAtomMPIIO::init_style()
 
 void DumpAtomMPIIO::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   (this->*header_choice)(ndump);
 }
 
diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp
index 32e09675a8..80adefa325 100644
--- a/src/MPIIO/dump_custom_mpiio.cpp
+++ b/src/MPIIO/dump_custom_mpiio.cpp
@@ -309,6 +309,8 @@ void DumpCustomMPIIO::init_style()
 
 void DumpCustomMPIIO::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   (this->*header_choice)(ndump);
 }
 
diff --git a/src/dump.cpp b/src/dump.cpp
index 372773bbb2..c1a246ada2 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -1,4 +1,4 @@
-// clang-format off
+  // clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -41,14 +41,20 @@ Dump *Dump::dumpptr;
 #define BIG 1.0e20
 #define EPSILON 1.0e-6
 
-enum{ASCEND,DESCEND};
+enum { ASCEND, DESCEND };
 
 /* ---------------------------------------------------------------------- */
 
-Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
+Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) :
+    Pointers(lmp), multiname(nullptr), refresh(nullptr), skipvar(nullptr), format(nullptr),
+    format_default(nullptr), format_line_user(nullptr), format_float_user(nullptr),
+    format_int_user(nullptr), format_bigint_user(nullptr), format_column_user(nullptr), fp(nullptr),
+    nameslist(nullptr), buf(nullptr), sbuf(nullptr), ids(nullptr), bufsort(nullptr),
+    idsort(nullptr), index(nullptr), proclist(nullptr), xpbc(nullptr), vpbc(nullptr),
+    imagepbc(nullptr), irregular(nullptr)
 {
-  MPI_Comm_rank(world,&me);
-  MPI_Comm_size(world,&nprocs);
+  MPI_Comm_rank(world, &me);
+  MPI_Comm_size(world, &nprocs);
 
   id = utils::strdup(arg[0]);
 
@@ -64,17 +70,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   first_flag = 0;
   flush_flag = 1;
 
-  format = nullptr;
-  format_default = nullptr;
-
-  format_line_user = nullptr;
-  format_float_user = nullptr;
-  format_int_user = nullptr;
-  format_bigint_user = nullptr;
-  format_column_user = nullptr;
-
   refreshflag = 0;
-  refresh = nullptr;
 
   clearstep = 0;
   sort_flag = 0;
@@ -92,25 +88,15 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   has_id = 1;
 
   skipflag = 0;
-  skipvar = nullptr;
 
   maxfiles = -1;
   numfiles = 0;
   fileidx = 0;
-  nameslist = nullptr;
 
   maxbuf = maxids = maxsort = maxproc = 0;
-  buf = bufsort = nullptr;
-  ids = idsort = nullptr;
-  index = proclist = nullptr;
-  irregular = nullptr;
-
   maxsbuf = 0;
-  sbuf = nullptr;
 
   maxpbc = -1;
-  xpbc = vpbc = nullptr;
-  imagepbc = nullptr;
 
   // parse filename for special syntax
   // if contains '%', write one file per proc and replace % with proc-ID
@@ -120,18 +106,17 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   //   else if ends in .gz or other known extensions -> compressed text file
   //   else ASCII text file
 
-  fp = nullptr;
   singlefile_opened = 0;
   compressed = 0;
   binary = 0;
   multifile = 0;
+  size_one = 0;
 
   multiproc = 0;
   nclusterprocs = nprocs;
   filewriter = 0;
   if (me == 0) filewriter = 1;
   fileproc = 0;
-  multiname = nullptr;
 
   char *ptr;
   if ((ptr = strchr(filename,'%'))) {
diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index 1d3862ab26..656eef8c9d 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -29,8 +28,10 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
+DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) :
+  Dump(lmp, narg, arg), header_choice(nullptr), pack_choice(nullptr)
 {
+  // clang-format off
   if (narg != 5) error->all(FLERR,"Illegal dump atom command");
 
   scale_flag = 1;
@@ -146,6 +147,8 @@ int DumpAtom::modify_param(int narg, char **arg)
 
 void DumpAtom::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   if (multiproc) (this->*header_choice)(ndump);
   else if (me == 0) (this->*header_choice)(ndump);
 }
@@ -154,6 +157,8 @@ void DumpAtom::write_header(bigint ndump)
 
 void DumpAtom::pack(tagint *ids)
 {
+  if (!pack_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   (this->*pack_choice)(ids);
 }
 
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 33cfba2cef..6a10641434 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -53,13 +52,14 @@ enum{LT,LE,GT,GE,EQ,NEQ,XOR};
 /* ---------------------------------------------------------------------- */
 
 DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
-  Dump(lmp, narg, arg), idregion(nullptr), thresh_array(nullptr), thresh_op(nullptr),
-  thresh_value(nullptr), thresh_last(nullptr), thresh_fix(nullptr), thresh_fixID(nullptr),
-  thresh_first(nullptr), earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr),
-  columns_default(nullptr), choose(nullptr), dchoose(nullptr), clist(nullptr),
-  field2index(nullptr), argindex(nullptr), id_compute(nullptr), compute(nullptr), id_fix(nullptr),
-  fix(nullptr), id_variable(nullptr), variable(nullptr), vbuf(nullptr), id_custom(nullptr),
-  custom(nullptr), custom_flag(nullptr), typenames(nullptr), pack_choice(nullptr)
+    Dump(lmp, narg, arg), idregion(nullptr), thresh_array(nullptr), thresh_op(nullptr),
+    thresh_value(nullptr), thresh_last(nullptr), thresh_fix(nullptr), thresh_fixID(nullptr),
+    thresh_first(nullptr), earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr),
+    columns_default(nullptr), choose(nullptr), dchoose(nullptr), clist(nullptr),
+    field2index(nullptr), argindex(nullptr), id_compute(nullptr), compute(nullptr), id_fix(nullptr),
+    fix(nullptr), id_variable(nullptr), variable(nullptr), vbuf(nullptr), id_custom(nullptr),
+    custom(nullptr), custom_flag(nullptr), typenames(nullptr), header_choice(nullptr),
+    pack_choice(nullptr)
 {
   if (narg == 5) error->all(FLERR,"No dump {} arguments specified", style);
 
@@ -352,6 +352,8 @@ void DumpCustom::init_style()
 
 void DumpCustom::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   if (multiproc) (this->*header_choice)(ndump);
   else if (me == 0) (this->*header_choice)(ndump);
 }
diff --git a/src/dump_grid.cpp b/src/dump_grid.cpp
index 056cac1095..39d80ade11 100644
--- a/src/dump_grid.cpp
+++ b/src/dump_grid.cpp
@@ -311,6 +311,8 @@ void DumpGrid::init_style()
 
 void DumpGrid::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   if (multiproc) (this->*header_choice)(ndump);
   else if (me == 0) (this->*header_choice)(ndump);
 }
diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp
index 83c4d180d6..241ec1c059 100644
--- a/src/dump_xyz.cpp
+++ b/src/dump_xyz.cpp
@@ -130,6 +130,8 @@ int DumpXYZ::modify_param(int narg, char **arg)
 void DumpXYZ::write_header(bigint n)
 {
   if (me == 0) {
+    if (!fp) error->one(FLERR, "Must not use 'run pre no' after creating a new dump");
+
     auto header = fmt::format("{}\n Atoms. Timestep: {}", n, update->ntimestep);
     if (time_flag) header += fmt::format(" Time: {:.6f}", compute_time());
     header += "\n";
@@ -177,9 +179,8 @@ int DumpXYZ::convert_string(int n, double *mybuf)
       memory->grow(sbuf,maxsbuf,"dump:sbuf");
     }
 
-    offset += sprintf(&sbuf[offset],format,
-                      typenames[static_cast<int> (mybuf[m+1])],
-                      mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+    offset += sprintf(&sbuf[offset], format, typenames[static_cast<int> (mybuf[m+1])],
+                      mybuf[m+2], mybuf[m+3], mybuf[m+4]);
     m += size_one;
   }
 

From 6d6f57aeff1db9d1a75d55d0d5b2c642e811441b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 20 Jun 2023 16:17:11 -0400
Subject: [PATCH 304/396] cosmetic

---
 src/variable.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/variable.cpp b/src/variable.cpp
index 456359de2f..4d07a9e3c2 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -3658,7 +3658,6 @@ int Variable::math_function(char *word, char *contents, Tree **tree, Tree **tree
         print_var_error(FLERR,"Invalid math function in variable formula",ivar);
       double value;
       if (update->ntimestep < ivalue1) value = ivalue1;
-      //else if (update->ntimestep <= ivalue3) {
       else {
         value = ivalue1;
         double logsp = ivalue1;

From e4b50a610e9b740bb8c9d7e072cd183a4bd7cc12 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 20 Jun 2023 13:31:16 -0400
Subject: [PATCH 305/396] avoid segfaults if a dump is created and followed by
 run pre no

---
 src/MPIIO/dump_atom_mpiio.cpp   |  2 ++
 src/MPIIO/dump_custom_mpiio.cpp |  2 ++
 src/dump.cpp                    | 39 ++++++++++-----------------------
 src/dump_atom.cpp               |  9 ++++++--
 src/dump_custom.cpp             | 18 ++++++++-------
 src/dump_grid.cpp               |  2 ++
 src/dump_xyz.cpp                |  7 +++---
 7 files changed, 39 insertions(+), 40 deletions(-)

diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp
index 4e0fd47a29..844d1a46e4 100644
--- a/src/MPIIO/dump_atom_mpiio.cpp
+++ b/src/MPIIO/dump_atom_mpiio.cpp
@@ -283,6 +283,8 @@ void DumpAtomMPIIO::init_style()
 
 void DumpAtomMPIIO::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   (this->*header_choice)(ndump);
 }
 
diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp
index 32e09675a8..80adefa325 100644
--- a/src/MPIIO/dump_custom_mpiio.cpp
+++ b/src/MPIIO/dump_custom_mpiio.cpp
@@ -309,6 +309,8 @@ void DumpCustomMPIIO::init_style()
 
 void DumpCustomMPIIO::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   (this->*header_choice)(ndump);
 }
 
diff --git a/src/dump.cpp b/src/dump.cpp
index 372773bbb2..c1a246ada2 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -1,4 +1,4 @@
-// clang-format off
+  // clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -41,14 +41,20 @@ Dump *Dump::dumpptr;
 #define BIG 1.0e20
 #define EPSILON 1.0e-6
 
-enum{ASCEND,DESCEND};
+enum { ASCEND, DESCEND };
 
 /* ---------------------------------------------------------------------- */
 
-Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
+Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) :
+    Pointers(lmp), multiname(nullptr), refresh(nullptr), skipvar(nullptr), format(nullptr),
+    format_default(nullptr), format_line_user(nullptr), format_float_user(nullptr),
+    format_int_user(nullptr), format_bigint_user(nullptr), format_column_user(nullptr), fp(nullptr),
+    nameslist(nullptr), buf(nullptr), sbuf(nullptr), ids(nullptr), bufsort(nullptr),
+    idsort(nullptr), index(nullptr), proclist(nullptr), xpbc(nullptr), vpbc(nullptr),
+    imagepbc(nullptr), irregular(nullptr)
 {
-  MPI_Comm_rank(world,&me);
-  MPI_Comm_size(world,&nprocs);
+  MPI_Comm_rank(world, &me);
+  MPI_Comm_size(world, &nprocs);
 
   id = utils::strdup(arg[0]);
 
@@ -64,17 +70,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   first_flag = 0;
   flush_flag = 1;
 
-  format = nullptr;
-  format_default = nullptr;
-
-  format_line_user = nullptr;
-  format_float_user = nullptr;
-  format_int_user = nullptr;
-  format_bigint_user = nullptr;
-  format_column_user = nullptr;
-
   refreshflag = 0;
-  refresh = nullptr;
 
   clearstep = 0;
   sort_flag = 0;
@@ -92,25 +88,15 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   has_id = 1;
 
   skipflag = 0;
-  skipvar = nullptr;
 
   maxfiles = -1;
   numfiles = 0;
   fileidx = 0;
-  nameslist = nullptr;
 
   maxbuf = maxids = maxsort = maxproc = 0;
-  buf = bufsort = nullptr;
-  ids = idsort = nullptr;
-  index = proclist = nullptr;
-  irregular = nullptr;
-
   maxsbuf = 0;
-  sbuf = nullptr;
 
   maxpbc = -1;
-  xpbc = vpbc = nullptr;
-  imagepbc = nullptr;
 
   // parse filename for special syntax
   // if contains '%', write one file per proc and replace % with proc-ID
@@ -120,18 +106,17 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   //   else if ends in .gz or other known extensions -> compressed text file
   //   else ASCII text file
 
-  fp = nullptr;
   singlefile_opened = 0;
   compressed = 0;
   binary = 0;
   multifile = 0;
+  size_one = 0;
 
   multiproc = 0;
   nclusterprocs = nprocs;
   filewriter = 0;
   if (me == 0) filewriter = 1;
   fileproc = 0;
-  multiname = nullptr;
 
   char *ptr;
   if ((ptr = strchr(filename,'%'))) {
diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index 1d3862ab26..656eef8c9d 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -29,8 +28,10 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
+DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) :
+  Dump(lmp, narg, arg), header_choice(nullptr), pack_choice(nullptr)
 {
+  // clang-format off
   if (narg != 5) error->all(FLERR,"Illegal dump atom command");
 
   scale_flag = 1;
@@ -146,6 +147,8 @@ int DumpAtom::modify_param(int narg, char **arg)
 
 void DumpAtom::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   if (multiproc) (this->*header_choice)(ndump);
   else if (me == 0) (this->*header_choice)(ndump);
 }
@@ -154,6 +157,8 @@ void DumpAtom::write_header(bigint ndump)
 
 void DumpAtom::pack(tagint *ids)
 {
+  if (!pack_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   (this->*pack_choice)(ids);
 }
 
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 33cfba2cef..6a10641434 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -53,13 +52,14 @@ enum{LT,LE,GT,GE,EQ,NEQ,XOR};
 /* ---------------------------------------------------------------------- */
 
 DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
-  Dump(lmp, narg, arg), idregion(nullptr), thresh_array(nullptr), thresh_op(nullptr),
-  thresh_value(nullptr), thresh_last(nullptr), thresh_fix(nullptr), thresh_fixID(nullptr),
-  thresh_first(nullptr), earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr),
-  columns_default(nullptr), choose(nullptr), dchoose(nullptr), clist(nullptr),
-  field2index(nullptr), argindex(nullptr), id_compute(nullptr), compute(nullptr), id_fix(nullptr),
-  fix(nullptr), id_variable(nullptr), variable(nullptr), vbuf(nullptr), id_custom(nullptr),
-  custom(nullptr), custom_flag(nullptr), typenames(nullptr), pack_choice(nullptr)
+    Dump(lmp, narg, arg), idregion(nullptr), thresh_array(nullptr), thresh_op(nullptr),
+    thresh_value(nullptr), thresh_last(nullptr), thresh_fix(nullptr), thresh_fixID(nullptr),
+    thresh_first(nullptr), earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr),
+    columns_default(nullptr), choose(nullptr), dchoose(nullptr), clist(nullptr),
+    field2index(nullptr), argindex(nullptr), id_compute(nullptr), compute(nullptr), id_fix(nullptr),
+    fix(nullptr), id_variable(nullptr), variable(nullptr), vbuf(nullptr), id_custom(nullptr),
+    custom(nullptr), custom_flag(nullptr), typenames(nullptr), header_choice(nullptr),
+    pack_choice(nullptr)
 {
   if (narg == 5) error->all(FLERR,"No dump {} arguments specified", style);
 
@@ -352,6 +352,8 @@ void DumpCustom::init_style()
 
 void DumpCustom::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   if (multiproc) (this->*header_choice)(ndump);
   else if (me == 0) (this->*header_choice)(ndump);
 }
diff --git a/src/dump_grid.cpp b/src/dump_grid.cpp
index 056cac1095..39d80ade11 100644
--- a/src/dump_grid.cpp
+++ b/src/dump_grid.cpp
@@ -311,6 +311,8 @@ void DumpGrid::init_style()
 
 void DumpGrid::write_header(bigint ndump)
 {
+  if (!header_choice) error->all(FLERR, "Must not use 'run pre no' after creating a new dump");
+
   if (multiproc) (this->*header_choice)(ndump);
   else if (me == 0) (this->*header_choice)(ndump);
 }
diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp
index 83c4d180d6..241ec1c059 100644
--- a/src/dump_xyz.cpp
+++ b/src/dump_xyz.cpp
@@ -130,6 +130,8 @@ int DumpXYZ::modify_param(int narg, char **arg)
 void DumpXYZ::write_header(bigint n)
 {
   if (me == 0) {
+    if (!fp) error->one(FLERR, "Must not use 'run pre no' after creating a new dump");
+
     auto header = fmt::format("{}\n Atoms. Timestep: {}", n, update->ntimestep);
     if (time_flag) header += fmt::format(" Time: {:.6f}", compute_time());
     header += "\n";
@@ -177,9 +179,8 @@ int DumpXYZ::convert_string(int n, double *mybuf)
       memory->grow(sbuf,maxsbuf,"dump:sbuf");
     }
 
-    offset += sprintf(&sbuf[offset],format,
-                      typenames[static_cast<int> (mybuf[m+1])],
-                      mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+    offset += sprintf(&sbuf[offset], format, typenames[static_cast<int> (mybuf[m+1])],
+                      mybuf[m+2], mybuf[m+3], mybuf[m+4]);
     m += size_one;
   }
 

From e95b10f24aef2735da23330bf64c4fa390b0e55a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 21 Jun 2023 06:42:19 -0400
Subject: [PATCH 306/396] update VMD plugin headers to the latest version

---
 lib/molfile/molfile_plugin.h | 1 -
 lib/molfile/vmdplugin.h      | 6 +++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/molfile/molfile_plugin.h b/lib/molfile/molfile_plugin.h
index 491cd375bb..a417b82e96 100644
--- a/lib/molfile/molfile_plugin.h
+++ b/lib/molfile/molfile_plugin.h
@@ -987,4 +987,3 @@ typedef struct {
 } molfile_plugin_t;
 
 #endif
-
diff --git a/lib/molfile/vmdplugin.h b/lib/molfile/vmdplugin.h
index 7afc358e97..9336d3e24f 100644
--- a/lib/molfile/vmdplugin.h
+++ b/lib/molfile/vmdplugin.h
@@ -11,7 +11,7 @@
  *
  *      $RCSfile: vmdplugin.h,v $
  *      $Author: johns $       $Locker:  $             $State: Exp $
- *      $Revision: 1.34 $       $Date: 2018/05/02 03:12:56 $
+ *      $Revision: 1.35 $       $Date: 2020/10/16 07:50:56 $
  *
  ***************************************************************************/
 
@@ -58,8 +58,8 @@
 /*@}*/
 
 
-/** "WIN32" is defined on both WIN32 and WIN64 platforms... */
-#if (defined(WIN32))
+/** Detect compilations targeting Windows x86 and x64 platforms */
+#if (defined(WIN32) || defined(WIN64) || defined(_MSC_VER))
 #define WIN32_LEAN_AND_MEAN
 #include <windows.h>
 

From ffda6596da1f44a920daa57b8719290476c0a1b1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 22 Jun 2023 10:48:07 -0400
Subject: [PATCH 307/396] detect and flag short reads with missing lines in
 utils::read_lines_from_file()

---
 src/utils.cpp | 67 +++++++++++++++++++++++++++++----------------------
 1 file changed, 38 insertions(+), 29 deletions(-)

diff --git a/src/utils.cpp b/src/utils.cpp
index bc4eee7385..eee1d5dd46 100644
--- a/src/utils.cpp
+++ b/src/utils.cpp
@@ -272,6 +272,7 @@ int utils::read_lines_from_file(FILE *fp, int nlines, int nmax, char *buffer, in
 {
   char *ptr = buffer;
   *ptr = '\0';
+  int mylines = 0;
 
   if (me == 0) {
     if (fp) {
@@ -282,13 +283,15 @@ int utils::read_lines_from_file(FILE *fp, int nlines, int nmax, char *buffer, in
         ptr += strlen(ptr);
         // ensure buffer is null terminated. null char is start of next line.
         *ptr = '\0';
+        // count line
+        ++mylines;
       }
     }
   }
 
   int n = strlen(buffer);
   MPI_Bcast(&n, 1, MPI_INT, 0, comm);
-  if (n == 0) return 1;
+  if ((n == 0) || (nlines != mylines)) return 1;
   MPI_Bcast(buffer, n + 1, MPI_CHAR, 0, comm);
   return 0;
 }
@@ -879,8 +882,8 @@ char *utils::expand_type(const char *file, int line, const std::string &str, int
      caller decides what to do if arg is not a COMPUTE or FIX reference
 ------------------------------------------------------------------------- */
 
-int utils::check_grid_reference(char *errstr, char *ref, int nevery,
-                                char *&id, int &igrid, int &idata, int &index, LAMMPS *lmp)
+int utils::check_grid_reference(char *errstr, char *ref, int nevery, char *&id, int &igrid,
+                                int &idata, int &index, LAMMPS *lmp)
 {
   ArgInfo argi(ref, ArgInfo::COMPUTE | ArgInfo::FIX);
   index = argi.get_index1();
@@ -889,80 +892,85 @@ int utils::check_grid_reference(char *errstr, char *ref, int nevery,
   switch (argi.get_type()) {
 
     case ArgInfo::UNKNOWN: {
-      lmp->error->all(FLERR,"%s grid reference %s is invalid",errstr,ref);
+      lmp->error->all(FLERR, "%s grid reference %s is invalid", errstr, ref);
     } break;
 
-    // compute value = c_ID
+      // compute value = c_ID
 
     case ArgInfo::COMPUTE: {
 
       // split name = idcompute:gname:dname into 3 strings
 
-      auto words = parse_grid_id(FLERR,name,lmp->error);
+      auto words = parse_grid_id(FLERR, name, lmp->error);
       const auto &idcompute = words[0];
       const auto &gname = words[1];
       const auto &dname = words[2];
 
       auto icompute = lmp->modify->get_compute_by_id(idcompute);
-      if (!icompute) lmp->error->all(FLERR,"{} compute ID {} not found",errstr,idcompute);
+      if (!icompute) lmp->error->all(FLERR, "{} compute ID {} not found", errstr, idcompute);
       if (icompute->pergrid_flag == 0)
-        lmp->error->all(FLERR,"{} compute {} does not compute per-grid info",errstr,idcompute);
+        lmp->error->all(FLERR, "{} compute {} does not compute per-grid info", errstr, idcompute);
 
       int dim;
-      igrid = icompute->get_grid_by_name(gname,dim);
+      igrid = icompute->get_grid_by_name(gname, dim);
       if (igrid < 0)
-        lmp->error->all(FLERR,"{} compute {} does not recognize grid name {}",errstr,idcompute,gname);
+        lmp->error->all(FLERR, "{} compute {} does not recognize grid name {}", errstr, idcompute,
+                        gname);
 
       int ncol;
-      idata = icompute->get_griddata_by_name(igrid,dname,ncol);
+      idata = icompute->get_griddata_by_name(igrid, dname, ncol);
       if (idata < 0)
-        lmp->error->all(FLERR,"{} compute {} does not recognize data name {}",errstr,idcompute,dname);
+        lmp->error->all(FLERR, "{} compute {} does not recognize data name {}", errstr, idcompute,
+                        dname);
 
       if (argi.get_dim() == 0 && ncol)
-        lmp->error->all(FLERR,"{} compute {} data {} is not per-grid vector",errstr,idcompute,dname);
+        lmp->error->all(FLERR, "{} compute {} data {} is not per-grid vector", errstr, idcompute,
+                        dname);
       if (argi.get_dim() && ncol == 0)
-        lmp->error->all(FLERR,"{} compute {} data {} is not per-grid array",errstr,idcompute,dname);
+        lmp->error->all(FLERR, "{} compute {} data {} is not per-grid array", errstr, idcompute,
+                        dname);
       if (argi.get_dim() && argi.get_index1() > ncol)
-        lmp->error->all(FLERR,"{} compute {} array {} is accessed out-of-range",errstr,idcompute,dname);
+        lmp->error->all(FLERR, "{} compute {} array {} is accessed out-of-range", errstr, idcompute,
+                        dname);
 
       id = utils::strdup(idcompute);
       return ArgInfo::COMPUTE;
     } break;
 
-    // fix value = f_ID
+      // fix value = f_ID
 
     case ArgInfo::FIX: {
 
       // split name = idfix:gname:dname into 3 strings
 
-      auto words = parse_grid_id(FLERR,name,lmp->error);
+      auto words = parse_grid_id(FLERR, name, lmp->error);
       const auto &idfix = words[0];
       const auto &gname = words[1];
       const auto &dname = words[2];
 
       auto ifix = lmp->modify->get_fix_by_id(idfix);
-      if (!ifix) lmp->error->all(FLERR,"{} fix ID {} not found",errstr,idfix);
+      if (!ifix) lmp->error->all(FLERR, "{} fix ID {} not found", errstr, idfix);
       if (ifix->pergrid_flag == 0)
-        lmp->error->all(FLERR,"{} fix {} does not compute per-grid info",errstr,idfix);
+        lmp->error->all(FLERR, "{} fix {} does not compute per-grid info", errstr, idfix);
       if (nevery % ifix->pergrid_freq)
-        lmp->error->all(FLERR,"{} fix {} not computed at compatible time",errstr,idfix);
+        lmp->error->all(FLERR, "{} fix {} not computed at compatible time", errstr, idfix);
 
       int dim;
-      igrid = ifix->get_grid_by_name(gname,dim);
+      igrid = ifix->get_grid_by_name(gname, dim);
       if (igrid < 0)
-        lmp->error->all(FLERR,"{} fix {} does not recognize grid name {}",errstr,idfix,gname);
+        lmp->error->all(FLERR, "{} fix {} does not recognize grid name {}", errstr, idfix, gname);
 
       int ncol;
-      idata = ifix->get_griddata_by_name(igrid,dname,ncol);
+      idata = ifix->get_griddata_by_name(igrid, dname, ncol);
       if (idata < 0)
-        lmp->error->all(FLERR,"{} fix {} does not recognize data name {}",errstr,idfix,dname);
+        lmp->error->all(FLERR, "{} fix {} does not recognize data name {}", errstr, idfix, dname);
 
       if (argi.get_dim() == 0 && ncol)
-        lmp->error->all(FLERR,"{} fix {} data {} is not per-grid vector",errstr,idfix,dname);
+        lmp->error->all(FLERR, "{} fix {} data {} is not per-grid vector", errstr, idfix, dname);
       if (argi.get_dim() > 0 && ncol == 0)
-        lmp->error->all(FLERR,"{} fix {} data {} is not per-grid array",errstr,idfix,dname);
+        lmp->error->all(FLERR, "{} fix {} data {} is not per-grid array", errstr, idfix, dname);
       if (argi.get_dim() > 0 && argi.get_index1() > ncol)
-        lmp->error->all(FLERR,"{} fix {} array {} is accessed out-of-range",errstr,idfix,dname);
+        lmp->error->all(FLERR, "{} fix {} array {} is accessed out-of-range", errstr, idfix, dname);
 
       id = utils::strdup(idfix);
       return ArgInfo::FIX;
@@ -1360,8 +1368,9 @@ bool utils::is_double(const std::string &str)
 {
   if (str.empty()) return false;
 
-  return strmatch(str, "^[+-]?\\d+\\.?\\d*$") || strmatch(str, "^[+-]?\\d+\\.?\\d*[eE][+-]?\\d+$") ||
-      strmatch(str, "^[+-]?\\d*\\.?\\d+$") || strmatch(str, "^[+-]?\\d*\\.?\\d+[eE][+-]?\\d+$");
+  return strmatch(str, "^[+-]?\\d+\\.?\\d*$") ||
+      strmatch(str, "^[+-]?\\d+\\.?\\d*[eE][+-]?\\d+$") || strmatch(str, "^[+-]?\\d*\\.?\\d+$") ||
+      strmatch(str, "^[+-]?\\d*\\.?\\d+[eE][+-]?\\d+$");
 }
 
 /* ----------------------------------------------------------------------

From e9a06a065451d82bc82e7c7a6b1b00f97ae9632e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 22 Jun 2023 11:49:56 -0400
Subject: [PATCH 308/396] correct and reformat error messages for short reads

---
 src/read_data.cpp | 21 +++++----------------
 1 file changed, 5 insertions(+), 16 deletions(-)

diff --git a/src/read_data.cpp b/src/read_data.cpp
index 2fea75f7c0..e3087ae215 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -2021,9 +2021,7 @@ void ReadData::pairIJcoeffs()
   if (eof) error->all(FLERR, "Unexpected end of data file");
 
   if (tlabelflag && !lmap->is_complete(Atom::ATOM))
-    error->all(FLERR,
-               "Label map is incomplete: "
-               "all types must be assigned a unique type label");
+    error->all(FLERR,"Label map is incomplete: all types must be assigned a unique type label");
 
   char *original = buf;
   for (i = 0; i < ntypes; i++)
@@ -2032,10 +2030,7 @@ void ReadData::pairIJcoeffs()
       *next = '\0';
       parse_coeffs(buf, nullptr, 0, 2, toffset, tlabelflag, lmap->lmap2lmap.atom);
       if (ncoeffarg == 0)
-        error->all(FLERR,
-                   "Unexpected empty line in PairIJCoeffs section. "
-                   "Expected {} lines.",
-                   (ntypes - 1) * ntypes);
+        error->all(FLERR, "Unexpected empty line in PairIJCoeffs section. Expected {} lines.", nsq);
       force->pair->coeff(ncoeffarg, coeffarg);
       buf = next + 1;
     }
@@ -2055,9 +2050,7 @@ void ReadData::bondcoeffs()
   if (eof) error->all(FLERR, "Unexpected end of data file");
 
   if (blabelflag && !lmap->is_complete(Atom::BOND))
-    error->all(FLERR,
-               "Label map is incomplete: "
-               "all types must be assigned a unique type label");
+    error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label");
 
   char *original = buf;
   for (int i = 0; i < nbondtypes; i++) {
@@ -2086,9 +2079,7 @@ void ReadData::anglecoeffs(int which)
   if (eof) error->all(FLERR, "Unexpected end of data file");
 
   if (alabelflag && !lmap->is_complete(Atom::ANGLE))
-    error->all(FLERR,
-               "Label map is incomplete: "
-               "all types must be assigned a unique type label");
+    error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label");
 
   char *original = buf;
   for (int i = 0; i < nangletypes; i++) {
@@ -2122,9 +2113,7 @@ void ReadData::dihedralcoeffs(int which)
   if (eof) error->all(FLERR, "Unexpected end of data file");
 
   if (dlabelflag && !lmap->is_complete(Atom::DIHEDRAL))
-    error->all(FLERR,
-               "Label map is incomplete: "
-               "all types must be assigned a unique type label");
+    error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label");
 
   char *original = buf;
   for (int i = 0; i < ndihedraltypes; i++) {

From a38e0fb47b586331f54bcb19a46995d5d8546fb8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 23 Jun 2023 08:22:31 -0400
Subject: [PATCH 309/396] restore clang-format comments

---
 src/dump.cpp        | 2 +-
 src/dump_atom.cpp   | 2 +-
 src/dump_custom.cpp | 1 +
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/dump.cpp b/src/dump.cpp
index c1a246ada2..39d8989c41 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -1,4 +1,4 @@
-  // clang-format off
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index 656eef8c9d..2d047dc0a0 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -31,7 +32,6 @@ using namespace LAMMPS_NS;
 DumpAtom::DumpAtom(LAMMPS *lmp, int narg, char **arg) :
   Dump(lmp, narg, arg), header_choice(nullptr), pack_choice(nullptr)
 {
-  // clang-format off
   if (narg != 5) error->all(FLERR,"Illegal dump atom command");
 
   scale_flag = 1;
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 6a10641434..bdbc8ec185 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -1,3 +1,4 @@
+// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories

From fab01c7d5fa771040485ba6f624badb1eeec82e3 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@outlook.com>
Date: Sat, 24 Jun 2023 20:26:08 -0600
Subject: [PATCH 310/396] Remove extra semicolons

---
 src/grid2d.h | 2 +-
 src/grid3d.h | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/grid2d.h b/src/grid2d.h
index bb1bfb25e1..fd6b5efd1e 100644
--- a/src/grid2d.h
+++ b/src/grid2d.h
@@ -67,7 +67,7 @@ protected:
   int stencil_grid_lo,stencil_grid_hi;    // grid cells accessed beyond owned cell
   double shift_grid;   // location of grid point within grid cell
                        // only affects which proc owns grid cell
-  double shift_atom_lo,shift_atom_hi;;   // max shift applied to atoms
+  double shift_atom_lo,shift_atom_hi;   // max shift applied to atoms
                        // when mapped to grid cell by caller
                        // can be different in lo/hi directions
                        // only affects extent of ghost cells
diff --git a/src/grid3d.h b/src/grid3d.h
index 97fcf5992a..c15d5ac7f2 100644
--- a/src/grid3d.h
+++ b/src/grid3d.h
@@ -69,7 +69,7 @@ class Grid3d : protected Pointers {
   int stencil_grid_lo,stencil_grid_hi;    // grid cells accessed beyond owned cell
   double shift_grid;   // location of grid point within grid cell
                        // only affects which proc owns grid cell
-  double shift_atom_lo,shift_atom_hi;;   // max shift applied to atoms
+  double shift_atom_lo,shift_atom_hi;   // max shift applied to atoms
                        // when mapped to grid cell by caller
                        // can be different in lo/hi directions
                        // only affects extent of ghost cells

From bfa39a37ff81e37a871e4ff6968edda648349ff8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 25 Jun 2023 05:47:21 -0400
Subject: [PATCH 311/396] apply clang-format

---
 src/grid2d.h | 30 +++++++++++++++---------------
 src/grid3d.h | 36 ++++++++++++++++++------------------
 2 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/src/grid2d.h b/src/grid2d.h
index fd6b5efd1e..6c1cca5f9d 100644
--- a/src/grid2d.h
+++ b/src/grid2d.h
@@ -53,7 +53,7 @@ class Grid2d : protected Pointers {
   void read_file(int, void *, FILE *, int, int);
   void write_file(int, void *, int, int, int, MPI_Datatype);
 
-protected:
+ protected:
   int me, nprocs;
   int layout;           // not TILED or TILED, same as Comm class
   MPI_Comm gridcomm;    // communicator for this class
@@ -61,18 +61,18 @@ protected:
 
   // inputs from caller via constructor
 
-  int nx, ny;          // size of global grid in both dims
-  double maxdist;      // distance owned atoms can move outside subdomain
-  int stencil_atom_lo,stencil_atom_hi;    // grid cells accessed beyond atom's cell
-  int stencil_grid_lo,stencil_grid_hi;    // grid cells accessed beyond owned cell
-  double shift_grid;   // location of grid point within grid cell
-                       // only affects which proc owns grid cell
-  double shift_atom_lo,shift_atom_hi;   // max shift applied to atoms
-                       // when mapped to grid cell by caller
-                       // can be different in lo/hi directions
-                       // only affects extent of ghost cells
-  int yextra;          // 1 if extra grid cells in Y, 0 if not
-  double yfactor;      // multiplier on extent of grid in Y direction
+  int nx, ny;                              // size of global grid in both dims
+  double maxdist;                          // distance owned atoms can move outside subdomain
+  int stencil_atom_lo, stencil_atom_hi;    // grid cells accessed beyond atom's cell
+  int stencil_grid_lo, stencil_grid_hi;    // grid cells accessed beyond owned cell
+  double shift_grid;                       // location of grid point within grid cell
+                                           // only affects which proc owns grid cell
+  double shift_atom_lo, shift_atom_hi;     // max shift applied to atoms
+                                           // when mapped to grid cell by caller
+                                           // can be different in lo/hi directions
+                                           // only affects extent of ghost cells
+  int yextra;                              // 1 if extra grid cells in Y, 0 if not
+  double yfactor;                          // multiplier on extent of grid in Y direction
 
   // extent of my owned and ghost cells
 
@@ -190,11 +190,11 @@ protected:
   // internal variables for OVERLAP operation
   // -------------------------------------------
 
-  int *overlap_procs;       // length of Nprocs in communicator
+  int *overlap_procs;    // length of Nprocs in communicator
 
   // BRICK decomposition
 
-  double *xsplit,*ysplit,*zsplit;
+  double *xsplit, *ysplit, *zsplit;
   int ***grid2proc;
 
   // TILED decomposition
diff --git a/src/grid3d.h b/src/grid3d.h
index c15d5ac7f2..e4a8e276f5 100644
--- a/src/grid3d.h
+++ b/src/grid3d.h
@@ -23,8 +23,8 @@ class Grid3d : protected Pointers {
   enum { KSPACE = 0, PAIR = 1, FIX = 2 };    // calling classes
 
   Grid3d(class LAMMPS *, MPI_Comm, int, int, int);
-  Grid3d(class LAMMPS *, MPI_Comm, int, int, int,
-         int, int, int, int, int, int, int, int, int, int, int, int);
+  Grid3d(class LAMMPS *, MPI_Comm, int, int, int, int, int, int, int, int, int, int, int, int, int,
+         int, int);
   ~Grid3d();
 
   void set_distance(double);
@@ -41,8 +41,8 @@ class Grid3d : protected Pointers {
   void get_bounds_owned(int &, int &, int &, int &, int &, int &);
   void get_bounds_ghost(int &, int &, int &, int &, int &, int &);
 
-  void setup_grid(int &, int &, int &, int &, int &, int &,
-                  int &, int &, int &, int &, int &, int &);
+  void setup_grid(int &, int &, int &, int &, int &, int &, int &, int &, int &, int &, int &,
+                  int &);
 
   void setup_comm(int &, int &);
   int ghost_adjacent();
@@ -63,18 +63,18 @@ class Grid3d : protected Pointers {
 
   // input from caller
 
-  int nx, ny, nz;      // size of global grid in all 3 dims
-  double maxdist;      // distance owned atoms can move outside subdomain
-  int stencil_atom_lo,stencil_atom_hi;    // grid cells accessed beyond atom's cell
-  int stencil_grid_lo,stencil_grid_hi;    // grid cells accessed beyond owned cell
-  double shift_grid;   // location of grid point within grid cell
-                       // only affects which proc owns grid cell
-  double shift_atom_lo,shift_atom_hi;   // max shift applied to atoms
-                       // when mapped to grid cell by caller
-                       // can be different in lo/hi directions
-                       // only affects extent of ghost cells
-  int zextra;          // 1 if extra grid cells in Z, 0 if not
-  double zfactor;      // multiplier on extent of grid in Z direction
+  int nx, ny, nz;                          // size of global grid in all 3 dims
+  double maxdist;                          // distance owned atoms can move outside subdomain
+  int stencil_atom_lo, stencil_atom_hi;    // grid cells accessed beyond atom's cell
+  int stencil_grid_lo, stencil_grid_hi;    // grid cells accessed beyond owned cell
+  double shift_grid;                       // location of grid point within grid cell
+                                           // only affects which proc owns grid cell
+  double shift_atom_lo, shift_atom_hi;     // max shift applied to atoms
+                                           // when mapped to grid cell by caller
+                                           // can be different in lo/hi directions
+                                           // only affects extent of ghost cells
+  int zextra;                              // 1 if extra grid cells in Z, 0 if not
+  double zfactor;                          // multiplier on extent of grid in Z direction
 
   // extent of my owned and ghost cells
 
@@ -196,11 +196,11 @@ class Grid3d : protected Pointers {
   // internal variables for OVERLAP operation
   // -------------------------------------------
 
-  int *overlap_procs;       // length of Nprocs in communicator
+  int *overlap_procs;    // length of Nprocs in communicator
 
   // BRICK decomposition
 
-  double *xsplit,*ysplit,*zsplit;
+  double *xsplit, *ysplit, *zsplit;
   int ***grid2proc;
 
   // TILED decomposition

From 92c118b29fc760a26aca9f38ad0db0fb2dd08fe8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 25 Jun 2023 05:56:51 -0400
Subject: [PATCH 312/396] replace for (;;) with while (true)

---
 src/EXTRA-COMPUTE/compute_ackland_atom.cpp     | 8 ++++----
 src/EXTRA-COMPUTE/compute_basal_atom.cpp       | 8 ++++----
 src/EXTRA-COMPUTE/compute_hexorder_atom.cpp    | 4 ++--
 src/KOKKOS/compute_orientorder_atom_kokkos.cpp | 4 ++--
 src/compute_centro_atom.cpp                    | 8 ++++----
 src/compute_orientorder_atom.cpp               | 4 ++--
 6 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_ackland_atom.cpp b/src/EXTRA-COMPUTE/compute_ackland_atom.cpp
index d8a77b9c2f..fd7a5fb05c 100644
--- a/src/EXTRA-COMPUTE/compute_ackland_atom.cpp
+++ b/src/EXTRA-COMPUTE/compute_ackland_atom.cpp
@@ -357,7 +357,7 @@ void ComputeAcklandAtom::select(int k, int n, double *arr)
   arr--;
   l = 1;
   ir = n;
-  for (;;) {
+  while (true) {
     if (ir <= l+1) {
       if (ir == l+1 && arr[ir] < arr[l]) {
         SWAP(arr[l],arr[ir])
@@ -378,7 +378,7 @@ void ComputeAcklandAtom::select(int k, int n, double *arr)
       i = l+1;
       j = ir;
       a = arr[l+1];
-      for (;;) {
+      while (true) {
         do i++; while (arr[i] < a);
         do j--; while (arr[j] > a);
         if (j < i) break;
@@ -403,7 +403,7 @@ void ComputeAcklandAtom::select2(int k, int n, double *arr, int *iarr)
   iarr--;
   l = 1;
   ir = n;
-  for (;;) {
+  while (true) {
     if (ir <= l+1) {
       if (ir == l+1 && arr[ir] < arr[l]) {
         SWAP(arr[l],arr[ir])
@@ -430,7 +430,7 @@ void ComputeAcklandAtom::select2(int k, int n, double *arr, int *iarr)
       j = ir;
       a = arr[l+1];
       ia = iarr[l+1];
-      for (;;) {
+      while (true) {
         do i++; while (arr[i] < a);
         do j--; while (arr[j] > a);
         if (j < i) break;
diff --git a/src/EXTRA-COMPUTE/compute_basal_atom.cpp b/src/EXTRA-COMPUTE/compute_basal_atom.cpp
index b149746fb4..8b65917111 100644
--- a/src/EXTRA-COMPUTE/compute_basal_atom.cpp
+++ b/src/EXTRA-COMPUTE/compute_basal_atom.cpp
@@ -442,7 +442,7 @@ void ComputeBasalAtom::select(int k, int n, double *arr)
   arr--;
   l = 1;
   ir = n;
-  for (;;) {
+  while (true) {
     if (ir <= l+1) {
       if (ir == l+1 && arr[ir] < arr[l]) {
         SWAP(arr[l],arr[ir])
@@ -463,7 +463,7 @@ void ComputeBasalAtom::select(int k, int n, double *arr)
       i = l+1;
       j = ir;
       a = arr[l+1];
-      for (;;) {
+      while (true) {
         do i++; while (arr[i] < a);
         do j--; while (arr[j] > a);
         if (j < i) break;
@@ -488,7 +488,7 @@ void ComputeBasalAtom::select2(int k, int n, double *arr, int *iarr)
   iarr--;
   l = 1;
   ir = n;
-  for (;;) {
+  while (true) {
     if (ir <= l+1) {
       if (ir == l+1 && arr[ir] < arr[l]) {
         SWAP(arr[l],arr[ir])
@@ -515,7 +515,7 @@ void ComputeBasalAtom::select2(int k, int n, double *arr, int *iarr)
       j = ir;
       a = arr[l+1];
       ia = iarr[l+1];
-      for (;;) {
+      while (true) {
         do i++; while (arr[i] < a);
         do j--; while (arr[j] > a);
         if (j < i) break;
diff --git a/src/EXTRA-COMPUTE/compute_hexorder_atom.cpp b/src/EXTRA-COMPUTE/compute_hexorder_atom.cpp
index a10e810e82..dc04c6b650 100644
--- a/src/EXTRA-COMPUTE/compute_hexorder_atom.cpp
+++ b/src/EXTRA-COMPUTE/compute_hexorder_atom.cpp
@@ -281,7 +281,7 @@ void ComputeHexOrderAtom::select2(int k, int n, double *arr, int *iarr)
   iarr--;
   l = 1;
   ir = n;
-  for (;;) {
+  while (true) {
     if (ir <= l+1) {
       if (ir == l+1 && arr[ir] < arr[l]) {
         SWAP(arr[l],arr[ir])
@@ -308,7 +308,7 @@ void ComputeHexOrderAtom::select2(int k, int n, double *arr, int *iarr)
       j = ir;
       a = arr[l+1];
       ia = iarr[l+1];
-      for (;;) {
+      while (true) {
         do i++; while (arr[i] < a);
         do j--; while (arr[j] > a);
         if (j < i) break;
diff --git a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp
index 157d41126f..263a070a3a 100644
--- a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp
+++ b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp
@@ -386,7 +386,7 @@ void ComputeOrientOrderAtomKokkos<DeviceType>::select3(int k, int n, int ii) con
 
   l = 0;
   ir = n-1;
-  for (;;) {
+  while (true) {
     if (ir <= l+1) {
       if (ir == l+1 && arr[ir] < arr[l]) {
         SWAP(arr,l,ir);
@@ -421,7 +421,7 @@ void ComputeOrientOrderAtomKokkos<DeviceType>::select3(int k, int n, int ii) con
       a3[0] = arr3(l+1,0);
       a3[1] = arr3(l+1,1);
       a3[2] = arr3(l+1,2);
-      for (;;) {
+      while (true) {
         do i++; while (arr[i] < a);
         do j--; while (arr[j] > a);
         if (j < i) break;
diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp
index ae6ef4901f..f726a95594 100644
--- a/src/compute_centro_atom.cpp
+++ b/src/compute_centro_atom.cpp
@@ -338,7 +338,7 @@ void ComputeCentroAtom::select(int k, int n, double *arr)
   arr--;
   l = 1;
   ir = n;
-  for (;;) {
+  while (true) {
     if (ir <= l + 1) {
       if (ir == l + 1 && arr[ir] < arr[l]) { SWAP(arr[l], arr[ir]) }
       return;
@@ -351,7 +351,7 @@ void ComputeCentroAtom::select(int k, int n, double *arr)
       i = l + 1;
       j = ir;
       a = arr[l + 1];
-      for (;;) {
+      while (true) {
         do i++;
         while (arr[i] < a);
         do j--;
@@ -378,7 +378,7 @@ void ComputeCentroAtom::select2(int k, int n, double *arr, int *iarr)
   iarr--;
   l = 1;
   ir = n;
-  for (;;) {
+  while (true) {
     if (ir <= l + 1) {
       if (ir == l + 1 && arr[ir] < arr[l]) {
         SWAP(arr[l], arr[ir])
@@ -405,7 +405,7 @@ void ComputeCentroAtom::select2(int k, int n, double *arr, int *iarr)
       j = ir;
       a = arr[l + 1];
       ia = iarr[l + 1];
-      for (;;) {
+      while (true) {
         do i++;
         while (arr[i] < a);
         do j--;
diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp
index 5682432c8e..6f1b2b4036 100644
--- a/src/compute_orientorder_atom.cpp
+++ b/src/compute_orientorder_atom.cpp
@@ -370,7 +370,7 @@ void ComputeOrientOrderAtom::select3(int k, int n, double *arr, int *iarr, doubl
   arr3--;
   l = 1;
   ir = n;
-  for (;;) {
+  while (true) {
     if (ir <= l + 1) {
       if (ir == l + 1 && arr[ir] < arr[l]) {
         SWAP(arr[l], arr[ir]);
@@ -405,7 +405,7 @@ void ComputeOrientOrderAtom::select3(int k, int n, double *arr, int *iarr, doubl
       a3[0] = arr3[l + 1][0];
       a3[1] = arr3[l + 1][1];
       a3[2] = arr3[l + 1][2];
-      for (;;) {
+      while (true) {
         do i++;
         while (arr[i] < a);
         do j--;

From d1980031efbb2a8b73ca5ca75596b5b4c314e445 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 25 Jun 2023 06:02:17 -0400
Subject: [PATCH 313/396] remove more duplicate semicolons

---
 src/BODY/pair_body_rounded_polyhedron.cpp         |  2 +-
 src/CG-DNA/bond_oxdna_fene.cpp                    |  2 +-
 src/CG-DNA/pair_oxdna2_coaxstk.cpp                |  2 +-
 src/CG-DNA/pair_oxdna2_dh.cpp                     |  2 +-
 src/CG-DNA/pair_oxdna_coaxstk.cpp                 |  2 +-
 src/CG-DNA/pair_oxdna_xstk.cpp                    |  2 +-
 src/CG-DNA/pair_oxrna2_xstk.cpp                   |  2 +-
 src/EXTRA-COMPUTE/compute_adf.cpp                 |  2 +-
 src/EXTRA-DUMP/dump_xtc.cpp                       |  2 +-
 src/EXTRA-FIX/fix_wall_ees.cpp                    |  2 +-
 src/INTEL/npair_full_bin_intel.cpp                |  2 +-
 src/INTEL/pppm_disp_intel.cpp                     |  2 +-
 src/KOKKOS/atom_vec_dpd_kokkos.cpp                | 12 ++++++------
 src/KOKKOS/dihedral_harmonic_kokkos.cpp           |  6 +++---
 src/KOKKOS/fix_wall_gran_old.cpp                  |  2 +-
 src/KSPACE/ewald.cpp                              |  2 +-
 src/KSPACE/pair_lj_charmmfsw_coul_long.cpp        |  6 +++---
 src/KSPACE/pppm.cpp                               |  2 +-
 src/KSPACE/pppm_disp.cpp                          |  2 +-
 src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp |  4 ++--
 src/RIGID/fix_shake.cpp                           |  2 +-
 src/SMTBQ/pair_smtbq.cpp                          |  2 +-
 src/SPIN/min_spin_lbfgs.cpp                       |  2 +-
 src/fix_ave_grid.cpp                              |  2 +-
 src/input.cpp                                     |  2 +-
 src/special.cpp                                   |  2 +-
 26 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp
index d9a79abad0..9425707ef1 100644
--- a/src/BODY/pair_body_rounded_polyhedron.cpp
+++ b/src/BODY/pair_body_rounded_polyhedron.cpp
@@ -1910,7 +1910,7 @@ void PairBodyRoundedPolyhedron::inside_polygon(int ibody, int face_index,
   iffirst = facfirst[ibody];
   rradi = rounded_radius[ibody];
   double rradsq = rradi*rradi;
-  anglesum1 = anglesum2 = 0;;
+  anglesum1 = anglesum2 = 0;
   for (i = 0; i < MAX_FACE_SIZE; i++) {
     npi1 = static_cast<int>(face[iffirst+face_index][i]);
     if (npi1 < 0) break;
diff --git a/src/CG-DNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp
index 2d471cbbe6..780b71e44c 100644
--- a/src/CG-DNA/bond_oxdna_fene.cpp
+++ b/src/CG-DNA/bond_oxdna_fene.cpp
@@ -146,7 +146,7 @@ void BondOxdnaFene::ev_tally_xyz(int i, int j, int nlocal, int newton_bond, doub
 void BondOxdnaFene::compute(int eflag, int vflag)
 {
   int a, b, in, type;
-  double delf[3], delta[3], deltb[3];    // force, torque increment;;
+  double delf[3], delta[3], deltb[3];    // force, torque increment
   double delr[3], ebond, fbond;
   double rsq, Deltasq, rlogarg;
   double r, rr0, rr0sq;
diff --git a/src/CG-DNA/pair_oxdna2_coaxstk.cpp b/src/CG-DNA/pair_oxdna2_coaxstk.cpp
index 844ba56577..527020076c 100644
--- a/src/CG-DNA/pair_oxdna2_coaxstk.cpp
+++ b/src/CG-DNA/pair_oxdna2_coaxstk.cpp
@@ -612,7 +612,7 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg)
         (0.5 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one) -
         k_cxst_one * 0.5 * (cut_cxst_0_one -cut_cxst_c_one) * (cut_cxst_0_one - cut_cxst_c_one)/k_cxst_one);
 
-  cut_cxst_lc_one = cut_cxst_lo_one - 0.5 * (cut_cxst_lo_one - cut_cxst_0_one)/b_cxst_lo_one;;
+  cut_cxst_lc_one = cut_cxst_lo_one - 0.5 * (cut_cxst_lo_one - cut_cxst_0_one)/b_cxst_lo_one;
 
   b_cxst_hi_one = 0.25 * (cut_cxst_hi_one - cut_cxst_0_one) * (cut_cxst_hi_one - cut_cxst_0_one)/
         (0.5 * (cut_cxst_hi_one - cut_cxst_0_one) * (cut_cxst_hi_one - cut_cxst_0_one) -
diff --git a/src/CG-DNA/pair_oxdna2_dh.cpp b/src/CG-DNA/pair_oxdna2_dh.cpp
index dcfe3f9ea1..a8114c84d7 100644
--- a/src/CG-DNA/pair_oxdna2_dh.cpp
+++ b/src/CG-DNA/pair_oxdna2_dh.cpp
@@ -79,7 +79,7 @@ void PairOxdna2Dh::compute_interaction_sites(double e1[3],
 
 void PairOxdna2Dh::compute(int eflag, int vflag)
 {
-  double delf[3],delta[3],deltb[3]; // force, torque increment;;
+  double delf[3],delta[3],deltb[3]; // force, torque increment
   double rtmp_s[3],delr[3];
   double evdwl,fpair,factor_lj;
   double r,rsq,rinv;
diff --git a/src/CG-DNA/pair_oxdna_coaxstk.cpp b/src/CG-DNA/pair_oxdna_coaxstk.cpp
index b9b34338fe..679bfbf18d 100644
--- a/src/CG-DNA/pair_oxdna_coaxstk.cpp
+++ b/src/CG-DNA/pair_oxdna_coaxstk.cpp
@@ -749,7 +749,7 @@ void PairOxdnaCoaxstk::coeff(int narg, char **arg)
         (0.5 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one) -
         k_cxst_one * 0.5 * (cut_cxst_0_one -cut_cxst_c_one) * (cut_cxst_0_one - cut_cxst_c_one)/k_cxst_one);
 
-  cut_cxst_lc_one = cut_cxst_lo_one - 0.5 * (cut_cxst_lo_one - cut_cxst_0_one)/b_cxst_lo_one;;
+  cut_cxst_lc_one = cut_cxst_lo_one - 0.5 * (cut_cxst_lo_one - cut_cxst_0_one)/b_cxst_lo_one;
 
   b_cxst_hi_one = 0.25 * (cut_cxst_hi_one - cut_cxst_0_one) * (cut_cxst_hi_one - cut_cxst_0_one)/
         (0.5 * (cut_cxst_hi_one - cut_cxst_0_one) * (cut_cxst_hi_one - cut_cxst_0_one) -
diff --git a/src/CG-DNA/pair_oxdna_xstk.cpp b/src/CG-DNA/pair_oxdna_xstk.cpp
index d95004f537..6ef6091889 100644
--- a/src/CG-DNA/pair_oxdna_xstk.cpp
+++ b/src/CG-DNA/pair_oxdna_xstk.cpp
@@ -696,7 +696,7 @@ void PairOxdnaXstk::coeff(int narg, char **arg)
         (0.5 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one) -
         k_xst_one * 0.5 * (cut_xst_0_one -cut_xst_c_one) * (cut_xst_0_one - cut_xst_c_one)/k_xst_one);
 
-  cut_xst_lc_one = cut_xst_lo_one - 0.5 * (cut_xst_lo_one - cut_xst_0_one)/b_xst_lo_one;;
+  cut_xst_lc_one = cut_xst_lo_one - 0.5 * (cut_xst_lo_one - cut_xst_0_one)/b_xst_lo_one;
 
   b_xst_hi_one = 0.25 * (cut_xst_hi_one - cut_xst_0_one) * (cut_xst_hi_one - cut_xst_0_one)/
         (0.5 * (cut_xst_hi_one - cut_xst_0_one) * (cut_xst_hi_one - cut_xst_0_one) -
diff --git a/src/CG-DNA/pair_oxrna2_xstk.cpp b/src/CG-DNA/pair_oxrna2_xstk.cpp
index cdba56e33a..e28b6573bf 100644
--- a/src/CG-DNA/pair_oxrna2_xstk.cpp
+++ b/src/CG-DNA/pair_oxrna2_xstk.cpp
@@ -639,7 +639,7 @@ void PairOxrna2Xstk::coeff(int narg, char **arg)
         (0.5 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one) -
         k_xst_one * 0.5 * (cut_xst_0_one -cut_xst_c_one) * (cut_xst_0_one - cut_xst_c_one)/k_xst_one);
 
-  cut_xst_lc_one = cut_xst_lo_one - 0.5 * (cut_xst_lo_one - cut_xst_0_one)/b_xst_lo_one;;
+  cut_xst_lc_one = cut_xst_lo_one - 0.5 * (cut_xst_lo_one - cut_xst_0_one)/b_xst_lo_one;
 
   b_xst_hi_one = 0.25 * (cut_xst_hi_one - cut_xst_0_one) * (cut_xst_hi_one - cut_xst_0_one)/
         (0.5 * (cut_xst_hi_one - cut_xst_0_one) * (cut_xst_hi_one - cut_xst_0_one) -
diff --git a/src/EXTRA-COMPUTE/compute_adf.cpp b/src/EXTRA-COMPUTE/compute_adf.cpp
index fc74cb8037..35ff8bfd33 100644
--- a/src/EXTRA-COMPUTE/compute_adf.cpp
+++ b/src/EXTRA-COMPUTE/compute_adf.cpp
@@ -288,7 +288,7 @@ void ComputeADF::init()
     rcutinnerk[0] = 0.0;
     rcutouterj[0] = force->pair->cutforce;
     rcutouterk[0] = force->pair->cutforce;
-    maxouter = force->pair->cutforce;;
+    maxouter = force->pair->cutforce;
   } else {
     for (int m = 0; m < ntriples; m++) {
       maxouter = MAX(rcutouterj[m],maxouter);
diff --git a/src/EXTRA-DUMP/dump_xtc.cpp b/src/EXTRA-DUMP/dump_xtc.cpp
index 6b0b97181b..ba3f740cf7 100644
--- a/src/EXTRA-DUMP/dump_xtc.cpp
+++ b/src/EXTRA-DUMP/dump_xtc.cpp
@@ -1046,7 +1046,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
         sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
       }
     }
-    if (buf[1] != 0) buf[0]++;;
+    if (buf[1] != 0) buf[0]++;
     xdr_int(xdrs, &(buf[0])); /* buf[0] holds the length in bytes */
     return errval * (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]));
   } else {
diff --git a/src/EXTRA-FIX/fix_wall_ees.cpp b/src/EXTRA-FIX/fix_wall_ees.cpp
index 230b8f6ac0..0e4d5aa1eb 100644
--- a/src/EXTRA-FIX/fix_wall_ees.cpp
+++ b/src/EXTRA-FIX/fix_wall_ees.cpp
@@ -116,7 +116,7 @@ void FixWallEES::wall_particle(int m, int which, double coord)
       nhat[(dim+2)%3] = 0 ;
 
 
-      double* shape = bonus[ellipsoid[i]].shape;;
+      double* shape = bonus[ellipsoid[i]].shape;
       MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
       MathExtra::transpose_matvec(A,nhat,tempvec);
       for (int k = 0; k<3; k++) {
diff --git a/src/INTEL/npair_full_bin_intel.cpp b/src/INTEL/npair_full_bin_intel.cpp
index 2f8af4c8af..285ed35ec9 100644
--- a/src/INTEL/npair_full_bin_intel.cpp
+++ b/src/INTEL/npair_full_bin_intel.cpp
@@ -62,7 +62,7 @@ fbi(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
   list->inum = nlocal;
   list->gnum = 0;
 
-  int host_start = _fix->host_start_neighbor();;
+  int host_start = _fix->host_start_neighbor();
   const int off_end = _fix->offload_end_neighbor();
 
   #ifdef _LMP_INTEL_OFFLOAD
diff --git a/src/INTEL/pppm_disp_intel.cpp b/src/INTEL/pppm_disp_intel.cpp
index cc4aa6ab93..6dac9fad99 100644
--- a/src/INTEL/pppm_disp_intel.cpp
+++ b/src/INTEL/pppm_disp_intel.cpp
@@ -1478,7 +1478,7 @@ void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> * /*buffers*/)
 
       int nxsum = nx + nlower;
       int nysum = ny + nlower;
-      int nzsum = nz + nlower;;
+      int nzsum = nz + nlower;
 
       FFT_SCALAR dx = nx+fshiftone - (x[i][0]-lo0)*xi;
       FFT_SCALAR dy = ny+fshiftone - (x[i][1]-lo1)*yi;
diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
index eda26a92dc..a8ce29f666 100644
--- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
@@ -116,22 +116,22 @@ void AtomVecDPDKokkos::grow_pointers()
   d_dpdTheta = atomKK->k_dpdTheta.d_view;
   h_dpdTheta = atomKK->k_dpdTheta.h_view;
   uCond = atomKK->uCond;
-  d_uCond = atomKK->k_uCond.d_view;;
+  d_uCond = atomKK->k_uCond.d_view;
   h_uCond = atomKK->k_uCond.h_view;
   uMech = atomKK->uMech;
-  d_uMech = atomKK->k_uMech.d_view;;
+  d_uMech = atomKK->k_uMech.d_view;
   h_uMech = atomKK->k_uMech.h_view;
   uChem = atomKK->uChem;
-  d_uChem = atomKK->k_uChem.d_view;;
+  d_uChem = atomKK->k_uChem.d_view;
   h_uChem = atomKK->k_uChem.h_view;
   uCG = atomKK->uCG;
-  d_uCG = atomKK->k_uCG.d_view;;
+  d_uCG = atomKK->k_uCG.d_view;
   h_uCG = atomKK->k_uCG.h_view;
   uCGnew = atomKK->uCGnew;
-  d_uCGnew = atomKK->k_uCGnew.d_view;;
+  d_uCGnew = atomKK->k_uCGnew.d_view;
   h_uCGnew = atomKK->k_uCGnew.h_view;
   duChem = atomKK->duChem;
-  d_duChem = atomKK->k_duChem.d_view;;
+  d_duChem = atomKK->k_duChem.d_view;
   h_duChem = atomKK->k_duChem.h_view;
 }
 
diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.cpp b/src/KOKKOS/dihedral_harmonic_kokkos.cpp
index 96287946ea..8ca0b368df 100644
--- a/src/KOKKOS/dihedral_harmonic_kokkos.cpp
+++ b/src/KOKKOS/dihedral_harmonic_kokkos.cpp
@@ -265,9 +265,9 @@ void DihedralHarmonicKokkos<DeviceType>::operator()(TagDihedralHarmonicCompute<N
 
   const F_FLOAT df = -d_k[type] * df1;
 
-  const F_FLOAT sx2  = df*dtgx;;
-  const F_FLOAT sy2  = df*dtgy;;
-  const F_FLOAT sz2  = df*dtgz;;
+  const F_FLOAT sx2  = df*dtgx;
+  const F_FLOAT sy2  = df*dtgy;
+  const F_FLOAT sz2  = df*dtgz;
 
   F_FLOAT f1[3],f2[3],f3[3],f4[3];
   f1[0] = df*dtfx;
diff --git a/src/KOKKOS/fix_wall_gran_old.cpp b/src/KOKKOS/fix_wall_gran_old.cpp
index 95aaa144e5..8c02e6146d 100644
--- a/src/KOKKOS/fix_wall_gran_old.cpp
+++ b/src/KOKKOS/fix_wall_gran_old.cpp
@@ -1470,7 +1470,7 @@ void FixWallGranOld::granular(double rsq, double dx, double dy, double dz,
   if (twist_model != TWIST_NONE) {
     magtwist = relrot1*nx + relrot2*ny + relrot3*nz; //Omega_T (eq 29 of Marshall)
     if (twist_model == TWIST_MARSHALL) {
-      k_twist = 0.5*k_tangential*a*a;; // eq 32 of Marshall paper
+      k_twist = 0.5*k_tangential*a*a; // eq 32 of Marshall paper
       damp_twist = 0.5*damp_tangential*a*a;
       mu_twist = TWOTHIRDS*a*tangential_coeffs[2];
     }
diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp
index b61a1d36c6..93470c60ac 100644
--- a/src/KSPACE/ewald.cpp
+++ b/src/KSPACE/ewald.cpp
@@ -857,7 +857,7 @@ void Ewald::coeffs()
         vg[kcount][3] = -vterm*unitk[0]*k*unitk[1]*l;
         vg[kcount][4] = 0.0;
         vg[kcount][5] = 0.0;
-        kcount++;;
+        kcount++;
       }
     }
   }
diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
index fd76d2fc00..b7635c49c7 100644
--- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
@@ -230,7 +230,7 @@ void PairLJCharmmfswCoulLong::compute(int eflag, int vflag)
               evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
                 (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
               evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
-                (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
+                (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);
               evdwl = evdwl12 + evdwl6;
             } else {
               evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
@@ -588,7 +588,7 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag)
               evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
                 (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
               evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
-                (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
+                (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);
               evdwl = evdwl12 + evdwl6;
             } else {
               evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
@@ -1015,7 +1015,7 @@ double PairLJCharmmfswCoulLong::single(int i, int j, int itype, int jtype,
       philj12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
         (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
       philj6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
-        (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
+        (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);
       philj = philj12 + philj6;
     } else {
       philj12 = r6inv*lj3[itype][jtype]*r6inv -
diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp
index 70f7c8f6b7..2f5b4fc670 100644
--- a/src/KSPACE/pppm.cpp
+++ b/src/KSPACE/pppm.cpp
@@ -3004,7 +3004,7 @@ double PPPM::memory_usage()
 
   if (group_allocate_flag) {
     bytes += (double)2 * nbrick * sizeof(FFT_SCALAR);
-    bytes += (double)2 * nfft_both * sizeof(FFT_SCALAR);;
+    bytes += (double)2 * nfft_both * sizeof(FFT_SCALAR);
   }
 
   // two Grid3d bufs
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index 78ebad512a..7ab76ad62a 100644
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -4651,7 +4651,7 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
       for (j = nylo_i; j <= nyhi_i; j++)
         for (i = nxlo_i; i <= nxhi_i; i++) {
           vz_brick[k][j][i] = wk2[n++];
-          u_pa[k][j][i] = -wk2[n++];;
+          u_pa[k][j][i] = -wk2[n++];
         }
   }
 
diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
index 5063c402c6..65caa46153 100644
--- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
+++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
@@ -188,7 +188,7 @@ void PairLJCharmmfswCoulCharmmfsh::compute(int eflag, int vflag)
               evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
                 (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
               evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
-                (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
+                (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);
               evdwl = evdwl12 + evdwl6;
             } else {
               evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
@@ -525,7 +525,7 @@ single(int i, int j, int itype, int jtype,
       philj12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
         (r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
       philj6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
-        (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
+        (r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);
       philj = philj12 + philj6;
     } else {
       philj12 = r6inv*lj3[itype][jtype]*r6inv -
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 94c7668453..b2c65220bc 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -877,7 +877,7 @@ void FixShake::find_clusters()
       tagprev = tag[i] - iatom - 1;
       npartner[i] = atommols[imol]->nspecial[iatom][0];
       for (j = 0; j < npartner[i]; j++)
-        partner_tag[i][j] = atommols[imol]->special[iatom][j] + tagprev;;
+        partner_tag[i][j] = atommols[imol]->special[iatom][j] + tagprev;
     }
   }
 
diff --git a/src/SMTBQ/pair_smtbq.cpp b/src/SMTBQ/pair_smtbq.cpp
index 15e5c2da5e..fdef0b6043 100644
--- a/src/SMTBQ/pair_smtbq.cpp
+++ b/src/SMTBQ/pair_smtbq.cpp
@@ -204,7 +204,7 @@ PairSMTBQ::~PairSMTBQ()
   memory->destroy(potcov);
 
   memory->destroy(nvsm);
-  memory->destroy(vsm);;
+  memory->destroy(vsm);
   memory->destroy(flag_QEq);
 
   memory->destroy(nQEqall);
diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp
index c9c84239b6..ae9d33a705 100644
--- a/src/SPIN/min_spin_lbfgs.cpp
+++ b/src/SPIN/min_spin_lbfgs.cpp
@@ -378,7 +378,7 @@ void MinSpinLBFGS::calc_search_direction()
       scaling = maximum_rotation(g_cur);
 
     for (int i = 0; i < 3 * nlocal; i++) {
-      p_s[i] = -g_cur[i] * factor * scaling;;
+      p_s[i] = -g_cur[i] * factor * scaling;
       g_old[i] = g_cur[i]  * factor;
       for (int k = 0; k < num_mem; k++) {
         ds[k][i] = 0.0;
diff --git a/src/fix_ave_grid.cpp b/src/fix_ave_grid.cpp
index 524def73a4..039c656fab 100644
--- a/src/fix_ave_grid.cpp
+++ b/src/fix_ave_grid.cpp
@@ -931,7 +931,7 @@ void FixAveGrid::atom2grid()
               vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
               if (rmass) one = rmass[i];
               else one = mass[type[i]];
-              array2d[bin[i][0]][bin[i][1]][m] += one*vsq;;
+              array2d[bin[i][0]][bin[i][1]][m] += one*vsq;
             }
           }
       } else {
diff --git a/src/input.cpp b/src/input.cpp
index 1dc2b00ebc..dbbc62df59 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -567,7 +567,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
   //   else $x becomes x followed by null char
   // beyond = points to text following variable
 
-  int i,n,paren_count,nchars;;
+  int i,n,paren_count,nchars;
   char immediate[256];
   char *var,*value,*beyond;
   int quoteflag = 0;
diff --git a/src/special.cpp b/src/special.cpp
index a210b6a82a..7e15ec9e80 100644
--- a/src/special.cpp
+++ b/src/special.cpp
@@ -958,7 +958,7 @@ void Special::combine()
 
 void Special::angle_trim()
 {
-  int i,j,k,m;;
+  int i,j,k,m;
 
   int *num_angle = atom->num_angle;
   int *num_dihedral = atom->num_dihedral;

From d8135194931b08efa7ae2b786e4e7a5c9617919b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 26 Jun 2023 10:52:12 -0400
Subject: [PATCH 314/396] make handling of masses consistent and simplify code

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp      | 37 +++++++---------
 .../compute_stress_mop_profile.cpp            | 44 +++++++------------
 2 files changed, 31 insertions(+), 50 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index 98e3bf7043..aa50f39ab9 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -432,16 +432,14 @@ void ComputeStressMop::compute_pairs()
           fi[1] = atom->f[i][1];
           fi[2] = atom->f[i][2];
 
-          //coordinates at t-dt (based on Velocity-Verlet alg.)
-          if (rmass) {
-            xj[0] = xi[0]-vi[0]*dt+fi[0]/2.0/rmass[i]*dt*dt*ftm2v;
-            xj[1] = xi[1]-vi[1]*dt+fi[1]/2.0/rmass[i]*dt*dt*ftm2v;
-            xj[2] = xi[2]-vi[2]*dt+fi[2]/2.0/rmass[i]*dt*dt*ftm2v;
-          } else {
-            xj[0] = xi[0]-vi[0]*dt+fi[0]/2.0/mass[itype]*dt*dt*ftm2v;
-            xj[1] = xi[1]-vi[1]*dt+fi[1]/2.0/mass[itype]*dt*dt*ftm2v;
-            xj[2] = xi[2]-vi[2]*dt+fi[2]/2.0/mass[itype]*dt*dt*ftm2v;
-          }
+          const double imass = (rmass) ? rmass[i] : mass[itype];
+          const double iterm = 0.5/imass*dt*ftm2v;
+
+          // coordinates at t-dt (based on Velocity-Verlet alg.)
+
+          xj[0] = xi[0]-vi[0]*dt+fi[0]*iterm*dt;
+          xj[1] = xi[1]-vi[1]*dt+fi[1]*iterm*dt;
+          xj[2] = xi[2]-vi[2]*dt+fi[2]*iterm*dt;
 
           // because LAMMPS does not put atoms back in the box
           // at each timestep, must check atoms going through the
@@ -453,23 +451,18 @@ void ComputeStressMop::compute_pairs()
           if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)) < 0) {
 
             // sgn = copysign(1.0,vi[dir]-vcm[dir]);
+
             sgn = copysign(1.0,vi[dir]);
 
             // approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
             double vcross[3];
-            if (rmass) {
-              vcross[0] = vi[0]-fi[0]/rmass[i]/2.0*ftm2v*dt;
-              vcross[1] = vi[1]-fi[1]/rmass[i]/2.0*ftm2v*dt;
-              vcross[2] = vi[2]-fi[2]/rmass[i]/2.0*ftm2v*dt;
-            } else {
-              vcross[0] = vi[0]-fi[0]/mass[itype]/2.0*ftm2v*dt;
-              vcross[1] = vi[1]-fi[1]/mass[itype]/2.0*ftm2v*dt;
-              vcross[2] = vi[2]-fi[2]/mass[itype]/2.0*ftm2v*dt;
-            }
+            vcross[0] = vi[0]-fi[0]*iterm;
+            vcross[1] = vi[1]-fi[1]*iterm;
+            vcross[2] = vi[2]-fi[2]*iterm;
 
-            values_local[m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
-            values_local[m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
-            values_local[m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
+            values_local[m] += imass*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
+            values_local[m+1] += imass*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
+            values_local[m+2] += imass*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
           }
         }
       }
diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index 1f1dc30733..12a02cbe63 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -435,16 +435,14 @@ void ComputeStressMopProfile::compute_pairs()
           fi[1] = atom->f[i][1];
           fi[2] = atom->f[i][2];
 
-          //coordinates at t-dt (based on Velocity-Verlet alg.)
-          if (rmass) {
-            xj[0] = xi[0]-vi[0]*dt+fi[0]/2/rmass[i]*dt*dt*ftm2v;
-            xj[1] = xi[1]-vi[1]*dt+fi[1]/2/rmass[i]*dt*dt*ftm2v;
-            xj[2] = xi[2]-vi[2]*dt+fi[2]/2/rmass[i]*dt*dt*ftm2v;
-          } else {
-            xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
-            xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
-            xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
-          }
+          const double imass = (rmass) ? rmass[i] : mass[itype];
+          const double iterm = 0.5/imass*dt*ftm2v;
+
+          // coordinates at t-dt (based on Velocity-Verlet alg.)
+
+          xj[0] = xi[0]-vi[0]*dt+fi[0]*iterm*dt;
+          xj[1] = xi[1]-vi[1]*dt+fi[1]*iterm*dt;
+          xj[2] = xi[2]-vi[2]*dt+fi[2]*iterm*dt;
 
           for (ibin = 0; ibin < nbins; ibin++) {
             pos = coord[ibin][0];
@@ -454,26 +452,16 @@ void ComputeStressMopProfile::compute_pairs()
 
               sgn = copysign(1.0,vi[dir]);
 
-              //approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
-              if (rmass) {
-                double vcross[3];
-                vcross[0] = vi[0]-fi[0]/rmass[i]/2*ftm2v*dt;
-                vcross[1] = vi[1]-fi[1]/rmass[i]/2*ftm2v*dt;
-                vcross[2] = vi[2]-fi[2]/rmass[i]/2*ftm2v*dt;
+              // approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
 
-                values_local[ibin][m] += rmass[i]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
-                values_local[ibin][m+1] += rmass[i]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
-                values_local[ibin][m+2] += rmass[i]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
-              } else {
-                double vcross[3];
-                vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
-                vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
-                vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
+              double vcross[3];
+              vcross[0] = vi[0]-fi[0]*iterm;
+              vcross[1] = vi[1]-fi[1]*iterm;
+              vcross[2] = vi[2]-fi[2]*iterm;
 
-                values_local[ibin][m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
-                values_local[ibin][m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
-                values_local[ibin][m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
-              }
+              values_local[ibin][m] += imass*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
+              values_local[ibin][m+1] += imass*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
+              values_local[ibin][m+2] += imass*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
             }
           }
         }

From d4e705b0598dc6489b9dffeb6533599a7371a005 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 26 Jun 2023 10:59:03 -0400
Subject: [PATCH 315/396] enable and apply clang-format

---
 src/EXTRA-COMPUTE/compute_stress_mop.cpp      | 308 ++++++++++--------
 .../compute_stress_mop_profile.cpp            | 269 ++++++++-------
 2 files changed, 314 insertions(+), 263 deletions(-)

diff --git a/src/EXTRA-COMPUTE/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
index aa50f39ab9..fc9de602a7 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop.cpp
@@ -41,11 +41,9 @@ using namespace LAMMPS_NS;
 enum { X, Y, Z };
 enum { TOTAL, CONF, KIN, PAIR, BOND, ANGLE };
 
-// clang-format off
 /* ---------------------------------------------------------------------- */
 
-ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg)
+ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
 {
   if (narg < 6) utils::missing_cmd_args(FLERR, "compute stress/mop", error);
 
@@ -54,37 +52,40 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
 
   // set compute mode and direction of plane(s) for pressure calculation
 
-  if (strcmp(arg[3],"x") == 0) {
+  if (strcmp(arg[3], "x") == 0) {
     dir = X;
-  } else if (strcmp(arg[3],"y") == 0) {
+  } else if (strcmp(arg[3], "y") == 0) {
     dir = Y;
-  } else if (strcmp(arg[3],"z") == 0) {
+  } else if (strcmp(arg[3], "z") == 0) {
     dir = Z;
-  } else error->all(FLERR,"Illegal compute stress/mop command");
+  } else
+    error->all(FLERR, "Illegal compute stress/mop command");
 
   // Position of the plane
 
-  if (strcmp(arg[4],"lower") == 0) {
+  if (strcmp(arg[4], "lower") == 0) {
     pos = domain->boxlo[dir];
-  } else if (strcmp(arg[4],"upper") == 0) {
+  } else if (strcmp(arg[4], "upper") == 0) {
     pos = domain->boxhi[dir];
-  } else if (strcmp(arg[4],"center") == 0) {
-    pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]);
-  } else pos = utils::numeric(FLERR,arg[4],false,lmp);
+  } else if (strcmp(arg[4], "center") == 0) {
+    pos = 0.5 * (domain->boxlo[dir] + domain->boxhi[dir]);
+  } else
+    pos = utils::numeric(FLERR, arg[4], false, lmp);
 
   // plane inside the box
+
   if ((pos > domain->boxhi[dir]) || (pos < domain->boxlo[dir])) {
     error->warning(FLERR, "The specified initial plane lies outside of the simulation box");
     double dx[3] = {0.0, 0.0, 0.0};
-    dx[dir] = pos - 0.5*(domain->boxhi[dir] + domain->boxlo[dir]);
+    dx[dir] = pos - 0.5 * (domain->boxhi[dir] + domain->boxlo[dir]);
     domain->minimum_image(dx[0], dx[1], dx[2]);
-    pos = 0.5*(domain->boxhi[dir] + domain->boxlo[dir]) + dx[dir];
+    pos = 0.5 * (domain->boxhi[dir] + domain->boxlo[dir]) + dx[dir];
 
     if ((pos > domain->boxhi[dir]) || (pos < domain->boxlo[dir]))
       error->all(FLERR, "Plane for compute stress/mop is out of bounds");
   }
 
-  if (pos < (domain->boxlo[dir]+domain->prd_half[dir])) {
+  if (pos < (domain->boxlo[dir] + domain->prd_half[dir])) {
     pos1 = pos + domain->prd[dir];
   } else {
     pos1 = pos - domain->prd[dir];
@@ -92,52 +93,53 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
 
   // parse values until one isn't recognized
 
-  which = new int[3*(narg-5)];
+  which = new int[3 * (narg - 5)];
   nvalues = 0;
   int i;
 
-  int iarg=5;
+  int iarg = 5;
   while (iarg < narg) {
-    if (strcmp(arg[iarg],"conf") == 0) {
-      for (i=0; i<3; i++) {
+    if (strcmp(arg[iarg], "conf") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = CONF;
         nvalues++;
       }
-    } else if (strcmp(arg[iarg],"kin") == 0) {
-      for (i=0; i<3; i++) {
+    } else if (strcmp(arg[iarg], "kin") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = KIN;
         nvalues++;
       }
-    } else if (strcmp(arg[iarg],"total") == 0) {
-      for (i=0; i<3; i++) {
+    } else if (strcmp(arg[iarg], "total") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = TOTAL;
         nvalues++;
       }
-    } else if (strcmp(arg[iarg],"pair") == 0) {
-      for (i=0; i<3; i++) {
+    } else if (strcmp(arg[iarg], "pair") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = PAIR;
         nvalues++;
       }
-    } else if (strcmp(arg[iarg],"bond") == 0) {
-      for (i=0; i<3; i++) {
+    } else if (strcmp(arg[iarg], "bond") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = BOND;
         nvalues++;
       }
-    } else if (strcmp(arg[iarg],"angle") == 0) {
-      for (i=0; i<3; i++) {
+    } else if (strcmp(arg[iarg], "angle") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = ANGLE;
         nvalues++;
       }
-    } else error->all(FLERR, "Illegal compute stress/mop command"); //break;
+    } else
+      error->all(FLERR, "Illegal compute stress/mop command");    //break;
 
     iarg++;
   }
 
-  // Error checks
+  // Error checks:
+
   // 3D only
 
-  if (domain->dimension != 3)
-    error->all(FLERR, "Compute stress/mop requires a 3d system");
+  if (domain->dimension != 3) error->all(FLERR, "Compute stress/mop requires a 3d system");
 
   // orthogonal simulation box
   if (domain->triclinic != 0)
@@ -153,18 +155,17 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
 
   // this fix produces a global vector
 
-  memory->create(vector,nvalues,"stress/mop:vector");
-  memory->create(values_local,nvalues,"stress/mop:values_local");
-  memory->create(values_global,nvalues,"stress/mop:values_global");
-  memory->create(bond_local,nvalues,"stress/mop:bond_local");
-  memory->create(bond_global,nvalues,"stress/mop:bond_global");
-  memory->create(angle_local,nvalues,"stress/mop:angle_local");
-  memory->create(angle_global,nvalues,"stress/mop:angle_global");
+  memory->create(vector, nvalues, "stress/mop:vector");
+  memory->create(values_local, nvalues, "stress/mop:values_local");
+  memory->create(values_global, nvalues, "stress/mop:values_global");
+  memory->create(bond_local, nvalues, "stress/mop:bond_local");
+  memory->create(bond_global, nvalues, "stress/mop:bond_global");
+  memory->create(angle_local, nvalues, "stress/mop:angle_local");
+  memory->create(angle_global, nvalues, "stress/mop:angle_global");
   size_vector = nvalues;
 
   vector_flag = 1;
   extvector = 0;
-
 }
 
 /* ---------------------------------------------------------------------- */
@@ -196,8 +197,8 @@ void ComputeStressMop::init()
 
   area = 1;
   int i;
-  for (i=0; i<3; i++) {
-    if (i!=dir) area = area*domain->prd[i];
+  for (i = 0; i < 3; i++) {
+    if (i != dir) area = area * domain->prd[i];
   }
 
   // Timestep Value
@@ -212,10 +213,9 @@ void ComputeStressMop::init()
 
   // This compute requires a pair style with pair_single method implemented
 
-  if (!force->pair)
-    error->all(FLERR,"No pair style is defined for compute stress/mop");
+  if (!force->pair) error->all(FLERR, "No pair style is defined for compute stress/mop");
   if (force->pair->single_enable == 0)
-    error->all(FLERR,"Pair style does not support compute stress/mop");
+    error->all(FLERR, "Pair style does not support compute stress/mop");
 
   // Errors
 
@@ -227,21 +227,23 @@ void ComputeStressMop::init()
     if (force->angle) {
       if (force->angle->born_matrix_enable == 0) {
         if ((strcmp(force->angle_style, "zero") != 0) && (strcmp(force->angle_style, "none") != 0))
-          error->all(FLERR,"compute stress/mop does not account for angle potentials");
+          error->all(FLERR, "compute stress/mop does not account for angle potentials");
       } else {
-         angleflag = 1;
+        angleflag = 1;
       }
     }
     if (force->dihedral) {
-      if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
-        error->all(FLERR,"compute stress/mop does not account for dihedral potentials");
+      if ((strcmp(force->dihedral_style, "zero") != 0) &&
+          (strcmp(force->dihedral_style, "none") != 0))
+        error->all(FLERR, "compute stress/mop does not account for dihedral potentials");
     }
     if (force->improper) {
-      if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
-        error->all(FLERR,"compute stress/mop does not account for improper potentials");
+      if ((strcmp(force->improper_style, "zero") != 0) &&
+          (strcmp(force->improper_style, "none") != 0))
+        error->all(FLERR, "compute stress/mop does not account for improper potentials");
     }
     if (force->kspace)
-      error->warning(FLERR,"compute stress/mop does not account for kspace contributions");
+      error->warning(FLERR, "compute stress/mop does not account for kspace contributions");
   }
 
   // need an occasional half neighbor list
@@ -255,7 +257,6 @@ void ComputeStressMop::init_list(int /* id */, NeighList *ptr)
   list = ptr;
 }
 
-
 /* ----------------------------------------------------------------------
    compute output vector
    ------------------------------------------------------------------------- */
@@ -264,38 +265,43 @@ void ComputeStressMop::compute_vector()
 {
   invoked_array = update->ntimestep;
 
-  //Compute pressures on separate procs
+  // Compute pressures on separate procs
+
   compute_pairs();
 
   // sum pressure contributions over all procs
-  MPI_Allreduce(values_local,values_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
+
+  MPI_Allreduce(values_local, values_global, nvalues, MPI_DOUBLE, MPI_SUM, world);
+
+  // Compute bond contribution on separate procs
 
   if (bondflag) {
-    //Compute bond contribution on separate procs
     compute_bonds();
   } else {
-    for (int i=0; i<nvalues; i++) bond_local[i] = 0.0;
+    for (int i = 0; i < nvalues; i++) bond_local[i] = 0.0;
   }
 
   // sum bond contribution over all procs
-  MPI_Allreduce(bond_local,bond_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
+
+  MPI_Allreduce(bond_local, bond_global, nvalues, MPI_DOUBLE, MPI_SUM, world);
+
+  // Compute angle contribution on separate procs
 
   if (angleflag) {
-    //Compute angle contribution on separate procs
     compute_angles();
   } else {
-    for (int i=0; i<nvalues; i++) angle_local[i] = 0.0;
+    for (int i = 0; i < nvalues; i++) angle_local[i] = 0.0;
   }
 
   // sum angle contribution over all procs
-  MPI_Allreduce(angle_local,angle_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
 
-  for (int m=0; m<nvalues; m++) {
+  MPI_Allreduce(angle_local, angle_global, nvalues, MPI_DOUBLE, MPI_SUM, world);
+
+  for (int m = 0; m < nvalues; m++) {
     vector[m] = values_global[m] + bond_global[m] + angle_global[m];
   }
 }
 
-
 /*------------------------------------------------------------------------
   compute pressure contribution of local proc
   -------------------------------------------------------------------------*/
@@ -303,10 +309,10 @@ void ComputeStressMop::compute_vector()
 void ComputeStressMop::compute_pairs()
 
 {
-  int i,j,m,ii,jj,inum,jnum,itype,jtype;
-  double delx,dely,delz;
-  double rsq,fpair,factor_coul,factor_lj;
-  int *ilist,*jlist,*numneigh,**firstneigh;
+  int i, j, m, ii, jj, inum, jnum, itype, jtype;
+  double delx, dely, delz;
+  double rsq, fpair, factor_coul, factor_lj;
+  int *ilist, *jlist, *numneigh, **firstneigh;
 
   double *mass = atom->mass;
   double *rmass = atom->rmass;
@@ -317,7 +323,6 @@ void ComputeStressMop::compute_pairs()
   double *special_lj = force->special_lj;
   int newton_pair = force->newton_pair;
 
-
   // zero out arrays for one sample
 
   for (i = 0; i < nvalues; i++) values_local[i] = 0.0;
@@ -373,7 +378,7 @@ void ComputeStressMop::compute_pairs()
           delx = xi[0] - xj[0];
           dely = xi[1] - xj[1];
           delz = xi[2] - xj[2];
-          rsq = delx*delx + dely*dely + delz*delz;
+          rsq = delx * delx + dely * dely + delz * delz;
           jtype = type[j];
           if (rsq >= cutsq[itype][jtype]) continue;
 
@@ -381,29 +386,29 @@ void ComputeStressMop::compute_pairs()
 
             //check if ij pair is across plane, add contribution to pressure
             if (((xi[dir] > pos) && (xj[dir] < pos)) || ((xi[dir] > pos1) && (xj[dir] < pos1))) {
-              pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-              values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
-              values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
-              values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
-            } else if (((xi[dir] < pos) && (xj[dir] > pos)) || ((xi[dir] < pos1) && (xj[dir] > pos1))) {
-              pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-              values_local[m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
-              values_local[m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
-              values_local[m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
+              pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
+              values_local[m] += fpair * (xi[0] - xj[0]) / area * nktv2p;
+              values_local[m + 1] += fpair * (xi[1] - xj[1]) / area * nktv2p;
+              values_local[m + 2] += fpair * (xi[2] - xj[2]) / area * nktv2p;
+            } else if (((xi[dir] < pos) && (xj[dir] > pos)) ||
+                       ((xi[dir] < pos1) && (xj[dir] > pos1))) {
+              pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
+              values_local[m] -= fpair * (xi[0] - xj[0]) / area * nktv2p;
+              values_local[m + 1] -= fpair * (xi[1] - xj[1]) / area * nktv2p;
+              values_local[m + 2] -= fpair * (xi[2] - xj[2]) / area * nktv2p;
             }
           } else {
             if (((xi[dir] > pos) && (xj[dir] < pos)) || ((xi[dir] > pos1) && (xj[dir] < pos1))) {
-              pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-              values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
-              values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
-              values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+              pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
+              values_local[m] += fpair * (xi[0] - xj[0]) / area * nktv2p;
+              values_local[m + 1] += fpair * (xi[1] - xj[1]) / area * nktv2p;
+              values_local[m + 2] += fpair * (xi[2] - xj[2]) / area * nktv2p;
             }
           }
         }
       }
     }
 
-
     // Compute kinetic contribution to pressure
     // counts local particles transfers across the plane
 
@@ -413,56 +418,61 @@ void ComputeStressMop::compute_pairs()
       for (int i = 0; i < nlocal; i++) {
 
         // skip if I is not in group
+
         if (mask[i] & groupbit) {
 
           itype = type[i];
 
-          //coordinates at t
+          // coordinates at t
+
           xi[0] = atom->x[i][0];
           xi[1] = atom->x[i][1];
           xi[2] = atom->x[i][2];
 
-          //velocities at t
+          // velocities at t
+
           vi[0] = atom->v[i][0];
           vi[1] = atom->v[i][1];
           vi[2] = atom->v[i][2];
 
-          //forces at t
+          // forces at t
+
           fi[0] = atom->f[i][0];
           fi[1] = atom->f[i][1];
           fi[2] = atom->f[i][2];
 
           const double imass = (rmass) ? rmass[i] : mass[itype];
-          const double iterm = 0.5/imass*dt*ftm2v;
+          const double iterm = 0.5 / imass * dt * ftm2v;
 
           // coordinates at t-dt (based on Velocity-Verlet alg.)
 
-          xj[0] = xi[0]-vi[0]*dt+fi[0]*iterm*dt;
-          xj[1] = xi[1]-vi[1]*dt+fi[1]*iterm*dt;
-          xj[2] = xi[2]-vi[2]*dt+fi[2]*iterm*dt;
+          xj[0] = xi[0] - vi[0] * dt + fi[0] * iterm * dt;
+          xj[1] = xi[1] - vi[1] * dt + fi[1] * iterm * dt;
+          xj[2] = xi[2] - vi[2] * dt + fi[2] * iterm * dt;
 
           // because LAMMPS does not put atoms back in the box
           // at each timestep, must check atoms going through the
           // image of the plane that is closest to the box
 
-          double pos_temp = pos+copysign(1.0,domain->prd_half[dir]-pos)*domain->prd[dir];
-          if (fabs(xi[dir]-pos)<fabs(xi[dir]-pos_temp)) pos_temp = pos;
+          double pos_temp = pos + copysign(1.0, domain->prd_half[dir] - pos) * domain->prd[dir];
+          if (fabs(xi[dir] - pos) < fabs(xi[dir] - pos_temp)) pos_temp = pos;
 
-          if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)) < 0) {
+          if (((xi[dir] - pos_temp) * (xj[dir] - pos_temp)) < 0) {
 
             // sgn = copysign(1.0,vi[dir]-vcm[dir]);
 
-            sgn = copysign(1.0,vi[dir]);
+            sgn = copysign(1.0, vi[dir]);
 
             // approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
-            double vcross[3];
-            vcross[0] = vi[0]-fi[0]*iterm;
-            vcross[1] = vi[1]-fi[1]*iterm;
-            vcross[2] = vi[2]-fi[2]*iterm;
 
-            values_local[m] += imass*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
-            values_local[m+1] += imass*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
-            values_local[m+2] += imass*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
+            double vcross[3];
+            vcross[0] = vi[0] - fi[0] * iterm;
+            vcross[1] = vi[1] - fi[1] * iterm;
+            vcross[2] = vi[2] - fi[2] * iterm;
+
+            values_local[m] += imass * vcross[0] * sgn / dt / area * nktv2p / ftm2v;
+            values_local[m + 1] += imass * vcross[1] * sgn / dt / area * nktv2p / ftm2v;
+            values_local[m + 2] += imass * vcross[2] * sgn / dt / area * nktv2p / ftm2v;
           }
         }
       }
@@ -504,9 +514,11 @@ void ComputeStressMop::compute_bonds()
   double local_contribution[3] = {0.0, 0.0, 0.0};
 
   // initialization
+
   for (int i = 0; i < nvalues; i++) bond_local[i] = 0.0;
 
   // loop over all bonded atoms in the current proc
+
   for (atom1 = 0; atom1 < nlocal; atom1++) {
     if (!(mask[atom1] & groupbit)) continue;
 
@@ -534,6 +546,7 @@ void ComputeStressMop::compute_bonds()
       if (btype <= 0) continue;
 
       // minimum image of atom1 with respect to the plane of interest
+
       dx[0] = x[atom1][0];
       dx[1] = x[atom1][1];
       dx[2] = x[atom1][2];
@@ -545,6 +558,7 @@ void ComputeStressMop::compute_bonds()
       x_bond_1[dir] += pos;
 
       // minimum image of atom2 with respect to atom1
+
       dx[0] = x[atom2][0] - x_bond_1[0];
       dx[1] = x[atom2][1] - x_bond_1[1];
       dx[2] = x[atom2][2] - x_bond_1[2];
@@ -554,6 +568,7 @@ void ComputeStressMop::compute_bonds()
       x_bond_2[2] = x_bond_1[2] + dx[2];
 
       // check if the bond vector crosses the plane of interest
+
       double tau = (x_bond_1[dir] - pos) / (x_bond_1[dir] - x_bond_2[dir]);
       if ((tau <= 1) && (tau >= 0)) {
         dx[0] = x_bond_1[0] - x_bond_2[0];
@@ -563,20 +578,21 @@ void ComputeStressMop::compute_bonds()
         bond->single(btype, rsq, atom1, atom2, fpair);
 
         double sgn = copysign(1.0, x_bond_1[dir] - pos);
-        local_contribution[0] += sgn*fpair*dx[0]/area*nktv2p;
-        local_contribution[1] += sgn*fpair*dx[1]/area*nktv2p;
-        local_contribution[2] += sgn*fpair*dx[2]/area*nktv2p;
+        local_contribution[0] += sgn * fpair * dx[0] / area * nktv2p;
+        local_contribution[1] += sgn * fpair * dx[1] / area * nktv2p;
+        local_contribution[2] += sgn * fpair * dx[2] / area * nktv2p;
       }
     }
   }
 
   // loop over the keywords and if necessary add the bond contribution
+
   int m = 0;
-  while (m<nvalues) {
+  while (m < nvalues) {
     if (which[m] == CONF || which[m] == TOTAL || which[m] == BOND) {
       bond_local[m] = local_contribution[0];
-      bond_local[m+1] = local_contribution[1];
-      bond_local[m+2] = local_contribution[2];
+      bond_local[m + 1] = local_contribution[1];
+      bond_local[m + 2] = local_contribution[2];
     }
     m += 3;
   }
@@ -623,6 +639,7 @@ void ComputeStressMop::compute_angles()
   double local_contribution[3] = {0.0, 0.0, 0.0};
 
   // initialization
+
   for (int i = 0; i < nvalues; i++) angle_local[i] = 0.0;
 
   for (atom2 = 0; atom2 < nlocal; atom2++) {
@@ -656,6 +673,7 @@ void ComputeStressMop::compute_angles()
       if (atype <= 0) continue;
 
       // minimum image of atom1 with respect to the plane of interest
+
       dx[0] = x[atom1][0];
       dx[1] = x[atom1][1];
       dx[2] = x[atom1][2];
@@ -665,7 +683,9 @@ void ComputeStressMop::compute_angles()
       x_angle_left[1] = dx[1];
       x_angle_left[2] = dx[2];
       x_angle_left[dir] += pos;
+
       // minimum image of atom2 with respect to atom1
+
       dx_left[0] = x[atom2][0] - x_angle_left[0];
       dx_left[1] = x[atom2][1] - x_angle_left[1];
       dx_left[2] = x[atom2][2] - x_angle_left[2];
@@ -675,6 +695,7 @@ void ComputeStressMop::compute_angles()
       x_angle_middle[2] = x_angle_left[2] + dx_left[2];
 
       // minimum image of atom3 with respect to atom2
+
       dx_right[0] = x[atom3][0] - x_angle_middle[0];
       dx_right[1] = x[atom3][1] - x_angle_middle[1];
       dx_right[2] = x[atom3][2] - x_angle_middle[2];
@@ -684,70 +705,83 @@ void ComputeStressMop::compute_angles()
       x_angle_right[2] = x_angle_middle[2] + dx_right[2];
 
       // check if any bond vector crosses the plane of interest
+
       double tau_right = (x_angle_right[dir] - pos) / (x_angle_right[dir] - x_angle_middle[dir]);
       double tau_left = (x_angle_middle[dir] - pos) / (x_angle_middle[dir] - x_angle_left[dir]);
-      bool right_cross = ((tau_right >=0) && (tau_right  <= 1));
-      bool left_cross = ((tau_left >=0) && (tau_left <= 1));
+      bool right_cross = ((tau_right >= 0) && (tau_right <= 1));
+      bool left_cross = ((tau_left >= 0) && (tau_left <= 1));
 
       // no bonds crossing the plane
+
       if (!right_cross && !left_cross) continue;
 
       // compute the cos(theta) of the angle
-      r1 = sqrt(dx_left[0]*dx_left[0] + dx_left[1]*dx_left[1] + dx_left[2]*dx_left[2]);
-      r2 = sqrt(dx_right[0]*dx_right[0] + dx_right[1]*dx_right[1] + dx_right[2]*dx_right[2]);
-      cos_theta = -(dx_right[0]*dx_left[0] + dx_right[1]*dx_left[1] + dx_right[2]*dx_left[2])/(r1*r2);
 
-      if (cos_theta >  1.0) cos_theta = 1.0;
+      r1 = sqrt(dx_left[0] * dx_left[0] + dx_left[1] * dx_left[1] + dx_left[2] * dx_left[2]);
+      r2 = sqrt(dx_right[0] * dx_right[0] + dx_right[1] * dx_right[1] + dx_right[2] * dx_right[2]);
+      cos_theta =
+          -(dx_right[0] * dx_left[0] + dx_right[1] * dx_left[1] + dx_right[2] * dx_left[2]) /
+          (r1 * r2);
+
+      if (cos_theta > 1.0) cos_theta = 1.0;
       if (cos_theta < -1.0) cos_theta = -1.0;
 
       // The method returns derivative with regards to cos(theta)
+
       angle->born_matrix(atype, atom1, atom2, atom3, duang, du2ang);
+
       // only right bond crossing the plane
-      if (right_cross && !left_cross)
-      {
+
+      if (right_cross && !left_cross) {
         double sgn = copysign(1.0, x_angle_right[dir] - pos);
-        dcos_theta[0] = sgn*(dx_right[0]*cos_theta/r2 + dx_left[0]/r1)/r2;
-        dcos_theta[1] = sgn*(dx_right[1]*cos_theta/r2 + dx_left[1]/r1)/r2;
-        dcos_theta[2] = sgn*(dx_right[2]*cos_theta/r2 + dx_left[2]/r1)/r2;
+        dcos_theta[0] = sgn * (dx_right[0] * cos_theta / r2 + dx_left[0] / r1) / r2;
+        dcos_theta[1] = sgn * (dx_right[1] * cos_theta / r2 + dx_left[1] / r1) / r2;
+        dcos_theta[2] = sgn * (dx_right[2] * cos_theta / r2 + dx_left[2] / r1) / r2;
       }
 
       // only left bond crossing the plane
-      if (!right_cross && left_cross)
-      {
+
+      if (!right_cross && left_cross) {
         double sgn = copysign(1.0, x_angle_left[dir] - pos);
-        dcos_theta[0] = -sgn*(dx_left[0]*cos_theta/r1 + dx_right[0]/r2)/r1;
-        dcos_theta[1] = -sgn*(dx_left[1]*cos_theta/r1 + dx_right[1]/r2)/r1;
-        dcos_theta[2] = -sgn*(dx_left[2]*cos_theta/r1 + dx_right[2]/r2)/r1;
+        dcos_theta[0] = -sgn * (dx_left[0] * cos_theta / r1 + dx_right[0] / r2) / r1;
+        dcos_theta[1] = -sgn * (dx_left[1] * cos_theta / r1 + dx_right[1] / r2) / r1;
+        dcos_theta[2] = -sgn * (dx_left[2] * cos_theta / r1 + dx_right[2] / r2) / r1;
       }
 
       // both bonds crossing the plane
-      if (right_cross && left_cross)
-      {
+
+      if (right_cross && left_cross) {
+
         // due to right bond
+
         double sgn = copysign(1.0, x_angle_middle[dir] - pos);
-        dcos_theta[0] = -sgn*(dx_right[0]*cos_theta/r2 + dx_left[0]/r1)/r2;
-        dcos_theta[1] = -sgn*(dx_right[1]*cos_theta/r2 + dx_left[1]/r1)/r2;
-        dcos_theta[2] = -sgn*(dx_right[2]*cos_theta/r2 + dx_left[2]/r1)/r2;
+        dcos_theta[0] = -sgn * (dx_right[0] * cos_theta / r2 + dx_left[0] / r1) / r2;
+        dcos_theta[1] = -sgn * (dx_right[1] * cos_theta / r2 + dx_left[1] / r1) / r2;
+        dcos_theta[2] = -sgn * (dx_right[2] * cos_theta / r2 + dx_left[2] / r1) / r2;
 
         // due to left bond
-        dcos_theta[0] += sgn*(dx_left[0]*cos_theta/r1 + dx_right[0]/r2)/r1;
-        dcos_theta[1] += sgn*(dx_left[1]*cos_theta/r1 + dx_right[1]/r2)/r1;
-        dcos_theta[2] += sgn*(dx_left[2]*cos_theta/r1 + dx_right[2]/r2)/r1;
+
+        dcos_theta[0] += sgn * (dx_left[0] * cos_theta / r1 + dx_right[0] / r2) / r1;
+        dcos_theta[1] += sgn * (dx_left[1] * cos_theta / r1 + dx_right[1] / r2) / r1;
+        dcos_theta[2] += sgn * (dx_left[2] * cos_theta / r1 + dx_right[2] / r2) / r1;
       }
 
       // final contribution of the given angle term
-      local_contribution[0] += duang*dcos_theta[0]/area*nktv2p;
-      local_contribution[1] += duang*dcos_theta[1]/area*nktv2p;
-      local_contribution[2] += duang*dcos_theta[2]/area*nktv2p;
+
+      local_contribution[0] += duang * dcos_theta[0] / area * nktv2p;
+      local_contribution[1] += duang * dcos_theta[1] / area * nktv2p;
+      local_contribution[2] += duang * dcos_theta[2] / area * nktv2p;
     }
   }
+
   // loop over the keywords and if necessary add the angle contribution
+
   int m = 0;
   while (m < nvalues) {
     if (which[m] == CONF || which[m] == TOTAL || which[m] == ANGLE) {
       angle_local[m] = local_contribution[0];
-      angle_local[m+1] = local_contribution[1];
-      angle_local[m+2] = local_contribution[2];
+      angle_local[m + 1] = local_contribution[1];
+      angle_local[m + 2] = local_contribution[2];
     }
     m += 3;
   }
diff --git a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
index 12a02cbe63..cc201fdbaa 100644
--- a/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
+++ b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
@@ -41,11 +41,10 @@ enum { X, Y, Z };
 enum { LOWER, CENTER, UPPER, COORD };
 enum { TOTAL, CONF, KIN, PAIR, BOND };
 
-// clang-format off
 /* ---------------------------------------------------------------------- */
 
 ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg)
+    Compute(lmp, narg, arg)
 {
   if (narg < 7) utils::missing_cmd_args(FLERR, "compute stress/mop/profile", error);
 
@@ -53,58 +52,64 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
 
   // set compute mode and direction of plane(s) for pressure calculation
 
-  if (strcmp(arg[3],"x") == 0) {
+  if (strcmp(arg[3], "x") == 0) {
     dir = X;
-  } else if (strcmp(arg[3],"y") == 0) {
+  } else if (strcmp(arg[3], "y") == 0) {
     dir = Y;
-  } else if (strcmp(arg[3],"z") == 0) {
+  } else if (strcmp(arg[3], "z") == 0) {
     dir = Z;
-  } else error->all(FLERR,"Illegal compute stress/mop/profile command");
+  } else
+    error->all(FLERR, "Illegal compute stress/mop/profile command");
 
   // bin parameters
 
-  if (strcmp(arg[4],"lower") == 0) originflag = LOWER;
-  else if (strcmp(arg[4],"center") == 0) originflag = CENTER;
-  else if (strcmp(arg[4],"upper") == 0) originflag = UPPER;
-  else originflag = COORD;
-  if (originflag == COORD) origin = utils::numeric(FLERR,arg[4],false,lmp);
-  delta = utils::numeric(FLERR,arg[5],false,lmp);
-  invdelta = 1.0/delta;
+  if (strcmp(arg[4], "lower") == 0)
+    originflag = LOWER;
+  else if (strcmp(arg[4], "center") == 0)
+    originflag = CENTER;
+  else if (strcmp(arg[4], "upper") == 0)
+    originflag = UPPER;
+  else
+    originflag = COORD;
+  if (originflag == COORD) origin = utils::numeric(FLERR, arg[4], false, lmp);
+  delta = utils::numeric(FLERR, arg[5], false, lmp);
+  invdelta = 1.0 / delta;
 
   // parse values until one isn't recognized
 
-  which = new int[3*(narg-6)];
+  which = new int[3 * (narg - 6)];
   nvalues = 0;
   int i;
 
-  int iarg=6;
+  int iarg = 6;
   while (iarg < narg) {
-    if (strcmp(arg[iarg],"conf") == 0) {
-      for (i=0; i<3; i++) {
+    if (strcmp(arg[iarg], "conf") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = CONF;
         nvalues++;
       }
-    } else if (strcmp(arg[iarg],"kin") == 0) {
-      for (i=0; i<3; i++) {
+    } else if (strcmp(arg[iarg], "kin") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = KIN;
         nvalues++;
       }
-    } else if (strcmp(arg[iarg],"total") == 0) {
-      for (i=0; i<3; i++) {
+    } else if (strcmp(arg[iarg], "total") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = TOTAL;
         nvalues++;
       }
-    } else if (strcmp(arg[iarg],"pair") == 0) {
-      for (i=0; i<3; i++) {
+    } else if (strcmp(arg[iarg], "pair") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = PAIR;
         nvalues++;
       }
-    } else if (strcmp(arg[iarg],"bond") == 0) {
-      for (i=0; i<3; i++) {
+    } else if (strcmp(arg[iarg], "bond") == 0) {
+      for (i = 0; i < 3; i++) {
         which[nvalues] = BOND;
         nvalues++;
       }
-    } else error->all(FLERR, "Illegal compute stress/mop/profile command"); //break;
+    } else
+      error->all(FLERR, "Illegal compute stress/mop/profile command");    //break;
 
     iarg++;
   }
@@ -136,7 +141,7 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
 
   // this fix produces a global array
 
-  memory->create(array,nbins,1+nvalues,"stress/mop/profile:array");
+  memory->create(array, nbins, 1 + nvalues, "stress/mop/profile:array");
   size_array_rows = nbins;
   size_array_cols = 1 + nvalues;
 
@@ -173,47 +178,49 @@ void ComputeStressMopProfile::init()
 
   area = 1;
   int i;
-  for (i=0; i<3; i++) {
-    if (i!=dir) area = area*domain->prd[i];
+  for (i = 0; i < 3; i++) {
+    if (i != dir) area = area * domain->prd[i];
   }
 
   // timestep Value
 
   dt = update->dt;
 
-  // Error check
+  // Error checks:
+
   // Compute stress/mop/profile requires fixed simulation box
 
   if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
     error->all(FLERR, "Compute stress/mop/profile requires a fixed simulation box");
 
-  //This compute requires a pair style with pair_single method implemented
+  // This compute requires a pair style with pair_single method implemented
 
-  if (!force->pair)
-    error->all(FLERR,"No pair style is defined for compute stress/mop/profile");
+  if (!force->pair) error->all(FLERR, "No pair style is defined for compute stress/mop/profile");
   if (force->pair->single_enable == 0)
-    error->all(FLERR,"Pair style does not support compute stress/mop/profile");
+    error->all(FLERR, "Pair style does not support compute stress/mop/profile");
 
   // Errors
 
   if (comm->me == 0) {
 
-    //Compute stress/mop/profile only accounts for pair interactions.
+    // Compute stress/mop/profile only accounts for pair interactions.
     // issue an error if any intramolecular potential or Kspace is defined.
 
     if (force->bond) bondflag = 1;
 
     if (force->angle)
       if ((strcmp(force->angle_style, "zero") != 0) && (strcmp(force->angle_style, "none") != 0))
-        error->all(FLERR,"compute stress/mop/profile does not account for angle potentials");
+        error->all(FLERR, "compute stress/mop/profile does not account for angle potentials");
     if (force->dihedral)
-      if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
-        error->all(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
+      if ((strcmp(force->dihedral_style, "zero") != 0) &&
+          (strcmp(force->dihedral_style, "none") != 0))
+        error->all(FLERR, "compute stress/mop/profile does not account for dihedral potentials");
     if (force->improper)
-      if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
-        error->all(FLERR,"compute stress/mop/profile does not account for improper potentials");
+      if ((strcmp(force->improper_style, "zero") != 0) &&
+          (strcmp(force->improper_style, "none") != 0))
+        error->all(FLERR, "compute stress/mop/profile does not account for improper potentials");
     if (force->kspace)
-      error->warning(FLERR,"compute stress/mop/profile does not account for kspace contributions");
+      error->warning(FLERR, "compute stress/mop/profile does not account for kspace contributions");
   }
 
   // need an occasional half neighbor list
@@ -228,7 +235,6 @@ void ComputeStressMopProfile::init_list(int /* id */, NeighList *ptr)
   list = ptr;
 }
 
-
 /* ----------------------------------------------------------------------
    compute output array
    ------------------------------------------------------------------------- */
@@ -237,39 +243,41 @@ void ComputeStressMopProfile::compute_array()
 {
   invoked_array = update->ntimestep;
 
-  //Compute pressures on separate procs
+  // Compute pressures on separate procs
+
   compute_pairs();
 
   // sum pressure contributions over all procs
-  MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,MPI_DOUBLE,MPI_SUM,world);
+
+  MPI_Allreduce(&values_local[0][0], &values_global[0][0], nbins * nvalues, MPI_DOUBLE, MPI_SUM,
+                world);
+
+  // Compute bond contribution on separate procs
 
   if (bondflag) {
-    //Compute bond contribution on separate procs
     compute_bonds();
   } else {
     for (int m = 0; m < nbins; m++) {
-      for (int i = 0; i < nvalues; i++) {
-        bond_local[m][i] = 0.0;
-      }
+      for (int i = 0; i < nvalues; i++) { bond_local[m][i] = 0.0; }
     }
   }
 
   // sum bond contribution over all procs
-  MPI_Allreduce(&bond_local[0][0],&bond_global[0][0],nbins*nvalues,MPI_DOUBLE,MPI_SUM,world);
 
-  for (int ibin=0; ibin<nbins; ibin++) {
+  MPI_Allreduce(&bond_local[0][0], &bond_global[0][0], nbins * nvalues, MPI_DOUBLE, MPI_SUM, world);
+
+  for (int ibin = 0; ibin < nbins; ibin++) {
     array[ibin][0] = coord[ibin][0];
 
     int mo = 1;
     int m = 0;
     while (m < nvalues) {
-      array[ibin][m+mo] = values_global[ibin][m] + bond_global[ibin][m];
+      array[ibin][m + mo] = values_global[ibin][m] + bond_global[ibin][m];
       m++;
     }
   }
 }
 
-
 /*------------------------------------------------------------------------
   compute pressure contribution of local proc
   -------------------------------------------------------------------------*/
@@ -277,11 +285,11 @@ void ComputeStressMopProfile::compute_array()
 void ComputeStressMopProfile::compute_pairs()
 
 {
-  int i,j,m,ii,jj,inum,jnum,itype,jtype,ibin;
-  double delx,dely,delz;
-  double rsq,fpair,factor_coul,factor_lj;
-  int *ilist,*jlist,*numneigh,**firstneigh;
-  double pos,pos1;
+  int i, j, m, ii, jj, inum, jnum, itype, jtype, ibin;
+  double delx, dely, delz;
+  double rsq, fpair, factor_coul, factor_lj;
+  int *ilist, *jlist, *numneigh, **firstneigh;
+  double pos, pos1;
 
   double *mass = atom->mass;
   double *rmass = atom->rmass;
@@ -292,8 +300,8 @@ void ComputeStressMopProfile::compute_pairs()
   double *special_lj = force->special_lj;
   int newton_pair = force->newton_pair;
 
-
   // zero out arrays for one sample
+
   for (m = 0; m < nbins; m++) {
     for (i = 0; i < nvalues; i++) values_local[m][i] = 0.0;
   }
@@ -351,53 +359,51 @@ void ComputeStressMopProfile::compute_pairs()
           delx = xi[0] - xj[0];
           dely = xi[1] - xj[1];
           delz = xi[2] - xj[2];
-          rsq = delx*delx + dely*dely + delz*delz;
+          rsq = delx * delx + dely * dely + delz * delz;
           jtype = type[j];
           if (rsq >= cutsq[itype][jtype]) continue;
 
           if (newton_pair || j < nlocal) {
 
-            for (ibin=0;ibin<nbins;ibin++) {
+            for (ibin = 0; ibin < nbins; ibin++) {
               pos = coord[ibin][0];
               pos1 = coordp[ibin][0];
 
-              //check if ij pair is across plane, add contribution to pressure
+              // check if ij pair is across plane, add contribution to pressure
 
-              if ( ((xi[dir]>pos) && (xj[dir]<pos))
-                   || ((xi[dir]>pos1) && (xj[dir]<pos1))) {
+              if (((xi[dir] > pos) && (xj[dir] < pos)) || ((xi[dir] > pos1) && (xj[dir] < pos1))) {
 
-                pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+                pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
 
-                values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
-                values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
-                values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+                values_local[ibin][m] += fpair * (xi[0] - xj[0]) / area * nktv2p;
+                values_local[ibin][m + 1] += fpair * (xi[1] - xj[1]) / area * nktv2p;
+                values_local[ibin][m + 2] += fpair * (xi[2] - xj[2]) / area * nktv2p;
 
-              } else if ( ((xi[dir]<pos) && (xj[dir]>pos))
-                          || ((xi[dir]<pos1) && (xj[dir]>pos1))) {
+              } else if (((xi[dir] < pos) && (xj[dir] > pos)) ||
+                         ((xi[dir] < pos1) && (xj[dir] > pos1))) {
 
-                pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+                pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
 
-                values_local[ibin][m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
-                values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
-                values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
+                values_local[ibin][m] -= fpair * (xi[0] - xj[0]) / area * nktv2p;
+                values_local[ibin][m + 1] -= fpair * (xi[1] - xj[1]) / area * nktv2p;
+                values_local[ibin][m + 2] -= fpair * (xi[2] - xj[2]) / area * nktv2p;
               }
             }
           } else {
 
-            for (ibin=0;ibin<nbins;ibin++) {
+            for (ibin = 0; ibin < nbins; ibin++) {
               pos = coord[ibin][0];
               pos1 = coordp[ibin][0];
 
               //check if ij pair is across plane, add contribution to pressure
 
-              if ( ((xi[dir]>pos) && (xj[dir]<pos))
-                   || ((xi[dir]>pos1) && (xj[dir]<pos1))) {
+              if (((xi[dir] > pos) && (xj[dir] < pos)) || ((xi[dir] > pos1) && (xj[dir] < pos1))) {
 
-                pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+                pair->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fpair);
 
-                values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
-                values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
-                values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+                values_local[ibin][m] += fpair * (xi[0] - xj[0]) / area * nktv2p;
+                values_local[ibin][m + 1] += fpair * (xi[1] - xj[1]) / area * nktv2p;
+                values_local[ibin][m + 2] += fpair * (xi[2] - xj[2]) / area * nktv2p;
               }
             }
           }
@@ -420,54 +426,57 @@ void ComputeStressMopProfile::compute_pairs()
 
           itype = type[i];
 
-          //coordinates at t
+          // coordinates at t
+
           xi[0] = atom->x[i][0];
           xi[1] = atom->x[i][1];
           xi[2] = atom->x[i][2];
 
-          //velocities at t
+          // velocities at t
+
           vi[0] = atom->v[i][0];
           vi[1] = atom->v[i][1];
           vi[2] = atom->v[i][2];
 
-          //forces at t
+          // forces at t
+
           fi[0] = atom->f[i][0];
           fi[1] = atom->f[i][1];
           fi[2] = atom->f[i][2];
 
           const double imass = (rmass) ? rmass[i] : mass[itype];
-          const double iterm = 0.5/imass*dt*ftm2v;
+          const double iterm = 0.5 / imass * dt * ftm2v;
 
           // coordinates at t-dt (based on Velocity-Verlet alg.)
 
-          xj[0] = xi[0]-vi[0]*dt+fi[0]*iterm*dt;
-          xj[1] = xi[1]-vi[1]*dt+fi[1]*iterm*dt;
-          xj[2] = xi[2]-vi[2]*dt+fi[2]*iterm*dt;
+          xj[0] = xi[0] - vi[0] * dt + fi[0] * iterm * dt;
+          xj[1] = xi[1] - vi[1] * dt + fi[1] * iterm * dt;
+          xj[2] = xi[2] - vi[2] * dt + fi[2] * iterm * dt;
 
           for (ibin = 0; ibin < nbins; ibin++) {
             pos = coord[ibin][0];
             pos1 = coordp[ibin][0];
 
-            if (((xi[dir]-pos)*(xj[dir]-pos)*(xi[dir]-pos1)*(xj[dir]-pos1)<0)) {
+            if (((xi[dir] - pos) * (xj[dir] - pos) * (xi[dir] - pos1) * (xj[dir] - pos1) < 0)) {
 
-              sgn = copysign(1.0,vi[dir]);
+              sgn = copysign(1.0, vi[dir]);
 
               // approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
 
               double vcross[3];
-              vcross[0] = vi[0]-fi[0]*iterm;
-              vcross[1] = vi[1]-fi[1]*iterm;
-              vcross[2] = vi[2]-fi[2]*iterm;
+              vcross[0] = vi[0] - fi[0] * iterm;
+              vcross[1] = vi[1] - fi[1] * iterm;
+              vcross[2] = vi[2] - fi[2] * iterm;
 
-              values_local[ibin][m] += imass*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
-              values_local[ibin][m+1] += imass*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
-              values_local[ibin][m+2] += imass*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
+              values_local[ibin][m] += imass * vcross[0] * sgn / dt / area * nktv2p / ftm2v;
+              values_local[ibin][m + 1] += imass * vcross[1] * sgn / dt / area * nktv2p / ftm2v;
+              values_local[ibin][m + 2] += imass * vcross[2] * sgn / dt / area * nktv2p / ftm2v;
             }
           }
         }
       }
     }
-    m+=3;
+    m += 3;
   }
 }
 
@@ -503,16 +512,16 @@ void ComputeStressMopProfile::compute_bonds()
   double x_bond_2[3] = {0.0, 0.0, 0.0};
 
   // initialization
+
   for (int m = 0; m < nbins; m++) {
-    for (int i = 0; i < nvalues; i++) {
-      bond_local[m][i] = 0.0;
-    }
+    for (int i = 0; i < nvalues; i++) { bond_local[m][i] = 0.0; }
     local_contribution[m][0] = 0.0;
     local_contribution[m][1] = 0.0;
     local_contribution[m][2] = 0.0;
   }
 
   // loop over all bonded atoms in the current proc
+
   for (atom1 = 0; atom1 < nlocal; atom1++) {
     if (!(mask[atom1] & groupbit)) continue;
 
@@ -539,10 +548,11 @@ void ComputeStressMopProfile::compute_bonds()
       if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
       if (btype <= 0) continue;
 
-      for (int ibin = 0; ibin<nbins; ibin++) {
+      for (int ibin = 0; ibin < nbins; ibin++) {
         double pos = coord[ibin][0];
 
         // minimum image of atom1 with respect to the plane of interest
+
         dx[0] = x[atom1][0];
         dx[1] = x[atom1][1];
         dx[2] = x[atom1][2];
@@ -554,6 +564,7 @@ void ComputeStressMopProfile::compute_bonds()
         x_bond_1[dir] += pos;
 
         // minimum image of atom2 with respect to atom1
+
         dx[0] = x[atom2][0] - x_bond_1[0];
         dx[1] = x[atom2][1] - x_bond_1[1];
         dx[2] = x[atom2][2] - x_bond_1[2];
@@ -563,6 +574,7 @@ void ComputeStressMopProfile::compute_bonds()
         x_bond_2[2] = x_bond_1[2] + dx[2];
 
         // check if the bond vector crosses the plane of interest
+
         double tau = (x_bond_1[dir] - pos) / (x_bond_1[dir] - x_bond_2[dir]);
         if ((tau <= 1) && (tau >= 0)) {
           dx[0] = x_bond_1[0] - x_bond_2[0];
@@ -572,22 +584,23 @@ void ComputeStressMopProfile::compute_bonds()
           bond->single(btype, rsq, atom1, atom2, fpair);
 
           double sgn = copysign(1.0, x_bond_1[dir] - pos);
-          local_contribution[ibin][0] += sgn*fpair*dx[0]/area*nktv2p;
-          local_contribution[ibin][1] += sgn*fpair*dx[1]/area*nktv2p;
-          local_contribution[ibin][2] += sgn*fpair*dx[2]/area*nktv2p;
+          local_contribution[ibin][0] += sgn * fpair * dx[0] / area * nktv2p;
+          local_contribution[ibin][1] += sgn * fpair * dx[1] / area * nktv2p;
+          local_contribution[ibin][2] += sgn * fpair * dx[2] / area * nktv2p;
         }
       }
     }
   }
 
   // loop over the keywords and if necessary add the bond contribution
+
   int m = 0;
   while (m < nvalues) {
     if ((which[m] == CONF) || (which[m] == TOTAL) || (which[m] == BOND)) {
       for (int ibin = 0; ibin < nbins; ibin++) {
         bond_local[ibin][m] = local_contribution[ibin][0];
-        bond_local[ibin][m+1] = local_contribution[ibin][1];
-        bond_local[ibin][m+2] = local_contribution[ibin][2];
+        bond_local[ibin][m + 1] = local_contribution[ibin][1];
+        bond_local[ibin][m + 2] = local_contribution[ibin][2];
       }
     }
     m += 3;
@@ -601,47 +614,51 @@ void ComputeStressMopProfile::compute_bonds()
 
 void ComputeStressMopProfile::setup_bins()
 {
-  int i,n;
+  int i, n;
   double lo = 0.0, hi = 0.0;
 
-  double *boxlo,*boxhi;
+  double *boxlo, *boxhi;
   boxlo = domain->boxlo;
   boxhi = domain->boxhi;
 
-  if (originflag == LOWER) origin = boxlo[dir];
-  else if (originflag == UPPER) origin = boxhi[dir];
+  if (originflag == LOWER)
+    origin = boxlo[dir];
+  else if (originflag == UPPER)
+    origin = boxhi[dir];
   else if (originflag == CENTER)
     origin = 0.5 * (boxlo[dir] + boxhi[dir]);
 
   if (origin < boxlo[dir]) {
-    error->all(FLERR,"Origin of bins for compute stress/mop/profile is out of bounds" );
+    error->all(FLERR, "Origin of bins for compute stress/mop/profile is out of bounds");
   } else {
-    n = static_cast<int> ((origin - boxlo[dir]) * invdelta);
-    lo = origin - n*delta;
+    n = static_cast<int>((origin - boxlo[dir]) * invdelta);
+    lo = origin - n * delta;
   }
   if (origin < boxhi[dir]) {
-    n = static_cast<int> ((boxhi[dir] - origin) * invdelta);
-    hi = origin + n*delta;
+    n = static_cast<int>((boxhi[dir] - origin) * invdelta);
+    hi = origin + n * delta;
   } else {
-    error->all(FLERR,"Origin of bins for compute stress/mop/profile is out of bounds" );
+    error->all(FLERR, "Origin of bins for compute stress/mop/profile is out of bounds");
   }
 
   offset = lo;
-  nbins = static_cast<int> ((hi-lo) * invdelta + 1.5);
+  nbins = static_cast<int>((hi - lo) * invdelta + 1.5);
 
-  //allocate bin arrays
-  memory->create(coord,nbins,1,"stress/mop/profile:coord");
-  memory->create(coordp,nbins,1,"stress/mop/profile:coordp");
-  memory->create(values_local,nbins,nvalues,"stress/mop/profile:values_local");
-  memory->create(values_global,nbins,nvalues,"stress/mop/profile:values_global");
-  memory->create(bond_local,nbins,nvalues,"stress/mop/profile:bond_local");
-  memory->create(bond_global,nbins,nvalues,"stress/mop/profile:bond_global");
-  memory->create(local_contribution,nbins,3,"stress/mop/profile:local_contribution");
+  // allocate bin arrays
+
+  memory->create(coord, nbins, 1, "stress/mop/profile:coord");
+  memory->create(coordp, nbins, 1, "stress/mop/profile:coordp");
+  memory->create(values_local, nbins, nvalues, "stress/mop/profile:values_local");
+  memory->create(values_global, nbins, nvalues, "stress/mop/profile:values_global");
+  memory->create(bond_local, nbins, nvalues, "stress/mop/profile:bond_local");
+  memory->create(bond_global, nbins, nvalues, "stress/mop/profile:bond_global");
+  memory->create(local_contribution, nbins, 3, "stress/mop/profile:local_contribution");
 
   // set bin coordinates
+
   for (i = 0; i < nbins; i++) {
-    coord[i][0] = offset + i*delta;
-    if (coord[i][0] < (domain->boxlo[dir]+domain->prd_half[dir])) {
+    coord[i][0] = offset + i * delta;
+    if (coord[i][0] < (domain->boxlo[dir] + domain->prd_half[dir])) {
       coordp[i][0] = coord[i][0] + domain->prd[dir];
     } else {
       coordp[i][0] = coord[i][0] - domain->prd[dir];

From 46a9f0a08c4e9d5a7777015f68ce57ca5a18e306 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@gmail.com>
Date: Mon, 26 Jun 2023 11:08:04 -0700
Subject: [PATCH 316/396] change QM Python wrappers to use ENERGY instead of PE
 as MDI command

---
 examples/QUANTUM/LATTE/latte_mdi.py   | 6 +++---
 examples/QUANTUM/NWChem/nwchem_mdi.py | 6 +++---
 examples/QUANTUM/PySCF/pyscf_mdi.py   | 6 +++---
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/examples/QUANTUM/LATTE/latte_mdi.py b/examples/QUANTUM/LATTE/latte_mdi.py
index 0170feee1f..ba1a83120a 100644
--- a/examples/QUANTUM/LATTE/latte_mdi.py
+++ b/examples/QUANTUM/LATTE/latte_mdi.py
@@ -153,7 +153,7 @@ def mdi_engine(other_options):
 
   # engine --> driver
 
-  mdi.MDI_Register_Command("@DEFAULT","<PE")
+  mdi.MDI_Register_Command("@DEFAULT","<ENERGY")
   mdi.MDI_Register_Command("@DEFAULT","<FORCES")
   mdi.MDI_Register_Command("@DEFAULT",">LATTICE_FORCES")
   mdi.MDI_Register_Command("@DEFAULT","<STRESS")
@@ -232,10 +232,10 @@ def execute_command(command,mdicomm,object_ptr):
   # MDI commands which retreive quantum results
   # each may also trigger the quantum calculation
   
-  elif command == "<PE":
+  elif command == "<ENERGY":
     evaluate()
     ierr = mdi.MDI_Send(qm_pe,1,mdi.MDI_DOUBLE,mdicomm)
-    if ierr: error("MDI: <PE data")
+    if ierr: error("MDI: <ENERGY data")
     
   elif command == "<FORCES":
     evaluate()
diff --git a/examples/QUANTUM/NWChem/nwchem_mdi.py b/examples/QUANTUM/NWChem/nwchem_mdi.py
index 170a15c732..ceb67aefdf 100644
--- a/examples/QUANTUM/NWChem/nwchem_mdi.py
+++ b/examples/QUANTUM/NWChem/nwchem_mdi.py
@@ -159,7 +159,7 @@ def mdi_engine(other_options):
 
   # engine --> driver
 
-  mdi.MDI_Register_Command("@DEFAULT","<PE")
+  mdi.MDI_Register_Command("@DEFAULT","<ENERGY")
   mdi.MDI_Register_Command("@DEFAULT","<FORCES")
   mdi.MDI_Register_Command("@DEFAULT",">LATTICE_FORCES")
   #mdi.MDI_Register_Command("@DEFAULT","<STRESS")
@@ -236,10 +236,10 @@ def execute_command(command,mdicomm,object_ptr):
   # MDI commands which retreive quantum results
   # each may also trigger the quantum calculation
   
-  elif command == "<PE":
+  elif command == "<ENERGY":
     evaluate()
     ierr = mdi.MDI_Send(qm_pe,1,mdi.MDI_DOUBLE,mdicomm)
-    if ierr: error("MDI: <PE data")
+    if ierr: error("MDI: <ENERGY data")
     
   elif command == "<FORCES":
     evaluate()
diff --git a/examples/QUANTUM/PySCF/pyscf_mdi.py b/examples/QUANTUM/PySCF/pyscf_mdi.py
index b48d9ae598..4272ee9c1f 100644
--- a/examples/QUANTUM/PySCF/pyscf_mdi.py
+++ b/examples/QUANTUM/PySCF/pyscf_mdi.py
@@ -189,7 +189,7 @@ def mdi_engine(other_options):
 
   # engine --> driver
 
-  mdi.MDI_Register_Command("@DEFAULT","<PE")
+  mdi.MDI_Register_Command("@DEFAULT","<ENERGY")
   mdi.MDI_Register_Command("@DEFAULT","<FORCES")
   mdi.MDI_Register_Command("@DEFAULT","<LATTICE_FORCES")
   #mdi.MDI_Register_Command("@DEFAULT","<STRESS")
@@ -262,10 +262,10 @@ def execute_command(command,mdicomm,object_ptr):
   # MDI commands which retreive quantum results
   # each may also trigger the quantum calculation
 
-  elif command == "<PE":
+  elif command == "<ENERGY":
     evaluate()
     ierr = mdi.MDI_Send(qm_pe,1,mdi.MDI_DOUBLE,mdicomm)
-    if ierr: error("MDI: <PE data")
+    if ierr: error("MDI: <ENERGY data")
 
   elif command == "<FORCES":
     evaluate()

From c3321039386ec9c3fd93ae1e66402affd360756c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 26 Jun 2023 15:20:29 -0400
Subject: [PATCH 317/396] make short read detection bugfix work in parallel

---
 src/utils.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/utils.cpp b/src/utils.cpp
index eee1d5dd46..dd18c4406d 100644
--- a/src/utils.cpp
+++ b/src/utils.cpp
@@ -290,8 +290,9 @@ int utils::read_lines_from_file(FILE *fp, int nlines, int nmax, char *buffer, in
   }
 
   int n = strlen(buffer);
+  if (nlines != mylines) n = 0;
   MPI_Bcast(&n, 1, MPI_INT, 0, comm);
-  if ((n == 0) || (nlines != mylines)) return 1;
+  if (n == 0) return 1;
   MPI_Bcast(buffer, n + 1, MPI_CHAR, 0, comm);
   return 0;
 }

From c347de78501d7e9693842559c37e22e17f0bf6a1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 26 Jun 2023 16:12:15 -0400
Subject: [PATCH 318/396] improve error messages

---
 src/create_bonds.cpp | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index 5355ce2b7c..fa063c7dc6 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -49,7 +49,7 @@ void CreateBonds::command(int narg, char **arg)
   if (atom->molecular != Atom::MOLECULAR)
     error->all(FLERR, "Cannot use create_bonds with non-molecular system");
 
-  if (narg < 4) error->all(FLERR, "Illegal create_bonds command");
+  if (narg < 4) utils::missing_cmd_args(FLERR, "create_bonds", error);
 
   // parse args
 
@@ -58,38 +58,38 @@ void CreateBonds::command(int narg, char **arg)
   int iarg = 0;
   if (strcmp(arg[0], "many") == 0) {
     style = MANY;
-    if (narg != 6) error->all(FLERR, "Illegal create_bonds command");
+    if (narg != 6) error->all(FLERR, "No optional keywords allowed with create_bonds many");
     igroup = group->find(arg[1]);
-    if (igroup == -1) error->all(FLERR, "Cannot find create_bonds group ID");
+    if (igroup == -1) error->all(FLERR, "Cannot find create_bonds first group ID {}",arg[1]);
     group1bit = group->bitmask[igroup];
     igroup = group->find(arg[2]);
-    if (igroup == -1) error->all(FLERR, "Cannot find create_bonds group ID");
+    if (igroup == -1) error->all(FLERR, "Cannot find create_bonds second group ID {}", arg[2]);
     group2bit = group->bitmask[igroup];
     btype = utils::inumeric(FLERR, arg[3], false, lmp);
     rmin = utils::numeric(FLERR, arg[4], false, lmp);
     rmax = utils::numeric(FLERR, arg[5], false, lmp);
-    if (rmin > rmax) error->all(FLERR, "Illegal create_bonds command");
+    if (rmin > rmax) error->all(FLERR, "Inconsistent cutoffs for create_bonds many");
     iarg = 6;
   } else if (strcmp(arg[0], "single/bond") == 0) {
     style = SBOND;
     btype = utils::inumeric(FLERR, arg[1], false, lmp);
     batom1 = utils::tnumeric(FLERR, arg[2], false, lmp);
     batom2 = utils::tnumeric(FLERR, arg[3], false, lmp);
-    if (batom1 == batom2) error->all(FLERR, "Illegal create_bonds command");
+    if (batom1 == batom2) error->all(FLERR, "Bond atoms must be different");
     iarg = 4;
   } else if (strcmp(arg[0], "single/angle") == 0) {
     style = SANGLE;
-    if (narg < 5) error->all(FLERR, "Illegal create_bonds command");
+    if (narg < 5) utils::missing_cmd_args(FLERR, "create_bonds single/angle", error);
     atype = utils::inumeric(FLERR, arg[1], false, lmp);
     aatom1 = utils::tnumeric(FLERR, arg[2], false, lmp);
     aatom2 = utils::tnumeric(FLERR, arg[3], false, lmp);
     aatom3 = utils::tnumeric(FLERR, arg[4], false, lmp);
     if ((aatom1 == aatom2) || (aatom1 == aatom3) || (aatom2 == aatom3))
-      error->all(FLERR, "Illegal create_bonds command");
+      error->all(FLERR, "Angle atoms must be different");
     iarg = 5;
   } else if (strcmp(arg[0], "single/dihedral") == 0) {
     style = SDIHEDRAL;
-    if (narg < 6) error->all(FLERR, "Illegal create_bonds command");
+    if (narg < 6) utils::missing_cmd_args(FLERR, "create_bonds single/dihedral", error);
     dtype = utils::inumeric(FLERR, arg[1], false, lmp);
     datom1 = utils::tnumeric(FLERR, arg[2], false, lmp);
     datom2 = utils::tnumeric(FLERR, arg[3], false, lmp);
@@ -101,7 +101,7 @@ void CreateBonds::command(int narg, char **arg)
     iarg = 6;
   } else if (strcmp(arg[0], "single/improper") == 0) {
     style = SIMPROPER;
-    if (narg < 6) error->all(FLERR, "Illegal create_bonds command");
+    if (narg < 6) utils::missing_cmd_args(FLERR, "create_bonds single/improper", error);
     dtype = utils::inumeric(FLERR, arg[1], false, lmp);
     datom1 = utils::tnumeric(FLERR, arg[2], false, lmp);
     datom2 = utils::tnumeric(FLERR, arg[3], false, lmp);

From 906eecdbd7346b2921b01ec9f998f18e1c8886f0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 27 Jun 2023 17:53:06 -0400
Subject: [PATCH 319/396] clarify the temperature computation in compute temp

---
 doc/src/compute_temp.rst                    | 28 +++++++++++++--------
 doc/utils/sphinx-config/false_positives.txt |  1 +
 2 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst
index 8f6f9f225f..e081280496 100644
--- a/doc/src/compute_temp.rst
+++ b/doc/src/compute_temp.rst
@@ -37,20 +37,24 @@ The temperature is calculated by the formula
 
 .. math::
 
-   \text{KE} = \frac{\text{dim}}{2} N k_B T,
+   T  = \frac{2 E_\mathrm{kin}}{N_\mathrm{DOF} k_B} \quad \mathrm{with} \quad
+   E_\mathrm{kin} = \sum^{N_\mathrm{atoms}}_{i=1} \frac{1}{2} m_i v^2_i \quad \mathrm{and} \quad
+   N_\mathrm{DOF} = n_\mathrm{dim} N_\mathrm{atoms} - n_\mathrm{dim} - N_\mathrm{fix DOFs}
 
-where KE = total kinetic energy of the group of atoms (sum of
-:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the
-simulation, :math:`N` is the number of atoms in the group, :math:`k_B`
-is the Boltzmann constant, and :math:`T` is the absolute temperature.
+where :math:`E_\mathrm{kin}` is the total kinetic energy of the group of
+atoms, :math:`n_\mathrm{dim}` is the dimensionality of the simulation
+(i.e. either 2 or 3), :math:`N_\mathrm{atoms}` is the number of atoms in
+the group, :math:`N_\mathrm{fix DOFs}` is the number of degrees of
+freedom removed by fix commands (see below), :math:`k_B` is the
+Boltzmann constant, and :math:`T` is the resulting computed temperature.
 
 A kinetic energy tensor, stored as a six-element vector, is also
 calculated by this compute for use in the computation of a pressure
-tensor.  The formula for the components of the tensor is the same as
-the above formula, except that :math:`v^2` is replaced by :math:`v_x
-v_y` for the :math:`xy` component, and so on.  The six components of
-the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`,
-:math:`xz`, :math:`yz`.
+tensor.  The formula for the components of the tensor is the same as the
+above expression for :math:`E_\mathrm{kin}`, except that :math:`v_i^2` is
+replaced by :math:`v_{i,x} v_{i,y}` for the :math:`xy` component, and so on.
+The six components of the vector are ordered :math:`xx`, :math:`yy`,
+:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
 
 The number of atoms contributing to the temperature is assumed to be
 constant for the duration of the run; use the *dynamic* option of the
@@ -62,6 +66,10 @@ constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
 atoms that include these constraints will be computed correctly.  If
 needed, the subtracted degrees-of-freedom can be altered using the
 *extra* option of the :doc:`compute_modify <compute_modify>` command.
+By default this *extra* component is initialized to
+:math:`n_\mathrm{dim}` (as shown in the formula above) to represent the
+degrees of freedom removed from a system due to its translation
+invariance due to periodic boundary conditions.
 
 A compute of this style with the ID of "thermo_temp" is created when
 LAMMPS starts up, as if this command were in the input script:
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 5791288a06..a68cd2714f 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -1559,6 +1559,7 @@ intramolecular
 ints
 inumeric
 inv
+invariance
 invariants
 inversed
 invertible

From a4cba99ff9851e5279e2521a45f2ce1e1d5dc2ca Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndactrung@gmail.com>
Date: Tue, 27 Jun 2023 23:55:57 -0500
Subject: [PATCH 320/396] Attempted to update slabcorr() in pppm/dielectric

---
 src/DIELECTRIC/fix_polarize_bem_icc.cpp | 2 ++
 src/DIELECTRIC/pppm_dielectric.cpp      | 6 +++---
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/DIELECTRIC/fix_polarize_bem_icc.cpp b/src/DIELECTRIC/fix_polarize_bem_icc.cpp
index 2b5664e4f5..4dc7dd2669 100644
--- a/src/DIELECTRIC/fix_polarize_bem_icc.cpp
+++ b/src/DIELECTRIC/fix_polarize_bem_icc.cpp
@@ -455,6 +455,7 @@ void FixPolarizeBEMICC::set_dielectric_params(double ediff, double emean, double
   double *ed = atom->ed;
   double *em = atom->em;
   double *q = atom->q;
+  double *q_scaled = atom->q_scaled;
   double *epsilon = atom->epsilon;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
@@ -466,6 +467,7 @@ void FixPolarizeBEMICC::set_dielectric_params(double ediff, double emean, double
       if (areai > 0) area[i] = areai;
       if (epsiloni > 0) epsilon[i] = epsiloni;
       if (set_charge) q[i] = qvalue;
+      q_scaled[i] = q[i] / epsilon[i];
     }
   }
 }
diff --git a/src/DIELECTRIC/pppm_dielectric.cpp b/src/DIELECTRIC/pppm_dielectric.cpp
index b9ae1d65ff..e308cb0826 100644
--- a/src/DIELECTRIC/pppm_dielectric.cpp
+++ b/src/DIELECTRIC/pppm_dielectric.cpp
@@ -575,7 +575,7 @@ void PPPMDielectric::slabcorr()
   int nlocal = atom->nlocal;
 
   double dipole = 0.0;
-  for (int i = 0; i < nlocal; i++) dipole += q[i]*x[i][2];
+  for (int i = 0; i < nlocal; i++) dipole += eps[i]*q[i]*x[i][2];
 
   // sum local contributions to get global dipole moment
 
@@ -588,7 +588,7 @@ void PPPMDielectric::slabcorr()
   double dipole_r2 = 0.0;
   if (eflag_atom || fabs(qsum) > SMALL) {
     for (int i = 0; i < nlocal; i++)
-      dipole_r2 += q[i]*x[i][2]*x[i][2];
+      dipole_r2 += eps[i]*q[i]*x[i][2]*x[i][2];
 
     // sum local contributions
 
@@ -621,6 +621,6 @@ void PPPMDielectric::slabcorr()
 
   for (int i = 0; i < nlocal; i++) {
     f[i][2] += ffact * eps[i]*q[i]*(dipole_all - qsum*x[i][2]);
-    efield[i][2] += ffact * eps[i]*(dipole_all - qsum*x[i][2]);
+    efield[i][2] += ffact * (dipole_all - qsum*x[i][2]);
   }
 }

From 5d027fc92c66e9875c165355f094dfac3adab74c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 28 Jun 2023 09:50:27 -0400
Subject: [PATCH 321/396] error out when many bonds creation cutoff is larger
 than periodic domain

---
 src/create_bonds.cpp | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index fa063c7dc6..2960eda766 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -60,7 +60,7 @@ void CreateBonds::command(int narg, char **arg)
     style = MANY;
     if (narg != 6) error->all(FLERR, "No optional keywords allowed with create_bonds many");
     igroup = group->find(arg[1]);
-    if (igroup == -1) error->all(FLERR, "Cannot find create_bonds first group ID {}",arg[1]);
+    if (igroup == -1) error->all(FLERR, "Cannot find create_bonds first group ID {}", arg[1]);
     group1bit = group->bitmask[igroup];
     igroup = group->find(arg[2]);
     if (igroup == -1) error->all(FLERR, "Cannot find create_bonds second group ID {}", arg[2]);
@@ -197,6 +197,10 @@ void CreateBonds::many()
   if (rmax > neighbor->cutneighmin && comm->me == 0)
     error->warning(FLERR, "Create_bonds max distance > minimum neighbor cutoff");
 
+  if ((domain->xperiodic && (rmax > domain->xprd)) ||
+      (domain->yperiodic && (rmax > domain->yprd)) || (domain->zperiodic && (rmax > domain->zprd)))
+    error->all(FLERR, "Bond creation cutoff is larger than periodic domain");
+
   // require special_bonds 1-2 weights = 0.0 and KSpace = nullptr
   // so that already bonded atom pairs do not appear in neighbor list
   // otherwise with newton_bond = 1,
@@ -205,7 +209,7 @@ void CreateBonds::many()
 
   if (force->special_lj[1] != 0.0 || force->special_coul[1] != 0.0)
     error->all(FLERR, "Create_bonds command requires special_bonds 1-2 weights be 0.0");
-  if (force->kspace) error->all(FLERR, "Create_bonds command requires no kspace_style be defined");
+  if (force->kspace) error->all(FLERR, "Create_bonds command is incompatible with Kspace styles");
 
   // setup domain, communication and neighboring
   // acquire ghosts and build standard neighbor lists

From a50993dac1255e3fb39e7d2436c69f9a34d38581 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 28 Jun 2023 10:06:31 -0400
Subject: [PATCH 322/396] update docs for create_bonds

---
 doc/src/create_bonds.rst | 45 ++++++++++++++++++++++++----------------
 1 file changed, 27 insertions(+), 18 deletions(-)

diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst
index d520f1a88e..53a9a1ca50 100644
--- a/doc/src/create_bonds.rst
+++ b/doc/src/create_bonds.rst
@@ -86,19 +86,20 @@ data file for a complex system of molecules.
 
 .. note::
 
-   If the system has no bonds (angles, dihedrals, impropers) to begin with,
-   or if more bonds per atom are being added than currently exist, then you
-   must ensure that the number of bond types and the maximum number of
-   bonds per atom are set to large enough values, and similarly for
-   angles, dihedrals, and impropers, otherwise an error may occur when too many
-   bonds (angles, dihedrals, impropers) are added to an atom.  If the
-   :doc:`read_data <read_data>` command is used to define the system, these
-   parameters can be set via the "bond types" and "extra bond per atom"
-   fields in the header section of the data file.  If the
-   :doc:`create_box <create_box>` command is used to define the system,
-   these two parameters can be set via its optional *bond/types* and
-   *extra/bond/per/atom* arguments, and similarly for angles, dihedrals, and
-   impropers.  See the doc pages for these two commands for details.
+   If the system has no bonds (angles, dihedrals, impropers) to begin
+   with, or if more bonds per atom are being added than currently exist,
+   then you must ensure that the number of bond types and the maximum
+   number of bonds per atom are set to large enough values, and
+   similarly for angles, dihedrals, impropers, and special neighbors,
+   otherwise an error may occur when too many bonds (angles, dihedrals,
+   impropers) are added to an atom.  If the :doc:`read_data <read_data>`
+   command is used to define the system, these parameters can be set via
+   its optional *extra/bond/types*, *extra/bond/per/atom*, and similar
+   keywords to the command.  If the :doc:`create_box <create_box>`
+   command is used to define the system, these two parameters can be set
+   via its optional *bond/types* and *extra/bond/per/atom* arguments,
+   and similarly for angles, dihedrals, and impropers.  See the
+   corresponding documentation pages for these two commands for details.
 
 ----------
 
@@ -112,7 +113,7 @@ For a bond to be created, an :math:`I,J` pair of atoms must be a distance
 :math:`D` apart such that :math:`r_\text{min} \le D \le r_\text{max}`.
 
 The following settings must have been made in an input script before
-this style is used:
+the *many* style is used:
 
 * special_bonds weight for 1--2 interactions must be 0.0
 * a :doc:`pair_style <pair_style>` must be defined
@@ -121,10 +122,13 @@ this style is used:
   skin :math:`\ge r_\text{max}`
 
 These settings are required so that a neighbor list can be created to
-search for nearby atoms.  Pairs of atoms that are already bonded
-cannot appear in the neighbor list, to avoid creation of duplicate
-bonds.  The neighbor list for all atom type pairs must also extend to
-a distance that encompasses the *rmax* for new bonds to create.
+search for nearby atoms.  Pairs of atoms that are already bonded cannot
+appear in the neighbor list, to avoid creation of duplicate bonds.  The
+neighbor list for all atom type pairs must also extend to a distance
+that encompasses the *rmax* for new bonds to create.  When using
+periodic boundary conditions, the box length in each periodic dimension
+must be larger than *rmax*, so that no bonds are created between the
+system and its own periodic image.
 
 .. note::
 
@@ -219,6 +223,11 @@ This command cannot be used with molecular systems defined using
 molecule template files via the :doc:`molecule <molecule>` and
 :doc:`atom_style template <atom_style>` commands.
 
+For style *many*, no :doc:`kspace style <kspace_style>` must be
+defined. Also, the *rmax* value must be smaller than any periodic box
+length and the neighbor list cutoff (largest pair cutoff plus neighbor
+skin).
+
 Related commands
 """"""""""""""""
 

From b0b26d9d3a329c76b6ca8d9d164b28f9d597645e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 29 Jun 2023 07:32:52 -0400
Subject: [PATCH 323/396] silence compiler warning

---
 src/lammps.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/lammps.cpp b/src/lammps.cpp
index 956793c20a..9ac4c98bc3 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -135,7 +135,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
   // append git descriptor info to update string when compiling development or maintenance version
 
   std::string update_string = UPDATE_STRING;
-  if (has_git_info() && (update_string == " - Development") || (update_string == " - Maintenance"))
+  if (has_git_info() && ((update_string == " - Development") || (update_string == " - Maintenance")))
     update_string += fmt::format(" - {}", git_descriptor());
 
   external_comm = 0;

From 14462d8f8064884452b3ca3904b3c2ed58920eef Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 29 Jun 2023 16:13:16 -0400
Subject: [PATCH 324/396] join strings

---
 src/neighbor.cpp | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 006101da64..23b4b9984e 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -839,8 +839,7 @@ int Neighbor::init_pair()
   if (style == Neighbor::BIN) {
     for (i = 0; i < nrequest; i++)
       if (requests[i]->occasional && requests[i]->ghost)
-        error->all(FLERR,"Cannot request an occasional binned neighbor list "
-                   "with ghost info");
+        error->all(FLERR,"Cannot request an occasional binned neighbor list with ghost info");
   }
 
   // morph requests in various ways
@@ -2672,8 +2671,7 @@ void Neighbor::modify_params(int narg, char **arg)
                  strcmp(arg[iarg+1],"molecule/intra") == 0) {
         if (iarg+3 > narg) utils::missing_cmd_args(FLERR, "neigh_modify exclude molecule", error);
         if (atom->molecule_flag == 0)
-          error->all(FLERR,"Neigh_modify exclude molecule "
-                     "requires atom attribute molecule");
+          error->all(FLERR,"Neigh_modify exclude molecule requires atom attribute molecule");
         if (nex_mol == maxex_mol) {
           maxex_mol += EXDELTA;
           memory->grow(ex_mol_group,maxex_mol,"neigh:ex_mol_group");

From b7024288b66c3930d87b5cfc1dc825366e0a7390 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 29 Jun 2023 21:20:07 -0400
Subject: [PATCH 325/396] add check to disallow custom neighbor list cutoffs
 larger than the communication cutoff.

---
 src/neighbor.cpp | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 23b4b9984e..df1547e5eb 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -837,9 +837,20 @@ int Neighbor::init_pair()
   //     similar to what vanilla Nbin::coord2atom() does now in atom2bin
 
   if (style == Neighbor::BIN) {
-    for (i = 0; i < nrequest; i++)
+    for (i = 0; i < nrequest; ++i)
       if (requests[i]->occasional && requests[i]->ghost)
-        error->all(FLERR,"Cannot request an occasional binned neighbor list with ghost info");
+        error->all(FLERR, "Cannot request an occasional binned neighbor list with ghost info");
+  }
+
+  // check requests with a custom neighbor list cutoff to make sure the cutoff is within
+  // the communication cutoff.  For perpetual lists, neighbor list skin is added later.
+
+  const double comm_cutoff = comm->get_comm_cutoff();
+  for (i = 0; i < nrequest; ++i) {
+    if (requests[i]->cut) {
+      if (comm_cutoff < (requests[i]->cutoff + (requests[i]->occasional ? 0.0 : skin)))
+        error->all(FLERR, "Custom neighbor list cutoff too large for communication cutoff");
+    }
   }
 
   // morph requests in various ways

From ab1e090e0e5aff5c943e25e64bc6e320d58c70a1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 29 Jun 2023 21:32:04 -0400
Subject: [PATCH 326/396] neighbor list skin is added to custom cutoff
 automatically

---
 src/KIM/pair_kim.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp
index ae2e6e6ea0..8ac6fe1f75 100644
--- a/src/KIM/pair_kim.cpp
+++ b/src/KIM/pair_kim.cpp
@@ -596,7 +596,7 @@ void PairKIM::init_style()
     if (kim_cutoff_values[i] <= neighbor->skin)
       error->all(FLERR,"Illegal neighbor request (force cutoff {:.3} <= skin {:.3})",
                  kim_cutoff_values[i], neighbor->skin);
-    req->set_cutoff(kim_cutoff_values[i] + neighbor->skin);
+    req->set_cutoff(kim_cutoff_values[i]);
   }
   // increment instance_me in case of need to change the neighbor list
   // request settings

From 02498925c57e86bbabdfc861fdf442babe10e03e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 29 Jun 2023 22:07:04 -0400
Subject: [PATCH 327/396] only fail on too small periodic domain in z direction
 if 3d system.

---
 src/create_bonds.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index 2960eda766..13a99a182f 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -198,7 +198,8 @@ void CreateBonds::many()
     error->warning(FLERR, "Create_bonds max distance > minimum neighbor cutoff");
 
   if ((domain->xperiodic && (rmax > domain->xprd)) ||
-      (domain->yperiodic && (rmax > domain->yprd)) || (domain->zperiodic && (rmax > domain->zprd)))
+      (domain->yperiodic && (rmax > domain->yprd)) ||
+      ((domain->dimension == 3) && domain->zperiodic && (rmax > domain->zprd)))
     error->all(FLERR, "Bond creation cutoff is larger than periodic domain");
 
   // require special_bonds 1-2 weights = 0.0 and KSpace = nullptr

From 83528f02e83cdfc84e627f7a9f4b54c766c52bcf Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 29 Jun 2023 22:10:31 -0400
Subject: [PATCH 328/396] whitespace

---
 examples/balance/in.balance               | 44 ++++++-------
 examples/balance/in.balance.bond.fast     | 44 ++++++-------
 examples/balance/in.balance.bond.slow     | 44 ++++++-------
 examples/balance/in.balance.clock.dynamic | 68 ++++++++++----------
 examples/balance/in.balance.clock.static  | 62 +++++++++---------
 examples/balance/in.balance.group.dynamic | 56 ++++++++--------
 examples/balance/in.balance.group.static  | 62 +++++++++---------
 examples/balance/in.balance.kspace        | 52 +++++++--------
 examples/balance/in.balance.neigh.dynamic | 66 +++++++++----------
 examples/balance/in.balance.neigh.rcb     | 66 +++++++++----------
 examples/balance/in.balance.neigh.static  | 58 ++++++++---------
 examples/balance/in.balance.var.dynamic   | 78 +++++++++++------------
 12 files changed, 350 insertions(+), 350 deletions(-)

diff --git a/examples/balance/in.balance b/examples/balance/in.balance
index e0fb5078aa..3a1298acfd 100644
--- a/examples/balance/in.balance
+++ b/examples/balance/in.balance
@@ -2,34 +2,34 @@
 
 variable        b index 0
 
-variable	x index 50
-variable	y index 20
-variable	d index 20
-variable	v index 5
-variable	w index 2
-                
-units		lj
+variable        x index 50
+variable        y index 20
+variable        d index 20
+variable        v index 5
+variable        w index 2
+
+units           lj
 dimension       2
-atom_style	atomic
+atom_style      atomic
 boundary        f f p
 
-lattice		hex 0.85
-region		box block 0 $x 0 $y -0.5 0.5
-create_box	1 box
-region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-create_atoms	1 region circle
-mass		1 1.0
+lattice         hex 0.85
+region          box block 0 $x 0 $y -0.5 0.5
+create_box      1 box
+region          circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+create_atoms    1 region circle
+mass            1 1.0
 
-velocity	all create 0.5 87287 loop geom
+velocity        all create 0.5 87287 loop geom
 velocity        all set $v $w 0 sum yes
 
-pair_style	lj/cut 2.5
-pair_coeff	1 1 10.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      1 1 10.0 1.0 2.5
 
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
 
-fix		1 all nve
+fix             1 all nve
 
 fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
 fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
@@ -49,6 +49,6 @@ fix             10 all balance 50 0.9 rcb
 #dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}
 
 thermo_style    custom step temp epair press f_10[3] f_10
-thermo          100                
+thermo          100
 
-run		10000
+run             10000
diff --git a/examples/balance/in.balance.bond.fast b/examples/balance/in.balance.bond.fast
index 3bfcea033e..ff54fb94cc 100644
--- a/examples/balance/in.balance.bond.fast
+++ b/examples/balance/in.balance.bond.fast
@@ -2,29 +2,29 @@
 
 variable        b index 0
 
-variable	x index 50
-variable	y index 20
-variable	d index 20
-variable	v index 5
-variable	w index 2
-                
-units		lj
+variable        x index 50
+variable        y index 20
+variable        d index 20
+variable        v index 5
+variable        w index 2
+
+units           lj
 dimension       2
-atom_style	bond
+atom_style      bond
 boundary        f f p
 
-lattice		hex 0.85
-region		box block 0 $x 0 $y -0.5 0.5
-create_box	1 box bond/types 1 extra/bond/per/atom 6
-region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-create_atoms	1 region circle
-mass		1 1.0
+lattice         hex 0.85
+region          box block 0 $x 0 $y -0.5 0.5
+create_box      1 box bond/types 1 extra/bond/per/atom 6
+region          circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+create_atoms    1 region circle
+mass            1 1.0
 
-velocity	all create 0.5 87287 loop geom
+velocity        all create 0.5 87287 loop geom
 velocity        all set $v $w 0 sum yes
 
-pair_style	lj/cut 2.5
-pair_coeff	1 1 10.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      1 1 10.0 1.0 2.5
 
 bond_style      harmonic
 bond_coeff      1 10.0 1.2
@@ -34,10 +34,10 @@ bond_coeff      1 10.0 1.2
 special_bonds   lj/coul 0 1 1
 create_bonds    many all all 1 1.0 1.5
 
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
 
-fix		1 all nve
+fix             1 all nve
 
 fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
 fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
@@ -58,6 +58,6 @@ fix             10 all balance 50 0.9 rcb
 #dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}
 
 thermo_style    custom step temp epair press f_10[3] f_10
-thermo          100                
+thermo          100
 
-run		10000
+run             10000
diff --git a/examples/balance/in.balance.bond.slow b/examples/balance/in.balance.bond.slow
index 68b1110c3d..1fd4ae4c85 100644
--- a/examples/balance/in.balance.bond.slow
+++ b/examples/balance/in.balance.bond.slow
@@ -2,42 +2,42 @@
 
 variable        b index 0
 
-variable	x index 50
-variable	y index 20
-variable	d index 20
+variable        x index 50
+variable        y index 20
+variable        d index 20
 
 # careful not to slam into wall too hard
 
-variable	v index 0.3
-variable	w index 0.08
-                
-units		lj
+variable        v index 0.3
+variable        w index 0.08
+
+units           lj
 dimension       2
-atom_style	bond
+atom_style      bond
 boundary        f f p
 
-lattice		hex 0.85
-region		box block 0 $x 0 $y -0.5 0.5
-create_box	1 box bond/types 1 extra/bond/per/atom 6
-region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
-create_atoms	1 region circle
-mass		1 1.0
+lattice         hex 0.85
+region          box block 0 $x 0 $y -0.5 0.5
+create_box      1 box bond/types 1 extra/bond/per/atom 6
+region          circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+create_atoms    1 region circle
+mass            1 1.0
 
-velocity	all create 0.5 87287 loop geom
+velocity        all create 0.5 87287 loop geom
 velocity        all set $v $w 0 sum yes
 
-pair_style	lj/cut 2.5
-pair_coeff	1 1 10.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      1 1 10.0 1.0 2.5
 
 bond_style      harmonic
 bond_coeff      1 10.0 1.2
 
 create_bonds    many all all 1 1.0 1.5
 
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
 
-fix		1 all nve
+fix             1 all nve
 
 fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
 fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
@@ -57,6 +57,6 @@ fix             10 all balance 50 0.9 rcb
 #dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}
 
 thermo_style    custom step temp epair press f_10[3] f_10
-thermo          100                
+thermo          100
 
-run		40000
+run             40000
diff --git a/examples/balance/in.balance.clock.dynamic b/examples/balance/in.balance.clock.dynamic
index a0bebd518d..aafaf34326 100644
--- a/examples/balance/in.balance.clock.dynamic
+++ b/examples/balance/in.balance.clock.dynamic
@@ -1,54 +1,54 @@
 # 3d Lennard-Jones melt
 
-units		lj
-atom_style	atomic
+units           lj
+atom_style      atomic
 processors      * 1 1
 
-lattice		fcc 0.8442
-region		box block 0 10 0 10 0 10
-create_box	3 box
-create_atoms	1 box
-mass		* 1.0
+lattice         fcc 0.8442
+region          box block 0 10 0 10 0 10
+create_box      3 box
+create_atoms    1 box
+mass            * 1.0
 
-region		long block 3 6 0 10 0 10
+region          long block 3 6 0 10 0 10
 set             region long type 2
 
-velocity	all create 1.0 87287
+velocity        all create 1.0 87287
 
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      * * 1.0 1.0 2.5
 pair_coeff      * 2 1.0 1.0 5.0
 
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
-fix		p all property/atom d_WEIGHT
-compute		p all property/atom d_WEIGHT
-fix		0 all balance 50 1.0 shift x 10 1.0 &
+neighbor        0.3 bin
+neigh_modify    every 2 delay 4 check yes
+fix             p all property/atom d_WEIGHT
+compute         p all property/atom d_WEIGHT
+fix             0 all balance 50 1.0 shift x 10 1.0 &
                 weight time 1.0 weight store WEIGHT
-variable	maximb equal f_0[1]
-variable	iter   equal f_0[2]
-variable 	prev   equal f_0[3]
-variable	final  equal f_0
+variable        maximb equal f_0[1]
+variable        iter   equal f_0[2]
+variable        prev   equal f_0[3]
+variable        final  equal f_0
 
-#fix		3 all print 50 "${iter} ${prev} ${final} ${maximb}"
+#fix            3 all print 50 "${iter} ${prev} ${final} ${maximb}"
 
-fix		1 all nve
+fix             1 all nve
 
-#dump		id all atom 50 dump.melt
-#dump		id all custom 50 dump.lammpstrj id type x y z c_p
+#dump           id all atom 50 dump.melt
+#dump           id all custom 50 dump.lammpstrj id type x y z c_p
 
-#dump		2 all image 25 image.*.jpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
+#dump           2 all image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    2 pad 3
 
-#dump		3 all movie 25 movie.mpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
+#dump           3 all movie 25 movie.mpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    3 pad 3
 
-thermo		50
-run		500
-run		500
-fix		0 all balance 50 1.0 shift x 5 1.0 &
+thermo          50
+run             500
+run             500
+fix             0 all balance 50 1.0 shift x 5 1.0 &
                 weight neigh 0.5 weight time 0.66 weight store WEIGHT
 run             500
 run             500
diff --git a/examples/balance/in.balance.clock.static b/examples/balance/in.balance.clock.static
index 6301e56fd0..519e567403 100644
--- a/examples/balance/in.balance.clock.static
+++ b/examples/balance/in.balance.clock.static
@@ -1,48 +1,48 @@
 # 3d Lennard-Jones melt
 
-units		lj
-atom_style	atomic
+units           lj
+atom_style      atomic
 processors      * 1 1
 
-variable	factor index 1.0
+variable        factor index 1.0
 
-lattice		fcc 0.8442
-region		box block 0 10 0 10 0 10
-create_box	3 box
-create_atoms	1 box
-mass		* 1.0
+lattice         fcc 0.8442
+region          box block 0 10 0 10 0 10
+create_box      3 box
+create_atoms    1 box
+mass            * 1.0
 
-region		long block 3 6 0 10 0 10
+region          long block 3 6 0 10 0 10
 set             region long type 2
 
-velocity	all create 1.0 87287
+velocity        all create 1.0 87287
 
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      * * 1.0 1.0 2.5
 pair_coeff      * 2 1.0 1.0 5.0
 
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
+neighbor        0.3 bin
+neigh_modify    every 2 delay 4 check yes
 
-group		fast type 1
-group		slow type 2
-balance		1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt 
+group           fast type 1
+group           slow type 2
+balance         1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt 
 
-fix		1 all nve
+fix             1 all nve
 
-#dump		id all atom 50 dump.melt
+#dump           id all atom 50 dump.melt
 
-#dump		2 all image 25 image.*.jpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
+#dump           2 all image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    2 pad 3
 
-#dump		3 all movie 25 movie.mpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
+#dump           3 all movie 25 movie.mpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    3 pad 3
 
-thermo		50
-run		250
-balance		1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt 
-run		250
-balance		1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt 
-run 		250
+thermo          50
+run             250
+balance         1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt 
+run             250
+balance         1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt 
+run             250
diff --git a/examples/balance/in.balance.group.dynamic b/examples/balance/in.balance.group.dynamic
index 3e2b44f897..04dc349197 100644
--- a/examples/balance/in.balance.group.dynamic
+++ b/examples/balance/in.balance.group.dynamic
@@ -1,47 +1,47 @@
 # 3d Lennard-Jones melt
 
-units		lj
-atom_style	atomic
+units           lj
+atom_style      atomic
 processors      * 1 1
 
-variable	factor index 1.0
+variable        factor index 1.0
 
-lattice		fcc 0.8442
-region		box block 0 10 0 10 0 10
-create_box	3 box
-create_atoms	1 box
-mass		* 1.0
+lattice         fcc 0.8442
+region          box block 0 10 0 10 0 10
+create_box      3 box
+create_atoms    1 box
+mass            * 1.0
 
-region		long block 3 6 0 10 0 10
+region          long block 3 6 0 10 0 10
 set             region long type 2
 
-velocity	all create 1.0 87287
+velocity        all create 1.0 87287
 
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      * * 1.0 1.0 2.5
 pair_coeff      * 2 1.0 1.0 5.0
 
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
+neighbor        0.3 bin
+neigh_modify    every 2 delay 4 check yes
 
-group		fast type 1
-group		slow type 2
-balance		1.0 shift x 5 1.1 &
+group           fast type 1
+group           slow type 2
+balance         1.0 shift x 5 1.1 &
                 weight group 2 fast 1.0 slow ${factor} # out weighted.txt
-fix		0 all balance 10 1.0 shift x 5 1.1 &
+fix             0 all balance 10 1.0 shift x 5 1.1 &
                 weight group 2 fast 1.0 slow ${factor}
 
-fix		1 all nve
+fix             1 all nve
 
-#dump		id all atom 50 dump.melt
+#dump           id all atom 50 dump.melt
 
-#dump		2 all image 25 image.*.jpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
+#dump           2 all image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    2 pad 3
 
-#dump		3 all movie 25 movie.mpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
+#dump           3 all movie 25 movie.mpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    3 pad 3
 
-thermo		50
-run		250
+thermo          50
+run             250
diff --git a/examples/balance/in.balance.group.static b/examples/balance/in.balance.group.static
index 92ff3e8cb4..ad45c5381d 100644
--- a/examples/balance/in.balance.group.static
+++ b/examples/balance/in.balance.group.static
@@ -1,54 +1,54 @@
 # 3d Lennard-Jones melt
 
-units		lj
-atom_style	atomic
+units           lj
+atom_style      atomic
 processors      * 1 1
 
-variable	factor index 1.0
+variable        factor index 1.0
 
-lattice		fcc 0.8442
-region		box block 0 10 0 10 0 10
-create_box	3 box
-create_atoms	1 box
-mass		* 1.0
+lattice         fcc 0.8442
+region          box block 0 10 0 10 0 10
+create_box      3 box
+create_atoms    1 box
+mass            * 1.0
 
-region		long block 3 6 0 10 0 10
+region          long block 3 6 0 10 0 10
 set             region long type 2
 
-velocity	all create 1.0 87287
+velocity        all create 1.0 87287
 
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      * * 1.0 1.0 2.5
 pair_coeff      * 2 1.0 1.0 5.0
 
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
+neighbor        0.3 bin
+neigh_modify    every 2 delay 4 check yes
 
-balance		1.0 shift x 5 1.1 # out unweighted.txt
+balance         1.0 shift x 5 1.1 # out unweighted.txt
 
-balance		1.0 x uniform
+balance         1.0 x uniform
 
 variable        weight atom (type==1)*1.0+(type==2)*v_factor
-balance		1.0 shift x 5 1.1 weight var weight # out weighted_var.txt
+balance         1.0 shift x 5 1.1 weight var weight # out weighted_var.txt
 
-balance		1.0 x uniform
+balance         1.0 x uniform
 
-group		fast type 1
-group		slow type 2
-balance		1.0 shift x 5 1.1 &
+group           fast type 1
+group           slow type 2
+balance         1.0 shift x 5 1.1 &
                 weight group 2 fast 1.0 slow ${factor} # out weighted_group.txt
 
-fix		1 all nve
+fix             1 all nve
 
-#dump		id all atom 50 dump.melt
+#dump           id all atom 50 dump.melt
 
-#dump		2 all image 25 image.*.jpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
+#dump           2 all image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    2 pad 3
 
-#dump		3 all movie 25 movie.mpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
+#dump           3 all movie 25 movie.mpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    3 pad 3
 
-thermo		50
-run		250
+thermo          50
+run             250
diff --git a/examples/balance/in.balance.kspace b/examples/balance/in.balance.kspace
index 5a2de11c70..c89024d76f 100644
--- a/examples/balance/in.balance.kspace
+++ b/examples/balance/in.balance.kspace
@@ -1,47 +1,47 @@
 # 3d Lennard-Jones melt
 
-units		lj
-#atom_style	charge
+units           lj
+#atom_style     charge
 processors      * 1 1
 
-lattice		fcc 0.8442
-region		box block 0 10 0 10 0 10
-create_box	3 box
-create_atoms	1 box
-mass		* 1.0
+lattice         fcc 0.8442
+region          box block 0 10 0 10 0 10
+create_box      3 box
+create_atoms    1 box
+mass            * 1.0
 
-region		long block 3 6 0 10 0 10
+region          long block 3 6 0 10 0 10
 set             region long type 2
 #set type 1:2    charge 0.0
 
-velocity	all create 1.0 87287
+velocity        all create 1.0 87287
 
-pair_style	lj/long/coul/long long off 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_style      lj/long/coul/long long off 2.5
+pair_coeff      * * 1.0 1.0 2.5
 pair_coeff      * 2 1.0 1.0 5.0
 
 kspace_style    pppm/disp 1.0e-4
 kspace_modify   gewald/disp 0.1
 
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
+neighbor        0.3 bin
+neigh_modify    every 2 delay 4 check yes
 
-group		fast type 1
-group		slow type 2
-fix		0 all balance 20 1.0 shift x 5 1.0 &
+group           fast type 1
+group           slow type 2
+fix             0 all balance 20 1.0 shift x 5 1.0 &
                 weight group 2 fast 1.0 slow 2.0 weight time 0.66
 
-fix		1 all nve
+fix             1 all nve
 
-#dump		id all atom 50 dump.melt
+#dump           id all atom 50 dump.melt
 
-#dump		2 all image 25 image.*.jpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
+#dump           2 all image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    2 pad 3
 
-#dump		3 all movie 25 movie.mpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
+#dump           3 all movie 25 movie.mpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    3 pad 3
 
-thermo		50
-run		500
+thermo          50
+run             500
diff --git a/examples/balance/in.balance.neigh.dynamic b/examples/balance/in.balance.neigh.dynamic
index 395f9f37eb..9217a1c3a6 100644
--- a/examples/balance/in.balance.neigh.dynamic
+++ b/examples/balance/in.balance.neigh.dynamic
@@ -1,53 +1,53 @@
 # 3d Lennard-Jones melt
 
-units		lj
-atom_style	atomic
+units           lj
+atom_style      atomic
 processors      * 1 1
 
-lattice		fcc 0.8442
-region		box block 0 10 0 10 0 10
-create_box	3 box
-create_atoms	1 box
-mass		* 1.0
+lattice         fcc 0.8442
+region          box block 0 10 0 10 0 10
+create_box      3 box
+create_atoms    1 box
+mass            * 1.0
 
-region		long block 3 6 0 10 0 10
+region          long block 3 6 0 10 0 10
 set             region long type 2
 
-velocity	all create 1.0 87287
+velocity        all create 1.0 87287
 
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      * * 1.0 1.0 2.5
 pair_coeff      * 2 1.0 1.0 5.0
 
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
-fix		p all property/atom d_WEIGHT
-fix		0 all balance 50 1.0 shift x 5 1.0 &
+neighbor        0.3 bin
+neigh_modify    every 2 delay 4 check yes
+fix             p all property/atom d_WEIGHT
+fix             0 all balance 50 1.0 shift x 5 1.0 &
                 weight neigh 0.8 weight store WEIGHT
-compute		p all property/atom d_WEIGHT
-variable	maximb equal f_0[1]
-variable	iter   equal f_0[2]
-variable 	prev   equal f_0[3]
-variable	final  equal f_0
+compute         p all property/atom d_WEIGHT
+variable        maximb equal f_0[1]
+variable        iter   equal f_0[2]
+variable        prev   equal f_0[3]
+variable        final  equal f_0
 
-#fix		3 all print 50 "${iter} ${prev} ${final} ${maximb}"
+#fix            3 all print 50 "${iter} ${prev} ${final} ${maximb}"
 
-fix		1 all nve
+fix             1 all nve
 
-#dump		id all atom 50 dump.melt
-#dump		id all custom 50 dump.lammpstrj id type x y z c_p
+#dump           id all atom 50 dump.melt
+#dump           id all custom 50 dump.lammpstrj id type x y z c_p
 
-#dump		2 all image 25 image.*.jpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
+#dump           2 all image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    2 pad 3
 
-#dump		3 all movie 25 movie.mp4 c_p type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3 amap 0.0 2.0 cf 0.1 3 min blue 0.5 green max red
+#dump           3 all movie 25 movie.mp4 c_p type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    3 pad 3 amap 0.0 2.0 cf 0.1 3 min blue 0.5 green max red
 
-thermo		50
-run		500
-run		500
+thermo          50
+run             500
+run             500
 run             500
 run             500
 
diff --git a/examples/balance/in.balance.neigh.rcb b/examples/balance/in.balance.neigh.rcb
index 0b2ca59441..040e47fcad 100644
--- a/examples/balance/in.balance.neigh.rcb
+++ b/examples/balance/in.balance.neigh.rcb
@@ -1,53 +1,53 @@
 # 3d Lennard-Jones melt
 
-units		lj
-atom_style	atomic
+units           lj
+atom_style      atomic
 processors      * 1 1
 
-lattice		fcc 0.8442
-region		box block 0 10 0 10 0 10
-create_box	3 box
-create_atoms	1 box
-mass		* 1.0
+lattice         fcc 0.8442
+region          box block 0 10 0 10 0 10
+create_box      3 box
+create_atoms    1 box
+mass            * 1.0
 
-region		long block 3 6 0 10 0 10
+region          long block 3 6 0 10 0 10
 set             region long type 2
 
-velocity	all create 1.0 87287
+velocity        all create 1.0 87287
 
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      * * 1.0 1.0 2.5
 pair_coeff      * 2 1.0 1.0 5.0
 
-comm_style	tiled
+comm_style      tiled
 
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
-fix		p all property/atom d_WEIGHT
-fix		0 all balance 50 1.0 rcb weight neigh 0.8 weight store WEIGHT
-compute		p all property/atom d_WEIGHT
-variable	maximb equal f_0[1]
-variable	iter   equal f_0[2]
-variable 	prev   equal f_0[3]
-variable	final  equal f_0
+neighbor        0.3 bin
+neigh_modify    every 2 delay 4 check yes
+fix             p all property/atom d_WEIGHT
+fix             0 all balance 50 1.0 rcb weight neigh 0.8 weight store WEIGHT
+compute         p all property/atom d_WEIGHT
+variable        maximb equal f_0[1]
+variable        iter   equal f_0[2]
+variable        prev   equal f_0[3]
+variable        final  equal f_0
 
-#fix		3 all print 50 "${iter} ${prev} ${final} ${maximb}"
+#fix            3 all print 50 "${iter} ${prev} ${final} ${maximb}"
 
-fix		1 all nve
+fix             1 all nve
 
-#dump		id all atom 50 dump.melt
-#dump		id all custom 50 dump.lammpstrj id type x y z c_p
+#dump           id all atom 50 dump.melt
+#dump           id all custom 50 dump.lammpstrj id type x y z c_p
 
-#dump		2 all image 25 image.*.jpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
+#dump           2 all image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    2 pad 3
 
-#dump		3 all movie 25 movie.mpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
+#dump           3 all movie 25 movie.mpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    3 pad 3
 
-thermo		50
+thermo          50
 
-run		250
+run             250
 run             250
 
diff --git a/examples/balance/in.balance.neigh.static b/examples/balance/in.balance.neigh.static
index c3c061bcbe..28fd5eaa9b 100644
--- a/examples/balance/in.balance.neigh.static
+++ b/examples/balance/in.balance.neigh.static
@@ -1,51 +1,51 @@
 # 3d Lennard-Jones melt
 
-units		lj
-atom_style	atomic
+units           lj
+atom_style      atomic
 processors      * 1 1
 
-variable	factor index 1.0
+variable        factor index 1.0
 
-lattice		fcc 0.8442
-region		box block 0 10 0 10 0 10
-create_box	3 box
-create_atoms	1 box
-mass		* 1.0
+lattice         fcc 0.8442
+region          box block 0 10 0 10 0 10
+create_box      3 box
+create_atoms    1 box
+mass            * 1.0
 
-region		long block 3 6 0 10 0 10
+region          long block 3 6 0 10 0 10
 set             region long type 2
 
-velocity	all create 1.0 87287
+velocity        all create 1.0 87287
 
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      * * 1.0 1.0 2.5
 pair_coeff      * 2 1.0 1.0 5.0
 
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
+neighbor        0.3 bin
+neigh_modify    every 2 delay 4 check yes
 
-balance		1.0 shift x 10 1.0 weight neigh 0.8 # out weighted_var.txt
+balance         1.0 shift x 10 1.0 weight neigh 0.8 # out weighted_var.txt
 
-fix		1 all nve
+fix             1 all nve
 
-#dump		id all atom 50 dump.melt
+#dump           id all atom 50 dump.melt
 
-#dump		2 all image 25 image.*.jpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
+#dump           2 all image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    2 pad 3
 
-#dump		3 all movie 25 movie.mpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
+#dump           3 all movie 25 movie.mpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    3 pad 3
 
-thermo		50
-run		250 post no
-balance		1.0 shift x 10 1.0 weight neigh 0.8
+thermo          50
 run             250 post no
-balance		1.0 shift x 10 1.0 weight neigh 0.8
+balance         1.0 shift x 10 1.0 weight neigh 0.8
 run             250 post no
-balance		1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
+balance         1.0 shift x 10 1.0 weight neigh 0.8
+run             250 post no
+balance         1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
 run             250
-balance		1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
+balance         1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6
 run             250
 
diff --git a/examples/balance/in.balance.var.dynamic b/examples/balance/in.balance.var.dynamic
index 0c49106cdf..846c0c1fdb 100644
--- a/examples/balance/in.balance.var.dynamic
+++ b/examples/balance/in.balance.var.dynamic
@@ -1,65 +1,65 @@
 # 3d Lennard-Jones melt
 
-units		lj
-atom_style	atomic
+units           lj
+atom_style      atomic
 processors      * 1 1
 
-lattice		fcc 0.8442
-region		box block 0 10 0 10 0 10
-create_box	3 box
-create_atoms	1 box
-mass		* 1.0
+lattice         fcc 0.8442
+region          box block 0 10 0 10 0 10
+create_box      3 box
+create_atoms    1 box
+mass            * 1.0
 
-region		long block 3 6 0 10 0 10
+region          long block 3 6 0 10 0 10
 set             region long type 2
 
-velocity	all create 1.0 87287
+velocity        all create 1.0 87287
 
-pair_style	lj/cut 2.5
-pair_coeff	* * 1.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      * * 1.0 1.0 2.5
 pair_coeff      * 2 1.0 1.0 5.0
 
-neighbor	0.3 bin
-neigh_modify	every 2 delay 4 check yes
-fix		p all property/atom d_WEIGHT
-compute		p all property/atom d_WEIGHT
+neighbor        0.3 bin
+neigh_modify    every 2 delay 4 check yes
+fix             p all property/atom d_WEIGHT
+compute         p all property/atom d_WEIGHT
 
-group		fast type 1
-group		slow type 2
-balance		1.0 shift x 10 1.0 &
+group           fast type 1
+group           slow type 2
+balance         1.0 shift x 10 1.0 &
                 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
-variable	lastweight atom c_p
+variable        lastweight atom c_p
 
-fix		0 all balance 50 1.0 shift x 10 1.0 &
+fix             0 all balance 50 1.0 shift x 10 1.0 &
                 weight var lastweight weight time 0.5 weight store WEIGHT
-variable	maximb equal f_0[1]
-variable	iter   equal f_0[2]
-variable 	prev   equal f_0[3]
-variable	final  equal f_0
+variable        maximb equal f_0[1]
+variable        iter   equal f_0[2]
+variable        prev   equal f_0[3]
+variable        final  equal f_0
 
-#fix		3 all print 50 "${iter} ${prev} ${final} ${maximb}"
+#fix            3 all print 50 "${iter} ${prev} ${final} ${maximb}"
 
-fix		1 all nve
+fix             1 all nve
 
-#dump		id all atom 50 dump.melt
-#dump		id all custom 50 dump.lammpstrj id type x y z c_p
+#dump           id all atom 50 dump.melt
+#dump           id all custom 50 dump.lammpstrj id type x y z c_p
 
-#dump		2 all image 25 image.*.jpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	2 pad 3
+#dump           2 all image 25 image.*.jpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    2 pad 3
 
-#dump		3 all movie 25 movie.mpg type type &
-#		axes yes 0.8 0.02 view 60 -30
-#dump_modify	3 pad 3
+#dump           3 all movie 25 movie.mpg type type &
+#               axes yes 0.8 0.02 view 60 -30
+#dump_modify    3 pad 3
 
-thermo		50
-run		500
-run		500
+thermo          50
+run             500
+run             500
 
-balance		1.0 shift x 10 1.0 &
+balance         1.0 shift x 10 1.0 &
                 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
 
-fix		0 all balance 50 1.0 shift x 5 1.0 &
+fix             0 all balance 50 1.0 shift x 5 1.0 &
                 weight var lastweight weight neigh 0.5 weight store WEIGHT
 
 run             500

From 55918ebabf2d18d43813dd5bfa81fc1a34aefb05 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 30 Jun 2023 16:17:04 -0400
Subject: [PATCH 329/396] sphinx-tabs 3.4.1 is now available directly

---
 doc/utils/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt
index 3f7bc065d0..9c8522948b 100644
--- a/doc/utils/requirements.txt
+++ b/doc/utils/requirements.txt
@@ -2,7 +2,7 @@ Sphinx >= 5.3.0, <7.1.0
 sphinxcontrib-spelling
 sphinxcontrib-jquery
 git+https://github.com/akohlmey/sphinx-fortran@parallel-read
-git+https://github.com/executablebooks/sphinx-tabs@v3.4.1
+sphinx-tabs>=3.4.1
 breathe
 Pygments
 six

From c1213c5222607860dda764b5915afd4d36092f35 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 30 Jun 2023 16:17:47 -0400
Subject: [PATCH 330/396] use dynamic/dof and extra/dof consistently. remove
 compatibility note in docs.

---
 doc/src/compute_modify.rst                    |  37 +++---
 doc/src/compute_rdf.rst                       |   2 +-
 doc/src/compute_temp_asphere.rst              |  49 ++++----
 doc/src/compute_temp_body.rst                 |  16 +--
 doc/src/compute_temp_drude.rst                |   3 +-
 doc/src/compute_temp_sphere.rst               |  35 +++---
 doc/src/fix_charge_regulation.rst             |   2 +-
 doc/src/fix_deposit.rst                       |  25 ++--
 doc/src/fix_evaporate.rst                     |  10 +-
 doc/src/fix_gcmc.rst                          | 114 +++++++++---------
 doc/src/fix_modify.rst                        |  33 ++---
 doc/src/fix_pour.rst                          |  22 ++--
 .../PACKAGES/atc/cauchy_born/in.flying_cube   |  16 +--
 .../PACKAGES/atc/cauchy_born/in.ftcb_constV   |  24 ++--
 examples/PACKAGES/atc/fluids/in.bar1d_fluids  |  84 ++++++-------
 examples/PACKAGES/atc/fluids/in.concentration |  76 ++++++------
 examples/PACKAGES/atc/fluids/in.shear_flow    |  64 +++++-----
 examples/PACKAGES/atc/hardy/in.eshelby_static |  42 +++----
 examples/PACKAGES/atc/hardy/in.nvt            |  26 ++--
 examples/PACKAGES/atc/thermal/in.bar1d        |  76 ++++++------
 .../PACKAGES/atc/thermal/in.bar1d_all_atoms   |  84 ++++++-------
 .../PACKAGES/atc/thermal/in.bar1d_combined    |  74 ++++++------
 examples/PACKAGES/atc/thermal/in.bar1d_flux   |  70 +++++------
 .../PACKAGES/atc/thermal/in.bar1d_frac_step   |  58 ++++-----
 examples/PACKAGES/atc/thermal/in.bar1d_hoover |  80 ++++++------
 .../PACKAGES/atc/thermal/in.bar1d_interpolate |  74 ++++++------
 examples/PACKAGES/atc/thermal/in.bar1d_lumped |  72 +++++------
 .../atc/two_temperature/in.uniform_heating    |  42 +++----
 .../PACKAGES/charge_regulation/in.chreg-acid  |   2 +-
 .../charge_regulation/in.chreg-acid-real      |  14 +--
 .../charge_regulation/in.chreg-polymer        |   2 +-
 examples/mc/in.gcmc.lj                        |  48 ++++----
 32 files changed, 688 insertions(+), 688 deletions(-)

diff --git a/doc/src/compute_modify.rst b/doc/src/compute_modify.rst
index 2c5f7d0e8e..028eb8b66d 100644
--- a/doc/src/compute_modify.rst
+++ b/doc/src/compute_modify.rst
@@ -12,16 +12,14 @@ Syntax
 
 * compute-ID = ID of the compute to modify
 * one or more keyword/value pairs may be listed
-* keyword = *extra/dof* or *extra* or *dynamic/dof* or *dynamic*
+* keyword = *extra/dof* or *dynamic/dof*
 
   .. parsed-literal::
 
        *extra/dof* value = N
          N = # of extra degrees of freedom to subtract
-       *extra* syntax is identical to *extra/dof*, will be disabled at some point
        *dynamic/dof* value = *yes* or *no*
          yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
-       *dynamic* syntax is identical to *dynamic/dof*, will be disabled at some point
 
 Examples
 """"""""
@@ -37,19 +35,18 @@ Description
 Modify one or more parameters of a previously defined compute.  Not
 all compute styles support all parameters.
 
-The *extra/dof* or *extra* keyword refers to how many degrees of
-freedom are subtracted (typically from :math:`3N`) as a normalizing
-factor in a temperature computation.  Only computes that compute a
-temperature use this option.  The default is 2 or 3 for :doc:`2d or 3d
-systems <dimension>` which is a correction factor for an ensemble of
-velocities with zero total linear momentum. For compute temp/partial,
-if one or more velocity components are excluded, the value used for
-*extra* is scaled accordingly. You can use a negative number for the
-*extra* parameter if you need to add degrees-of-freedom.  See the
-:doc:`compute temp/asphere <compute_temp_asphere>` command for an
-example.
+The *extra/dof* keyword refers to how many degrees of freedom are
+subtracted (typically from :math:`3N`) as a normalizing factor in a
+temperature computation.  Only computes that compute a temperature use
+this option.  The default is 2 or 3 for :doc:`2d or 3d systems
+<dimension>` which is a correction factor for an ensemble of velocities
+with zero total linear momentum. For compute temp/partial, if one or
+more velocity components are excluded, the value used for *extra/dof* is
+scaled accordingly. You can use a negative number for the *extra/dof*
+parameter if you need to add degrees-of-freedom.  See the :doc:`compute
+temp/asphere <compute_temp_asphere>` command for an example.
 
-The *dynamic/dof* or *dynamic* keyword determines whether the number
+The *dynamic/dof* keyword determines whether the number
 of atoms :math:`N` in the compute group and their associated degrees
 of freedom (DOF) are re-computed each time a temperature is computed.
 Only compute styles that calculate a temperature use this option.  By
@@ -61,12 +58,6 @@ are adding atoms or molecules to the system (see the :doc:`fix pour
 <fix_evaporate>`), then this option should be used to ensure the
 temperature is correctly normalized.
 
-.. note::
-
-   The *extra* and *dynamic* keywords should not be used as they
-   are deprecated (March 2017) and will eventually be disabled.  Instead,
-   use the equivalent *extra/dof* and *dynamic/dof* keywords.
-
 Restrictions
 """"""""""""
  none
@@ -79,5 +70,5 @@ Related commands
 Default
 """""""
 
-The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and
-dynamic/dof = *no*.
+The option defaults are extra/dof = 2 or 3 for 2d or 3d systems,
+respectively, and dynamic/dof = *no*.
diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst
index 88bd7ec74c..ed73800f82 100644
--- a/doc/src/compute_rdf.rst
+++ b/doc/src/compute_rdf.rst
@@ -202,7 +202,7 @@ change from zero to one at the location of the spike in :math:`g(r)`.
    parallel efficiency and scaling. For systems, where only the type
    of atoms changes (e.g., when using :doc:`fix atom/swap <fix_atom_swap>`),
    you need to explicitly request the dynamic normalization updates
-   via :doc:`compute_modify dynamic yes <compute_modify>`
+   via :doc:`compute_modify dynamic/dof yes <compute_modify>`
 
 Related commands
 """"""""""""""""
diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst
index cba52a68b4..5741db76aa 100644
--- a/doc/src/compute_temp_asphere.rst
+++ b/doc/src/compute_temp_asphere.rst
@@ -49,25 +49,26 @@ rotational).
 
 .. note::
 
-   This choice for degrees of freedom (DOF) assumes that all
-   finite-size aspherical or spherical particles in your model will
-   freely rotate, sampling all their rotational DOF.  It is possible to
-   use a combination of interaction potentials and fixes that induce no
-   torque or otherwise constrain some of all of your particles so that
-   this is not the case.  Then there are fewer DOF and you should use the
-   :doc:`compute_modify extra <compute_modify>` command to adjust the DOF
-   accordingly.
+   This choice for degrees of freedom (DOF) assumes that all finite-size
+   aspherical or spherical particles in your model will freely rotate,
+   sampling all their rotational DOF.  It is possible to use a
+   combination of interaction potentials and fixes that induce no torque
+   or otherwise constrain some of all of your particles so that this is
+   not the case.  Then there are fewer DOF and you should use the
+   :doc:`compute_modify extra/dof <compute_modify>` command to adjust
+   the DOF accordingly.
 
 For example, an aspherical particle with all three of its shape
-parameters the same is a sphere.  If it does not rotate, then it
-should have 3 DOF instead of 6 in 3d (or two instead of three in 2d).
-A uniaxial aspherical particle has two of its three shape parameters the
+parameters the same is a sphere.  If it does not rotate, then it should
+have 3 DOF instead of 6 in 3d (or two instead of three in 2d).  A
+uniaxial aspherical particle has two of its three shape parameters the
 same.  If it does not rotate around the axis perpendicular to its
 circular cross section, then it should have 5 DOF instead of 6 in 3d.
-The latter is the case for uniaxial ellipsoids in a :doc:`GayBerne model <pair_gayberne>` since there is no induced torque around the
-optical axis.  It will also be the case for biaxial ellipsoids when
-exactly two of the semiaxes have the same length and the corresponding
-relative well depths are equal.
+The latter is the case for uniaxial ellipsoids in a :doc:`GayBerne model
+<pair_gayberne>` since there is no induced torque around the optical
+axis.  It will also be the case for biaxial ellipsoids when exactly two
+of the semiaxes have the same length and the corresponding relative well
+depths are equal.
 
 The translational kinetic energy is computed the same as is described
 by the :doc:`compute temp <compute_temp>` command.  The rotational
@@ -90,15 +91,17 @@ inertia tensor are used.  The six components of the vector are ordered
 :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
 
 The number of atoms contributing to the temperature is assumed to be
-constant for the duration of the run; use the *dynamic* option of the
-:doc:`compute_modify <compute_modify>` command if this is not the case.
+constant for the duration of the run; use the *dynamic/dof* option of
+the :doc:`compute_modify <compute_modify>` command if this is not the
+case.
 
-This compute subtracts out translational degrees-of-freedom due to
-fixes that constrain molecular motion, such as :doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>`.  This means the
-temperature of groups of atoms that include these constraints will be
-computed correctly.  If needed, the subtracted degrees-of-freedom can
-be altered using the *extra* option of the
-:doc:`compute_modify <compute_modify>` command.
+This compute subtracts out translational degrees-of-freedom due to fixes
+that constrain molecular motion, such as :doc:`fix shake <fix_shake>`
+and :doc:`fix rigid <fix_rigid>`.  This means the temperature of groups
+of atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees-of-freedom can be altered using the
+*extra/dof* option of the :doc:`compute_modify <compute_modify>`
+command.
 
 See the :doc:`Howto thermostat <Howto_thermostat>` page for a
 discussion of different ways to compute temperature and perform
diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst
index 64f5ce9a0f..f29ca5c39b 100644
--- a/doc/src/compute_temp_body.rst
+++ b/doc/src/compute_temp_body.rst
@@ -51,11 +51,10 @@ rotational).
    This choice for degrees of freedom (DOF) assumes that all body
    particles in your model will freely rotate, sampling all their
    rotational DOF.  It is possible to use a combination of interaction
-   potentials and fixes that induce no torque or otherwise constrain some
-   of all of your particles so that this is not the case.  Then there are
-   less DOF and you should use the
-   :doc:`compute_modify extra <compute_modify>` command to adjust the DOF
-   accordingly.
+   potentials and fixes that induce no torque or otherwise constrain
+   some of all of your particles so that this is not the case.  Then
+   there are less DOF and you should use the :doc:`compute_modify
+   extra/dof <compute_modify>` command to adjust the DOF accordingly.
 
 The translational kinetic energy is computed the same as is described
 by the :doc:`compute temp <compute_temp>` command.  The rotational
@@ -72,15 +71,16 @@ used.  The six components of the vector are ordered :math:`xx`, :math:`yy`,
 :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
 
 The number of atoms contributing to the temperature is assumed to be
-constant for the duration of the run; use the *dynamic* option of the
-:doc:`compute_modify <compute_modify>` command if this is not the case.
+constant for the duration of the run; use the *dynamic/dof* option of
+the :doc:`compute_modify <compute_modify>` command if this is not the
+case.
 
 This compute subtracts out translational degrees-of-freedom due to
 fixes that constrain molecular motion, such as :doc:`fix shake <fix_shake>`
 and :doc:`fix rigid <fix_rigid>`.  This means the
 temperature of groups of atoms that include these constraints will be
 computed correctly.  If needed, the subtracted degrees-of-freedom can
-be altered using the *extra* option of the
+be altered using the *extra/dof* option of the
 :doc:`compute_modify <compute_modify>` command.
 
 See the :doc:`Howto thermostat <Howto_thermostat>` page for a
diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst
index 8602bc3589..be09afc6a4 100644
--- a/doc/src/compute_temp_drude.rst
+++ b/doc/src/compute_temp_drude.rst
@@ -75,7 +75,8 @@ Restrictions
 
 The number of degrees of freedom contributing to the temperature is
 assumed to be constant for the duration of the run unless the
-*fix_modify* command sets the option *dynamic yes*\ .
+:doc:`fix_modify command <fix_modify>` sets the option *dynamic/dof
+yes*\ .
 
 Related commands
 """"""""""""""""
diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst
index 5c7c73a8d2..d1891f64bf 100644
--- a/doc/src/compute_temp_sphere.rst
+++ b/doc/src/compute_temp_sphere.rst
@@ -49,14 +49,13 @@ each has three degrees of freedom (two translational, one rotational).
 
 .. note::
 
-   This choice for degrees of freedom (DOF) assumes that all
-   finite-size spherical particles in your model will freely rotate,
-   sampling all their rotational DOF.  It is possible to use a
-   combination of interaction potentials and fixes that induce no torque
-   or otherwise constrain some of all of your particles so that this is
-   not the case.  Then there are less DOF and you should use the
-   :doc:`compute_modify extra <compute_modify>` command to adjust the DOF
-   accordingly.
+   This choice for degrees of freedom (DOF) assumes that all finite-size
+   spherical particles in your model will freely rotate, sampling all
+   their rotational DOF.  It is possible to use a combination of
+   interaction potentials and fixes that induce no torque or otherwise
+   constrain some of all of your particles so that this is not the case.
+   Then there are less DOF and you should use the :doc:`compute_modify
+   extra/dof <compute_modify>` command to adjust the DOF accordingly.
 
 The translational kinetic energy is computed the same as is described
 by the :doc:`compute temp <compute_temp>` command.  The rotational
@@ -73,20 +72,22 @@ velocity.
 A kinetic energy tensor, stored as a six-element vector, is also
 calculated by this compute.  The formula for the components of the
 tensor is the same as the above formulas, except that :math:`v^2` and
-:math:`\omega^2` are replaced by :math:`v_x v_y` and :math:`\omega_x \omega_y`
-for the :math:`xy` component.  The six components of the vector are ordered
-:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
+:math:`\omega^2` are replaced by :math:`v_x v_y` and :math:`\omega_x
+\omega_y` for the :math:`xy` component.  The six components of the
+vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`,
+:math:`xz`, :math:`yz`.
 
 The number of atoms contributing to the temperature is assumed to be
 constant for the duration of the run; use the *dynamic* option of the
 :doc:`compute_modify <compute_modify>` command if this is not the case.
 
-This compute subtracts out translational degrees-of-freedom due to
-fixes that constrain molecular motion, such as :doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>`.  This means the
-temperature of groups of atoms that include these constraints will be
-computed correctly.  If needed, the subtracted degrees of freedom can
-be altered using the *extra* option of the
-:doc:`compute_modify <compute_modify>` command.
+This compute subtracts out translational degrees-of-freedom due to fixes
+that constrain molecular motion, such as :doc:`fix shake <fix_shake>`
+and :doc:`fix rigid <fix_rigid>`.  This means the temperature of groups
+of atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees of freedom can be altered using the
+*extra/dof* option of the :doc:`compute_modify <compute_modify>`
+command.
 
 See the :doc:`Howto thermostat <Howto_thermostat>` page for a
 discussion of different ways to compute temperature and perform
diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst
index c1e790c691..203d40951d 100644
--- a/doc/src/fix_charge_regulation.rst
+++ b/doc/src/fix_charge_regulation.rst
@@ -171,7 +171,7 @@ Langevin thermostat:
 .. code-block:: LAMMPS
 
     compute dtemp all temp
-    compute_modify dtemp dynamic yes
+    compute_modify dtemp dynamic/dof yes
     fix fT all langevin 1.0 1.0 1.0 123
     fix_modify fT temp dtemp
 
diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst
index 7d19e93148..c8746bcf9c 100644
--- a/doc/src/fix_deposit.rst
+++ b/doc/src/fix_deposit.rst
@@ -95,10 +95,9 @@ default group "all" and the group specified in the fix deposit command
 (which can also be "all").
 
 If you are computing temperature values which include inserted
-particles, you will want to use the
-:doc:`compute_modify <compute_modify>` dynamic option, which ensures the
-current number of atoms is used as a normalizing factor each time the
-temperature is computed.
+particles, you will want to use the :doc:`compute_modify dynamic/dof yes
+<compute_modify>` option, which ensures the current number of atoms is
+used as a normalizing factor each time the temperature is computed.
 
 Care must be taken that inserted particles are not too near existing
 atoms, using the options described below.  When inserting particles
@@ -160,15 +159,17 @@ command which also appears in your input script.
 
 .. note::
 
-   If you wish the new rigid molecules (and other rigid molecules)
-   to be thermostatted correctly via :doc:`fix rigid/small/nvt <fix_rigid>`
-   or :doc:`fix rigid/small/npt <fix_rigid>`, then you need to use the
-   "fix_modify dynamic/dof yes" command for the rigid fix.  This is to
-   inform that fix that the molecule count will vary dynamically.
+   If you wish the new rigid molecules (and other rigid molecules) to be
+   thermostatted correctly via :doc:`fix rigid/small/nvt <fix_rigid>` or
+   :doc:`fix rigid/small/npt <fix_rigid>`, then you need to use the
+   :doc:`fix_modify dynamic/dof yes <fix_modify>` command for the rigid
+   fix.  This is to inform that fix that the molecule count will vary
+   dynamically.
 
 If you wish to insert molecules via the *mol* keyword, that will have
 their bonds or angles constrained via SHAKE, use the *shake* keyword,
-specifying as its value the ID of a separate :doc:`fix shake <fix_shake>` command which also appears in your input script.
+specifying as its value the ID of a separate :doc:`fix shake
+<fix_shake>` command which also appears in your input script.
 
 Each timestep a particle is inserted, the coordinates for its atoms
 are chosen as follows.  For insertion of individual atoms, the
@@ -268,8 +269,8 @@ units of distance or velocity.
 
    If you are monitoring the temperature of a system where the atom
    count is changing due to adding particles, you typically should use
-   the :doc:`compute_modify dynamic yes <compute_modify>` command for the
-   temperature compute you are using.
+   the :doc:`compute_modify dynamic/dof yes <compute_modify>` command
+   for the temperature compute you are using.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst
index 4c5ea01e13..c8e46631a3 100644
--- a/doc/src/fix_evaporate.rst
+++ b/doc/src/fix_evaporate.rst
@@ -69,14 +69,15 @@ incur overhead due to the cost of building neighbor lists.
 
    If you are monitoring the temperature of a system where the atom
    count is changing due to evaporation, you typically should use the
-   :doc:`compute_modify dynamic yes <compute_modify>` command for the
+   :doc:`compute_modify dynamic/dof yes <compute_modify>` command for the
    temperature compute you are using.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
-are relevant to this fix.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
+relevant to this fix.
 
 This fix computes a global scalar, which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the cumulative
@@ -84,7 +85,8 @@ number of deleted atoms.  The scalar value calculated by this fix is
 "intensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst
index c348e2a44f..c0fa990d6e 100644
--- a/doc/src/fix_gcmc.rst
+++ b/doc/src/fix_gcmc.rst
@@ -146,8 +146,8 @@ center-of-mass is inside the specified region.
 If used with :doc:`fix nvt <fix_nh>`, the temperature of the imaginary
 reservoir, T, should be set to be equivalent to the target temperature
 used in fix nvt. Otherwise, the imaginary reservoir will not be in
-thermal equilibrium with the simulation cell. Also, it is important
-that the temperature used by fix nvt be dynamic/dof, which can be
+thermal equilibrium with the simulation cell. Also, it is important that
+the temperature used by *fix nvt* is dynamically updated, which can be
 achieved as follows:
 
 .. code-block:: LAMMPS
@@ -197,15 +197,17 @@ which also appears in your input script.
 
 .. note::
 
-   If you wish the new rigid molecules (and other rigid molecules)
-   to be thermostatted correctly via :doc:`fix rigid/small/nvt <fix_rigid>`
-   or :doc:`fix rigid/small/npt <fix_rigid>`, then you need to use the
-   "fix_modify dynamic/dof yes" command for the rigid fix.  This is to
-   inform that fix that the molecule count will vary dynamically.
+   If you wish the new rigid molecules (and other rigid molecules) to be
+   thermostatted correctly via :doc:`fix rigid/small/nvt <fix_rigid>` or
+   :doc:`fix rigid/small/npt <fix_rigid>`, then you need to use the
+   :doc:`fix_modify dynamic/dof yes <fix_modify>` command for the rigid
+   fix.  This is to inform that fix that the molecule count will vary
+   dynamically.
 
 If you wish to insert molecules via the *mol* keyword, that will have
 their bonds or angles constrained via SHAKE, use the *shake* keyword,
-specifying as its value the ID of a separate :doc:`fix shake <fix_shake>` command which also appears in your input script.
+specifying as its value the ID of a separate :doc:`fix shake
+<fix_shake>` command which also appears in your input script.
 
 Optionally, users may specify the relative amounts of different MC
 moves using the *mcmoves* keyword. The values *Patomtrans*,
@@ -335,31 +337,30 @@ temperature.
 Some fixes have an associated potential energy. Examples of such fixes
 include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
 :doc:`addforce <fix_addforce>`, :doc:`langevin <fix_langevin>`,
-:doc:`restrain <fix_restrain>`,
-:doc:`temp/berendsen <fix_temp_berendsen>`,
-:doc:`temp/rescale <fix_temp_rescale>`, and :doc:`wall fixes <fix_wall>`.
-For that energy to be included in the total potential energy of the
-system (the quantity used when performing GCMC exchange and MC moves),
-you MUST enable
-the :doc:`fix_modify <fix_modify>` *energy* option for that fix.  The
-doc pages for individual :doc:`fix <fix>` commands specify if this
-should be done.
+:doc:`restrain <fix_restrain>`, :doc:`temp/berendsen
+<fix_temp_berendsen>`, :doc:`temp/rescale <fix_temp_rescale>`, and
+:doc:`wall fixes <fix_wall>`.  For that energy to be included in the
+total potential energy of the system (the quantity used when performing
+GCMC exchange and MC moves), you MUST enable the :doc:`fix_modify
+<fix_modify>` *energy* option for that fix.  The doc pages for
+individual :doc:`fix <fix>` commands specify if this should be done.
 
 Use the *charge* option to insert atoms with a user-specified point
-charge. Note that doing so will cause the system to become
-non-neutral.  LAMMPS issues a warning when using long-range
-electrostatics (kspace) with non-neutral systems. See the :doc:`compute group/group <compute_group_group>` documentation for more details
-about simulating non-neutral systems with kspace on.
+charge. Note that doing so will cause the system to become non-neutral.
+LAMMPS issues a warning when using long-range electrostatics (kspace)
+with non-neutral systems. See the :doc:`compute group/group
+<compute_group_group>` documentation for more details about simulating
+non-neutral systems with kspace on.
 
 Use of this fix typically will cause the number of atoms to fluctuate,
-therefore, you will want to use the
-:doc:`compute_modify dynamic/dof <compute_modify>` command to ensure that the
-current number of atoms is used as a normalizing factor each time
-temperature is computed. A simple example of this is:
+therefore, you will want to use the :doc:`compute_modify dynamic/dof
+<compute_modify>` command to ensure that the current number of atoms is
+used as a normalizing factor each time temperature is computed. A simple
+example of this is:
 
 .. code-block:: LAMMPS
 
-   compute_modify thermo_temp dynamic yes
+   compute_modify thermo_temp dynamic/dof yes
 
 A more complicated example is listed earlier on this page
 in the context of NVT dynamics.
@@ -369,31 +370,29 @@ in the context of NVT dynamics.
    If the density of the cell is initially very small or zero, and
    increases to a much larger density after a period of equilibration,
    then certain quantities that are only calculated once at the start
-   (kspace parameters) may no longer be accurate.  The
-   solution is to start a new simulation after the equilibrium density
-   has been reached.
+   (kspace parameters) may no longer be accurate.  The solution is to
+   start a new simulation after the equilibrium density has been
+   reached.
 
 With some pair_styles, such as :doc:`Buckingham <pair_buck>`,
-:doc:`Born-Mayer-Huggins <pair_born>` and :doc:`ReaxFF <pair_reaxff>`, two
-atoms placed close to each other may have an arbitrary large, negative
-potential energy due to the functional form of the potential.  While
-these unphysical configurations are inaccessible to typical dynamical
-trajectories, they can be generated by Monte Carlo moves. The
-*overlap_cutoff* keyword suppresses these moves by effectively
-assigning an infinite positive energy to all new configurations that
-place any pair of atoms closer than the specified overlap cutoff
-distance.
+:doc:`Born-Mayer-Huggins <pair_born>` and :doc:`ReaxFF <pair_reaxff>`,
+two atoms placed close to each other may have an arbitrary large,
+negative potential energy due to the functional form of the potential.
+While these unphysical configurations are inaccessible to typical
+dynamical trajectories, they can be generated by Monte Carlo moves. The
+*overlap_cutoff* keyword suppresses these moves by effectively assigning
+an infinite positive energy to all new configurations that place any
+pair of atoms closer than the specified overlap cutoff distance.
 
-The *max* and *min* keywords allow for the restriction of the number
-of atoms in the simulation. They automatically reject all insertion
-or deletion moves that would take the system beyond the set boundaries.
+The *max* and *min* keywords allow for the restriction of the number of
+atoms in the simulation. They automatically reject all insertion or
+deletion moves that would take the system beyond the set boundaries.
 Should the system already be beyond the boundary, only moves that bring
 the system closer to the bounds may be accepted.
 
-The *group* keyword adds all inserted atoms to the
-:doc:`group <group>` of the group-ID value. The *grouptype* keyword
-adds all inserted atoms of the specified type to the
-:doc:`group <group>` of the group-ID value.
+The *group* keyword adds all inserted atoms to the :doc:`group <group>`
+of the group-ID value. The *grouptype* keyword adds all inserted atoms
+of the specified type to the :doc:`group <group>` of the group-ID value.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -446,22 +445,21 @@ called.  Reneighboring is required.
 
 Only usable for 3D simulations.
 
-Can be run in parallel, but aspects of the GCMC part will not scale
-well in parallel. Currently, molecule translations and rotations
-are not supported with more than one MPI process.
-It is still possible to do parallel molecule exchange without
-translation and rotation moves by setting MC moves to zero
-and/or by using the *mcmoves* keyword with *Pmoltrans* = *Pmolrotate* = 0 .
+This fix can be run in parallel, but aspects of the GCMC part will not
+scale well in parallel.  Currently, molecule translations and rotations
+are not supported with more than one MPI process.  It is still possible
+to do parallel molecule exchange without translation and rotation moves
+by setting MC moves to zero and/or by using the *mcmoves* keyword with
+*Pmoltrans* = *Pmolrotate* = 0 .
 
 
-When using fix gcmc in combination with fix shake or fix rigid,
-only GCMC exchange moves are supported, so the argument
-*M* must be zero.
+When using fix gcmc in combination with fix shake or fix rigid, only
+GCMC exchange moves are supported, so the argument *M* must be zero.
 
-When using fix gcmc in combination with fix rigid, deletion
-of the last remaining molecule is not allowed for technical reasons,
-and so the molecule count will never drop below 1, regardless of the
-specified chemical potential.
+When using fix gcmc in combination with fix rigid, deletion of the last
+remaining molecule is not allowed for technical reasons, and so the
+molecule count will never drop below 1, regardless of the specified
+chemical potential.
 
 Note that very lengthy simulations involving insertions/deletions of
 billions of gas molecules may run out of atom or molecule IDs and
diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst
index 175d02dd8f..265803c213 100644
--- a/doc/src/fix_modify.rst
+++ b/doc/src/fix_modify.rst
@@ -131,24 +131,24 @@ with their specified level at the beginning of a r-RESPA run.
 The *dynamic/dof* keyword determines whether the number of atoms N in
 the fix group and their associated degrees of freedom are re-computed
 each time a temperature is computed.  Only fix styles that calculate
-their own internal temperature use this option.  Currently this is
-only the :doc:`fix rigid/nvt/small <fix_rigid>` and :doc:`fix
-rigid/npt/small <fix_rigid>` commands for the purpose of
-thermostatting rigid body translation and rotation.  By default, N and
-their DOF are assumed to be constant.  If you are adding atoms or
-molecules to the system (see the :doc:`fix pour <fix_pour>`, :doc:`fix
-deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or
-expect atoms or molecules to be lost (e.g. due to exiting the
-simulation box or via :doc:`fix evaporate <fix_evaporate>`), then this
-option should be used to ensure the temperature is correctly
-normalized.
+their own internal temperature use this option.  Currently this is only
+the :doc:`fix rigid/nvt/small <fix_rigid>` and :doc:`fix rigid/npt/small
+<fix_rigid>` commands for the purpose of thermostatting rigid body
+translation and rotation.  By default, N and their DOF are assumed to be
+constant.  If you are adding atoms or molecules to the system (see the
+:doc:`fix pour <fix_pour>`, :doc:`fix deposit <fix_deposit>`, and
+:doc:`fix gcmc <fix_gcmc>` commands) or expect atoms or molecules to be
+lost (e.g. due to exiting the simulation box or via :doc:`fix evaporate
+<fix_evaporate>`), then this option should be used to ensure the
+temperature is correctly normalized.
 
 .. note::
 
-   Other thermostatting fixes, such as :doc:`fix nvt <fix_nh>`, do
-   not use the *dynamic/dof* keyword because they use a temperature
-   compute to calculate temperature.  See the :doc:`compute_modify dynamic/dof <compute_modify>` command for a similar way to ensure
-   correct temperature normalization for those thermostats.
+   Other thermostatting fixes, such as :doc:`fix nvt <fix_nh>`, do not
+   use the *dynamic/dof* keyword because they use a temperature compute
+   to calculate temperature.  See the :doc:`compute_modify dynamic/dof
+   <compute_modify>` command for a similar way to ensure correct
+   temperature normalization for those thermostats.
 
 The *bodyforces* keyword determines whether the forces and torques
 acting on rigid bodies are computed *early* at the post-force stage of
@@ -156,7 +156,8 @@ each timestep (right after per-atom forces have been computed and
 communicated among processors), or *late* at the final-integrate stage
 of each timestep (after any other fixes have finished their post-force
 tasks).  Only the rigid-body integration fixes use this option, which
-includes :doc:`fix rigid <fix_rigid>` and :doc:`fix rigid/small <fix_rigid>`, and their variants, and also :doc:`fix poems <fix_poems>`.
+includes :doc:`fix rigid <fix_rigid>` and :doc:`fix rigid/small
+<fix_rigid>`, and their variants, and also :doc:`fix poems <fix_poems>`.
 
 The default is *late*\ .  If there are other fixes that add forces to
 individual atoms, then the rigid-body constraints will include these
diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst
index 6ef18ea800..8a7000662e 100644
--- a/doc/src/fix_pour.rst
+++ b/doc/src/fix_pour.rst
@@ -123,15 +123,17 @@ command which also appears in your input script.
 
 .. note::
 
-   If you wish the new rigid molecules (and other rigid molecules)
-   to be thermostatted correctly via :doc:`fix rigid/small/nvt <fix_rigid>`
-   or :doc:`fix rigid/small/npt <fix_rigid>`, then you need to use the
-   "fix_modify dynamic/dof yes" command for the rigid fix.  This is to
-   inform that fix that the molecule count will vary dynamically.
+   If you wish the new rigid molecules (and other rigid molecules) to be
+   thermostatted correctly via :doc:`fix rigid/small/nvt <fix_rigid>` or
+   :doc:`fix rigid/small/npt <fix_rigid>`, then you need to use the
+   :doc:`fix_modify dynamic/dof yes <fix_modify>` command for the rigid
+   fix.  This is to inform that fix that the molecule count will vary
+   dynamically.
 
 If you wish to insert molecules via the *mol* keyword, that will have
 their bonds or angles constrained via SHAKE, use the *shake* keyword,
-specifying as its value the ID of a separate :doc:`fix shake <fix_shake>` command which also appears in your input script.
+specifying as its value the ID of a separate :doc:`fix shake
+<fix_shake>` command which also appears in your input script.
 
 Each timestep particles are inserted, they are placed randomly inside
 the insertion volume so as to mimic a stream of poured particles.  If
@@ -148,10 +150,10 @@ many timesteps until the desired # of particles has been inserted.
 
 .. note::
 
-   If you are monitoring the temperature of a system where the
-   particle count is changing due to adding particles, you typically
-   should use the :doc:`compute_modify dynamic yes <compute_modify>`
-   command for the temperature compute you are using.
+   If you are monitoring the temperature of a system where the particle
+   count is changing due to adding particles, you typically should use
+   the :doc:`compute_modify dynamic/dof yes <compute_modify>` command
+   for the temperature compute you are using.
 
 ----------
 
diff --git a/examples/PACKAGES/atc/cauchy_born/in.flying_cube b/examples/PACKAGES/atc/cauchy_born/in.flying_cube
index 23bd7a5ae0..9b81fcf6a0 100644
--- a/examples/PACKAGES/atc/cauchy_born/in.flying_cube
+++ b/examples/PACKAGES/atc/cauchy_born/in.flying_cube
@@ -1,11 +1,11 @@
 # This test evaluates Hardy fields for a small block of LJ material
-# that's undergoing translation in the x-direction through the 
+# that's undergoing translation in the x-direction through the
 # periodic boundary.
 echo both
-log            log.flying_cube 
+log            log.flying_cube
 units          real
 atom_style     atomic
-variable       lattice_constant equal 5.256227487 
+variable       lattice_constant equal 5.256227487
 variable       c equal 6
 variable       L equal (${lattice_constant}*$c)
 variable       V equal $L*$L*$L
@@ -23,15 +23,15 @@ create_box     1 box
 create_atoms   1 region box
 mass           1 $m
 group          all region box
-pair_style     lj/cut 13.5  
-pair_coeff     1 1 0.238 3.405 
+pair_style     lj/cut 13.5
+pair_coeff     1 1 0.238 3.405
 # define region
 neighbor       1.0 bin
 neigh_modify   delay 0 every 200 check no
 # neigh_modify   delay 0 every $n
 reset_timestep 0
 thermo         $s
-compute_modify thermo_temp extra 0
+compute_modify thermo_temp extra/dof 0
 thermo_style   custom step temp pxx pyy pzz etotal lx ly lz
 timestep       ${dt}
 min_modify     line quadratic
@@ -46,10 +46,10 @@ variable       zHI equal zhi
 # region         BOX block ${xLO} ${xHI} ${yLO} ${yHI} ${zLO} ${zHI} units box
 region         BOX block ${xLO} ${xHI} -0.5 31.7 -0.5 31.7 units box
 fix            ATC all atc field
-fix_modify     ATC mesh create 1 1 1 box p p p 
+fix_modify     ATC mesh create 1 1 1 box p p p
 fix_modify     ATC  fields add stress velocity displacement
 fix_modify     ATC  fields add temperature kinetic_temperature
-fix_modify     ATC  fields add internal_energy energy 
+fix_modify     ATC  fields add internal_energy energy
 fix_modify     ATC  output flying_cubeFE $s text binary tensor_components
 # fix_modify     ATC  atomic_output flying_cubeMD $m text binary tensor_components
 dump           dumpfc all atom $s flying_cube.dmp
diff --git a/examples/PACKAGES/atc/cauchy_born/in.ftcb_constV b/examples/PACKAGES/atc/cauchy_born/in.ftcb_constV
index 431fe15ddd..2b54a50739 100644
--- a/examples/PACKAGES/atc/cauchy_born/in.ftcb_constV
+++ b/examples/PACKAGES/atc/cauchy_born/in.ftcb_constV
@@ -1,34 +1,34 @@
 # This test compares Hardy and Cauchy-Born metrics of energy density and stress
 # for an Ar system undergoing dynamics at a finite temperature.
 echo both
-log            ftcb_constV.log  
+log            ftcb_constV.log
 units          real
 atom_style     atomic
-variable       lattice_constant equal 5.256227487 
+variable       lattice_constant equal 5.256227487
 variable       c equal 6
 variable       L equal (${lattice_constant}*$c)
 variable       V equal $L*$L*$L
 print          "Volume : $V"
-variable       Ti equal 0.0001 
+variable       Ti equal 0.0001
 variable       dT equal 0.2
 variable       n equal 10000
 variable       m equal 200
 variable       dt equal 0.1
 # create system
-lattice        fcc ${lattice_constant} 
+lattice        fcc ${lattice_constant}
 region         box block 0 $c 0 $c 0 $c
 boundary       p p p
-pair_style     lj/cut 13.5  
+pair_style     lj/cut 13.5
 read_data      ftcb_constV_setup.init
 mass           1 39.95
-pair_coeff     1 1 0.238 3.405 
+pair_coeff     1 1 0.238 3.405
 # define region
 neighbor       1.0 bin
 neigh_modify   delay 0 every 2000 check no
 reset_timestep 0
 thermo         $m
-compute_modify thermo_temp extra 0
-variable       nrepeat equal $n/$m 
+compute_modify thermo_temp extra/dof 0
+variable       nrepeat equal $n/$m
 variable       sxx equal -pxx
 variable       intenergy equal etotal
 fix            TDAVE all ave/time $m ${nrepeat} $n c_thermo_temp v_sxx v_intenergy ave one file ftcb_constV.profile
@@ -37,7 +37,7 @@ timestep       ${dt}
 # filtered
 fix            ATCFILT all atc field Ar_CauchyBorn.mat
 #fix_modify     ATCFILT  reset_atomic_reference_positions ftcb_constV_setup.data
-fix_modify     ATCFILT mesh create 1 1 1 box p p p 
+fix_modify     ATCFILT mesh create 1 1 1 box p p p
 fix_modify     ATCFILT  fields none
 fix_modify     ATCFILT  fields add internal_energy stress cauchy_born_energy cauchy_born_stress
 fix_modify     ATCFILT  fields add temperature displacement
@@ -51,7 +51,7 @@ fix_modify     ATCFILT  filter type step
 # not filtered
 fix            ATC all atc field Ar_CauchyBorn.mat
 #fix_modify     ATC  reset_atomic_reference_positions ftcb_constV_setup.data
-fix_modify     ATC mesh create 1 1 1 box p p p 
+fix_modify     ATC mesh create 1 1 1 box p p p
 fix_modify     ATC  fields none
 fix_modify     ATC  fields add internal_energy stress cauchy_born_energy cauchy_born_stress
 fix_modify     ATC  fields add temperature displacement
@@ -59,7 +59,7 @@ fix_modify     ATC  gradients add displacement
 fix_modify     ATC  output ftcb_constVFE $m text binary tensor_components
 velocity       all create ${Ti} 102486 mom yes rot yes dist gaussian
 # step iu T,V space
-variable i loop 1 
+variable i loop 1
 label loop_i
   print ">>> step $i, T: ${Ti}, V: $V"
   variable Tf equal ${Ti}+${dT}
@@ -69,6 +69,6 @@ label loop_i
   fix NVT all nvt temp ${Tf} ${Tf} 20 drag 0.5 tchain 1
   run  $n
   unfix NVT
-  variable Ti equal ${Tf} 
+  variable Ti equal ${Tf}
 next i
 jump in.ftcb_constV loop_i
diff --git a/examples/PACKAGES/atc/fluids/in.bar1d_fluids b/examples/PACKAGES/atc/fluids/in.bar1d_fluids
index 79a6c8a4c2..69a2df6900 100644
--- a/examples/PACKAGES/atc/fluids/in.bar1d_fluids
+++ b/examples/PACKAGES/atc/fluids/in.bar1d_fluids
@@ -5,50 +5,50 @@
 # out # to the FEM on the right.  Insufficient time is captured to reach the
 # linear # steady state, but heat crossing both boundaries should be observed.
 log bar1d_fluids.log
-units		real
-atom_style	atomic
+units           real
+atom_style      atomic
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
 # NOTE following 3 lines added for restart
 boundary        f p p
 pair_style      lj/cut 13.5
 read_data       temp.init
-#read_restart	post_eq.dat
+#read_restart   post_eq.dat
 lattice         fcc 5.405 origin 0.25 0.25 0.25
 # create atoms, NOTE commented out for restart
-#region		mdRegion block -7 7 -3 3 -3 3
-#boundary	f p p
-#create_box	2 mdRegion
-#create_atoms	1 region mdRegion
-#mass		* 39.95
+#region         mdRegion block -7 7 -3 3 -3 3
+#boundary       f p p
+#create_box     2 mdRegion
+#create_atoms   1 region mdRegion
+#mass           * 39.95
 # specify interal/ghost atoms
-#region		mdInternal block -6 6 -3 3 -3 3
-#region		mdGhost block -6 6 -3 3 -3 3 side out
+#region         mdInternal block -6 6 -3 3 -3 3
+#region         mdGhost block -6 6 -3 3 -3 3 side out
 #create_atoms    1 region mdGhost
 #lattice         fcc 6.5 origin 0.25 0.25 0.25
-#create_atoms	2 region mdInternal
-group		internal type 2
-group		ghost type 1
+#create_atoms   2 region mdInternal
+group           internal type 2
+group           ghost type 1
 # velocities have Vcm = 0, NOTE next four lines commented out for restart
-#velocity	internal create 100. 87287 mom yes loop geom
-#pair_style	lj/cut 13.5
-##pair_coeff	1 1 0.010323166 3.405 13.5
-#pair_coeff  	* * .238 3.405 13.5
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
-#write_restart	tinit.dat
+#velocity       internal create 100. 87287 mom yes loop geom
+#pair_style     lj/cut 13.5
+##pair_coeff    1 1 0.010323166 3.405 13.5
+#pair_coeff     * * .238 3.405 13.5
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
+#write_restart  tinit.dat
 #               ID  group atc PhysicsType ParameterFile
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		atcRegion block -6.25 6.25 -3 3 -3 3
+region          atcRegion block -6.25 6.25 -3 3 -3 3
 fix             AtC internal   atc thermal     Ar_thermal.mat
 #               ID  part keywords    nx ny nz region    periodicity
 fix_modify      AtC mesh create 6 1  1   atcRegion f p p
 fix_modify      AtC time_integration fractional_step
-fix_modify	AtC atom_element_map eulerian 10 # NOTE this introduces a minor amount of time integration error tracking the atomic temperature
+fix_modify      AtC atom_element_map eulerian 10 # NOTE this introduces a minor amount of time integration error tracking the atomic temperature
 fix_modify      AtC  internal_quadrature off
-#fix_modify	AtC  mass_matrix fe
+#fix_modify     AtC  mass_matrix fe
 # fix a temperature
-fix_modify     	AtC  fix temperature all 100.
+fix_modify      AtC  fix temperature all 100.
 # add nodesets
 #               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
 fix_modify      AtC mesh create_nodeset lbc -6.3 -6.2   -INF  INF   -INF  INF
@@ -56,43 +56,43 @@ fix_modify      AtC mesh create_nodeset rbc  6.2  6.3   -INF  INF   -INF  INF
 #fix_modify      AtC  fix temperature lbc 120.
 #fix_modify      AtC  fix temperature rbc 100.
 #used for restarting
-#fix_modify	AtC  consistent_fe_initialization on
+#fix_modify     AtC  consistent_fe_initialization on
 #fix_modify     AtC  initial temperature all 100.
 # turn on thermostat
-fix_modify	AtC control  thermal rescale 10
+fix_modify      AtC control  thermal rescale 10
 # equilibrate MD field
 variable xdof equal 3*count(ghost)
-compute_modify thermo_temp extra ${xdof}
+compute_modify thermo_temp extra/dof ${xdof}
 thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
 thermo_modify  format 1 %6i format 2 %7.2g
 #fix_modify      AtC  output bar1d_fluids_eqFE 200 text binary
 #dump            D1 all atom 200 dump_eq.bar1d
-timestep	2
-thermo		200
-run 		2000
-#write_restart	post_eq.dat
+timestep        2
+thermo          200
+run             2000
+#write_restart  post_eq.dat
 # change thermostat to hoover
 reset_timestep 0
-fix_modify	AtC  reset_time
+fix_modify      AtC  reset_time
 fix_modify      AtC  unfix temperature all
 variable deltaT equal 2.*2000.
 fix_modify      AtC  fix temperature lbc temporal_ramp 100. 120. ${deltaT}
-#fix_modify	AtC  fix temperature lbc 100.
+#fix_modify     AtC  fix temperature lbc 100.
 fix_modify      AtC  fix temperature rbc 100.
 fix_modify      AtC control thermal flux no_boundary
-fix_modify	AtC control tolerance 1.e-14
-fix_modify	AtC control localized_lambda on
+fix_modify      AtC control tolerance 1.e-14
+fix_modify      AtC control localized_lambda on
 fix_modify      AtC  filter type exponential
 fix_modify      AtC  filter scale 1000.0
 fix_modify      AtC  filter on
 # output commands
 fix_modify      AtC  output bar1d_fluidsFE 100 text
 #undump          D1
-#dump		D2 all atom 200 dump.bar1d
-#dump		D2 all custom 200 dump.bar1d id type xs ys zs vx vy vz
+#dump           D2 all atom 200 dump.bar1d
+#dump           D2 all custom 200 dump.bar1d id type xs ys zs vx vy vz
 # set-up non-equilibrium IC
-thermo		100
-run 		2000
+thermo          100
+run             2000
 # run non-equilibrium condition
-fix_modify	AtC  fix temperature lbc 120.
-run		4000
+fix_modify      AtC  fix temperature lbc 120.
+run             4000
diff --git a/examples/PACKAGES/atc/fluids/in.concentration b/examples/PACKAGES/atc/fluids/in.concentration
index 255524bc0a..f5c2a37cbb 100644
--- a/examples/PACKAGES/atc/fluids/in.concentration
+++ b/examples/PACKAGES/atc/fluids/in.concentration
@@ -1,10 +1,10 @@
 echo both
-units     	real
+units           real
 atom_style full # charge
 ### NOTE p p p is required for both lammps & atc since periodic images are employed in ExtrinsicModelElectrostatic::correct_electrostatic_forces
 ########### BEGIN PARAMETERS ####################################
-variable T equal 300 
-variable a equal 1.0 # 5.719025032  
+variable T equal 300
+variable a equal 1.0 # 5.719025032
 variable i equal 10 # thermo
 variable f equal 50 # neighbor & conc interval
 variable s equal 100 # 10 # 100 # output
@@ -12,18 +12,18 @@ variable n equal 800 # 20 # 200 # 300 # duration
 variable x equal 4 # 40 #  2 # 4 # exchanges
 variable e equal 100. # 1. # 100. # 10. # energy
 variable h equal 5 # nelems
-variable dt equal 4. #1. # 0 # 4.0 
+variable dt equal 4. #1. # 0 # 4.0
 ##############  END PARAMETERS #################################
-dimension 	3
-boundary  	p p p
-pair_style  	lj/cut/coul/cut 13.0
-lattice   	sc  $a 
+dimension       3
+boundary        p p p
+pair_style      lj/cut/coul/cut 13.0
+lattice         sc  $a
 read_data concentration_init.data
 atom_modify sort 0 1
 mass       * 39.948
 pair_coeff * * 0.2381 3.405
 pair_coeff 1 * 0.4    3.405
-dielectric 80.0 
+dielectric 80.0
 variable xlo equal xlo
 variable xhi equal xhi
 variable xmid equal 0.5*(${xhi}+${xlo})
@@ -37,9 +37,9 @@ region FLUID block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
 region R     block ${xmid} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
 group SOLID type 1
 variable xdof equal 3*count(SOLID)
-compute_modify thermo_temp extra ${xdof}
-#set group SOLID charge 0 
-group NEUTRAL type 2 
+compute_modify thermo_temp extra/dof ${xdof}
+#set group SOLID charge 0
+group NEUTRAL type 2
 group FLUID type 2 3 4
 group NION type 3
 group PION type 4
@@ -72,16 +72,16 @@ compute PMIN PION reduce min x
 compute PMAX PION reduce max x
 compute NMIN NION reduce min x
 compute NMAX NION reduce max x
-timestep  	${dt}
+timestep        ${dt}
 #neighbor 13 bin
 neigh_modify every $i check no
 # coulombic interactions
-fix         ATC FLUID   atc species_electrostatic  Ar_electrostatic.mat 
+fix         ATC FLUID   atc species_electrostatic  Ar_electrostatic.mat
 #fix_modify  ATC parallel_consistency off
 fix_modify  ATC extrinsic short_range off
 #fix_modify  ATC boundary SOLID
 fix_modify  ATC atom_element_map eulerian $i
-fix_modify  ATC internal_quadrature off 
+fix_modify  ATC internal_quadrature off
 fix_modify  ATC consistent_fe_initialization on
 fix_modify  ATC filter type exponential
 fix_modify  ATC filter scale $i
@@ -97,31 +97,31 @@ fix_modify ATC mesh create_elementset BOX BOX
 fix_modify ATC mass_matrix fe
 fix_modify ATC include atomic_charge
 fix_modify ATC add_species N type 3
-fix_modify ATC add_species P type 4 
+fix_modify ATC add_species P type 4
 fix_modify ATC add_species Nt type 5
-fix_modify ATC add_species Pt type 6 
+fix_modify ATC add_species Pt type 6
 ## CC
 fix_modify ATC control concentration N R 0.001 Nt  # deletions R
-fix_modify ATC control concentration N frequency $f 
-fix_modify ATC control concentration N max_energy $e 
+fix_modify ATC control concentration N frequency $f
+fix_modify ATC control concentration N max_energy $e
 fix_modify ATC control concentration N max_attempts 100
 fix_modify ATC control concentration N max_exchanges $x
 #-
 fix_modify ATC control concentration P R 0.002 Pt # addtions R
-fix_modify ATC control concentration P frequency $f 
+fix_modify ATC control concentration P frequency $f
 fix_modify ATC control concentration P max_energy $e
-fix_modify ATC control concentration P max_attempts 100 
+fix_modify ATC control concentration P max_attempts 100
 fix_modify ATC control concentration P max_exchanges $x
 fix_modify ATC output volume_integral all mass_density
 fix_modify ATC output volume_integral all charge_density
 # data reduction
 fix        PP all   atc field
-#fix_modify PP add_species ions type 3 4 
+#fix_modify PP add_species ions type 3 4
 #fix_modify PP add_species IONS type 3 4 1 2
-fix_modify PP add_species n type 3 
-fix_modify PP add_species p type 4 
-fix_modify PP add_species s type 1 
-fix_modify PP add_species o type 2 
+fix_modify PP add_species n type 3
+fix_modify PP add_species p type 4
+fix_modify PP add_species s type 1
+fix_modify PP add_species o type 2
 fix_modify PP fields add species_concentration mass_density charge_density temperature
 fix_modify PP fields add charge_flux species_flux
 fix_modify  PP output volume_integral all mass_density
@@ -129,7 +129,7 @@ fix_modify  PP output volume_integral all charge_density
 fix_modify PP mesh  create $h 1 1 BOX f p p
 fix_modify PP atom_element_map eulerian $i
 # output
-thermo    $i	
+thermo    $i
 variable dN equal f_ATC[1]
 variable dP equal f_ATC[2]
 variable Nc equal f_ATC[3]
@@ -141,19 +141,19 @@ variable Nu equal f_ATC[7]
 variable Pu equal f_ATC[8]
 variable Ng equal f_ATC[9]
 variable Pg equal f_ATC[10]
-thermo_style 	custom step temp etotal &
+thermo_style    custom step temp etotal &
 atoms v_F v_P v_N v_dP v_dN v_Pc v_Nc v_Pr v_Nr v_Pt v_Nt &
 c_PMIN c_NMIN c_PMAX c_NMAX c_Q c_M c_Qf c_Mf v_Pu v_Nu v_Pg v_Ng
-# NOTE this doesn't seem to work 
-#thermo_modify format 4 %5d format 5 %5d format 6 %5d format 7 %5d format 8 %5d 
-#thermo_modify format 4 %5d 
-#thermo_modify format 5 %5d 
-#thermo_modify format 6 %5d 
-#thermo_modify format 7 %5d 
-#thermo_modify format 8 %5d 
-#thermo_modify format 9 %5d 
-#thermo_modify format 10 %5d 
-#thermo_modify format 11 %5d 
+# NOTE this doesn't seem to work
+#thermo_modify format 4 %5d format 5 %5d format 6 %5d format 7 %5d format 8 %5d
+#thermo_modify format 4 %5d
+#thermo_modify format 5 %5d
+#thermo_modify format 6 %5d
+#thermo_modify format 7 %5d
+#thermo_modify format 8 %5d
+#thermo_modify format 9 %5d
+#thermo_modify format 10 %5d
+#thermo_modify format 11 %5d
 log concentration.log
 fix_modify  ATC output concentrationFE $s text binary
 fix_modify   PP output concentrationPP $s text
diff --git a/examples/PACKAGES/atc/fluids/in.shear_flow b/examples/PACKAGES/atc/fluids/in.shear_flow
index 3c06676c64..29327dfb1c 100644
--- a/examples/PACKAGES/atc/fluids/in.shear_flow
+++ b/examples/PACKAGES/atc/fluids/in.shear_flow
@@ -2,42 +2,42 @@
 # This benchmark tests momentum flux as a BC to the MD region to generate shear flow.
 # Currently heat will be generated as it will have no where to go.
 log shear_flow.log
-units		real
-atom_style	atomic
+units           real
+atom_style      atomic
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
 # NOTE following 3 lines added for restart
 boundary        f p p
 pair_style      lj/cut 13.5
 #read_data       temp.init
-read_data	post_eq.init
+read_data       post_eq.init
 lattice         fcc 5.405 origin 0.25 0.25 0.25
 # create atoms, NOTE commented out for restart
-#region		mdRegion block -8 8 -3 3 -3 3
-#boundary	f p p
-#create_box	2 mdRegion
-#create_atoms	1 region mdRegion
-#mass		* 39.95
+#region         mdRegion block -8 8 -3 3 -3 3
+#boundary       f p p
+#create_box     2 mdRegion
+#create_atoms   1 region mdRegion
+#mass           * 39.95
 # specify interal/ghost atoms
-#region		mdInternal block -6 6 -3 3 -3 3
-#region		mdGhost block -6 6 -3 3 -3 3 side out
+#region         mdInternal block -6 6 -3 3 -3 3
+#region         mdGhost block -6 6 -3 3 -3 3 side out
 #create_atoms    1 region mdGhost
 #lattice         fcc 6.5 origin 0.25 0.25 0.25
-#create_atoms	2 region mdInternal
-group		internal type 2
-group		ghost type 1
+#create_atoms   2 region mdInternal
+group           internal type 2
+group           ghost type 1
 # velocities have Vcm = 0, NOTE next four lines commented out for restart
-#velocity	internal create 100. 87287 mom yes loop geom
-#pair_style	lj/cut 13.5
-##pair_coeff	1 1 0.010323166 3.405 13.5
-#pair_coeff  	* * .238 3.405 13.5
+#velocity       internal create 100. 87287 mom yes loop geom
+#pair_style     lj/cut 13.5
+##pair_coeff    1 1 0.010323166 3.405 13.5
+#pair_coeff     * * .238 3.405 13.5
 #write_restart  tinit.dat
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
 
 # equilibrate MD field
 variable xdof equal 3*count(ghost)
-compute_modify thermo_temp extra ${xdof}
+compute_modify thermo_temp extra/dof ${xdof}
 thermo_style custom step cpu etotal pe temp
 thermo_modify  format 1 %6i format 2 %7.2g
 #fix             NVT internal nvt temp 100 100 10 drag 0.2
@@ -49,28 +49,28 @@ timestep        2
 
 #               ID  group atc PhysicsType ParameterFile
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		atcRegion block -6.25 6.25 -3 3 -3 3
+region          atcRegion block -6.25 6.25 -3 3 -3 3
 fix             AtC internal   atc shear     Ar_viscosity.mat
 #               ID  part keywords    nx ny nz region    periodicity
 fix_modify      AtC mesh create 6 1  1   atcRegion f p p
 #fix_modify      AtC  time_integration fractional_step
-##fix_modify	AtC atom_element_map eulerian 10 # NOTE this introduces a minor amount of time integration error tracking the atomic temperature
+##fix_modify    AtC atom_element_map eulerian 10 # NOTE this introduces a minor amount of time integration error tracking the atomic temperature
 fix_modify      AtC  internal_quadrature off
-#fix_modify	AtC  mass_matrix fe
+#fix_modify     AtC  mass_matrix fe
 # add nodesets
 #               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
 fix_modify      AtC mesh create_elementset rbc  4.12  6.3   -INF  INF   -INF  INF
 #used for restarting
-fix_modify	AtC  consistent_fe_initialization on
+fix_modify      AtC  consistent_fe_initialization on
 #fix_modify     AtC  initial velocity x all 0.
 
 # turn on kinetostat
 reset_timestep 0
-fix_modify	AtC  reset_time
-fix_modify	AtC  source velocity y rbc .0000001
+fix_modify      AtC  reset_time
+fix_modify      AtC  source velocity y rbc .0000001
 fix_modify      AtC control momentum flux no_boundary
-fix_modify	AtC control tolerance 1.e-14
-fix_modify	AtC control localized_lambda on
+fix_modify      AtC control tolerance 1.e-14
+fix_modify      AtC control localized_lambda on
 #fix_modify      AtC  filter type exponential
 #fix_modify      AtC  filter scale 1000.0
 #fix_modify      AtC  filter on
@@ -78,7 +78,7 @@ fix_modify	AtC control localized_lambda on
 # output commands
 fix_modify      AtC  output shear_flowFE 100 text #binary
 #undump          D1
-#dump		D1 all custom 100 shear_flow.dmp id type xs ys zs vx vy vz
+#dump           D1 all custom 100 shear_flow.dmp id type xs ys zs vx vy vz
 # set-up non-equilibrium IC
-thermo		100
-run 		2000
+thermo          100
+run             2000
diff --git a/examples/PACKAGES/atc/hardy/in.eshelby_static b/examples/PACKAGES/atc/hardy/in.eshelby_static
index b0ccc94af5..b00dcd1185 100644
--- a/examples/PACKAGES/atc/hardy/in.eshelby_static
+++ b/examples/PACKAGES/atc/hardy/in.eshelby_static
@@ -1,4 +1,4 @@
-# This test calculates the J-integral for a sequence of different loads 
+# This test calculates the J-integral for a sequence of different loads
 # for a system with a crack tip.
 #
 # loops around crack and one around undefected material
@@ -7,17 +7,17 @@
 # loop 2 - medium   contour around left crack tip
 # loop 3 - largest  contour around left crack tip
 # loop 4 - medium   contour around right crack tip
-#for Lennard-Jones potential for gold: 
-# surface energy (gamma) of 0.1599 eV/Å^2 = 2.56191 J/m2. 
+#for Lennard-Jones potential for gold:
+# surface energy (gamma) of 0.1599 eV/Å^2 = 2.56191 J/m2.
 # 2*gamma = 0.3198 eV/Å^2 = 5.12382 J/m2
-# using the internal nktv2p conversion factor, 
+# using the internal nktv2p conversion factor,
 # the units of eshelby_stress are eV/Å^3, and
 # the resulting boundary integral is eV/Å since we also include thickness (a
 # boundary surface area rather than a periphery). If we multiply the 2*gamma
 # quantity times the thickness t = 3*4.08 = 12.24 Å, we obtain 2*gamma*t =
-# 3.914352 eV/Å, which agrees with the mesh calculation.  
+# 3.914352 eV/Å, which agrees with the mesh calculation.
 echo both
-log    eshelby_static.log  
+log    eshelby_static.log
 units    metal
 dimension  3
 boundary  p p p
@@ -29,12 +29,12 @@ lattice fcc 4.08 origin 0.25 0.25 0.25
 region    SYSTEM    block -10 10 -10 10 0 3
 region    UPPER     block -10 10   0 10 0 3
 region    LOWER     block -10  0 -10 10 0 3
-create_box  1 SYSTEM 
+create_box  1 SYSTEM
 create_atoms  1 region SYSTEM
 mass    1 63.55
-group    internal region SYSTEM 
-group    upper region UPPER 
-group    lower region LOWER 
+group    internal region SYSTEM
+group    upper region UPPER
+group    lower region LOWER
 #pair_style  eam
 #pair_coeff  * * ../../../../potentials/Cu_u3.eam
 #pair_style lj/smooth 8.0 10.0
@@ -42,27 +42,27 @@ group    lower region LOWER
 pair_style  lj/smooth/linear 5.456108274435118
 pair_coeff    * * 0.7242785984051078 2.598146797350056
 # define region
-region  abovecrack block -2.01 2.01  0 8 INF INF units lattice 
+region  abovecrack block -2.01 2.01  0 8 INF INF units lattice
 group   abovecrack region abovecrack
-region  belowcrack block -2.01 2.01 -8 0 INF INF units lattice 
+region  belowcrack block -2.01 2.01 -8 0 INF INF units lattice
 group   belowcrack region belowcrack
 neighbor  1.0 bin
 neigh_modify  delay 1000000
-neigh_modify  exclude group abovecrack belowcrack 
+neigh_modify  exclude group abovecrack belowcrack
 thermo    10
-compute_modify  thermo_temp extra 0
+compute_modify  thermo_temp extra/dof 0
 region  FORCECHECK block -6  0  6 10 0 3
 group   FORCECHECK region FORCECHECK
 compute   fxsum FORCECHECK reduce sum fx
 compute   fysum FORCECHECK reduce sum fy
 compute   fzsum FORCECHECK reduce sum fz
 thermo_style  custom step ke pe press c_fxsum c_fysum c_fzsum
-thermo_modify  format 1 %4i  format 2 %3.1g  format 3 %20.16g 
+thermo_modify  format 1 %4i  format 2 %3.1g  format 3 %20.16g
 timestep  0.0
 # (1) minimize the system to get a relaxed configuration
 min_modify line quadratic
 variable tol equal 1.e-11
-minimize  0.0 ${tol} 100000 1000000  
+minimize  0.0 ${tol} 100000 1000000
 write_restart  eshelby.restart
 # (2) pull crack apart
 reset_timestep  0
@@ -70,13 +70,13 @@ fix             PK1 internal atc field
 # NOTE tune this relative to lattice size
 fix_modify      PK1 mesh create 10 10 1 SYSTEM p f p
 fix_modify      PK1 fields none
-fix_modify      PK1 fields add mass_density internal_energy temperature stress displacement 
-fix_modify	PK1 fields add eshelby_stress transformed_stress
-fix_modify      PK1 gradients add displacement 
+fix_modify      PK1 fields add mass_density internal_energy temperature stress displacement
+fix_modify      PK1 fields add eshelby_stress transformed_stress
+fix_modify      PK1 gradients add displacement
 fix_modify      PK1 set reference_potential_energy
 fix_modify      PK1 output eshelby_staticFE 1 text binary tensor_components
-#fix_modify	PK1  on_the_fly
-#-- make concentric loops around one/both of the crack tips 
+#fix_modify     PK1  on_the_fly
+#-- make concentric loops around one/both of the crack tips
 #-- & another around undefected material (loop0)
 fix_modify      PK1 mesh create_faceset loop0 box -6  0  6 10 -INF INF outward
 fix_modify      PK1 output boundary_integral eshelby_stress faceset loop0
diff --git a/examples/PACKAGES/atc/hardy/in.nvt b/examples/PACKAGES/atc/hardy/in.nvt
index 68ba2eba17..c6de0842f9 100644
--- a/examples/PACKAGES/atc/hardy/in.nvt
+++ b/examples/PACKAGES/atc/hardy/in.nvt
@@ -5,12 +5,12 @@ atom_style  atomic
 echo both
 dimension 3
 boundary  p p p
-lattice 	fcc  5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
-region  	box block 0 5 0 5 0 5
-read_data	nvt.init
+lattice         fcc  5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
+region          box block 0 5 0 5 0 5
+read_data       nvt.init
 pair_style  lj/cut 13.0
-pair_coeff	1 1 0.2381 3.405
-group		internal region box
+pair_coeff      1 1 0.2381 3.405
+group           internal region box
 
 fix         ATC internal atc field
 fix_modify  ATC mesh create 1 1 1 box p p p
@@ -27,12 +27,12 @@ fix_modify  PP  atom_element_map eulerian 100
 fix_modify  PP  fields add mass_density energy stress temperature kinetic_temperature
 fix_modify  PP  fields add velocity thermal_energy kinetic_energy
 fix_modify  PP  output nvtPP 100 text
-thermo		100
-compute_modify	thermo_temp extra 0
-thermo_style 	custom step temp etotal ke pe press vol
-timestep 	4.0
-reset_timestep	0
+thermo          100
+compute_modify  thermo_temp extra/dof 0
+thermo_style    custom step temp etotal ke pe press vol
+timestep        4.0
+reset_timestep  0
 # NOTE fixes performing time integration (init_integrate/final_integrate) should be defined after atc
-fix 		NVT all nvt temp 30 30 10.0 drag 0.2 tchain 1
-log		nvt.log
-run 		1000
+fix             NVT all nvt temp 30 30 10.0 drag 0.2 tchain 1
+log             nvt.log
+run             1000
diff --git a/examples/PACKAGES/atc/thermal/in.bar1d b/examples/PACKAGES/atc/thermal/in.bar1d
index 3f70577ec3..9fe5617ec3 100644
--- a/examples/PACKAGES/atc/thermal/in.bar1d
+++ b/examples/PACKAGES/atc/thermal/in.bar1d
@@ -1,38 +1,38 @@
 #AtC Thermal Coupling
 # This benchmark tests heat conducting into and out of the MD region.  The
 # temperature is initially 20 everywhere and the left boundary BC is fixed at 40.
-# The result should show heat diffusing through the FEM to the MD and back out 
-# to the FEM on the right.  Insufficient time is captured to reach the linear 
+# The result should show heat diffusing through the FEM to the MD and back out
+# to the FEM on the right.  Insufficient time is captured to reach the linear
 # steady state, but heat crossing both boundaries should be observed.
- 
-units		real
-atom_style	atomic
+
+units           real
+atom_style      atomic
 echo both
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
 # NOTE following 3 lines added for restart
 boundary        f p p
 pair_style      lj/cut 13.5
 read_data       temp.init
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		simRegion block -12 12 -3 3 -3 3
+region          simRegion block -12 12 -3 3 -3 3
 # create atoms, NOTE commented out for restart
-#region		mdRegion block -5 5 -3 3 -3 3
-#boundary	f p p
-#create_box	1 mdRegion
-#create_atoms	1 region mdRegion
-#mass		1 39.95
+#region         mdRegion block -5 5 -3 3 -3 3
+#boundary       f p p
+#create_box     1 mdRegion
+#create_atoms   1 region mdRegion
+#mass           1 39.95
 # specify interal/ghost atoms
-region		mdInternal block -4 4 -3 3 -3 3
-group		internal region mdInternal
-group		ghost subtract all internal
+region          mdInternal block -4 4 -3 3 -3 3
+group           internal region mdInternal
+group           ghost subtract all internal
 # velocities have Vcm = 0, NOTE next four lines commented out for restart
-#velocity	internal create 40. 87287 mom yes loop geom
-#pair_style	lj/cut 13.5
-##pair_coeff	1 1 0.010323166 3.405 13.5
-#pair_coeff  	1 1 .238 3.405 13.5
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
+#velocity       internal create 40. 87287 mom yes loop geom
+#pair_style     lj/cut 13.5
+##pair_coeff    1 1 0.010323166 3.405 13.5
+#pair_coeff     1 1 .238 3.405 13.5
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
 #               ID  group atc PhysicsType ParameterFile
 fix             AtC internal   atc thermal     Ar_thermal.mat
 fix_modify      AtC boundary ghost
@@ -40,26 +40,26 @@ fix_modify      AtC boundary ghost
 fix_modify      AtC mesh create 12 1  1  simRegion f p p
 fix_modify      AtC internal_quadrature off
 # fix a temperature
-fix_modify     	AtC  fix temperature all 20.
+fix_modify      AtC  fix temperature all 20.
 # turn on thermostat
-fix_modify	AtC  control thermal rescale 10
+fix_modify      AtC  control thermal rescale 10
 # equilibrate MD field
 #dump            D1 all atom 100 dump.bar1d
 #fix_modify      AtC  output bar1dfe 100
-timestep	5
+timestep        5
 variable xdof equal 3*count(ghost)
-compute_modify thermo_temp extra ${xdof}
-thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] 
+compute_modify thermo_temp extra/dof ${xdof}
+thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
 thermo_modify  format 1 %6i format 2 %7.2g
-thermo		100
-run 		400
+thermo          100
+run             400
 # change thermostat to hoover
-fix_modify	AtC  unfix temperature all
-fix_modify     	AtC  control thermal hoover
-#fix_modify	AtC  localized_lambda on
-fix_modify	AtC  filter type exponential
-fix_modify	AtC  filter scale 10000.0
-fix_modify	AtC  filter on
+fix_modify      AtC  unfix temperature all
+fix_modify      AtC  control thermal hoover
+#fix_modify     AtC  localized_lambda on
+fix_modify      AtC  filter type exponential
+fix_modify      AtC  filter scale 10000.0
+fix_modify      AtC  filter on
 # add nodesets
 #               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
 fix_modify      AtC mesh create_nodeset lbc -12.1  -11.9   -INF  INF   -INF  INF
@@ -67,13 +67,13 @@ fix_modify      AtC mesh create_nodeset rbc  11.9   12.1   -INF  INF   -INF  INF
 fix_modify      AtC  fix temperature lbc 40.
 fix_modify      AtC  fix temperature rbc 20.
 # initialize filter
-thermo		1
-run		100
+thermo          1
+run             100
 # set up output, should be before a "run"
 fix_modify      AtC  output bar1dFE 100 text binary
 # output command
 #dump            D1 all atom 1000 dump.bar1d
 # run with FE
 reset_timestep 0
-thermo		100
-run 		10000
+thermo          100
+run             10000
diff --git a/examples/PACKAGES/atc/thermal/in.bar1d_all_atoms b/examples/PACKAGES/atc/thermal/in.bar1d_all_atoms
index 2219b803ec..1faf24427d 100644
--- a/examples/PACKAGES/atc/thermal/in.bar1d_all_atoms
+++ b/examples/PACKAGES/atc/thermal/in.bar1d_all_atoms
@@ -4,33 +4,33 @@
 # 40.# The result should show heat diffusing through the FEM to the MD and back
 # out # to the FEM on the right.  Insufficient time is captured to reach the
 # linear # steady state, but heat crossing both boundaries should be observed.
-units		real
-atom_style	atomic
+units           real
+atom_style      atomic
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
 # NOTE following 3 lines added for restart
 boundary        f p p
 pair_style      lj/cut 13.5
 read_data       all_atoms.init
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		simRegion block -7 7 -3 3 -3 3
+region          simRegion block -7 7 -3 3 -3 3
 # create atoms, NOTE commented out for restart
-#boundary	f p p
-#create_box	1 simRegion
-#create_atoms	1 region simRegion
-#mass		1 39.95
+#boundary       f p p
+#create_box     1 simRegion
+#create_atoms   1 region simRegion
+#mass           1 39.95
 # specify interal/ghost atoms
-region		mdInternal block -6 6 -3 3 -3 3
-group		internal region mdInternal
-group		ghost subtract all internal
+region          mdInternal block -6 6 -3 3 -3 3
+group           internal region mdInternal
+group           ghost subtract all internal
 # velocities have Vcm = 0, NOTE next four lines commented out for restart
-#velocity	internal create 40. 87287 mom yes loop geom
-#pair_style	lj/cut 13.5
-##pair_coeff	1 1 0.010323166 3.405 13.5
-#pair_coeff  	1 1 .238 3.405 13.5
-#write_restart	all_atoms.init
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
+#velocity       internal create 40. 87287 mom yes loop geom
+#pair_style     lj/cut 13.5
+##pair_coeff    1 1 0.010323166 3.405 13.5
+#pair_coeff     1 1 .238 3.405 13.5
+#write_restart  all_atoms.init
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
 #               ID  group atc PhysicsType ParameterFile
 fix             AtC internal   atc thermal     Ar_thermal.mat
 #               ID  part keywords    nx ny nz region
@@ -39,34 +39,34 @@ fix_modify      AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF out
 fix_modify      AtC mesh create_faceset lbndy box -6.0 16.0 -INF INF -INF INF outward
 fix_modify      AtC mesh create_faceset rbndy box -16.0 6.0 -INF INF -INF INF outward
 # fix a temperature
-fix_modify     	AtC  fix temperature all 20.
+fix_modify      AtC  fix temperature all 20.
 # turn on thermostat
-fix_modify	AtC  control thermal rescale 10
+fix_modify      AtC  control thermal rescale 10
 fix_modify      AtC  internal_quadrature off
 # equilibrate MD field
 #dump            D1 all atom 100 dump.bar1d
 #fix_modify      AtC  output bar1dfe 100
-#fix_modify	AtC  time_integration frac_step
-timestep	5
+#fix_modify     AtC  time_integration frac_step
+timestep        5
 variable xdof equal 3*count(ghost)
-compute_modify thermo_temp extra ${xdof}
+compute_modify thermo_temp extra/dof ${xdof}
 thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
 thermo_modify  format 1 %6i format 2 %7.2g
-thermo		100
-run 		400
+thermo          100
+run             400
 # change thermostat to hoover
-fix_modify	AtC  control thermal hoover
-#fix_modify	AtC  thermal control flux interpolate
-#fix_modify	AtC  thermal control flux faceset obndy
-fix_modify	AtC  filter scale 1000.0
-#fix_modify	AtC  filter equilibrate
-#fix_modify	AtC  filter on
-#fix_modify	AtC  localized_lambda on
+fix_modify      AtC  control thermal hoover
+#fix_modify     AtC  thermal control flux interpolate
+#fix_modify     AtC  thermal control flux faceset obndy
+fix_modify      AtC  filter scale 1000.0
+#fix_modify     AtC  filter equilibrate
+#fix_modify     AtC  filter on
+#fix_modify     AtC  localized_lambda on
 fix_modify      AtC  boundary_faceset is obndy
 # initialize filter
 #fix_modify      AtC  output bar1d_all_atoms_preqFE 1
 reset_timestep  0
-thermo		1
+thermo          1
 #run             5000
 # add nodesets and ramp temperature
 #               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
@@ -76,26 +76,26 @@ thermo		1
 #fix_modify      AtC  fix temperature rbc 20.
 # initialize filter
 #fix_modify      AtC  output bar1d_all_atoms_eqFE 200
-reset_timestep	0
-fix_modify	AtC  reset_time
+reset_timestep  0
+fix_modify      AtC  reset_time
 #run             5000
 # release and let run
-#fix_modify	AtC  filter on
-fix_modify	AtC  unfix temperature all
+#fix_modify     AtC  filter on
+fix_modify      AtC  unfix temperature all
 #fix_modify      AtC  localized_lambda on
-fix_modify	AtC  control lumped_lambda_solve on
+fix_modify      AtC  control lumped_lambda_solve on
 # dirichlet boundaries
 #fix_modify      AtC  fix temperature lbc 40.
 #fix_modify      AtC  fix temperature rbc 20.
 # neumann boundaries
 fix_modify      AtC  control thermal flux no_boundary
-fix_modify	AtC  fix_flux temperature lbndy  0.0000000001
+fix_modify      AtC  fix_flux temperature lbndy  0.0000000001
 fix_modify      AtC  fix_flux temperature rbndy -0.0000000001
 # set up output, should be before a "run"
 fix_modify      AtC  output bar1d_all_atomsFE 200 text binary
 # output command
 #dump            D1 all atom 1000 dump.bar1d
 # run with FE
-reset_timestep 	0
-thermo		200
-run 		5000
+reset_timestep  0
+thermo          200
+run             5000
diff --git a/examples/PACKAGES/atc/thermal/in.bar1d_combined b/examples/PACKAGES/atc/thermal/in.bar1d_combined
index 70dafe72be..23b01139f2 100644
--- a/examples/PACKAGES/atc/thermal/in.bar1d_combined
+++ b/examples/PACKAGES/atc/thermal/in.bar1d_combined
@@ -6,62 +6,62 @@
 # linear # steady state, but heat crossing the boundaries should be observed,
 # as should the interaction of the two themostat types.
 #echo both
-units		real
-atom_style	atomic
+units           real
+atom_style      atomic
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
 # NOTE following 3 lines added for restart
-boundary	f p p
-pair_style	lj/cut 13.5
+boundary        f p p
+pair_style      lj/cut 13.5
 read_data       temp.init
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		simRegion block -16 4 -3 3 -3 3
+region          simRegion block -16 4 -3 3 -3 3
 # create atoms, NOTE commented out for restart
-#region		mdRegion block -5 5 -3 3 -3 3
-#boundary	f p p
-#create_box	1 mdRegion
-#create_atoms	1 region mdRegion
-#mass		1 39.95
+#region         mdRegion block -5 5 -3 3 -3 3
+#boundary       f p p
+#create_box     1 mdRegion
+#create_atoms   1 region mdRegion
+#mass           1 39.95
 # specify interal/ghost atoms
-region		mdInternal block -4 4 -3 3 -3 3
-group		internal region mdInternal
-region		mdGhost block -5 -4 -3 3 -3 3
-group		ghost region mdGhost
+region          mdInternal block -4 4 -3 3 -3 3
+group           internal region mdInternal
+region          mdGhost block -5 -4 -3 3 -3 3
+group           ghost region mdGhost
 # velocities have Vcm = 0, NOTE next four lines commented out for restart
-#velocity	internal create 40. 87287 mom yes loop geom
-#pair_style	lj/cut 13.5
-##pair_coeff	1 1 0.010323166 3.405 13.5
-#pair_coeff  	1 1 .238 3.405 13.5
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
-#write_restart	tinit.dat
+#velocity       internal create 40. 87287 mom yes loop geom
+#pair_style     lj/cut 13.5
+##pair_coeff    1 1 0.010323166 3.405 13.5
+#pair_coeff     1 1 .238 3.405 13.5
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
+#write_restart  tinit.dat
 #               ID  group atc PhysicsType ParameterFile
 fix             AtC internal   atc thermal     Ar_thermal.mat
 fix_modify      AtC boundary ghost
 fix_modify      AtC time_integration fractional_step
-fix_modify	AtC internal_quadrature off
+fix_modify      AtC internal_quadrature off
 #               ID  part keywords    nx ny nz region
 fix_modify      AtC mesh create 10 1  1  simRegion f p p
 fix_modify      AtC mesh create_faceset ibndy box -4.0 40.0 -INF INF -INF INF in
 fix_modify      AtC mesh create_faceset obndy box -4.0 40.0 -INF INF -INF INF outward
 # fix a temperature
-fix_modify     	AtC  fix temperature all 20.
+fix_modify      AtC  fix temperature all 20.
 # turn on thermostat
-fix_modify	AtC  control thermal rescale 10
+fix_modify      AtC  control thermal rescale 10
 variable xdof equal 3*count(ghost)
-compute_modify thermo_temp extra ${xdof}
+compute_modify thermo_temp extra/dof ${xdof}
 thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
 thermo_modify  format 1 %6i format 2 %7.2g
 # equilibrate MD field
 #fix_modify      AtC  output bar1dfe_combined_init 100
-timestep	5
-thermo		10
-run 		400
+timestep        5
+thermo          10
+run             400
 # change thermostat to flux
-fix_modify	AtC unfix temperature all
-fix_modify  	AtC control thermal flux faceset obndy 
-#fix_modify	AtC control thermal hoover
-fix_modify	AtC control localized_lambda on
+fix_modify      AtC unfix temperature all
+fix_modify      AtC control thermal flux faceset obndy 
+#fix_modify     AtC control thermal hoover
+fix_modify      AtC control localized_lambda on
 #fix_modify      AtC  control tolerance 1.e-16 # this tolerance seems necessary to prevent noticeable drift
 # add nodesets
 #               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
@@ -74,8 +74,8 @@ fix_modify      AtC  fix temperature rbc 20.
 fix_modify      AtC  filter type exponential
 fix_modify      AtC  filter scale 1000.0
 #fix_modify      AtC  filter on
-thermo		100
-#run		100
+thermo          100
+#run            100
 
 # set up output, should be before a "run"
 fix_modify      AtC  output bar1d_combinedFE 100 text
@@ -83,5 +83,5 @@ fix_modify      AtC  output bar1d_combinedFE 100 text
 #dump            D1 all atom 100 dump.bar1d_combined
 # run with FE
 reset_timestep 0
-thermo		100
-run 		5000
+thermo          100
+run             5000
diff --git a/examples/PACKAGES/atc/thermal/in.bar1d_flux b/examples/PACKAGES/atc/thermal/in.bar1d_flux
index 2b79aa6339..6f7fdcca21 100644
--- a/examples/PACKAGES/atc/thermal/in.bar1d_flux
+++ b/examples/PACKAGES/atc/thermal/in.bar1d_flux
@@ -5,34 +5,34 @@
 # out # to the FEM on the right.  Insufficient time is captured to reach the
 # linear # steady state, but heat crossing both boundaries should be observed.
 #echo both
-units		real
-atom_style	atomic
+units           real
+atom_style      atomic
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
 # NOTE following 3 lines added for restart
-boundary	f p p
-pair_style	lj/cut 13.5
+boundary        f p p
+pair_style      lj/cut 13.5
 read_data       temp.init
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		simRegion block -12 12 -3 3 -3 3
+region          simRegion block -12 12 -3 3 -3 3
 # create atoms, NOTE commented out for restart
-#region		mdRegion block -5 5 -3 3 -3 3
-#boundary	f p p
-#create_box	1 mdRegion
-#create_atoms	1 region mdRegion
-#mass		1 39.95
+#region         mdRegion block -5 5 -3 3 -3 3
+#boundary       f p p
+#create_box     1 mdRegion
+#create_atoms   1 region mdRegion
+#mass           1 39.95
 # specify interal/ghost atoms
-region		mdInternal block -4 4 -3 3 -3 3
-group		internal region mdInternal
-group		ghost subtract all internal
+region          mdInternal block -4 4 -3 3 -3 3
+group           internal region mdInternal
+group           ghost subtract all internal
 # velocities have Vcm = 0, NOTE next four lines commented out for restart
-#velocity	internal create 40. 87287 mom yes loop geom
-#pair_style	lj/cut 13.5
-##pair_coeff	1 1 0.010323166 3.405 13.5
-#pair_coeff  	1 1 .238 3.405 13.5
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
-#write_restart	tinit.dat
+#velocity       internal create 40. 87287 mom yes loop geom
+#pair_style     lj/cut 13.5
+##pair_coeff    1 1 0.010323166 3.405 13.5
+#pair_coeff     1 1 .238 3.405 13.5
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
+#write_restart  tinit.dat
 #               ID  group atc PhysicsType ParameterFile
 fix             AtC internal   atc thermal     Ar_thermal.mat
 fix_modify      AtC boundary ghost
@@ -42,25 +42,25 @@ fix_modify      AtC mesh create 12 1  1  simRegion f p p
 fix_modify      AtC mesh create_faceset ibndy box -4.0 4.0 -INF INF -INF INF in
 fix_modify      AtC mesh create_faceset obndy box -4.0 4.0 -INF INF -INF INF outward
 # fix a temperature
-fix_modify     	AtC  fix temperature all 20.
-#fix_modify	AtC  fix temperature all linear 0 0 0 -0.154 0 0 30.
+fix_modify      AtC  fix temperature all 20.
+#fix_modify     AtC  fix temperature all linear 0 0 0 -0.154 0 0 30.
 # turn on thermostat
-fix_modify	AtC  control thermal rescale 10
+fix_modify      AtC  control thermal rescale 10
 variable xdof equal 3*count(ghost)
-compute_modify thermo_temp extra ${xdof}
+compute_modify thermo_temp extra/dof ${xdof}
 thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
 thermo_modify  format 1 %6i format 2 %7.2g
 # equilibrate MD field
 #fix_modify      AtC  output bar1dfe_flux_init 100
-timestep	5
-thermo		10
-run 		400
+timestep        5
+thermo          10
+run             400
 # change thermostat to hoover
-fix_modify	AtC  unfix temperature all
-fix_modify  	AtC  control thermal flux faceset obndy 
+fix_modify      AtC  unfix temperature all
+fix_modify      AtC  control thermal flux faceset obndy 
 fix_modify      AtC  filter type exponential
-fix_modify	AtC  filter scale 10000.0
-#fix_modify	AtC  filter on
+fix_modify      AtC  filter scale 10000.0
+#fix_modify     AtC  filter on
 # add nodesets
 #               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
 fix_modify      AtC mesh create_nodeset lbc -12.1  -11.9   -INF INF   -INF INF
@@ -68,12 +68,12 @@ fix_modify      AtC mesh create_nodeset rbc  11.9   12.1   -INF INF   -INF INF
 fix_modify      AtC  fix temperature lbc 40.
 fix_modify      AtC  fix temperature rbc 20.
 # initialize filter
-run		100
+run             100
 # set up output, should be before a "run"
 fix_modify      AtC  output bar1d_fluxFE 100 text binary
 # output command
 #dump            D1 all atom 1000 dump.bar1d
 # run with FE
 reset_timestep 0
-thermo		100
-run 		10000
+thermo          100
+run             10000
diff --git a/examples/PACKAGES/atc/thermal/in.bar1d_frac_step b/examples/PACKAGES/atc/thermal/in.bar1d_frac_step
index e8540d9151..09295cab24 100644
--- a/examples/PACKAGES/atc/thermal/in.bar1d_frac_step
+++ b/examples/PACKAGES/atc/thermal/in.bar1d_frac_step
@@ -4,33 +4,33 @@
 # 40.# The result should show heat diffusing through the FEM to the MD and back
 # out # to the FEM on the right.  Insufficient time is captured to reach the
 # linear # steady state, but heat crossing both boundaries should be observed.
-units		real
-atom_style	atomic
+units           real
+atom_style      atomic
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
 # NOTE following 3 lines added for restart
 boundary        f p p
 pair_style      lj/cut 13.5
 read_data       temp.init
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		simRegion block -12 12 -3 3 -3 3
+region          simRegion block -12 12 -3 3 -3 3
 # create atoms, NOTE commented out for restart
-#region		mdRegion block -5 5 -3 3 -3 3
-#boundary	f p p
-#create_box	1 mdRegion
-#create_atoms	1 region mdRegion
-#mass		1 39.95
+#region         mdRegion block -5 5 -3 3 -3 3
+#boundary       f p p
+#create_box     1 mdRegion
+#create_atoms   1 region mdRegion
+#mass           1 39.95
 # specify interal/ghost atoms
-region		mdInternal block -4 4 -3 3 -3 3
-group		internal region mdInternal
-group		ghost subtract all internal
+region          mdInternal block -4 4 -3 3 -3 3
+group           internal region mdInternal
+group           ghost subtract all internal
 # velocities have Vcm = 0, NOTE next four lines commented out for restart
-#velocity	internal create 40. 87287 mom yes loop geom
-#pair_style	lj/cut 13.5
-##pair_coeff	1 1 0.010323166 3.405 13.5
-#pair_coeff  	1 1 .238 3.405 13.5
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
+#velocity       internal create 40. 87287 mom yes loop geom
+#pair_style     lj/cut 13.5
+##pair_coeff    1 1 0.010323166 3.405 13.5
+#pair_coeff     1 1 .238 3.405 13.5
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
 #               ID  group atc PhysicsType ParameterFile
 fix             AtC internal   atc thermal     Ar_thermal.mat
 #               ID  part keywords    nx ny nz region
@@ -40,7 +40,7 @@ fix_modify  AtC  internal_atom_integrate off
 fix iNVE internal nve
 fix_modify      AtC  internal_quadrature off
 # fix a temperature
-fix_modify     	AtC  fix temperature all 20.
+fix_modify      AtC  fix temperature all 20.
 # add nodesets
 #               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
 fix_modify      AtC mesh create_nodeset lbc -4.1  -3.9   -INF INF   -INF INF
@@ -48,25 +48,25 @@ fix_modify      AtC mesh create_nodeset rbc  3.9   4.1   -INF INF   -INF INF
 fix_modify      AtC  fix temperature lbc 40.
 fix_modify      AtC  fix temperature rbc 20.
 # turn on thermostat
-fix_modify	AtC  control thermal rescale 10
+fix_modify      AtC  control thermal rescale 10
 # equilibrate MD field
 #dump            D1 all atom 100 dump.bar1d
 #fix_modify      AtC  output bar1dfe 100 text
-timestep	5
+timestep        5
 variable xdof equal 3*count(ghost)
-compute_modify thermo_temp extra ${xdof}
+compute_modify thermo_temp extra/dof ${xdof}
 thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
 thermo_modify  format 1 %6i format 2 %7.2g
-thermo		100
-run 		400
+thermo          100
+run             400
 # change thermostat to hoover
 fix_modify      AtC  unfix temperature all
 fix_modify      AtC  fix temperature lbc 40.
 fix_modify      AtC  fix temperature rbc 20.
 fix_modify      AtC  control thermal flux no_boundary
-fix_modify	AtC  control tolerance 1.e-9 # this is to remove looser benchmark tolerance because the lambda solution was reacting to numerical noise, but it results in a slight drift in the constraints
-#fix_modify	AtC  thermal control none
-fix_modify	AtC  control localized_lambda on
+fix_modify      AtC  control tolerance 1.e-9 # this is to remove looser benchmark tolerance because the lambda solution was reacting to numerical noise, but it results in a slight drift in the constraints
+#fix_modify     AtC  thermal control none
+fix_modify      AtC  control localized_lambda on
 fix_modify      AtC  filter type exponential
 fix_modify      AtC  filter scale 1000.0
 fix_modify      AtC  filter on
@@ -76,5 +76,5 @@ fix_modify      AtC  output bar1d_frac_stepFE 200 text
 #dump            D1 all atom 1000 dump.bar1d
 # run with FE
 reset_timestep 0
-thermo		100
-run 		10000
+thermo          100
+run             10000
diff --git a/examples/PACKAGES/atc/thermal/in.bar1d_hoover b/examples/PACKAGES/atc/thermal/in.bar1d_hoover
index 2f0518d0d2..477a2bf08d 100644
--- a/examples/PACKAGES/atc/thermal/in.bar1d_hoover
+++ b/examples/PACKAGES/atc/thermal/in.bar1d_hoover
@@ -4,35 +4,35 @@
 # 40.# The result should show heat diffusing through the FEM to the MD and back
 # out # to the FEM on the right.  Insufficient time is captured to reach the
 # linear # steady state, but heat crossing both boundaries should be observed.
-units		real
-atom_style	atomic
+units           real
+atom_style      atomic
 log bar1d_hoover.log
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
 # NOTE following 3 lines added for restart
 boundary        f p p
 pair_style      lj/cut 13.5
 read_data       all_atoms.init
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		simRegion block -7 7 -3 3 -3 3
+region          simRegion block -7 7 -3 3 -3 3
 # create atoms, NOTE commented out for restart
-#boundary	f p p
-#create_box	1 simRegion
-#create_atoms	1 region simRegion
-#mass		1 39.95
-#atom_modify	sort 0 0
+#boundary       f p p
+#create_box     1 simRegion
+#create_atoms   1 region simRegion
+#mass           1 39.95
+#atom_modify    sort 0 0
 # specify interal/ghost atoms
-region		mdInternal block -6 6 -3 3 -3 3
-group		internal region mdInternal
-group		ghost subtract all internal
+region          mdInternal block -6 6 -3 3 -3 3
+group           internal region mdInternal
+group           ghost subtract all internal
 # velocities have Vcm = 0, NOTE next four lines commented out for restart
-#velocity	internal create 40. 87287 mom yes loop geom
-#pair_style	lj/cut 13.5
-##pair_coeff	1 1 0.010323166 3.405 13.5
-#pair_coeff  	1 1 .238 3.405 13.5
-#write_restart	all_atoms.init
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
+#velocity       internal create 40. 87287 mom yes loop geom
+#pair_style     lj/cut 13.5
+##pair_coeff    1 1 0.010323166 3.405 13.5
+#pair_coeff     1 1 .238 3.405 13.5
+#write_restart  all_atoms.init
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
 #               ID  group atc PhysicsType ParameterFile
 fix             AtC internal   atc thermal     Ar_thermal.mat
 #               ID  part keywords    nx ny nz region
@@ -40,9 +40,9 @@ fix             AtC internal   atc thermal     Ar_thermal.mat
 # switch depending on application of BCs or coupling
 #variable nEls equal 6 # for boundary conditions
 variable nEls equal 12 # for coupling
-fix_modify	AtC boundary ghost # for coupling
+fix_modify      AtC boundary ghost # for coupling
 
-region		atcRegion block -${nEls} ${nEls} -3 3 -3 3
+region          atcRegion block -${nEls} ${nEls} -3 3 -3 3
 fix_modify      AtC mesh  create ${nEls} 1  1  atcRegion f p p
 fix_modify      AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
 fix_modify      AtC mesh create_faceset lbndy box -6.0 16.0 -INF INF -INF INF outward
@@ -50,39 +50,39 @@ fix_modify      AtC mesh create_faceset rbndy box -16.0 6.0 -INF INF -INF INF ou
 variable tol equal 0.1
 variable uBnd equal ${nEls}+${tol}
 variable lBnd equal ${nEls}-${tol}
-fix_modify	AtC mesh create_nodeset lbc -${uBnd}  -${lBnd}   -INF INF   -INF INF
+fix_modify      AtC mesh create_nodeset lbc -${uBnd}  -${lBnd}   -INF INF   -INF INF
 fix_modify      AtC mesh create_nodeset rbc  ${lBnd}   ${uBnd}   -INF INF   -INF INF
 # fix a temperature
-fix_modify     	AtC  fix temperature all 20.
-#fix_modify	AtC initial temperature all 20.
-#fix_modify	AtC consistent_fe_initialization on
+fix_modify      AtC  fix temperature all 20.
+#fix_modify     AtC initial temperature all 20.
+#fix_modify     AtC consistent_fe_initialization on
 # turn on thermostat
-fix_modify	AtC  control thermal rescale 10
+fix_modify      AtC  control thermal rescale 10
 fix_modify      AtC  internal_quadrature off
 # equilibrate MD field
 #dump            D1 all atom 100 dump.bar1d_hoover_init
 #fix_modify      AtC  output bar1d_hoover_init 100 text binary
-fix_modify	AtC  time_integration fractional_step
-fix_modify	AtC  temperature_definition total
-timestep	5
+fix_modify      AtC  time_integration fractional_step
+fix_modify      AtC  temperature_definition total
+timestep        5
 variable xdof equal 3*count(ghost)
-compute_modify thermo_temp extra ${xdof}
+compute_modify thermo_temp extra/dof ${xdof}
 thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
 thermo_modify  format 1 %6i format 2 %7.2g
-thermo		100
-run 		400
+thermo          100
+run             400
 
-fix_modify	AtC  unfix temperature all
+fix_modify      AtC  unfix temperature all
 
-fix_modify	AtC  filter type exponential
+fix_modify      AtC  filter type exponential
 fix_modify      AtC  filter scale 1000.0
 fix_modify      AtC  filter on
 
 
 # boundary conditions------------------------
 # dirichlet with ramp (unstable when filtered due to instantaneous change in rate)
-#fix_modify	AtC  fix temperature lbc temporal_ramp 20. 40. 25000.
-#fix_modify	AtC  fix temperature rbc 20.
+#fix_modify     AtC  fix temperature lbc temporal_ramp 20. 40. 25000.
+#fix_modify     AtC  fix temperature rbc 20.
 #fix_modify      AtC  localized_lambda on
 #fix_modify      AtC  control thermal flux no_boundary
 #fix_modify      AtC  output test_rampFE 200 text binary
@@ -94,7 +94,7 @@ fix_modify      AtC  filter on
 #fix_modify      AtC  fix temperature lbc 40.
 
 # dirichlet with rescaling
-#fix_modify	AtC  filter off
+#fix_modify     AtC  filter off
 #fix_modify      AtC  fix temperature all 20.
 #fix_modify      AtC  fix temperature lbc 40.
 #fix_modify      AtC  output test_rampFE 200 text binary
@@ -126,13 +126,13 @@ fix_modify      AtC  fix temperature rbc 20.
 #fix_modify      AtC  lumped_lambda_solve on
 
 # hoover
-fix_modify	AtC  control thermal hoover
+fix_modify      AtC  control thermal hoover
 fix_modify      AtC  control localized_lambda on
 
-fix_modify	AtC  control tolerance 1.e-14
+fix_modify      AtC  control tolerance 1.e-14
 fix_modify      AtC  output bar1d_hooverFE 200 text binary
 #dump            D1 all atom 200 dump.bar1d_hoover
 reset_timestep  0
 fix_modify      AtC  reset_time
-thermo		100
+thermo          100
 run             5000
diff --git a/examples/PACKAGES/atc/thermal/in.bar1d_interpolate b/examples/PACKAGES/atc/thermal/in.bar1d_interpolate
index 0333bf117d..7e1d6295b4 100644
--- a/examples/PACKAGES/atc/thermal/in.bar1d_interpolate
+++ b/examples/PACKAGES/atc/thermal/in.bar1d_interpolate
@@ -4,65 +4,65 @@
 # 40.# The result should show heat diffusing through the FEM to the MD and back
 # out # to the FEM on the right.  Insufficient time is captured to reach the
 # linear # steady state, but heat crossing both boundaries should be observed.
-units		real
-atom_style	atomic
+units           real
+atom_style      atomic
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
 # NOTE following 3 lines added for restart
 boundary        f p p
 pair_style      lj/cut 13.5
 read_data       temp.init
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		simRegion block -12 12 -3 3 -3 3
+region          simRegion block -12 12 -3 3 -3 3
 # create atoms, NOTE commented out for restart
-#region		mdRegion block -5 5 -3 3 -3 3
-#boundary	f p p
-#create_box	1 mdRegion
-#create_atoms	1 region mdRegion
-#mass		1 39.95
+#region         mdRegion block -5 5 -3 3 -3 3
+#boundary       f p p
+#create_box     1 mdRegion
+#create_atoms   1 region mdRegion
+#mass           1 39.95
 # specify interal/ghost atoms
-region		mdInternal block -4 4 -3 3 -3 3
-group		internal region mdInternal
-group		ghost subtract all internal
+region          mdInternal block -4 4 -3 3 -3 3
+group           internal region mdInternal
+group           ghost subtract all internal
 # velocities have Vcm = 0, NOTE next three lines commented out for restart
-#velocity	internal create 40. 87287 mom yes loop geom
-#pair_style	lj/cut 13.5
-#pair_coeff  	1 1 .238 3.405 13.5
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
+#velocity       internal create 40. 87287 mom yes loop geom
+#pair_style     lj/cut 13.5
+#pair_coeff     1 1 .238 3.405 13.5
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
 #               ID  group atc PhysicsType ParameterFile
 fix             AtC internal   atc thermal     Ar_thermal.mat
 fix_modify      AtC boundary ghost
 # numerical parameters
-fix_modify	AtC time_integration fractional_step
+fix_modify      AtC time_integration fractional_step
 #               ID  part keywords    nx ny nz region
 fix_modify      AtC mesh create 12 1  1  simRegion f p p
 fix_modify      AtC mesh create_faceset ibndy box -4.0 4.0 -INF INF -INF INF in
 fix_modify      AtC mesh create_faceset obndy box -4.0 4.0 -INF INF -INF INF outward
 # fix a temperature
-fix_modify     	AtC  fix temperature all 20.
-#fix_modify	AtC  fix temperature all linear 0 0 0 -0.154 0 0 30.
-#fix_modify	AtC  fix temperature all quadratic 0 0 0 -0.154 0 0 30. 0.01 0.0 0.0 0 0 0 
+fix_modify      AtC  fix temperature all 20.
+#fix_modify     AtC  fix temperature all linear 0 0 0 -0.154 0 0 30.
+#fix_modify     AtC  fix temperature all quadratic 0 0 0 -0.154 0 0 30. 0.01 0.0 0.0 0 0 0 
 # turn on thermostat
-fix_modify	AtC  control thermal rescale 10
+fix_modify      AtC  control thermal rescale 10
 # equilibrate MD field
 #fix_modify      AtC  output bar1dfe_flux_init 100
-timestep	5
+timestep        5
 variable xdof equal 3*count(ghost)
-compute_modify thermo_temp extra ${xdof}
+compute_modify thermo_temp extra/dof ${xdof}
 thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
 thermo_modify  format 1 %6i format 2 %7.2g
-thermo		100
-run 		400
+thermo          100
+run             400
 # change thermostat to hoover
-fix_modify	AtC  unfix temperature all
-fix_modify	AtC  control thermal none
-fix_modify	AtC  control thermal flux interpolate
-fix_modify	AtC  control localized_lambda on
-#fix_modify	AtC  thermal control flux faceset obndy
+fix_modify      AtC  unfix temperature all
+fix_modify      AtC  control thermal none
+fix_modify      AtC  control thermal flux interpolate
+fix_modify      AtC  control localized_lambda on
+#fix_modify     AtC  thermal control flux faceset obndy
 fix_modify      AtC  filter type exponential
-fix_modify	AtC  filter scale 10000.0
-fix_modify	AtC  filter on
+fix_modify      AtC  filter scale 10000.0
+fix_modify      AtC  filter on
 # add nodesets
 #               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
 fix_modify      AtC mesh create_nodeset lbc -12.1  -11.9   -INF INF   -INF INF
@@ -70,11 +70,11 @@ fix_modify      AtC mesh create_nodeset rbc  11.9   12.1   -INF INF   -INF INF
 fix_modify      AtC  fix temperature lbc 40.
 fix_modify      AtC  fix temperature rbc 20.
 # initialize filter
-run		100
+run             100
 # set up output, should be before a "run"
 fix_modify      AtC  output bar1d_interpolateFE 100 text
 # run with FE
 reset_timestep 0
-thermo		100
-#run 		10
-run 		10000
+thermo          100
+#run            10
+run             10000
diff --git a/examples/PACKAGES/atc/thermal/in.bar1d_lumped b/examples/PACKAGES/atc/thermal/in.bar1d_lumped
index 153f7b632d..5321c45eb4 100644
--- a/examples/PACKAGES/atc/thermal/in.bar1d_lumped
+++ b/examples/PACKAGES/atc/thermal/in.bar1d_lumped
@@ -5,32 +5,32 @@
 # out # to the FEM on the right.  Insufficient time is captured to reach the
 # linear # steady state, but heat crossing both boundaries should be observed.
 echo both
-units		real
-atom_style	atomic
+units           real
+atom_style      atomic
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
 # NOTE following 3 lines added for restart
 boundary        f p p
 pair_style      lj/cut 13.5
 read_data       temp.init
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		simRegion block -12 12 -3 3 -3 3
+region          simRegion block -12 12 -3 3 -3 3
 # create atoms, NOTE commented out for restart
-#region		mdRegion block -5 5 -3 3 -3 3
-#boundary	f p p
-#create_box	1 mdRegion
-#create_atoms	1 region mdRegion
-#mass		1 39.95
+#region         mdRegion block -5 5 -3 3 -3 3
+#boundary       f p p
+#create_box     1 mdRegion
+#create_atoms   1 region mdRegion
+#mass           1 39.95
 # specify interal/ghost atoms
-region		mdInternal block -4 4 -3 3 -3 3
-group		internal region mdInternal
-group		ghost subtract all internal
+region          mdInternal block -4 4 -3 3 -3 3
+group           internal region mdInternal
+group           ghost subtract all internal
 # velocities have Vcm = 0, NOTE next three lines commented out for restart
-#velocity	internal create 40. 87287 mom yes loop geom
-#pair_style	lj/cut 13.5
-#pair_coeff  	1 1 .238 3.405 13.5
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
+#velocity       internal create 40. 87287 mom yes loop geom
+#pair_style     lj/cut 13.5
+#pair_coeff     1 1 .238 3.405 13.5
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
 #               ID  group atc PhysicsType ParameterFile
 fix             AtC internal   atc thermal     Ar_thermal.mat
 fix_modify      AtC boundary ghost
@@ -42,30 +42,30 @@ fix_modify      AtC mesh create 12 1  1  simRegion f p p
 fix_modify      AtC mesh create_faceset ibndy box -4.0 4.0 -INF INF -INF INF in
 fix_modify      AtC mesh create_faceset obndy box -4.0 4.0 -INF INF -INF INF outward
 # fix a temperature
-fix_modify     	AtC  fix temperature all 20.
-#fix_modify	AtC  fix temperature all linear 0 0 0 -0.154 0 0 30.
-#fix_modify	AtC  fix temperature all quadratic 0 0 0 -0.154 0 0 30. 0.01 0.0 0.0 0 0 0 
+fix_modify      AtC  fix temperature all 20.
+#fix_modify     AtC  fix temperature all linear 0 0 0 -0.154 0 0 30.
+#fix_modify     AtC  fix temperature all quadratic 0 0 0 -0.154 0 0 30. 0.01 0.0 0.0 0 0 0 
 # turn on thermostat
-fix_modify	AtC  control thermal rescale 10
+fix_modify      AtC  control thermal rescale 10
 # output
-thermo		100
+thermo          100
 variable xdof equal 3*count(ghost)
-compute_modify thermo_temp extra ${xdof}
+compute_modify thermo_temp extra/dof ${xdof}
 thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
 thermo_modify  format 1 %6i format 2 %7.2g
 # equilibrate MD field
 #fix_modify      AtC  output bar1d_lumped_initFE 1 text
-timestep	5
-run 		400
-#run 		100
+timestep        5
+run             400
+#run            100
 # change thermostat to hoover
-fix_modify	AtC  unfix temperature all
-#fix_modify	AtC  thermal control flux interpolate
-fix_modify	AtC  control thermal flux faceset obndy
-fix_modify	AtC  control localized_lambda on
+fix_modify      AtC  unfix temperature all
+#fix_modify     AtC  thermal control flux interpolate
+fix_modify      AtC  control thermal flux faceset obndy
+fix_modify      AtC  control localized_lambda on
 fix_modify      AtC  filter type exponential
-fix_modify	AtC  filter scale 10000.0
-fix_modify	AtC  filter on
+fix_modify      AtC  filter scale 10000.0
+fix_modify      AtC  filter on
 # add nodesets
 #               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
 fix_modify      AtC mesh create_nodeset lbc -12.1  -11.9   -INF INF   -INF INF
@@ -73,13 +73,13 @@ fix_modify      AtC mesh create_nodeset rbc  11.9   12.1   -INF INF   -INF INF
 fix_modify      AtC  fix temperature lbc 80.
 fix_modify      AtC  fix temperature rbc 80.
 # initialize
-thermo		10
-run		100
+thermo          10
+run             100
 # relax
 fix_modify      AtC  unfix temperature all
 # output
 fix_modify      AtC  output bar1d_lumpedFE 100 text
 # run with FE
 reset_timestep 0
-thermo		100
-run 		10000
+thermo          100
+run             10000
diff --git a/examples/PACKAGES/atc/two_temperature/in.uniform_heating b/examples/PACKAGES/atc/two_temperature/in.uniform_heating
index 0565fe8449..81a649e847 100644
--- a/examples/PACKAGES/atc/two_temperature/in.uniform_heating
+++ b/examples/PACKAGES/atc/two_temperature/in.uniform_heating
@@ -1,41 +1,41 @@
 # needs description
 #AtC Thermal Coupling
 echo both
-units		real
-atom_style	atomic
-boundary	f p p
+units           real
+atom_style      atomic
+boundary        f p p
 # create domain
-#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
-pair_style	lj/cut 13.5
-read_data	uniform_heating.init
+#lattice        type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
+pair_style      lj/cut 13.5
+read_data       uniform_heating.init
 lattice         fcc 5.405 origin 0.25 0.25 0.25
-region		mdRegion block   -8 8 -3 3 -3 3
-region		mdInternal block -6 6 -3 3 -3 3
-group		internal region mdInternal
-neighbor	5. bin
-neigh_modify	every 10 delay 0 check no
+region          mdRegion block   -8 8 -3 3 -3 3
+region          mdInternal block -6 6 -3 3 -3 3
+group           internal region mdInternal
+neighbor        5. bin
+neigh_modify    every 10 delay 0 check no
 #               ID  group atc PhysicsType ParameterFile
 fix             AtC internal   atc two_temperature Ar_ttm.mat
 #               ID  part keywords    nx ny nz region
 fix_modify      AtC mesh create 6 1  1  mdInternal f p p
 fix_modify AtC  internal_quadrature on
 # fix a temperature
-fix_modify     	AtC  initial temperature all 20.
-fix_modify     	AtC  fix     temperature all 20.
-fix_modify     	AtC  initial electron_temperature all 20.
-fix_modify     	AtC  fix     electron_temperature all 20.
+fix_modify      AtC  initial temperature all 20.
+fix_modify      AtC  fix     temperature all 20.
+fix_modify      AtC  initial electron_temperature all 20.
+fix_modify      AtC  fix     electron_temperature all 20.
 # turn on thermostat
-fix_modify	AtC  control thermal rescale 10
+fix_modify      AtC  control thermal rescale 10
 # output
 thermo_style custom step cpu pe etotal temp f_AtC[1] f_AtC[2]
-thermo		100
+thermo          100
 log uniform_heating.log
 # make thermo output the correct temperature by removing ghost dof
 # variable xdof equal 3*count(ghost)
-# compute_modify thermo_temp extra ${xdof}
+# compute_modify thermo_temp extra/dof ${xdof}
 # equilibrate MD field
-timestep	5
-run 		400
+timestep        5
+run             400
 # change thermostat
 fix_modify  AtC  output uniform_heatingFE 100 text
 fix_modify  AtC  unfix temperature all
@@ -50,4 +50,4 @@ fix_modify AtC  fix temperature rbc 20.
 fix_modify AtC  source temperature  all 6.3363e-10
 # run with FE
 reset_timestep 0
-run 		1000
+run             1000
diff --git a/examples/PACKAGES/charge_regulation/in.chreg-acid b/examples/PACKAGES/charge_regulation/in.chreg-acid
index 68ef5e1b7c..30ae13c6da 100644
--- a/examples/PACKAGES/charge_regulation/in.chreg-acid
+++ b/examples/PACKAGES/charge_regulation/in.chreg-acid
@@ -25,7 +25,7 @@ pair_modify     shift yes
 #########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
 fix             fnve all nve
 compute         dtemp all temp
-compute_modify  dtemp dynamic yes
+compute_modify  dtemp dynamic/dof yes
 fix             fT all langevin 1.0 1.0 1.0 123
 fix_modify      fT temp dtemp
 
diff --git a/examples/PACKAGES/charge_regulation/in.chreg-acid-real b/examples/PACKAGES/charge_regulation/in.chreg-acid-real
index d7225f33ea..361027c596 100644
--- a/examples/PACKAGES/charge_regulation/in.chreg-acid-real
+++ b/examples/PACKAGES/charge_regulation/in.chreg-acid-real
@@ -6,12 +6,12 @@ neighbor        10.0 bin
 read_data       data.chreg-acid-real
 
 #real units
-variable 	sigma equal 7.2	              # particle diameter 0.72 nm	    	
-variable	temperature equal 298         # temperature 298 K
+variable        sigma equal 7.2               # particle diameter 0.72 nm
+variable        temperature equal 298         # temperature 298 K
 variable        kb index 0.0019872067         # kB in Kcal/mol/K
-variable 	epsilon equal ${kb}*${temperature}
-variable	tunit   equal 	2000          # time unit is 2000 fs    
-variable	timestep equal 0.005*${tunit}
+variable        epsilon equal ${kb}*${temperature}
+variable        tunit   equal   2000          # time unit is 2000 fs
+variable        timestep equal 0.005*${tunit}
 
 variable        cut_long equal 12.5*${sigma}
 variable        nevery equal 100
@@ -27,13 +27,13 @@ velocity        all create ${temperature} 8008 loop geom
 pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
 pair_coeff      * *  ${epsilon} ${sigma}
 kspace_style    pppm 1.0e-3
-dielectric	78
+dielectric      78
 pair_modify     shift yes
 
 #########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
 fix             fnve all nve
 compute         dtemp all temp
-compute_modify  dtemp dynamic yes
+compute_modify  dtemp dynamic/dof yes
 fix             fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
 fix_modify      fT temp dtemp
 
diff --git a/examples/PACKAGES/charge_regulation/in.chreg-polymer b/examples/PACKAGES/charge_regulation/in.chreg-polymer
index 055032c018..068fe35c90 100644
--- a/examples/PACKAGES/charge_regulation/in.chreg-polymer
+++ b/examples/PACKAGES/charge_regulation/in.chreg-polymer
@@ -17,7 +17,7 @@ dielectric      1.0
 #########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
 fix             fnve all nve
 compute         dtemp all temp
-compute_modify  dtemp dynamic yes
+compute_modify  dtemp dynamic/dof yes
 fix             fT all langevin 1.0 1.0 1.0 123
 fix_modify      fT temp dtemp
 
diff --git a/examples/mc/in.gcmc.lj b/examples/mc/in.gcmc.lj
index a1c7c6eb10..5f007fbf40 100644
--- a/examples/mc/in.gcmc.lj
+++ b/examples/mc/in.gcmc.lj
@@ -3,35 +3,35 @@
 # rho ~ 0.5
 # p ~ 1.5
 # mu_ex ~ 0.0
-# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8 
+# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8
 
 # variables modifiable using -var command line switch
 
 variable        mu index -1.25
 variable        temp index 2.0
-variable	disp index 1.0
+variable        disp index 1.0
 variable        lbox index 5.0
 
 # global model settings
 
 units           lj
 atom_style      atomic
-pair_style      lj/cut 3.0 
-pair_modify	tail no # turn of to avoid triggering full_energy
+pair_style      lj/cut 3.0
+pair_modify     tail no # turn of to avoid triggering full_energy
 
 # box
 
-region		box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
-create_box	1 box
+region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
+create_box      1 box
 
 # lj parameters
 
-pair_coeff	* * 1.0 1.0
-mass		* 1.0
+pair_coeff      * * 1.0 1.0
+mass            * 1.0
 
 # we recommend setting up a dedicated group for gcmc
 
-group		gcmcgroup type 1
+group           gcmcgroup type 1
 
 # gcmc
 
@@ -39,29 +39,29 @@ fix             mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
 
 # atom count
 
-variable 	type1 atom "type==1"
-group 		type1 dynamic gcmcgroup var type1
+variable        type1 atom "type==1"
+group           type1 dynamic gcmcgroup var type1
 variable        n1 equal count(type1)
 
 # averaging
 
-variable	rho equal density
-variable	p equal press
-variable	nugget equal 1.0e-8
+variable        rho equal density
+variable        p equal press
+variable        nugget equal 1.0e-8
 variable        lambda equal 1.0
-variable     	muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
-fix 		ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
-variable	rhoav equal f_ave[1]
-variable	pav equal f_ave[2]
-variable	muexav equal f_ave[3]
-variable	n1av equal f_ave[4]
+variable        muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
+fix             ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
+variable        rhoav equal f_ave[1]
+variable        pav equal f_ave[2]
+variable        muexav equal f_ave[3]
+variable        n1av equal f_ave[4]
 
 # output
 
-variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
-variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
-variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
-compute_modify  thermo_temp dynamic yes
+variable        tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
+variable        iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
+variable        dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
+compute_modify  thermo_temp dynamic/dof yes
 thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
 thermo          1000
 

From 900c6cf545fe74bacb3adfa0721fa87c9ec5b2db Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 1 Jul 2023 18:27:35 -0400
Subject: [PATCH 331/396] remove unused variable

---
 src/REACTION/fix_bond_react.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp
index 83442ecb25..cf99efd099 100644
--- a/src/REACTION/fix_bond_react.cpp
+++ b/src/REACTION/fix_bond_react.cpp
@@ -2223,7 +2223,7 @@ note: currently uses global rxnID and onemol variables
 
 double FixBondReact::get_totalcharge()
 {
-  int j,jj,ilocal;
+  int j,jj;
   double *q = atom->q;
   double sim_total_charge = 0.0;
   for (j = 0; j < onemol->natoms; j++) {

From 5878040f26b273c7ff9f56fe6c70c6d194b5d80c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 1 Jul 2023 18:44:57 -0400
Subject: [PATCH 332/396] skip undesired 'make install' targets from bundled
 Kokkos library

---
 cmake/Modules/Packages/KOKKOS.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake
index 8b695667ae..795b087bcb 100644
--- a/cmake/Modules/Packages/KOKKOS.cmake
+++ b/cmake/Modules/Packages/KOKKOS.cmake
@@ -88,7 +88,7 @@ else()
   if(CMAKE_REQUEST_PIC)
     set(CMAKE_POSITION_INDEPENDENT_CODE ON)
   endif()
-  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR} EXCLUDE_FROM_ALL)
 
   set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src

From b7bfc86eaf6cdd354553cd76b670b4ae0d7fdece Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 2 Jul 2023 07:07:12 -0400
Subject: [PATCH 333/396] remove unused files still available and used in
 download-build-jpeg-png branch

---
 cmake/CMakeLists.jpeg | 615 -----------------------------------
 cmake/CMakeLists.png  | 741 ------------------------------------------
 cmake/CMakeLists.zlib | 195 -----------
 3 files changed, 1551 deletions(-)
 delete mode 100644 cmake/CMakeLists.jpeg
 delete mode 100644 cmake/CMakeLists.png
 delete mode 100644 cmake/CMakeLists.zlib

diff --git a/cmake/CMakeLists.jpeg b/cmake/CMakeLists.jpeg
deleted file mode 100644
index f0bd85a90d..0000000000
--- a/cmake/CMakeLists.jpeg
+++ /dev/null
@@ -1,615 +0,0 @@
-cmake_minimum_required(VERSION 3.10)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-if(CMAKE_EXECUTABLE_SUFFIX)
-  set(CMAKE_EXECUTABLE_SUFFIX_TMP ${CMAKE_EXECUTABLE_SUFFIX})
-endif()
-
-project(libjpeg-turbo C)
-set(VERSION 2.1.3)
-set(COPYRIGHT_YEAR "1991-2022")
-string(REPLACE "." ";" VERSION_TRIPLET ${VERSION})
-list(GET VERSION_TRIPLET 0 VERSION_MAJOR)
-list(GET VERSION_TRIPLET 1 VERSION_MINOR)
-list(GET VERSION_TRIPLET 2 VERSION_REVISION)
-function(pad_number NUMBER OUTPUT_LEN)
-  string(LENGTH "${${NUMBER}}" INPUT_LEN)
-  if(INPUT_LEN LESS OUTPUT_LEN)
-    math(EXPR ZEROES "${OUTPUT_LEN} - ${INPUT_LEN} - 1")
-    set(NUM ${${NUMBER}})
-    foreach(C RANGE ${ZEROES})
-      set(NUM "0${NUM}")
-    endforeach()
-    set(${NUMBER} ${NUM} PARENT_SCOPE)
-  endif()
-endfunction()
-pad_number(VERSION_MINOR 3)
-pad_number(VERSION_REVISION 3)
-set(LIBJPEG_TURBO_VERSION_NUMBER ${VERSION_MAJOR}${VERSION_MINOR}${VERSION_REVISION})
-
-# CMake 3.14 and later sets CMAKE_MACOSX_BUNDLE to TRUE by default when
-# CMAKE_SYSTEM_NAME is iOS, tvOS, or watchOS, which breaks the libjpeg-turbo
-# build.  (Specifically, when CMAKE_MACOSX_BUNDLE is TRUE, executables for
-# Apple platforms are built as application bundles, which causes CMake to
-# complain that our install() directives for executables do not specify a
-# BUNDLE DESTINATION.  Even if CMake did not complain, building executables as
-# application bundles would break our iOS packages.)
-set(CMAKE_MACOSX_BUNDLE FALSE)
-
-string(TIMESTAMP DEFAULT_BUILD "%Y%m%d")
-set(BUILD ${DEFAULT_BUILD} CACHE STRING "Build string (default: ${DEFAULT_BUILD})")
-
-# NOTE: On Windows, this does nothing except when using MinGW or Cygwin.
-# CMAKE_BUILD_TYPE has no meaning in Visual Studio, and it always defaults to
-# Debug when using NMake.
-if(NOT CMAKE_BUILD_TYPE)
-  set(CMAKE_BUILD_TYPE Release)
-endif()
-message(STATUS "CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
-
-message(STATUS "VERSION = ${VERSION}, BUILD = ${BUILD}")
-
-include(cmakescripts/PackageInfo.cmake)
-
-# Detect CPU type and whether we're building 64-bit or 32-bit code
-math(EXPR BITS "${CMAKE_SIZEOF_VOID_P} * 8")
-string(TOLOWER ${CMAKE_SYSTEM_PROCESSOR} CMAKE_SYSTEM_PROCESSOR_LC)
-set(COUNT 1)
-foreach(ARCH ${CMAKE_OSX_ARCHITECTURES})
-  if(COUNT GREATER 1)
-    message(FATAL_ERROR "The libjpeg-turbo build system does not support multiple values in CMAKE_OSX_ARCHITECTURES.")
-  endif()
-  math(EXPR COUNT "${COUNT}+1")
-endforeach()
-if(CMAKE_SYSTEM_PROCESSOR_LC MATCHES "x86_64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "amd64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "i[0-9]86" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "x86" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "ia32")
-  if(BITS EQUAL 64 OR CMAKE_C_COMPILER_ABI MATCHES "ELF X32")
-    set(CPU_TYPE x86_64)
-  else()
-    set(CPU_TYPE i386)
-  endif()
-  if(NOT CMAKE_SYSTEM_PROCESSOR STREQUAL ${CPU_TYPE})
-    set(CMAKE_SYSTEM_PROCESSOR ${CPU_TYPE})
-  endif()
-elseif(CMAKE_SYSTEM_PROCESSOR_LC STREQUAL "aarch64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^arm")
-  if(BITS EQUAL 64)
-    set(CPU_TYPE arm64)
-  else()
-    set(CPU_TYPE arm)
-  endif()
-elseif(CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^ppc" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^powerpc")
-  set(CPU_TYPE powerpc)
-else()
-  set(CPU_TYPE ${CMAKE_SYSTEM_PROCESSOR_LC})
-endif()
-if(CMAKE_OSX_ARCHITECTURES MATCHES "x86_64" OR
-  CMAKE_OSX_ARCHITECTURES MATCHES "arm64" OR
-  CMAKE_OSX_ARCHITECTURES MATCHES "i386")
-  set(CPU_TYPE ${CMAKE_OSX_ARCHITECTURES})
-endif()
-if(CMAKE_OSX_ARCHITECTURES MATCHES "ppc")
-  set(CPU_TYPE powerpc)
-endif()
-if(MSVC_IDE AND CMAKE_GENERATOR_PLATFORM MATCHES "arm64")
-  set(CPU_TYPE arm64)
-endif()
-
-message(STATUS "${BITS}-bit build (${CPU_TYPE})")
-
-macro(report_directory var)
-  if(CMAKE_INSTALL_${var} STREQUAL CMAKE_INSTALL_FULL_${var})
-    message(STATUS "CMAKE_INSTALL_${var} = ${CMAKE_INSTALL_${var}}")
-  else()
-    message(STATUS "CMAKE_INSTALL_${var} = ${CMAKE_INSTALL_${var}} (${CMAKE_INSTALL_FULL_${var}})")
-  endif()
-  mark_as_advanced(CLEAR CMAKE_INSTALL_${var})
-endmacro()
-
-set(DIRLIST "BINDIR;DATAROOTDIR;DOCDIR;INCLUDEDIR;LIBDIR")
-if(UNIX)
-  list(APPEND DIRLIST "MANDIR")
-endif()
-foreach(dir ${DIRLIST})
-  report_directory(${dir})
-endforeach()
-
-
-###############################################################################
-# CONFIGURATION OPTIONS
-###############################################################################
-
-macro(boolean_number var)
-  if(${var})
-    set(${var} 1 ${ARGN})
-  else()
-    set(${var} 0 ${ARGN})
-  endif()
-endmacro()
-
-option(ENABLE_SHARED "Build shared libraries" FALSE)
-boolean_number(ENABLE_SHARED)
-option(ENABLE_STATIC "Build static libraries" TRUE)
-boolean_number(ENABLE_STATIC)
-option(REQUIRE_SIMD "Generate a fatal error if SIMD extensions are not available for this platform (default is to fall back to a non-SIMD build)" FALSE)
-boolean_number(REQUIRE_SIMD)
-option(WITH_12BIT "Encode/decode JPEG images with 12-bit samples (implies WITH_ARITH_DEC=0 WITH_ARITH_ENC=0 WITH_JAVA=0 WITH_SIMD=0 WITH_TURBOJPEG=0 )" FALSE)
-boolean_number(WITH_12BIT)
-option(WITH_ARITH_DEC "Include arithmetic decoding support when emulating the libjpeg v6b API/ABI" TRUE)
-boolean_number(WITH_ARITH_DEC)
-option(WITH_ARITH_ENC "Include arithmetic encoding support when emulating the libjpeg v6b API/ABI" TRUE)
-boolean_number(WITH_ARITH_ENC)
-if(CMAKE_C_COMPILER_ABI MATCHES "ELF X32")
-  set(WITH_JAVA 0)
-else()
-  option(WITH_JAVA "Build Java wrapper for the TurboJPEG API library (implies ENABLE_SHARED=1)" FALSE)
-  boolean_number(WITH_JAVA)
-endif()
-option(WITH_JPEG7 "Emulate libjpeg v7 API/ABI (this makes ${CMAKE_PROJECT_NAME} backward-incompatible with libjpeg v6b)" FALSE)
-boolean_number(WITH_JPEG7)
-option(WITH_JPEG8 "Emulate libjpeg v8 API/ABI (this makes ${CMAKE_PROJECT_NAME} backward-incompatible with libjpeg v6b)" FALSE)
-boolean_number(WITH_JPEG8)
-option(WITH_MEM_SRCDST "Include in-memory source/destination manager functions when emulating the libjpeg v6b or v7 API/ABI" TRUE)
-boolean_number(WITH_MEM_SRCDST)
-option(WITH_SIMD "Include SIMD extensions, if available for this platform" FALSE)
-boolean_number(WITH_SIMD)
-option(WITH_TURBOJPEG "Include the TurboJPEG API library and associated test programs" FALSE)
-boolean_number(WITH_TURBOJPEG)
-option(WITH_FUZZ "Build fuzz targets" FALSE)
-
-macro(report_option var desc)
-  if(${var})
-    message(STATUS "${desc} enabled (${var} = ${${var}})")
-  else()
-    message(STATUS "${desc} disabled (${var} = ${${var}})")
-  endif()
-endmacro()
-
-if(WITH_JAVA)
-  set(ENABLE_SHARED 1)
-endif()
-
-# Explicitly setting CMAKE_POSITION_INDEPENDENT_CODE=FALSE disables PIC for all
-# targets, which will cause the shared library builds to fail.  Thus, if shared
-# libraries are enabled and CMAKE_POSITION_INDEPENDENT_CODE is explicitly set
-# to FALSE, we need to unset it, thus restoring the default behavior
-# (automatically using PIC for shared library targets.)
-if(DEFINED CMAKE_POSITION_INDEPENDENT_CODE AND
-  NOT CMAKE_POSITION_INDEPENDENT_CODE AND ENABLE_SHARED)
-  unset(CMAKE_POSITION_INDEPENDENT_CODE CACHE)
-endif()
-
-report_option(ENABLE_SHARED "Shared libraries")
-report_option(ENABLE_STATIC "Static libraries")
-
-if(ENABLE_SHARED)
-  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
-endif()
-
-if(WITH_JPEG8 OR WITH_JPEG7)
-  set(WITH_ARITH_ENC 1)
-  set(WITH_ARITH_DEC 1)
-endif()
-if(WITH_JPEG8)
-  set(WITH_MEM_SRCDST 0)
-endif()
-
-if(WITH_12BIT)
-  set(WITH_ARITH_DEC 0)
-  set(WITH_ARITH_ENC 0)
-  set(WITH_JAVA 0)
-  set(WITH_SIMD 0)
-  set(WITH_TURBOJPEG 0)
-  set(BITS_IN_JSAMPLE 12)
-else()
-  set(BITS_IN_JSAMPLE 8)
-endif()
-report_option(WITH_12BIT "12-bit JPEG support")
-
-if(WITH_ARITH_DEC)
-  set(D_ARITH_CODING_SUPPORTED 1)
-endif()
-if(NOT WITH_12BIT)
-  report_option(WITH_ARITH_DEC "Arithmetic decoding support")
-endif()
-
-if(WITH_ARITH_ENC)
-  set(C_ARITH_CODING_SUPPORTED 1)
-endif()
-if(NOT WITH_12BIT)
-  report_option(WITH_ARITH_ENC "Arithmetic encoding support")
-endif()
-
-if(NOT WITH_12BIT)
-  report_option(WITH_TURBOJPEG "TurboJPEG API library")
-  report_option(WITH_JAVA "TurboJPEG Java wrapper")
-endif()
-
-if(WITH_MEM_SRCDST)
-  set(MEM_SRCDST_SUPPORTED 1)
-  set(MEM_SRCDST_FUNCTIONS "global:  jpeg_mem_dest;  jpeg_mem_src;")
-endif()
-if(NOT WITH_JPEG8)
-  report_option(WITH_MEM_SRCDST "In-memory source/destination managers")
-endif()
-
-set(SO_AGE 2)
-if(WITH_MEM_SRCDST)
-  set(SO_AGE 3)
-endif()
-
-if(WITH_JPEG8)
-  set(JPEG_LIB_VERSION 80)
-elseif(WITH_JPEG7)
-  set(JPEG_LIB_VERSION 70)
-else()
-  set(JPEG_LIB_VERSION 62)
-endif()
-
-math(EXPR JPEG_LIB_VERSION_DIV10 "${JPEG_LIB_VERSION} / 10")
-math(EXPR JPEG_LIB_VERSION_MOD10 "${JPEG_LIB_VERSION} % 10")
-if(JPEG_LIB_VERSION STREQUAL "62")
-  set(DEFAULT_SO_MAJOR_VERSION ${JPEG_LIB_VERSION})
-else()
-  set(DEFAULT_SO_MAJOR_VERSION ${JPEG_LIB_VERSION_DIV10})
-endif()
-if(JPEG_LIB_VERSION STREQUAL "80")
-  set(DEFAULT_SO_MINOR_VERSION 2)
-else()
-  set(DEFAULT_SO_MINOR_VERSION 0)
-endif()
-
-# This causes SO_MAJOR_VERSION/SO_MINOR_VERSION to reset to defaults if
-# WITH_JPEG7 or WITH_JPEG8 has changed.
-if((DEFINED WITH_JPEG7_INT AND NOT WITH_JPEG7 EQUAL WITH_JPEG7_INT) OR
-  (DEFINED WITH_JPEG8_INT AND NOT WITH_JPEG8 EQUAL WITH_JPEG8_INT))
-  set(FORCE_SO_VERSION "FORCE")
-endif()
-set(WITH_JPEG7_INT ${WITH_JPEG7} CACHE INTERNAL "")
-set(WITH_JPEG8_INT ${WITH_JPEG8} CACHE INTERNAL "")
-
-set(SO_MAJOR_VERSION ${DEFAULT_SO_MAJOR_VERSION} CACHE STRING
-  "Major version of the libjpeg API shared library (default: ${DEFAULT_SO_MAJOR_VERSION})"
-  ${FORCE_SO_VERSION})
-set(SO_MINOR_VERSION ${DEFAULT_SO_MINOR_VERSION} CACHE STRING
-  "Minor version of the libjpeg API shared library (default: ${DEFAULT_SO_MINOR_VERSION})"
-  ${FORCE_SO_VERSION})
-
-set(JPEG_LIB_VERSION_DECIMAL "${JPEG_LIB_VERSION_DIV10}.${JPEG_LIB_VERSION_MOD10}")
-message(STATUS "Emulating libjpeg API/ABI v${JPEG_LIB_VERSION_DECIMAL} (WITH_JPEG7 = ${WITH_JPEG7}, WITH_JPEG8 = ${WITH_JPEG8})")
-message(STATUS "libjpeg API shared library version = ${SO_MAJOR_VERSION}.${SO_AGE}.${SO_MINOR_VERSION}")
-
-# Because the TurboJPEG API library uses versioned symbols and changes the
-# names of functions whenever they are modified in a backward-incompatible
-# manner, it is always backward-ABI-compatible with itself, so the major and
-# minor SO versions don't change.  However, we increase the middle number (the
-# SO "age") whenever functions are added to the API.
-set(TURBOJPEG_SO_MAJOR_VERSION 0)
-set(TURBOJPEG_SO_AGE 2)
-set(TURBOJPEG_SO_VERSION 0.${TURBOJPEG_SO_AGE}.0)
-
-
-###############################################################################
-# COMPILER SETTINGS
-###############################################################################
-
-if(MSVC)
-  option(WITH_CRT_DLL
-    "Link all ${CMAKE_PROJECT_NAME} libraries and executables with the C run-time DLL (msvcr*.dll) instead of the static C run-time library (libcmt*.lib.)  The default is to use the C run-time DLL only with the libraries and executables that need it."
-    FALSE)
-  if(NOT WITH_CRT_DLL)
-    # Use the static C library for all build types
-    foreach(var CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
-      CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
-      if(${var} MATCHES "/MD")
-        string(REGEX REPLACE "/MD" "/MT" ${var} "${${var}}")
-      endif()
-    endforeach()
-  endif()
-  add_definitions(-D_CRT_NONSTDC_NO_WARNINGS)
-endif()
-
-if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_C_COMPILER_ID STREQUAL "Clang")
-  # Use the maximum optimization level for release builds
-  foreach(var CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO)
-    if(${var} MATCHES "-O2")
-      string(REGEX REPLACE "-O2" "-O3" ${var} "${${var}}")
-    endif()
-  endforeach()
-endif()
-
-if(CMAKE_SYSTEM_NAME STREQUAL "SunOS")
-  if(CMAKE_C_COMPILER_ID MATCHES "SunPro")
-    # Use the maximum optimization level for release builds
-    foreach(var CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO)
-      if(${var} MATCHES "-xO3")
-        string(REGEX REPLACE "-xO3" "-xO5" ${var} "${${var}}")
-      endif()
-      if(${var} MATCHES "-xO2")
-        string(REGEX REPLACE "-xO2" "-xO5" ${var} "${${var}}")
-      endif()
-    endforeach()
-  endif()
-endif()
-
-string(TOUPPER ${CMAKE_BUILD_TYPE} CMAKE_BUILD_TYPE_UC)
-
-set(EFFECTIVE_C_FLAGS "${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE_UC}}")
-message(STATUS "Compiler flags = ${EFFECTIVE_C_FLAGS}")
-
-set(EFFECTIVE_LD_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS_${CMAKE_BUILD_TYPE_UC}}")
-message(STATUS "Linker flags = ${EFFECTIVE_LD_FLAGS}")
-
-include(CheckCSourceCompiles)
-include(CheckIncludeFiles)
-include(CheckTypeSize)
-
-check_type_size("size_t" SIZE_T)
-check_type_size("unsigned long" UNSIGNED_LONG)
-
-if(SIZE_T EQUAL UNSIGNED_LONG)
-  check_c_source_compiles("int main(int argc, char **argv) { unsigned long a = argc;  return __builtin_ctzl(a); }"
-    HAVE_BUILTIN_CTZL)
-endif()
-if(MSVC)
-  check_include_files("intrin.h" HAVE_INTRIN_H)
-endif()
-
-if(UNIX)
-  if(CMAKE_CROSSCOMPILING)
-    set(RIGHT_SHIFT_IS_UNSIGNED 0)
-  else()
-    include(CheckCSourceRuns)
-    check_c_source_runs("
-      #include <stdio.h>
-      #include <stdlib.h>
-      int is_shifting_signed (long arg) {
-        long res = arg >> 4;
-        if (res == -0x7F7E80CL)
-          return 1; /* right shift is signed */
-        /* see if unsigned-shift hack will fix it. */
-        /* we can't just test exact value since it depends on width of long... */
-        res |= (~0L) << (32-4);
-        if (res == -0x7F7E80CL)
-          return 0; /* right shift is unsigned */
-        printf(\"Right shift isn't acting as I expect it to.\\\\n\");
-        printf(\"I fear the JPEG software will not work at all.\\\\n\\\\n\");
-        return 0; /* try it with unsigned anyway */
-      }
-      int main (void) {
-        exit(is_shifting_signed(-0x7F7E80B1L));
-      }" RIGHT_SHIFT_IS_UNSIGNED)
-  endif()
-endif()
-
-if(MSVC)
-  set(INLINE_OPTIONS "__inline;inline")
-else()
-  set(INLINE_OPTIONS "__inline__;inline")
-endif()
-option(FORCE_INLINE "Force function inlining" TRUE)
-boolean_number(FORCE_INLINE)
-if(FORCE_INLINE)
-  if(MSVC)
-    list(INSERT INLINE_OPTIONS 0 "__forceinline")
-  else()
-    list(INSERT INLINE_OPTIONS 0 "inline __attribute__((always_inline))")
-    list(INSERT INLINE_OPTIONS 0 "__inline__ __attribute__((always_inline))")
-  endif()
-endif()
-foreach(inline ${INLINE_OPTIONS})
-  check_c_source_compiles("${inline} static int foo(void) { return 0; } int main(void) { return foo(); }"
-    INLINE_WORKS)
-  if(INLINE_WORKS)
-    set(INLINE ${inline})
-    break()
-  endif()
-endforeach()
-if(NOT INLINE_WORKS)
-  message(FATAL_ERROR "Could not determine how to inline functions.")
-endif()
-message(STATUS "INLINE = ${INLINE} (FORCE_INLINE = ${FORCE_INLINE})")
-
-if(WITH_TURBOJPEG)
-  if(MSVC)
-    set(THREAD_LOCAL "__declspec(thread)")
-  else()
-    set(THREAD_LOCAL "__thread")
-  endif()
-  check_c_source_compiles("${THREAD_LOCAL} int i;  int main(void) { i = 0;  return i; }" HAVE_THREAD_LOCAL)
-  if(HAVE_THREAD_LOCAL)
-    message(STATUS "THREAD_LOCAL = ${THREAD_LOCAL}")
-  else()
-    message(WARNING "Thread-local storage is not available.  The TurboJPEG API library's global error handler will not be thread-safe.")
-    unset(THREAD_LOCAL)
-  endif()
-endif()
-
-if(UNIX AND NOT APPLE)
-  file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map "VERS_1 { global: *; };")
-  set(CMAKE_REQUIRED_FLAGS
-    "-Wl,--version-script,${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-  check_c_source_compiles("int main(void) { return 0; }" HAVE_VERSION_SCRIPT)
-  set(CMAKE_REQUIRED_FLAGS)
-  file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map)
-  if(HAVE_VERSION_SCRIPT)
-    message(STATUS "Linker supports GNU-style version scripts")
-    set(MAPFLAG "-Wl,--version-script,")
-    set(TJMAPFLAG "-Wl,--version-script,")
-  else()
-    message(STATUS "Linker does not support GNU-style version scripts")
-    if(CMAKE_SYSTEM_NAME STREQUAL "SunOS")
-      # The Solaris linker doesn't like our version script for the libjpeg API
-      # library, but the version script for the TurboJPEG API library should
-      # still work.
-      file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map
-        "VERS_1 { global: foo;  local: *; }; VERS_2 { global: foo2; } VERS_1;")
-      set(CMAKE_REQUIRED_FLAGS "-Wl,-M,${CMAKE_CURRENT_BINARY_DIR}/conftest.map -shared")
-      check_c_source_compiles("int foo() { return 0; } int foo2() { return 2; }"
-        HAVE_MAPFILE)
-      set(CMAKE_REQUIRED_FLAGS)
-      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map)
-      if(HAVE_MAPFILE)
-        message(STATUS "Linker supports mapfiles")
-        set(TJMAPFLAG "-Wl,-M,")
-      else()
-        message(STATUS "Linker does not support mapfiles")
-      endif()
-    endif()
-  endif()
-endif()
-
-# Generate files
-if(WIN32)
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/win/jconfig.h.in jconfig.h)
-else()
-  configure_file(jconfig.h.in jconfig.h)
-endif()
-configure_file(jconfigint.h.in jconfigint.h)
-configure_file(jversion.h.in jversion.h)
-if(UNIX)
-  configure_file(libjpeg.map.in libjpeg.map)
-endif()
-
-# Include directories and compiler definitions
-include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR})
-
-
-###############################################################################
-# TARGETS
-###############################################################################
-
-if(CMAKE_EXECUTABLE_SUFFIX_TMP)
-  set(CMAKE_EXECUTABLE_SUFFIX ${CMAKE_EXECUTABLE_SUFFIX_TMP})
-endif()
-message(STATUS "CMAKE_EXECUTABLE_SUFFIX = ${CMAKE_EXECUTABLE_SUFFIX}")
-
-set(JPEG_SOURCES jcapimin.c jcapistd.c jccoefct.c jccolor.c jcdctmgr.c jchuff.c
-  jcicc.c jcinit.c jcmainct.c jcmarker.c jcmaster.c jcomapi.c jcparam.c
-  jcphuff.c jcprepct.c jcsample.c jctrans.c jdapimin.c jdapistd.c jdatadst.c
-  jdatasrc.c jdcoefct.c jdcolor.c jddctmgr.c jdhuff.c jdicc.c jdinput.c
-  jdmainct.c jdmarker.c jdmaster.c jdmerge.c jdphuff.c jdpostct.c jdsample.c
-  jdtrans.c jerror.c jfdctflt.c jfdctfst.c jfdctint.c jidctflt.c jidctfst.c
-  jidctint.c jidctred.c jquant1.c jquant2.c jutils.c jmemmgr.c jmemnobs.c)
-
-if(WITH_ARITH_ENC OR WITH_ARITH_DEC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jaricom.c)
-endif()
-
-if(WITH_ARITH_ENC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jcarith.c)
-endif()
-
-if(WITH_ARITH_DEC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jdarith.c)
-endif()
-
-if(WITH_SIMD)
-  add_subdirectory(simd)
-  if(NEON_INTRINSICS)
-    add_definitions(-DNEON_INTRINSICS)
-  endif()
-elseif(NOT WITH_12BIT)
-  message(STATUS "SIMD extensions: None (WITH_SIMD = ${WITH_SIMD})")
-endif()
-if(WITH_SIMD)
-  message(STATUS "SIMD extensions: ${CPU_TYPE} (WITH_SIMD = ${WITH_SIMD})")
-  if(MSVC_IDE OR XCODE)
-    set_source_files_properties(${SIMD_OBJS} PROPERTIES GENERATED 1)
-  endif()
-else()
-  add_library(simd OBJECT jsimd_none.c)
-  if(NOT WIN32 AND (CMAKE_POSITION_INDEPENDENT_CODE OR ENABLE_SHARED))
-    set_target_properties(simd PROPERTIES POSITION_INDEPENDENT_CODE 1)
-  endif()
-endif()
-
-if(WITH_JAVA)
-  add_subdirectory(java)
-endif()
-
-if(ENABLE_SHARED)
-  add_subdirectory(sharedlib)
-endif()
-
-if(ENABLE_STATIC)
-  add_library(jpeg-static STATIC ${JPEG_SOURCES} $<TARGET_OBJECTS:simd>
-    ${SIMD_OBJS})
-  if(NOT MSVC)
-    set_target_properties(jpeg-static PROPERTIES OUTPUT_NAME jpeg)
-  endif()
-endif()
-
-if(WITH_TURBOJPEG)
-  if(ENABLE_SHARED)
-    set(TURBOJPEG_SOURCES ${JPEG_SOURCES} $<TARGET_OBJECTS:simd> ${SIMD_OBJS}
-      turbojpeg.c transupp.c jdatadst-tj.c jdatasrc-tj.c rdbmp.c rdppm.c
-      wrbmp.c wrppm.c)
-    set(TJMAPFILE ${CMAKE_CURRENT_SOURCE_DIR}/turbojpeg-mapfile)
-    if(WITH_JAVA)
-      set(TURBOJPEG_SOURCES ${TURBOJPEG_SOURCES} turbojpeg-jni.c)
-      include_directories(${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2})
-      set(TJMAPFILE ${CMAKE_CURRENT_SOURCE_DIR}/turbojpeg-mapfile.jni)
-    endif()
-    if(MSVC)
-      configure_file(${CMAKE_SOURCE_DIR}/win/turbojpeg.rc.in
-        ${CMAKE_BINARY_DIR}/win/turbojpeg.rc)
-      set(TURBOJPEG_SOURCES ${TURBOJPEG_SOURCES}
-        ${CMAKE_BINARY_DIR}/win/turbojpeg.rc)
-    endif()
-    add_library(turbojpeg SHARED ${TURBOJPEG_SOURCES})
-    set_property(TARGET turbojpeg PROPERTY COMPILE_FLAGS
-      "-DBMP_SUPPORTED -DPPM_SUPPORTED")
-    if(WIN32)
-      set_target_properties(turbojpeg PROPERTIES DEFINE_SYMBOL DLLDEFINE)
-    endif()
-    if(MINGW)
-      set_target_properties(turbojpeg PROPERTIES LINK_FLAGS -Wl,--kill-at)
-    endif()
-    if(APPLE AND (NOT CMAKE_OSX_DEPLOYMENT_TARGET OR
-                  CMAKE_OSX_DEPLOYMENT_TARGET VERSION_GREATER 10.4))
-      if(NOT CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG)
-        set(CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG "-Wl,-rpath,")
-      endif()
-      set_target_properties(turbojpeg PROPERTIES MACOSX_RPATH 1)
-    endif()
-    set_target_properties(turbojpeg PROPERTIES
-      SOVERSION ${TURBOJPEG_SO_MAJOR_VERSION} VERSION ${TURBOJPEG_SO_VERSION})
-    if(TJMAPFLAG)
-      set_target_properties(turbojpeg PROPERTIES
-        LINK_FLAGS "${TJMAPFLAG}${TJMAPFILE}")
-    endif()
-  endif()
-
-  if(ENABLE_STATIC)
-    add_library(turbojpeg-static STATIC ${JPEG_SOURCES} $<TARGET_OBJECTS:simd>
-      ${SIMD_OBJS} turbojpeg.c transupp.c jdatadst-tj.c jdatasrc-tj.c rdbmp.c
-      rdppm.c wrbmp.c wrppm.c)
-    set_property(TARGET turbojpeg-static PROPERTY COMPILE_FLAGS
-      "-DBMP_SUPPORTED -DPPM_SUPPORTED")
-    if(NOT MSVC)
-      set_target_properties(turbojpeg-static PROPERTIES OUTPUT_NAME turbojpeg)
-    endif()
-  endif()
-endif()
-
-if(WIN32)
-  set(USE_SETMODE "-DUSE_SETMODE")
-endif()
-if(WITH_12BIT)
-  set(COMPILE_FLAGS "-DGIF_SUPPORTED -DPPM_SUPPORTED ${USE_SETMODE}")
-else()
-  set(COMPILE_FLAGS "-DBMP_SUPPORTED -DGIF_SUPPORTED -DPPM_SUPPORTED -DTARGA_SUPPORTED ${USE_SETMODE}")
-  set(CJPEG_BMP_SOURCES rdbmp.c rdtarga.c)
-  set(DJPEG_BMP_SOURCES wrbmp.c wrtarga.c)
-endif()
\ No newline at end of file
diff --git a/cmake/CMakeLists.png b/cmake/CMakeLists.png
deleted file mode 100644
index 2521ab41be..0000000000
--- a/cmake/CMakeLists.png
+++ /dev/null
@@ -1,741 +0,0 @@
-# CMakeLists.txt
-
-# Copyright (C) 2018 Cosmin Truta
-# Copyright (C) 2007,2009-2018 Glenn Randers-Pehrson
-# Written by Christian Ehrlicher, 2007
-# Revised by Roger Lowman, 2009-2010
-# Revised by Clifford Yapp, 2011-2012,2017
-# Revised by Roger Leigh, 2016
-# Revised by Andreas Franek, 2016
-# Revised by Sam Serrels, 2017
-# Revised by Vadim Barkov, 2017
-# Revised by Vicky Pfau, 2018
-# Revised by Cameron Cawley, 2018
-# Revised by Cosmin Truta, 2018
-# Revised by Kyle Bentley, 2018
-
-# This code is released under the libpng license.
-# For conditions of distribution and use, see the disclaimer
-# and license in png.h
-
-cmake_minimum_required(VERSION 3.10)
-cmake_policy(VERSION 3.1)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
-
-project(libpng C ASM)
-enable_testing()
-
-set(PNGLIB_MAJOR 1)
-set(PNGLIB_MINOR 6)
-set(PNGLIB_RELEASE 37)
-set(PNGLIB_NAME libpng${PNGLIB_MAJOR}${PNGLIB_MINOR})
-set(PNGLIB_VERSION ${PNGLIB_MAJOR}.${PNGLIB_MINOR}.${PNGLIB_RELEASE})
-
-include(GNUInstallDirs)
-
-# needed packages
-
-# Allow users to specify location of Zlib.
-# Useful if zlib is being built alongside this as a sub-project.
-option(PNG_BUILD_ZLIB "Custom zlib Location, else find_package is used" ON)
-
-if(NOT PNG_BUILD_ZLIB)
-  find_package(ZLIB REQUIRED)
-  include_directories(${ZLIB_INCLUDE_DIR})
-endif()
-
-if(UNIX AND NOT APPLE AND NOT BEOS AND NOT HAIKU)
-  find_library(M_LIBRARY m)
-else()
-  # libm is not needed and/or not available
-  set(M_LIBRARY "")
-endif()
-
-# COMMAND LINE OPTIONS
-option(PNG_SHARED "Build shared lib" OFF)
-option(PNG_STATIC "Build static lib" ON)
-option(PNG_TESTS  "Build libpng tests" OFF)
-
-# Many more configuration options could be added here
-option(PNG_FRAMEWORK "Build OS X framework" OFF)
-option(PNG_DEBUG "Build with debug output" OFF)
-option(PNG_HARDWARE_OPTIMIZATIONS "Enable hardware optimizations" OFF)
-
-set(PNG_PREFIX "" CACHE STRING "Prefix to add to the API function names")
-set(DFA_XTRA "" CACHE FILEPATH "File containing extra configuration settings")
-
-if(PNG_HARDWARE_OPTIMIZATIONS)
-
-# set definitions and sources for arm
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm" OR
-  CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64")
-  set(PNG_ARM_NEON_POSSIBLE_VALUES check on off)
-  set(PNG_ARM_NEON "check" CACHE STRING "Enable ARM NEON optimizations:
-     check: (default) use internal checking code;
-     off: disable the optimizations;
-     on: turn on unconditionally.")
-  set_property(CACHE PNG_ARM_NEON PROPERTY STRINGS
-     ${PNG_ARM_NEON_POSSIBLE_VALUES})
-  list(FIND PNG_ARM_NEON_POSSIBLE_VALUES ${PNG_ARM_NEON} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_ARM_NEON must be one of [${PNG_ARM_NEON_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_ARM_NEON} STREQUAL "off")
-    set(libpng_arm_sources
-      arm/arm_init.c
-      arm/filter_neon.S
-      arm/filter_neon_intrinsics.c
-      arm/palette_neon_intrinsics.c)
-
-    if(${PNG_ARM_NEON} STREQUAL "on")
-      add_definitions(-DPNG_ARM_NEON_OPT=2)
-    elseif(${PNG_ARM_NEON} STREQUAL "check")
-      add_definitions(-DPNG_ARM_NEON_CHECK_SUPPORTED)
-    endif()
-  else()
-    add_definitions(-DPNG_ARM_NEON_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for powerpc
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^powerpc*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^ppc64*")
-  set(PNG_POWERPC_VSX_POSSIBLE_VALUES on off)
-  set(PNG_POWERPC_VSX "on" CACHE STRING "Enable POWERPC VSX optimizations:
-     off: disable the optimizations.")
-  set_property(CACHE PNG_POWERPC_VSX PROPERTY STRINGS
-     ${PNG_POWERPC_VSX_POSSIBLE_VALUES})
-  list(FIND PNG_POWERPC_VSX_POSSIBLE_VALUES ${PNG_POWERPC_VSX} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_POWERPC_VSX must be one of [${PNG_POWERPC_VSX_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_POWERPC_VSX} STREQUAL "off")
-    set(libpng_powerpc_sources
-      powerpc/powerpc_init.c
-      powerpc/filter_vsx_intrinsics.c)
-    if(${PNG_POWERPC_VSX} STREQUAL "on")
-      add_definitions(-DPNG_POWERPC_VSX_OPT=2)
-    endif()
-  else()
-    add_definitions(-DPNG_POWERPC_VSX_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for intel
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^i?86" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64*")
-  set(PNG_INTEL_SSE_POSSIBLE_VALUES on off)
-  set(PNG_INTEL_SSE "on" CACHE STRING "Enable INTEL_SSE optimizations:
-     off: disable the optimizations")
-  set_property(CACHE PNG_INTEL_SSE PROPERTY STRINGS
-     ${PNG_INTEL_SSE_POSSIBLE_VALUES})
-  list(FIND PNG_INTEL_SSE_POSSIBLE_VALUES ${PNG_INTEL_SSE} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_INTEL_SSE must be one of [${PNG_INTEL_SSE_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_INTEL_SSE} STREQUAL "off")
-    set(libpng_intel_sources
-      intel/intel_init.c
-      intel/filter_sse2_intrinsics.c)
-    if(${PNG_INTEL_SSE} STREQUAL "on")
-      add_definitions(-DPNG_INTEL_SSE_OPT=1)
-    endif()
-  else()
-    add_definitions(-DPNG_INTEL_SSE_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for MIPS
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "mipsel*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "mips64el*")
-  set(PNG_MIPS_MSA_POSSIBLE_VALUES on off)
-  set(PNG_MIPS_MSA "on" CACHE STRING "Enable MIPS_MSA optimizations:
-     off: disable the optimizations")
-  set_property(CACHE PNG_MIPS_MSA PROPERTY STRINGS
-     ${PNG_MIPS_MSA_POSSIBLE_VALUES})
-  list(FIND PNG_MIPS_MSA_POSSIBLE_VALUES ${PNG_MIPS_MSA} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_MIPS_MSA must be one of [${PNG_MIPS_MSA_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_MIPS_MSA} STREQUAL "off")
-    set(libpng_mips_sources
-      mips/mips_init.c
-      mips/filter_msa_intrinsics.c)
-    if(${PNG_MIPS_MSA} STREQUAL "on")
-      add_definitions(-DPNG_MIPS_MSA_OPT=2)
-    endif()
-  else()
-    add_definitions(-DPNG_MIPS_MSA_OPT=0)
-  endif()
-endif()
-
-else(PNG_HARDWARE_OPTIMIZATIONS)
-
-# set definitions and sources for arm
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64")
-  add_definitions(-DPNG_ARM_NEON_OPT=0)
-endif()
-
-# set definitions and sources for powerpc
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^powerpc*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^ppc64*")
-  add_definitions(-DPNG_POWERPC_VSX_OPT=0)
-endif()
-
-# set definitions and sources for intel
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^i?86" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64*")
-  add_definitions(-DPNG_INTEL_SSE_OPT=0)
-endif()
-
-# set definitions and sources for MIPS
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "mipsel*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "mips64el*")
-  add_definitions(-DPNG_MIPS_MSA_OPT=0)
-endif()
-
-endif(PNG_HARDWARE_OPTIMIZATIONS)
-
-# SET LIBNAME
-set(PNG_LIB_NAME png${PNGLIB_MAJOR}${PNGLIB_MINOR})
-
-# to distinguish between debug and release lib
-set(CMAKE_DEBUG_POSTFIX "d")
-
-include(CheckCSourceCompiles)
-option(ld-version-script "Enable linker version script" ON)
-if(ld-version-script AND NOT APPLE)
-  # Check if LD supports linker scripts.
-  file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/conftest.map" "VERS_1 {
-        global: sym;
-        local: *;
-};
-
-VERS_2 {
-        global: sym2;
-                main;
-} VERS_1;
-")
-  set(CMAKE_REQUIRED_FLAGS_SAVE ${CMAKE_REQUIRED_FLAGS})
-  set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS} "-Wl,--version-script='${CMAKE_CURRENT_BINARY_DIR}/conftest.map'")
-  check_c_source_compiles("void sym(void) {}
-void sym2(void) {}
-int main(void) {return 0;}
-" HAVE_LD_VERSION_SCRIPT)
-  if(NOT HAVE_LD_VERSION_SCRIPT)
-    set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE} "-Wl,-M -Wl,${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-  check_c_source_compiles("void sym(void) {}
-void sym2(void) {}
-int main(void) {return 0;}
-" HAVE_SOLARIS_LD_VERSION_SCRIPT)
-  endif()
-  set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE})
-  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-endif()
-
-# Find symbol prefix.  Likely obsolete and unnecessary with recent
-# toolchains (it's not done in many other projects).
-function(symbol_prefix)
-  set(SYMBOL_PREFIX)
-
-  execute_process(COMMAND "${CMAKE_C_COMPILER}" "-E" "-"
-                  INPUT_FILE /dev/null
-                  OUTPUT_VARIABLE OUT
-                  RESULT_VARIABLE STATUS)
-
-  if(CPP_FAIL)
-    message(WARNING "Failed to run the C preprocessor")
-  endif()
-
-  string(REPLACE "\n" ";" OUT "${OUT}")
-  foreach(line ${OUT})
-    string(REGEX MATCH "^PREFIX=" found_match "${line}")
-    if(found_match)
-      string(REGEX REPLACE "^PREFIX=(.*\)" "\\1" prefix "${line}")
-      string(REGEX MATCH "__USER_LABEL_PREFIX__" found_match "${prefix}")
-      if(found_match)
-        string(REGEX REPLACE "(.*)__USER_LABEL_PREFIX__(.*)" "\\1\\2" prefix "${prefix}")
-      endif()
-      set(SYMBOL_PREFIX "${prefix}")
-    endif()
-  endforeach()
-
-  message(STATUS "Symbol prefix: ${SYMBOL_PREFIX}")
-  set(SYMBOL_PREFIX "${SYMBOL_PREFIX}" PARENT_SCOPE)
-endfunction()
-
-if(UNIX)
-  symbol_prefix()
-endif()
-
-find_program(AWK NAMES gawk awk)
-
-include_directories(${CMAKE_CURRENT_BINARY_DIR})
-
-if(NOT AWK OR ANDROID)
-  # No awk available to generate sources; use pre-built pnglibconf.h
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.h.prebuilt
-                 ${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h)
-  add_custom_target(genfiles) # Dummy
-else()
-  include(CMakeParseArguments)
-  # Generate .chk from .out with awk
-  # generate_chk(INPUT inputfile OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_chk)
-    set(options)
-    set(oneValueArgs INPUT OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GC "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GC_INPUT)
-      message(FATAL_ERROR "generate_chk: Missing INPUT argument")
-    endif()
-    if(NOT _GC_OUTPUT)
-      message(FATAL_ERROR "generate_chk: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${_GC_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DINPUT=${_GC_INPUT}"
-                               "-DOUTPUT=${_GC_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/genchk.cmake"
-                       DEPENDS "${_GC_INPUT}" ${_GC_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Generate .out from .c with awk
-  # generate_out(INPUT inputfile OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_out)
-    set(options)
-    set(oneValueArgs INPUT OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GO "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GO_INPUT)
-      message(FATAL_ERROR "generate_out: Missing INPUT argument")
-    endif()
-    if(NOT _GO_OUTPUT)
-      message(FATAL_ERROR "generate_out: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${_GO_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DINPUT=${_GO_INPUT}"
-                               "-DOUTPUT=${_GO_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/genout.cmake"
-                       DEPENDS "${_GO_INPUT}" ${_GO_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Generate specific source file with awk
-  # generate_source(OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_source)
-    set(options)
-    set(oneValueArgs OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GSO "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GSO_OUTPUT)
-      message(FATAL_ERROR "generate_source: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/${_GSO_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DOUTPUT=${_GSO_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake"
-                       DEPENDS ${_GSO_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Copy file
-  function(generate_copy source destination)
-    add_custom_command(OUTPUT "${destination}"
-                       COMMAND "${CMAKE_COMMAND}" -E remove "${destination}"
-                       COMMAND "${CMAKE_COMMAND}" -E copy "${source}"
-                                                          "${destination}"
-                       DEPENDS "${source}")
-  endfunction()
-
-  # Generate scripts/pnglibconf.h
-  generate_source(OUTPUT "scripts/pnglibconf.c"
-                  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.dfa"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/scripts/options.awk"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h")
-
-  # Generate pnglibconf.c
-  generate_source(OUTPUT "pnglibconf.c"
-                  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.dfa"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/scripts/options.awk"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h")
-
-  if(PNG_PREFIX)
-    set(PNGLIBCONF_H_EXTRA_DEPENDS
-        "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-        "${CMAKE_CURRENT_SOURCE_DIR}/scripts/macro.lst")
-    set(PNGPREFIX_H_EXTRA_DEPENDS
-        "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out")
-  endif()
-
-  generate_out(INPUT "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out")
-
-  # Generate pnglibconf.h
-  generate_source(OUTPUT "pnglibconf.h"
-                  DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out"
-                          ${PNGLIBCONF_H_EXTRA_DEPENDS})
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/intprefix.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out"
-               DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/prefix.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out")
-
-  # Generate pngprefix.h
-  generate_source(OUTPUT "pngprefix.h"
-                  DEPENDS ${PNGPREFIX_H_EXTRA_DEPENDS})
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/sym.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-               DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/symbols.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.h.prebuilt")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/vers.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_chk(INPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/checksym.awk"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/scripts/symbols.def")
-
-  add_custom_target(symbol-check DEPENDS
-                    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk")
-
-  generate_copy("${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-                "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym")
-  generate_copy("${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out"
-                "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers")
-
-  add_custom_target(genvers DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers")
-  add_custom_target(gensym DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym")
-
-  add_custom_target("genprebuilt"
-                    COMMAND "${CMAKE_COMMAND}"
-                            "-DOUTPUT=scripts/pnglibconf.h.prebuilt"
-                            -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake"
-                    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-
-  # A single target handles generation of all generated files.  If
-  # they are depended upon separately by multiple targets, this
-  # confuses parallel make (it would require a separate top-level
-  # target for each file to track the dependencies properly).
-  add_custom_target(genfiles DEPENDS
-    "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym"
-    "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.c"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/pngprefix.h"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/pnglibconf.c"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out")
-endif(NOT AWK OR ANDROID)
-
-# OUR SOURCES
-set(libpng_public_hdrs
-  png.h
-  pngconf.h
-  "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h"
-)
-set(libpng_private_hdrs
-  pngpriv.h
-  pngdebug.h
-  pnginfo.h
-  pngstruct.h
-)
-if(AWK AND NOT ANDROID)
-  list(APPEND libpng_private_hdrs "${CMAKE_CURRENT_BINARY_DIR}/pngprefix.h")
-endif()
-set(libpng_sources
-  ${libpng_public_hdrs}
-  ${libpng_private_hdrs}
-  png.c
-  pngerror.c
-  pngget.c
-  pngmem.c
-  pngpread.c
-  pngread.c
-  pngrio.c
-  pngrtran.c
-  pngrutil.c
-  pngset.c
-  pngtrans.c
-  pngwio.c
-  pngwrite.c
-  pngwtran.c
-  pngwutil.c
-  ${libpng_arm_sources}
-  ${libpng_intel_sources}
-  ${libpng_mips_sources}
-  ${libpng_powerpc_sources}
-)
-set(pngtest_sources
-  pngtest.c
-)
-set(pngvalid_sources
-  contrib/libtests/pngvalid.c
-)
-set(pngstest_sources
-  contrib/libtests/pngstest.c
-)
-set(pngunknown_sources
-  contrib/libtests/pngunknown.c
-)
-set(pngimage_sources
-  contrib/libtests/pngimage.c
-)
-set(pngfix_sources
-  contrib/tools/pngfix.c
-)
-set(png_fix_itxt_sources
-  contrib/tools/png-fix-itxt.c
-)
-
-if(MSVC)
-  add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
-endif()
-
-if(PNG_DEBUG)
-  add_definitions(-DPNG_DEBUG)
-endif()
-
-# NOW BUILD OUR TARGET
-include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${ZLIB_INCLUDE_DIR})
-
-unset(PNG_LIB_TARGETS)
-
-if(PNG_STATIC)
-  # does not work without changing name
-  set(PNG_LIB_NAME_STATIC png_static)
-  add_library(png_static STATIC ${libpng_sources})
-  add_dependencies(png_static genfiles)
-  # MSVC doesn't use a different file extension for shared vs. static
-  # libs.  We are able to change OUTPUT_NAME to remove the _static
-  # for all other platforms.
-  if(NOT MSVC)
-    set_target_properties(png_static PROPERTIES
-      OUTPUT_NAME "${PNG_LIB_NAME}"
-      CLEAN_DIRECT_OUTPUT 1)
-  else()
-    set_target_properties(png_static PROPERTIES
-      OUTPUT_NAME "${PNG_LIB_NAME}_static"
-      CLEAN_DIRECT_OUTPUT 1)
-  endif()
-  list(APPEND PNG_LIB_TARGETS png_static)
-  if(MSVC)
-    # msvc does not append 'lib' - do it here to have consistent name
-    set_target_properties(png_static PROPERTIES PREFIX "lib")
-  endif()
-  target_link_libraries(png_static ${M_LIBRARY})
-endif()
-
-if(NOT PNG_LIB_TARGETS)
-  message(SEND_ERROR
-    "No library variant selected to build. "
-    "Please enable at least one of the following options: "
-    "PNG_STATIC, PNG_SHARED, PNG_FRAMEWORK")
-endif()
-
-# Set a variable with CMake code which:
-# Creates a symlink from src to dest (if possible) or alternatively
-# copies if different.
-include(CMakeParseArguments)
-
-function(create_symlink DEST_FILE)
-
-  cmake_parse_arguments(S "" "FILE;TARGET" "" ${ARGN})
-
-  if(NOT S_TARGET AND NOT S_FILE)
-    message(FATAL_ERROR "create_symlink: Missing TARGET or FILE argument")
-  endif()
-
-  if(S_TARGET AND S_FILE)
-    message(FATAL_ERROR "create_symlink: Both source file ${S_FILE} and build target ${S_TARGET} arguments are present; can only have one.")
-  endif()
-
-  if(S_FILE)
-    # If we don't need to symlink something that's coming from a build target,
-    # we can go ahead and symlink/copy at configure time.
-    if(CMAKE_HOST_WIN32 AND NOT CYGWIN)
-      execute_process(
-        COMMAND "${CMAKE_COMMAND}" -E copy_if_different ${S_FILE} ${DEST_FILE}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-    else()
-      execute_process(
-        COMMAND ${CMAKE_COMMAND} -E create_symlink ${S_FILE} ${DEST_FILE}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-    endif()
-  endif()
-
-  if(S_TARGET)
-    # We need to use generator expressions, which can be a bit tricky, so for
-    # simplicity make the symlink a POST_BUILD step and use the TARGET
-    # signature of add_custom_command.
-    if(CMAKE_HOST_WIN32 AND NOT CYGWIN)
-      add_custom_command(TARGET ${S_TARGET} POST_BUILD
-        COMMAND "${CMAKE_COMMAND}" -E copy_if_different $<TARGET_LINKER_FILE_NAME:${S_TARGET}> $<TARGET_LINKER_FILE_DIR:${S_TARGET}>/${DEST_FILE})
-    else()
-      add_custom_command(TARGET ${S_TARGET} POST_BUILD
-        COMMAND "${CMAKE_COMMAND}" -E create_symlink $<TARGET_LINKER_FILE_NAME:${S_TARGET}> $<TARGET_LINKER_FILE_DIR:${S_TARGET}>/${DEST_FILE})
-    endif()
-  endif()
-
-endfunction()
-
-# Create source generation scripts.
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/genchk.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/genchk.cmake @ONLY)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/genout.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/genout.cmake @ONLY)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/gensrc.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake @ONLY)
-
-# libpng is a library so default to 'lib'
-if(NOT DEFINED CMAKE_INSTALL_LIBDIR)
-  set(CMAKE_INSTALL_LIBDIR lib)
-endif()
-
-# CREATE PKGCONFIG FILES
-# We use the same files like ./configure, so we have to set its vars.
-# Only do this on Windows for Cygwin - the files don't make much sense outside
-# of a UNIX look-alike.
-if(NOT WIN32 OR CYGWIN OR MINGW)
-  set(prefix      ${CMAKE_INSTALL_PREFIX})
-  set(exec_prefix ${CMAKE_INSTALL_PREFIX})
-  set(libdir      ${CMAKE_INSTALL_FULL_LIBDIR})
-  set(includedir  ${CMAKE_INSTALL_FULL_INCLUDEDIR})
-  set(LIBS        "-lz -lm")
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng.pc.in
-    ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc @ONLY)
-  create_symlink(libpng.pc FILE ${PNGLIB_NAME}.pc)
-
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng-config.in
-    ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config @ONLY)
-  create_symlink(libpng-config FILE ${PNGLIB_NAME}-config)
-endif()
-
-# SET UP LINKS
-if(PNG_SHARED)
-  set_target_properties(png PROPERTIES
-#   VERSION 16.${PNGLIB_RELEASE}.1.6.37
-    VERSION 16.${PNGLIB_RELEASE}.0
-    SOVERSION 16
-    CLEAN_DIRECT_OUTPUT 1)
-endif()
-
-# INSTALL
-if(NOT SKIP_INSTALL_LIBRARIES AND NOT SKIP_INSTALL_ALL)
-  install(TARGETS ${PNG_LIB_TARGETS}
-          EXPORT libpng
-          RUNTIME DESTINATION bin
-          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-          FRAMEWORK DESTINATION ${CMAKE_INSTALL_LIBDIR})
-
-  if(PNG_SHARED)
-    # Create a symlink for libpng.dll.a => libpng16.dll.a on Cygwin
-    if(CYGWIN OR MINGW)
-      create_symlink(libpng${CMAKE_IMPORT_LIBRARY_SUFFIX} TARGET png)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png>/libpng${CMAKE_IMPORT_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-
-    if(NOT WIN32)
-      create_symlink(libpng${CMAKE_SHARED_LIBRARY_SUFFIX} TARGET png)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png>/libpng${CMAKE_SHARED_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-  endif()
-
-  if(PNG_STATIC)
-    if(NOT WIN32 OR CYGWIN OR MINGW)
-      create_symlink(libpng${CMAKE_STATIC_LIBRARY_SUFFIX} TARGET png_static)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png_static>/libpng${CMAKE_STATIC_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-  endif()
-endif()
-
-if(NOT SKIP_INSTALL_HEADERS AND NOT SKIP_INSTALL_ALL)
-  install(FILES ${libpng_public_hdrs} DESTINATION include)
-  install(FILES ${libpng_public_hdrs} DESTINATION include/${PNGLIB_NAME})
-endif()
-if(NOT SKIP_INSTALL_EXECUTABLES AND NOT SKIP_INSTALL_ALL)
-  if(NOT WIN32 OR CYGWIN OR MINGW)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config DESTINATION bin)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config DESTINATION bin)
-  endif()
-endif()
-
-if(NOT SKIP_INSTALL_PROGRAMS AND NOT SKIP_INSTALL_ALL)
-  install(TARGETS ${PNG_BIN_TARGETS}
-          RUNTIME DESTINATION bin)
-endif()
-
-if(NOT SKIP_INSTALL_FILES AND NOT SKIP_INSTALL_ALL)
-  # Install man pages
-  if(NOT PNG_MAN_DIR)
-    set(PNG_MAN_DIR "share/man")
-  endif()
-  install(FILES libpng.3 libpngpf.3 DESTINATION ${PNG_MAN_DIR}/man3)
-  install(FILES png.5 DESTINATION ${PNG_MAN_DIR}/man5)
-  # Install pkg-config files
-  if(NOT CMAKE_HOST_WIN32 OR CYGWIN OR MINGW)
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libpng.pc
-            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config
-            DESTINATION bin)
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc
-            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config
-            DESTINATION bin)
-  endif()
-endif()
-
-# Create an export file that CMake users can include() to import our targets.
-if(NOT SKIP_INSTALL_EXPORT AND NOT SKIP_INSTALL_ALL)
-  install(EXPORT libpng DESTINATION lib/libpng FILE lib${PNG_LIB_NAME}.cmake)
-endif()
-
-# what's with libpng-manual.txt and all the extra files?
-
-# UNINSTALL
-# do we need this?
-
-# DIST
-# do we need this?
-
-# to create msvc import lib for mingw compiled shared lib
-# pexports libpng.dll > libpng.def
-# lib /def:libpng.def /machine:x86
diff --git a/cmake/CMakeLists.zlib b/cmake/CMakeLists.zlib
deleted file mode 100644
index a33f14ce64..0000000000
--- a/cmake/CMakeLists.zlib
+++ /dev/null
@@ -1,195 +0,0 @@
-cmake_minimum_required(VERSION 3.10)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
-
-project(zlib C)
-
-set(VERSION "1.2.11")
-
-option(ASM686 "Enable building i686 assembly implementation" OFF)
-option(AMD64 "Enable building amd64 assembly implementation" OFF)
-
-set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables")
-set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries")
-set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers")
-set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages")
-set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files")
-
-include(CheckTypeSize)
-include(CheckFunctionExists)
-include(CheckIncludeFile)
-include(CheckCSourceCompiles)
-
-check_include_file(sys/types.h HAVE_SYS_TYPES_H)
-check_include_file(stdint.h    HAVE_STDINT_H)
-check_include_file(stddef.h    HAVE_STDDEF_H)
-
-#
-# Check to see if we have large file support
-#
-set(CMAKE_REQUIRED_DEFINITIONS -D_LARGEFILE64_SOURCE=1)
-# We add these other definitions here because CheckTypeSize.cmake
-# in CMake 2.4.x does not automatically do so and we want
-# compatibility with CMake 2.4.x.
-if(HAVE_SYS_TYPES_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_SYS_TYPES_H)
-endif()
-if(HAVE_STDINT_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDINT_H)
-endif()
-if(HAVE_STDDEF_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDDEF_H)
-endif()
-check_type_size(off64_t OFF64_T)
-check_type_size(off64_t OFF64_T)
-if(HAVE_OFF64_T)
-   add_definitions(-D_LARGEFILE64_SOURCE=1)
-endif()
-set(CMAKE_REQUIRED_DEFINITIONS) # clear variable
-
-#
-# Check for fseeko
-#
-check_function_exists(fseeko HAVE_FSEEKO)
-if(NOT HAVE_FSEEKO)
-    add_definitions(-DNO_FSEEKO)
-endif()
-
-#
-# Check for unistd.h
-#
-check_include_file(unistd.h Z_HAVE_UNISTD_H)
-
-if(MSVC)
-    set(CMAKE_DEBUG_POSTFIX "d")
-    add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
-    add_definitions(-D_CRT_NONSTDC_NO_DEPRECATE)
-    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-endif()
-
-if(NOT CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
-    # If we're doing an out of source build and the user has a zconf.h
-    # in their source tree...
-    if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h)
-        file(RENAME ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.included)
-  endif()
-endif()
-
-set(ZLIB_PC ${CMAKE_CURRENT_BINARY_DIR}/zlib.pc)
-configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/zlib.pc.cmakein
-		${ZLIB_PC} @ONLY)
-configure_file(	${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.cmakein
-		${CMAKE_CURRENT_BINARY_DIR}/zconf.h @ONLY)
-include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_SOURCE_DIR})
-
-
-#============================================================================
-# zlib
-#============================================================================
-
-set(ZLIB_PUBLIC_HDRS
-    ${CMAKE_CURRENT_BINARY_DIR}/zconf.h
-    zlib.h
-)
-set(ZLIB_PRIVATE_HDRS
-    crc32.h
-    deflate.h
-    gzguts.h
-    inffast.h
-    inffixed.h
-    inflate.h
-    inftrees.h
-    trees.h
-    zutil.h
-)
-set(ZLIB_SRCS
-    adler32.c
-    compress.c
-    crc32.c
-    deflate.c
-    gzclose.c
-    gzlib.c
-    gzread.c
-    gzwrite.c
-    inflate.c
-    infback.c
-    inftrees.c
-    inffast.c
-    trees.c
-    uncompr.c
-    zutil.c
-)
-
-if(NOT MINGW)
-    set(ZLIB_DLL_SRCS
-        win32/zlib1.rc # If present will override custom build rule below.
-    )
-endif()
-
-if(CMAKE_COMPILER_IS_GNUCC)
-    if(ASM686)
-        set(ZLIB_ASMS contrib/asm686/match.S)
-    elseif (AMD64)
-        set(ZLIB_ASMS contrib/amd64/amd64-match.S)
-    endif ()
-
-	if(ZLIB_ASMS)
-		add_definitions(-DASMV)
-		set_source_files_properties(${ZLIB_ASMS} PROPERTIES LANGUAGE C COMPILE_FLAGS -DNO_UNDERLINE)
-	endif()
-endif()
-
-if(MSVC)
-    if(ASM686)
-		ENABLE_LANGUAGE(ASM_MASM)
-        set(ZLIB_ASMS
-			contrib/masmx86/inffas32.asm
-			contrib/masmx86/match686.asm
-		)
-    elseif (AMD64)
-		ENABLE_LANGUAGE(ASM_MASM)
-        set(ZLIB_ASMS
-			contrib/masmx64/gvmat64.asm
-			contrib/masmx64/inffasx64.asm
-		)
-    endif()
-
-	if(ZLIB_ASMS)
-		add_definitions(-DASMV -DASMINF)
-	endif()
-endif()
-
-# parse the full version number from zlib.h and include in ZLIB_FULL_VERSION
-file(READ ${CMAKE_CURRENT_SOURCE_DIR}/zlib.h _zlib_h_contents)
-string(REGEX REPLACE ".*#define[ \t]+ZLIB_VERSION[ \t]+\"([-0-9A-Za-z.]+)\".*"
-    "\\1" ZLIB_FULL_VERSION ${_zlib_h_contents})
-
-if(MINGW)
-    # This gets us DLL resource information when compiling on MinGW.
-    if(NOT CMAKE_RC_COMPILER)
-        set(CMAKE_RC_COMPILER windres.exe)
-    endif()
-
-    add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
-                       COMMAND ${CMAKE_RC_COMPILER}
-                            -D GCC_WINDRES
-                            -I ${CMAKE_CURRENT_SOURCE_DIR}
-                            -I ${CMAKE_CURRENT_BINARY_DIR}
-                            -o ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
-                            -i ${CMAKE_CURRENT_SOURCE_DIR}/win32/zlib1.rc)
-    set(ZLIB_DLL_SRCS ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj)
-endif(MINGW)
-
-add_library(zlibstatic STATIC ${ZLIB_SRCS} ${ZLIB_ASMS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
-
-if(UNIX)
-    # On unix-like platforms the library is almost always called libz
-   set_target_properties(zlibstatic PROPERTIES OUTPUT_NAME z)
-endif()
\ No newline at end of file

From d23cebf9f16908ba8d7a587f203570b7ce90b44a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 3 Jul 2023 09:53:59 -0400
Subject: [PATCH 334/396] must copy wheel to olddir when -w flag is not given

---
 python/install.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/python/install.py b/python/install.py
index 25784791b4..853479e9f6 100644
--- a/python/install.py
+++ b/python/install.py
@@ -11,7 +11,7 @@ independently and used to build the wheel without installing it.
 """
 
 from __future__ import print_function
-import sys,os,shutil,glob,subprocess
+import sys, os, shutil, glob, subprocess
 from argparse import ArgumentParser
 
 parser = ArgumentParser(prog='install.py',
@@ -105,12 +105,12 @@ os.system(sys.executable + ' makewheel.py')
 for wheel in glob.glob('lammps-*.whl'):
   if args.wheeldir:
     shutil.copy(wheel, args.wheeldir)
-
-print('wheel = ', wheel)
+  else:
+    shutil.copy(wheel, olddir)
 
 # remove temporary folders and files
 os.chdir(olddir)
-shutil.rmtree('build-python',True)
+shutil.rmtree('build-python', True)
 
 # stop here if we were asked not to install the wheel we created
 if args.noinstall:

From 268faf935b050097cf873f1e233c9405998466b6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 3 Jul 2023 10:32:24 -0400
Subject: [PATCH 335/396] avoid overeager flagging of errors for arguments to
 derived classes

---
 src/dump_custom.cpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index bdbc8ec185..dba72c7478 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -1464,10 +1464,14 @@ int DumpCustom::parse_fields(int narg, char **arg)
       switch (argi.get_type()) {
 
       case ArgInfo::UNKNOWN:
-      case ArgInfo::NONE:
         error->all(FLERR,"Invalid attribute {} in dump {} command",arg[iarg],style);
         break;
 
+      case ArgInfo::NONE:
+        // ignore because this may be a valid argument for a derived dump style class
+        return iarg;
+        break;
+
       // compute value = c_ID
       // if no trailing [], then arg is set to 0, else arg is int between []
 

From 677ff15740c5e993b2a8305d173c1f34db3d75b3 Mon Sep 17 00:00:00 2001
From: "Dan S. Bolintineanu" <dsbolin@sandia.gov>
Date: Mon, 3 Jul 2023 11:52:41 -0600
Subject: [PATCH 336/396] Gran/heat changes

---
 doc/src/pair_granular.rst          | 31 +++++++++++++++++++++++-----
 src/GRANULAR/fix_heat_flow.cpp     | 20 ++++++++----------
 src/GRANULAR/gran_sub_mod_heat.cpp | 33 +++++++++++++++++++++++++++---
 src/GRANULAR/gran_sub_mod_heat.h   | 15 +++++++++++++-
 4 files changed, 79 insertions(+), 20 deletions(-)

diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst
index 37ff8fcbfe..fb5d5c6338 100644
--- a/doc/src/pair_granular.rst
+++ b/doc/src/pair_granular.rst
@@ -641,22 +641,36 @@ The optional *heat* keyword enables heat conduction. The options currently
 supported are:
 
 1. *none*
-2. *area* : :math:`k_{s}`
+2. *radius* : :math:`k_{s}`
+3. *area* : :math:`h_{s}`
 
 If the *heat* keyword is not specified, the model defaults to *none*.
 
+For *heat* *radius*, the heat
+:math:`Q` conducted between two particles is given by
+
+.. math::
+
+   Q = 2 k_{s} a \Delta T
+
+where :math:`\Delta T` is the difference in the two particles' temperature,
+:math:`k_{s}` is a non-negative numeric value for the conductivity (in units
+of power/(length*temperature)), and :math:`a` is the radius of the contact and 
+depends on the normal force model. This is the model proposed by 
+:ref:`Vargas and McCarthy <VargasMcCarthy2001>`
+
 For *heat* *area*, the heat
 :math:`Q` conducted between two particles is given by
 
 .. math::
 
-   Q = k_{s} A \Delta T
-
+   Q = h_{s} A \Delta T
 
 
 where :math:`\Delta T` is the difference in the two particles' temperature,
-:math:`k_{s}` is a non-negative numeric value for the conductivity, and
-:math:`A` is the area of the contact and depends on the normal force model.
+:math:`h_{s}` is a non-negative numeric value for the heat transfer 
+coefficient (in units of power/(area*temperature)), and :math:`A=\pi a^2` is
+the area of the contact and depends on the normal force model.
 
 Note that the option *none* must either be used in all or none of of the
 *pair_coeff* calls. See :doc:`fix heat/flow <fix_heat_flow>` and
@@ -894,3 +908,10 @@ J. Appl. Mech., ASME 20, 327-344.
 **(Agnolin and Roux 2007)** Agnolin, I. & Roux, J-N. (2007).
 Internal states of model isotropic granular packings.
 I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302.
+
+.. _VargasMcCarthy2001:
+
+**(Vargas and McCarthy 2001)** Vargas, W.L. and McCarthy, J.J. (2001). 
+Heat conduction in granular materials. 
+AIChE Journal, 47(5), 1052-1059.
+
diff --git a/src/GRANULAR/fix_heat_flow.cpp b/src/GRANULAR/fix_heat_flow.cpp
index a9c110a2e7..16f7755d44 100644
--- a/src/GRANULAR/fix_heat_flow.cpp
+++ b/src/GRANULAR/fix_heat_flow.cpp
@@ -89,23 +89,21 @@ void FixHeatFlow::init()
 
 void FixHeatFlow::setup(int /*vflag*/)
 {
-  // Identify whether this is the first instance of fix heat/flow
-  first_flag = 0;
-
-  int i = 0;
-  auto fixlist = modify->get_fix_by_style("heat/flow");
-  for (const auto &ifix : fixlist) {
-    if (strcmp(ifix->id, id) == 0) break;
-    i++;
-  }
-
-  if (i == 0) first_flag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixHeatFlow::setup_pre_force(int /*vflag*/)
 {
+  // Identify whether this is the first instance of fix heat/flow
+  first_flag = 0;
+  int i = 0;
+  auto fixlist = modify->get_fix_by_style("heat/flow");
+  for (const auto &ifix : fixlist) {
+    if (strcmp(ifix->id, id) == 0) break;
+    i++;
+  }
+  if (i == 0) first_flag = 1;
   pre_force(0);
 }
 
diff --git a/src/GRANULAR/gran_sub_mod_heat.cpp b/src/GRANULAR/gran_sub_mod_heat.cpp
index 75dcd30b73..dc6d50f7ec 100644
--- a/src/GRANULAR/gran_sub_mod_heat.cpp
+++ b/src/GRANULAR/gran_sub_mod_heat.cpp
@@ -41,6 +41,33 @@ double GranSubModHeatNone::calculate_heat()
   return 0.0;
 }
 
+/* ----------------------------------------------------------------------
+   Radius-based heat conduction
+------------------------------------------------------------------------- */
+
+GranSubModHeatRadius::GranSubModHeatRadius(GranularModel *gm, LAMMPS *lmp) : GranSubModHeat(gm, lmp)
+{
+  num_coeffs = 1;
+  contact_radius_flag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GranSubModHeatRadius::coeffs_to_local()
+{
+  conductivity = coeffs[0];
+
+  if (conductivity < 0.0) error->all(FLERR, "Illegal radius heat model");
+}
+
+/* ---------------------------------------------------------------------- */
+
+double GranSubModHeatRadius::calculate_heat()
+{
+  return 2 * conductivity * gm->contact_radius * (gm->Tj - gm->Ti);
+}
+
+
 /* ----------------------------------------------------------------------
    Area-based heat conduction
 ------------------------------------------------------------------------- */
@@ -55,14 +82,14 @@ GranSubModHeatArea::GranSubModHeatArea(GranularModel *gm, LAMMPS *lmp) : GranSub
 
 void GranSubModHeatArea::coeffs_to_local()
 {
-  conductivity = coeffs[0];
+  heat_transfer_coeff = coeffs[0];
 
-  if (conductivity < 0.0) error->all(FLERR, "Illegal area heat model");
+  if (heat_transfer_coeff < 0.0) error->all(FLERR, "Illegal area heat model");
 }
 
 /* ---------------------------------------------------------------------- */
 
 double GranSubModHeatArea::calculate_heat()
 {
-  return conductivity * MY_PI * gm->contact_radius * gm->contact_radius * (gm->Tj - gm->Ti);
+  return heat_transfer_coeff * MY_PI * gm->contact_radius * gm->contact_radius * (gm->Tj - gm->Ti);
 }
diff --git a/src/GRANULAR/gran_sub_mod_heat.h b/src/GRANULAR/gran_sub_mod_heat.h
index 8e5dc2693d..1098a0aa78 100644
--- a/src/GRANULAR/gran_sub_mod_heat.h
+++ b/src/GRANULAR/gran_sub_mod_heat.h
@@ -14,6 +14,7 @@
 #ifdef GRAN_SUB_MOD_CLASS
 // clang-format off
 GranSubModStyle(none,GranSubModHeatNone,HEAT);
+GranSubModStyle(radius,GranSubModHeatRadius,HEAT);
 GranSubModStyle(area,GranSubModHeatArea,HEAT);
 // clang-format on
 #else
@@ -39,6 +40,18 @@ namespace Granular_NS {
     GranSubModHeatNone(class GranularModel *, class LAMMPS *);
     double calculate_heat() override;
   };
+    
+  /* ---------------------------------------------------------------------- */
+
+  class GranSubModHeatRadius : public GranSubModHeat {
+   public:
+    GranSubModHeatRadius(class GranularModel *, class LAMMPS *);
+    void coeffs_to_local() override;
+    double calculate_heat() override;
+
+   protected:
+    double conductivity;
+  };
 
   /* ---------------------------------------------------------------------- */
 
@@ -49,7 +62,7 @@ namespace Granular_NS {
     double calculate_heat() override;
 
    protected:
-    double conductivity;
+    double heat_transfer_coeff;
   };
 
 }    // namespace Granular_NS

From 9dd5ceaf4eee1a81bdd824952368dddcdef2a491 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Mon, 3 Jul 2023 15:06:23 -0600
Subject: [PATCH 337/396] Kokkos Makefiles

---
 ...le.spock_kokkos => Makefile.aurora_kokkos} | 25 ++++++++-----------
 ...rusher_kokkos => Makefile.frontier_kokkos} |  4 +--
 2 files changed, 11 insertions(+), 18 deletions(-)
 rename src/MAKE/MACHINES/{Makefile.spock_kokkos => Makefile.aurora_kokkos} (82%)
 rename src/MAKE/MACHINES/{Makefile.crusher_kokkos => Makefile.frontier_kokkos} (94%)

diff --git a/src/MAKE/MACHINES/Makefile.spock_kokkos b/src/MAKE/MACHINES/Makefile.aurora_kokkos
similarity index 82%
rename from src/MAKE/MACHINES/Makefile.spock_kokkos
rename to src/MAKE/MACHINES/Makefile.aurora_kokkos
index 8f7e5bd63d..a263d4cb8c 100644
--- a/src/MAKE/MACHINES/Makefile.spock_kokkos
+++ b/src/MAKE/MACHINES/Makefile.aurora_kokkos
@@ -1,4 +1,4 @@
-# spock_kokkos = KOKKOS/HIP, AMD MI100 GPU and AMD EPYC 7662 "Rome" CPU, Cray MPICH, hipcc compiler, hipFFT
+# aurora_kokkos = KOKKOS/SYCL, Intel Data Center Max (Ponte Vecchio) GPU, Intel Sapphire Rapids CPU, mpicxx compiler
 
 SHELL = /bin/sh
 
@@ -6,14 +6,12 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
-
-CC =		hipcc
-CCFLAGS =	-g -O3 -DNDEBUG -DKOKKOS_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS
+CC =		mpicxx
+CCFLAGS =	-g -O3 -DNDEBUG
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		hipcc
+LINK =		mpicxx
 LINKFLAGS =	-g -O3
 LIB = 
 SIZE =		size
@@ -21,8 +19,8 @@ SIZE =		size
 ARCHIVE =	ar
 ARFLAGS =	-rc
 SHLIBFLAGS =	-shared
-KOKKOS_DEVICES = HIP
-KOKKOS_ARCH = Zen2,Vega908
+KOKKOS_DEVICES = SYCL
+KOKKOS_ARCH = PVC,SPR
 
 # ---------------------------------------------------------------------
 # LAMMPS-specific settings, all OPTIONAL
@@ -43,9 +41,9 @@ LMP_INC =	-DLAMMPS_GZIP
 # PATH = path for MPI library
 # LIB = name of MPI library
 
-MPI_INC =       -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I${MPICH_DIR}/include
+MPI_INC =       -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
 MPI_PATH = 
-MPI_LIB = -L${MPICH_DIR}/lib -lmpi -L${CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_hsa
+MPI_LIB =
 
 # FFT library
 # see discussion in Section 3.5.2 of manual
@@ -54,12 +52,9 @@ MPI_LIB = -L${MPICH_DIR}/lib -lmpi -L${CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_hsa
 # PATH = path for FFT library
 # LIB = name of FFT library
 
-MY_HIP_EXE = $(shell which hipcc)
-MY_HIP_PATH = $(dir ${MY_HIP_EXE})
-
-FFT_INC = -DFFT_HIPFFT
+FFT_INC =
 FFT_PATH =
-FFT_LIB = -L${MY_HIP_PATH}../lib -lhipfft
+FFT_LIB =
 
 # JPEG and/or PNG library
 # see discussion in Section 3.5.4 of manual
diff --git a/src/MAKE/MACHINES/Makefile.crusher_kokkos b/src/MAKE/MACHINES/Makefile.frontier_kokkos
similarity index 94%
rename from src/MAKE/MACHINES/Makefile.crusher_kokkos
rename to src/MAKE/MACHINES/Makefile.frontier_kokkos
index d6332805f7..ade90e6ffb 100644
--- a/src/MAKE/MACHINES/Makefile.crusher_kokkos
+++ b/src/MAKE/MACHINES/Makefile.frontier_kokkos
@@ -1,4 +1,4 @@
-# crusher_kokkos = KOKKOS/HIP, AMD MI250X GPU and AMD EPYC 7A53 "Optimized 3rd Gen EPYC" CPU, Cray MPICH, hipcc compiler, hipFFT
+# frontier_kokkos = KOKKOS/HIP, AMD MI250X GPU and AMD EPYC 7A53 "Optimized 3rd Gen EPYC" CPU, Cray MPICH, hipcc compiler, hipFFT
 
 SHELL = /bin/sh
 
@@ -6,8 +6,6 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
-
 CC =		hipcc
 CCFLAGS =	-g -O3 -munsafe-fp-atomics -DNDEBUG -DKOKKOS_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS
 SHFLAGS =	-fPIC

From 9031d7979161afd541f27b268416176158f04d3c Mon Sep 17 00:00:00 2001
From: Stan Moore <stanmoore1@gmail.com>
Date: Mon, 3 Jul 2023 21:47:47 +0000
Subject: [PATCH 338/396] Add Makefile for Perlmutter

---
 src/MAKE/MACHINES/Makefile.frontier_kokkos   |   2 +-
 src/MAKE/MACHINES/Makefile.perlmutter_kokkos | 128 +++++++++++++++++++
 2 files changed, 129 insertions(+), 1 deletion(-)
 create mode 100644 src/MAKE/MACHINES/Makefile.perlmutter_kokkos

diff --git a/src/MAKE/MACHINES/Makefile.frontier_kokkos b/src/MAKE/MACHINES/Makefile.frontier_kokkos
index ade90e6ffb..86cddd12b7 100644
--- a/src/MAKE/MACHINES/Makefile.frontier_kokkos
+++ b/src/MAKE/MACHINES/Makefile.frontier_kokkos
@@ -20,7 +20,7 @@ ARCHIVE =	ar
 ARFLAGS =	-rc
 SHLIBFLAGS =	-shared
 KOKKOS_DEVICES = HIP
-KOKKOS_ARCH = Zen3,Vega90A
+KOKKOS_ARCH = Vega90A,Zen3
 
 # ---------------------------------------------------------------------
 # LAMMPS-specific settings, all OPTIONAL
diff --git a/src/MAKE/MACHINES/Makefile.perlmutter_kokkos b/src/MAKE/MACHINES/Makefile.perlmutter_kokkos
new file mode 100644
index 0000000000..2882fb6260
--- /dev/null
+++ b/src/MAKE/MACHINES/Makefile.perlmutter_kokkos
@@ -0,0 +1,128 @@
+# perlmutter_kokkos = KOKKOS/CUDA, NVIDIA A100 GPU and AMD EPYC 7763 (Milan) CPU, Cray MPICH, nvcc compiler with gcc
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
+
+CC =		$(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
+CCFLAGS =	-g -O3 -DNDEBUG -Xcudafe --diag_suppress=unrecognized_pragma
+SHFLAGS =	-fPIC
+DEPFLAGS =	-M
+
+LINK =		$(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
+LINKFLAGS =	-g -O3
+LIB = 
+SIZE =		size
+
+ARCHIVE =	ar
+ARFLAGS =	-rc
+SHLIBFLAGS =	-shared
+KOKKOS_DEVICES = Cuda
+KOKKOS_ARCH = Ampere80,Zen3
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings, all OPTIONAL
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings
+# see possible settings in Section 3.5 of the manual
+
+LMP_INC =	-DLAMMPS_GZIP
+
+# MPI library
+# see discussion in Section 3.4 of the manual
+# MPI wrapper compiler/linker can provide this info
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I${MPICH_DIR}/include
+MPI_PATH =
+MPI_LIB = -L${MPICH_DIR}/lib -lmpi -L${CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_cuda
+
+# FFT library
+# see discussion in Section 3.5.2 of manual
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_CUFFT
+FFT_PATH = 
+FFT_LIB = -lcufft
+
+# JPEG and/or PNG library
+# see discussion in Section 3.5.4 of manual
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =
+JPG_PATH =
+JPG_LIB =
+
+#  library for loading shared objects (defaults to -ldl, should be empty on Windows)
+# uncomment to change the default
+
+# override DYN_LIB =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# do not edit this section
+
+include Makefile.package.settings
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
+EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
+EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
+	$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
+	$(SIZE) $@
+
+# Library targets
+
+$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
+	@rm -f ../$(ARLIB)
+	$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
+	@rm -f $(ARLIB)
+	@ln -s ../$(ARLIB) $(ARLIB)
+
+$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
+		$(OBJ) $(EXTRA_LIB) $(LIB)
+	@rm -f $(SHLIB)
+	@ln -s ../$(SHLIB) $(SHLIB)
+
+# Compilation rules
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+# Individual dependencies
+
+depend : fastdep.exe $(SRC)
+	@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
+
+fastdep.exe: ../DEPEND/fastdep.c
+	cc -O -o $@ $<
+
+sinclude .depend

From d57e1be9420699863dce18491fae67842f933285 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 4 Jul 2023 08:13:06 -0400
Subject: [PATCH 339/396] avoid division by zero in angle style dipole

---
 src/DIPOLE/angle_dipole.cpp | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/DIPOLE/angle_dipole.cpp b/src/DIPOLE/angle_dipole.cpp
index f6508022db..6ad4a0fb4c 100644
--- a/src/DIPOLE/angle_dipole.cpp
+++ b/src/DIPOLE/angle_dipole.cpp
@@ -31,6 +31,8 @@
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
+static constexpr double SMALL = 1.0e-100;
+
 /* ---------------------------------------------------------------------- */
 
 AngleDipole::AngleDipole(LAMMPS *lmp) : Angle(lmp)
@@ -72,7 +74,7 @@ void AngleDipole::compute(int eflag, int vflag)
 
   double **f = atom->f;
   double delTx, delTy, delTz;
-  double fx, fy, fz, fmod, fmod_sqrtff;
+  double fx, fy, fz, fmod, fmod_len, len;
 
   if (!newton_bond) error->all(FLERR, "'newton' flag for bonded interactions must be 'on'");
 
@@ -87,6 +89,7 @@ void AngleDipole::compute(int eflag, int vflag)
     delz = x[iRef][2] - x[iDip][2];
 
     r = sqrt(delx * delx + dely * dely + delz * delz);
+    if (r < SMALL) continue;
 
     rmu = r * mu[iDip][3];
     cosGamma = (mu[iDip][0] * delx + mu[iDip][1] * dely + mu[iDip][2] * delz) / rmu;
@@ -111,11 +114,13 @@ void AngleDipole::compute(int eflag, int vflag)
     fz = delx * delTy - dely * delTx;
 
     fmod = sqrt(delTx * delTx + delTy * delTy + delTz * delTz) / r;    // magnitude
-    fmod_sqrtff = fmod / sqrt(fx * fx + fy * fy + fz * fz);
+    len = sqrt(fx * fx + fy * fy + fz * fz);
+    if (len < SMALL) continue;
+    fmod_len = fmod / len;
 
-    fi[0] = fx * fmod_sqrtff;
-    fi[1] = fy * fmod_sqrtff;
-    fi[2] = fz * fmod_sqrtff;
+    fi[0] = fx * fmod_len;
+    fi[1] = fy * fmod_len;
+    fi[2] = fz * fmod_len;
 
     fj[0] = -fi[0];
     fj[1] = -fi[1];
@@ -249,6 +254,8 @@ double AngleDipole::single(int type, int iRef, int iDip, int /*iDummy*/)
   domain->minimum_image(delx, dely, delz);
 
   double r = sqrt(delx * delx + dely * dely + delz * delz);
+  if (r < SMALL) return 0.0;
+
   double rmu = r * mu[iDip][3];
   double cosGamma = (mu[iDip][0] * delx + mu[iDip][1] * dely + mu[iDip][2] * delz) / rmu;
   double deltaGamma = cosGamma - cos(gamma0[type]);

From fcf30f4c582003ad6f0fef5b096158694330469d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Jul 2023 09:16:58 -0400
Subject: [PATCH 340/396] modernize example for dumping ellipsoid info to
 visualize with OVITO

---
 examples/ASPHERE/ellipsoid/in.ellipsoid    | 127 +++++++++++----------
 examples/ASPHERE/ellipsoid/in.ellipsoid.mp | 127 +++++++++++----------
 2 files changed, 132 insertions(+), 122 deletions(-)

diff --git a/examples/ASPHERE/ellipsoid/in.ellipsoid b/examples/ASPHERE/ellipsoid/in.ellipsoid
index 5e9a20f6e0..2dda95a029 100644
--- a/examples/ASPHERE/ellipsoid/in.ellipsoid
+++ b/examples/ASPHERE/ellipsoid/in.ellipsoid
@@ -1,23 +1,23 @@
 # SRD diffusion demo - ellipsoids
 
-units		lj
-atom_style	ellipsoid
-atom_modify	first big
-dimension	2
+units           lj
+atom_style      ellipsoid
+atom_modify     first big
+dimension       2
 
 # create big ellipsoidal particles
 
-lattice		sq 0.14
-region		box block 0 10 0 10 -0.5 0.5
-create_box	2 box
-create_atoms	1 region box
+lattice         sq 0.14
+region          box block 0 10 0 10 -0.5 0.5
+create_box      2 box
+create_atoms    1 region box
 
-set		type 1 mass 1.0
-set		type 1 shape 3.0 1.0 1.0
-group		big type 1
-set		group big quat/random 29898
+set             type 1 mass 1.0
+set             type 1 shape 3.0 1.0 1.0
+group           big type 1
+set             group big quat/random 29898
 
-velocity	big create 1.44 87287 loop geom
+velocity        big create 1.44 87287 loop geom
 
 # equilibrate big particles
 
@@ -26,57 +26,60 @@ pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
 pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
 pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
 
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
 
-fix		1 big nve/asphere
-fix		2 all enforce2d
+fix             1 big nve/asphere
+fix             2 all enforce2d
 
-compute		rot big temp/asphere
+compute         rot big temp/asphere
+compute         0 all property/atom quatw quati quatj quatk shapex shapey shapez
 
-#dump		1 all custom 10 dump.ellipsoid.equil id type x y z &
-#		  quatw quati quatj quatk
+#dump           1 all custom 10 dump.ellipsoid.equil id type x y z &
+#                 c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
+#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
+#                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
 
-thermo_style	custom step temp c_rot epair etotal press
-thermo		100
+thermo_style    custom step temp c_rot epair etotal press
+thermo          100
 
-run		1000
+run             1000
 
-#undump		1
-unfix		1
-unfix		2
+#undump         1
+unfix           1
+unfix           2
 
 # add small particles as hi density lattice
 
-region		plane block INF INF INF INF -0.001 0.001 units box
-lattice		sq 120.0
-create_atoms	2 region plane
+region          plane block INF INF INF INF -0.001 0.001 units box
+lattice         sq 120.0
+create_atoms    2 region plane
 
-set		type 2 mass 0.01
-group		small type 2
-velocity	small create 1.0 593849 loop geom
+set             type 2 mass 0.01
+group           small type 2
+velocity        small create 1.0 593849 loop geom
 
 # delete overlaps
 # must set 1-2 cutoff to non-zero value
 
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 2.0
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 2.0
 
-neigh_modify	one 10000
+neigh_modify    one 10000
 
-delete_atoms	overlap 1.6 small big
+delete_atoms    overlap 1.6 small big
 
 # SRD run
 
-reset_timestep	0
+reset_timestep  0
 
-neighbor	0.3 multi
-neigh_modify	delay 0 every 1 check yes
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
 
-comm_modify	mode multi group big vel yes
-neigh_modify	include big
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
 
 # no pairwise interactions with small particles
 
@@ -88,29 +91,31 @@ pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
 # use fix SRD to push small particles out from inside big ones
 # if comment out, big particles won't see SRD particles
 
-timestep	0.0005
+timestep        0.0005
 
-fix		1 big nve/asphere
-fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
-		  collision noslip search 0.2 inside ignore exact no bounce 50
-fix		3 all enforce2d
+fix             1 big nve/asphere
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
+                  collision noslip search 0.2 inside ignore exact no bounce 50
+fix             3 all enforce2d
 
 # diagnostics
 
-compute		tbig big temp/asphere
-variable	pebig equal pe*atoms/count(big)
-variable	ebig equal etotal*atoms/count(big)
-thermo_style	custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
-		f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
-		f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+compute         tbig big temp/asphere
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+thermo_style    custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
+                f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
+                f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
 
-thermo_modify	temp tbig
-thermo		1000
+thermo_modify   temp tbig
+thermo          1000
 
-#dump		1 all custom 1000 dump.ellipsoid id type x y z &
-#                quatw quati quatj quatk
+#dump           1 all custom 1000 dump.ellipsoid id type x y z &
+#                 c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
+#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
+#                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
 
-#dump		1 all image 1000 image.*.jpg type type zoom 1.6
-#dump_modify	1 pad 6 adiam 1 1 adiam 2 0.2
+#dump           2 all image 1000 image.*.jpg type type zoom 1.6
+#dump_modify    2 pad 6 adiam 1 1 adiam 2 0.2
 
-run		100000
+run             100000
diff --git a/examples/ASPHERE/ellipsoid/in.ellipsoid.mp b/examples/ASPHERE/ellipsoid/in.ellipsoid.mp
index 7ce01ad4e1..e950cc86f5 100644
--- a/examples/ASPHERE/ellipsoid/in.ellipsoid.mp
+++ b/examples/ASPHERE/ellipsoid/in.ellipsoid.mp
@@ -1,23 +1,23 @@
 # SRD viscosity demo - ellipsoids
 
-units		lj
-atom_style	ellipsoid
-atom_modify	first big
-dimension	2
+units           lj
+atom_style      ellipsoid
+atom_modify     first big
+dimension       2
 
 # create big ellipsoidal particles
 
-lattice		sq 0.14
-region		box block 0 10 0 10 -0.5 0.5
-create_box	2 box
-create_atoms	1 region box
+lattice         sq 0.14
+region          box block 0 10 0 10 -0.5 0.5
+create_box      2 box
+create_atoms    1 region box
 
-set		type 1 mass 1.0
-set		type 1 shape 3.0 1.0 1.0
-group		big type 1
-set		group big quat/random 29898
+set             type 1 mass 1.0
+set             type 1 shape 3.0 1.0 1.0
+group           big type 1
+set             group big quat/random 29898
 
-velocity	big create 1.44 87287 loop geom
+velocity        big create 1.44 87287 loop geom
 
 # equilibrate big particles
 
@@ -26,57 +26,60 @@ pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
 pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
 pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
 
-neighbor	0.3 bin
-neigh_modify	delay 0 every 1 check yes
+neighbor        0.3 bin
+neigh_modify    delay 0 every 1 check yes
 
-fix		1 big nve/asphere
-fix		2 all enforce2d
+fix             1 big nve/asphere
+fix             2 all enforce2d
 
-compute		rot big temp/asphere
+compute         rot big temp/asphere
+compute         0 all property/atom quatw quati quatj quatk shapex shapey shapez
 
-#dump		1 all custom 10 dump.ellipsoid.equil id type x y z &
-#		  quatw quati quatj quatk
+#dump           1 all custom 10 dump.ellipsoid.equil id type x y z &
+#                 c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
+#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
+#                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
 
-thermo_style	custom step temp c_rot epair etotal press
-thermo		100
+thermo_style    custom step temp c_rot epair etotal press
+thermo          100
 
-run		1000
+run             1000
 
-#undump		1
-unfix		1
-unfix		2
+#undump         1
+unfix           1
+unfix           2
 
 # add small particles as hi density lattice
 
-region		plane block INF INF INF INF -0.001 0.001 units box
-lattice		sq 120.0
-create_atoms	2 region plane
+region          plane block INF INF INF INF -0.001 0.001 units box
+lattice         sq 120.0
+create_atoms    2 region plane
 
-set		type 2 mass 0.01
-group		small type 2
-velocity	small create 1.0 593849 loop geom
+set             type 2 mass 0.01
+group           small type 2
+velocity        small create 1.0 593849 loop geom
 
 # delete overlaps
 # must set 1-2 cutoff to non-zero value
 
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 2.0
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0
+pair_coeff      2 2 0.0 1.0 0.0
+pair_coeff      1 2 0.0 1.0 2.0
 
-neigh_modify	one 10000
+neigh_modify    one 10000
 
-delete_atoms	overlap 1.6 small big
+delete_atoms    overlap 1.6 small big
 
 # SRD run
 
-reset_timestep	0
+reset_timestep  0
 
-neighbor	0.3 multi
-neigh_modify	delay 0 every 1 check yes
+neighbor        0.3 multi
+neigh_modify    delay 0 every 1 check yes
 
-comm_modify	mode multi group big vel yes
-neigh_modify	include big
+comm_modify     mode multi group big vel yes
+neigh_modify    include big
 
 # no pairwise interactions with small particles
 
@@ -88,30 +91,32 @@ pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0
 # use fix SRD to push small particles out from inside big ones
 # if comment out, big particles won't see SRD particles
 
-timestep	0.0005
+timestep        0.0005
 
-fix		1 big nve/asphere
-fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
+fix             1 big nve/asphere
+fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
                   collision noslip search 0.2 inside ignore exact no bounce 50
-fix		3 small viscosity 20 x y 50
-fix		4 all enforce2d
+fix             3 small viscosity 20 x y 50
+fix             4 all enforce2d
 
 # diagnostics
 
-compute		tbig big temp/asphere
-variable	pebig equal pe*atoms/count(big)
-variable	ebig equal etotal*atoms/count(big)
-thermo_style	custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
-		f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
-		f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
+compute         tbig big temp/asphere
+variable        pebig equal pe*atoms/count(big)
+variable        ebig equal etotal*atoms/count(big)
+thermo_style    custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
+                f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
+                f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
 
-thermo_modify	temp tbig
-thermo		1000
+thermo_modify   temp tbig
+thermo          1000
 
-#dump		1 all custom 500 dump.ellipsoid.mp id type x y z &
-#                quatw quati quatj quatk
+#dump           1 all custom 500 dump.ellipsoid id type x y z &
+#                 c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
+#dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
+#                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
 
-#dump		1 all image 500 image.*.jpg type type zoom 1.6
-#dump_modify	1 pad 6 adiam 1 1 adiam 2 0.2
+#dump           1 all image 500 image.*.jpg type type zoom 1.6
+#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2
 
-run		50000
+run             50000

From 8ae5ab57fcac05783a82c674ce9727ac1c819b56 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Jul 2023 09:17:27 -0400
Subject: [PATCH 341/396] non-ellipsoid particles you have a 1,0,0,0 quaternion
 and 1,1,1 shape

---
 src/compute_property_atom.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp
index fc7089fa01..fbb9129b6e 100644
--- a/src/compute_property_atom.cpp
+++ b/src/compute_property_atom.cpp
@@ -1268,7 +1268,7 @@ void ComputePropertyAtom::pack_shapex(int n)
   for (int i = 0; i < nlocal; i++) {
     if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
       buf[n] = 2.0*bonus[ellipsoid[i]].shape[0];
-    else buf[n] = 0.0;
+    else buf[n] = 1.0;
     n += nvalues;
   }
 }
@@ -1285,7 +1285,7 @@ void ComputePropertyAtom::pack_shapey(int n)
   for (int i = 0; i < nlocal; i++) {
     if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
       buf[n] = 2.0*bonus[ellipsoid[i]].shape[1];
-    else buf[n] = 0.0;
+    else buf[n] = 1.0;
     n += nvalues;
   }
 }
@@ -1302,7 +1302,7 @@ void ComputePropertyAtom::pack_shapez(int n)
   for (int i = 0; i < nlocal; i++) {
     if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
       buf[n] = 2.0*bonus[ellipsoid[i]].shape[2];
-    else buf[n] = 0.0;
+    else buf[n] = 1.0;
     n += nvalues;
   }
 }
@@ -1320,7 +1320,7 @@ void ComputePropertyAtom::pack_quatw(int n)
     for (int i = 0; i < nlocal; i++) {
       if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
         buf[n] = bonus[ellipsoid[i]].quat[0];
-      else buf[n] = 0.0;
+      else buf[n] = 1.0;
       n += nvalues;
     }
 

From 02845483d2038b42aecd77d327028d7a0fed9d09 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@gmail.com>
Date: Thu, 6 Jul 2023 09:08:15 -0700
Subject: [PATCH 342/396] add gravity keyword info to fix rigid doc page

---
 doc/src/fix_rigid.rst | 32 ++++++++++++++++++++++++++++----
 1 file changed, 28 insertions(+), 4 deletions(-)

diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst
index 884d883f5a..098b900050 100644
--- a/doc/src/fix_rigid.rst
+++ b/doc/src/fix_rigid.rst
@@ -610,10 +610,12 @@ such attributes: the total mass of the rigid body, its center-of-mass
 position, its 6 moments of inertia, its center-of-mass velocity, and
 the 3 image flags of the center-of-mass position.  For rigid bodies
 consisting of point particles or non-overlapping finite-size
-particles, LAMMPS can compute these values accurately.  However, for
-rigid bodies consisting of finite-size particles which overlap each
-other, LAMMPS will ignore the overlaps when computing these 4
-attributes.  The amount of error this induces depends on the amount of
+particles, LAMMPS can compute these values accurately.
+
+However, for rigid bodies consisting of finite-size particles which
+overlap each other, LAMMPS will ignore the overlaps when computing
+these 4 attributes, which means the dynamics of the bodies will be
+incorrect.  The amount of error this induces depends on the amount of
 overlap.  To avoid this issue, the values can be pre-computed
 (e.g. using Monte Carlo integration).
 
@@ -677,6 +679,28 @@ cross periodic boundaries during the simulation.
    auxiliary file will contain one line for every rigid body, even if the
    original file only listed a subset of the rigid bodies.
 
+If the system has rigid bodies with finite-size overlapping particles
+and the model uses the :doc:`fix gravity <fix_gravity>` command to
+apply a gravitational force to the rigid bodies, then the *gravity*
+keyword should be used in the following manner.
+
+First, the group specified for the :doc:`fix gravity <fix_gravity>`
+command should not include any atoms in rigid bodies which have
+overlapping particles.  It can be empty (see the :doc:`group empty
+<group>` command) or only contain single particles not in rigid
+bodies, e.g. background particles.
+
+Second, the *infile* keyword should be used to specify the total mass
+and other properties of the rigid bodies with overlaps, so that their
+dyamics will be modeled correctly, as explained above.
+
+Third, the *gravity* keyword should be used the with the ID of the
+:doc:`fix gravity <fix_gravity>` command as its argument.  The rigid
+fixes will access gravity fix to extract the current direction of the
+gravity vector at each timestep (which can be static or dynamic).  A
+gravity force will then be applied to each rigid body at its
+center-of-mass position using its total mass.
+
 ----------
 
 If you use a :doc:`temperature compute <compute>` with a group that

From 6e41ac7ead41188a9660ddd8074aa76a9f1d342c Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@gmail.com>
Date: Thu, 6 Jul 2023 09:14:00 -0700
Subject: [PATCH 343/396] fix typo

---
 doc/src/fix_rigid.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst
index 098b900050..7650822626 100644
--- a/doc/src/fix_rigid.rst
+++ b/doc/src/fix_rigid.rst
@@ -696,9 +696,9 @@ dyamics will be modeled correctly, as explained above.
 
 Third, the *gravity* keyword should be used the with the ID of the
 :doc:`fix gravity <fix_gravity>` command as its argument.  The rigid
-fixes will access gravity fix to extract the current direction of the
-gravity vector at each timestep (which can be static or dynamic).  A
-gravity force will then be applied to each rigid body at its
+fixes will access the gravity fix to extract the current direction of
+the gravity vector at each timestep (which can be static or dynamic).
+A gravity force will then be applied to each rigid body at its
 center-of-mass position using its total mass.
 
 ----------

From cac82473836961e7fddbdc068e3848939a07ae29 Mon Sep 17 00:00:00 2001
From: "Dan S. Bolintineanu" <dsbolin@sandia.gov>
Date: Thu, 6 Jul 2023 11:19:22 -0600
Subject: [PATCH 344/396] Modified doc page for pair granular to include flux
 as extra pairwise quantity

---
 doc/src/pair_granular.rst | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst
index fb5d5c6338..730eff9eee 100644
--- a/doc/src/pair_granular.rst
+++ b/doc/src/pair_granular.rst
@@ -763,15 +763,17 @@ The single() function of these pair styles returns 0.0 for the energy
 of a pairwise interaction, since energy is not conserved in these
 dissipative potentials.  It also returns only the normal component of
 the pairwise interaction force.  However, the single() function also
-calculates 12 extra pairwise quantities.  The first 3 are the
+calculates 13 extra pairwise quantities.  The first 3 are the
 components of the tangential force between particles I and J, acting
 on particle I.  The fourth is the magnitude of this tangential force.
 The next 3 (5-7) are the components of the rolling torque acting on
 particle I. The next entry (8) is the magnitude of the rolling torque.
 The next entry (9) is the magnitude of the twisting torque acting
 about the vector connecting the two particle centers.
-The last 3 (10-12) are the components of the vector connecting
-the centers of the two particles (x_I - x_J).
+The next 3 (10-12) are the components of the vector connecting
+the centers of the two particles (x_I - x_J). The last quantity (13)
+is the heat flow between the two particles, set to 0 if no heat model
+is active.
 
 These extra quantities can be accessed by the :doc:`compute pair/local <compute_pair_local>` command, as *p1*, *p2*, ...,
 *p12*\ .

From b66a5cd225e7a8b020cf3d5518f43e722acbb1c5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Jul 2023 13:31:00 -0400
Subject: [PATCH 345/396] fix another typo

---
 doc/src/fix_rigid.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst
index 7650822626..b6c2c99071 100644
--- a/doc/src/fix_rigid.rst
+++ b/doc/src/fix_rigid.rst
@@ -692,7 +692,7 @@ bodies, e.g. background particles.
 
 Second, the *infile* keyword should be used to specify the total mass
 and other properties of the rigid bodies with overlaps, so that their
-dyamics will be modeled correctly, as explained above.
+dynamics will be modeled correctly, as explained above.
 
 Third, the *gravity* keyword should be used the with the ID of the
 :doc:`fix gravity <fix_gravity>` command as its argument.  The rigid

From 55b7b3d9992a22522bd85553389b5eda16a8ad65 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Jul 2023 14:03:07 -0400
Subject: [PATCH 346/396] whitespace fixes

---
 doc/src/pair_granular.rst        | 10 +++++-----
 src/GRANULAR/gran_sub_mod_heat.h |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst
index 730eff9eee..c54df44d95 100644
--- a/doc/src/pair_granular.rst
+++ b/doc/src/pair_granular.rst
@@ -655,8 +655,8 @@ For *heat* *radius*, the heat
 
 where :math:`\Delta T` is the difference in the two particles' temperature,
 :math:`k_{s}` is a non-negative numeric value for the conductivity (in units
-of power/(length*temperature)), and :math:`a` is the radius of the contact and 
-depends on the normal force model. This is the model proposed by 
+of power/(length*temperature)), and :math:`a` is the radius of the contact and
+depends on the normal force model. This is the model proposed by
 :ref:`Vargas and McCarthy <VargasMcCarthy2001>`
 
 For *heat* *area*, the heat
@@ -668,7 +668,7 @@ For *heat* *area*, the heat
 
 
 where :math:`\Delta T` is the difference in the two particles' temperature,
-:math:`h_{s}` is a non-negative numeric value for the heat transfer 
+:math:`h_{s}` is a non-negative numeric value for the heat transfer
 coefficient (in units of power/(area*temperature)), and :math:`A=\pi a^2` is
 the area of the contact and depends on the normal force model.
 
@@ -913,7 +913,7 @@ I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302.
 
 .. _VargasMcCarthy2001:
 
-**(Vargas and McCarthy 2001)** Vargas, W.L. and McCarthy, J.J. (2001). 
-Heat conduction in granular materials. 
+**(Vargas and McCarthy 2001)** Vargas, W.L. and McCarthy, J.J. (2001).
+Heat conduction in granular materials.
 AIChE Journal, 47(5), 1052-1059.
 
diff --git a/src/GRANULAR/gran_sub_mod_heat.h b/src/GRANULAR/gran_sub_mod_heat.h
index 1098a0aa78..5f264cb913 100644
--- a/src/GRANULAR/gran_sub_mod_heat.h
+++ b/src/GRANULAR/gran_sub_mod_heat.h
@@ -40,7 +40,7 @@ namespace Granular_NS {
     GranSubModHeatNone(class GranularModel *, class LAMMPS *);
     double calculate_heat() override;
   };
-    
+
   /* ---------------------------------------------------------------------- */
 
   class GranSubModHeatRadius : public GranSubModHeat {

From 3e4b66378a4a31b243249cc2893efa54360b496a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Jul 2023 14:06:31 -0400
Subject: [PATCH 347/396] typo

---
 doc/src/pair_granular.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst
index c54df44d95..bc469412d9 100644
--- a/doc/src/pair_granular.rst
+++ b/doc/src/pair_granular.rst
@@ -657,7 +657,7 @@ where :math:`\Delta T` is the difference in the two particles' temperature,
 :math:`k_{s}` is a non-negative numeric value for the conductivity (in units
 of power/(length*temperature)), and :math:`a` is the radius of the contact and
 depends on the normal force model. This is the model proposed by
-:ref:`Vargas and McCarthy <VargasMcCarthy2001>`
+:ref:`Vargas and McCarthy <VargasMcCarthy2001>`.
 
 For *heat* *area*, the heat
 :math:`Q` conducted between two particles is given by

From bf0372280e42d46f02d12d392fc30a3d97a29d71 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Jul 2023 14:59:09 -0400
Subject: [PATCH 348/396] remove dead code

---
 src/GRANULAR/fix_heat_flow.cpp | 6 ------
 src/GRANULAR/fix_heat_flow.h   | 1 -
 2 files changed, 7 deletions(-)

diff --git a/src/GRANULAR/fix_heat_flow.cpp b/src/GRANULAR/fix_heat_flow.cpp
index 16f7755d44..e948e5454f 100644
--- a/src/GRANULAR/fix_heat_flow.cpp
+++ b/src/GRANULAR/fix_heat_flow.cpp
@@ -87,12 +87,6 @@ void FixHeatFlow::init()
 
 /* ---------------------------------------------------------------------- */
 
-void FixHeatFlow::setup(int /*vflag*/)
-{
-}
-
-/* ---------------------------------------------------------------------- */
-
 void FixHeatFlow::setup_pre_force(int /*vflag*/)
 {
   // Identify whether this is the first instance of fix heat/flow
diff --git a/src/GRANULAR/fix_heat_flow.h b/src/GRANULAR/fix_heat_flow.h
index 5a06eed4d3..89fabc5a4d 100644
--- a/src/GRANULAR/fix_heat_flow.h
+++ b/src/GRANULAR/fix_heat_flow.h
@@ -30,7 +30,6 @@ class FixHeatFlow : public Fix {
 
   int setmask() override;
   void init() override;
-  void setup(int) override;
   void setup_pre_force(int) override;
   void pre_force(int) override;
   void final_integrate() override;

From 6d8f5a38ea44270cad55d208076ddd3a149b7f90 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Jul 2023 15:03:38 -0400
Subject: [PATCH 349/396] improve error messages

---
 src/GRANULAR/fix_heat_flow.cpp | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/GRANULAR/fix_heat_flow.cpp b/src/GRANULAR/fix_heat_flow.cpp
index e948e5454f..519b7f731d 100644
--- a/src/GRANULAR/fix_heat_flow.cpp
+++ b/src/GRANULAR/fix_heat_flow.cpp
@@ -33,7 +33,7 @@ enum {NONE, CONSTANT, TYPE};
 FixHeatFlow::FixHeatFlow(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg)
 {
-  if (narg < 4) error->all(FLERR,"Illegal fix command");
+  if (narg < 4) utils::missing_cmd_args(FLERR,"fix heat/flow", error);
 
   cp_style = NONE;
   comm_forward = 1;
@@ -41,24 +41,24 @@ FixHeatFlow::FixHeatFlow(LAMMPS *lmp, int narg, char **arg) :
 
   int ntypes = atom->ntypes;
   if (strcmp(arg[3],"constant") == 0) {
-    if (narg != 5) error->all(FLERR,"Illegal fix command");
+    if (narg != 5) error->all(FLERR,"Illegal fix heat/flow constant command");
     cp_style = CONSTANT;
     cp = utils::numeric(FLERR,arg[4],false,lmp);
-    if (cp < 0.0) error->all(FLERR,"Illegal fix command");
+    if (cp < 0.0) error->all(FLERR,"Illegal fix heat/flow constant command value");
   } else if (strcmp(arg[3],"type") == 0) {
-    if (narg != 4 + ntypes) error->all(FLERR,"Illegal fix command");
+    if (narg != 4 + ntypes) error->all(FLERR,"Illegal fix heat/flow type command");
     cp_style = TYPE;
-    memory->create(cp_type,ntypes+1,"fix/temp/integrate:cp_type");
+    memory->create(cp_type,ntypes+1,"fix_heat_flow:cp_type");
     for (int i = 1; i <= ntypes; i++) {
       cp_type[i] = utils::numeric(FLERR,arg[3+i],false,lmp);
-      if (cp_type[i] < 0.0) error->all(FLERR,"Illegal fix command");
+      if (cp_type[i] < 0.0) error->all(FLERR,"Illegal fix heat/flow type command value");
     }
   } else {
-    error->all(FLERR,"Illegal fix command");
+    error->all(FLERR,"Unknown fix heat/flow keyword {}", arg[3]);
   }
 
   if (cp_style == NONE)
-    error->all(FLERR, "Must specify specific heat in fix temp/integrate");
+    error->all(FLERR, "Must specify specific heat in fix heat/flow");
   dynamic_group_allow = 1;
 }
 
@@ -80,9 +80,9 @@ void FixHeatFlow::init()
   dt = update->dt;
 
   if (!atom->temperature_flag)
-    error->all(FLERR,"Fix temp/integrate requires atom style with temperature property");
+    error->all(FLERR,"Fix heat/flow requires atom style with temperature property");
   if (!atom->heatflow_flag)
-    error->all(FLERR,"Fix temp/integrate requires atom style with heatflow property");
+    error->all(FLERR,"Fix heat/flow requires atom style with heatflow property");
 }
 
 /* ---------------------------------------------------------------------- */

From 6f289df9806de41c8c0231067bef45510f0c9b4a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Jul 2023 15:05:36 -0400
Subject: [PATCH 350/396] enable and apply clang-format

---
 src/GRANULAR/fix_heat_flow.cpp | 53 ++++++++++++++--------------------
 1 file changed, 21 insertions(+), 32 deletions(-)

diff --git a/src/GRANULAR/fix_heat_flow.cpp b/src/GRANULAR/fix_heat_flow.cpp
index 519b7f731d..d0d7a73ce6 100644
--- a/src/GRANULAR/fix_heat_flow.cpp
+++ b/src/GRANULAR/fix_heat_flow.cpp
@@ -1,4 +1,3 @@
-// clang-format off
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -26,39 +25,37 @@
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
-enum {NONE, CONSTANT, TYPE};
+enum { NONE, CONSTANT, TYPE };
 
 /* ---------------------------------------------------------------------- */
 
-FixHeatFlow::FixHeatFlow(LAMMPS *lmp, int narg, char **arg) :
-  Fix(lmp, narg, arg)
+FixHeatFlow::FixHeatFlow(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
 {
-  if (narg < 4) utils::missing_cmd_args(FLERR,"fix heat/flow", error);
+  if (narg < 4) utils::missing_cmd_args(FLERR, "fix heat/flow", error);
 
   cp_style = NONE;
   comm_forward = 1;
   comm_reverse = 1;
 
   int ntypes = atom->ntypes;
-  if (strcmp(arg[3],"constant") == 0) {
-    if (narg != 5) error->all(FLERR,"Illegal fix heat/flow constant command");
+  if (strcmp(arg[3], "constant") == 0) {
+    if (narg != 5) error->all(FLERR, "Illegal fix heat/flow constant command");
     cp_style = CONSTANT;
-    cp = utils::numeric(FLERR,arg[4],false,lmp);
-    if (cp < 0.0) error->all(FLERR,"Illegal fix heat/flow constant command value");
-  } else if (strcmp(arg[3],"type") == 0) {
-    if (narg != 4 + ntypes) error->all(FLERR,"Illegal fix heat/flow type command");
+    cp = utils::numeric(FLERR, arg[4], false, lmp);
+    if (cp < 0.0) error->all(FLERR, "Illegal fix heat/flow constant command value");
+  } else if (strcmp(arg[3], "type") == 0) {
+    if (narg != 4 + ntypes) error->all(FLERR, "Illegal fix heat/flow type command");
     cp_style = TYPE;
-    memory->create(cp_type,ntypes+1,"fix_heat_flow:cp_type");
+    memory->create(cp_type, ntypes + 1, "fix_heat_flow:cp_type");
     for (int i = 1; i <= ntypes; i++) {
-      cp_type[i] = utils::numeric(FLERR,arg[3+i],false,lmp);
-      if (cp_type[i] < 0.0) error->all(FLERR,"Illegal fix heat/flow type command value");
+      cp_type[i] = utils::numeric(FLERR, arg[3 + i], false, lmp);
+      if (cp_type[i] < 0.0) error->all(FLERR, "Illegal fix heat/flow type command value");
     }
   } else {
-    error->all(FLERR,"Unknown fix heat/flow keyword {}", arg[3]);
+    error->all(FLERR, "Unknown fix heat/flow keyword {}", arg[3]);
   }
 
-  if (cp_style == NONE)
-    error->all(FLERR, "Must specify specific heat in fix heat/flow");
+  if (cp_style == NONE) error->all(FLERR, "Must specify specific heat in fix heat/flow");
   dynamic_group_allow = 1;
 }
 
@@ -80,9 +77,9 @@ void FixHeatFlow::init()
   dt = update->dt;
 
   if (!atom->temperature_flag)
-    error->all(FLERR,"Fix heat/flow requires atom style with temperature property");
+    error->all(FLERR, "Fix heat/flow requires atom style with temperature property");
   if (!atom->heatflow_flag)
-    error->all(FLERR,"Fix heat/flow requires atom style with heatflow property");
+    error->all(FLERR, "Fix heat/flow requires atom style with heatflow property");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -130,19 +127,14 @@ void FixHeatFlow::final_integrate()
   if (igroup == atom->firstgroup) nlocal = atom->nfirst;
 
   // add ghost contributions to heatflow if first instance of fix
-  if (first_flag)
-    comm->reverse_comm(this);
+  if (first_flag) comm->reverse_comm(this);
 
   if (rmass) {
     for (int i = 0; i < nlocal; i++)
-      if (mask[i] & groupbit) {
-        temperature[i] += dt * heatflow[i] / (calc_cp(i) * rmass[i]);
-      }
+      if (mask[i] & groupbit) temperature[i] += dt * heatflow[i] / (calc_cp(i) * rmass[i]);
   } else {
     for (int i = 0; i < nlocal; i++)
-      if (mask[i] & groupbit) {
-        temperature[i] += dt * heatflow[i] / (calc_cp(i) * mass[type[i]]);
-      }
+      if (mask[i] & groupbit) temperature[i] += dt * heatflow[i] / (calc_cp(i) * mass[type[i]]);
   }
 }
 
@@ -211,9 +203,7 @@ int FixHeatFlow::pack_reverse_comm(int n, int first, double *buf)
   int last = first + n;
   double *heatflow = atom->heatflow;
 
-  for (int i = first; i < last; i++) {
-    buf[m++] = heatflow[i];
-  }
+  for (int i = first; i < last; i++) { buf[m++] = heatflow[i]; }
 
   return m;
 }
@@ -225,6 +215,5 @@ void FixHeatFlow::unpack_reverse_comm(int n, int *list, double *buf)
   int m = 0;
   double *heatflow = atom->heatflow;
 
-  for (int i = 0; i < n; i++)
-    heatflow[list[i]] += buf[m++];
+  for (int i = 0; i < n; i++) heatflow[list[i]] += buf[m++];
 }

From a3b9914f62423731607a5d7f5d7e2b41658656b4 Mon Sep 17 00:00:00 2001
From: jbcouli <jbcouli@sandia.gov>
Date: Thu, 6 Jul 2023 17:48:49 -0600
Subject: [PATCH 351/396] make error messages consistent with keyword values
 yes/no. Allow coul weight for 1-2 bonds to be zero for break no to eliminate
 bonded atoms from neighbor list when bonds cannot break

---
 doc/src/Howto_bpm.rst           |  6 +++++-
 doc/src/bond_bpm_rotational.rst |  4 ++--
 doc/src/bond_bpm_spring.rst     |  4 ++--
 src/BPM/bond_bpm.cpp            | 18 +++++++++---------
 4 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst
index 8b84e96b99..1c30b177e7 100644
--- a/doc/src/Howto_bpm.rst
+++ b/doc/src/Howto_bpm.rst
@@ -107,7 +107,11 @@ bond lists is expensive.  By setting the lj weight for 1-2 bonds to
 zero, this turns off pairwise interactions.  Even though there are no
 charges in BPM models, setting a nonzero coul weight for 1-2 bonds
 ensures all bonded neighbors are still included in the neighbor list
-in case bonds break between neighbor list builds.
+in case bonds break between neighbor list builds. If bond breakage is
+disabled during a simulation run by setting the *break* keyword to *no*,
+a zero coul weight for 1-2 bonds can be used to exclude bonded neighbors
+from the neighbor list builds. This can be useful for post-processing,
+or to determine pair interaction properties between distinct bonded particles.
 
 To monitor the fracture of bonds in the system, all BPM bond styles
 have the ability to record instances of bond breakage to output using
diff --git a/doc/src/bond_bpm_rotational.rst b/doc/src/bond_bpm_rotational.rst
index cfacfde2cd..7459d491d6 100644
--- a/doc/src/bond_bpm_rotational.rst
+++ b/doc/src/bond_bpm_rotational.rst
@@ -234,8 +234,8 @@ This bond style is part of the BPM package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-By default if pair interactions are to be disabled, this bond style
-requires setting
+By default if pair interactions between bonded atoms are to be disabled,
+this bond style requires setting
 
 .. code-block:: LAMMPS
 
diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst
index 2376b8e077..04ff4d5991 100644
--- a/doc/src/bond_bpm_spring.rst
+++ b/doc/src/bond_bpm_spring.rst
@@ -191,8 +191,8 @@ This bond style is part of the BPM package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-By default if pair interactions are to be disabled, this bond style
-requires setting
+By default if pair interactions between bonded atoms are to be disabled,
+this bond style requires setting
 
 .. code-block:: LAMMPS
 
diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp
index d965a19067..4f3577b2ca 100644
--- a/src/BPM/bond_bpm.cpp
+++ b/src/BPM/bond_bpm.cpp
@@ -96,7 +96,7 @@ void BondBPM::init_style()
   if (overlay_flag) {
     if (force->special_lj[1] != 1.0)
       error->all(FLERR,
-                 "With overlay/pair, BPM bond styles require special_bonds weight of 1.0 for "
+                 "With overlay/pair yes, BPM bond styles require special_bonds weight of 1.0 for "
                  "first neighbors");
     if (id_fix_update) {
       modify->delete_fix(id_fix_update);
@@ -106,18 +106,18 @@ void BondBPM::init_style()
   } else {
     // Require atoms know about all of their bonds and if they break
     if (force->newton_bond && break_flag)
-      error->all(FLERR, "Without overlay/pair or break/no, BPM bond styles require Newton bond off");
+      error->all(FLERR, "With overlay/pair no, or break no, BPM bond styles require Newton bond off");
 
     // special lj must be 0 1 1 to censor pair forces between bonded particles
-    // special coulomb must be 1 1 1 to ensure all pairs are included in the
-    //   neighbor list and 1-3 and 1-4 special bond lists are skipped
     if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
       error->all(FLERR,
-                 "Without overlay/pair, BPM bond styles requires special LJ weights = 0,1,1");
-    if (force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 ||
-        force->special_coul[3] != 1.0)
+                 "With overlay/pair no, BPM bond styles require special LJ weights = 0,1,1");
+    // if bonds can break, special coulomb must be 1 1 1 to ensure all pairs are included in the
+    //    neighbor list and 1-3 and 1-4 special bond lists are skipped
+    if (break_flag && (force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 ||
+        force->special_coul[3] != 1.0))
       error->all(FLERR,
-                 "Without overlay/pair, BPM bond styles requires special Coulomb weights = 1,1,1");
+                 "With overlay/pair no, and break yes, BPM bond styles requires special Coulomb weights = 1,1,1");
 
     if (id_fix_dummy && break_flag) {
       id_fix_update = utils::strdup("BPM_UPDATE_SPECIAL_BONDS");
@@ -335,7 +335,7 @@ void BondBPM::read_restart(FILE *fp)
 void BondBPM::process_broken(int i, int j)
 {
   if (!break_flag)
-    error->one(FLERR, "BPM bond broke with break/no option");
+    error->one(FLERR, "BPM bond broke with break no option");
   if (fix_store_local) {
     for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j);
 

From 651ed1960d19de9c88b4822630b59d346cae8d64 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 7 Jul 2023 18:29:28 -0400
Subject: [PATCH 352/396] add per-atom data bugfix from Stan for fix ave/histo
 and fix ave/histo/weight

---
 src/fix_ave_histo.cpp        | 2 +-
 src/fix_ave_histo_weight.cpp | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index 157e43610a..0a2975bb2e 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -590,7 +590,7 @@ void FixAveHisto::end_of_step()
       } else if (kind == PERATOM) {
         if (j == 0) bin_atoms(val.val.f->vector_atom,1);
         else if (val.val.f->array_atom)
-          bin_atoms(val.val.f->array_atom[j-1],val.val.f->size_peratom_cols);
+          bin_atoms(&val.val.f->array_atom[0][j-1],val.val.f->size_peratom_cols);
 
       } else if (kind == LOCAL) {
         if (j == 0) bin_vector(val.val.f->size_local_rows,val.val.f->vector_local,1);
diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp
index 17dd00440e..181aa2a79d 100644
--- a/src/fix_ave_histo_weight.cpp
+++ b/src/fix_ave_histo_weight.cpp
@@ -212,7 +212,7 @@ void FixAveHistoWeight::end_of_step()
         weights = val.val.f->vector_atom;
         stride = 1;
       } else if (val.val.f->array_atom) {
-        weights = val.val.f->array_atom[j-1];
+        weights = &val.val.f->array_atom[0][j-1];
         stride = val.val.f->size_peratom_cols;
       }
     } else if (kind == LOCAL) {
@@ -339,7 +339,7 @@ void FixAveHistoWeight::end_of_step()
       if (j == 0)
         bin_atoms_weights(val.val.f->vector_atom,1,weights,stride);
       else if (val.val.f->array_atom)
-        bin_atoms_weights(val.val.f->array_atom[j-1],val.val.f->size_peratom_cols,
+        bin_atoms_weights(&val.val.f->array_atom[0][j-1],val.val.f->size_peratom_cols,
                           weights,stride);
 
 

From d6412dc97b86c0dc95a8f9a014ab75796bd6c12f Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndactrung@gmail.com>
Date: Sat, 8 Jul 2023 00:50:19 -0500
Subject: [PATCH 353/396] Attempted to resolve issues with switching from
 acctyp4 to acctyp3 in tep, fieldp since the changes in PR #3675, noting some
 changes with Intel OCL PR #3663

---
 lib/gpu/lal_base_amoeba.cpp |  5 +++++
 lib/gpu/lal_base_amoeba.h   |  2 +-
 lib/gpu/lal_hippo.cpp       | 16 ++++++++++------
 src/GPU/pair_amoeba_gpu.cpp | 30 +++++++++++++++---------------
 src/GPU/pair_hippo_gpu.cpp  | 30 +++++++++++++++---------------
 5 files changed, 46 insertions(+), 37 deletions(-)

diff --git a/lib/gpu/lal_base_amoeba.cpp b/lib/gpu/lal_base_amoeba.cpp
index 0821a33b06..c41c66fb5f 100644
--- a/lib/gpu/lal_base_amoeba.cpp
+++ b/lib/gpu/lal_base_amoeba.cpp
@@ -420,6 +420,11 @@ void BaseAmoebaT::compute_udirect2b(int *host_amtype, int *host_amgroup, double
   cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
   atom->add_extra_data();
 
+  if (_max_tep_size>_max_fieldp_size) {
+    _max_fieldp_size = _max_tep_size;
+    _fieldp.resize(_max_fieldp_size*6);
+  }
+
   *fieldp_ptr=_fieldp.host.begin();
 
   // specify the correct cutoff and alpha values
diff --git a/lib/gpu/lal_base_amoeba.h b/lib/gpu/lal_base_amoeba.h
index 0eaaafeb1e..f415b30334 100644
--- a/lib/gpu/lal_base_amoeba.h
+++ b/lib/gpu/lal_base_amoeba.h
@@ -203,7 +203,7 @@ class BaseAmoeba {
   virtual void update_fieldp(void **fieldp_ptr) {
     *fieldp_ptr=_fieldp.host.begin();
      // _fieldp store both arrays, one after another
-    _fieldp.update_host(_max_fieldp_size*8,false);
+    _fieldp.update_host(_max_fieldp_size*6,false);
   }
 
   /// setup a plan for FFT, where size is the number of elements
diff --git a/lib/gpu/lal_hippo.cpp b/lib/gpu/lal_hippo.cpp
index 24ffae8de2..8d6ad5dfb2 100644
--- a/lib/gpu/lal_hippo.cpp
+++ b/lib/gpu/lal_hippo.cpp
@@ -211,7 +211,7 @@ void HippoT::compute_repulsion(const int /*ago*/, const int inum_full,
 
   if (inum_full>this->_max_tep_size) {
     this->_max_tep_size=static_cast<int>(static_cast<double>(inum_full)*1.10);
-    this->_tep.resize(this->_max_tep_size*4);
+    this->_tep.resize(this->_max_tep_size*3);
   }
   *tep_ptr=this->_tep.host.begin();
 
@@ -226,7 +226,7 @@ void HippoT::compute_repulsion(const int /*ago*/, const int inum_full,
   repulsion(this->_eflag,this->_vflag);
 
   // copy tep from device to host
-  this->_tep.update_host(this->_max_tep_size*4,false);
+  this->_tep.update_host(this->_max_tep_size*3,false);
 }
 
 // ---------------------------------------------------------------------------
@@ -366,7 +366,7 @@ void HippoT::compute_multipole_real(const int /*ago*/, const int inum_full,
 
   if (inum_full>this->_max_tep_size) {
     this->_max_tep_size=static_cast<int>(static_cast<double>(inum_full)*1.10);
-    this->_tep.resize(this->_max_tep_size*4);
+    this->_tep.resize(this->_max_tep_size*3);
   }
   *tep_ptr=this->_tep.host.begin();
 
@@ -376,7 +376,7 @@ void HippoT::compute_multipole_real(const int /*ago*/, const int inum_full,
   multipole_real(this->_eflag,this->_vflag);
 
   // copy tep from device to host
-  this->_tep.update_host(this->_max_tep_size*4,false);
+  this->_tep.update_host(this->_max_tep_size*3,false);
 }
 
 // ---------------------------------------------------------------------------
@@ -434,6 +434,10 @@ void HippoT::compute_udirect2b(int * /*host_amtype*/, int * /*host_amgroup*/, do
   this->cast_extra_data(nullptr, nullptr, nullptr, host_uind, host_uinp, host_pval);
   this->atom->add_extra_data();
 
+  if (this->_max_tep_size>this->_max_fieldp_size) {
+    this->_max_fieldp_size = this->_max_tep_size;
+    this->_fieldp.resize(this->_max_fieldp_size*6);
+  }
   *fieldp_ptr=this->_fieldp.host.begin();
 
   this->_off2_polar = off2_polar;
@@ -442,7 +446,7 @@ void HippoT::compute_udirect2b(int * /*host_amtype*/, int * /*host_amgroup*/, do
 
   // copy field and fieldp from device to host (_fieldp store both arrays, one after another)
 
-  this->_fieldp.update_host(this->_max_fieldp_size*8,false);
+  this->_fieldp.update_host(this->_max_fieldp_size*6,false);
 }
 
 // ---------------------------------------------------------------------------
@@ -580,7 +584,7 @@ void HippoT::compute_polar_real(int * /*host_amtype*/, int * /*host_amgroup*/, d
   this->device->add_ans_object(this->ans);
 
   // copy tep from device to host
-  this->_tep.update_host(this->_max_tep_size*4,false);
+  this->_tep.update_host(this->_max_tep_size*3,false);
 }
 
 // ---------------------------------------------------------------------------
diff --git a/src/GPU/pair_amoeba_gpu.cpp b/src/GPU/pair_amoeba_gpu.cpp
index b7e1f8e118..8b3cf2cfea 100644
--- a/src/GPU/pair_amoeba_gpu.cpp
+++ b/src/GPU/pair_amoeba_gpu.cpp
@@ -745,15 +745,15 @@ void PairAmoebaGPU::udirect2b(double **field, double **fieldp)
     auto field_ptr = (float *)fieldp_pinned;
 
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       field[i][0] += field_ptr[idx];
       field[i][1] += field_ptr[idx+1];
       field[i][2] += field_ptr[idx+2];
     }
 
-    field_ptr += 4*inum;
+    field_ptr += 3*inum;
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       fieldp[i][0] += field_ptr[idx];
       fieldp[i][1] += field_ptr[idx+1];
       fieldp[i][2] += field_ptr[idx+2];
@@ -762,15 +762,15 @@ void PairAmoebaGPU::udirect2b(double **field, double **fieldp)
     auto field_ptr = (double *)fieldp_pinned;
 
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       field[i][0] += field_ptr[idx];
       field[i][1] += field_ptr[idx+1];
       field[i][2] += field_ptr[idx+2];
     }
 
-    field_ptr += 4*inum;
+    field_ptr += 3*inum;
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       fieldp[i][0] += field_ptr[idx];
       fieldp[i][1] += field_ptr[idx+1];
       fieldp[i][2] += field_ptr[idx+2];
@@ -976,15 +976,15 @@ void PairAmoebaGPU::ufield0c(double **field, double **fieldp)
     auto field_ptr = (float *)fieldp_pinned;
 
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       field[i][0] += field_ptr[idx];
       field[i][1] += field_ptr[idx+1];
       field[i][2] += field_ptr[idx+2];
     }
 
-    field_ptr += 4*inum;
+    field_ptr += 3*inum;
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       fieldp[i][0] += field_ptr[idx];
       fieldp[i][1] += field_ptr[idx+1];
       fieldp[i][2] += field_ptr[idx+2];
@@ -993,15 +993,15 @@ void PairAmoebaGPU::ufield0c(double **field, double **fieldp)
     auto field_ptr = (double *)fieldp_pinned;
 
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       field[i][0] += field_ptr[idx];
       field[i][1] += field_ptr[idx+1];
       field[i][2] += field_ptr[idx+2];
     }
 
-    field_ptr += 4*inum;
+    field_ptr += 3*inum;
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       fieldp[i][0] += field_ptr[idx];
       fieldp[i][1] += field_ptr[idx+1];
       fieldp[i][2] += field_ptr[idx+2];
@@ -2029,9 +2029,9 @@ void PairAmoebaGPU::compute_force_from_torque(const numtyp* tq_ptr,
   int nlocal = atom->nlocal;
 
   for (i = 0; i < nlocal; i++) {
-    _tq[0] = tq_ptr[4*i];
-    _tq[1] = tq_ptr[4*i+1];
-    _tq[2] = tq_ptr[4*i+2];
+    _tq[0] = tq_ptr[3*i];
+    _tq[1] = tq_ptr[3*i+1];
+    _tq[2] = tq_ptr[3*i+2];
     torque2force(i,_tq,fix,fiy,fiz,force_comp);
 
     iz = zaxis2local[i];
diff --git a/src/GPU/pair_hippo_gpu.cpp b/src/GPU/pair_hippo_gpu.cpp
index f87676ec08..256b4088d8 100644
--- a/src/GPU/pair_hippo_gpu.cpp
+++ b/src/GPU/pair_hippo_gpu.cpp
@@ -859,15 +859,15 @@ void PairHippoGPU::udirect2b(double **field, double **fieldp)
     auto field_ptr = (float *)fieldp_pinned;
 
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       field[i][0] += field_ptr[idx];
       field[i][1] += field_ptr[idx+1];
       field[i][2] += field_ptr[idx+2];
     }
 
-    field_ptr += 4*inum;
+    field_ptr += 3*inum;
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       fieldp[i][0] += field_ptr[idx];
       fieldp[i][1] += field_ptr[idx+1];
       fieldp[i][2] += field_ptr[idx+2];
@@ -877,15 +877,15 @@ void PairHippoGPU::udirect2b(double **field, double **fieldp)
 
     auto field_ptr = (double *)fieldp_pinned;
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       field[i][0] += field_ptr[idx];
       field[i][1] += field_ptr[idx+1];
       field[i][2] += field_ptr[idx+2];
     }
 
-    field_ptr += 4*inum;
+    field_ptr += 3*inum;
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       fieldp[i][0] += field_ptr[idx];
       fieldp[i][1] += field_ptr[idx+1];
       fieldp[i][2] += field_ptr[idx+2];
@@ -1087,15 +1087,15 @@ void PairHippoGPU::ufield0c(double **field, double **fieldp)
     auto *field_ptr = (float *)fieldp_pinned;
 
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       field[i][0] += field_ptr[idx];
       field[i][1] += field_ptr[idx+1];
       field[i][2] += field_ptr[idx+2];
     }
 
-    field_ptr += 4*inum;
+    field_ptr += 3*inum;
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       fieldp[i][0] += field_ptr[idx];
       fieldp[i][1] += field_ptr[idx+1];
       fieldp[i][2] += field_ptr[idx+2];
@@ -1105,15 +1105,15 @@ void PairHippoGPU::ufield0c(double **field, double **fieldp)
     auto *field_ptr = (double *)fieldp_pinned;
 
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       field[i][0] += field_ptr[idx];
       field[i][1] += field_ptr[idx+1];
       field[i][2] += field_ptr[idx+2];
     }
 
-    field_ptr += 4*inum;
+    field_ptr += 3*inum;
     for (int i = 0; i < nlocal; i++) {
-      int idx = 4*i;
+      int idx = 3*i;
       fieldp[i][0] += field_ptr[idx];
       fieldp[i][1] += field_ptr[idx+1];
       fieldp[i][2] += field_ptr[idx+2];
@@ -1456,9 +1456,9 @@ void PairHippoGPU::compute_force_from_torque(const numtyp* tq_ptr,
   int nlocal = atom->nlocal;
 
   for (i = 0; i < nlocal; i++) {
-    _tq[0] = tq_ptr[4*i];
-    _tq[1] = tq_ptr[4*i+1];
-    _tq[2] = tq_ptr[4*i+2];
+    _tq[0] = tq_ptr[3*i];
+    _tq[1] = tq_ptr[3*i+1];
+    _tq[2] = tq_ptr[3*i+2];
     torque2force(i,_tq,fix,fiy,fiz,force_comp);
 
     iz = zaxis2local[i];

From 75a2557e826eab29aaf277f2960b9bb7f438173e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 9 Jul 2023 15:41:39 -0400
Subject: [PATCH 354/396] fix bugs where an Atom::tag value was stored in an
 int and not a tagint

---
 src/MANYBODY/pair_gw.cpp                       | 3 ++-
 src/MGPT/pair_mgpt.cpp                         | 3 +--
 src/OPENMP/npair_half_nsq_newton_omp.cpp       | 4 ++--
 src/OPENMP/npair_half_respa_nsq_newton_omp.cpp | 4 ++--
 src/OPENMP/npair_half_size_nsq_newton_omp.cpp  | 4 ++--
 src/npair_half_respa_nsq_newton.cpp            | 4 ++--
 src/npair_half_size_nsq_newton.cpp             | 4 ++--
 7 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp
index be2a1e41f3..1fd98b80f0 100644
--- a/src/MANYBODY/pair_gw.cpp
+++ b/src/MANYBODY/pair_gw.cpp
@@ -73,7 +73,8 @@ PairGW::~PairGW()
 void PairGW::compute(int eflag, int vflag)
 {
   int i,j,k,ii,jj,kk,inum,jnum;
-  int itag,jtag,itype,jtype,ktype,iparam_ij,iparam_ijk;
+  int itype,jtype,ktype,iparam_ij,iparam_ijk;
+  tagint itag,jtag;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
   double rsq,rsq1,rsq2;
   double delr1[3],delr2[3],fi[3],fj[3],fk[3];
diff --git a/src/MGPT/pair_mgpt.cpp b/src/MGPT/pair_mgpt.cpp
index 5c4b889f8a..c924cbea84 100644
--- a/src/MGPT/pair_mgpt.cpp
+++ b/src/MGPT/pair_mgpt.cpp
@@ -589,8 +589,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
                           double *e_s,double *e_p,double *e_t,double *e_q,
                           int evflag,int newton_pair) {
   Hash<bond_data,Doublet> bond_hash(100000);
-  int i,j,k,m,ix,jx,kx,mx,itag,jtag,p;
-
+  int i,j,k,m,ix,jx,kx,mx,p;
   double e_single,e_pair,e_triplet,e_triplet_c,e_quad;
   double volvir2;
 
diff --git a/src/OPENMP/npair_half_nsq_newton_omp.cpp b/src/OPENMP/npair_half_nsq_newton_omp.cpp
index cb08cb7f7a..5996cd2013 100644
--- a/src/OPENMP/npair_half_nsq_newton_omp.cpp
+++ b/src/OPENMP/npair_half_nsq_newton_omp.cpp
@@ -49,8 +49,8 @@ void NPairHalfNsqNewtonOmp::build(NeighList *list)
 #endif
   NPAIR_OMP_SETUP(nlocal);
 
-  int i,j,n,itype,jtype,itag,jtag,which,imol,iatom;
-  tagint tagprev;
+  int i,j,n,itype,jtype,which,imol,iatom;
+  tagint itag,jtag,tagprev;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   int *neighptr;
 
diff --git a/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp b/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp
index 6604861f74..61d9165b1e 100644
--- a/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp
+++ b/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp
@@ -55,8 +55,8 @@ void NPairHalfRespaNsqNewtonOmp::build(NeighList *list)
 #endif
   NPAIR_OMP_SETUP(nlocal);
 
-  int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle,imol,iatom;
-  tagint tagprev;
+  int i,j,n,itype,jtype,n_inner,n_middle,imol,iatom;
+  tagint itag,jtag,tagprev;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   int *neighptr,*neighptr_inner,*neighptr_middle;
 
diff --git a/src/OPENMP/npair_half_size_nsq_newton_omp.cpp b/src/OPENMP/npair_half_size_nsq_newton_omp.cpp
index 35dc42ec5b..fe2a1be3da 100644
--- a/src/OPENMP/npair_half_size_nsq_newton_omp.cpp
+++ b/src/OPENMP/npair_half_size_nsq_newton_omp.cpp
@@ -58,8 +58,8 @@ void NPairHalfSizeNsqNewtonOmp::build(NeighList *list)
 #endif
   NPAIR_OMP_SETUP(nlocal);
 
-  int i,j,jh,n,itag,jtag,which,imol,iatom;
-  tagint tagprev;
+  int i,j,jh,n,which,imol,iatom;
+  tagint itag,jtag,tagprev;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   double radi,radsum,cutsq;
   int *neighptr;
diff --git a/src/npair_half_respa_nsq_newton.cpp b/src/npair_half_respa_nsq_newton.cpp
index 77d6af141f..d231cddb87 100644
--- a/src/npair_half_respa_nsq_newton.cpp
+++ b/src/npair_half_respa_nsq_newton.cpp
@@ -38,9 +38,9 @@ NPairHalfRespaNsqNewton::NPairHalfRespaNsqNewton(LAMMPS *lmp) : NPair(lmp) {}
 
 void NPairHalfRespaNsqNewton::build(NeighList *list)
 {
-  int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle,bitmask;
+  int i,j,n,itype,jtype,n_inner,n_middle,bitmask;
   int imol,iatom,moltemplate;
-  tagint tagprev;
+  tagint itag,jtag,tagprev;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   int *neighptr,*neighptr_inner,*neighptr_middle;
 
diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp
index 8b596e6968..93d65c7a45 100644
--- a/src/npair_half_size_nsq_newton.cpp
+++ b/src/npair_half_size_nsq_newton.cpp
@@ -39,8 +39,8 @@ NPairHalfSizeNsqNewton::NPairHalfSizeNsqNewton(LAMMPS *lmp) : NPair(lmp) {}
 
 void NPairHalfSizeNsqNewton::build(NeighList *list)
 {
-  int i,j,jh,n,itag,jtag,bitmask,which,imol,iatom,moltemplate;
-  tagint tagprev;
+  int i,j,jh,n,bitmask,which,imol,iatom,moltemplate;
+  tagint itag,jtag,tagprev;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   double radi,radsum,cutsq;
   int *neighptr;

From 0718114a67cdf5ff970965a4a457c280cd1f59d6 Mon Sep 17 00:00:00 2001
From: jbcouli <jbcouli@sandia.gov>
Date: Sun, 9 Jul 2023 17:43:39 -0600
Subject: [PATCH 355/396] fix typo for broken links in doc

---
 doc/src/fix_ave_grid.rst | 4 ++--
 doc/src/variable.rst     | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/doc/src/fix_ave_grid.rst b/doc/src/fix_ave_grid.rst
index 5760bb4508..da0d1f957b 100644
--- a/doc/src/fix_ave_grid.rst
+++ b/doc/src/fix_ave_grid.rst
@@ -129,12 +129,12 @@ overlays the simulation box.  For 2d simulations, *Nz* must be 1.  The
 very coarse compared to the particle count, or very fine.  If one or
 more of the values = 1, then bins are 2d planes or 1d slices of the
 simulation domain.  Note that if the total number of grid cells is
-small, it may be more efficient to use the doc:`fix ave/chunk
+small, it may be more efficient to use the :doc:`fix ave/chunk
 <fix_ave_chunk>` command which can treat a grid defined by the
 :doc:`compute chunk/atom <compute_chunk_atom>` command as a global
 grid where each processor owns a copy of all the grid cells.  If *Nx*
 = *Ny* = *Nz* = 1 is used, the same calculation would be more
-efficiently performed by the doc:`fix ave/atom <fix_ave_atom>`
+efficiently performed by the :doc:`fix ave/atom <fix_ave_atom>`
 command.
 
 If the simulation box size or shape changes during a simulation, the
diff --git a/doc/src/variable.rst b/doc/src/variable.rst
index 67600af62d..a9d21bab9b 100644
--- a/doc/src/variable.rst
+++ b/doc/src/variable.rst
@@ -1441,7 +1441,7 @@ timestep that the variable needs the tallies.  An input script can
 also request variables be evaluated before or after or in between
 runs, e.g. by including them in a :doc:`print <print>` command.
 
-LAMMPS keeps track of all of this as it performs a doc:`run <run>` or
+LAMMPS keeps track of all of this as it performs a :doc:`run <run>` or
 :doc:`minimize <minimize>` simulation, as well as in between
 simulations.  An error will be generated if you attempt to evaluate a
 variable when LAMMPS knows it cannot produce accurate values.  For
@@ -1453,7 +1453,7 @@ command, then an error will occur.
 
 However, there are two special cases to be aware when a variable
 requires invocation of a compute (directly or indirectly).  The first
-is if the variable is evaluated before the first doc:`run <run>` or
+is if the variable is evaluated before the first :doc:`run <run>` or
 :doc:`minimize <minimize>` command in the input script.  In this case,
 LAMMPS will generate an error.  This is because many computes require
 initializations which have not yet taken place.  One example is the
@@ -1463,10 +1463,10 @@ energy or virial quantities; these values are not tallied until the
 first simulation begins.
 
 The second special case is when a variable that depends on a compute
-is evaluated in between doc:`run <run>` or :doc:`minimize <minimize>`
+is evaluated in between :doc:`run <run>` or :doc:`minimize <minimize>`
 commands.  It is possible for other input script commands issued
 following the previous run, but before the variable is evaluated, to
-change the system.  For example, the doc:`delete_atoms <delete_atoms>`
+change the system.  For example, the :doc:`delete_atoms <delete_atoms>`
 command could be used to remove atoms.  Since the compute will not
 re-initialize itself until the next simulation or it may depend on
 energy/virial computations performed before the system was changed, it

From 60b45f97661a6d6506f771602f716620a39d1ce3 Mon Sep 17 00:00:00 2001
From: jbcouli <jbcouli@sandia.gov>
Date: Sun, 9 Jul 2023 18:01:19 -0600
Subject: [PATCH 356/396] correct error message

---
 doc/src/Howto_bpm.rst | 2 +-
 src/BPM/bond_bpm.cpp  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst
index 1c30b177e7..448a43a654 100644
--- a/doc/src/Howto_bpm.rst
+++ b/doc/src/Howto_bpm.rst
@@ -109,7 +109,7 @@ charges in BPM models, setting a nonzero coul weight for 1-2 bonds
 ensures all bonded neighbors are still included in the neighbor list
 in case bonds break between neighbor list builds. If bond breakage is
 disabled during a simulation run by setting the *break* keyword to *no*,
-a zero coul weight for 1-2 bonds can be used to exclude bonded neighbors
+a zero coul weight for 1-2 bonds can be used to exclude bonded atoms
 from the neighbor list builds. This can be useful for post-processing,
 or to determine pair interaction properties between distinct bonded particles.
 
diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp
index 4f3577b2ca..023988b64d 100644
--- a/src/BPM/bond_bpm.cpp
+++ b/src/BPM/bond_bpm.cpp
@@ -106,7 +106,7 @@ void BondBPM::init_style()
   } else {
     // Require atoms know about all of their bonds and if they break
     if (force->newton_bond && break_flag)
-      error->all(FLERR, "With overlay/pair no, or break no, BPM bond styles require Newton bond off");
+      error->all(FLERR, "With overlay/pair no, or break yes, BPM bond styles require Newton bond off");
 
     // special lj must be 0 1 1 to censor pair forces between bonded particles
     if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)

From 91b16c59452c64e7df22864c6fd3ad74442fb554 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 9 Jul 2023 21:10:44 -0400
Subject: [PATCH 357/396] make certain conductivity class member is always
 initialized

---
 src/GRANULAR/gran_sub_mod_heat.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/GRANULAR/gran_sub_mod_heat.cpp b/src/GRANULAR/gran_sub_mod_heat.cpp
index 75dcd30b73..c3dd9ea5dc 100644
--- a/src/GRANULAR/gran_sub_mod_heat.cpp
+++ b/src/GRANULAR/gran_sub_mod_heat.cpp
@@ -49,6 +49,7 @@ GranSubModHeatArea::GranSubModHeatArea(GranularModel *gm, LAMMPS *lmp) : GranSub
 {
   num_coeffs = 1;
   contact_radius_flag = 1;
+  conductivity = 0.0;
 }
 
 /* ---------------------------------------------------------------------- */

From 2607212363d2697a7d5d82f3f8615254b6fde20a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 9 Jul 2023 21:21:39 -0400
Subject: [PATCH 358/396] update for upstream changes

---
 src/GRANULAR/gran_sub_mod_heat.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/GRANULAR/gran_sub_mod_heat.cpp b/src/GRANULAR/gran_sub_mod_heat.cpp
index 9dffdfa7d7..5378a72fd4 100644
--- a/src/GRANULAR/gran_sub_mod_heat.cpp
+++ b/src/GRANULAR/gran_sub_mod_heat.cpp
@@ -49,6 +49,7 @@ GranSubModHeatRadius::GranSubModHeatRadius(GranularModel *gm, LAMMPS *lmp) : Gra
 {
   num_coeffs = 1;
   contact_radius_flag = 1;
+  conductivity = 0.0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -76,7 +77,7 @@ GranSubModHeatArea::GranSubModHeatArea(GranularModel *gm, LAMMPS *lmp) : GranSub
 {
   num_coeffs = 1;
   contact_radius_flag = 1;
-  conductivity = 0.0;
+  heat_transfer_coeff = 0.0;
 }
 
 /* ---------------------------------------------------------------------- */

From 55343d715c3597ff11d50a583a04d1e2d3b7dd00 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 9 Jul 2023 21:39:51 -0400
Subject: [PATCH 359/396] update URL

---
 doc/src/Bibliography.rst          | 2 +-
 doc/src/fix_electron_stopping.rst | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst
index 2d27d2e6f9..e9ea8b0925 100644
--- a/doc/src/Bibliography.rst
+++ b/doc/src/Bibliography.rst
@@ -203,7 +203,7 @@ Bibliography
    A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)
 
 **(CasP)**
-   CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
+   CasP webpage: http://www.casp-program.org/
 
 **(Cawkwell2012)**
    A.\  M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012).
diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst
index fa0fc763f5..a90d0932ee 100644
--- a/doc/src/fix_electron_stopping.rst
+++ b/doc/src/fix_electron_stopping.rst
@@ -204,7 +204,7 @@ The default is no limitation by region, and minneigh = 1.
 
 .. _CasP:
 
-**(CasP)** CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
+**(CasP)** CasP webpage: http://www.casp-program.org/
 
 .. _PASS:
 

From a4b3306b7cf1fccff293a6b75403c7036f98aac5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 10 Jul 2023 18:48:13 -0400
Subject: [PATCH 360/396] fix error message

---
 src/compute_property_atom.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp
index fbb9129b6e..c3c101b995 100644
--- a/src/compute_property_atom.cpp
+++ b/src/compute_property_atom.cpp
@@ -376,7 +376,7 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
       index[i] = atom->avec->property_atom(arg[iarg]);
       if (index[i] < 0)
         error->all(FLERR,"Invalid keyword {} for atom style {} in compute property/atom command ",
-                   atom->get_style(), arg[iarg]);
+                   arg[iarg], atom->get_style());
       pack_choice[i] = &ComputePropertyAtom::pack_atom_style;
     }
   }

From c63c9711d5942c6eea177bbb04f94713d28d3ca0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 10 Jul 2023 19:42:48 -0400
Subject: [PATCH 361/396] update remaining ellipsoid example dump output for
 OVITO compatibility

---
 examples/ASPHERE/ellipsoid/in.ellipsoid    |  6 +--
 examples/ASPHERE/ellipsoid/in.ellipsoid.mp |  6 +--
 examples/ellipse/in.ellipse.gayberne       | 53 ++++++++++----------
 examples/ellipse/in.ellipse.resquared      | 56 ++++++++++++----------
 4 files changed, 61 insertions(+), 60 deletions(-)

diff --git a/examples/ASPHERE/ellipsoid/in.ellipsoid b/examples/ASPHERE/ellipsoid/in.ellipsoid
index 2dda95a029..1ee59597da 100644
--- a/examples/ASPHERE/ellipsoid/in.ellipsoid
+++ b/examples/ASPHERE/ellipsoid/in.ellipsoid
@@ -35,8 +35,7 @@ fix             2 all enforce2d
 compute         rot big temp/asphere
 compute         0 all property/atom quatw quati quatj quatk shapex shapey shapez
 
-#dump           1 all custom 10 dump.ellipsoid.equil id type x y z &
-#                 c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
+#dump           1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
 #dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
 #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
 
@@ -110,8 +109,7 @@ thermo_style    custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
 thermo_modify   temp tbig
 thermo          1000
 
-#dump           1 all custom 1000 dump.ellipsoid id type x y z &
-#                 c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
+#dump           1 all custom 1000 dump.ellipsoid id type x y z c_0[*]
 #dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
 #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
 
diff --git a/examples/ASPHERE/ellipsoid/in.ellipsoid.mp b/examples/ASPHERE/ellipsoid/in.ellipsoid.mp
index e950cc86f5..31fe79eb58 100644
--- a/examples/ASPHERE/ellipsoid/in.ellipsoid.mp
+++ b/examples/ASPHERE/ellipsoid/in.ellipsoid.mp
@@ -35,8 +35,7 @@ fix             2 all enforce2d
 compute         rot big temp/asphere
 compute         0 all property/atom quatw quati quatj quatk shapex shapey shapez
 
-#dump           1 all custom 10 dump.ellipsoid.equil id type x y z &
-#                 c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
+#dump           1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
 #dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
 #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
 
@@ -111,8 +110,7 @@ thermo_style    custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
 thermo_modify   temp tbig
 thermo          1000
 
-#dump           1 all custom 500 dump.ellipsoid id type x y z &
-#                 c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
+#dump           1 all custom 500 dump.ellipsoid id type x y z c_0[*]
 #dump_modify    1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
 #                 colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
 
diff --git a/examples/ellipse/in.ellipse.gayberne b/examples/ellipse/in.ellipse.gayberne
index fe783ac6de..0e6b21797a 100644
--- a/examples/ellipse/in.ellipse.gayberne
+++ b/examples/ellipse/in.ellipse.gayberne
@@ -1,23 +1,23 @@
 # GayBerne ellipsoids in LJ background fluid
 
-units	     lj
+units        lj
 atom_style   ellipsoid
 dimension    2
 
-lattice	     sq 0.02
-region	     box block 0 20 0 20 -0.5 0.5
+lattice      sq 0.02
+region       box block 0 20 0 20 -0.5 0.5
 create_box   2 box
 create_atoms 1 box
 
-set	     group all type/fraction 2 0.1 95392
-set 	     type 1 mass 1.0
-set 	     type 2 mass 1.5
-set 	     type 1 shape 1 1 1
-set 	     type 2 shape 3 1 1
-set	     group all quat/random 18238
+set          group all type/fraction 2 0.1 95392
+set          type 1 mass 1.0
+set          type 2 mass 1.5
+set          type 1 shape 1 1 1
+set          type 2 shape 3 1 1
+set          group all quat/random 18238
 
-compute	     rot all temp/asphere
-group	     spheroid type 1
+compute      rot all temp/asphere
+group        spheroid type 1
 variable     dof equal count(spheroid)+2
 compute_modify rot extra/dof ${dof}
 
@@ -31,36 +31,37 @@ pair_coeff   2 2 1.0 1.0 1 1 0.2 0 0 0
 neighbor     0.8 bin
 
 thermo_style custom step c_rot epair etotal press vol
-thermo	     100
+thermo       100
 
 timestep     0.002
 
-compute	     q all property/atom quatw quati quatj quatk
+compute      0 all property/atom quatw quati quatj quatk shapex shapey shapez
 
-#dump	     1 all custom 100 dump.ellipse.gayberne &
-#	     id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
+dump        1 all custom 100 dump.ellipse.gayberne id type x y z c_0[*]
+dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
+              colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
 
-#dump	     2 all image 100 image.*.jpg type type &
-#	     zoom 1.6 center d 0.5 0.5 0.5
+#dump        2 all image 100 image.*.jpg type type &
+#            zoom 1.6 center d 0.5 0.5 0.5
 #dump_modify  2 pad 4 adiam 1 1.0 adiam 2 2.0
 
-#dump	     3 all movie 100 movie.mpg type type &
-#	     zoom 1.6 center d 0.5 0.5 0.5
+#dump        3 all movie 100 movie.mpg type type &
+#            zoom 1.6 center d 0.5 0.5 0.5
 #dump_modify  3 pad 4 adiam 1 1.0 adiam 2 2.0
 
-fix	     1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
-	       mtk no pchain 0 tchain 1
-fix	     2 all enforce2d
+fix          1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
+               mtk no pchain 0 tchain 1
+fix          2 all enforce2d
 
 compute_modify 1_temp extra/dof ${dof}
 
 # equilibrate to shrink box around dilute system
 
-run	     2000
+run          2000
 
 # run dynamics on dense system
 
-unfix	     1
-fix	     1 all nve/asphere
+unfix        1
+fix          1 all nve/asphere
 
-run	     2000
+run          2000
diff --git a/examples/ellipse/in.ellipse.resquared b/examples/ellipse/in.ellipse.resquared
index 82398987f8..d5bc8897cb 100644
--- a/examples/ellipse/in.ellipse.resquared
+++ b/examples/ellipse/in.ellipse.resquared
@@ -1,23 +1,23 @@
 # RESquared ellipsoids in LJ background fluid
 
-units	     lj
+units        lj
 atom_style   ellipsoid
 dimension    2
 
-lattice	     sq 0.02
-region	     box block 0 20 0 20 -0.5 0.5
+lattice      sq 0.02
+region       box block 0 20 0 20 -0.5 0.5
 create_box   2 box
 create_atoms 1 box
 
-set	     group all type/fraction 2 0.1 95392
-set 	     type 1 mass 1.0
-set 	     type 2 mass 1.5
-set 	     type 1 shape 1 1 1
-set 	     type 2 shape 3 1 1
-set	     group all quat/random 18238
+set          group all type/fraction 2 0.1 95392
+set          type 1 mass 1.0
+set          type 2 mass 1.5
+set          type 1 shape 1 1 1
+set          type 2 shape 3 1 1
+set          group all quat/random 18238
 
-compute	     rot all temp/asphere
-group	     spheroid type 1
+compute      rot all temp/asphere
+group        spheroid type 1
 variable     dof equal count(spheroid)+2
 compute_modify rot extra/dof ${dof}
 
@@ -31,36 +31,40 @@ pair_coeff   2 2 1.0 1 1 1 0.2 0 0 0
 neighbor     0.8 bin
 
 thermo_style custom step c_rot epair etotal press vol
-thermo	     100
+thermo       100
 
 timestep     0.002
 
-compute	     q all property/atom quatw quati quatj quatk
+compute      0 all property/atom quatw quati quatj quatk shapex shapey shapez
 
-#dump	     1 all custom 100 dump.ellipse.resquared &
-#	     id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
+dump        1 all custom 100 dump.ellipse.resquared id type x y z c_0[*]
+dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
+              colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
 
-#dump	     2 all image 100 image.*.jpg type type &
-#	     zoom 1.6 center d 0.5 0.5 0.5
+#dump        1 all custom 100 dump.ellipse.resquared &
+#            id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
+
+#dump        2 all image 100 image.*.jpg type type &
+#            zoom 1.6 center d 0.5 0.5 0.5
 #dump_modify  2 pad 4 adiam 1 1.0 adiam 2 2.0
 
-#dump	     3 all movie 100 movie.mpg type type &
-#	     zoom 1.6 center d 0.5 0.5 0.5
+#dump        3 all movie 100 movie.mpg type type &
+#            zoom 1.6 center d 0.5 0.5 0.5
 #dump_modify  3 pad 4 adiam 1 1.0 adiam 2 2.0
 
-fix	     1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
-	       mtk no pchain 0 tchain 1
-fix	     2 all enforce2d
+fix          1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
+               mtk no pchain 0 tchain 1
+fix          2 all enforce2d
 
 compute_modify 1_temp extra/dof ${dof}
 
 # equilibrate to shrink box around dilute system
 
-run	     2000
+run          2000
 
 # run dynamics on dense system
 
-unfix	     1
-fix	     1 all nve/asphere
+unfix        1
+fix          1 all nve/asphere
 
-run	     2000
+run          2000

From 4d8ef552c4e4f2d894be6458054d186f246a0f3f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 10 Jul 2023 22:42:49 -0400
Subject: [PATCH 362/396] remove dead code, trim namespace imports

---
 src/DIELECTRIC/fix_polarize_bem_gmres.cpp  | 1 -
 src/DIELECTRIC/fix_polarize_functional.cpp | 9 +++------
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp
index 3945b76641..40f7d0c853 100644
--- a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp
+++ b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp
@@ -350,7 +350,6 @@ void FixPolarizeBEMGMRES::compute_induced_charges()
   double *ed = atom->ed;
   double *em = atom->em;
   double *epsilon = atom->epsilon;
-  int *mask = atom->mask;
   int nlocal = atom->nlocal;
   int eflag = 1;
   int vflag = 0;
diff --git a/src/DIELECTRIC/fix_polarize_functional.cpp b/src/DIELECTRIC/fix_polarize_functional.cpp
index ab039f9c48..dd0c0eb648 100644
--- a/src/DIELECTRIC/fix_polarize_functional.cpp
+++ b/src/DIELECTRIC/fix_polarize_functional.cpp
@@ -55,9 +55,9 @@
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
-using namespace MathExtra;
-using namespace MathConst;
-using namespace MathSpecial;
+using MathConst::MY_PI;
+using MathConst::MY_PIS;
+using MathSpecial::square;
 
 //#define _POLARIZE_DEBUG
 
@@ -378,10 +378,7 @@ void FixPolarizeFunctional::update_induced_charges()
   // assign charges to the particles in the group
 
   double *q_scaled = atom->q_scaled;
-  double *q = atom->q;
-  double *epsilon = atom->epsilon;
   int nlocal = atom->nlocal;
-  double tmp = 0;
 
   for (int i = 0; i < nlocal; i++) {
     if (induced_charge_idx[i] < 0) continue;

From 564a8e88c127926ae1ce84a75cbf1d4c129acf6a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 11 Jul 2023 10:31:16 -0400
Subject: [PATCH 363/396] use blanks on both sides of comparison operators not
 only one, remove blanks next to parenthesis

---
 purge-workflows.py                            | 22 +++++++++++++++++++
 src/EFF/pair_eff_cut.cpp                      |  4 ++--
 src/EXTRA-DUMP/dump_xtc.cpp                   |  2 +-
 src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp |  2 +-
 src/EXTRA-PAIR/pair_lj_relres.cpp             |  2 +-
 src/INTEL/fix_intel.cpp                       |  2 +-
 src/INTERLAYER/pair_ilp_tmd.cpp               |  4 ++--
 src/KIM/pair_kim.cpp                          |  3 +--
 src/KOKKOS/mliap_so3_kokkos.cpp               |  2 +-
 src/KOKKOS/neigh_bond_kokkos.cpp              |  4 ++--
 src/MANYBODY/pair_comb3.cpp                   |  6 ++---
 src/MANYBODY/pair_lcbop.cpp                   |  2 +-
 src/MISC/fix_ipi.cpp                          | 12 +++++-----
 src/MISC/pair_agni.cpp                        |  2 +-
 src/OPENMP/npair_full_bin_ghost_omp.cpp       |  2 +-
 src/OPENMP/npair_full_bin_omp.cpp             |  2 +-
 src/OPENMP/npair_full_nsq_ghost_omp.cpp       |  2 +-
 src/OPENMP/npair_full_nsq_omp.cpp             |  2 +-
 .../npair_half_bin_newtoff_ghost_omp.cpp      |  2 +-
 src/OPENMP/npair_half_bin_newtoff_omp.cpp     |  2 +-
 src/OPENMP/npair_half_bin_newton_omp.cpp      |  4 ++--
 src/OPENMP/npair_half_bin_newton_tri_omp.cpp  |  2 +-
 .../npair_half_multi_old_newtoff_omp.cpp      |  2 +-
 .../npair_half_multi_old_newton_omp.cpp       |  4 ++--
 .../npair_half_multi_old_newton_tri_omp.cpp   |  2 +-
 .../npair_half_nsq_newtoff_ghost_omp.cpp      |  2 +-
 src/OPENMP/npair_half_nsq_newtoff_omp.cpp     |  2 +-
 src/OPENMP/npair_half_nsq_newton_omp.cpp      |  2 +-
 .../npair_half_respa_bin_newtoff_omp.cpp      |  2 +-
 .../npair_half_respa_bin_newton_omp.cpp       |  4 ++--
 .../npair_half_respa_bin_newton_tri_omp.cpp   |  2 +-
 .../npair_half_respa_nsq_newtoff_omp.cpp      |  2 +-
 .../npair_half_respa_nsq_newton_omp.cpp       |  2 +-
 .../npair_half_size_bin_newtoff_omp.cpp       |  2 +-
 src/OPENMP/npair_half_size_bin_newton_omp.cpp |  4 ++--
 .../npair_half_size_bin_newton_tri_omp.cpp    |  2 +-
 .../npair_half_size_multi_newtoff_omp.cpp     |  4 ++--
 .../npair_half_size_multi_newton_omp.cpp      |  4 ++--
 .../npair_half_size_multi_newton_tri_omp.cpp  |  2 +-
 .../npair_half_size_multi_old_newtoff_omp.cpp |  2 +-
 .../npair_half_size_multi_old_newton_omp.cpp  |  4 ++--
 ...air_half_size_multi_old_newton_tri_omp.cpp |  2 +-
 .../npair_half_size_nsq_newtoff_omp.cpp       |  2 +-
 src/OPENMP/npair_half_size_nsq_newton_omp.cpp |  2 +-
 src/PHONON/dynamical_matrix.cpp               |  2 +-
 src/PHONON/third_order.cpp                    |  2 +-
 src/REACTION/fix_bond_react.cpp               |  6 ++---
 src/REAXFF/fix_reaxff_bonds.cpp               |  2 +-
 src/SMTBQ/pair_smtbq.cpp                      | 16 +++++++-------
 src/VTK/dump_vtk.cpp                          |  2 +-
 src/atom.cpp                                  |  8 +++----
 src/library.cpp                               | 20 ++++++++---------
 src/read_restart.cpp                          | 14 ++++++------
 src/variable.cpp                              |  6 ++---
 54 files changed, 121 insertions(+), 100 deletions(-)
 create mode 100644 purge-workflows.py

diff --git a/purge-workflows.py b/purge-workflows.py
new file mode 100644
index 0000000000..73b7d22f7a
--- /dev/null
+++ b/purge-workflows.py
@@ -0,0 +1,22 @@
+from yaml import load
+import subprocess
+try:
+    from yaml import CLoader as Loader
+except ImportError:
+    from yaml import Loader
+
+runs = subprocess.check_output('gh api repos/lammps/lammps/actions/runs',shell=True)
+data = load(runs,Loader=Loader)
+while data['total_count'] > 3:
+    print('remaining: ', data['total_count'])
+    num=1
+    for d in data['workflow_runs']:
+        print(num, d['id'],d['name'],d['run_number'])
+        num += 1
+        if num > 4:
+            subprocess.call('gh api -X DELETE repos/lammps/lammps/actions/runs/' + str(d['id']), shell=True)
+            #print('gh api -X DELETE repos/lammps/lammps/actions/runs/' + str(d['id']))
+        else:
+            print('skip')
+    runs = subprocess.check_output('gh api repos/lammps/lammps/actions/runs',shell=True)
+    data = load(runs,Loader=Loader)
diff --git a/src/EFF/pair_eff_cut.cpp b/src/EFF/pair_eff_cut.cpp
index 1cfe5cd1dd..5f32de9912 100644
--- a/src/EFF/pair_eff_cut.cpp
+++ b/src/EFF/pair_eff_cut.cpp
@@ -921,13 +921,13 @@ void PairEffCut::coeff(int narg, char **arg)
   } else {
     int ecp;
     ecp = utils::inumeric(FLERR,arg[0],false,lmp);
-    if (strcmp(arg[1],"s") ==0) {
+    if (strcmp(arg[1],"s") == 0) {
       PAULI_CORE_A[ecp_type[ecp]] = utils::numeric(FLERR,arg[2],false,lmp);
       PAULI_CORE_B[ecp_type[ecp]] = utils::numeric(FLERR,arg[3],false,lmp);
       PAULI_CORE_C[ecp_type[ecp]] = utils::numeric(FLERR,arg[4],false,lmp);
       PAULI_CORE_D[ecp_type[ecp]] = 0.0;
       PAULI_CORE_E[ecp_type[ecp]] = 0.0;
-    } else if (strcmp(arg[1],"p") ==0) {
+    } else if (strcmp(arg[1],"p") == 0) {
       PAULI_CORE_A[ecp_type[ecp]] = utils::numeric(FLERR,arg[2],false,lmp);
       PAULI_CORE_B[ecp_type[ecp]] = utils::numeric(FLERR,arg[3],false,lmp);
       PAULI_CORE_C[ecp_type[ecp]] = utils::numeric(FLERR,arg[4],false,lmp);
diff --git a/src/EXTRA-DUMP/dump_xtc.cpp b/src/EXTRA-DUMP/dump_xtc.cpp
index ba3f740cf7..798bdcb391 100644
--- a/src/EXTRA-DUMP/dump_xtc.cpp
+++ b/src/EXTRA-DUMP/dump_xtc.cpp
@@ -740,7 +740,7 @@ static void receiveints(int buf[], const int num_of_ints, int num_of_bits,
   }
   for (i = num_of_ints-1; i > 0; i--) {
     num = 0;
-    for (j = num_of_bytes-1; j >=0; j--) {
+    for (j = num_of_bytes-1; j >= 0; j--) {
       num = (num << 8) | bytes[j];
       p = num / sizes[i];
       bytes[j] = p;
diff --git a/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp b/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp
index c0b44530e8..c435cc14ae 100644
--- a/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp
+++ b/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp
@@ -109,7 +109,7 @@ FixWallReflectStochastic(LAMMPS *lmp, int narg, char **arg) :
       for (int dir = 0; dir < 3; dir++) {
         wallvel[nwall][dir]= utils::numeric(FLERR,arg[iarg+dir+3],false,lmp);
         int dim = wallwhich[nwall] / 2;
-        if ((wallvel[nwall][dir] !=0) & (dir == dim))
+        if ((wallvel[nwall][dir] != 0) & (dir == dim))
           error->all(FLERR,"The wall velocity must be tangential");
 
         // DIFFUSIVE = no accommodation coeffs
diff --git a/src/EXTRA-PAIR/pair_lj_relres.cpp b/src/EXTRA-PAIR/pair_lj_relres.cpp
index 85d0a04bf9..1826f3f1db 100644
--- a/src/EXTRA-PAIR/pair_lj_relres.cpp
+++ b/src/EXTRA-PAIR/pair_lj_relres.cpp
@@ -453,7 +453,7 @@ double PairLJRelRes::init_one(int i, int j)
     offset[i][j] = 0.0;
   }
 
-  if (epsilonf[i][j] != 0 ) {  // fg (cut=cutf coefficients)
+  if (epsilonf[i][j] != 0) {  // fg (cut=cutf coefficients)
     ljf1[i][j] = 48.0 * epsilonf[i][j] * pow(sigmaf[i][j],12.0);
     ljf2[i][j] = 24.0 * epsilonf[i][j] * pow(sigmaf[i][j],6.0);
     ljf3[i][j] = 4.0 * epsilonf[i][j] * pow(sigmaf[i][j],12.0);
diff --git a/src/INTEL/fix_intel.cpp b/src/INTEL/fix_intel.cpp
index 4c46608677..0a3d27a978 100644
--- a/src/INTEL/fix_intel.cpp
+++ b/src/INTEL/fix_intel.cpp
@@ -430,7 +430,7 @@ void FixIntel::pair_init_check(const bool cdmessage)
     double *time1 = off_watch_pair();
     double *time2 = off_watch_neighbor();
     int *overflow = get_off_overflow_flag();
-    if (_offload_balance !=0.0) {
+    if (_offload_balance != 0.0) {
       #pragma offload_transfer target(mic:_cop)  \
         nocopy(time1,time2:length(1) alloc_if(1) free_if(0)) \
         in(overflow:length(5) alloc_if(1) free_if(0))
diff --git a/src/INTERLAYER/pair_ilp_tmd.cpp b/src/INTERLAYER/pair_ilp_tmd.cpp
index fd3a2f8c6f..8b08de39c0 100644
--- a/src/INTERLAYER/pair_ilp_tmd.cpp
+++ b/src/INTERLAYER/pair_ilp_tmd.cpp
@@ -481,11 +481,11 @@ void PairILPTMD::calc_normal()
           jH2 = atom->map(tag[i] - 2);
           iH1 = map[type[jH1]];
           iH2 = map[type[jH2]];
-          if (strcmp(elements[iH1], "Ow") == 0 ) {
+          if (strcmp(elements[iH1], "Ow") == 0) {
             vect[0][0] = x[jH1][0] - xtp;
             vect[0][1] = x[jH1][1] - ytp;
             vect[0][2] = x[jH1][2] - ztp;
-          } else if (strcmp(elements[iH2], "Ow") == 0 ) {
+          } else if (strcmp(elements[iH2], "Ow") == 0) {
             vect[0][0] = x[jH2][0] - xtp;
             vect[0][1] = x[jH2][1] - ytp;
             vect[0][2] = x[jH2][2] - ztp;
diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp
index 8ac6fe1f75..e0fc90ea46 100644
--- a/src/KIM/pair_kim.cpp
+++ b/src/KIM/pair_kim.cpp
@@ -198,8 +198,7 @@ PairKIM::~PairKIM()
 void PairKIM::set_contributing()
 {
   int const nall = atom->nlocal + atom->nghost;
-  for (int i = 0; i < nall; ++i)
-    kim_particleContributing[i] = ( (i < atom->nlocal) ? 1 : 0 );
+  for (int i = 0; i < nall; ++i) kim_particleContributing[i] = (i < atom->nlocal) ? 1 : 0;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/mliap_so3_kokkos.cpp b/src/KOKKOS/mliap_so3_kokkos.cpp
index 128e0f0a0c..bfdf4af0aa 100644
--- a/src/KOKKOS/mliap_so3_kokkos.cpp
+++ b/src/KOKKOS/mliap_so3_kokkos.cpp
@@ -856,7 +856,7 @@ void MLIAP_SO3Kokkos<DeviceType>::spectrum_dxdr(int nlocal, DAT::tdual_int_1d nu
     memoryKK->create_kokkos(m_clisttot_i, nlocal, m_nmax, m_numYlms, "MLIAP_SO3Kokkos:m_clisttot_i");
     int num_of_temp = std::min(nlocal, m_chunk_size);
     int delta=num_of_temp-m_ulist_r.extent(0);
-    if (delta > 0 ){
+    if (delta > 0){
       memoryKK->destroy_kokkos(m_ulist_r);
       memoryKK->create_kokkos(m_ulist_r, num_of_temp, m_idxu_count, "MLIAP_SO3Kokkos:m_ulist_r");
       memoryKK->destroy_kokkos(m_ulist_i);
diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp
index 9067284426..4cfe440b1f 100644
--- a/src/KOKKOS/neigh_bond_kokkos.cpp
+++ b/src/KOKKOS/neigh_bond_kokkos.cpp
@@ -266,7 +266,7 @@ void NeighBondKokkos<DeviceType>::bond_all()
 
   int all;
   MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
-  if (all && me ==0)
+  if (all && me == 0)
     error->warning(FLERR,"Bond atoms missing at step {}", update->ntimestep);
 
   k_bondlist.modify<DeviceType>();
@@ -345,7 +345,7 @@ void NeighBondKokkos<DeviceType>::bond_partial()
 
   int all;
   MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
-  if (all && me ==0)
+  if (all && me == 0)
     error->warning(FLERR,"Bond atoms missing at step {}", update->ntimestep);
 
   k_bondlist.modify<DeviceType>();
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index ac1ac0ea62..a6a6ed37fd 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -593,9 +593,9 @@ void PairComb3::read_file(char *file)
 
       if (params[nparams].lambda < 0.0 || params[nparams].powern < 0.0 ||
           params[nparams].beta < 0.0 || params[nparams].alpha1 < 0.0 ||
-          params[nparams].bigB1< 0.0 || params[nparams].bigA< 0.0 ||
-          params[nparams].bigB2< 0.0 || params[nparams].alpha2 <0.0 ||
-          params[nparams].bigB3< 0.0 || params[nparams].alpha3 <0.0 ||
+          params[nparams].bigB1 < 0.0 || params[nparams].bigA < 0.0 ||
+          params[nparams].bigB2 < 0.0 || params[nparams].alpha2 < 0.0 ||
+          params[nparams].bigB3 < 0.0 || params[nparams].alpha3 < 0.0 ||
           params[nparams].bigr < 0.0 || params[nparams].bigd < 0.0 ||
           params[nparams].bigd > params[nparams].bigr ||
           params[nparams].powerm - params[nparams].powermint != 0.0 ||
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index 65191ae85e..ed085c4b98 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -115,7 +115,7 @@ void PairLCBOP::allocate()
 ------------------------------------------------------------------------- */
 
 void PairLCBOP::settings(int narg, char **/*arg*/) {
-  if (narg != 0 ) error->all(FLERR,"Illegal pair_style command");
+  if (narg != 0) error->all(FLERR,"Illegal pair_style command");
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/MISC/fix_ipi.cpp b/src/MISC/fix_ipi.cpp
index 9411fa763d..69e0f2a7f3 100644
--- a/src/MISC/fix_ipi.cpp
+++ b/src/MISC/fix_ipi.cpp
@@ -284,17 +284,17 @@ void FixIPI::initial_integrate(int /*vflag*/)
       // while i-PI just asks for status, signal we are ready and wait
       readbuffer(ipisock, header, MSGLEN, error); header[MSGLEN]=0;
 
-      if (strcmp(header,"STATUS      ") == 0 )
+      if (strcmp(header,"STATUS      ") == 0)
         writebuffer(ipisock,"READY       ",MSGLEN, error);
       else break;
     }
 
-    if (strcmp(header,"EXIT        ") == 0 )
+    if (strcmp(header,"EXIT        ") == 0)
       error->one(FLERR, "Got EXIT message from i-PI. Now leaving!");
 
     // when i-PI signals it has positions to evaluate new forces,
     // read positions and cell data
-    if (strcmp(header,"POSDATA     ") == 0 )  {
+    if (strcmp(header,"POSDATA     ") == 0)  {
       readbuffer(ipisock, (char*) cellh, 9*8, error);
       readbuffer(ipisock, (char*) cellih, 9*8, error);
       readbuffer(ipisock, (char*) &nat, 4, error);
@@ -454,15 +454,15 @@ void FixIPI::final_integrate()
     while (true) {
       readbuffer(ipisock, header, MSGLEN, error); header[MSGLEN]=0;
 
-      if (strcmp(header,"STATUS      ") == 0 )
+      if (strcmp(header,"STATUS      ") == 0)
         writebuffer(ipisock,"HAVEDATA    ",MSGLEN, error);
       else break;
     }
 
-    if (strcmp(header,"EXIT        ") == 0 )
+    if (strcmp(header,"EXIT        ") == 0)
       error->one(FLERR, "Got EXIT message from i-PI. Now leaving!");
 
-    if (strcmp(header,"GETFORCE    ") == 0 )  {
+    if (strcmp(header,"GETFORCE    ") == 0)  {
       writebuffer(ipisock,"FORCEREADY  ",MSGLEN, error);
       writebuffer(ipisock,(char*) &pot,8, error);
       writebuffer(ipisock,(char*) &nat,4, error);
diff --git a/src/MISC/pair_agni.cpp b/src/MISC/pair_agni.cpp
index 539c0ca00f..8597e5db93 100644
--- a/src/MISC/pair_agni.cpp
+++ b/src/MISC/pair_agni.cpp
@@ -347,7 +347,7 @@ void PairAGNI::read_file(char *filename)
             curparam = -1;
           } else error->warning(FLERR,"Ignoring unknown tag '{}' in AGNI potential file.",tag);
         } else {
-          if (params && wantdata >=0) {
+          if (params && wantdata >= 0) {
             if ((int)values.count() == params[wantdata].numeta + 2) {
               for (k = 0; k < params[wantdata].numeta; ++k)
                 params[wantdata].xU[k][fp_counter] = values.next_double();
diff --git a/src/OPENMP/npair_full_bin_ghost_omp.cpp b/src/OPENMP/npair_full_bin_ghost_omp.cpp
index 5723a418f5..0825d61b49 100644
--- a/src/OPENMP/npair_full_bin_ghost_omp.cpp
+++ b/src/OPENMP/npair_full_bin_ghost_omp.cpp
@@ -114,7 +114,7 @@ void NPairFullBinGhostOmp::build(NeighList *list)
             if (molecular != Atom::ATOMIC) {
               if (!moltemplate)
                 which = find_special(special[i],nspecial[i],tag[j]);
-              else if (imol >=0)
+              else if (imol >= 0)
                 which = find_special(onemols[imol]->special[iatom],
                                      onemols[imol]->nspecial[iatom],
                                      tag[j]-tagprev);
diff --git a/src/OPENMP/npair_full_bin_omp.cpp b/src/OPENMP/npair_full_bin_omp.cpp
index 94668002a9..65af519850 100644
--- a/src/OPENMP/npair_full_bin_omp.cpp
+++ b/src/OPENMP/npair_full_bin_omp.cpp
@@ -108,7 +108,7 @@ void NPairFullBinOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_full_nsq_ghost_omp.cpp b/src/OPENMP/npair_full_nsq_ghost_omp.cpp
index 05f402a99d..c1270d9fdc 100644
--- a/src/OPENMP/npair_full_nsq_ghost_omp.cpp
+++ b/src/OPENMP/npair_full_nsq_ghost_omp.cpp
@@ -108,7 +108,7 @@ void NPairFullNsqGhostOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_full_nsq_omp.cpp b/src/OPENMP/npair_full_nsq_omp.cpp
index 6349906771..695cb1bc48 100644
--- a/src/OPENMP/npair_full_nsq_omp.cpp
+++ b/src/OPENMP/npair_full_nsq_omp.cpp
@@ -108,7 +108,7 @@ void NPairFullNsqOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp b/src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp
index 2255033204..e10d181a8c 100644
--- a/src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp
+++ b/src/OPENMP/npair_half_bin_newtoff_ghost_omp.cpp
@@ -122,7 +122,7 @@ void NPairHalfBinNewtoffGhostOmp::build(NeighList *list)
             if (molecular != Atom::ATOMIC) {
               if (!moltemplate)
                 which = find_special(special[i],nspecial[i],tag[j]);
-              else if (imol >=0)
+              else if (imol >= 0)
                 which = find_special(onemols[imol]->special[iatom],
                                      onemols[imol]->nspecial[iatom],
                                      tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_bin_newtoff_omp.cpp
index 36997d9bcb..9d32cc7e2b 100644
--- a/src/OPENMP/npair_half_bin_newtoff_omp.cpp
+++ b/src/OPENMP/npair_half_bin_newtoff_omp.cpp
@@ -113,7 +113,7 @@ void NPairHalfBinNewtoffOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_bin_newton_omp.cpp b/src/OPENMP/npair_half_bin_newton_omp.cpp
index 1663a2f14c..d2da12962c 100644
--- a/src/OPENMP/npair_half_bin_newton_omp.cpp
+++ b/src/OPENMP/npair_half_bin_newton_omp.cpp
@@ -114,7 +114,7 @@ void NPairHalfBinNewtonOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
@@ -145,7 +145,7 @@ void NPairHalfBinNewtonOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_bin_newton_tri_omp.cpp
index e754456ef1..4d93d06d75 100644
--- a/src/OPENMP/npair_half_bin_newton_tri_omp.cpp
+++ b/src/OPENMP/npair_half_bin_newton_tri_omp.cpp
@@ -119,7 +119,7 @@ void NPairHalfBinNewtonTriOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_multi_old_newtoff_omp.cpp b/src/OPENMP/npair_half_multi_old_newtoff_omp.cpp
index ac5e9dae04..4447b4414e 100644
--- a/src/OPENMP/npair_half_multi_old_newtoff_omp.cpp
+++ b/src/OPENMP/npair_half_multi_old_newtoff_omp.cpp
@@ -120,7 +120,7 @@ void NPairHalfMultiOldNewtoffOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_multi_old_newton_omp.cpp b/src/OPENMP/npair_half_multi_old_newton_omp.cpp
index baa9dd0724..29c551f17d 100644
--- a/src/OPENMP/npair_half_multi_old_newton_omp.cpp
+++ b/src/OPENMP/npair_half_multi_old_newton_omp.cpp
@@ -116,7 +116,7 @@ void NPairHalfMultiOldNewtonOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
@@ -153,7 +153,7 @@ void NPairHalfMultiOldNewtonOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp b/src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp
index e4895ff1a9..1d906b1fa5 100644
--- a/src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp
+++ b/src/OPENMP/npair_half_multi_old_newton_tri_omp.cpp
@@ -129,7 +129,7 @@ void NPairHalfMultiOldNewtonTriOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp b/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp
index 388e51e1af..54de8b9607 100644
--- a/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp
+++ b/src/OPENMP/npair_half_nsq_newtoff_ghost_omp.cpp
@@ -117,7 +117,7 @@ void NPairHalfNsqNewtoffGhostOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_nsq_newtoff_omp.cpp
index 002ea37e6b..54a90d9f2b 100644
--- a/src/OPENMP/npair_half_nsq_newtoff_omp.cpp
+++ b/src/OPENMP/npair_half_nsq_newtoff_omp.cpp
@@ -109,7 +109,7 @@ void NPairHalfNsqNewtoffOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_nsq_newton_omp.cpp b/src/OPENMP/npair_half_nsq_newton_omp.cpp
index 5996cd2013..c010a3b024 100644
--- a/src/OPENMP/npair_half_nsq_newton_omp.cpp
+++ b/src/OPENMP/npair_half_nsq_newton_omp.cpp
@@ -127,7 +127,7 @@ void NPairHalfNsqNewtonOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp
index c6be04419d..e1d4ee59b1 100644
--- a/src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp
+++ b/src/OPENMP/npair_half_respa_bin_newtoff_omp.cpp
@@ -144,7 +144,7 @@ void NPairHalfRespaBinNewtoffOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_respa_bin_newton_omp.cpp b/src/OPENMP/npair_half_respa_bin_newton_omp.cpp
index 51fc7a2ed8..ce8a103170 100644
--- a/src/OPENMP/npair_half_respa_bin_newton_omp.cpp
+++ b/src/OPENMP/npair_half_respa_bin_newton_omp.cpp
@@ -146,7 +146,7 @@ void NPairHalfRespaBinNewtonOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
@@ -190,7 +190,7 @@ void NPairHalfRespaBinNewtonOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp
index c998f71290..73f2102dba 100644
--- a/src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp
+++ b/src/OPENMP/npair_half_respa_bin_newton_tri_omp.cpp
@@ -151,7 +151,7 @@ void NPairHalfRespaBinNewtonTriOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp
index 1167a7601b..428ca778e8 100644
--- a/src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp
+++ b/src/OPENMP/npair_half_respa_nsq_newtoff_omp.cpp
@@ -141,7 +141,7 @@ void NPairHalfRespaNsqNewtoffOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp b/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp
index 61d9165b1e..4bcba0fbef 100644
--- a/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp
+++ b/src/OPENMP/npair_half_respa_nsq_newton_omp.cpp
@@ -159,7 +159,7 @@ void NPairHalfRespaNsqNewtonOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_bin_newtoff_omp.cpp b/src/OPENMP/npair_half_size_bin_newtoff_omp.cpp
index c205b67539..478e28a5f4 100644
--- a/src/OPENMP/npair_half_size_bin_newtoff_omp.cpp
+++ b/src/OPENMP/npair_half_size_bin_newtoff_omp.cpp
@@ -125,7 +125,7 @@ void NPairHalfSizeBinNewtoffOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_bin_newton_omp.cpp b/src/OPENMP/npair_half_size_bin_newton_omp.cpp
index 628057d41d..dba392781e 100644
--- a/src/OPENMP/npair_half_size_bin_newton_omp.cpp
+++ b/src/OPENMP/npair_half_size_bin_newton_omp.cpp
@@ -126,7 +126,7 @@ void NPairHalfSizeBinNewtonOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
@@ -161,7 +161,7 @@ void NPairHalfSizeBinNewtonOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp
index c320296442..160cf64194 100644
--- a/src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp
+++ b/src/OPENMP/npair_half_size_bin_newton_tri_omp.cpp
@@ -132,7 +132,7 @@ void NPairHalfSizeBinNewtonTriOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_multi_newtoff_omp.cpp b/src/OPENMP/npair_half_size_multi_newtoff_omp.cpp
index 73564a150c..ba0dfc16be 100644
--- a/src/OPENMP/npair_half_size_multi_newtoff_omp.cpp
+++ b/src/OPENMP/npair_half_size_multi_newtoff_omp.cpp
@@ -124,7 +124,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list)
 
       for (k = 0; k < ns; k++) {
         js = binhead_multi[jcollection][jbin + s[k]];
-        for (j = js; j >=0; j = bins[j]) {
+        for (j = js; j >= 0; j = bins[j]) {
           if (j <= i) continue;
 
           jtype = type[j];
@@ -145,7 +145,7 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list)
             if (molecular != Atom::ATOMIC) {
               if (!moltemplate)
                 which = find_special(special[i],nspecial[i],tag[j]);
-              else if (imol >=0)
+              else if (imol >= 0)
                 which = find_special(onemols[imol]->special[iatom],
                                      onemols[imol]->nspecial[iatom],
                                      tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_multi_newton_omp.cpp b/src/OPENMP/npair_half_size_multi_newton_omp.cpp
index 0ed843ea0b..4bc17f911c 100644
--- a/src/OPENMP/npair_half_size_multi_newton_omp.cpp
+++ b/src/OPENMP/npair_half_size_multi_newton_omp.cpp
@@ -155,7 +155,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list)
             if (molecular != Atom::ATOMIC) {
               if (!moltemplate)
                 which = find_special(special[i],nspecial[i],tag[j]);
-              else if (imol >=0)
+              else if (imol >= 0)
                 which = find_special(onemols[imol]->special[iatom],
                                      onemols[imol]->nspecial[iatom],
                                      tag[j]-tagprev);
@@ -198,7 +198,7 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list)
             if (molecular != Atom::ATOMIC) {
               if (!moltemplate)
                 which = find_special(special[i],nspecial[i],tag[j]);
-              else if (imol >=0)
+              else if (imol >= 0)
                 which = find_special(onemols[imol]->special[iatom],
                                      onemols[imol]->nspecial[iatom],
                                      tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp
index 9a0ead482b..73e11a2745 100644
--- a/src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp
+++ b/src/OPENMP/npair_half_size_multi_newton_tri_omp.cpp
@@ -160,7 +160,7 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list)
             if (molecular != Atom::ATOMIC) {
               if (!moltemplate)
                 which = find_special(special[i],nspecial[i],tag[j]);
-              else if (imol >=0)
+              else if (imol >= 0)
                 which = find_special(onemols[imol]->special[iatom],
                                      onemols[imol]->nspecial[iatom],
                                      tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp b/src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp
index c368e71095..e4169482bc 100644
--- a/src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp
+++ b/src/OPENMP/npair_half_size_multi_old_newtoff_omp.cpp
@@ -132,7 +132,7 @@ void NPairHalfSizeMultiOldNewtoffOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_multi_old_newton_omp.cpp b/src/OPENMP/npair_half_size_multi_old_newton_omp.cpp
index 187efe04d1..7d6a3de871 100644
--- a/src/OPENMP/npair_half_size_multi_old_newton_omp.cpp
+++ b/src/OPENMP/npair_half_size_multi_old_newton_omp.cpp
@@ -127,7 +127,7 @@ void NPairHalfSizeMultiOldNewtonOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
@@ -170,7 +170,7 @@ void NPairHalfSizeMultiOldNewtonOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp b/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp
index c74b191f66..caa993ed38 100644
--- a/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp
+++ b/src/OPENMP/npair_half_size_multi_old_newton_tri_omp.cpp
@@ -140,7 +140,7 @@ void NPairHalfSizeMultiOldNewtonTriOmp::build(NeighList *list)
           if (molecular != Atom::ATOMIC) {
             if (!moltemplate)
               which = find_special(special[i],nspecial[i],tag[j]);
-            else if (imol >=0)
+            else if (imol >= 0)
               which = find_special(onemols[imol]->special[iatom],
                                    onemols[imol]->nspecial[iatom],
                                    tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp b/src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp
index 020551bd8e..2982586a18 100644
--- a/src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp
+++ b/src/OPENMP/npair_half_size_nsq_newtoff_omp.cpp
@@ -122,7 +122,7 @@ void NPairHalfSizeNsqNewtoffOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
diff --git a/src/OPENMP/npair_half_size_nsq_newton_omp.cpp b/src/OPENMP/npair_half_size_nsq_newton_omp.cpp
index fe2a1be3da..0a80da9422 100644
--- a/src/OPENMP/npair_half_size_nsq_newton_omp.cpp
+++ b/src/OPENMP/npair_half_size_nsq_newton_omp.cpp
@@ -140,7 +140,7 @@ void NPairHalfSizeNsqNewtonOmp::build(NeighList *list)
         if (molecular != Atom::ATOMIC) {
           if (!moltemplate)
             which = find_special(special[i],nspecial[i],tag[j]);
-          else if (imol >=0)
+          else if (imol >= 0)
             which = find_special(onemols[imol]->special[iatom],
                                  onemols[imol]->nspecial[iatom],
                                  tag[j]-tagprev);
diff --git a/src/PHONON/dynamical_matrix.cpp b/src/PHONON/dynamical_matrix.cpp
index 8e4f8557a2..c2ba34c4c2 100644
--- a/src/PHONON/dynamical_matrix.cpp
+++ b/src/PHONON/dynamical_matrix.cpp
@@ -365,7 +365,7 @@ void DynamicalMatrix::calculateMatrix()
     delete [] fdynmat[i];
   delete [] fdynmat;
 
-  if (screen && me ==0 ) fprintf(screen,"Finished Calculating Dynamical Matrix\n");
+  if (screen && me == 0) fprintf(screen,"Finished Calculating Dynamical Matrix\n");
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/PHONON/third_order.cpp b/src/PHONON/third_order.cpp
index 4a8948de77..c31aae0086 100644
--- a/src/PHONON/third_order.cpp
+++ b/src/PHONON/third_order.cpp
@@ -412,7 +412,7 @@ void ThirdOrder::calculateMatrix()
   delete [] dynmat;
   delete [] fdynmat;
 
-  if (screen && me ==0)
+  if (screen && me == 0)
     fprintf(screen,"Finished Calculating Third Order Tensor\n");
 }
 
diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp
index cf99efd099..d124b06dc2 100644
--- a/src/REACTION/fix_bond_react.cpp
+++ b/src/REACTION/fix_bond_react.cpp
@@ -412,7 +412,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
       } else if (strcmp(arg[iarg],"modify_create") == 0) {
         if (iarg++ > narg) error->all(FLERR,"Illegal fix bond/react command: "
                                       "'modify_create' has too few arguments");
-        while (iarg < narg && strcmp(arg[iarg],"react") != 0 ) {
+        while (iarg < narg && strcmp(arg[iarg],"react") != 0) {
           if (strcmp(arg[iarg],"fit") == 0) {
             if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
                                           "'modify_create' has too few arguments");
@@ -1394,7 +1394,7 @@ void FixBondReact::superimpose_algorithm()
         }
 
         for (int i = 0; i < onemol->natoms; i++) {
-          if (glove[i][0] !=0 && pioneer_count[i] < onemol_nxspecial[i][0] && edge[i][rxnID] == 0) {
+          if (glove[i][0] != 0 && pioneer_count[i] < onemol_nxspecial[i][0] && edge[i][rxnID] == 0) {
             pioneers[i] = 1;
           }
         }
@@ -1837,7 +1837,7 @@ void FixBondReact::inner_crosscheck_loop()
   for (int i=1; i < num_choices; ++i) {
     tagint hold = tag_choices[i];
     int j = i - 1;
-    while ((j >=0) && (tag_choices[j] > hold)) {
+    while ((j >= 0) && (tag_choices[j] > hold)) {
       tag_choices[j+1] = tag_choices[j];
       --j;
     }
diff --git a/src/REAXFF/fix_reaxff_bonds.cpp b/src/REAXFF/fix_reaxff_bonds.cpp
index 393e22930f..8bd7ed0020 100644
--- a/src/REAXFF/fix_reaxff_bonds.cpp
+++ b/src/REAXFF/fix_reaxff_bonds.cpp
@@ -295,7 +295,7 @@ void FixReaxFFBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local,
     MPI_Isend(&buf[0],nbuf_local,MPI_DOUBLE,0,0,world,&irequest2);
     MPI_Wait(&irequest2,MPI_STATUS_IGNORE);
   }
-  if (me ==0) fputs("# \n",fp);
+  if (me == 0) fputs("# \n",fp);
 
 }
 
diff --git a/src/SMTBQ/pair_smtbq.cpp b/src/SMTBQ/pair_smtbq.cpp
index fdef0b6043..4f924a6fca 100644
--- a/src/SMTBQ/pair_smtbq.cpp
+++ b/src/SMTBQ/pair_smtbq.cpp
@@ -446,7 +446,7 @@ void PairSMTBQ::read_file(char *file)
       params[i].chi = values.next_double();
       params[i].dj = values.next_double();
 
-      if (strcmp(params[i].nom, "O") !=0) {
+      if (strcmp(params[i].nom, "O") != 0) {
         params[i].R = values.next_double();
         if ((comm->me == 0) && VERBOSE)
           utils::logmesg(lmp, " {} {} {} {} {}\n",label,params[i].ne,params[i].chi,
@@ -782,7 +782,7 @@ void PairSMTBQ::read_file(char *file)
         if (intparams[m].intsm == 0) continue;
 
         intparams[m].neig_cut = 1.2*intparams[m].r0;
-        if (strcmp(intparams[m].typepot,"second_moment") == 0 )
+        if (strcmp(intparams[m].typepot,"second_moment") == 0)
           if ((comm->me == 0) && VERBOSE)
             utils::logmesg(lmp, " Rc 1er voisin, typepot {} -> {} Ang\n",
                            intparams[m].typepot,intparams[m].neig_cut);
@@ -1020,7 +1020,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
 
       //    ----------------------------------------------
       if ( strcmp(intparams[m].typepot,"buck") == 0 ||
-           strcmp(intparams[m].typepot,"buckPlusAttr") ==0) {
+           strcmp(intparams[m].typepot,"buckPlusAttr") == 0) {
         //    ----------------------------------------------
 
         evdwl = 0.0; fpair =0.0;
@@ -1070,7 +1070,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
 
 
       //    -----------------------------------------------------------------
-      if (strcmp(intparams[m].typepot,"second_moment") != 0 ) continue;
+      if (strcmp(intparams[m].typepot,"second_moment") != 0) continue;
       //    -----------------------------------------------------------------
 
 
@@ -2575,7 +2575,7 @@ void PairSMTBQ::Charge()
   if (me == 0 && strcmp(Bavard,"false") != 0) {
     for (gp = 0; gp < nteam+1; gp++) {
       printf (" ++++ Groupe %d - Nox %d Ncat %d\n",gp,nQEqaall[gp],nQEqcall[gp]);
-      if (nQEqcall[gp] !=0 && nQEqaall[gp] !=0 )
+      if (nQEqcall[gp] != 0 && nQEqaall[gp] !=0 )
         printf (" neutralite des charges %f\n qtotc %f qtota %f\n",
                 qtotll,qtotcll[gp]/nQEqcall[gp],qtotall[gp]/nQEqaall[gp]);
       printf (" ---------------------------- \n");}
@@ -2641,7 +2641,7 @@ void PairSMTBQ::Charge()
 
     for (i = 0; i < nteam+1; i++) {
 
-      if (nQEqall[i] !=0) TransfAll[i] /= static_cast<double>(nQEqall[i]);
+      if (nQEqall[i] != 0) TransfAll[i] /= static_cast<double>(nQEqall[i]);
       enegchk[i] = enegmax[i] = 0.0;
     }
 
@@ -2665,7 +2665,7 @@ void PairSMTBQ::Charge()
 
 
     for (gp = 0; gp < nteam+1; gp++) {
-      if (nQEqall[gp] !=0) {
+      if (nQEqall[gp] != 0) {
         enegchk[gp] = enegchkall[gp]/static_cast<double>(nQEqall[gp]);
         enegmax[gp] = enegmaxall[gp];
       }
@@ -2729,7 +2729,7 @@ void PairSMTBQ::Charge()
   //   Statistique (ecart type)
   //   ------------------------
   for (i=0; i<nteam+1; i++) {
-    if (nQEqcall[i] !=0)
+    if (nQEqcall[i] != 0)
       { TransfAll[i+cluster] /= static_cast<double>(nQEqcall[i]) ;
         TransfAll[i+2*cluster] /= static_cast<double>(nQEqaall[i]) ;}
     sigmaa[i] = sigmac[i] = 0.0;
diff --git a/src/VTK/dump_vtk.cpp b/src/VTK/dump_vtk.cpp
index 3667180bc9..a77f5b2e11 100644
--- a/src/VTK/dump_vtk.cpp
+++ b/src/VTK/dump_vtk.cpp
@@ -1933,7 +1933,7 @@ void DumpVTK::identify_vectors()
     // assume components are grouped together and in correct order
     if (name.count(it->first + 1) && name.count(it->first + 2)) { // more attributes?
       if (it->second.compare(0,it->second.length()-3,name[it->first + 1],0,it->second.length()-3) == 0  && // same attributes?
-         it->second.compare(0,it->second.length()-3,name[it->first + 2],0,it->second.length()-3) == 0 )
+         it->second.compare(0,it->second.length()-3,name[it->first + 2],0,it->second.length()-3) == 0)
       {
         it->second.erase(it->second.length()-1);
         std::ostringstream oss;
diff --git a/src/atom.cpp b/src/atom.cpp
index 08e9639440..6b014fc9c8 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -966,10 +966,10 @@ void Atom::bonus_check()
   bigint local_bodies = 0, num_global;
 
   for (int i = 0; i < nlocal; ++i) {
-    if (ellipsoid && (ellipsoid[i] >=0)) ++local_ellipsoids;
-    if (line && (line[i] >=0)) ++local_lines;
-    if (tri && (tri[i] >=0)) ++local_tris;
-    if (body && (body[i] >=0)) ++local_bodies;
+    if (ellipsoid && (ellipsoid[i] >= 0)) ++local_ellipsoids;
+    if (line && (line[i] >= 0)) ++local_lines;
+    if (tri && (tri[i] >= 0)) ++local_tris;
+    if (body && (body[i] >= 0)) ++local_bodies;
   }
 
   MPI_Allreduce(&local_ellipsoids,&num_global,1,MPI_LMP_BIGINT,MPI_SUM,world);
diff --git a/src/library.cpp b/src/library.cpp
index 872b59693f..8cec7c4505 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -2328,7 +2328,7 @@ void *lammps_extract_variable(void *handle, const char *name, const char *group)
     } else if (lmp->input->variable->vectorstyle(ivar)) {
       double *values = nullptr;
       int nvector = lmp->input->variable->compute_vector(ivar, &values);
-      if ( group != nullptr && strcmp(group,"LMP_SIZE_VECTOR") == 0 ) {
+      if (group != nullptr && strcmp(group,"LMP_SIZE_VECTOR") == 0) {
           int* nvecptr = (int *) malloc(sizeof(int));
           *nvecptr = nvector;
           return (void *) nvecptr;
@@ -2372,7 +2372,7 @@ int lammps_extract_variable_datatype(void *handle, const char *name)
   BEGIN_CAPTURE
   {
     int ivar = lmp->input->variable->find(name);
-    if ( ivar < 0 ) return -1;
+    if (ivar < 0) return -1;
 
     if (lmp->input->variable->equalstyle(ivar))
       return LMP_VAR_EQUAL;
@@ -5199,7 +5199,7 @@ int lammps_find_pair_neighlist(void *handle, const char *style, int exact, int n
     // find neigh list
     for (int i = 0; i < lmp->neighbor->nlist; i++) {
       NeighList *list = lmp->neighbor->lists[i];
-      if ( (list->requestor_type == NeighList::PAIR)
+      if ((list->requestor_type == NeighList::PAIR)
            && (pair == list->requestor)
            && (list->id == reqid) ) return i;
     }
@@ -5229,7 +5229,7 @@ int lammps_find_fix_neighlist(void *handle, const char *id, int reqid) {
   // find neigh list
   for (int i = 0; i < lmp->neighbor->nlist; i++) {
     NeighList *list = lmp->neighbor->lists[i];
-    if ( (list->requestor_type == NeighList::FIX)
+    if ((list->requestor_type == NeighList::FIX)
          && (fix == list->requestor)
          && (list->id == reqid) ) return i;
   }
@@ -5258,7 +5258,7 @@ int lammps_find_compute_neighlist(void *handle, const char *id, int reqid) {
   // find neigh list
   for (int i = 0; i < lmp->neighbor->nlist; i++) {
     NeighList * list = lmp->neighbor->lists[i];
-    if ( (list->requestor_type == NeighList::COMPUTE)
+    if ((list->requestor_type == NeighList::COMPUTE)
          && (compute == list->requestor)
          && (list->id == reqid) ) return i;
   }
@@ -5709,7 +5709,7 @@ int lammps_style_name(void *handle, const char *category, int idx,
   Info info(lmp);
   auto styles = info.get_available_styles(category);
 
-  if ((idx >=0) && (idx < (int) styles.size())) {
+  if ((idx >= 0) && (idx < (int) styles.size())) {
     strncpy(buffer, styles[idx].c_str(), buf_size);
     return 1;
   }
@@ -5844,23 +5844,23 @@ int lammps_id_name(void *handle, const char *category, int idx, char *buffer, in
       return 1;
     }
   } else if (strcmp(category,"group") == 0) {
-    if ((idx >=0) && (idx < lmp->group->ngroup)) {
+    if ((idx >= 0) && (idx < lmp->group->ngroup)) {
       strncpy(buffer, lmp->group->names[idx], buf_size);
       return 1;
     }
   } else if (strcmp(category,"molecule") == 0) {
-    if ((idx >=0) && (idx < lmp->atom->nmolecule)) {
+    if ((idx >= 0) && (idx < lmp->atom->nmolecule)) {
       strncpy(buffer, lmp->atom->molecules[idx]->id, buf_size);
       return 1;
     }
   } else if (strcmp(category,"region") == 0) {
     auto regions = lmp->domain->get_region_list();
-    if ((idx >=0) && (idx < (int) regions.size())) {
+    if ((idx >= 0) && (idx < (int) regions.size())) {
       strncpy(buffer, regions[idx]->id, buf_size);
       return 1;
     }
   } else if (strcmp(category,"variable") == 0) {
-    if ((idx >=0) && (idx < lmp->input->variable->nvar)) {
+    if ((idx >= 0) && (idx < lmp->input->variable->nvar)) {
       strncpy(buffer, lmp->input->variable->names[idx], buf_size);
       return 1;
     }
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index aa9f5fe8ee..0de36ebe1e 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -768,7 +768,7 @@ void ReadRestart::header()
       for (int i = 0; i < nargcopy; i++)
         argcopy[i] = read_string();
       atom->create_avec(style,nargcopy,argcopy,1);
-      if (comm->me ==0)
+      if (comm->me == 0)
         utils::logmesg(lmp,"  restoring atom style {} from restart\n",atom->atom_style);
       for (int i = 0; i < nargcopy; i++) delete[] argcopy[i];
       delete[] argcopy;
@@ -921,14 +921,14 @@ void ReadRestart::force_fields()
       style = read_string();
       force->create_pair(style,1);
       delete[] style;
-      if (comm->me ==0)
+      if (comm->me == 0)
         utils::logmesg(lmp,"  restoring pair style {} from restart\n",
                        force->pair_style);
       force->pair->read_restart(fp);
 
     } else if (flag == NO_PAIR) {
       style = read_string();
-      if (comm->me ==0)
+      if (comm->me == 0)
         utils::logmesg(lmp,"  pair style {} stores no restart info\n", style);
       force->create_pair("none",0);
       force->pair_restart = style;
@@ -937,7 +937,7 @@ void ReadRestart::force_fields()
       style = read_string();
       force->create_bond(style,1);
       delete[] style;
-      if (comm->me ==0)
+      if (comm->me == 0)
         utils::logmesg(lmp,"  restoring bond style {} from restart\n",
                        force->bond_style);
       force->bond->read_restart(fp);
@@ -946,7 +946,7 @@ void ReadRestart::force_fields()
       style = read_string();
       force->create_angle(style,1);
       delete[] style;
-      if (comm->me ==0)
+      if (comm->me == 0)
         utils::logmesg(lmp,"  restoring angle style {} from restart\n",
                        force->angle_style);
       force->angle->read_restart(fp);
@@ -955,7 +955,7 @@ void ReadRestart::force_fields()
       style = read_string();
       force->create_dihedral(style,1);
       delete[] style;
-      if (comm->me ==0)
+      if (comm->me == 0)
         utils::logmesg(lmp,"  restoring dihedral style {} from restart\n",
                        force->dihedral_style);
       force->dihedral->read_restart(fp);
@@ -964,7 +964,7 @@ void ReadRestart::force_fields()
       style = read_string();
       force->create_improper(style,1);
       delete[] style;
-      if (comm->me ==0)
+      if (comm->me == 0)
         utils::logmesg(lmp,"  restoring improper style {} from restart\n",
                        force->improper_style);
       force->improper->read_restart(fp);
diff --git a/src/variable.cpp b/src/variable.cpp
index 4d07a9e3c2..3264cfa1ee 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -2726,7 +2726,7 @@ double Variable::collapse_tree(Tree *tree)
     if (tree->first->type != VALUE || tree->second->type != VALUE ||
         tree->extra[0]->type != VALUE) return 0.0;
     tree->type = VALUE;
-    if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0 )
+    if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0)
       error->all(FLERR,"Invalid math function in variable formula");
     if (update->ntimestep < ivalue1) tree->value = ivalue1;
     else {
@@ -3097,7 +3097,7 @@ double Variable::eval_tree(Tree *tree, int i)
     auto  ivalue1 = static_cast<bigint> (eval_tree(tree->first,i));
     auto  ivalue2 = static_cast<bigint> (eval_tree(tree->second,i));
     auto  ivalue3 = static_cast<bigint> (eval_tree(tree->extra[0],i));
-    if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0 )
+    if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0)
       error->all(FLERR,"Invalid math function in variable formula");
     if (update->ntimestep < ivalue1) arg = ivalue1;
     else {
@@ -3628,7 +3628,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree, Tree **tree
       auto  ivalue1 = static_cast<bigint> (value1);
       auto  ivalue2 = static_cast<bigint> (value2);
       auto  ivalue3 = static_cast<bigint> (values[0]);
-      if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0 )
+      if (ivalue1 <= 0 || ivalue2 <= 0 || ivalue3 <= 0)
         print_var_error(FLERR,"Invalid math function in variable formula",ivar);
       double value;
       if (update->ntimestep < ivalue1) value = ivalue1;

From 0f89a8b2caf50226c002b2a958d5eb18e41dc39d Mon Sep 17 00:00:00 2001
From: jbcouli <jbcouli@sandia.gov>
Date: Tue, 11 Jul 2023 10:42:26 -0600
Subject: [PATCH 364/396] explicit special_bonds commands for 1-2 coul weight
 equal to zero

---
 doc/src/Howto_bpm.rst | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst
index 448a43a654..380c114866 100644
--- a/doc/src/Howto_bpm.rst
+++ b/doc/src/Howto_bpm.rst
@@ -110,8 +110,14 @@ ensures all bonded neighbors are still included in the neighbor list
 in case bonds break between neighbor list builds. If bond breakage is
 disabled during a simulation run by setting the *break* keyword to *no*,
 a zero coul weight for 1-2 bonds can be used to exclude bonded atoms
-from the neighbor list builds. This can be useful for post-processing,
-or to determine pair interaction properties between distinct bonded particles.
+from the neighbor list builds
+
+   .. code-block:: LAMMPS
+
+      special_bonds lj 0 1 1 coul 0 1 1
+
+This can be useful for post-processing, or to determine pair interaction
+properties between distinct bonded particles.
 
 To monitor the fracture of bonds in the system, all BPM bond styles
 have the ability to record instances of bond breakage to output using

From 6123883324c95190713bba64b543a5449eef253a Mon Sep 17 00:00:00 2001
From: Karl Hammond <hammondkd@missouri.edu>
Date: Tue, 11 Jul 2023 17:57:22 -0500
Subject: [PATCH 365/396] Replaced parsed-literal:: with code-block:: LAMMPS
 under "Syntax"

---
 doc/src/atc_add_molecule.rst                 | 2 +-
 doc/src/atc_add_species.rst                  | 2 +-
 doc/src/atc_atom_element_map.rst             | 2 +-
 doc/src/atc_atom_weight.rst                  | 2 +-
 doc/src/atc_atomic_charge.rst                | 2 +-
 doc/src/atc_boundary_dynamics.rst            | 2 +-
 doc/src/atc_boundary_faceset.rst             | 2 +-
 doc/src/atc_boundary_type.rst                | 2 +-
 doc/src/atc_consistent_fe_initialization.rst | 2 +-
 doc/src/atc_control_localized_lambda.rst     | 2 +-
 doc/src/atc_control_momentum.rst             | 2 +-
 doc/src/atc_control_thermal.rst              | 2 +-
 doc/src/atc_decomposition.rst                | 2 +-
 doc/src/atc_electron_integration.rst         | 2 +-
 doc/src/atc_equilibrium_start.rst            | 2 +-
 doc/src/atc_extrinsic_exchange.rst           | 2 +-
 doc/src/atc_fe_md_boundary.rst               | 2 +-
 doc/src/atc_filter_scale.rst                 | 2 +-
 doc/src/atc_filter_type.rst                  | 2 +-
 doc/src/atc_fix.rst                          | 2 +-
 doc/src/atc_fix_flux.rst                     | 2 +-
 doc/src/atc_hardy_computes.rst               | 2 +-
 doc/src/atc_hardy_fields.rst                 | 2 +-
 doc/src/atc_hardy_gradients.rst              | 2 +-
 doc/src/atc_hardy_kernel.rst                 | 2 +-
 doc/src/atc_hardy_on_the_fly.rst             | 2 +-
 doc/src/atc_hardy_rates.rst                  | 2 +-
 doc/src/atc_initial.rst                      | 2 +-
 doc/src/atc_internal_element_set.rst         | 2 +-
 doc/src/atc_internal_quadrature.rst          | 2 +-
 doc/src/atc_kernel_bandwidth.rst             | 2 +-
 doc/src/atc_lumped_lambda_solve.rst          | 2 +-
 doc/src/atc_mask_direction.rst               | 2 +-
 doc/src/atc_mass_matrix.rst                  | 2 +-
 doc/src/atc_material.rst                     | 2 +-
 doc/src/atc_mesh_add_to_nodeset.rst          | 2 +-
 doc/src/atc_mesh_create.rst                  | 2 +-
 doc/src/atc_mesh_create_elementset.rst       | 2 +-
 doc/src/atc_mesh_create_faceset_box.rst      | 2 +-
 doc/src/atc_mesh_create_faceset_plane.rst    | 2 +-
 doc/src/atc_mesh_create_nodeset.rst          | 2 +-
 doc/src/atc_mesh_delete_elements.rst         | 2 +-
 doc/src/atc_mesh_nodeset_to_elementset.rst   | 2 +-
 doc/src/atc_mesh_output.rst                  | 2 +-
 doc/src/atc_mesh_quadrature.rst              | 2 +-
 doc/src/atc_mesh_read.rst                    | 2 +-
 doc/src/atc_mesh_write.rst                   | 2 +-
 doc/src/atc_output.rst                       | 2 +-
 doc/src/atc_output_boundary_integral.rst     | 2 +-
 doc/src/atc_output_contour_integral.rst      | 2 +-
 doc/src/atc_output_nodeset.rst               | 2 +-
 doc/src/atc_output_volume_integral.rst       | 2 +-
 doc/src/atc_pair_interactions.rst            | 2 +-
 doc/src/atc_poisson_solver.rst               | 2 +-
 doc/src/atc_read_restart.rst                 | 2 +-
 doc/src/atc_remove_molecule.rst              | 2 +-
 doc/src/atc_remove_source.rst                | 2 +-
 doc/src/atc_remove_species.rst               | 2 +-
 doc/src/atc_reset_atomic_reference.rst       | 2 +-
 doc/src/atc_reset_time.rst                   | 2 +-
 doc/src/atc_sample_frequency.rst             | 2 +-
 doc/src/atc_set_reference_pe.rst             | 2 +-
 doc/src/atc_source.rst                       | 2 +-
 doc/src/atc_source_integration.rst           | 2 +-
 doc/src/atc_temperature_definition.rst       | 2 +-
 doc/src/atc_time_filter.rst                  | 2 +-
 doc/src/atc_time_integration.rst             | 2 +-
 doc/src/atc_track_displacement.rst           | 2 +-
 doc/src/atc_unfix.rst                        | 2 +-
 doc/src/atc_unfix_flux.rst                   | 2 +-
 doc/src/atc_write_atom_weights.rst           | 2 +-
 doc/src/atc_write_restart.rst                | 2 +-
 doc/src/compute_property_grid.rst            | 2 +-
 doc/src/compute_reduce_chunk.rst             | 2 +-
 doc/src/compute_saed.rst                     | 2 +-
 doc/src/compute_slice.rst                    | 2 +-
 doc/src/compute_smd_contact_radius.rst       | 2 +-
 doc/src/compute_smd_damage.rst               | 2 +-
 doc/src/compute_smd_hourglass_error.rst      | 2 +-
 doc/src/compute_smd_internal_energy.rst      | 2 +-
 doc/src/compute_smd_plastic_strain.rst       | 2 +-
 doc/src/compute_smd_plastic_strain_rate.rst  | 2 +-
 doc/src/compute_smd_rho.rst                  | 2 +-
 doc/src/compute_smd_tlsph_defgrad.rst        | 2 +-
 doc/src/compute_smd_tlsph_dt.rst             | 2 +-
 doc/src/compute_smd_tlsph_num_neighs.rst     | 2 +-
 doc/src/compute_smd_tlsph_shape.rst          | 2 +-
 doc/src/compute_smd_tlsph_strain.rst         | 2 +-
 doc/src/compute_smd_tlsph_strain_rate.rst    | 2 +-
 doc/src/compute_smd_tlsph_stress.rst         | 2 +-
 doc/src/compute_smd_triangle_vertices.rst    | 2 +-
 doc/src/compute_smd_vol.rst                  | 2 +-
 doc/src/compute_sna_atom.rst                 | 2 +-
 doc/src/compute_sph_e_atom.rst               | 2 +-
 doc/src/compute_sph_rho_atom.rst             | 2 +-
 doc/src/compute_sph_t_atom.rst               | 2 +-
 doc/src/dump_image.rst                       | 2 +-
 doc/src/dump_molfile.rst                     | 2 +-
 doc/src/dump_netcdf.rst                      | 2 +-
 doc/src/fitpod_command.rst                   | 2 +-
 doc/src/fix_alchemy.rst                      | 2 +-
 doc/src/fix_ave_grid.rst                     | 2 +-
 doc/src/fix_bond_swap.rst                    | 2 +-
 doc/src/fix_box_relax.rst                    | 2 +-
 doc/src/fix_charge_regulation.rst            | 4 ++--
 doc/src/fix_cmap.rst                         | 2 +-
 doc/src/fix_colvars.rst                      | 2 +-
 doc/src/fix_controller.rst                   | 2 +-
 doc/src/fix_damping_cundall.rst              | 2 +-
 doc/src/fix_deform.rst                       | 2 +-
 doc/src/fix_deposit.rst                      | 2 +-
 doc/src/fix_dpd_energy.rst                   | 2 +-
 doc/src/fix_dpd_source.rst                   | 2 +-
 doc/src/fix_drag.rst                         | 2 +-
 doc/src/fix_drude.rst                        | 2 +-
 doc/src/fix_drude_transform.rst              | 2 +-
 doc/src/fix_dt_reset.rst                     | 2 +-
 doc/src/fix_efield.rst                       | 2 +-
 doc/src/fix_ehex.rst                         | 2 +-
 doc/src/fix_electron_stopping.rst            | 2 +-
 doc/src/fix_enforce2d.rst                    | 2 +-
 doc/src/fix_eos_cv.rst                       | 2 +-
 doc/src/fix_eos_table.rst                    | 2 +-
 doc/src/fix_eos_table_rx.rst                 | 2 +-
 doc/src/fix_evaporate.rst                    | 2 +-
 doc/src/fix_external.rst                     | 2 +-
 doc/src/fix_ffl.rst                          | 2 +-
 doc/src/fix_filter_corotate.rst              | 2 +-
 doc/src/fix_flow_gauss.rst                   | 2 +-
 doc/src/fix_freeze.rst                       | 2 +-
 doc/src/fix_gcmc.rst                         | 2 +-
 doc/src/fix_gld.rst                          | 2 +-
 doc/src/fix_gle.rst                          | 2 +-
 doc/src/fix_gravity.rst                      | 2 +-
 doc/src/fix_grem.rst                         | 2 +-
 doc/src/fix_halt.rst                         | 2 +-
 doc/src/fix_heat.rst                         | 2 +-
 doc/src/fix_heat_flow.rst                    | 2 +-
 doc/src/fix_hyper_global.rst                 | 2 +-
 doc/src/fix_hyper_local.rst                  | 2 +-
 doc/src/fix_imd.rst                          | 2 +-
 doc/src/fix_indent.rst                       | 2 +-
 doc/src/fix_ipi.rst                          | 2 +-
 doc/src/fix_langevin.rst                     | 2 +-
 doc/src/fix_langevin_drude.rst               | 2 +-
 doc/src/fix_langevin_eff.rst                 | 2 +-
 doc/src/fix_langevin_spin.rst                | 2 +-
 doc/src/fix_lb_fluid.rst                     | 2 +-
 doc/src/fix_lb_momentum.rst                  | 2 +-
 doc/src/fix_lb_viscous.rst                   | 2 +-
 doc/src/fix_lineforce.rst                    | 2 +-
 doc/src/fix_manifoldforce.rst                | 2 +-
 doc/src/fix_mdi_qm.rst                       | 2 +-
 doc/src/fix_mdi_qmmm.rst                     | 2 +-
 doc/src/fix_meso_move.rst                    | 2 +-
 doc/src/fix_mol_swap.rst                     | 2 +-
 doc/src/fix_momentum.rst                     | 2 +-
 doc/src/fix_move.rst                         | 2 +-
 doc/src/fix_mscg.rst                         | 2 +-
 doc/src/fix_msst.rst                         | 2 +-
 doc/src/fix_mvv_dpd.rst                      | 2 +-
 doc/src/fix_neb.rst                          | 2 +-
 doc/src/fix_neb_spin.rst                     | 2 +-
 doc/src/fix_nh.rst                           | 2 +-
 doc/src/fix_nh_eff.rst                       | 2 +-
 doc/src/fix_nh_uef.rst                       | 2 +-
 doc/src/fix_nph_asphere.rst                  | 2 +-
 doc/src/fix_nph_body.rst                     | 2 +-
 doc/src/fix_nph_sphere.rst                   | 2 +-
 doc/src/fix_nphug.rst                        | 2 +-
 doc/src/fix_npt_asphere.rst                  | 2 +-
 doc/src/fix_npt_body.rst                     | 2 +-
 doc/src/fix_npt_cauchy.rst                   | 2 +-
 doc/src/fix_npt_sphere.rst                   | 2 +-
 doc/src/fix_numdiff.rst                      | 2 +-
 doc/src/fix_numdiff_virial.rst               | 2 +-
 doc/src/fix_nve.rst                          | 2 +-
 doc/src/fix_nve_asphere.rst                  | 2 +-
 doc/src/fix_nve_asphere_noforce.rst          | 2 +-
 doc/src/fix_nve_awpmd.rst                    | 2 +-
 doc/src/fix_nve_body.rst                     | 2 +-
 doc/src/fix_nve_bpm_sphere.rst               | 2 +-
 doc/src/fix_nve_dot.rst                      | 2 +-
 doc/src/fix_nve_dotc_langevin.rst            | 2 +-
 doc/src/fix_nve_eff.rst                      | 2 +-
 doc/src/fix_nve_limit.rst                    | 2 +-
 doc/src/fix_nve_line.rst                     | 2 +-
 doc/src/fix_nve_manifold_rattle.rst          | 2 +-
 doc/src/fix_nve_noforce.rst                  | 2 +-
 doc/src/fix_nve_sphere.rst                   | 2 +-
 doc/src/fix_nve_spin.rst                     | 2 +-
 doc/src/fix_nve_tri.rst                      | 2 +-
 doc/src/fix_nvk.rst                          | 2 +-
 doc/src/fix_nvt_asphere.rst                  | 2 +-
 doc/src/fix_nvt_body.rst                     | 2 +-
 doc/src/fix_nvt_manifold_rattle.rst          | 2 +-
 doc/src/fix_nvt_sllod.rst                    | 2 +-
 doc/src/fix_nvt_sllod_eff.rst                | 2 +-
 doc/src/fix_nvt_sphere.rst                   | 2 +-
 doc/src/fix_oneway.rst                       | 2 +-
 doc/src/fix_orient.rst                       | 2 +-
 doc/src/fix_pafi.rst                         | 2 +-
 doc/src/fix_pair.rst                         | 2 +-
 doc/src/fix_phonon.rst                       | 2 +-
 doc/src/fix_pimd.rst                         | 2 +-
 doc/src/fix_planeforce.rst                   | 2 +-
 doc/src/fix_plumed.rst                       | 2 +-
 doc/src/fix_poems.rst                        | 2 +-
 doc/src/fix_polarize.rst                     | 2 +-
 doc/src/fix_pour.rst                         | 2 +-
 doc/src/fix_press_berendsen.rst              | 2 +-
 doc/src/fix_print.rst                        | 2 +-
 doc/src/fix_propel_self.rst                  | 2 +-
 doc/src/fix_property_atom.rst                | 2 +-
 doc/src/fix_python_invoke.rst                | 2 +-
 doc/src/fix_python_move.rst                  | 2 +-
 doc/src/fix_qbmsst.rst                       | 2 +-
 doc/src/fix_qeq.rst                          | 2 +-
 doc/src/fix_qeq_comb.rst                     | 2 +-
 doc/src/fix_qeq_reaxff.rst                   | 2 +-
 doc/src/fix_qmmm.rst                         | 2 +-
 doc/src/fix_qtb.rst                          | 2 +-
 doc/src/fix_reaxff_bonds.rst                 | 2 +-
 doc/src/fix_reaxff_species.rst               | 2 +-
 doc/src/fix_recenter.rst                     | 2 +-
 doc/src/fix_rhok.rst                         | 2 +-
 doc/src/fix_rigid.rst                        | 2 +-
 doc/src/fix_rigid_meso.rst                   | 2 +-
 doc/src/fix_rx.rst                           | 2 +-
 doc/src/fix_saed_vtk.rst                     | 2 +-
 doc/src/fix_setforce.rst                     | 2 +-
 doc/src/fix_sgcmc.rst                        | 2 +-
 doc/src/fix_shake.rst                        | 2 +-
 doc/src/fix_shardlow.rst                     | 2 +-
 doc/src/fix_smd.rst                          | 2 +-
 doc/src/fix_smd_setvel.rst                   | 2 +-
 doc/src/fix_sph.rst                          | 2 +-
 doc/src/fix_sph_stationary.rst               | 2 +-
 doc/src/fix_spring.rst                       | 2 +-
 doc/src/fix_spring_chunk.rst                 | 2 +-
 doc/src/fix_spring_rg.rst                    | 2 +-
 doc/src/fix_spring_self.rst                  | 2 +-
 doc/src/fix_srd.rst                          | 2 +-
 doc/src/fix_store_force.rst                  | 2 +-
 doc/src/fix_store_state.rst                  | 2 +-
 doc/src/fix_temp_berendsen.rst               | 2 +-
 doc/src/fix_temp_csvr.rst                    | 2 +-
 doc/src/fix_temp_rescale.rst                 | 2 +-
 doc/src/fix_temp_rescale_eff.rst             | 2 +-
 doc/src/fix_tfmc.rst                         | 2 +-
 doc/src/fix_tgnh_drude.rst                   | 2 +-
 doc/src/fix_thermal_conductivity.rst         | 2 +-
 doc/src/fix_ti_spring.rst                    | 2 +-
 doc/src/fix_tmd.rst                          | 2 +-
 doc/src/fix_ttm.rst                          | 2 +-
 doc/src/fix_tune_kspace.rst                  | 2 +-
 doc/src/fix_vector.rst                       | 2 +-
 doc/src/fix_viscosity.rst                    | 2 +-
 doc/src/fix_viscous.rst                      | 2 +-
 doc/src/fix_viscous_sphere.rst               | 2 +-
 doc/src/fix_wall.rst                         | 2 +-
 doc/src/fix_wall_body_polygon.rst            | 2 +-
 doc/src/fix_wall_body_polyhedron.rst         | 2 +-
 doc/src/fix_wall_ees.rst                     | 2 +-
 doc/src/fix_wall_gran.rst                    | 2 +-
 doc/src/fix_wall_gran_region.rst             | 2 +-
 doc/src/fix_wall_piston.rst                  | 2 +-
 doc/src/fix_wall_reflect.rst                 | 2 +-
 doc/src/fix_wall_reflect_stochastic.rst      | 2 +-
 doc/src/fix_wall_region.rst                  | 2 +-
 doc/src/fix_wall_srd.rst                     | 2 +-
 doc/src/fix_widom.rst                        | 2 +-
 doc/src/group2ndx.rst                        | 2 +-
 doc/src/hyper.rst                            | 2 +-
 doc/src/include.rst                          | 2 +-
 doc/src/info.rst                             | 2 +-
 doc/src/jump.rst                             | 2 +-
 doc/src/label.rst                            | 2 +-
 doc/src/lattice.rst                          | 2 +-
 doc/src/log.rst                              | 2 +-
 doc/src/mass.rst                             | 2 +-
 doc/src/min_style.rst                        | 2 +-
 doc/src/minimize.rst                         | 2 +-
 doc/src/molecule.rst                         | 2 +-
 doc/src/neb.rst                              | 2 +-
 doc/src/neb_spin.rst                         | 2 +-
 doc/src/neighbor.rst                         | 2 +-
 doc/src/newton.rst                           | 2 +-
 doc/src/next.rst                             | 2 +-
 doc/src/package.rst                          | 2 +-
 doc/src/partition.rst                        | 2 +-
 doc/src/plugin.rst                           | 2 +-
 doc/src/prd.rst                              | 2 +-
 doc/src/print.rst                            | 2 +-
 doc/src/processors.rst                       | 2 +-
 doc/src/python.rst                           | 2 +-
 doc/src/quit.rst                             | 2 +-
 doc/src/region.rst                           | 2 +-
 doc/src/replicate.rst                        | 2 +-
 doc/src/rerun.rst                            | 2 +-
 doc/src/restart.rst                          | 2 +-
 doc/src/run.rst                              | 2 +-
 doc/src/set.rst                              | 2 +-
 doc/src/shell.rst                            | 2 +-
 doc/src/suffix.rst                           | 2 +-
 doc/src/tad.rst                              | 2 +-
 doc/src/temper.rst                           | 2 +-
 doc/src/temper_grem.rst                      | 2 +-
 doc/src/temper_npt.rst                       | 2 +-
 doc/src/thermo.rst                           | 2 +-
 doc/src/timer.rst                            | 2 +-
 doc/src/timestep.rst                         | 2 +-
 doc/src/uncompute.rst                        | 2 +-
 doc/src/undump.rst                           | 2 +-
 doc/src/unfix.rst                            | 2 +-
 doc/src/units.rst                            | 2 +-
 doc/src/variable.rst                         | 2 +-
 doc/src/velocity.rst                         | 2 +-
 318 files changed, 319 insertions(+), 319 deletions(-)

diff --git a/doc/src/atc_add_molecule.rst b/doc/src/atc_add_molecule.rst
index dc0f0318ac..68330da256 100644
--- a/doc/src/atc_add_molecule.rst
+++ b/doc/src/atc_add_molecule.rst
@@ -6,7 +6,7 @@ fix_modify AtC add_molecule command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> add_molecule <small|large> <tag> <group-ID>
 
diff --git a/doc/src/atc_add_species.rst b/doc/src/atc_add_species.rst
index 0b39379e62..3fc2bcb2d3 100644
--- a/doc/src/atc_add_species.rst
+++ b/doc/src/atc_add_species.rst
@@ -6,7 +6,7 @@ fix_modify AtC add_species command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> add_species <tag> <group|type> <ID>
 
diff --git a/doc/src/atc_atom_element_map.rst b/doc/src/atc_atom_element_map.rst
index 96895acc8e..f614e8f350 100644
--- a/doc/src/atc_atom_element_map.rst
+++ b/doc/src/atc_atom_element_map.rst
@@ -6,7 +6,7 @@ fix_modify AtC atom_element_map command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> atom_element_map <eulerian|lagrangian> [<frequency>]
 
diff --git a/doc/src/atc_atom_weight.rst b/doc/src/atc_atom_weight.rst
index 50e7ea146d..1e1d771ef1 100644
--- a/doc/src/atc_atom_weight.rst
+++ b/doc/src/atc_atom_weight.rst
@@ -6,7 +6,7 @@ fix_modify AtC atom_weight command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> atom_weight <method> <args>
 
diff --git a/doc/src/atc_atomic_charge.rst b/doc/src/atc_atomic_charge.rst
index 4b3d34b815..1207043324 100644
--- a/doc/src/atc_atomic_charge.rst
+++ b/doc/src/atc_atomic_charge.rst
@@ -6,7 +6,7 @@ fix_modify AtC atomic_charge command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> <include|omit> atomic_charge
 
diff --git a/doc/src/atc_boundary_dynamics.rst b/doc/src/atc_boundary_dynamics.rst
index 696d091094..6b571f53d0 100644
--- a/doc/src/atc_boundary_dynamics.rst
+++ b/doc/src/atc_boundary_dynamics.rst
@@ -6,7 +6,7 @@ fix_modify AtC boundary_dynamics command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> boundary_dynamics <on|damped_harmonic|prescribed|coupled|none>
 
diff --git a/doc/src/atc_boundary_faceset.rst b/doc/src/atc_boundary_faceset.rst
index c33239b833..7c0654cc00 100644
--- a/doc/src/atc_boundary_faceset.rst
+++ b/doc/src/atc_boundary_faceset.rst
@@ -6,7 +6,7 @@ fix_modify AtC boundary_faceset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> boundary_faceset <is|add> <faceset_name>
 
diff --git a/doc/src/atc_boundary_type.rst b/doc/src/atc_boundary_type.rst
index 26b40e5a12..a43c17a658 100644
--- a/doc/src/atc_boundary_type.rst
+++ b/doc/src/atc_boundary_type.rst
@@ -6,7 +6,7 @@ fix_modify AtC boundary type command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> boundary type <atom-type-id>
 
diff --git a/doc/src/atc_consistent_fe_initialization.rst b/doc/src/atc_consistent_fe_initialization.rst
index 3241752262..78f7699906 100644
--- a/doc/src/atc_consistent_fe_initialization.rst
+++ b/doc/src/atc_consistent_fe_initialization.rst
@@ -6,7 +6,7 @@ fix_modify AtC consistent_fe_initialization command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> consistent_fe_initialization <on|off>
 
diff --git a/doc/src/atc_control_localized_lambda.rst b/doc/src/atc_control_localized_lambda.rst
index eb286756b7..ca0bba30d5 100644
--- a/doc/src/atc_control_localized_lambda.rst
+++ b/doc/src/atc_control_localized_lambda.rst
@@ -6,7 +6,7 @@ fix_modify AtC control localized_lambda command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> control localized_lambda <on|off>
 
diff --git a/doc/src/atc_control_momentum.rst b/doc/src/atc_control_momentum.rst
index e87bd789b9..fcc3570e06 100644
--- a/doc/src/atc_control_momentum.rst
+++ b/doc/src/atc_control_momentum.rst
@@ -6,7 +6,7 @@ fix_modify AtC control momentum command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> control <physics_type> <solution_parameter> <value>
    fix_modify AtC control momentum none
diff --git a/doc/src/atc_control_thermal.rst b/doc/src/atc_control_thermal.rst
index 7a17701c5c..c14e52ac8f 100644
--- a/doc/src/atc_control_thermal.rst
+++ b/doc/src/atc_control_thermal.rst
@@ -6,7 +6,7 @@ fix_modify AtC control thermal command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> control <physics_type> <solution_parameter> <value>
    fix_modify <AtC fixID> control thermal <control_type> <optional_args>
diff --git a/doc/src/atc_decomposition.rst b/doc/src/atc_decomposition.rst
index 50d11bf52f..182a27d915 100644
--- a/doc/src/atc_decomposition.rst
+++ b/doc/src/atc_decomposition.rst
@@ -6,7 +6,7 @@ fix_modify AtC decomposition command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> decomposition <type>
 
diff --git a/doc/src/atc_electron_integration.rst b/doc/src/atc_electron_integration.rst
index 2f3fd9eee2..b3cd858e3d 100644
--- a/doc/src/atc_electron_integration.rst
+++ b/doc/src/atc_electron_integration.rst
@@ -6,7 +6,7 @@ fix_modify AtC extrinsic electron_integration command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> extrinsic electron_integration <integration_type> [<num_subcycle_steps>]
 
diff --git a/doc/src/atc_equilibrium_start.rst b/doc/src/atc_equilibrium_start.rst
index 0068dc02c3..b1ef99dc11 100644
--- a/doc/src/atc_equilibrium_start.rst
+++ b/doc/src/atc_equilibrium_start.rst
@@ -6,7 +6,7 @@ fix_modify AtC equilibrium_start command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> equilibrium_start <on|off>
 
diff --git a/doc/src/atc_extrinsic_exchange.rst b/doc/src/atc_extrinsic_exchange.rst
index 03d794115b..55aa4115b5 100644
--- a/doc/src/atc_extrinsic_exchange.rst
+++ b/doc/src/atc_extrinsic_exchange.rst
@@ -6,7 +6,7 @@ fix_modify AtC extrinsic exchange command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> extrinsic exchange <on|off>
 
diff --git a/doc/src/atc_fe_md_boundary.rst b/doc/src/atc_fe_md_boundary.rst
index ad66bf6d49..ebc783c333 100644
--- a/doc/src/atc_fe_md_boundary.rst
+++ b/doc/src/atc_fe_md_boundary.rst
@@ -6,7 +6,7 @@ fix_modify AtC fe_md_boundary command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> fe_md_boundary <faceset|interpolate|no_boundary>
 
diff --git a/doc/src/atc_filter_scale.rst b/doc/src/atc_filter_scale.rst
index ce62a589eb..100906d9f7 100644
--- a/doc/src/atc_filter_scale.rst
+++ b/doc/src/atc_filter_scale.rst
@@ -6,7 +6,7 @@ fix_modify AtC filter scale command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> filter scale <scale>
 
diff --git a/doc/src/atc_filter_type.rst b/doc/src/atc_filter_type.rst
index 5e2da80755..605c84c192 100644
--- a/doc/src/atc_filter_type.rst
+++ b/doc/src/atc_filter_type.rst
@@ -6,7 +6,7 @@ fix_modify AtC filter type command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> filter type <exponential|step|no_filter>
 
diff --git a/doc/src/atc_fix.rst b/doc/src/atc_fix.rst
index d3ba972508..77bc37ccef 100644
--- a/doc/src/atc_fix.rst
+++ b/doc/src/atc_fix.rst
@@ -6,7 +6,7 @@ fix_modify AtC fix command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> fix <field> <nodeset> <constant|function>
 
diff --git a/doc/src/atc_fix_flux.rst b/doc/src/atc_fix_flux.rst
index 12699e9163..71513eb1f9 100644
--- a/doc/src/atc_fix_flux.rst
+++ b/doc/src/atc_fix_flux.rst
@@ -6,7 +6,7 @@ fix_modify AtC fix_flux command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> fix_flux <field> <face_set> <value|function>
 
diff --git a/doc/src/atc_hardy_computes.rst b/doc/src/atc_hardy_computes.rst
index 609740fe99..fe42a6265f 100644
--- a/doc/src/atc_hardy_computes.rst
+++ b/doc/src/atc_hardy_computes.rst
@@ -6,7 +6,7 @@ fix_modify AtC computes command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> computes <add|delete> <per-atom compute-ID> <volume|number>
 
diff --git a/doc/src/atc_hardy_fields.rst b/doc/src/atc_hardy_fields.rst
index bef051bbe8..0159bb55ab 100644
--- a/doc/src/atc_hardy_fields.rst
+++ b/doc/src/atc_hardy_fields.rst
@@ -6,7 +6,7 @@ fix_modify AtC fields command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> fields <all|none>
    fix_modify <AtC fixID> fields <add|delete> <list_of_fields>
diff --git a/doc/src/atc_hardy_gradients.rst b/doc/src/atc_hardy_gradients.rst
index 2e7649d73c..52d05eac7c 100644
--- a/doc/src/atc_hardy_gradients.rst
+++ b/doc/src/atc_hardy_gradients.rst
@@ -6,7 +6,7 @@ fix_modify AtC gradients command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> gradients <add|delete> <list_of_fields>
 
diff --git a/doc/src/atc_hardy_kernel.rst b/doc/src/atc_hardy_kernel.rst
index 74316ec8b2..b3a10e8e99 100644
--- a/doc/src/atc_hardy_kernel.rst
+++ b/doc/src/atc_hardy_kernel.rst
@@ -6,7 +6,7 @@ fix_modify AtC kernel command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> kernel <type> <parameters>
 
diff --git a/doc/src/atc_hardy_on_the_fly.rst b/doc/src/atc_hardy_on_the_fly.rst
index fe7c688387..4635d72d13 100644
--- a/doc/src/atc_hardy_on_the_fly.rst
+++ b/doc/src/atc_hardy_on_the_fly.rst
@@ -6,7 +6,7 @@ fix_modify AtC on_the_fly command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> on_the_fly <bond|kernel> <on|off>
 
diff --git a/doc/src/atc_hardy_rates.rst b/doc/src/atc_hardy_rates.rst
index 56166087d7..0c23e211ba 100644
--- a/doc/src/atc_hardy_rates.rst
+++ b/doc/src/atc_hardy_rates.rst
@@ -6,7 +6,7 @@ fix_modify AtC rates command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> rates <add|delete> <list_of_fields>
 
diff --git a/doc/src/atc_initial.rst b/doc/src/atc_initial.rst
index 7d62251c6c..721f0f3538 100644
--- a/doc/src/atc_initial.rst
+++ b/doc/src/atc_initial.rst
@@ -6,7 +6,7 @@ fix_modify AtC initial command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> initial <field> <nodeset> <constant|function>
 
diff --git a/doc/src/atc_internal_element_set.rst b/doc/src/atc_internal_element_set.rst
index 4a376f55a3..e50463feed 100644
--- a/doc/src/atc_internal_element_set.rst
+++ b/doc/src/atc_internal_element_set.rst
@@ -6,7 +6,7 @@ fix_modify AtC internal_element_set command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> internal_element_set <element_set_name>
 
diff --git a/doc/src/atc_internal_quadrature.rst b/doc/src/atc_internal_quadrature.rst
index b171914021..d8e241572c 100644
--- a/doc/src/atc_internal_quadrature.rst
+++ b/doc/src/atc_internal_quadrature.rst
@@ -6,7 +6,7 @@ fix_modify AtC internal_quadrature command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> internal_quadrature <on|off> [region]
 
diff --git a/doc/src/atc_kernel_bandwidth.rst b/doc/src/atc_kernel_bandwidth.rst
index 02707cfd30..f166a063e3 100644
--- a/doc/src/atc_kernel_bandwidth.rst
+++ b/doc/src/atc_kernel_bandwidth.rst
@@ -6,7 +6,7 @@ fix_modify AtC kernel_bandwidth command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> kernel_bandwidth <value>
 
diff --git a/doc/src/atc_lumped_lambda_solve.rst b/doc/src/atc_lumped_lambda_solve.rst
index e777116da5..b64ffb2d01 100644
--- a/doc/src/atc_lumped_lambda_solve.rst
+++ b/doc/src/atc_lumped_lambda_solve.rst
@@ -6,7 +6,7 @@ fix_modify AtC control lumped_lambda_solve command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> control lumped_lambda_solve <on|off>
 
diff --git a/doc/src/atc_mask_direction.rst b/doc/src/atc_mask_direction.rst
index ed5c605834..0e55cc7190 100644
--- a/doc/src/atc_mask_direction.rst
+++ b/doc/src/atc_mask_direction.rst
@@ -6,7 +6,7 @@ fix_modify AtC control mask_direction command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> control mask_direction <direction> <on|off>
 
diff --git a/doc/src/atc_mass_matrix.rst b/doc/src/atc_mass_matrix.rst
index eb586b933b..7763044ec8 100644
--- a/doc/src/atc_mass_matrix.rst
+++ b/doc/src/atc_mass_matrix.rst
@@ -6,7 +6,7 @@ fix_modify AtC mass_matrix command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mass_matrix <fe|md_fe>
 
diff --git a/doc/src/atc_material.rst b/doc/src/atc_material.rst
index 471bffffb2..eef5dbdd0e 100644
--- a/doc/src/atc_material.rst
+++ b/doc/src/atc_material.rst
@@ -6,7 +6,7 @@ fix_modify AtC material command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> material <elementset_name> <material_id>
 
diff --git a/doc/src/atc_mesh_add_to_nodeset.rst b/doc/src/atc_mesh_add_to_nodeset.rst
index f9f6f575fe..0944a51099 100644
--- a/doc/src/atc_mesh_add_to_nodeset.rst
+++ b/doc/src/atc_mesh_add_to_nodeset.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh add_to_nodeset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
 
diff --git a/doc/src/atc_mesh_create.rst b/doc/src/atc_mesh_create.rst
index b17bb8ac0d..289c0e5c56 100644
--- a/doc/src/atc_mesh_create.rst
+++ b/doc/src/atc_mesh_create.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh create command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh create <nx> <ny> <nz> <region-ID> <f|p> <f|p> <f|p>
 
diff --git a/doc/src/atc_mesh_create_elementset.rst b/doc/src/atc_mesh_create_elementset.rst
index 3cb406e7bc..35086b0fc9 100644
--- a/doc/src/atc_mesh_create_elementset.rst
+++ b/doc/src/atc_mesh_create_elementset.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh create_elementset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
 
diff --git a/doc/src/atc_mesh_create_faceset_box.rst b/doc/src/atc_mesh_create_faceset_box.rst
index 09b099d179..29dcfa69ad 100644
--- a/doc/src/atc_mesh_create_faceset_box.rst
+++ b/doc/src/atc_mesh_create_faceset_box.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh create_faceset box command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]
 
diff --git a/doc/src/atc_mesh_create_faceset_plane.rst b/doc/src/atc_mesh_create_faceset_plane.rst
index 035e584044..e36990de40 100644
--- a/doc/src/atc_mesh_create_faceset_plane.rst
+++ b/doc/src/atc_mesh_create_faceset_plane.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh create_faceset plane command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]
 
diff --git a/doc/src/atc_mesh_create_nodeset.rst b/doc/src/atc_mesh_create_nodeset.rst
index a2f9d74d07..943d1c7d19 100644
--- a/doc/src/atc_mesh_create_nodeset.rst
+++ b/doc/src/atc_mesh_create_nodeset.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh create_nodeset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>
 
diff --git a/doc/src/atc_mesh_delete_elements.rst b/doc/src/atc_mesh_delete_elements.rst
index 9785f0adf6..2c9d83d506 100644
--- a/doc/src/atc_mesh_delete_elements.rst
+++ b/doc/src/atc_mesh_delete_elements.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh delete_elements command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh delete_elements <id>
 
diff --git a/doc/src/atc_mesh_nodeset_to_elementset.rst b/doc/src/atc_mesh_nodeset_to_elementset.rst
index d8721cc295..1838aa120f 100644
--- a/doc/src/atc_mesh_nodeset_to_elementset.rst
+++ b/doc/src/atc_mesh_nodeset_to_elementset.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh nodeset_to_elementset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh nodeset_to_elementset <nodeset_id> <elementset_id> <max/min>
 
diff --git a/doc/src/atc_mesh_output.rst b/doc/src/atc_mesh_output.rst
index 63756df98e..237b88eff6 100644
--- a/doc/src/atc_mesh_output.rst
+++ b/doc/src/atc_mesh_output.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh output command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh output <file_prefix>
 
diff --git a/doc/src/atc_mesh_quadrature.rst b/doc/src/atc_mesh_quadrature.rst
index 0c9bd4b30f..4cc94d77e2 100644
--- a/doc/src/atc_mesh_quadrature.rst
+++ b/doc/src/atc_mesh_quadrature.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh quadrature command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh quatrature <quad>
 
diff --git a/doc/src/atc_mesh_read.rst b/doc/src/atc_mesh_read.rst
index 9848e12b07..dcc999166f 100644
--- a/doc/src/atc_mesh_read.rst
+++ b/doc/src/atc_mesh_read.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh read command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh read <f|p> <f|p> <f|p>
 
diff --git a/doc/src/atc_mesh_write.rst b/doc/src/atc_mesh_write.rst
index dbb8f9c219..2636f51fc5 100644
--- a/doc/src/atc_mesh_write.rst
+++ b/doc/src/atc_mesh_write.rst
@@ -6,7 +6,7 @@ fix_modify AtC mesh write command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> mesh write <f|p> <f|p> <f|p>
 
diff --git a/doc/src/atc_output.rst b/doc/src/atc_output.rst
index 5003817daa..13df4c7d58 100644
--- a/doc/src/atc_output.rst
+++ b/doc/src/atc_output.rst
@@ -6,7 +6,7 @@ fix_modify AtC output command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> output <filename_prefix> <frequency> [text|full_text|binary|vector_components|tensor_components]
    fix_modify <AtC fixID> output index [step|time]
diff --git a/doc/src/atc_output_boundary_integral.rst b/doc/src/atc_output_boundary_integral.rst
index 71a3e03ac2..65ad6e835e 100644
--- a/doc/src/atc_output_boundary_integral.rst
+++ b/doc/src/atc_output_boundary_integral.rst
@@ -6,7 +6,7 @@ fix_modify AtC output boundary_integral command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> output boundary_integral <fieldname> faceset [name]
 
diff --git a/doc/src/atc_output_contour_integral.rst b/doc/src/atc_output_contour_integral.rst
index 24678ef6cc..fa6ab8c9d1 100644
--- a/doc/src/atc_output_contour_integral.rst
+++ b/doc/src/atc_output_contour_integral.rst
@@ -6,7 +6,7 @@ fix_modify AtC output contour_integral command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> output contour_integral <fieldname> faceset <name> [axis [x|y|z]]
 
diff --git a/doc/src/atc_output_nodeset.rst b/doc/src/atc_output_nodeset.rst
index eb12a2344e..e5d1580274 100644
--- a/doc/src/atc_output_nodeset.rst
+++ b/doc/src/atc_output_nodeset.rst
@@ -6,7 +6,7 @@ fix_modify AtC output nodeset command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> output nodeset <nodeset_name> <operation>
 
diff --git a/doc/src/atc_output_volume_integral.rst b/doc/src/atc_output_volume_integral.rst
index 464d43cbce..a740c56e8b 100644
--- a/doc/src/atc_output_volume_integral.rst
+++ b/doc/src/atc_output_volume_integral.rst
@@ -6,7 +6,7 @@ fix_modify AtC output volume_integral command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> output volume_integral <elementset_name> <field>
 
diff --git a/doc/src/atc_pair_interactions.rst b/doc/src/atc_pair_interactions.rst
index 73ada09001..d8de219d89 100644
--- a/doc/src/atc_pair_interactions.rst
+++ b/doc/src/atc_pair_interactions.rst
@@ -9,7 +9,7 @@ fix_modify AtC bond_interactions command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> pair_interactions <on|off>
    fix_modify <AtC fixID> bond_interactions <on|off>
diff --git a/doc/src/atc_poisson_solver.rst b/doc/src/atc_poisson_solver.rst
index d37f214b97..e203c3dc51 100644
--- a/doc/src/atc_poisson_solver.rst
+++ b/doc/src/atc_poisson_solver.rst
@@ -6,7 +6,7 @@ fix_modify AtC poisson_solver command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> poisson_solver mesh create <nx> <ny> <nz> <region-ID> <f|p> <f|p> <f|p>
 
diff --git a/doc/src/atc_read_restart.rst b/doc/src/atc_read_restart.rst
index 11ba4519a4..32badbd3a8 100644
--- a/doc/src/atc_read_restart.rst
+++ b/doc/src/atc_read_restart.rst
@@ -6,7 +6,7 @@ fix_modify AtC read_restart command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> read_restart <file_name>
 
diff --git a/doc/src/atc_remove_molecule.rst b/doc/src/atc_remove_molecule.rst
index a654cd5c1d..13c0856307 100644
--- a/doc/src/atc_remove_molecule.rst
+++ b/doc/src/atc_remove_molecule.rst
@@ -6,7 +6,7 @@ fix_modify AtC remove_molecule command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> remove_molecule <tag>
 
diff --git a/doc/src/atc_remove_source.rst b/doc/src/atc_remove_source.rst
index d98b7933da..253166cd3c 100644
--- a/doc/src/atc_remove_source.rst
+++ b/doc/src/atc_remove_source.rst
@@ -6,7 +6,7 @@ fix_modify AtC remove_source command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> remove_source <field> <element_set>
 
diff --git a/doc/src/atc_remove_species.rst b/doc/src/atc_remove_species.rst
index 5c4fd771ba..b7718a6874 100644
--- a/doc/src/atc_remove_species.rst
+++ b/doc/src/atc_remove_species.rst
@@ -6,7 +6,7 @@ fix_modify AtC remove_species command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> remove_species <tag>
 
diff --git a/doc/src/atc_reset_atomic_reference.rst b/doc/src/atc_reset_atomic_reference.rst
index 8f53cbfbe9..43acc9b4b2 100644
--- a/doc/src/atc_reset_atomic_reference.rst
+++ b/doc/src/atc_reset_atomic_reference.rst
@@ -6,7 +6,7 @@ fix_modify AtC reset_atomic_reference_positions command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> reset_atomic_reference_positions
 
diff --git a/doc/src/atc_reset_time.rst b/doc/src/atc_reset_time.rst
index 147a6ab910..f02c723011 100644
--- a/doc/src/atc_reset_time.rst
+++ b/doc/src/atc_reset_time.rst
@@ -6,7 +6,7 @@ fix_modify AtC reset_time command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> reset_time <value>
 
diff --git a/doc/src/atc_sample_frequency.rst b/doc/src/atc_sample_frequency.rst
index 5b0da6d9dd..e61e9fd6ed 100644
--- a/doc/src/atc_sample_frequency.rst
+++ b/doc/src/atc_sample_frequency.rst
@@ -6,7 +6,7 @@ fix_modify AtC sample_frequency command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> sample_frequency <freq>
 
diff --git a/doc/src/atc_set_reference_pe.rst b/doc/src/atc_set_reference_pe.rst
index 8053a1df98..f85e3f7ebc 100644
--- a/doc/src/atc_set_reference_pe.rst
+++ b/doc/src/atc_set_reference_pe.rst
@@ -6,7 +6,7 @@ fix_modify AtC set reference_potential_energy command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> set reference_potential_energy [<value|filename>]
 
diff --git a/doc/src/atc_source.rst b/doc/src/atc_source.rst
index 6df4b67d1c..ce712c8186 100644
--- a/doc/src/atc_source.rst
+++ b/doc/src/atc_source.rst
@@ -6,7 +6,7 @@ fix_modify AtC source command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> source <field> <element_set> <value|function>
 
diff --git a/doc/src/atc_source_integration.rst b/doc/src/atc_source_integration.rst
index b10e6c7e2a..a145a7c9f1 100644
--- a/doc/src/atc_source_integration.rst
+++ b/doc/src/atc_source_integration.rst
@@ -6,7 +6,7 @@ fix_modify AtC source_integration command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> source_integration <fe|atom>
 
diff --git a/doc/src/atc_temperature_definition.rst b/doc/src/atc_temperature_definition.rst
index b5a27467ca..0194e38314 100644
--- a/doc/src/atc_temperature_definition.rst
+++ b/doc/src/atc_temperature_definition.rst
@@ -6,7 +6,7 @@ fix_modify AtC temperature_definition command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> temperature_definition <kinetic|total>
 
diff --git a/doc/src/atc_time_filter.rst b/doc/src/atc_time_filter.rst
index 0a97c83259..76163a77b5 100644
--- a/doc/src/atc_time_filter.rst
+++ b/doc/src/atc_time_filter.rst
@@ -6,7 +6,7 @@ fix_modify AtC filter command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> filter <on|off|equilibrate>
 
diff --git a/doc/src/atc_time_integration.rst b/doc/src/atc_time_integration.rst
index cf746dde0d..3eae147a6e 100644
--- a/doc/src/atc_time_integration.rst
+++ b/doc/src/atc_time_integration.rst
@@ -6,7 +6,7 @@ fix_modify AtC time_integration command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> time_integration <descriptor>
 
diff --git a/doc/src/atc_track_displacement.rst b/doc/src/atc_track_displacement.rst
index 043f42ea9c..f5a2d1742c 100644
--- a/doc/src/atc_track_displacement.rst
+++ b/doc/src/atc_track_displacement.rst
@@ -6,7 +6,7 @@ fix_modify AtC track_displacement command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> track_displacement <on|off>
 
diff --git a/doc/src/atc_unfix.rst b/doc/src/atc_unfix.rst
index 12ee37bbde..c6ada6dcca 100644
--- a/doc/src/atc_unfix.rst
+++ b/doc/src/atc_unfix.rst
@@ -6,7 +6,7 @@ fix_modify AtC unfix command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> unfix <field> <nodeset>
 
diff --git a/doc/src/atc_unfix_flux.rst b/doc/src/atc_unfix_flux.rst
index da9d1b4aba..73ef5b17af 100644
--- a/doc/src/atc_unfix_flux.rst
+++ b/doc/src/atc_unfix_flux.rst
@@ -6,7 +6,7 @@ fix_modify AtC unfix_flux command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> unfix_flux <field> <face_set> <value|function>
 
diff --git a/doc/src/atc_write_atom_weights.rst b/doc/src/atc_write_atom_weights.rst
index ecb69b5deb..40af619356 100644
--- a/doc/src/atc_write_atom_weights.rst
+++ b/doc/src/atc_write_atom_weights.rst
@@ -6,7 +6,7 @@ fix_modify AtC write_atom_weights command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> write_atom_weights <filename> <frequency>
 
diff --git a/doc/src/atc_write_restart.rst b/doc/src/atc_write_restart.rst
index e4f19dea10..75945e1715 100644
--- a/doc/src/atc_write_restart.rst
+++ b/doc/src/atc_write_restart.rst
@@ -6,7 +6,7 @@ fix_modify AtC write_restart command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix_modify <AtC fixID> write_restart <file_name>
 
diff --git a/doc/src/compute_property_grid.rst b/doc/src/compute_property_grid.rst
index e65e822516..44389320d6 100644
--- a/doc/src/compute_property_grid.rst
+++ b/doc/src/compute_property_grid.rst
@@ -6,7 +6,7 @@ compute property/grid command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID property/grid Nx Ny Nz input1 input2 ...
 
diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst
index 43fee39cf2..8ec19ade66 100644
--- a/doc/src/compute_reduce_chunk.rst
+++ b/doc/src/compute_reduce_chunk.rst
@@ -6,7 +6,7 @@ compute reduce/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID reduce/chunk chunkID mode input1 input2 ...
 
diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst
index deb6a61f7c..9ec455d03b 100644
--- a/doc/src/compute_saed.rst
+++ b/doc/src/compute_saed.rst
@@ -6,7 +6,7 @@ compute saed command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID saed lambda type1 type2 ... typeN keyword value ...
 
diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst
index 9b4e7df626..0da7c99573 100644
--- a/doc/src/compute_slice.rst
+++ b/doc/src/compute_slice.rst
@@ -6,7 +6,7 @@ compute slice command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID slice Nstart Nstop Nskip input1 input2 ...
 
diff --git a/doc/src/compute_smd_contact_radius.rst b/doc/src/compute_smd_contact_radius.rst
index 4911ac4e27..2ac039a3b5 100644
--- a/doc/src/compute_smd_contact_radius.rst
+++ b/doc/src/compute_smd_contact_radius.rst
@@ -6,7 +6,7 @@ compute smd/contact/radius command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/contact/radius
 
diff --git a/doc/src/compute_smd_damage.rst b/doc/src/compute_smd_damage.rst
index fe5d94fa83..72307bc184 100644
--- a/doc/src/compute_smd_damage.rst
+++ b/doc/src/compute_smd_damage.rst
@@ -6,7 +6,7 @@ compute smd/damage command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/damage
 
diff --git a/doc/src/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst
index 7e0aadd6d2..533c0f03c0 100644
--- a/doc/src/compute_smd_hourglass_error.rst
+++ b/doc/src/compute_smd_hourglass_error.rst
@@ -6,7 +6,7 @@ compute smd/hourglass/error command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/hourglass/error
 
diff --git a/doc/src/compute_smd_internal_energy.rst b/doc/src/compute_smd_internal_energy.rst
index 36bd816e8f..91c671c6a1 100644
--- a/doc/src/compute_smd_internal_energy.rst
+++ b/doc/src/compute_smd_internal_energy.rst
@@ -6,7 +6,7 @@ compute smd/internal/energy command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/internal/energy
 
diff --git a/doc/src/compute_smd_plastic_strain.rst b/doc/src/compute_smd_plastic_strain.rst
index 00c6cb9a4a..b1e5719249 100644
--- a/doc/src/compute_smd_plastic_strain.rst
+++ b/doc/src/compute_smd_plastic_strain.rst
@@ -6,7 +6,7 @@ compute smd/plastic/strain command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/plastic/strain
 
diff --git a/doc/src/compute_smd_plastic_strain_rate.rst b/doc/src/compute_smd_plastic_strain_rate.rst
index 681573be9b..bf9b3b23f4 100644
--- a/doc/src/compute_smd_plastic_strain_rate.rst
+++ b/doc/src/compute_smd_plastic_strain_rate.rst
@@ -6,7 +6,7 @@ compute smd/plastic/strain/rate command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/plastic/strain/rate
 
diff --git a/doc/src/compute_smd_rho.rst b/doc/src/compute_smd_rho.rst
index 605dd5b79c..8ecb09f318 100644
--- a/doc/src/compute_smd_rho.rst
+++ b/doc/src/compute_smd_rho.rst
@@ -6,7 +6,7 @@ compute smd/rho command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/rho
 
diff --git a/doc/src/compute_smd_tlsph_defgrad.rst b/doc/src/compute_smd_tlsph_defgrad.rst
index 399e54d055..aceecc1722 100644
--- a/doc/src/compute_smd_tlsph_defgrad.rst
+++ b/doc/src/compute_smd_tlsph_defgrad.rst
@@ -6,7 +6,7 @@ compute smd/tlsph/defgrad command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/defgrad
 
diff --git a/doc/src/compute_smd_tlsph_dt.rst b/doc/src/compute_smd_tlsph_dt.rst
index 9490f7da14..1cafecdb7c 100644
--- a/doc/src/compute_smd_tlsph_dt.rst
+++ b/doc/src/compute_smd_tlsph_dt.rst
@@ -6,7 +6,7 @@ compute smd/tlsph/dt command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/dt
 
diff --git a/doc/src/compute_smd_tlsph_num_neighs.rst b/doc/src/compute_smd_tlsph_num_neighs.rst
index ef8c19d49c..8bf244a8db 100644
--- a/doc/src/compute_smd_tlsph_num_neighs.rst
+++ b/doc/src/compute_smd_tlsph_num_neighs.rst
@@ -6,7 +6,7 @@ compute smd/tlsph/num/neighs command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/num/neighs
 
diff --git a/doc/src/compute_smd_tlsph_shape.rst b/doc/src/compute_smd_tlsph_shape.rst
index 4a5abd868b..b682e72fdd 100644
--- a/doc/src/compute_smd_tlsph_shape.rst
+++ b/doc/src/compute_smd_tlsph_shape.rst
@@ -6,7 +6,7 @@ compute smd/tlsph/shape command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/shape
 
diff --git a/doc/src/compute_smd_tlsph_strain.rst b/doc/src/compute_smd_tlsph_strain.rst
index 053488886b..89b9bee132 100644
--- a/doc/src/compute_smd_tlsph_strain.rst
+++ b/doc/src/compute_smd_tlsph_strain.rst
@@ -6,7 +6,7 @@ compute smd/tlsph/strain command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/strain
 
diff --git a/doc/src/compute_smd_tlsph_strain_rate.rst b/doc/src/compute_smd_tlsph_strain_rate.rst
index 2f3d561cee..83797edd49 100644
--- a/doc/src/compute_smd_tlsph_strain_rate.rst
+++ b/doc/src/compute_smd_tlsph_strain_rate.rst
@@ -6,7 +6,7 @@ compute smd/tlsph/strain/rate command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/strain/rate
 
diff --git a/doc/src/compute_smd_tlsph_stress.rst b/doc/src/compute_smd_tlsph_stress.rst
index 4f0473f30a..12539ffda7 100644
--- a/doc/src/compute_smd_tlsph_stress.rst
+++ b/doc/src/compute_smd_tlsph_stress.rst
@@ -6,7 +6,7 @@ compute smd/tlsph/stress command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/tlsph/stress
 
diff --git a/doc/src/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst
index 309c4260e9..2e7dd0cfd0 100644
--- a/doc/src/compute_smd_triangle_vertices.rst
+++ b/doc/src/compute_smd_triangle_vertices.rst
@@ -6,7 +6,7 @@ compute smd/triangle/vertices command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/triangle/vertices
 
diff --git a/doc/src/compute_smd_vol.rst b/doc/src/compute_smd_vol.rst
index d31eb53785..94372c23ce 100644
--- a/doc/src/compute_smd_vol.rst
+++ b/doc/src/compute_smd_vol.rst
@@ -6,7 +6,7 @@ compute smd/vol command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID smd/vol
 
diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst
index d604ca9d29..8d06868f3d 100644
--- a/doc/src/compute_sna_atom.rst
+++ b/doc/src/compute_sna_atom.rst
@@ -26,7 +26,7 @@ compute sna/grid/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
    compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
diff --git a/doc/src/compute_sph_e_atom.rst b/doc/src/compute_sph_e_atom.rst
index 5e6706fa27..d557eb7920 100644
--- a/doc/src/compute_sph_e_atom.rst
+++ b/doc/src/compute_sph_e_atom.rst
@@ -6,7 +6,7 @@ compute sph/e/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID sph/e/atom
 
diff --git a/doc/src/compute_sph_rho_atom.rst b/doc/src/compute_sph_rho_atom.rst
index 7fcec0c9da..6e8579476a 100644
--- a/doc/src/compute_sph_rho_atom.rst
+++ b/doc/src/compute_sph_rho_atom.rst
@@ -6,7 +6,7 @@ compute sph/rho/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID sph/rho/atom
 
diff --git a/doc/src/compute_sph_t_atom.rst b/doc/src/compute_sph_t_atom.rst
index 702d81027d..3383c26145 100644
--- a/doc/src/compute_sph_t_atom.rst
+++ b/doc/src/compute_sph_t_atom.rst
@@ -6,7 +6,7 @@ compute sph/t/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID sph/t/atom
 
diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst
index dd3354faaa..25d1efff7d 100644
--- a/doc/src/dump_image.rst
+++ b/doc/src/dump_image.rst
@@ -98,7 +98,7 @@ dump_modify options for dump image/movie
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump_modify dump-ID keyword values ...
 
diff --git a/doc/src/dump_molfile.rst b/doc/src/dump_molfile.rst
index ffc0b443e0..2878bc7b73 100644
--- a/doc/src/dump_molfile.rst
+++ b/doc/src/dump_molfile.rst
@@ -6,7 +6,7 @@ dump molfile command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump ID group-ID molfile N file format path
 
diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst
index 296b725e20..f7495e29a8 100644
--- a/doc/src/dump_netcdf.rst
+++ b/doc/src/dump_netcdf.rst
@@ -10,7 +10,7 @@ dump netcdf/mpiio command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    dump ID group-ID netcdf N file args
    dump ID group-ID netcdf/mpiio N file args
diff --git a/doc/src/fitpod_command.rst b/doc/src/fitpod_command.rst
index fc21caec70..28afb990ff 100644
--- a/doc/src/fitpod_command.rst
+++ b/doc/src/fitpod_command.rst
@@ -6,7 +6,7 @@ fitpod command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fitpod Ta_param.pod Ta_data.pod
 
diff --git a/doc/src/fix_alchemy.rst b/doc/src/fix_alchemy.rst
index 4f0ad06fd4..14273d65c4 100644
--- a/doc/src/fix_alchemy.rst
+++ b/doc/src/fix_alchemy.rst
@@ -6,7 +6,7 @@ fix alchemy command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID alchemy v_name
 
diff --git a/doc/src/fix_ave_grid.rst b/doc/src/fix_ave_grid.rst
index da0d1f957b..a79a6cf486 100644
--- a/doc/src/fix_ave_grid.rst
+++ b/doc/src/fix_ave_grid.rst
@@ -6,7 +6,7 @@ fix ave/grid command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ave/grid Nevery Nrepeat Nfreq Nx Ny Nz value1 value2 ... keyword args ...
 
diff --git a/doc/src/fix_bond_swap.rst b/doc/src/fix_bond_swap.rst
index c7535c21b1..6448dd6e1c 100644
--- a/doc/src/fix_bond_swap.rst
+++ b/doc/src/fix_bond_swap.rst
@@ -6,7 +6,7 @@ fix bond/swap command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID bond/swap Nevery fraction cutoff seed
 
diff --git a/doc/src/fix_box_relax.rst b/doc/src/fix_box_relax.rst
index 5efbfcab1b..9f1dade765 100644
--- a/doc/src/fix_box_relax.rst
+++ b/doc/src/fix_box_relax.rst
@@ -6,7 +6,7 @@ fix box/relax command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID box/relax keyword value ...
 
diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst
index 203d40951d..bc2651a55b 100644
--- a/doc/src/fix_charge_regulation.rst
+++ b/doc/src/fix_charge_regulation.rst
@@ -7,7 +7,7 @@ fix charge/regulation command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
     fix ID group-ID charge/regulation cation_type anion_type keyword value(s)
 
@@ -45,10 +45,10 @@ Syntax
 
 Examples
 """"""""
+
 .. code-block:: LAMMPS
 
     fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5.0 pKb 6.0 pH 7.0 pIp 3.0 pIm 3.0 nevery 200 nmc 200 seed 123 tempfixid fT
-
     fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0
 
 Description
diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst
index 19d8cd2d52..316ad5d038 100644
--- a/doc/src/fix_cmap.rst
+++ b/doc/src/fix_cmap.rst
@@ -6,7 +6,7 @@ fix cmap command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID cmap filename
 
diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst
index 77a90cc54f..5acd79ba34 100644
--- a/doc/src/fix_colvars.rst
+++ b/doc/src/fix_colvars.rst
@@ -6,7 +6,7 @@ fix colvars command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID colvars configfile keyword values ...
 
diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst
index d03d9a123c..fc8186ef29 100644
--- a/doc/src/fix_controller.rst
+++ b/doc/src/fix_controller.rst
@@ -6,7 +6,7 @@ fix controller command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID controller Nevery alpha Kp Ki Kd pvar setpoint cvar
 
diff --git a/doc/src/fix_damping_cundall.rst b/doc/src/fix_damping_cundall.rst
index 262291c0b8..5c532f08d0 100644
--- a/doc/src/fix_damping_cundall.rst
+++ b/doc/src/fix_damping_cundall.rst
@@ -6,7 +6,7 @@ fix damping/cundall command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID damping/cundall gamma_l gamma_a keyword values ...
 
diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst
index 9adf5b4aa2..ee010f5645 100644
--- a/doc/src/fix_deform.rst
+++ b/doc/src/fix_deform.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *deform/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID deform N parameter args ... keyword value ...
 
diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst
index c8746bcf9c..7d2d28bfa9 100644
--- a/doc/src/fix_deposit.rst
+++ b/doc/src/fix_deposit.rst
@@ -6,7 +6,7 @@ fix deposit command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID deposit N type M seed keyword values ...
 
diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst
index d6e8dd7230..ef5a5ed073 100644
--- a/doc/src/fix_dpd_energy.rst
+++ b/doc/src/fix_dpd_energy.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *dpd/energy/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID dpd/energy
 
diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst
index 71894161f1..8ec5163854 100644
--- a/doc/src/fix_dpd_source.rst
+++ b/doc/src/fix_dpd_source.rst
@@ -10,7 +10,7 @@ fix tdpd/source command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID edpd/source keyword values ...
    fix ID group-ID tdpd/source cc_index keyword values ...
diff --git a/doc/src/fix_drag.rst b/doc/src/fix_drag.rst
index 3bfc5420de..9e29762cf5 100644
--- a/doc/src/fix_drag.rst
+++ b/doc/src/fix_drag.rst
@@ -6,7 +6,7 @@ fix drag command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID drag x y z fmag delta
 
diff --git a/doc/src/fix_drude.rst b/doc/src/fix_drude.rst
index 5300d1f490..679d6eb4bf 100644
--- a/doc/src/fix_drude.rst
+++ b/doc/src/fix_drude.rst
@@ -6,7 +6,7 @@ fix drude command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID drude flag1 flag2 ... flagN
 
diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst
index bd63a411be..399bf2dd45 100644
--- a/doc/src/fix_drude_transform.rst
+++ b/doc/src/fix_drude_transform.rst
@@ -10,7 +10,7 @@ fix drude/transform/inverse command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style keyword value ...
 
diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst
index 5757f0ec99..03b07776e6 100644
--- a/doc/src/fix_dt_reset.rst
+++ b/doc/src/fix_dt_reset.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *dt/reset/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ...
 
diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst
index e38e1e6894..2958d89794 100644
--- a/doc/src/fix_efield.rst
+++ b/doc/src/fix_efield.rst
@@ -10,7 +10,7 @@ fix efield/tip4p command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style ex ey ez keyword value ...
 
diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst
index 186ed7065e..d7c09ce36c 100644
--- a/doc/src/fix_ehex.rst
+++ b/doc/src/fix_ehex.rst
@@ -6,7 +6,7 @@ fix ehex command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ehex nevery F keyword value
 
diff --git a/doc/src/fix_electron_stopping.rst b/doc/src/fix_electron_stopping.rst
index fa0fc763f5..681a000321 100644
--- a/doc/src/fix_electron_stopping.rst
+++ b/doc/src/fix_electron_stopping.rst
@@ -10,7 +10,7 @@ fix electron/stopping/fit command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style args
 
diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst
index a8061e5eaa..5dd0b79057 100644
--- a/doc/src/fix_enforce2d.rst
+++ b/doc/src/fix_enforce2d.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *enforce2d/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID enforce2d
 
diff --git a/doc/src/fix_eos_cv.rst b/doc/src/fix_eos_cv.rst
index c43b5461b1..3f5c87cd38 100644
--- a/doc/src/fix_eos_cv.rst
+++ b/doc/src/fix_eos_cv.rst
@@ -6,7 +6,7 @@ fix eos/cv command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID eos/cv cv
 
diff --git a/doc/src/fix_eos_table.rst b/doc/src/fix_eos_table.rst
index bfb8ec2c3c..533904b0e7 100644
--- a/doc/src/fix_eos_table.rst
+++ b/doc/src/fix_eos_table.rst
@@ -6,7 +6,7 @@ fix eos/table command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID eos/table style file N keyword
 
diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst
index c9f134f985..104fa79c20 100644
--- a/doc/src/fix_eos_table_rx.rst
+++ b/doc/src/fix_eos_table_rx.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *eos/table/rx/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID eos/table/rx style file1 N keyword ...
 
diff --git a/doc/src/fix_evaporate.rst b/doc/src/fix_evaporate.rst
index c8e46631a3..1df58aa5d5 100644
--- a/doc/src/fix_evaporate.rst
+++ b/doc/src/fix_evaporate.rst
@@ -6,7 +6,7 @@ fix evaporate command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID evaporate N M region-ID seed
 
diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst
index a3677a350c..44dd0929ee 100644
--- a/doc/src/fix_external.rst
+++ b/doc/src/fix_external.rst
@@ -6,7 +6,7 @@ fix external command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID external mode args
 
diff --git a/doc/src/fix_ffl.rst b/doc/src/fix_ffl.rst
index 6058b0ed3e..04e4d9be90 100644
--- a/doc/src/fix_ffl.rst
+++ b/doc/src/fix_ffl.rst
@@ -6,7 +6,7 @@ fix ffl command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID id-group ffl tau Tstart Tstop seed [flip-type]
 
diff --git a/doc/src/fix_filter_corotate.rst b/doc/src/fix_filter_corotate.rst
index c0a2216be3..7c091140df 100644
--- a/doc/src/fix_filter_corotate.rst
+++ b/doc/src/fix_filter_corotate.rst
@@ -6,7 +6,7 @@ fix filter/corotate command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID filter/corotate keyword value ...
 
diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst
index 87ab283923..6100c5d635 100644
--- a/doc/src/fix_flow_gauss.rst
+++ b/doc/src/fix_flow_gauss.rst
@@ -6,7 +6,7 @@ fix flow/gauss command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID flow/gauss xflag yflag zflag keyword
 
diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst
index ce79ce3caf..9b579633b1 100644
--- a/doc/src/fix_freeze.rst
+++ b/doc/src/fix_freeze.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *freeze/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID freeze
 
diff --git a/doc/src/fix_gcmc.rst b/doc/src/fix_gcmc.rst
index c0fa990d6e..13ae509684 100644
--- a/doc/src/fix_gcmc.rst
+++ b/doc/src/fix_gcmc.rst
@@ -6,7 +6,7 @@ fix gcmc command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
 
diff --git a/doc/src/fix_gld.rst b/doc/src/fix_gld.rst
index d0fd6a4c9e..ba26f7a51b 100644
--- a/doc/src/fix_gld.rst
+++ b/doc/src/fix_gld.rst
@@ -6,7 +6,7 @@ fix gld command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ...
 
diff --git a/doc/src/fix_gle.rst b/doc/src/fix_gle.rst
index 03add9d354..d28a9bbf0d 100644
--- a/doc/src/fix_gle.rst
+++ b/doc/src/fix_gle.rst
@@ -6,7 +6,7 @@ fix gle command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID id-group gle Ns Tstart Tstop seed Amatrix [noneq Cmatrix] [every stride]
 
diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst
index 6d34cc1bf3..cd7cfcc3df 100644
--- a/doc/src/fix_gravity.rst
+++ b/doc/src/fix_gravity.rst
@@ -10,7 +10,7 @@ Accelerator Variants: *gravity/omp*, *gravity/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group gravity magnitude style args
 
diff --git a/doc/src/fix_grem.rst b/doc/src/fix_grem.rst
index 3e3ec02994..9cc6e3f43e 100644
--- a/doc/src/fix_grem.rst
+++ b/doc/src/fix_grem.rst
@@ -6,7 +6,7 @@ fix grem command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID grem lambda eta H0 thermostat-ID
 
diff --git a/doc/src/fix_halt.rst b/doc/src/fix_halt.rst
index 56e86208cd..4231c77cc5 100644
--- a/doc/src/fix_halt.rst
+++ b/doc/src/fix_halt.rst
@@ -6,7 +6,7 @@ fix halt command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID halt N attribute operator avalue keyword value ...
 
diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst
index 19bc3d84ca..1badf08bff 100644
--- a/doc/src/fix_heat.rst
+++ b/doc/src/fix_heat.rst
@@ -6,7 +6,7 @@ fix heat command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID heat N eflux
 
diff --git a/doc/src/fix_heat_flow.rst b/doc/src/fix_heat_flow.rst
index ee73d7d4f2..1ca99a1686 100644
--- a/doc/src/fix_heat_flow.rst
+++ b/doc/src/fix_heat_flow.rst
@@ -6,7 +6,7 @@ fix heat/flow command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID heat/flow style values ...
 
diff --git a/doc/src/fix_hyper_global.rst b/doc/src/fix_hyper_global.rst
index c8643b3b86..2ac1e5e4f3 100644
--- a/doc/src/fix_hyper_global.rst
+++ b/doc/src/fix_hyper_global.rst
@@ -6,7 +6,7 @@ fix hyper/global command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID hyper/global cutbond qfactor Vmax Tequil
 
diff --git a/doc/src/fix_hyper_local.rst b/doc/src/fix_hyper_local.rst
index b5350e9765..76b17cddc4 100644
--- a/doc/src/fix_hyper_local.rst
+++ b/doc/src/fix_hyper_local.rst
@@ -6,7 +6,7 @@ fix hyper/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID hyper/local cutbond qfactor Vmax Tequil Dcut alpha Btarget
 
diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst
index cb1831d174..520af505a1 100644
--- a/doc/src/fix_imd.rst
+++ b/doc/src/fix_imd.rst
@@ -6,7 +6,7 @@ fix imd command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID imd trate port keyword values ...
 
diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst
index c8349e9381..15790e15d0 100644
--- a/doc/src/fix_indent.rst
+++ b/doc/src/fix_indent.rst
@@ -6,7 +6,7 @@ fix indent command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID indent K keyword values ...
 
diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst
index 5e13d25971..7705f211e8 100644
--- a/doc/src/fix_ipi.rst
+++ b/doc/src/fix_ipi.rst
@@ -6,7 +6,7 @@ fix ipi command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ipi address port [unix] [reset]
 
diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst
index c09fc7b928..e04805427e 100644
--- a/doc/src/fix_langevin.rst
+++ b/doc/src/fix_langevin.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *langevin/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID langevin Tstart Tstop damp seed keyword values ...
 
diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst
index 5e62e4f416..c53c29b3ac 100644
--- a/doc/src/fix_langevin_drude.rst
+++ b/doc/src/fix_langevin_drude.rst
@@ -6,7 +6,7 @@ fix langevin/drude command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ...
 
diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst
index 506b5052d5..21cdc4a789 100644
--- a/doc/src/fix_langevin_eff.rst
+++ b/doc/src/fix_langevin_eff.rst
@@ -6,7 +6,7 @@ fix langevin/eff command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ...
 
diff --git a/doc/src/fix_langevin_spin.rst b/doc/src/fix_langevin_spin.rst
index 0ca291a732..c82751a755 100644
--- a/doc/src/fix_langevin_spin.rst
+++ b/doc/src/fix_langevin_spin.rst
@@ -6,7 +6,7 @@ fix langevin/spin command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID langevin/spin T Tdamp seed
 
diff --git a/doc/src/fix_lb_fluid.rst b/doc/src/fix_lb_fluid.rst
index 04f306156a..a461175f71 100644
--- a/doc/src/fix_lb_fluid.rst
+++ b/doc/src/fix_lb_fluid.rst
@@ -6,7 +6,7 @@ fix lb/fluid command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID lb/fluid nevery viscosity density keyword values ...
 
diff --git a/doc/src/fix_lb_momentum.rst b/doc/src/fix_lb_momentum.rst
index 8b2c5e6ae2..67a8d86d5f 100644
--- a/doc/src/fix_lb_momentum.rst
+++ b/doc/src/fix_lb_momentum.rst
@@ -6,7 +6,7 @@ fix lb/momentum command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID lb/momentum nevery keyword values ...
 
diff --git a/doc/src/fix_lb_viscous.rst b/doc/src/fix_lb_viscous.rst
index 6e0ec21b7e..5557cba57f 100644
--- a/doc/src/fix_lb_viscous.rst
+++ b/doc/src/fix_lb_viscous.rst
@@ -6,7 +6,7 @@ fix lb/viscous command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID lb/viscous
 
diff --git a/doc/src/fix_lineforce.rst b/doc/src/fix_lineforce.rst
index e82f6ed556..9b1d30e832 100644
--- a/doc/src/fix_lineforce.rst
+++ b/doc/src/fix_lineforce.rst
@@ -6,7 +6,7 @@ fix lineforce command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID lineforce x y z
 
diff --git a/doc/src/fix_manifoldforce.rst b/doc/src/fix_manifoldforce.rst
index 2d72743707..cd5fffc881 100644
--- a/doc/src/fix_manifoldforce.rst
+++ b/doc/src/fix_manifoldforce.rst
@@ -6,7 +6,7 @@ fix manifoldforce command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID manifoldforce manifold manifold-args ...
 
diff --git a/doc/src/fix_mdi_qm.rst b/doc/src/fix_mdi_qm.rst
index 3d0b350407..0868cbbac8 100644
--- a/doc/src/fix_mdi_qm.rst
+++ b/doc/src/fix_mdi_qm.rst
@@ -6,7 +6,7 @@ fix mdi/qm command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID mdi/qm keyword value(s) keyword value(s) ...
 
diff --git a/doc/src/fix_mdi_qmmm.rst b/doc/src/fix_mdi_qmmm.rst
index 1afce0f7e4..a39f8ba71d 100644
--- a/doc/src/fix_mdi_qmmm.rst
+++ b/doc/src/fix_mdi_qmmm.rst
@@ -6,7 +6,7 @@ fix mdi/qmmm command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID mdi/qmmm mode keyword value(s) keyword value(s) ...
 
diff --git a/doc/src/fix_meso_move.rst b/doc/src/fix_meso_move.rst
index 7b3609a8c7..55d54b2107 100644
--- a/doc/src/fix_meso_move.rst
+++ b/doc/src/fix_meso_move.rst
@@ -6,7 +6,7 @@ fix meso/move command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID meso/move style args keyword values ...
 
diff --git a/doc/src/fix_mol_swap.rst b/doc/src/fix_mol_swap.rst
index 737536fa0d..b344b9c0e6 100644
--- a/doc/src/fix_mol_swap.rst
+++ b/doc/src/fix_mol_swap.rst
@@ -6,7 +6,7 @@ fix mol/swap command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID mol/swap N X itype jtype seed T keyword value ...
 
diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst
index dff30fffc4..727cb176a1 100644
--- a/doc/src/fix_momentum.rst
+++ b/doc/src/fix_momentum.rst
@@ -13,7 +13,7 @@ fix momentum/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID momentum N keyword values ...
 
diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst
index ff1f8403df..3fde5f0861 100644
--- a/doc/src/fix_move.rst
+++ b/doc/src/fix_move.rst
@@ -6,7 +6,7 @@ fix move command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID move style args keyword values ...
 
diff --git a/doc/src/fix_mscg.rst b/doc/src/fix_mscg.rst
index 3255f3fbe9..91eb0fe772 100644
--- a/doc/src/fix_mscg.rst
+++ b/doc/src/fix_mscg.rst
@@ -6,7 +6,7 @@ fix mscg command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID mscg N keyword args ...
 
diff --git a/doc/src/fix_msst.rst b/doc/src/fix_msst.rst
index 9502fe21b8..6750934f61 100644
--- a/doc/src/fix_msst.rst
+++ b/doc/src/fix_msst.rst
@@ -6,7 +6,7 @@ fix msst command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID msst dir shockvel keyword value ...
 
diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst
index c2f8a50391..ff5b169f97 100644
--- a/doc/src/fix_mvv_dpd.rst
+++ b/doc/src/fix_mvv_dpd.rst
@@ -14,7 +14,7 @@ fix mvv/tdpd command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID mvv/dpd lambda
 
diff --git a/doc/src/fix_neb.rst b/doc/src/fix_neb.rst
index 5f22acfb2b..ccd0f9b83d 100644
--- a/doc/src/fix_neb.rst
+++ b/doc/src/fix_neb.rst
@@ -6,7 +6,7 @@ fix neb command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID neb Kspring keyword value
 
diff --git a/doc/src/fix_neb_spin.rst b/doc/src/fix_neb_spin.rst
index 16baba44c0..d04ba367c4 100644
--- a/doc/src/fix_neb_spin.rst
+++ b/doc/src/fix_neb_spin.rst
@@ -6,7 +6,7 @@ fix neb/spin command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID neb/spin Kspring
 
diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst
index 7f2ec69f9b..0cfbc8f921 100644
--- a/doc/src/fix_nh.rst
+++ b/doc/src/fix_nh.rst
@@ -30,7 +30,7 @@ Accelerator Variants: *nph/kk*, *nph/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style_name keyword value ...
 
diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst
index 11990d365b..7f0f8ee8f1 100644
--- a/doc/src/fix_nh_eff.rst
+++ b/doc/src/fix_nh_eff.rst
@@ -14,7 +14,7 @@ fix nph/eff command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style_name keyword value ...
 
diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst
index 922c2d515a..a515375746 100644
--- a/doc/src/fix_nh_uef.rst
+++ b/doc/src/fix_nh_uef.rst
@@ -10,7 +10,7 @@ fix npt/uef command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style_name erate edot_x edot_y temp Tstart Tstop Tdamp keyword value ...
 
diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst
index a1028efacc..93938fdd58 100644
--- a/doc/src/fix_nph_asphere.rst
+++ b/doc/src/fix_nph_asphere.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *nph/asphere/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nph/asphere args keyword value ...
 
diff --git a/doc/src/fix_nph_body.rst b/doc/src/fix_nph_body.rst
index 1b740a5ae2..9ee0bd7669 100644
--- a/doc/src/fix_nph_body.rst
+++ b/doc/src/fix_nph_body.rst
@@ -6,7 +6,7 @@ fix nph/body command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nph/body args keyword value ...
 
diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst
index 2ef85953e5..9d47cedc28 100644
--- a/doc/src/fix_nph_sphere.rst
+++ b/doc/src/fix_nph_sphere.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *nph/sphere/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nph/sphere args keyword value ...
 
diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst
index 1cedfa909a..ce63f5eddd 100644
--- a/doc/src/fix_nphug.rst
+++ b/doc/src/fix_nphug.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *nphug/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nphug keyword value ...
 
diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst
index 64e1c45be7..0d195821ad 100644
--- a/doc/src/fix_npt_asphere.rst
+++ b/doc/src/fix_npt_asphere.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *npt/asphere/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID npt/asphere keyword value ...
 
diff --git a/doc/src/fix_npt_body.rst b/doc/src/fix_npt_body.rst
index ff98638b63..31ef1653b8 100644
--- a/doc/src/fix_npt_body.rst
+++ b/doc/src/fix_npt_body.rst
@@ -6,7 +6,7 @@ fix npt/body command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID npt/body keyword value ...
 
diff --git a/doc/src/fix_npt_cauchy.rst b/doc/src/fix_npt_cauchy.rst
index 36b22037bf..6764f88eee 100644
--- a/doc/src/fix_npt_cauchy.rst
+++ b/doc/src/fix_npt_cauchy.rst
@@ -6,7 +6,7 @@ fix npt/cauchy command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style_name keyword value ...
 
diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst
index afaa2c9d67..f881bc2dfe 100644
--- a/doc/src/fix_npt_sphere.rst
+++ b/doc/src/fix_npt_sphere.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *npt/sphere/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID npt/sphere keyword value ...
 
diff --git a/doc/src/fix_numdiff.rst b/doc/src/fix_numdiff.rst
index b5fdfb12e6..9b3d3bf7da 100644
--- a/doc/src/fix_numdiff.rst
+++ b/doc/src/fix_numdiff.rst
@@ -6,7 +6,7 @@ fix numdiff command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID numdiff Nevery delta
 
diff --git a/doc/src/fix_numdiff_virial.rst b/doc/src/fix_numdiff_virial.rst
index f909d41111..2075d1d05f 100644
--- a/doc/src/fix_numdiff_virial.rst
+++ b/doc/src/fix_numdiff_virial.rst
@@ -6,7 +6,7 @@ fix numdiff/virial command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID numdiff/virial Nevery delta
 
diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst
index c50bc4d62f..3757233bcc 100644
--- a/doc/src/fix_nve.rst
+++ b/doc/src/fix_nve.rst
@@ -12,7 +12,7 @@ Accelerator Variants: *nve/gpu*, *nve/intel*, *nve/kk*, *nve/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve
 
diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst
index fbba2bc8dd..cf956bd0c4 100644
--- a/doc/src/fix_nve_asphere.rst
+++ b/doc/src/fix_nve_asphere.rst
@@ -10,7 +10,7 @@ Accelerator Variants: *nve/asphere/gpu*, *nve/asphere/intel*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/asphere
 
diff --git a/doc/src/fix_nve_asphere_noforce.rst b/doc/src/fix_nve_asphere_noforce.rst
index 7d904bef1c..9e6f35b56b 100644
--- a/doc/src/fix_nve_asphere_noforce.rst
+++ b/doc/src/fix_nve_asphere_noforce.rst
@@ -6,7 +6,7 @@ fix nve/asphere/noforce command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/asphere/noforce
 
diff --git a/doc/src/fix_nve_awpmd.rst b/doc/src/fix_nve_awpmd.rst
index c716a94a84..f835758e00 100644
--- a/doc/src/fix_nve_awpmd.rst
+++ b/doc/src/fix_nve_awpmd.rst
@@ -6,7 +6,7 @@ fix nve/awpmd command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/awpmd
 
diff --git a/doc/src/fix_nve_body.rst b/doc/src/fix_nve_body.rst
index 45beee0659..9f562ef59e 100644
--- a/doc/src/fix_nve_body.rst
+++ b/doc/src/fix_nve_body.rst
@@ -6,7 +6,7 @@ fix nve/body command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/body
 
diff --git a/doc/src/fix_nve_bpm_sphere.rst b/doc/src/fix_nve_bpm_sphere.rst
index ef170605a4..fb3bd9e466 100644
--- a/doc/src/fix_nve_bpm_sphere.rst
+++ b/doc/src/fix_nve_bpm_sphere.rst
@@ -6,7 +6,7 @@ fix nve/bpm/sphere command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/bpm/sphere
 
diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst
index 0a99e11452..0d6e0ab5c3 100644
--- a/doc/src/fix_nve_dot.rst
+++ b/doc/src/fix_nve_dot.rst
@@ -6,7 +6,7 @@ fix nve/dot command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/dot
 
diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst
index e47e8f4a2a..51efa06a02 100644
--- a/doc/src/fix_nve_dotc_langevin.rst
+++ b/doc/src/fix_nve_dotc_langevin.rst
@@ -6,7 +6,7 @@ fix nve/dotc/langevin command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value
 
diff --git a/doc/src/fix_nve_eff.rst b/doc/src/fix_nve_eff.rst
index 60bece43d0..1cf954a88d 100644
--- a/doc/src/fix_nve_eff.rst
+++ b/doc/src/fix_nve_eff.rst
@@ -6,7 +6,7 @@ fix nve/eff command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/eff
 
diff --git a/doc/src/fix_nve_limit.rst b/doc/src/fix_nve_limit.rst
index 0c572c6c6a..b00a5d64ca 100644
--- a/doc/src/fix_nve_limit.rst
+++ b/doc/src/fix_nve_limit.rst
@@ -6,7 +6,7 @@ fix nve/limit command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/limit xmax
 
diff --git a/doc/src/fix_nve_line.rst b/doc/src/fix_nve_line.rst
index 5bb6fd4213..7574110041 100644
--- a/doc/src/fix_nve_line.rst
+++ b/doc/src/fix_nve_line.rst
@@ -6,7 +6,7 @@ fix nve/line command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/line
 
diff --git a/doc/src/fix_nve_manifold_rattle.rst b/doc/src/fix_nve_manifold_rattle.rst
index 63632ebac0..6adf72ac55 100644
--- a/doc/src/fix_nve_manifold_rattle.rst
+++ b/doc/src/fix_nve_manifold_rattle.rst
@@ -6,7 +6,7 @@ fix nve/manifold/rattle command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/manifold/rattle tol maxit manifold manifold-args keyword value ...
 
diff --git a/doc/src/fix_nve_noforce.rst b/doc/src/fix_nve_noforce.rst
index ed13123403..9b9c30d325 100644
--- a/doc/src/fix_nve_noforce.rst
+++ b/doc/src/fix_nve_noforce.rst
@@ -6,7 +6,7 @@ fix nve/noforce command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve
 
diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst
index df177a2eca..9340e4af22 100644
--- a/doc/src/fix_nve_sphere.rst
+++ b/doc/src/fix_nve_sphere.rst
@@ -10,7 +10,7 @@ Accelerator Variants: *nve/sphere/omp*, *nve/sphere/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/sphere
 
diff --git a/doc/src/fix_nve_spin.rst b/doc/src/fix_nve_spin.rst
index e35647aef4..6edc9da09a 100644
--- a/doc/src/fix_nve_spin.rst
+++ b/doc/src/fix_nve_spin.rst
@@ -6,7 +6,7 @@ fix nve/spin command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/spin keyword values
 
diff --git a/doc/src/fix_nve_tri.rst b/doc/src/fix_nve_tri.rst
index b511d9b318..1bcecb71db 100644
--- a/doc/src/fix_nve_tri.rst
+++ b/doc/src/fix_nve_tri.rst
@@ -6,7 +6,7 @@ fix nve/tri command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nve/tri
 
diff --git a/doc/src/fix_nvk.rst b/doc/src/fix_nvk.rst
index 0d83a4b1be..d74ec1639c 100644
--- a/doc/src/fix_nvk.rst
+++ b/doc/src/fix_nvk.rst
@@ -6,7 +6,7 @@ fix nvk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nvk
 
diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst
index 7ce3aec125..b456516e3c 100644
--- a/doc/src/fix_nvt_asphere.rst
+++ b/doc/src/fix_nvt_asphere.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *nvt/asphere/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nvt/asphere keyword value ...
 
diff --git a/doc/src/fix_nvt_body.rst b/doc/src/fix_nvt_body.rst
index 7b9e996a5b..4397159515 100644
--- a/doc/src/fix_nvt_body.rst
+++ b/doc/src/fix_nvt_body.rst
@@ -6,7 +6,7 @@ fix nvt/body command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nvt/body keyword value ...
 
diff --git a/doc/src/fix_nvt_manifold_rattle.rst b/doc/src/fix_nvt_manifold_rattle.rst
index 91a5f28649..921022d743 100644
--- a/doc/src/fix_nvt_manifold_rattle.rst
+++ b/doc/src/fix_nvt_manifold_rattle.rst
@@ -6,7 +6,7 @@ fix nvt/manifold/rattle command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nvt/manifold/rattle tol maxit manifold manifold-args keyword value ...
 
diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst
index 48d0bb5946..430ed31c14 100644
--- a/doc/src/fix_nvt_sllod.rst
+++ b/doc/src/fix_nvt_sllod.rst
@@ -11,7 +11,7 @@ Accelerator Variants: *nvt/sllod/intel*, *nvt/sllod/omp*, *nvt/sllod/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nvt/sllod keyword value ...
 
diff --git a/doc/src/fix_nvt_sllod_eff.rst b/doc/src/fix_nvt_sllod_eff.rst
index dd4dd469ef..71a7e75b80 100644
--- a/doc/src/fix_nvt_sllod_eff.rst
+++ b/doc/src/fix_nvt_sllod_eff.rst
@@ -6,7 +6,7 @@ fix nvt/sllod/eff command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nvt/sllod/eff keyword value ...
 
diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst
index f107940af9..6baa79532c 100644
--- a/doc/src/fix_nvt_sphere.rst
+++ b/doc/src/fix_nvt_sphere.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *nvt/sphere/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID nvt/sphere keyword value ...
 
diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst
index 272797fa17..b4a55e9968 100644
--- a/doc/src/fix_oneway.rst
+++ b/doc/src/fix_oneway.rst
@@ -6,7 +6,7 @@ fix oneway command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID oneway N region-ID direction
 
diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst
index 68522209b7..7e30b7bb01 100644
--- a/doc/src/fix_orient.rst
+++ b/doc/src/fix_orient.rst
@@ -10,7 +10,7 @@ fix orient/bcc command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1
    fix ID group-ID orient/bcc nstats dir alat dE cutlo cuthi file0 file1
diff --git a/doc/src/fix_pafi.rst b/doc/src/fix_pafi.rst
index c8830316a2..a57fc658fc 100644
--- a/doc/src/fix_pafi.rst
+++ b/doc/src/fix_pafi.rst
@@ -6,7 +6,7 @@ fix pafi command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID pafi compute-ID Temp Tdamp seed keyword values...
 
diff --git a/doc/src/fix_pair.rst b/doc/src/fix_pair.rst
index 07e934d1c0..ec4a5bcb3f 100644
--- a/doc/src/fix_pair.rst
+++ b/doc/src/fix_pair.rst
@@ -6,7 +6,7 @@ fix pair command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID pair N pstyle name flag ...
 
diff --git a/doc/src/fix_phonon.rst b/doc/src/fix_phonon.rst
index 527498bb21..e99d2b6891 100644
--- a/doc/src/fix_phonon.rst
+++ b/doc/src/fix_phonon.rst
@@ -6,7 +6,7 @@ fix phonon command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ...
 
diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst
index c08a4005f5..5b51b97c52 100644
--- a/doc/src/fix_pimd.rst
+++ b/doc/src/fix_pimd.rst
@@ -10,7 +10,7 @@ fix pimd/nvt command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style keyword value ...
 
diff --git a/doc/src/fix_planeforce.rst b/doc/src/fix_planeforce.rst
index d0f1b8102e..f4032cf829 100644
--- a/doc/src/fix_planeforce.rst
+++ b/doc/src/fix_planeforce.rst
@@ -6,7 +6,7 @@ fix planeforce command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID planeforce x y z
 
diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst
index c562ecc81d..ca56f83958 100644
--- a/doc/src/fix_plumed.rst
+++ b/doc/src/fix_plumed.rst
@@ -6,7 +6,7 @@ fix plumed command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID plumed keyword value ...
 
diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst
index 7ecb4eef7d..a43e552fbb 100644
--- a/doc/src/fix_poems.rst
+++ b/doc/src/fix_poems.rst
@@ -6,7 +6,7 @@ fix poems command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID poems keyword values
 
diff --git a/doc/src/fix_polarize.rst b/doc/src/fix_polarize.rst
index f35e34bc67..93ef1e4276 100644
--- a/doc/src/fix_polarize.rst
+++ b/doc/src/fix_polarize.rst
@@ -14,7 +14,7 @@ fix polarize/functional command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style nevery tolerance
 
diff --git a/doc/src/fix_pour.rst b/doc/src/fix_pour.rst
index 8a7000662e..eca1f70c41 100644
--- a/doc/src/fix_pour.rst
+++ b/doc/src/fix_pour.rst
@@ -6,7 +6,7 @@ fix pour command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID pour N type seed keyword values ...
 
diff --git a/doc/src/fix_press_berendsen.rst b/doc/src/fix_press_berendsen.rst
index dee93c5b8b..09ec44e673 100644
--- a/doc/src/fix_press_berendsen.rst
+++ b/doc/src/fix_press_berendsen.rst
@@ -6,7 +6,7 @@ fix press/berendsen command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID press/berendsen keyword value ...
 
diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst
index 05abbe3c98..1ec643a635 100644
--- a/doc/src/fix_print.rst
+++ b/doc/src/fix_print.rst
@@ -6,7 +6,7 @@ fix print command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID print N string keyword value ...
 
diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst
index 863d43b6f2..0b932c7316 100644
--- a/doc/src/fix_propel_self.rst
+++ b/doc/src/fix_propel_self.rst
@@ -6,7 +6,7 @@ fix propel/self command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID propel/self mode magnitude keyword values
 
diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst
index d09c15d192..b177fe9a96 100644
--- a/doc/src/fix_property_atom.rst
+++ b/doc/src/fix_property_atom.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *property/atom/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID property/atom name1 name2 ... keyword value ...
 
diff --git a/doc/src/fix_python_invoke.rst b/doc/src/fix_python_invoke.rst
index c82fb91a27..ad55882270 100644
--- a/doc/src/fix_python_invoke.rst
+++ b/doc/src/fix_python_invoke.rst
@@ -6,7 +6,7 @@ fix python/invoke command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID python/invoke N callback function_name
 
diff --git a/doc/src/fix_python_move.rst b/doc/src/fix_python_move.rst
index b338dcbfac..63898f3aa1 100644
--- a/doc/src/fix_python_move.rst
+++ b/doc/src/fix_python_move.rst
@@ -6,7 +6,7 @@ fix python/move command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix python/move pymodule.CLASS
 
diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst
index 5428eeb637..3234335b6b 100644
--- a/doc/src/fix_qbmsst.rst
+++ b/doc/src/fix_qbmsst.rst
@@ -6,7 +6,7 @@ fix qbmsst command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID qbmsst dir shockvel keyword value ...
 
diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst
index 73cf013fb9..bace7af0ca 100644
--- a/doc/src/fix_qeq.rst
+++ b/doc/src/fix_qeq.rst
@@ -22,7 +22,7 @@ fix qeq/fire command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ...
 
diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst
index 0c04a8c4a7..f93a650c17 100644
--- a/doc/src/fix_qeq_comb.rst
+++ b/doc/src/fix_qeq_comb.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *qeq/comb/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID qeq/comb Nevery precision keyword value ...
 
diff --git a/doc/src/fix_qeq_reaxff.rst b/doc/src/fix_qeq_reaxff.rst
index 00cfb6d3ce..e90842ea6a 100644
--- a/doc/src/fix_qeq_reaxff.rst
+++ b/doc/src/fix_qeq_reaxff.rst
@@ -10,7 +10,7 @@ Accelerator Variants: *qeq/reaxff/kk*, *qeq/reaxff/omp*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID qeq/reaxff Nevery cutlo cuthi tolerance params args
 
diff --git a/doc/src/fix_qmmm.rst b/doc/src/fix_qmmm.rst
index 546635520c..eabbdbba03 100644
--- a/doc/src/fix_qmmm.rst
+++ b/doc/src/fix_qmmm.rst
@@ -6,7 +6,7 @@ fix qmmm command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID qmmm
 
diff --git a/doc/src/fix_qtb.rst b/doc/src/fix_qtb.rst
index c41a58a8f4..2112a0f14b 100644
--- a/doc/src/fix_qtb.rst
+++ b/doc/src/fix_qtb.rst
@@ -6,7 +6,7 @@ fix qtb command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID qtb keyword value ...
 
diff --git a/doc/src/fix_reaxff_bonds.rst b/doc/src/fix_reaxff_bonds.rst
index 15b2eb6da9..15fd9abafa 100644
--- a/doc/src/fix_reaxff_bonds.rst
+++ b/doc/src/fix_reaxff_bonds.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *reaxff/bonds/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID reaxff/bonds Nevery filename
 
diff --git a/doc/src/fix_reaxff_species.rst b/doc/src/fix_reaxff_species.rst
index 6a171ede5e..9bf1a82933 100644
--- a/doc/src/fix_reaxff_species.rst
+++ b/doc/src/fix_reaxff_species.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *reaxff/species/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID reaxff/species Nevery Nrepeat Nfreq filename keyword value ...
 
diff --git a/doc/src/fix_recenter.rst b/doc/src/fix_recenter.rst
index 520564677a..9991904b37 100644
--- a/doc/src/fix_recenter.rst
+++ b/doc/src/fix_recenter.rst
@@ -6,7 +6,7 @@ fix recenter command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID recenter x y z keyword value ...
 
diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst
index 9d6114328f..7ac40e1bed 100644
--- a/doc/src/fix_rhok.rst
+++ b/doc/src/fix_rhok.rst
@@ -6,7 +6,7 @@ fix rhok command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID rhok nx ny nz K a
 
diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst
index b6c2c99071..89759da817 100644
--- a/doc/src/fix_rigid.rst
+++ b/doc/src/fix_rigid.rst
@@ -60,7 +60,7 @@ fix rigid/nph/small command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style bodystyle args keyword values ...
 
diff --git a/doc/src/fix_rigid_meso.rst b/doc/src/fix_rigid_meso.rst
index 1c70092092..c8c994fd26 100644
--- a/doc/src/fix_rigid_meso.rst
+++ b/doc/src/fix_rigid_meso.rst
@@ -6,7 +6,7 @@ fix rigid/meso command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID rigid/meso bodystyle args keyword values ...
 
diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst
index 4028a4e7e1..631b227449 100644
--- a/doc/src/fix_rx.rst
+++ b/doc/src/fix_rx.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *rx/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID rx file localTemp matrix solver minSteps ...
 
diff --git a/doc/src/fix_saed_vtk.rst b/doc/src/fix_saed_vtk.rst
index cd3cad7c72..e0cf251780 100644
--- a/doc/src/fix_saed_vtk.rst
+++ b/doc/src/fix_saed_vtk.rst
@@ -6,7 +6,7 @@ fix saed/vtk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
 
diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst
index e115c52991..e194ad4c11 100644
--- a/doc/src/fix_setforce.rst
+++ b/doc/src/fix_setforce.rst
@@ -13,7 +13,7 @@ fix setforce/spin command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID setforce fx fy fz keyword value ...
 
diff --git a/doc/src/fix_sgcmc.rst b/doc/src/fix_sgcmc.rst
index fd6f8beab4..63cfaf22da 100644
--- a/doc/src/fix_sgcmc.rst
+++ b/doc/src/fix_sgcmc.rst
@@ -6,7 +6,7 @@ fix sgcmc command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID sgcmc every_nsteps swap_fraction temperature deltamu ...
 
diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst
index 2483b9431a..73caa9c668 100644
--- a/doc/src/fix_shake.rst
+++ b/doc/src/fix_shake.rst
@@ -13,7 +13,7 @@ fix rattle command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style tol iter N constraint values ... keyword value ...
 
diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst
index 468985be1b..bc2684af53 100644
--- a/doc/src/fix_shardlow.rst
+++ b/doc/src/fix_shardlow.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *shardlow/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID shardlow
 
diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst
index 4c682e66c0..14892227fd 100644
--- a/doc/src/fix_smd.rst
+++ b/doc/src/fix_smd.rst
@@ -6,7 +6,7 @@ fix smd command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID smd type values keyword values
 
diff --git a/doc/src/fix_smd_setvel.rst b/doc/src/fix_smd_setvel.rst
index 9dcc3c636c..31b92491ab 100644
--- a/doc/src/fix_smd_setvel.rst
+++ b/doc/src/fix_smd_setvel.rst
@@ -6,7 +6,7 @@ fix smd/setvel command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID smd/setvel vx vy vz keyword value ...
 
diff --git a/doc/src/fix_sph.rst b/doc/src/fix_sph.rst
index 1133142f05..4932485b03 100644
--- a/doc/src/fix_sph.rst
+++ b/doc/src/fix_sph.rst
@@ -6,7 +6,7 @@ fix sph command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID sph
 
diff --git a/doc/src/fix_sph_stationary.rst b/doc/src/fix_sph_stationary.rst
index 4496a10eca..07bedad4c3 100644
--- a/doc/src/fix_sph_stationary.rst
+++ b/doc/src/fix_sph_stationary.rst
@@ -6,7 +6,7 @@ fix sph/stationary command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID sph/stationary
 
diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst
index 007f2cd278..b85fe26813 100644
--- a/doc/src/fix_spring.rst
+++ b/doc/src/fix_spring.rst
@@ -6,7 +6,7 @@ fix spring command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID spring keyword values
 
diff --git a/doc/src/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst
index 3d3069c53e..63a225e878 100644
--- a/doc/src/fix_spring_chunk.rst
+++ b/doc/src/fix_spring_chunk.rst
@@ -6,7 +6,7 @@ fix spring/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID spring/chunk K chunkID comID
 
diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst
index aba35c8134..e615771d2a 100644
--- a/doc/src/fix_spring_rg.rst
+++ b/doc/src/fix_spring_rg.rst
@@ -6,7 +6,7 @@ fix spring/rg command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID spring/rg K RG0
 
diff --git a/doc/src/fix_spring_self.rst b/doc/src/fix_spring_self.rst
index 6cf0a9e0e7..3383f27ebb 100644
--- a/doc/src/fix_spring_self.rst
+++ b/doc/src/fix_spring_self.rst
@@ -6,7 +6,7 @@ fix spring/self command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID spring/self K dir
 
diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst
index 04eaeed251..1fc574a7ad 100644
--- a/doc/src/fix_srd.rst
+++ b/doc/src/fix_srd.rst
@@ -6,7 +6,7 @@ fix srd command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ...
 
diff --git a/doc/src/fix_store_force.rst b/doc/src/fix_store_force.rst
index f6bed4d4af..487d4f0352 100644
--- a/doc/src/fix_store_force.rst
+++ b/doc/src/fix_store_force.rst
@@ -6,7 +6,7 @@ fix store/force command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID store/force
 
diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst
index b47b6900aa..4a0bef2f74 100644
--- a/doc/src/fix_store_state.rst
+++ b/doc/src/fix_store_state.rst
@@ -6,7 +6,7 @@ fix store/state command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID store/state N input1 input2 ... keyword value ...
 
diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst
index 473c30aced..67e496e6c5 100644
--- a/doc/src/fix_temp_berendsen.rst
+++ b/doc/src/fix_temp_berendsen.rst
@@ -6,7 +6,7 @@ fix temp/berendsen command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID temp/berendsen Tstart Tstop Tdamp
 
diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst
index 5fc6e8eae7..781ce97d96 100644
--- a/doc/src/fix_temp_csvr.rst
+++ b/doc/src/fix_temp_csvr.rst
@@ -10,7 +10,7 @@ fix temp/csld command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID temp/csvr Tstart Tstop Tdamp seed
    fix ID group-ID temp/csld Tstart Tstop Tdamp seed
diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst
index 41ad8709cc..bfdcaa90f8 100644
--- a/doc/src/fix_temp_rescale.rst
+++ b/doc/src/fix_temp_rescale.rst
@@ -6,7 +6,7 @@ fix temp/rescale command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID temp/rescale N Tstart Tstop window fraction
 
diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst
index ea3996e9b6..b92feccfed 100644
--- a/doc/src/fix_temp_rescale_eff.rst
+++ b/doc/src/fix_temp_rescale_eff.rst
@@ -6,7 +6,7 @@ fix temp/rescale/eff command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction
 
diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst
index 7eb4d24935..f3379c1e2f 100644
--- a/doc/src/fix_tfmc.rst
+++ b/doc/src/fix_tfmc.rst
@@ -6,7 +6,7 @@ fix tfmc command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID tfmc Delta Temp seed keyword value
 
diff --git a/doc/src/fix_tgnh_drude.rst b/doc/src/fix_tgnh_drude.rst
index d1f5cf19a4..0a67af291f 100644
--- a/doc/src/fix_tgnh_drude.rst
+++ b/doc/src/fix_tgnh_drude.rst
@@ -11,7 +11,7 @@ fix tgnpt/drude command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style_name keyword values ...
 
diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst
index 0652810267..041fde8be5 100644
--- a/doc/src/fix_thermal_conductivity.rst
+++ b/doc/src/fix_thermal_conductivity.rst
@@ -6,7 +6,7 @@ fix thermal/conductivity command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID thermal/conductivity N edim Nbin keyword value ...
 
diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst
index d519f36157..6273164d52 100644
--- a/doc/src/fix_ti_spring.rst
+++ b/doc/src/fix_ti_spring.rst
@@ -6,7 +6,7 @@ fix ti/spring command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ti/spring k t_s t_eq keyword value ...
 
diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst
index ccebb35823..3ee7f2a5c8 100644
--- a/doc/src/fix_tmd.rst
+++ b/doc/src/fix_tmd.rst
@@ -6,7 +6,7 @@ fix tmd command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID tmd rho_final file1 N file2
 
diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst
index 413c5f5c3c..ccf7f16554 100644
--- a/doc/src/fix_ttm.rst
+++ b/doc/src/fix_ttm.rst
@@ -14,7 +14,7 @@ fix ttm/mod command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz keyword value ...
    fix ID group-ID ttm/mod seed init_file Nx Ny Nz keyword value ...
diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst
index 6a3cba16e4..17e0710be8 100644
--- a/doc/src/fix_tune_kspace.rst
+++ b/doc/src/fix_tune_kspace.rst
@@ -6,7 +6,7 @@ fix tune/kspace command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID tune/kspace N
 
diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst
index f4eee41269..95ec350e12 100644
--- a/doc/src/fix_vector.rst
+++ b/doc/src/fix_vector.rst
@@ -6,7 +6,7 @@ fix vector command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID vector Nevery value1 value2 ...
 
diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst
index c99196e09b..187d723d68 100644
--- a/doc/src/fix_viscosity.rst
+++ b/doc/src/fix_viscosity.rst
@@ -6,7 +6,7 @@ fix viscosity command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID viscosity N vdim pdim Nbin keyword value ...
 
diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst
index d5fd794020..68d2568529 100644
--- a/doc/src/fix_viscous.rst
+++ b/doc/src/fix_viscous.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *viscous/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID viscous gamma keyword values ...
 
diff --git a/doc/src/fix_viscous_sphere.rst b/doc/src/fix_viscous_sphere.rst
index 13463c8c11..678cb9904f 100644
--- a/doc/src/fix_viscous_sphere.rst
+++ b/doc/src/fix_viscous_sphere.rst
@@ -6,7 +6,7 @@ fix viscous/sphere command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID viscous/sphere gamma keyword values ...
 
diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst
index 42cd94978d..eb8219e157 100644
--- a/doc/src/fix_wall.rst
+++ b/doc/src/fix_wall.rst
@@ -37,7 +37,7 @@ fix wall/table command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style [tabstyle] [N] face args ... keyword value ...
 
diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst
index ac0a58f55c..504ded6aaf 100644
--- a/doc/src/fix_wall_body_polygon.rst
+++ b/doc/src/fix_wall_body_polygon.rst
@@ -6,7 +6,7 @@ fix wall/body/polygon command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID wall/body/polygon k_n c_n c_t wallstyle args keyword values ...
 
diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst
index 9930c10f74..86bd35ae02 100644
--- a/doc/src/fix_wall_body_polyhedron.rst
+++ b/doc/src/fix_wall_body_polyhedron.rst
@@ -6,7 +6,7 @@ fix wall/body/polyhedron command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID wall/body/polyhedron k_n c_n c_t wallstyle args keyword values ...
 
diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst
index 9c7f82e015..7bcfc830e2 100644
--- a/doc/src/fix_wall_ees.rst
+++ b/doc/src/fix_wall_ees.rst
@@ -10,7 +10,7 @@ fix wall/region/ees command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style args
 
diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst
index 27d19d60b5..f6465d1159 100644
--- a/doc/src/fix_wall_gran.rst
+++ b/doc/src/fix_wall_gran.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *wall/gran/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID wall/gran fstyle fstyle_params wallstyle args keyword values ...
 
diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst
index 94edebbcf1..0a4343493b 100644
--- a/doc/src/fix_wall_gran_region.rst
+++ b/doc/src/fix_wall_gran_region.rst
@@ -6,7 +6,7 @@ fix wall/gran/region command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID keyword values ...
 
diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst
index 1237d1ac7c..d60d8cb731 100644
--- a/doc/src/fix_wall_piston.rst
+++ b/doc/src/fix_wall_piston.rst
@@ -6,7 +6,7 @@ fix wall/piston command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID wall/piston face ... keyword value ...
 
diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst
index 8bb895280c..c2f4c3a6ab 100644
--- a/doc/src/fix_wall_reflect.rst
+++ b/doc/src/fix_wall_reflect.rst
@@ -9,7 +9,7 @@ Accelerator Variants: *wall/reflect/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID wall/reflect face arg ... keyword value ...
 
diff --git a/doc/src/fix_wall_reflect_stochastic.rst b/doc/src/fix_wall_reflect_stochastic.rst
index 64e3d759c1..5a93950a5d 100644
--- a/doc/src/fix_wall_reflect_stochastic.rst
+++ b/doc/src/fix_wall_reflect_stochastic.rst
@@ -6,7 +6,7 @@ fix wall/reflect/stochastic command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID wall/reflect/stochastic rstyle seed face args ... keyword value ...
 
diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst
index adfd8402c6..466319c12e 100644
--- a/doc/src/fix_wall_region.rst
+++ b/doc/src/fix_wall_region.rst
@@ -6,7 +6,7 @@ fix wall/region command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID wall/region region-ID style args ... cutoff
 
diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst
index a8cbdd1619..dfb6560ffd 100644
--- a/doc/src/fix_wall_srd.rst
+++ b/doc/src/fix_wall_srd.rst
@@ -6,7 +6,7 @@ fix wall/srd command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID wall/srd face arg ... keyword value ...
 
diff --git a/doc/src/fix_widom.rst b/doc/src/fix_widom.rst
index 5be93100b3..ff66095db5 100644
--- a/doc/src/fix_widom.rst
+++ b/doc/src/fix_widom.rst
@@ -6,7 +6,7 @@ fix widom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID widom N M type seed T keyword values ...
 
diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst
index e465c4629f..122341f7f6 100644
--- a/doc/src/group2ndx.rst
+++ b/doc/src/group2ndx.rst
@@ -10,7 +10,7 @@ ndx2group command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    group2ndx file group-ID ...
    ndx2group file group-ID ...
diff --git a/doc/src/hyper.rst b/doc/src/hyper.rst
index 9266a95523..c707c6b3fc 100644
--- a/doc/src/hyper.rst
+++ b/doc/src/hyper.rst
@@ -6,7 +6,7 @@ hyper command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    hyper N Nevent fix-ID compute-ID keyword values ...
 
diff --git a/doc/src/include.rst b/doc/src/include.rst
index 6d146061db..5e19f4a377 100644
--- a/doc/src/include.rst
+++ b/doc/src/include.rst
@@ -6,7 +6,7 @@ include command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    include file
 
diff --git a/doc/src/info.rst b/doc/src/info.rst
index 853e5020fc..958542e3c8 100644
--- a/doc/src/info.rst
+++ b/doc/src/info.rst
@@ -6,7 +6,7 @@ info command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    info args
 
diff --git a/doc/src/jump.rst b/doc/src/jump.rst
index e8047222ef..bf56934d8f 100644
--- a/doc/src/jump.rst
+++ b/doc/src/jump.rst
@@ -6,7 +6,7 @@ jump command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    jump file label
 
diff --git a/doc/src/label.rst b/doc/src/label.rst
index 430587135f..bf232431d7 100644
--- a/doc/src/label.rst
+++ b/doc/src/label.rst
@@ -6,7 +6,7 @@ label command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    label ID
 
diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst
index d4d69c7af0..7dc9c579e5 100644
--- a/doc/src/lattice.rst
+++ b/doc/src/lattice.rst
@@ -6,7 +6,7 @@ lattice command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    lattice style scale keyword values ...
 
diff --git a/doc/src/log.rst b/doc/src/log.rst
index 5d4036dc06..46784f6ea6 100644
--- a/doc/src/log.rst
+++ b/doc/src/log.rst
@@ -6,7 +6,7 @@ log command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    log file keyword
 
diff --git a/doc/src/mass.rst b/doc/src/mass.rst
index f359ccf3a5..88bd14950c 100644
--- a/doc/src/mass.rst
+++ b/doc/src/mass.rst
@@ -6,7 +6,7 @@ mass command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    mass I value
 
diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst
index 2f43308610..b89ae6d398 100644
--- a/doc/src/min_style.rst
+++ b/doc/src/min_style.rst
@@ -27,7 +27,7 @@ min_style fire command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    min_style style
 
diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst
index 6221d33aad..c71c8e3632 100644
--- a/doc/src/minimize.rst
+++ b/doc/src/minimize.rst
@@ -9,7 +9,7 @@ minimize/kk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    minimize etol ftol maxiter maxeval
 
diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst
index b42bece327..480e175e7b 100644
--- a/doc/src/molecule.rst
+++ b/doc/src/molecule.rst
@@ -6,7 +6,7 @@ molecule command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    molecule ID file1 keyword values ... file2 keyword values ... fileN ...
 
diff --git a/doc/src/neb.rst b/doc/src/neb.rst
index a959eee01b..0bc5de010b 100644
--- a/doc/src/neb.rst
+++ b/doc/src/neb.rst
@@ -6,7 +6,7 @@ neb command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    neb etol ftol N1 N2 Nevery file-style arg keyword values
 
diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst
index 9f714096dc..1d42ff884c 100644
--- a/doc/src/neb_spin.rst
+++ b/doc/src/neb_spin.rst
@@ -6,7 +6,7 @@ neb/spin command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    neb/spin etol ttol N1 N2 Nevery file-style arg keyword
 
diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst
index 9dcdd1daf2..12d6d91fde 100644
--- a/doc/src/neighbor.rst
+++ b/doc/src/neighbor.rst
@@ -6,7 +6,7 @@ neighbor command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    neighbor skin style
 
diff --git a/doc/src/newton.rst b/doc/src/newton.rst
index c1a015c3e6..f77c8c54c4 100644
--- a/doc/src/newton.rst
+++ b/doc/src/newton.rst
@@ -6,7 +6,7 @@ newton command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    newton flag
    newton flag1 flag2
diff --git a/doc/src/next.rst b/doc/src/next.rst
index 46d39660eb..d86c15c5fb 100644
--- a/doc/src/next.rst
+++ b/doc/src/next.rst
@@ -6,7 +6,7 @@ next command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    next variables
 
diff --git a/doc/src/package.rst b/doc/src/package.rst
index 0f28598029..63a7f095ad 100644
--- a/doc/src/package.rst
+++ b/doc/src/package.rst
@@ -6,7 +6,7 @@ package command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    package style args
 
diff --git a/doc/src/partition.rst b/doc/src/partition.rst
index f05c3fa446..6b1866d8d8 100644
--- a/doc/src/partition.rst
+++ b/doc/src/partition.rst
@@ -6,7 +6,7 @@ partition command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    partition style N command ...
 
diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst
index 41e2621fef..f8f668789d 100644
--- a/doc/src/plugin.rst
+++ b/doc/src/plugin.rst
@@ -6,7 +6,7 @@ plugin command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    plugin command args
 
diff --git a/doc/src/prd.rst b/doc/src/prd.rst
index 7c6af3abb5..fd20fa4a3b 100644
--- a/doc/src/prd.rst
+++ b/doc/src/prd.rst
@@ -6,7 +6,7 @@ prd command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
 
diff --git a/doc/src/print.rst b/doc/src/print.rst
index a221ed04b6..f5ba16d8b5 100644
--- a/doc/src/print.rst
+++ b/doc/src/print.rst
@@ -6,7 +6,7 @@ print command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    print string keyword value
 
diff --git a/doc/src/processors.rst b/doc/src/processors.rst
index 676f339725..921bbcc667 100644
--- a/doc/src/processors.rst
+++ b/doc/src/processors.rst
@@ -6,7 +6,7 @@ processors command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    processors Px Py Pz keyword args ...
 
diff --git a/doc/src/python.rst b/doc/src/python.rst
index b05de7094d..99f32e7c80 100644
--- a/doc/src/python.rst
+++ b/doc/src/python.rst
@@ -6,7 +6,7 @@ python command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    python mode keyword args ...
 
diff --git a/doc/src/quit.rst b/doc/src/quit.rst
index ba6b4037be..2355fb238b 100644
--- a/doc/src/quit.rst
+++ b/doc/src/quit.rst
@@ -6,7 +6,7 @@ quit command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    quit status
 
diff --git a/doc/src/region.rst b/doc/src/region.rst
index 4589e6deb1..36c7c799dc 100644
--- a/doc/src/region.rst
+++ b/doc/src/region.rst
@@ -6,7 +6,7 @@ region command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    region ID style args keyword arg ...
 
diff --git a/doc/src/replicate.rst b/doc/src/replicate.rst
index ed4e844c35..6bfbeab891 100644
--- a/doc/src/replicate.rst
+++ b/doc/src/replicate.rst
@@ -6,7 +6,7 @@ replicate command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    replicate nx ny nz *keyword*
 
diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst
index cfed2e2872..1c1b4fb570 100644
--- a/doc/src/rerun.rst
+++ b/doc/src/rerun.rst
@@ -6,7 +6,7 @@ rerun command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    rerun file1 file2 ... keyword args ...
 
diff --git a/doc/src/restart.rst b/doc/src/restart.rst
index 5de2d3d75c..10394de80e 100644
--- a/doc/src/restart.rst
+++ b/doc/src/restart.rst
@@ -6,7 +6,7 @@ restart command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    restart 0
    restart N root keyword value ...
diff --git a/doc/src/run.rst b/doc/src/run.rst
index 8bcf469052..c3dd171f6b 100644
--- a/doc/src/run.rst
+++ b/doc/src/run.rst
@@ -6,7 +6,7 @@ run command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    run N keyword values ...
 
diff --git a/doc/src/set.rst b/doc/src/set.rst
index 2ba1057ef5..8a6510f88f 100644
--- a/doc/src/set.rst
+++ b/doc/src/set.rst
@@ -6,7 +6,7 @@ set command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    set style ID keyword values ...
 
diff --git a/doc/src/shell.rst b/doc/src/shell.rst
index fb9baffe08..378ebdc479 100644
--- a/doc/src/shell.rst
+++ b/doc/src/shell.rst
@@ -6,7 +6,7 @@ shell command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    shell command args
 
diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst
index 4789229800..6c723657a5 100644
--- a/doc/src/suffix.rst
+++ b/doc/src/suffix.rst
@@ -6,7 +6,7 @@ suffix command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    suffix style args
 
diff --git a/doc/src/tad.rst b/doc/src/tad.rst
index cc6d52d415..b35bc3dfbb 100644
--- a/doc/src/tad.rst
+++ b/doc/src/tad.rst
@@ -6,7 +6,7 @@ tad command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...
 
diff --git a/doc/src/temper.rst b/doc/src/temper.rst
index 363e0102fc..d8bbcb959b 100644
--- a/doc/src/temper.rst
+++ b/doc/src/temper.rst
@@ -6,7 +6,7 @@ temper command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    temper N M temp fix-ID seed1 seed2 index
 
diff --git a/doc/src/temper_grem.rst b/doc/src/temper_grem.rst
index 312df21254..0963ea98c1 100644
--- a/doc/src/temper_grem.rst
+++ b/doc/src/temper_grem.rst
@@ -6,7 +6,7 @@ temper/grem command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    temper/grem N M lambda fix-ID thermostat-ID seed1 seed2 index
 
diff --git a/doc/src/temper_npt.rst b/doc/src/temper_npt.rst
index a8f5999dbe..0659ba2c03 100644
--- a/doc/src/temper_npt.rst
+++ b/doc/src/temper_npt.rst
@@ -6,7 +6,7 @@ temper/npt command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    temper/npt  N M temp fix-ID seed1 seed2 pressure index
 
diff --git a/doc/src/thermo.rst b/doc/src/thermo.rst
index 5621b554c8..f918810cc2 100644
--- a/doc/src/thermo.rst
+++ b/doc/src/thermo.rst
@@ -6,7 +6,7 @@ thermo command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    thermo N
 
diff --git a/doc/src/timer.rst b/doc/src/timer.rst
index a604cc2212..13d5a92473 100644
--- a/doc/src/timer.rst
+++ b/doc/src/timer.rst
@@ -6,7 +6,7 @@ timer command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    timer args
 
diff --git a/doc/src/timestep.rst b/doc/src/timestep.rst
index 3142509611..037b3f8642 100644
--- a/doc/src/timestep.rst
+++ b/doc/src/timestep.rst
@@ -6,7 +6,7 @@ timestep command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    timestep dt
 
diff --git a/doc/src/uncompute.rst b/doc/src/uncompute.rst
index 24b7c028d5..e65cbb2038 100644
--- a/doc/src/uncompute.rst
+++ b/doc/src/uncompute.rst
@@ -6,7 +6,7 @@ uncompute command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    uncompute compute-ID
 
diff --git a/doc/src/undump.rst b/doc/src/undump.rst
index 9320338854..89874457b0 100644
--- a/doc/src/undump.rst
+++ b/doc/src/undump.rst
@@ -6,7 +6,7 @@ undump command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    undump dump-ID
 
diff --git a/doc/src/unfix.rst b/doc/src/unfix.rst
index 419559a118..aeb640201d 100644
--- a/doc/src/unfix.rst
+++ b/doc/src/unfix.rst
@@ -6,7 +6,7 @@ unfix command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    unfix fix-ID
 
diff --git a/doc/src/units.rst b/doc/src/units.rst
index 2554806fb5..3f0904f162 100644
--- a/doc/src/units.rst
+++ b/doc/src/units.rst
@@ -6,7 +6,7 @@ units command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    units style
 
diff --git a/doc/src/variable.rst b/doc/src/variable.rst
index a9d21bab9b..28c0d29799 100644
--- a/doc/src/variable.rst
+++ b/doc/src/variable.rst
@@ -6,7 +6,7 @@ variable command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    variable name style args ...
 
diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst
index ee1d546d79..48b0526df9 100644
--- a/doc/src/velocity.rst
+++ b/doc/src/velocity.rst
@@ -6,7 +6,7 @@ velocity command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    velocity group-ID style args keyword value ...
 

From 6efa8526ba2740838659d4fbf9fcf5c521a8c004 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 11 Jul 2023 19:39:54 -0400
Subject: [PATCH 366/396] work around pygments issue

---
 doc/src/group2ndx.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst
index 122341f7f6..e3d8999714 100644
--- a/doc/src/group2ndx.rst
+++ b/doc/src/group2ndx.rst
@@ -12,11 +12,11 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   group2ndx file group-ID ...
-   ndx2group file group-ID ...
+   group2ndx file group-ID args
+   ndx2group file group-ID args
 
 * file = name of index file to write out or read in
-* zero or more group IDs may be appended
+* args = zero or more group IDs may be appended
 
 Examples
 """"""""

From fe2a275531a16610e8ad38e027f0a03b23e9ae60 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 11 Jul 2023 19:40:14 -0400
Subject: [PATCH 367/396] update list of known commands

---
 doc/utils/sphinx-config/LAMMPSLexer.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py
index c8826a9ed6..9a4a1e2bc6 100644
--- a/doc/utils/sphinx-config/LAMMPSLexer.py
+++ b/doc/utils/sphinx-config/LAMMPSLexer.py
@@ -2,14 +2,15 @@ from pygments.lexer import RegexLexer, words, include, default
 from pygments.token import *
 
 LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify",
-                   "atom_style", "balance", "bond_coeff", "bond_style",
-                   "bond_write", "boundary", "clear", "comm_modify",
-                   "comm_style", "compute_modify", "create_atoms",
-                   "create_bonds", "create_box", "delete_atoms",
-                   "delete_bonds", "dielectric", "dihedral_coeff",
-                   "dihedral_style", "dimension", "displace_atoms",
-                   "dump_modify", "dynamical_matrix", "echo", "elif",
-                   "else", "fix_modify", "group2ndx", "hyper", "if",
+                   "atom_style", "angle_write", "balance", "bond_coeff",
+                   "bond_style", "bond_write", "boundary", "clear",
+                   "comm_modify", "comm_style", "compute_modify",
+                   "create_atoms", "create_bonds", "create_box",
+                   "delete_atoms", "delete_bonds", "dielectric",
+                   "dihedral_coeff", "dihedral_style", "dihedral_write",
+                   "dimension", "displace_atoms", "dump_modify",
+                   "dynamical_matrix", "echo", "elif", "else", "fitpod",
+                   "fix_modify", "group2ndx", "hyper", "if",
                    "improper_coeff", "improper_style", "include",
                    "info", "jump", "kim", "kspace_modify",
                    "kspace_style", "label", "labelmap", "lattice",

From 9e049147bee35b3b861fce68701f5cefcab4cb00 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 11 Jul 2023 19:50:37 -0400
Subject: [PATCH 368/396] remove accidental commit

---
 purge-workflows.py | 22 ----------------------
 1 file changed, 22 deletions(-)
 delete mode 100644 purge-workflows.py

diff --git a/purge-workflows.py b/purge-workflows.py
deleted file mode 100644
index 73b7d22f7a..0000000000
--- a/purge-workflows.py
+++ /dev/null
@@ -1,22 +0,0 @@
-from yaml import load
-import subprocess
-try:
-    from yaml import CLoader as Loader
-except ImportError:
-    from yaml import Loader
-
-runs = subprocess.check_output('gh api repos/lammps/lammps/actions/runs',shell=True)
-data = load(runs,Loader=Loader)
-while data['total_count'] > 3:
-    print('remaining: ', data['total_count'])
-    num=1
-    for d in data['workflow_runs']:
-        print(num, d['id'],d['name'],d['run_number'])
-        num += 1
-        if num > 4:
-            subprocess.call('gh api -X DELETE repos/lammps/lammps/actions/runs/' + str(d['id']), shell=True)
-            #print('gh api -X DELETE repos/lammps/lammps/actions/runs/' + str(d['id']))
-        else:
-            print('skip')
-    runs = subprocess.check_output('gh api repos/lammps/lammps/actions/runs',shell=True)
-    data = load(runs,Loader=Loader)

From 3b859094bffa575cc7488f87c3d24ad9b039133b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 12 Jul 2023 12:26:55 -0400
Subject: [PATCH 369/396] there is no mandatory group-ID for both commands

---
 doc/src/group2ndx.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst
index e3d8999714..077f88e3e8 100644
--- a/doc/src/group2ndx.rst
+++ b/doc/src/group2ndx.rst
@@ -12,8 +12,8 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   group2ndx file group-ID args
-   ndx2group file group-ID args
+   group2ndx file args
+   ndx2group file args
 
 * file = name of index file to write out or read in
 * args = zero or more group IDs may be appended

From 751dc1cfb6922fbd1a4b3ef6d45c406670d1f9e4 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 12 Jul 2023 12:28:03 -0400
Subject: [PATCH 370/396] improve pygments lexer to detect more text to
 highlight and for more consistency

---
 doc/utils/sphinx-config/LAMMPSLexer.py | 32 ++++++++++++++++++--------
 1 file changed, 23 insertions(+), 9 deletions(-)

diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py
index 9a4a1e2bc6..48c52d6460 100644
--- a/doc/utils/sphinx-config/LAMMPSLexer.py
+++ b/doc/utils/sphinx-config/LAMMPSLexer.py
@@ -46,15 +46,24 @@ class LAMMPSLexer(RegexLexer):
     tokens = {
         'root': [
             (r'fix\s+', Keyword, 'fix'),
+            (r'fix_modify\s+', Keyword, 'modify_cmd'),
             (r'compute\s+', Keyword, 'compute'),
+            (r'compute_modify\s+', Keyword, 'modify_cmd'),
             (r'dump\s+', Keyword, 'dump'),
+            (r'dump_modify\s+', Keyword, 'modify_cmd'),
             (r'region\s+', Keyword, 'region'),
             (r'^\s*variable\s+', Keyword, 'variable_cmd'),
             (r'group\s+', Keyword, 'group'),
             (r'change_box\s+', Keyword, 'change_box'),
-            (r'uncompute\s+', Keyword, 'uncompute'),
-            (r'unfix\s+', Keyword, 'unfix'),
-            (r'undump\s+', Keyword, 'undump'),
+            (r'create_box\s+', Keyword, 'create_box'),
+            (r'delete_bonds\s+', Keyword, 'id_cmd'),
+            (r'displace_atoms\s+', Keyword, 'id_cmd'),
+            (r'dynamical_matrix\s+', Keyword, 'id_cmd'),
+            (r'group2ndx\s+', Keyword, 'ndx_cmd'),
+            (r'ndx2group\s+', Keyword, 'ndx_cmd'),
+            (r'uncompute\s+', Keyword, 'id_cmd'),
+            (r'unfix\s+', Keyword, 'id_cmd'),
+            (r'undump\s+', Keyword, 'id_cmd'),
             (r'write_dump\s+', Keyword, 'write_dump'),
             include('keywords'),
             (r'#.*?\n', Comment),
@@ -91,6 +100,10 @@ class LAMMPSLexer(RegexLexer):
             ('\(', Name.Variable, 'expression'),
             ('\)', Name.Variable, '#pop'),
         ],
+        'modify_cmd' : [
+            (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
+            default('#pop')
+        ],
         'fix' : [
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             (r'\s+', Whitespace, 'group_id'),
@@ -122,15 +135,16 @@ class LAMMPSLexer(RegexLexer):
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')
         ],
-        'unfix' : [
+        'create_box' : [
+            (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
+            (r'\s+', Whitespace, 'group_id'),
+            default('#pop')
+        ],
+        'id_cmd' : [
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')
         ],
-        'undump' : [
-            (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
-            default('#pop')
-        ],
-        'uncompute' : [
+        'ndx_cmd' : [
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')
         ],

From fe95dbc82f9d0c258923501a60dde34f3ca0e922 Mon Sep 17 00:00:00 2001
From: jbcouli <jbcouli@sandia.gov>
Date: Wed, 12 Jul 2023 11:37:17 -0600
Subject: [PATCH 371/396] enforce all special_bonds weights to be 1.0 when
 overlay/pair is used

---
 doc/src/Howto_bpm.rst | 6 +++---
 src/BPM/bond_bpm.cpp  | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst
index 380c114866..0ca4e85fbb 100644
--- a/doc/src/Howto_bpm.rst
+++ b/doc/src/Howto_bpm.rst
@@ -79,9 +79,9 @@ As bonds can be broken between neighbor list builds, the
 bond styles. There are two possible settings which determine how pair
 interactions work between bonded particles.  First, one can overlay
 pair forces with bond forces such that all bonded particles also
-feel pair interactions. This can be accomplished by using the *overlay/pair*
-keyword present in all bpm bond styles and by using the following special
-bond settings
+feel pair interactions. This can be accomplished by setting the *overlay/pair*
+keyword present in all bpm bond styles to *yes* and requires using the
+following special bond settings
 
    .. code-block:: LAMMPS
 
diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp
index 023988b64d..3ebeed3f1d 100644
--- a/src/BPM/bond_bpm.cpp
+++ b/src/BPM/bond_bpm.cpp
@@ -94,10 +94,10 @@ void BondBPM::init_style()
   }
 
   if (overlay_flag) {
-    if (force->special_lj[1] != 1.0)
+    if (force->special_lj[1] != 1.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 ||
+        force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
       error->all(FLERR,
-                 "With overlay/pair yes, BPM bond styles require special_bonds weight of 1.0 for "
-                 "first neighbors");
+                 "With overlay/pair yes, BPM bond styles require a value of 1.0 for all special_bonds weights");
     if (id_fix_update) {
       modify->delete_fix(id_fix_update);
       delete[] id_fix_update;

From 24de6377d34fb2685513ce459b679df9534fa119 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 12 Jul 2023 14:43:04 -0400
Subject: [PATCH 372/396] handle more commands with arguments for more
 consistent syntax highlighting

---
 doc/utils/sphinx-config/LAMMPSLexer.py | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py
index 48c52d6460..d09dda5302 100644
--- a/doc/utils/sphinx-config/LAMMPSLexer.py
+++ b/doc/utils/sphinx-config/LAMMPSLexer.py
@@ -61,10 +61,18 @@ class LAMMPSLexer(RegexLexer):
             (r'dynamical_matrix\s+', Keyword, 'id_cmd'),
             (r'group2ndx\s+', Keyword, 'ndx_cmd'),
             (r'ndx2group\s+', Keyword, 'ndx_cmd'),
+            (r'jump\s+', Keyword, 'jump_cmd'),
+            (r'label\s+', Keyword, 'jump_cmd'),
+            (r'next\s+', Keyword, 'id_cmd'),
+            (r'kim\s+', Keyword, 'kim_cmd'),
             (r'uncompute\s+', Keyword, 'id_cmd'),
             (r'unfix\s+', Keyword, 'id_cmd'),
             (r'undump\s+', Keyword, 'id_cmd'),
+            (r'velocity\s+', Keyword, 'id_cmd'),
+            (r'write_coeff\s+', Keyword, 'ndx_cmd'),
+            (r'write_data\s+', Keyword, 'ndx_cmd'),
             (r'write_dump\s+', Keyword, 'write_dump'),
+            (r'write_restart\s+', Keyword, 'ndx_cmd'),
             include('keywords'),
             (r'#.*?\n', Comment),
             ('"', String, 'string'),
@@ -80,7 +88,7 @@ class LAMMPSLexer(RegexLexer):
             (r'[\~\.\w_:,@\-\/\\0-9]+', Text),
         ],
         'keywords' : [
-            (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword)
+            (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^\s*'), Keyword)
         ]
         ,
         'variable' : [
@@ -148,6 +156,14 @@ class LAMMPSLexer(RegexLexer):
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')
         ],
+        'jump_cmd' : [
+            (r'[\w_\-\.\[\]]+', Literal.String.Char),
+            default('#pop')
+        ],
+        'kim_cmd' : [
+            (r'[\w_\-\.\[\]]+', Literal.String.Single),
+            default('#pop')
+        ],
         'write_dump' : [
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')

From 6907543e9df06e9868396ba41b4fa26ad474670d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 12 Jul 2023 20:25:49 -0400
Subject: [PATCH 373/396] highlight if/then/elif/else everywhere, but revert
 for general keywords

---
 doc/utils/sphinx-config/LAMMPSLexer.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py
index d09dda5302..a7ba5d92a8 100644
--- a/doc/utils/sphinx-config/LAMMPSLexer.py
+++ b/doc/utils/sphinx-config/LAMMPSLexer.py
@@ -9,8 +9,8 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify",
                    "delete_atoms", "delete_bonds", "dielectric",
                    "dihedral_coeff", "dihedral_style", "dihedral_write",
                    "dimension", "displace_atoms", "dump_modify",
-                   "dynamical_matrix", "echo", "elif", "else", "fitpod",
-                   "fix_modify", "group2ndx", "hyper", "if",
+                   "dynamical_matrix", "echo", "fitpod",
+                   "fix_modify", "group2ndx", "hyper",
                    "improper_coeff", "improper_style", "include",
                    "info", "jump", "kim", "kspace_modify",
                    "kspace_style", "label", "labelmap", "lattice",
@@ -24,7 +24,7 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify",
                    "read_restart", "replicate", "rerun", "reset_atoms",
                    "reset_timestep", "restart", "run", "run_style",
                    "server", "set", "shell", "special_bonds", "suffix",
-                   "tad", "temper", "temper/grem", "temper/npt", "then",
+                   "tad", "temper", "temper/grem", "temper/npt",
                    "thermo", "thermo_modify", "thermo_style",
                    "third_order", "timer", "timestep", "units",
                    "velocity", "write_coeff", "write_data",
@@ -52,7 +52,7 @@ class LAMMPSLexer(RegexLexer):
             (r'dump\s+', Keyword, 'dump'),
             (r'dump_modify\s+', Keyword, 'modify_cmd'),
             (r'region\s+', Keyword, 'region'),
-            (r'^\s*variable\s+', Keyword, 'variable_cmd'),
+            (r'variable\s+', Keyword, 'variable_cmd'),
             (r'group\s+', Keyword, 'group'),
             (r'change_box\s+', Keyword, 'change_box'),
             (r'create_box\s+', Keyword, 'create_box'),
@@ -73,6 +73,7 @@ class LAMMPSLexer(RegexLexer):
             (r'write_data\s+', Keyword, 'ndx_cmd'),
             (r'write_dump\s+', Keyword, 'write_dump'),
             (r'write_restart\s+', Keyword, 'ndx_cmd'),
+            include('conditionals'),
             include('keywords'),
             (r'#.*?\n', Comment),
             ('"', String, 'string'),
@@ -87,6 +88,10 @@ class LAMMPSLexer(RegexLexer):
             (r'[\+\-\*\^\|\/\!%&=<>]', Operator),
             (r'[\~\.\w_:,@\-\/\\0-9]+', Text),
         ],
+        'conditionals' : [
+            (words(('if','else','elif','then'), suffix=r'\b', prefix=r'\b'), Keyword)
+        ]
+        ,
         'keywords' : [
             (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^\s*'), Keyword)
         ]

From acb0b89833f873e77d2def92192c792b64f9a17a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 12 Jul 2023 20:48:14 -0400
Subject: [PATCH 374/396] fix typos

---
 doc/src/Howto_2d.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst
index be223c076a..ae58711063 100644
--- a/doc/src/Howto_2d.rst
+++ b/doc/src/Howto_2d.rst
@@ -13,9 +13,9 @@ box with a single z plane of atoms - e.g.
 
 .. code-block:: LAMMPS
 
-   create box 1 -10 10 -10 10 -0.25 0.25
+   create_box 1 -10 10 -10 10 -0.25 0.25
 
-If using the :doc:`read data <read_data>` command to read in a file of
+If using the :doc:`read_data <read_data>` command to read in a file of
 atom coordinates, set the "zlo zhi" values to be finite but narrow,
 similar to the create_box command settings just described.  For each
 atom in the file, assign a z coordinate so it falls inside the

From 02d189fb23d7b61f1cacb3bbf38bc5e157ad8739 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 13 Jul 2023 10:53:56 -0400
Subject: [PATCH 375/396] avoid false positive with static code analysis

---
 src/compute_count_type.cpp | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/compute_count_type.cpp b/src/compute_count_type.cpp
index 3cb2e6bc3a..3d4815f9ff 100644
--- a/src/compute_count_type.cpp
+++ b/src/compute_count_type.cpp
@@ -159,6 +159,8 @@ void ComputeCountType::compute_vector()
     nvec = count_dihedrals();
   else if (mode == IMPROPER)
     nvec = count_impropers();
+  else
+    nvec = 0;
 
   // sum across procs as bigint, then convert to double
   // correct for multiple counting if newton_bond off

From 620c60122a9e68ec036e824fc51bd50517a11fdc Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 14 Jul 2023 10:08:09 -0400
Subject: [PATCH 376/396] should not use pow() for computing cube, use
 multiplication.

---
 lib/gpu/lal_amoeba.cu | 3 ++-
 lib/gpu/lal_hippo.cu  | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/gpu/lal_amoeba.cu b/lib/gpu/lal_amoeba.cu
index 82a42cff6c..799cfe6d63 100644
--- a/lib/gpu/lal_amoeba.cu
+++ b/lib/gpu/lal_amoeba.cu
@@ -992,7 +992,8 @@ __kernel void k_amoeba_umutual2b(const __global numtyp4 *restrict x_,
       numtyp damp = pdi * coeff[jtype].x; // pdamp[jtype]
       if (damp != (numtyp)0.0) {
         numtyp pgamma = MIN(pti,coeff[jtype].y); // thole[jtype]
-        damp = pgamma * ucl_powr(r/damp,(numtyp)3.0);
+        numtyp rdamp = r/damp;
+        damp = pgamma * rdamp*rdamp*rdamp;
         if (damp < (numtyp)50.0) {
           numtyp expdamp = ucl_exp(-damp);
           scale3 = (numtyp)1.0 - expdamp;
diff --git a/lib/gpu/lal_hippo.cu b/lib/gpu/lal_hippo.cu
index 0a0f4f02be..92cb55f69b 100644
--- a/lib/gpu/lal_hippo.cu
+++ b/lib/gpu/lal_hippo.cu
@@ -845,7 +845,7 @@ __kernel void k_hippo_dispersion(const __global numtyp4 *restrict x_,
       numtyp scale = factor_disp * damp*damp;
       scale = scale - (numtyp)1.0;
       numtyp e = -ci * ck * (expa+scale) / r6;
-      numtyp rterm = -ucl_powr(ralpha2,(numtyp)3.0) * expterm / r;
+      numtyp rterm = -ralpha2*ralpha2*ralpha2 * expterm / r;
       numtyp de = (numtyp)-6.0*e/r2 - ci*ck*rterm/r7 - (numtyp)2.0*ci*ck*factor_disp*damp*ddamp/r7;
 
       energy+= e;

From be2e437cecf47a20fcb5266277984b5a20a81bbd Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 14 Jul 2023 10:08:59 -0400
Subject: [PATCH 377/396] use approximation for erfc() on OpenCL for Intel
 since the OpenCL version seems broken

---
 lib/gpu/lal_amoeba.cu | 20 ++++++++++++++++++++
 lib/gpu/lal_hippo.cu  | 20 ++++++++++++++++++++
 2 files changed, 40 insertions(+)

diff --git a/lib/gpu/lal_amoeba.cu b/lib/gpu/lal_amoeba.cu
index 799cfe6d63..e7c313301e 100644
--- a/lib/gpu/lal_amoeba.cu
+++ b/lib/gpu/lal_amoeba.cu
@@ -585,7 +585,12 @@ __kernel void k_amoeba_multipole(const __global numtyp4 *restrict x_,
       numtyp ralpha = aewald * r;
       numtyp exp2a = ucl_exp(-ralpha*ralpha);
       numtyp bn[6];
+#ifdef INTEL_OCL
+      numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*ralpha);
+      bn[0] = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * exp2a * rinv;
+#else
       bn[0] = ucl_erfc(ralpha) * rinv;
+#endif
 
       numtyp alsq2 = (numtyp)2.0 * aewald*aewald;
       numtyp alsq2n = (numtyp)0.0;
@@ -802,7 +807,12 @@ __kernel void k_amoeba_udirect2b(const __global numtyp4 *restrict x_,
       numtyp ralpha = aewald * r;
       numtyp exp2a = ucl_exp(-ralpha*ralpha);
       numtyp bn[4], bcn[3];
+#ifdef INTEL_OCL
+      numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*ralpha);
+      bn[0] = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * exp2a * rinv;
+#else
       bn[0] = ucl_erfc(ralpha) * rinv;
+#endif
 
       numtyp aefac = aesq2n;
       for (int m = 1; m <= 3; m++) {
@@ -976,7 +986,12 @@ __kernel void k_amoeba_umutual2b(const __global numtyp4 *restrict x_,
       numtyp ralpha = aewald * r;
       numtyp exp2a = ucl_exp(-ralpha*ralpha);
       numtyp bn[4];
+#ifdef INTEL_OCL
+      numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*ralpha);
+      bn[0] = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * exp2a * rinv;
+#else
       bn[0] = ucl_erfc(ralpha) * rinv;
+#endif
 
       numtyp aefac = aesq2n;
       for (int m = 1; m <= 3; m++) {
@@ -1231,7 +1246,12 @@ __kernel void k_amoeba_polar(const __global numtyp4 *restrict x_,
       numtyp ralpha = aewald * r;
       numtyp exp2a = ucl_exp(-ralpha*ralpha);
       numtyp bn[5];
+#ifdef INTEL_OCL
+      numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*ralpha);
+      bn[0] = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * exp2a * rinv;
+#else
       bn[0] = ucl_erfc(ralpha) * rinv;
+#endif
 
       numtyp alsq2 = (numtyp)2.0 * aewald*aewald;
       numtyp alsq2n = (numtyp)0.0;
diff --git a/lib/gpu/lal_hippo.cu b/lib/gpu/lal_hippo.cu
index 92cb55f69b..7de7bd594f 100644
--- a/lib/gpu/lal_hippo.cu
+++ b/lib/gpu/lal_hippo.cu
@@ -1072,7 +1072,12 @@ __kernel void k_hippo_multipole(const __global numtyp4 *restrict x_,
       numtyp ralpha = aewald * r;
       numtyp exp2a = ucl_exp(-ralpha*ralpha);
       numtyp bn[6];
+#ifdef INTEL_OCL
+      numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*ralpha);
+      bn[0] = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * exp2a * rinv;
+#else
       bn[0] = ucl_erfc(ralpha) * rinv;
+#endif
 
       numtyp alsq2 = (numtyp)2.0 * aewald*aewald;
       numtyp alsq2n = (numtyp)0.0;
@@ -1319,7 +1324,12 @@ __kernel void k_hippo_udirect2b(const __global numtyp4 *restrict x_,
       numtyp ralpha = aewald * r;
       numtyp exp2a = ucl_exp(-ralpha*ralpha);
       numtyp bn[4];
+#ifdef INTEL_OCL
+      numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*ralpha);
+      bn[0] = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * exp2a * rinv;
+#else
       bn[0] = ucl_erfc(ralpha) * rinv;
+#endif
 
       numtyp aefac = aesq2n;
       for (int m = 1; m <= 3; m++) {
@@ -1477,7 +1487,12 @@ __kernel void k_hippo_umutual2b(const __global numtyp4 *restrict x_,
       numtyp ralpha = aewald * r;
       numtyp exp2a = ucl_exp(-ralpha*ralpha);
       numtyp bn[4];
+#ifdef INTEL_OCL
+      numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*ralpha);
+      bn[0] = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * exp2a * rinv;
+#else
       bn[0] = ucl_erfc(ralpha) * rinv;
+#endif
 
       numtyp aefac = aesq2n;
       for (int m = 1; m <= 3; m++) {
@@ -1702,7 +1717,12 @@ __kernel void k_hippo_polar(const __global numtyp4 *restrict x_,
       numtyp ralpha = aewald * r;
       numtyp exp2a = ucl_exp(-ralpha*ralpha);
       numtyp bn[5];
+#ifdef INTEL_OCL
+      numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*ralpha);
+      bn[0] = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * exp2a * rinv;
+#else
       bn[0] = ucl_erfc(ralpha) * rinv;
+#endif
 
       numtyp alsq2 = (numtyp)2.0 * aewald*aewald;
       numtyp alsq2n = (numtyp)0.0;

From 78d3d4948f281c62e57e4f5ec200afcca5145ef2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 14 Jul 2023 20:06:31 -0400
Subject: [PATCH 378/396] fix off-by-one bug in argument parsing

---
 src/REPLICA/temper_npt.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/REPLICA/temper_npt.cpp b/src/REPLICA/temper_npt.cpp
index 6567cb83e1..6aa895e813 100644
--- a/src/REPLICA/temper_npt.cpp
+++ b/src/REPLICA/temper_npt.cpp
@@ -89,7 +89,9 @@ void TemperNPT::command(int narg, char **arg)
   seed_boltz = utils::inumeric(FLERR,arg[5],false,lmp);
 
   my_set_temp = universe->iworld;
-  if (narg == 8) my_set_temp = utils::inumeric(FLERR,arg[6],false,lmp);
+  if (narg == 8) my_set_temp = utils::inumeric(FLERR,arg[7],false,lmp);
+  if ((my_set_temp < 0) || (my_set_temp > 7))
+    error->universe_all(FLERR,"Invalid partition number for temperature index keyword");
 
   // swap frequency must evenly divide total # of timesteps
 

From e6873bb7c816cea6e5f46ad47f8b650b4b70ec79 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 14 Jul 2023 20:07:09 -0400
Subject: [PATCH 379/396] modernize code

---
 src/REPLICA/temper_npt.cpp | 35 ++++++++++++++++-------------------
 src/REPLICA/temper_npt.h   |  3 +--
 2 files changed, 17 insertions(+), 21 deletions(-)

diff --git a/src/REPLICA/temper_npt.cpp b/src/REPLICA/temper_npt.cpp
index 6aa895e813..303eff59b3 100644
--- a/src/REPLICA/temper_npt.cpp
+++ b/src/REPLICA/temper_npt.cpp
@@ -52,10 +52,10 @@ TemperNPT::~TemperNPT()
   MPI_Comm_free(&roots);
   if (ranswap) delete ranswap;
   delete ranboltz;
-  delete [] set_temp;
-  delete [] temp2world;
-  delete [] world2temp;
-  delete [] world2root;
+  delete[] set_temp;
+  delete[] temp2world;
+  delete[] world2temp;
+  delete[] world2root;
 }
 
 /* ----------------------------------------------------------------------
@@ -68,8 +68,7 @@ void TemperNPT::command(int narg, char **arg)
     error->all(FLERR,"Must have more than one processor partition to temper");
   if (domain->box_exist == 0)
     error->all(FLERR,"temper/npt command before simulation box is defined");
-  if (narg != 7 && narg != 8)
-    error->universe_all(FLERR,"Illegal temper/npt command");
+  if (narg != 7 && narg != 8) error->universe_all(FLERR,"Illegal temper/npt command");
 
   int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
   nevery = utils::inumeric(FLERR,arg[1],false,lmp);
@@ -80,10 +79,9 @@ void TemperNPT::command(int narg, char **arg)
 
   if (timer->is_timeout()) return;
 
-  for (whichfix = 0; whichfix < modify->nfix; whichfix++)
-    if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
-  if (whichfix == modify->nfix)
-    error->universe_all(FLERR,"Tempering fix ID is not defined");
+  whichfix = modify->get_fix_by_id(arg[3]);
+  if (!whichfix)
+    error->universe_all(FLERR,fmt::format("Tempering fix ID {} is not defined", arg[3]));
 
   seed_swap = utils::inumeric(FLERR,arg[4],false,lmp);
   seed_boltz = utils::inumeric(FLERR,arg[5],false,lmp);
@@ -106,8 +104,8 @@ void TemperNPT::command(int narg, char **arg)
   // change the volume. This currently only applies to fix npt and
   // fix rigid/npt variants
 
-  if ( (!utils::strmatch(modify->fix[whichfix]->style,"^npt")) &&
-       (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/npt")) )
+  if ( (!utils::strmatch(whichfix->style,"^npt")) &&
+       (!utils::strmatch(whichfix->style,"^rigid/npt")) )
     error->universe_all(FLERR,"Tempering temperature and pressure fix is not supported");
 
   // setup for long tempering run
@@ -118,8 +116,7 @@ void TemperNPT::command(int narg, char **arg)
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
-  if (update->laststep < 0)
-    error->all(FLERR,"Too many timesteps");
+  if (update->laststep < 0) error->all(FLERR,"Too many timesteps");
 
   lmp->init();
 
@@ -135,9 +132,9 @@ void TemperNPT::command(int narg, char **arg)
   // pe_compute = ptr to thermo_pe compute
   // notify compute it will be called at first swap
 
-  int id = modify->find_compute("thermo_pe");
-  if (id < 0) error->all(FLERR,"Tempering could not find thermo_pe compute");
-  Compute *pe_compute = modify->compute[id];
+  Compute *pe_compute = modify->get_compute_by_id("thermo_pe");
+  if (!pe_compute) error->all(FLERR,"Tempering could not find thermo_pe compute");
+
   pe_compute->addstep(update->ntimestep + nevery);
 
   // create MPI communicator for root proc from each world
@@ -186,7 +183,7 @@ void TemperNPT::command(int narg, char **arg)
 
   if (narg == 8) {
     double new_temp = set_temp[my_set_temp];
-    modify->fix[whichfix]->reset_target(new_temp);
+    whichfix->reset_target(new_temp);
   }
 
   // setup tempering runs
@@ -327,7 +324,7 @@ void TemperNPT::command(int narg, char **arg)
 
     if (swap) {
       new_temp = set_temp[partner_set_temp];
-      modify->fix[whichfix]->reset_target(new_temp);
+      whichfix->reset_target(new_temp);
     }
 
     // update my_set_temp and temp2world on every proc
diff --git a/src/REPLICA/temper_npt.h b/src/REPLICA/temper_npt.h
index 3a51fc74e4..2e831c55ef 100644
--- a/src/REPLICA/temper_npt.h
+++ b/src/REPLICA/temper_npt.h
@@ -42,8 +42,7 @@ class TemperNPT : public Command {
   int nswaps;                           // # of tempering swaps to perform
   int seed_swap;                        // 0 = toggle swaps, n = RNG for swap direction
   int seed_boltz;                       // seed for Boltz factor comparison
-  int whichfix;                         // index of temperature fix to use
-  int fixstyle;                         // what kind of temperature fix is used
+  class Fix *whichfix;                  // index of temperature fix to use
 
   int my_set_temp;     // which set temp I am simulating
   double *set_temp;    // static list of replica set temperatures

From baac049aed55d644783289d424ed0528c81e0ad3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 15 Jul 2023 12:25:03 -0400
Subject: [PATCH 380/396] update LAMMPS input file syntax highlighting for
 recent changes

---
 tools/vim/lammps.vim | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/tools/vim/lammps.vim b/tools/vim/lammps.vim
index 008ae1ee3f..9565d0a86e 100644
--- a/tools/vim/lammps.vim
+++ b/tools/vim/lammps.vim
@@ -1,23 +1,27 @@
 " Vim syntax file
-" Language:              Lammps Simulation Script File
+" Language:          Lammps Simulation Script File
 " Maintainer:        Gerolf Ziegenhain <gerolf@ziegenhain.com>
 " Updates:           Axel Kohlmeyer <akohlmey@gmail.com>, Sam Bateman <sam.bateman@nrlssc.navy.mil>, Daniel Möller Montull <d.moller.m@gmail.com>, Eryk Skalinski <eskalinski@protonmail.com>
-" Latest Revision:   2022-08-17
+" Latest Revision:   2023-07-15
 
 syn clear
 
-syn keyword     lammpsOutput    log write_data write_dump info shell write_restart restart dump undump thermo thermo_modify thermo_style print timer
+" Add '/' to list of valid keyword characters
+set iskeyword+=/
+
+syn keyword     lammpsOutput    log write_data write_dump write_coeff info shell write_restart restart dump undump thermo thermo_modify
+syn keyword     lammpsOutput    thermo_style print timer
 syn keyword     lammpsRead      include read_restart read_data read_dump molecule
 syn keyword     lammpsLattice   boundary units atom_style lattice region create_box create_atoms dielectric
 syn keyword     lammpsLattice   delete_atoms displace_atoms change_box dimension replicate
-syn keyword     lammpsParticle  pair_coeff pair_style pair_modify pair_write mass velocity angle_coeff angle_style
+syn keyword     lammpsParticle  pair_coeff pair_style pair_modify pair_write mass velocity angle_coeff angle_style angle_write
 syn keyword     lammpsParticle  atom_modify atom_style bond_coeff bond_style bond_write create_bonds delete_bonds kspace_style
-syn keyword     lammpsParticle  kspace_modify dihedral_style dihedral_coeff improper_style improper_coeff
-syn keyword     lammpsSetup     min_style fix_modify run_style timestep neighbor neigh_modify fix unfix suffix special_bonds
-syn keyword     lammpsSetup     balance box clear comm_modify comm_style newton package processors reset_ids reset_timestep
-syn keyword     lammpsRun       minimize run rerun tad neb prd quit server temper temper/grem temper/npt
-syn keyword     lammpsRun       min/spin message hyper dynamical_matrix
-syn keyword     lammpsDefine    variable group compute python set uncompute kim_query
+syn keyword     lammpsParticle  kspace_modify dihedral_style dihedral_coeff dihedral_write improper_style improper_coeff labelmap
+syn keyword     lammpsSetup     min_style min_modify fix_modify run_style timestep neighbor neigh_modify fix unfix suffix special_bonds
+syn keyword     lammpsSetup     balance box clear comm_modify comm_style newton package processors reset_atoms reset_ids reset_timestep
+syn keyword     lammpsRun       minimize minimize/kk run rerun tad neb neb/spin prd quit server temper/npt temper/grem temper
+syn keyword     lammpsRun       message hyper dynamical_matrix dynamical_matrix/kk third_order third_order/kk fitpod
+syn keyword     lammpsDefine    variable group compute python set uncompute kim_query kim group2ndx ndx2group mdi
 
 syn keyword     lammpsRepeat    jump next loop
 

From 77bdcb3e19679ae43ed1b4b969e5b818939be5f1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 15 Jul 2023 12:36:41 -0400
Subject: [PATCH 381/396] small doc style update

---
 doc/src/dynamical_matrix.rst | 2 +-
 doc/src/minimize.rst         | 4 ++--
 doc/src/third_order.rst      | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst
index 93e4c2a1aa..0243fb49db 100644
--- a/doc/src/dynamical_matrix.rst
+++ b/doc/src/dynamical_matrix.rst
@@ -4,7 +4,7 @@
 dynamical_matrix command
 ========================
 
-Accelerator Variants: dynamical_matrix/kk
+Accelerator Variant: dynamical_matrix/kk
 
 Syntax
 """"""
diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst
index c71c8e3632..56efa12f44 100644
--- a/doc/src/minimize.rst
+++ b/doc/src/minimize.rst
@@ -1,10 +1,10 @@
 .. index:: minimize
+.. index:: minimize/kk
 
 minimize command
 ================
 
-minimize/kk command
-===================
+Accelerator Variant: minimize/kk
 
 Syntax
 """"""
diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst
index 2635c92f84..bbbf424c44 100644
--- a/doc/src/third_order.rst
+++ b/doc/src/third_order.rst
@@ -4,7 +4,7 @@
 third_order command
 ===================
 
-Accelerator Variants: third_order/kk
+Accelerator Variant: third_order/kk
 
 Syntax
 """"""

From fd0a72eab53889af860c33d406b1390fd59ce609 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 15 Jul 2023 12:37:12 -0400
Subject: [PATCH 382/396] modernize and consolidate style across all three
 temper command variants

---
 src/REPLICA/temper.cpp      | 58 +++++++++++++---------------
 src/REPLICA/temper.h        |  3 +-
 src/REPLICA/temper_grem.cpp | 75 ++++++++++++++++++-------------------
 src/REPLICA/temper_grem.h   |  4 +-
 src/REPLICA/temper_npt.cpp  | 33 ++++++++--------
 5 files changed, 82 insertions(+), 91 deletions(-)

diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp
index 9e7e67d79d..adbdb4d742 100644
--- a/src/REPLICA/temper.cpp
+++ b/src/REPLICA/temper.cpp
@@ -37,7 +37,7 @@
 
 using namespace LAMMPS_NS;
 
-// #define TEMPER_DEBUG 1
+#define TEMPER_DEBUG 0
 
 /* ---------------------------------------------------------------------- */
 
@@ -50,10 +50,10 @@ Temper::~Temper()
   MPI_Comm_free(&roots);
   if (ranswap) delete ranswap;
   delete ranboltz;
-  delete [] set_temp;
-  delete [] temp2world;
-  delete [] world2temp;
-  delete [] world2root;
+  delete[] set_temp;
+  delete[] temp2world;
+  delete[] world2temp;
+  delete[] world2root;
 }
 
 /* ----------------------------------------------------------------------
@@ -63,11 +63,10 @@ Temper::~Temper()
 void Temper::command(int narg, char **arg)
 {
   if (universe->nworlds == 1)
-    error->all(FLERR,"Must have more than one processor partition to temper");
+    error->universe_all(FLERR,"More than one processor partition required for temper command");
   if (domain->box_exist == 0)
-    error->all(FLERR,"Temper command before simulation box is defined");
-  if (narg != 6 && narg != 7)
-    error->universe_all(FLERR,"Illegal temper command");
+    error->universe_all(FLERR,"Temper command before simulation box is defined");
+  if (narg != 6 && narg != 7) error->universe_all(FLERR,"Illegal temper command");
 
   int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
   nevery = utils::inumeric(FLERR,arg[1],false,lmp);
@@ -77,10 +76,9 @@ void Temper::command(int narg, char **arg)
 
   if (timer->is_timeout()) return;
 
-  for (whichfix = 0; whichfix < modify->nfix; whichfix++)
-    if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
-  if (whichfix == modify->nfix)
-    error->universe_all(FLERR,"Tempering fix ID is not defined");
+  whichfix = modify->get_fix_by_id(arg[3]);
+  if (!whichfix)
+    error->universe_all(FLERR,fmt::format("Tempering fix ID {} is not defined", arg[3]));
 
   seed_swap = utils::inumeric(FLERR,arg[4],false,lmp);
   seed_boltz = utils::inumeric(FLERR,arg[5],false,lmp);
@@ -88,7 +86,7 @@ void Temper::command(int narg, char **arg)
   my_set_temp = universe->iworld;
   if (narg == 7) my_set_temp = utils::inumeric(FLERR,arg[6],false,lmp);
   if ((my_set_temp < 0) || (my_set_temp >= universe->nworlds))
-    error->universe_one(FLERR,"Illegal temperature index");
+    error->universe_one(FLERR,"Invalid temperature index value");
 
   // swap frequency must evenly divide total # of timesteps
 
@@ -101,11 +99,11 @@ void Temper::command(int narg, char **arg)
   // fix style must be appropriate for temperature control, i.e. it needs
   // to provide a working Fix::reset_target() and must not change the volume.
 
-  if ((!utils::strmatch(modify->fix[whichfix]->style,"^nvt")) &&
-      (!utils::strmatch(modify->fix[whichfix]->style,"^langevin")) &&
-      (!utils::strmatch(modify->fix[whichfix]->style,"^gl[de]$")) &&
-      (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/nvt")) &&
-      (!utils::strmatch(modify->fix[whichfix]->style,"^temp/")))
+  if ((!utils::strmatch(whichfix->style,"^nvt")) &&
+      (!utils::strmatch(whichfix->style,"^langevin")) &&
+      (!utils::strmatch(whichfix->style,"^gl[de]$")) &&
+      (!utils::strmatch(whichfix->style,"^rigid/nvt")) &&
+      (!utils::strmatch(whichfix->style,"^temp/")))
     error->universe_all(FLERR,"Tempering temperature fix is not supported");
 
   // setup for long tempering run
@@ -116,8 +114,7 @@ void Temper::command(int narg, char **arg)
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
-  if (update->laststep < 0)
-    error->all(FLERR,"Too many timesteps");
+  if (update->laststep < 0) error->all(FLERR,"Too many timesteps");
 
   lmp->init();
 
@@ -132,9 +129,9 @@ void Temper::command(int narg, char **arg)
   // pe_compute = ptr to thermo_pe compute
   // notify compute it will be called at first swap
 
-  int id = modify->find_compute("thermo_pe");
-  if (id < 0) error->all(FLERR,"Tempering could not find thermo_pe compute");
-  Compute *pe_compute = modify->compute[id];
+  Compute *pe_compute = modify->get_compute_by_id("thermo_pe");
+  if (!pe_compute) error->all(FLERR,"Tempering could not find thermo_pe compute");
+
   pe_compute->addstep(update->ntimestep + nevery);
 
   // create MPI communicator for root proc from each world
@@ -183,7 +180,7 @@ void Temper::command(int narg, char **arg)
 
   if (narg == 7) {
     double new_temp = set_temp[my_set_temp];
-    modify->fix[whichfix]->reset_target(new_temp);
+    whichfix->reset_target(new_temp);
   }
 
   // setup tempering runs
@@ -289,13 +286,12 @@ void Temper::command(int narg, char **arg)
       else
         MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,MPI_STATUS_IGNORE);
 
-#ifdef TEMPER_DEBUG
+#if TEMPER_DEBUG
       if (me_universe < partner)
-        printf("SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
-               me_universe,partner,swap,my_set_temp,partner_set_temp,
-               pe,pe_partner,boltz_factor,exp(boltz_factor));
+        fprintf(universe->uscreen,"SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
+                me_universe,partner,swap,my_set_temp,partner_set_temp,
+                pe,pe_partner,boltz_factor,exp(boltz_factor));
 #endif
-
     }
 
     // bcast swap result to other procs in my world
@@ -310,7 +306,7 @@ void Temper::command(int narg, char **arg)
 
     if (swap) {
       new_temp = set_temp[partner_set_temp];
-      modify->fix[whichfix]->reset_target(new_temp);
+      whichfix->reset_target(new_temp);
     }
 
     // update my_set_temp and temp2world on every proc
diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h
index b557e8ddd8..d959892587 100644
--- a/src/REPLICA/temper.h
+++ b/src/REPLICA/temper.h
@@ -40,8 +40,7 @@ class Temper : public Command {
   int nswaps;                           // # of tempering swaps to perform
   int seed_swap;                        // 0 = toggle swaps, n = RNG for swap direction
   int seed_boltz;                       // seed for Boltz factor comparison
-  int whichfix;                         // index of temperature fix to use
-  int fixstyle;                         // what kind of temperature fix is used
+  class Fix *whichfix;                  // index of temperature fix to use
 
   int my_set_temp;     // which set temp I am simulating
   double *set_temp;    // static list of replica set temperatures
diff --git a/src/REPLICA/temper_grem.cpp b/src/REPLICA/temper_grem.cpp
index 68fbb4eef6..303f502309 100644
--- a/src/REPLICA/temper_grem.cpp
+++ b/src/REPLICA/temper_grem.cpp
@@ -24,6 +24,7 @@
 #include "finish.h"
 #include "fix.h"
 #include "fix_grem.h"
+#include "fix_nh.h"
 #include "force.h"
 #include "integrate.h"
 #include "modify.h"
@@ -37,7 +38,7 @@
 
 using namespace LAMMPS_NS;
 
-//#define TEMPER_DEBUG 1
+#define TEMPER_DEBUG 0
 
 /* ---------------------------------------------------------------------- */
 
@@ -50,11 +51,10 @@ TemperGrem::~TemperGrem()
   MPI_Comm_free(&roots);
   if (ranswap) delete ranswap;
   delete ranboltz;
-  delete [] set_lambda;
-  delete [] lambda2world;
-  delete [] world2lambda;
-  delete [] world2root;
-  delete [] id_nh;
+  delete[] set_lambda;
+  delete[] lambda2world;
+  delete[] world2lambda;
+  delete[] world2root;
 }
 
 /* ----------------------------------------------------------------------
@@ -64,46 +64,50 @@ TemperGrem::~TemperGrem()
 void TemperGrem::command(int narg, char **arg)
 {
   if (universe->nworlds == 1)
-    error->all(FLERR,"Must have more than one processor partition to temper");
+    error->universe_all(FLERR,"More than one processor partition required for temper/grem command");
   if (domain->box_exist == 0)
-    error->all(FLERR,"Temper/gREM command before simulation box is defined");
-  if (narg != 7 && narg != 8)
-    error->universe_all(FLERR,"Illegal temper command");
+    error->universe_all(FLERR,"Temper/grem command before simulation box is defined");
+  if (narg != 7 && narg != 8) error->universe_all(FLERR,"Illegal temper/grem command");
 
   int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
   nevery = utils::inumeric(FLERR,arg[1],false,lmp);
   double lambda = utils::numeric(FLERR,arg[2],false,lmp);
 
   // ignore temper command, if walltime limit was already reached
+
   if (timer->is_timeout()) return;
 
-  // Get and check if gREM fix exists
-  for (whichfix = 0; whichfix < modify->nfix; whichfix++)
-    if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
-  if (whichfix == modify->nfix)
-    error->universe_all(FLERR,"Tempering fix ID is not defined");
-  fix_grem = dynamic_cast<FixGrem*>(modify->fix[whichfix]);
+  // Get and check if gREM fix exists and is correct style
+
+  auto ifix = modify->get_fix_by_id(arg[3]);
+  if (!ifix) error->universe_all(FLERR,fmt::format("Tempering fix ID {} is not defined", arg[3]));
+
+  fix_grem = dynamic_cast<FixGrem*>(ifix);
+  if (!fix_grem || (strcmp(ifix->style,"grem") != 0))
+    error->universe_all(FLERR,"Tempering temperature fix is of incorrect style");
 
   // Check input values lambdas should be equal, assign other gREM values
   if (lambda != fix_grem->lambda)
-    error->universe_all(FLERR,"Lambda from tempering and fix in the same world"
-        " must be the same");
+    error->universe_all(FLERR,"Lambda from tempering and fix in the same world must be the same");
   double eta = fix_grem->eta;
   double h0 = fix_grem->h0;
   double pressref = 0;
 
   // Get and check for nh fix
-  id_nh = utils::strdup(arg[4]);
-  int ifix = modify->find_fix(id_nh);
-  if (ifix < 0)
-    error->all(FLERR,"Fix id for nvt or npt fix does not exist");
-  Fix *nh = modify->fix[ifix];
+
+  FixNH *nh = dynamic_cast<FixNH *>(modify->get_fix_by_id(arg[4]));
+  if (!nh)
+    error->all(FLERR,fmt::format("Fix {} for Nose-Hoover fix does not exist", arg[4]));
 
   // get result from nvt vs npt check from fix_grem
+
   int pressflag = fix_grem->pressflag;
+
   // fix_grem does all the checking...
+
   if (pressflag) {
-    auto p_start = (double *) nh->extract("p_start",ifix);
+    int dummy;
+    auto p_start = (double *) nh->extract("p_start",dummy);
     pressref = p_start[0];
   }
 
@@ -123,11 +127,6 @@ void TemperGrem::command(int narg, char **arg)
   if (nswaps*nevery != nsteps)
     error->universe_all(FLERR,"Non integer # of swaps in temper command");
 
-  // Must be used with fix_grem
-
-  if (strcmp(modify->fix[whichfix]->style,"grem") != 0)
-    error->universe_all(FLERR,"Tempering temperature fix is not supported");
-
   // setup for long tempering run
 
   update->whichflag = 1;
@@ -136,8 +135,7 @@ void TemperGrem::command(int narg, char **arg)
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
-  if (update->laststep < 0)
-    error->all(FLERR,"Too many timesteps");
+  if (update->laststep < 0) error->all(FLERR,"Too many timesteps");
 
   lmp->init();
 
@@ -152,9 +150,9 @@ void TemperGrem::command(int narg, char **arg)
   // pe_compute = ptr to thermo_pe compute
   // notify compute it will be called at first swap
 
-  int id = modify->find_compute("thermo_pe");
-  if (id < 0) error->all(FLERR,"Tempering could not find thermo_pe compute");
-  Compute *pe_compute = modify->compute[id];
+  Compute *pe_compute = modify->get_compute_by_id("thermo_pe");
+  if (!pe_compute) error->all(FLERR,"Tempering could not find thermo_pe compute");
+
   pe_compute->addstep(update->ntimestep + nevery);
 
   // create MPI communicator for root proc from each world
@@ -319,13 +317,12 @@ void TemperGrem::command(int narg, char **arg)
       else
         MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,MPI_STATUS_IGNORE);
 
-#ifdef TEMPER_DEBUG
+#if TEMPER_DEBUG
       if (me_universe < partner)
-        printf("SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
-               me_universe,partner,swap,my_set_lambda,partner_set_lambda,
-               weight,weight_partner,boltz_factor,exp(boltz_factor));
+        fprintf(universe->uscreen,"SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
+                me_universe,partner,swap,my_set_lambda,partner_set_lambda,
+                weight,weight_partner,boltz_factor,exp(boltz_factor));
 #endif
-
     }
 
     // bcast swap result to other procs in my world
diff --git a/src/REPLICA/temper_grem.h b/src/REPLICA/temper_grem.h
index 3c41f9b082..c66239a794 100644
--- a/src/REPLICA/temper_grem.h
+++ b/src/REPLICA/temper_grem.h
@@ -40,8 +40,7 @@ class TemperGrem : public Command {
   int nswaps;                           // # of tempering swaps to perform
   int seed_swap;                        // 0 = toggle swaps, n = RNG for swap direction
   int seed_boltz;                       // seed for Boltz factor comparison
-  int whichfix;                         // index of temperature fix to use
-  int fixstyle;                         // what kind of temperature fix is used
+  class Fix *whichfix;                  // index of temperature fix to use
 
   int my_set_lambda;     // which set lambda I am simulating
   double *set_lambda;    // static list of replica set lambdas
@@ -54,7 +53,6 @@ class TemperGrem : public Command {
   class FixGrem *fix_grem;
 
  protected:
-  char *id_nh;
   int pressflag;
 };
 
diff --git a/src/REPLICA/temper_npt.cpp b/src/REPLICA/temper_npt.cpp
index 303eff59b3..d814bf6725 100644
--- a/src/REPLICA/temper_npt.cpp
+++ b/src/REPLICA/temper_npt.cpp
@@ -65,9 +65,9 @@ TemperNPT::~TemperNPT()
 void TemperNPT::command(int narg, char **arg)
 {
   if (universe->nworlds == 1)
-    error->all(FLERR,"Must have more than one processor partition to temper");
+    error->universe_all(FLERR,"More than one processor partition required for temper/npt command");
   if (domain->box_exist == 0)
-    error->all(FLERR,"temper/npt command before simulation box is defined");
+    error->universe_all(FLERR,"Temper/npt command before simulation box is defined");
   if (narg != 7 && narg != 8) error->universe_all(FLERR,"Illegal temper/npt command");
 
   int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
@@ -88,8 +88,8 @@ void TemperNPT::command(int narg, char **arg)
 
   my_set_temp = universe->iworld;
   if (narg == 8) my_set_temp = utils::inumeric(FLERR,arg[7],false,lmp);
-  if ((my_set_temp < 0) || (my_set_temp > 7))
-    error->universe_all(FLERR,"Invalid partition number for temperature index keyword");
+  if ((my_set_temp < 0) || (my_set_temp >= universe->nworlds))
+    error->universe_one(FLERR,"Invalid temperature index value");
 
   // swap frequency must evenly divide total # of timesteps
 
@@ -278,22 +278,23 @@ void TemperNPT::command(int narg, char **arg)
 
     swap = 0;
     if (partner != -1) {
-      if (me_universe > partner) {
+      if (me_universe > partner)
         MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld);
-        }
-      else {
+      else
         MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE);
-        }
-      if (me_universe > partner) {
+
+      if (me_universe > partner)
         MPI_Send(&vol,1, MPI_DOUBLE,partner,0,universe->uworld);
-        }
-      else {
+      else
         MPI_Recv(&vol_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE);
-        }
-    // Acceptance criteria changed for NPT ensemble
+
+    // Acceptance criteria changed versus temper command for NPT ensemble
       if (me_universe < partner) {
         press_units = press_set/nktv2p;
-        delr = (pe_partner - pe)*(1.0/(boltz*set_temp[my_set_temp]) - 1.0/(boltz*set_temp[partner_set_temp])) + press_units*(1.0/(boltz*set_temp[my_set_temp]) - 1.0/(boltz*set_temp[partner_set_temp]))*(vol_partner - vol);
+        delr = (pe_partner - pe)*(1.0/(boltz*set_temp[my_set_temp])
+                                  - 1.0/(boltz*set_temp[partner_set_temp]))
+          + press_units*(1.0/(boltz*set_temp[my_set_temp])
+                         - 1.0/(boltz*set_temp[partner_set_temp]))*(vol_partner - vol);
         boltz_factor = -delr;
         if (boltz_factor >= 0.0) swap = 1;
         else if (ranboltz->uniform() < exp(boltz_factor)) swap = 1;
@@ -303,13 +304,13 @@ void TemperNPT::command(int narg, char **arg)
         MPI_Send(&swap,1,MPI_INT,partner,0,universe->uworld);
       else
         MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,MPI_STATUS_IGNORE);
-#ifdef TEMPER_DEBUG
+
+#if TEMPER_DEBUG
       if (me_universe < partner)
         fprintf(universe->uscreen,"SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g, vol = %g %g\n",
                me_universe,partner,swap,my_set_temp,partner_set_temp,
                pe,pe_partner,boltz_factor,exp(boltz_factor), vol, vol_partner);
 #endif
-
     }
 
     // bcast swap result to other procs in my world

From 89d82fde22eb625bcf42cdba8d8b5d489ffddba2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 16 Jul 2023 15:20:36 -0400
Subject: [PATCH 383/396] modernize access to list of fixes

---
 src/fix_wall_reflect.cpp | 9 ++++-----
 src/reset_atoms_id.cpp   | 6 +++---
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp
index 60a055fbd6..00ef968828 100644
--- a/src/fix_wall_reflect.cpp
+++ b/src/fix_wall_reflect.cpp
@@ -176,12 +176,11 @@ void FixWallReflect::init()
   }
 
   int nrigid = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    if (modify->fix[i]->rigid_flag) nrigid++;
+  for (const auto &ifix : modify->get_fix_list())
+    if (ifix->rigid_flag) nrigid++;
 
-  if (nrigid && comm->me == 0)
-    error->warning(FLERR,"Should not allow rigid bodies to bounce off "
-                   "relecting walls");
+  if (nrigid && (comm->me == 0))
+    error->warning(FLERR,"Should not use reflecting walls with rigid bodies");
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/reset_atoms_id.cpp b/src/reset_atoms_id.cpp
index c0fce95326..9e8ba3630d 100644
--- a/src/reset_atoms_id.cpp
+++ b/src/reset_atoms_id.cpp
@@ -55,9 +55,9 @@ void ResetAtomsID::command(int narg, char **arg)
     error->all(FLERR, "Reset_atoms id command before simulation box is defined");
   if (atom->tag_enable == 0) error->all(FLERR, "Cannot use reset_atoms id unless atoms have IDs");
 
-  for (int i = 0; i < modify->nfix; i++)
-    if (modify->fix[i]->stores_ids)
-      error->all(FLERR, "Cannot use reset_atoms id when a fix exists that stores atom IDs");
+  for (const auto &ifix : modify->get_fix_list())
+    if (ifix->stores_ids)
+      error->all(FLERR, "Cannot use reset_atoms id with a fix {} storing atom IDs", ifix->style);
 
   if (comm->me == 0) utils::logmesg(lmp, "Resetting atom IDs ...\n");
 

From 27aa6898f8b137d3db9e6504774f1a83f64d82fd Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 16 Jul 2023 20:05:52 -0400
Subject: [PATCH 384/396] modernize access for fixes and computes

---
 src/atom.cpp                        | 13 ++++++-------
 src/atom_vec_sphere.cpp             | 15 +++++++++++----
 src/compute_aggregate_atom.cpp      |  6 ++----
 src/compute_centro_atom.cpp         |  8 +++-----
 src/compute_cluster_atom.cpp        |  6 ++----
 src/compute_cna_atom.cpp            | 14 +++++---------
 src/compute_coord_atom.cpp          | 16 ++++++++++------
 src/compute_erotate_sphere_atom.cpp |  7 ++-----
 src/compute_fragment_atom.cpp       |  7 ++-----
 src/compute_ke_atom.cpp             |  6 ++----
 10 files changed, 45 insertions(+), 53 deletions(-)

diff --git a/src/atom.cpp b/src/atom.cpp
index 6b014fc9c8..c4521a244e 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -1818,17 +1818,16 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
 
 void Atom::data_fix_compute_variable(int nprev, int nnew)
 {
-  for (const auto &fix : modify->get_fix_list()) {
-    if (fix->create_attribute)
+  for (const auto &ifix : modify->get_fix_list()) {
+    if (ifix->create_attribute)
       for (int i = nprev; i < nnew; i++)
-        fix->set_arrays(i);
+        ifix->set_arrays(i);
   }
 
-  for (int m = 0; m < modify->ncompute; m++) {
-    Compute *compute = modify->compute[m];
-    if (compute->create_attribute)
+  for (const auto &icompute : modify->get_compute_list()) {
+    if (icompute->create_attribute)
       for (int i = nprev; i < nnew; i++)
-        compute->set_arrays(i);
+        icompute->set_arrays(i);
   }
 
   for (int i = nprev; i < nnew; i++)
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index d2f9c51880..27ea4b6fef 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -17,6 +17,7 @@
 #include "error.h"
 #include "fix.h"
 #include "fix_adapt.h"
+#include "fix_adapt_fep.h"
 #include "math_const.h"
 #include "modify.h"
 
@@ -88,12 +89,18 @@ void AtomVecSphere::init()
 
   // check if optional radvary setting should have been set to 1
 
-  for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style, "adapt") == 0) {
-      auto fix = dynamic_cast<FixAdapt *>(modify->fix[i]);
-      if (fix->diamflag && radvary == 0)
+  for (auto &ifix : modify->get_fix_by_style("^adapt")) {
+    if (utils::strmatch(ifix->style, "^adapt$")) {
+      auto fix = dynamic_cast<FixAdapt *>(ifix);
+      if (fix && fix->diamflag && radvary == 0)
         error->all(FLERR, "Fix adapt changes particle radii but atom_style sphere is not dynamic");
     }
+    if (utils::strmatch(ifix->style, "^adapt/fep$")) {
+      auto fix = dynamic_cast<FixAdaptFEP *>(ifix);
+      if (fix && fix->diamflag && radvary == 0)
+        error->all(FLERR, "Fix adapt/fep changes particle radii but atom_style sphere is not dynamic");
+    }
+  }
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp
index 05526494c0..e68062b73e 100644
--- a/src/compute_aggregate_atom.cpp
+++ b/src/compute_aggregate_atom.cpp
@@ -82,10 +82,8 @@ void ComputeAggregateAtom::init()
 
   neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
 
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style, "aggregate/atom") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute aggregate/atom");
+  if (modify->get_compute_by_style(style).size() > 1)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp
index f726a95594..10d2a79c45 100644
--- a/src/compute_centro_atom.cpp
+++ b/src/compute_centro_atom.cpp
@@ -93,14 +93,12 @@ void ComputeCentroAtom::init()
   if (force->pair == nullptr)
     error->all(FLERR, "Compute centro/atom requires a pair style be defined");
 
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style, "centro/atom") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute centro/atom");
-
   // need an occasional full neighbor list
 
   neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
+
+  if (modify->get_compute_by_style(style).size() > 1)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp
index 0a0a36debd..ae44fbcd37 100644
--- a/src/compute_cluster_atom.cpp
+++ b/src/compute_cluster_atom.cpp
@@ -69,10 +69,8 @@ void ComputeClusterAtom::init()
 
   neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
 
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style, "cluster/atom") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute cluster/atom");
+  if (modify->get_compute_by_style(style).size() > 1)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp
index ccb4183707..a09a671c07 100644
--- a/src/compute_cna_atom.cpp
+++ b/src/compute_cna_atom.cpp
@@ -76,19 +76,15 @@ void ComputeCNAAtom::init()
 
   // cannot use neighbor->cutneighmax b/c neighbor has not yet been init
 
-  if (2.0 * sqrt(cutsq) > force->pair->cutforce + neighbor->skin && comm->me == 0)
-    error->warning(FLERR,
-                   "Compute cna/atom cutoff may be too large to find "
-                   "ghost atom neighbors");
-
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style, "cna/atom") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute cna/atom defined");
+  if ((2.0 * sqrt(cutsq)) > (force->pair->cutforce + neighbor->skin) && (comm->me == 0))
+    error->warning(FLERR, "Compute cna/atom cutoff may be too large to find ghost atom neighbors");
 
   // need an occasional full neighbor list
 
   neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
+
+  if (modify->get_compute_by_style(style).size() > 1)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp
index 0d56ea6573..ea19f01b91 100644
--- a/src/compute_coord_atom.cpp
+++ b/src/compute_coord_atom.cpp
@@ -82,10 +82,11 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
 
     id_orientorder = utils::strdup(arg[4]);
 
-    int iorientorder = modify->find_compute(id_orientorder);
-    if (iorientorder < 0) error->all(FLERR, "Could not find compute coord/atom compute ID");
-    if (!utils::strmatch(modify->compute[iorientorder]->style, "^orientorder/atom"))
-      error->all(FLERR, "Compute coord/atom compute ID is not orientorder/atom");
+    auto iorientorder = modify->get_compute_by_id(id_orientorder);
+    if (!iorientorder)
+      error->all(FLERR, "Could not find compute coord/atom compute ID {}", id_orientorder);
+    if (!utils::strmatch(iorientorder->style, "^orientorder/atom"))
+      error->all(FLERR, "Compute coord/atom compute ID {} is not orientorder/atom", id_orientorder);
 
     threshold = utils::numeric(FLERR, arg[5], false, lmp);
     if (threshold <= -1.0 || threshold >= 1.0)
@@ -128,8 +129,11 @@ ComputeCoordAtom::~ComputeCoordAtom()
 void ComputeCoordAtom::init()
 {
   if (cstyle == ORIENT) {
-    int iorientorder = modify->find_compute(id_orientorder);
-    c_orientorder = dynamic_cast<ComputeOrientOrderAtom *>(modify->compute[iorientorder]);
+    c_orientorder =
+        dynamic_cast<ComputeOrientOrderAtom *>(modify->get_compute_by_id(id_orientorder));
+    if (!c_orientorder)
+      error->all(FLERR, "Could not find compute coord/atom compute ID {}", id_orientorder);
+
     cutsq = c_orientorder->cutsq;
     l = c_orientorder->qlcomp;
     //  communicate real and imaginary 2*l+1 components of the normalized vector
diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp
index 9bfa0afaea..3ec0f402a8 100644
--- a/src/compute_erotate_sphere_atom.cpp
+++ b/src/compute_erotate_sphere_atom.cpp
@@ -57,11 +57,8 @@ ComputeErotateSphereAtom::~ComputeErotateSphereAtom()
 
 void ComputeErotateSphereAtom::init()
 {
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style,"erotate/sphere/atom") == 0) count++;
-  if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one compute erotate/sphere/atom");
+  if (modify->get_compute_by_style(style).size() > 1)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
 
   pfactor = 0.5 * force->mvv2e * INERTIA;
 }
diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp
index 810ffa4d66..035f554c8d 100644
--- a/src/compute_fragment_atom.cpp
+++ b/src/compute_fragment_atom.cpp
@@ -84,11 +84,8 @@ void ComputeFragmentAtom::init()
   if (atom->molecular != Atom::MOLECULAR)
     error->all(FLERR,"Compute fragment/atom requires a molecular system");
 
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style,"fragment/atom") == 0) count++;
-  if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one compute fragment/atom");
+  if (modify->get_compute_by_style(style).size() > 1)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp
index aab687755e..9a329232b3 100644
--- a/src/compute_ke_atom.cpp
+++ b/src/compute_ke_atom.cpp
@@ -47,10 +47,8 @@ ComputeKEAtom::~ComputeKEAtom()
 
 void ComputeKEAtom::init()
 {
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style, "ke/atom") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute ke/atom");
+  if (modify->get_compute_by_style(style).size() > 1)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
 }
 
 /* ---------------------------------------------------------------------- */

From 3568cced4bd6b5c42841a9c61ee658ae3031d325 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 17 Jul 2023 09:52:44 -0400
Subject: [PATCH 385/396] update comment

---
 src/REPLICA/temper.h      | 2 +-
 src/REPLICA/temper_grem.h | 2 +-
 src/REPLICA/temper_npt.h  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h
index d959892587..46a6666f07 100644
--- a/src/REPLICA/temper.h
+++ b/src/REPLICA/temper.h
@@ -40,7 +40,7 @@ class Temper : public Command {
   int nswaps;                           // # of tempering swaps to perform
   int seed_swap;                        // 0 = toggle swaps, n = RNG for swap direction
   int seed_boltz;                       // seed for Boltz factor comparison
-  class Fix *whichfix;                  // index of temperature fix to use
+  class Fix *whichfix;                  // temperature fix to use
 
   int my_set_temp;     // which set temp I am simulating
   double *set_temp;    // static list of replica set temperatures
diff --git a/src/REPLICA/temper_grem.h b/src/REPLICA/temper_grem.h
index c66239a794..8fe49ae804 100644
--- a/src/REPLICA/temper_grem.h
+++ b/src/REPLICA/temper_grem.h
@@ -40,7 +40,7 @@ class TemperGrem : public Command {
   int nswaps;                           // # of tempering swaps to perform
   int seed_swap;                        // 0 = toggle swaps, n = RNG for swap direction
   int seed_boltz;                       // seed for Boltz factor comparison
-  class Fix *whichfix;                  // index of temperature fix to use
+  class Fix *whichfix;                  // temperature fix to use
 
   int my_set_lambda;     // which set lambda I am simulating
   double *set_lambda;    // static list of replica set lambdas
diff --git a/src/REPLICA/temper_npt.h b/src/REPLICA/temper_npt.h
index 2e831c55ef..3ea29a21f6 100644
--- a/src/REPLICA/temper_npt.h
+++ b/src/REPLICA/temper_npt.h
@@ -42,7 +42,7 @@ class TemperNPT : public Command {
   int nswaps;                           // # of tempering swaps to perform
   int seed_swap;                        // 0 = toggle swaps, n = RNG for swap direction
   int seed_boltz;                       // seed for Boltz factor comparison
-  class Fix *whichfix;                  // index of temperature fix to use
+  class Fix *whichfix;                  // temperature fix to use
 
   int my_set_temp;     // which set temp I am simulating
   double *set_temp;    // static list of replica set temperatures

From 1057fa9b0008345e0bd5288a4a41e23f6b0f19e6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 17 Jul 2023 22:17:05 -0400
Subject: [PATCH 386/396] move diamflag from fix adapt and adapt/fep to base
 class for cleaner code

---
 src/BPM/atom_vec_bpm_sphere.cpp | 12 +++---------
 src/FEP/fix_adapt_fep.cpp       |  9 ++++-----
 src/FEP/fix_adapt_fep.h         |  1 -
 src/atom_vec_sphere.cpp         | 15 +++------------
 src/fix.cpp                     |  1 +
 src/fix.h                       |  1 +
 src/fix_adapt.cpp               | 11 +++++------
 src/fix_adapt.h                 |  1 -
 8 files changed, 17 insertions(+), 34 deletions(-)

diff --git a/src/BPM/atom_vec_bpm_sphere.cpp b/src/BPM/atom_vec_bpm_sphere.cpp
index 375a33c28d..9428d5e9e4 100644
--- a/src/BPM/atom_vec_bpm_sphere.cpp
+++ b/src/BPM/atom_vec_bpm_sphere.cpp
@@ -17,7 +17,6 @@
 #include "comm.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_adapt.h"
 #include "math_const.h"
 #include "modify.h"
 
@@ -99,14 +98,9 @@ void AtomVecBPMSphere::init()
   // check if optional radvary setting should have been set to 1
 
   for (auto ifix : modify->get_fix_by_style("^adapt")) {
-    if (radvary == 0) {
-      if ((strcmp(ifix->style, "adapt") == 0) && (dynamic_cast<FixAdapt *>(ifix)->diamflag))
-        error->all(FLERR, "Fix adapt changes atom radii but atom_style bpm/sphere is not dynamic");
-      // cannot properly check for fix adapt/fep since its header is optional
-      if ((strcmp(ifix->style, "adapt/fep") == 0) && (comm->me == 0))
-        error->warning(
-            FLERR, "Fix adapt/fep may change atom radii but atom_style bpm/sphere is not dynamic");
-    }
+    if (ifix->diam_flag && (radvary == 0))
+      error->all(FLERR, "Fix {} changes atom radii but atom_style bpm/sphere is not dynamic",
+        ifix->style);
   }
 }
 
diff --git a/src/FEP/fix_adapt_fep.cpp b/src/FEP/fix_adapt_fep.cpp
index 6e38c90ef2..e050b8cf21 100644
--- a/src/FEP/fix_adapt_fep.cpp
+++ b/src/FEP/fix_adapt_fep.cpp
@@ -82,7 +82,6 @@ FixAdaptFEP::FixAdaptFEP(LAMMPS *lmp, int narg, char **arg) :
   // parse keywords
 
   nadapt = 0;
-  diamflag = 0;
   chgflag = 0;
 
   iarg = 4;
@@ -114,7 +113,7 @@ FixAdaptFEP::FixAdaptFEP(LAMMPS *lmp, int narg, char **arg) :
       adapt[nadapt].which = ATOM;
       if (strcmp(arg[iarg+1],"diameter") == 0) {
         adapt[nadapt].aparam = DIAMETER;
-        diamflag = 1;
+        diam_flag = 1;
       } else if (strcmp(arg[iarg+1],"charge") == 0) {
         adapt[nadapt].aparam = CHARGE;
         chgflag = 1;
@@ -201,7 +200,7 @@ int FixAdaptFEP::setmask()
 void FixAdaptFEP::post_constructor()
 {
   if (!resetflag) return;
-  if (!diamflag && !chgflag) return;
+  if (!diam_flag && !chgflag) return;
 
   // new id = fix-ID + FIX_STORE_ATTRIBUTE
   // new fix group = group for this fix
@@ -209,7 +208,7 @@ void FixAdaptFEP::post_constructor()
   id_fix_diam = nullptr;
   id_fix_chg = nullptr;
 
-  if (diamflag) {
+  if (diam_flag) {
     id_fix_diam = utils::strdup(id + std::string("_FIX_STORE_DIAM"));
     fix_diam = dynamic_cast<FixStoreAtom *>(
       modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
@@ -513,7 +512,7 @@ void FixAdaptFEP::restore_settings()
       *kspace_scale = 1.0;
 
     } else if (ad->which == ATOM) {
-      if (diamflag) {
+      if (diam_flag) {
         double density;
 
         double *vec = fix_diam->vstore;
diff --git a/src/FEP/fix_adapt_fep.h b/src/FEP/fix_adapt_fep.h
index 370a34a0f3..97749abcb6 100644
--- a/src/FEP/fix_adapt_fep.h
+++ b/src/FEP/fix_adapt_fep.h
@@ -26,7 +26,6 @@ namespace LAMMPS_NS {
 
 class FixAdaptFEP : public Fix {
  public:
-  int diamflag;    // 1 if atom diameters will vary, for AtomVecGranular
   int chgflag;
 
   FixAdaptFEP(class LAMMPS *, int, char **);
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index 27ea4b6fef..5599ef4370 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -16,8 +16,6 @@
 #include "atom.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_adapt.h"
-#include "fix_adapt_fep.h"
 #include "math_const.h"
 #include "modify.h"
 
@@ -90,16 +88,9 @@ void AtomVecSphere::init()
   // check if optional radvary setting should have been set to 1
 
   for (auto &ifix : modify->get_fix_by_style("^adapt")) {
-    if (utils::strmatch(ifix->style, "^adapt$")) {
-      auto fix = dynamic_cast<FixAdapt *>(ifix);
-      if (fix && fix->diamflag && radvary == 0)
-        error->all(FLERR, "Fix adapt changes particle radii but atom_style sphere is not dynamic");
-    }
-    if (utils::strmatch(ifix->style, "^adapt/fep$")) {
-      auto fix = dynamic_cast<FixAdaptFEP *>(ifix);
-      if (fix && fix->diamflag && radvary == 0)
-        error->all(FLERR, "Fix adapt/fep changes particle radii but atom_style sphere is not dynamic");
-    }
+    if (ifix->diam_flag && (radvary == 0))
+      error->all(FLERR, "Fix {} changes atom radii but atom_style sphere is not dynamic",
+        ifix->style);
   }
 }
 
diff --git a/src/fix.cpp b/src/fix.cpp
index 82389ba433..70e4133cdd 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -79,6 +79,7 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
   maxexchange_dynamic = 0;
   pre_exchange_migrate = 0;
   stores_ids = 0;
+  diam_flag = 0;
 
   scalar_flag = vector_flag = array_flag = 0;
   peratom_flag = local_flag = pergrid_flag = 0;
diff --git a/src/fix.h b/src/fix.h
index 30373ab6f2..5d55048c28 100644
--- a/src/fix.h
+++ b/src/fix.h
@@ -79,6 +79,7 @@ class Fix : protected Pointers {
   int maxexchange_dynamic;     // 1 if fix sets maxexchange dynamically
   int pre_exchange_migrate;    // 1 if fix migrates atoms in pre_exchange()
   int stores_ids;              // 1 if fix stores atom IDs
+  int diam_flag;               // 1 if fix may change partical diameter
 
   int scalar_flag;                 // 0/1 if compute_scalar() function exists
   int vector_flag;                 // 0/1 if compute_vector() function exists
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index 0b4ec9a638..660e3f6107 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -90,7 +90,6 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
   // parse keywords
 
   nadapt = 0;
-  diamflag = 0;
   chgflag = 0;
 
   iarg = 4;
@@ -149,7 +148,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
       if (strcmp(arg[iarg+1],"diameter") == 0 ||
           strcmp(arg[iarg+1],"diameter/disc") == 0) {
         adapt[nadapt].atomparam = DIAMETER;
-        diamflag = 1;
+        diam_flag = 1;
         discflag = 0;
         if (strcmp(arg[iarg+1],"diameter/disc") == 0) discflag = 1;
       } else if (strcmp(arg[iarg+1],"charge") == 0) {
@@ -190,7 +189,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
   // then previous step scale factors are written to restart file
   // initialize them here in case one is used and other is never defined
 
-  if (scaleflag && (diamflag || chgflag)) restart_global = 1;
+  if (scaleflag && (diam_flag || chgflag)) restart_global = 1;
   previous_diam_scale = previous_chg_scale = 1.0;
 
   // allocate pair style arrays
@@ -260,7 +259,7 @@ int FixAdapt::setmask()
 void FixAdapt::post_constructor()
 {
   if (!resetflag) return;
-  if (!diamflag && !chgflag) return;
+  if (!diam_flag && !chgflag) return;
 
   // new id = fix-ID + FIX_STORE_ATTRIBUTE
   // new fix group = group for this fix
@@ -268,7 +267,7 @@ void FixAdapt::post_constructor()
   id_fix_diam = nullptr;
   id_fix_chg = nullptr;
 
-  if (diamflag && atom->radius_flag) {
+  if (diam_flag && atom->radius_flag) {
     id_fix_diam = utils::strdup(id + std::string("_FIX_STORE_DIAM"));
     fix_diam = dynamic_cast<FixStoreAtom *>(
       modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
@@ -707,7 +706,7 @@ void FixAdapt::restore_settings()
       *kspace_scale = 1.0;
 
     } else if (ad->which == ATOM) {
-      if (diamflag) {
+      if (diam_flag) {
         double scale;
 
         double *vec = fix_diam->vstore;
diff --git a/src/fix_adapt.h b/src/fix_adapt.h
index f8477f7259..20964a8b12 100644
--- a/src/fix_adapt.h
+++ b/src/fix_adapt.h
@@ -26,7 +26,6 @@ namespace LAMMPS_NS {
 
 class FixAdapt : public Fix {
  public:
-  int diamflag;    // 1 if atom diameters will vary, for AtomVecGranular
   int chgflag;
 
   FixAdapt(class LAMMPS *, int, char **);

From 7a04e048fed83f85a37b7a5122a8f0009346affc Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 18 Jul 2023 11:08:59 -0400
Subject: [PATCH 387/396] make certain radvary is initialized in constructor

---
 src/BPM/atom_vec_bpm_sphere.cpp | 1 +
 src/atom_vec_sphere.cpp         | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/BPM/atom_vec_bpm_sphere.cpp b/src/BPM/atom_vec_bpm_sphere.cpp
index 9428d5e9e4..d3070383e5 100644
--- a/src/BPM/atom_vec_bpm_sphere.cpp
+++ b/src/BPM/atom_vec_bpm_sphere.cpp
@@ -32,6 +32,7 @@ AtomVecBPMSphere::AtomVecBPMSphere(LAMMPS *_lmp) : AtomVec(_lmp)
   mass_type = PER_ATOM;
   molecular = Atom::MOLECULAR;
   bonds_allow = 1;
+  radvary = 0;
 
   atom->molecule_flag = 1;
   atom->sphere_flag = 1;
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index 5599ef4370..5a98d78abc 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -30,6 +30,7 @@ AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
 {
   mass_type = PER_ATOM;
   molecular = Atom::ATOMIC;
+  radvary = 0;
 
   atom->sphere_flag = 1;
   atom->radius_flag = atom->rmass_flag = atom->omega_flag = atom->torque_flag = 1;

From cea202ebe90a13d5bf4277f61366576e0805ff9d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 18 Jul 2023 11:09:09 -0400
Subject: [PATCH 388/396] include file is not needed

---
 src/KOKKOS/atom_vec_sphere_kokkos.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp
index a9b64fc835..5a1c2beee3 100644
--- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp
@@ -20,7 +20,6 @@
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_adapt.h"
 #include "math_const.h"
 #include "memory.h"
 #include "memory_kokkos.h"

From 2e2624d719ebbe4b5ffba0b0dec65deb1b069070 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 18 Jul 2023 11:10:18 -0400
Subject: [PATCH 389/396] update loop over adapt fixes logic

---
 src/BPM/atom_vec_bpm_sphere.cpp | 11 ++++++-----
 src/atom_vec_sphere.cpp         | 11 ++++++-----
 2 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/BPM/atom_vec_bpm_sphere.cpp b/src/BPM/atom_vec_bpm_sphere.cpp
index d3070383e5..2820a74c8a 100644
--- a/src/BPM/atom_vec_bpm_sphere.cpp
+++ b/src/BPM/atom_vec_bpm_sphere.cpp
@@ -98,11 +98,12 @@ void AtomVecBPMSphere::init()
 
   // check if optional radvary setting should have been set to 1
 
-  for (auto ifix : modify->get_fix_by_style("^adapt")) {
-    if (ifix->diam_flag && (radvary == 0))
-      error->all(FLERR, "Fix {} changes atom radii but atom_style bpm/sphere is not dynamic",
-        ifix->style);
-  }
+  if (radvary == 0)
+    for (const auto &ifix : modify->get_fix_by_style("^adapt")) {
+      if (ifix->diam_flag)
+        error->all(FLERR, "Fix {} changes atom radii but atom_style bpm/sphere is not dynamic",
+                   ifix->style);
+    }
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index 5a98d78abc..8769c316d9 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -88,11 +88,12 @@ void AtomVecSphere::init()
 
   // check if optional radvary setting should have been set to 1
 
-  for (auto &ifix : modify->get_fix_by_style("^adapt")) {
-    if (ifix->diam_flag && (radvary == 0))
-      error->all(FLERR, "Fix {} changes atom radii but atom_style sphere is not dynamic",
-        ifix->style);
-  }
+  if (radvary == 0)
+    for (const auto &ifix : modify->get_fix_by_style("^adapt")) {
+      if (ifix->diam_flag)
+        error->all(FLERR, "Fix {} changes atom radii but atom_style sphere is not dynamic",
+                   ifix->style);
+    }
 }
 
 /* ----------------------------------------------------------------------

From 7d46165c2a935b18a96bee124ccbe6a762ac7907 Mon Sep 17 00:00:00 2001
From: Stan Gerald Moore <stamoor@sandia.gov>
Date: Thu, 20 Jul 2023 13:31:34 -0600
Subject: [PATCH 390/396] Fix compile bug in Kokkos MEAM styles

---
 src/KOKKOS/pair_meam_kokkos.cpp    |  2 +-
 src/KOKKOS/pair_meam_ms_kokkos.cpp |  2 +-
 src/KOKKOS/pppm_kokkos.h           | 15 ++++++++++++++-
 3 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/src/KOKKOS/pair_meam_kokkos.cpp b/src/KOKKOS/pair_meam_kokkos.cpp
index c2b03c2054..daf9c1e18b 100644
--- a/src/KOKKOS/pair_meam_kokkos.cpp
+++ b/src/KOKKOS/pair_meam_kokkos.cpp
@@ -980,7 +980,7 @@ void PairMEAMKokkos<DeviceType>::update_meam_views()
 
 namespace LAMMPS_NS {
 template class PairMEAMKokkos<LMPDeviceType>;
-#ifdef KOKKOS_ENABLE_CUDA
+#ifdef LMP_KOKKOS_GPU
 template class PairMEAMKokkos<LMPHostType>;
 #endif
 }
diff --git a/src/KOKKOS/pair_meam_ms_kokkos.cpp b/src/KOKKOS/pair_meam_ms_kokkos.cpp
index 491fc0273c..eaa7d500b9 100644
--- a/src/KOKKOS/pair_meam_ms_kokkos.cpp
+++ b/src/KOKKOS/pair_meam_ms_kokkos.cpp
@@ -26,7 +26,7 @@ PairMEAMMSKokkos<DeviceType>::PairMEAMMSKokkos(LAMMPS *lmp) : PairMEAMKokkos<Dev
 
 namespace LAMMPS_NS {
 template class PairMEAMMSKokkos<LMPDeviceType>;
-#ifdef KOKKOS_ENABLE_CUDA
+#ifdef LMP_KOKKOS_GPU
 template class PairMEAMMSKokkos<LMPHostType>;
 #endif
 }
diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h
index 2c6dcc4e15..d621313873 100644
--- a/src/KOKKOS/pppm_kokkos.h
+++ b/src/KOKKOS/pppm_kokkos.h
@@ -33,7 +33,7 @@ KSpaceStyle(pppm/kk/host,PPPMKokkos<LMPHostType>);
 
 // clang-format off
 
-// fix up FFT defines for KOKKOS with CUDA
+// fix up FFT defines for KOKKOS with CUDA and HIP
 
 #ifdef KOKKOS_ENABLE_CUDA
 # if defined(FFT_FFTW)
@@ -48,6 +48,19 @@ KSpaceStyle(pppm/kk/host,PPPMKokkos<LMPHostType>);
 # if !defined(FFT_CUFFT) && !defined(FFT_KISSFFT)
 #  define FFT_KISSFFT
 # endif
+#elif defined(KOKKOS_ENABLE_HIP)
+# if defined(FFT_FFTW)
+#  undef FFT_FFTW
+# endif
+# if defined(FFT_FFTW3)
+#  undef FFT_FFTW3
+# endif
+# if defined(FFT_MKL)
+#  undef FFT_MKL
+# endif
+# if !defined(FFT_HIPFFT) && !defined(FFT_KISSFFT)
+#  define FFT_KISSFFT
+# endif
 #endif
 
 #include "pppm.h"

From 6c6258371b774b2f44b75adb5a574dcde9d3f75e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 20 Jul 2023 20:31:16 -0400
Subject: [PATCH 391/396] add init_flags() and is_initialized() methods

---
 src/compute.cpp | 10 ++++++++++
 src/compute.h   |  6 +++++-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/compute.cpp b/src/compute.cpp
index dcad4954fc..2bd1544fd7 100644
--- a/src/compute.cpp
+++ b/src/compute.cpp
@@ -74,6 +74,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) :
   dynamic = 0;
   dynamic_group_allow = 1;
 
+  initialized_flag = 0;
   invoked_scalar = invoked_vector = invoked_array = -1;
   invoked_peratom = invoked_local = -1;
   invoked_flag = INVOKED_NONE;
@@ -111,6 +112,15 @@ Compute::~Compute()
 
 /* ---------------------------------------------------------------------- */
 
+void Compute::init_flags()
+{
+  initialized_flag = 1;
+  invoked_scalar = invoked_vector = invoked_array = -1;
+  invoked_peratom = invoked_local = -1;
+}
+
+/* ---------------------------------------------------------------------- */
+
 void Compute::modify_params(int narg, char **arg)
 {
   if (narg == 0) error->all(FLERR,"Illegal compute_modify command");
diff --git a/src/compute.h b/src/compute.h
index 72b0075fd6..8ae01a4469 100644
--- a/src/compute.h
+++ b/src/compute.h
@@ -62,7 +62,7 @@ class Compute : protected Pointers {
   int size_local_rows;    // rows in local vector or array
   int size_local_cols;    // 0 = vector, N = columns in local array
 
-  int pergrid_flag;       // 0/1 if compute_pergrid() function exists
+  int pergrid_flag;    // 0/1 if compute_pergrid() function exists
 
   int extscalar;    // 0/1 if global scalar is intensive/extensive
   int extvector;    // 0/1/-1 if global vector is all int/ext/extlist
@@ -88,6 +88,7 @@ class Compute : protected Pointers {
   int maxtime;      // max # of entries time list can hold
   bigint *tlist;    // list of timesteps the Compute is called on
 
+  int initialized_flag;      // 1 if compute is initialized, 0 if not
   int invoked_flag;          // non-zero if invoked or accessed this step, 0 if not
   bigint invoked_scalar;     // last timestep on which compute_scalar() was invoked
   bigint invoked_vector;     // ditto for compute_vector()
@@ -114,6 +115,7 @@ class Compute : protected Pointers {
   void modify_params(int, char **);
   virtual void reset_extra_dof();
 
+  void init_flags();
   virtual void init() = 0;
   virtual void init_list(int, class NeighList *) {}
   virtual void setup() {}
@@ -161,6 +163,8 @@ class Compute : protected Pointers {
   int matchstep(bigint);
   void clearstep();
 
+  bool is_initialized() const { return initialized_flag == 1; }
+
   virtual double memory_usage() { return 0.0; }
 
   virtual void pair_setup_callback(int, int) {}

From c7996b506a4f0f1663cf039dffac7051aeff51f0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 20 Jul 2023 20:31:48 -0400
Subject: [PATCH 392/396] make use of Compute::is_initialized() and
 Compute::init_flags()

---
 src/modify.cpp   |  6 +-----
 src/thermo.cpp   | 16 ++++++++--------
 src/variable.cpp | 44 ++++++++++++++++++++++----------------------
 3 files changed, 31 insertions(+), 35 deletions(-)

diff --git a/src/modify.cpp b/src/modify.cpp
index d0656d3895..427c4e259b 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -191,11 +191,7 @@ void Modify::init()
 
   for (i = 0; i < ncompute; i++) {
     compute[i]->init();
-    compute[i]->invoked_scalar = -1;
-    compute[i]->invoked_vector = -1;
-    compute[i]->invoked_array = -1;
-    compute[i]->invoked_peratom = -1;
-    compute[i]->invoked_local = -1;
+    compute[i]->init_flags();
   }
   addstep_compute_all(update->ntimestep);
 
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 6122edec83..bdf2b8cf7b 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -1134,8 +1134,8 @@ void Thermo::check_temp(const std::string &keyword)
   if (!temperature)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init temperature",
                keyword);
-  if (update->first_update == 0)
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before first run",keyword);
+  if (!temperature->is_initialized())
+    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialized by run",keyword);
   if (!(temperature->invoked_flag & Compute::INVOKED_SCALAR)) {
     temperature->compute_scalar();
     temperature->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1153,8 +1153,8 @@ void Thermo::check_pe(const std::string &keyword)
   if (!pe)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init potential energy",
                keyword);
-  if (update->first_update == 0)
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before first run",keyword);
+  if (!pe->is_initialized())
+    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialized by run",keyword);
   if (!(pe->invoked_flag & Compute::INVOKED_SCALAR)) {
     pe->compute_scalar();
     pe->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1169,8 +1169,8 @@ void Thermo::check_press_scalar(const std::string &keyword)
 {
   if (!pressure)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init press", keyword);
-  if (update->first_update == 0)
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before first run",keyword);
+  if (!pressure->is_initialized())
+    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialized by run",keyword);
   if (!(pressure->invoked_flag & Compute::INVOKED_SCALAR)) {
     pressure->compute_scalar();
     pressure->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1185,8 +1185,8 @@ void Thermo::check_press_vector(const std::string &keyword)
 {
   if (!pressure)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init press", keyword);
-  if (update->first_update == 0)
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before first run",keyword);
+  if (!pressure->is_initialized())
+    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialized by run",keyword);
   if (!(pressure->invoked_flag & Compute::INVOKED_VECTOR)) {
     pressure->compute_vector();
     pressure->invoked_flag |= Compute::INVOKED_VECTOR;
diff --git a/src/variable.cpp b/src/variable.cpp
index 3264cfa1ee..7cbd43b7c6 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -1505,8 +1505,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
 
         if (nbracket == 0 && compute->scalar_flag && lowercase) {
 
-          if (update->first_update == 0)
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+          if (!compute->is_initialized())
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_SCALAR)) {
             compute->compute_scalar();
             compute->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1527,8 +1527,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
           if (index1 > compute->size_vector &&
               compute->size_vector_variable == 0)
             print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range",ivar,0);
-          if (update->first_update == 0)
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+          if (!compute->is_initialized())
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
             compute->compute_vector();
             compute->invoked_flag |= Compute::INVOKED_VECTOR;
@@ -1553,8 +1553,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
             print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
           if (index2 > compute->size_array_cols)
             print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
-          if (update->first_update == 0)
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+          if (!compute->is_initialized())
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
             compute->compute_array();
             compute->invoked_flag |= Compute::INVOKED_ARRAY;
@@ -1580,8 +1580,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
             print_var_error(FLERR,"Compute global vector in atom-style variable formula",ivar);
           if (compute->size_vector == 0)
             print_var_error(FLERR,"Variable formula compute vector is zero length",ivar);
-          if (update->first_update == 0)
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+          if (!compute->is_initialized())
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
             compute->compute_vector();
             compute->invoked_flag |= Compute::INVOKED_VECTOR;
@@ -1604,8 +1604,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
             print_var_error(FLERR,"Compute global vector in atom-style variable formula",ivar);
           if (compute->size_array_rows == 0)
             print_var_error(FLERR,"Variable formula compute array is zero length",ivar);
-          if (update->first_update == 0)
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+          if (!compute->is_initialized())
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
             compute->compute_array();
             compute->invoked_flag |= Compute::INVOKED_ARRAY;
@@ -1623,8 +1623,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
         } else if (nbracket == 1 && compute->peratom_flag &&
                    compute->size_peratom_cols == 0) {
 
-          if (update->first_update == 0)
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+          if (!compute->is_initialized())
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
             compute->compute_peratom();
             compute->invoked_flag |= Compute::INVOKED_PERATOM;
@@ -1640,8 +1640,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
 
           if (index2 > compute->size_peratom_cols)
             print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
-          if (update->first_update == 0)
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+          if (!compute->is_initialized())
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
             compute->compute_peratom();
             compute->invoked_flag |= Compute::INVOKED_PERATOM;
@@ -1663,8 +1663,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
             print_var_error(FLERR,"Per-atom compute in equal-style variable formula",ivar);
           if (treetype == VECTOR)
             print_var_error(FLERR,"Per-atom compute in vector-style variable formula",ivar);
-          if (update->first_update == 0)
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+          if (!compute->is_initialized())
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
             compute->compute_peratom();
             compute->invoked_flag |= Compute::INVOKED_PERATOM;
@@ -1687,8 +1687,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
             print_var_error(FLERR,"Per-atom compute in vector-style variable formula",ivar);
           if (index1 > compute->size_peratom_cols)
             print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
-          if (update->first_update == 0)
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+          if (!compute->is_initialized())
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
             compute->compute_peratom();
             compute->invoked_flag |= Compute::INVOKED_PERATOM;
@@ -4163,8 +4163,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
         print_var_error(FLERR,mesg,ivar);
       }
       if (index == 0 && compute->vector_flag) {
-        if (update->first_update == 0)
-          print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+        if (!compute->is_initialized())
+          print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
         if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
           compute->compute_vector();
           compute->invoked_flag |= Compute::INVOKED_VECTOR;
@@ -4174,8 +4174,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
       } else if (index && compute->array_flag) {
         if (index > compute->size_array_cols)
           print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
-        if (update->first_update == 0)
-          print_var_error(FLERR,"Variable formula compute cannot be invoked before first run",ivar);
+        if (!compute->is_initialized())
+          print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
         if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
           compute->compute_array();
           compute->invoked_flag |= Compute::INVOKED_ARRAY;

From 78880c909915f00b44c4efb52e9da7ae8695a56f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 20 Jul 2023 21:28:45 -0400
Subject: [PATCH 393/396] update reset_atoms image to call Compute::init_flag()
 as a workaround

---
 src/reset_atoms_image.cpp | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/src/reset_atoms_image.cpp b/src/reset_atoms_image.cpp
index d39ea0fec1..7e9dd45a17 100644
--- a/src/reset_atoms_image.cpp
+++ b/src/reset_atoms_image.cpp
@@ -93,15 +93,16 @@ void ResetAtomsImage::command(int narg, char **arg)
                                    "c_ifmax_r_i_f[*] c_ifmin_r_i_f[*]");
 
   // trigger computes
-  // need to ensure update->first_update = 1
-  //   to allow this input script command prior to first run/minimize
-  //   this is b/c internal variables are evaulated which invoke computes
-  //   that will trigger an error unless first_update = 1
-  // reset update->first_update when done
-
-  int first_update_saved = update->first_update;
-  update->first_update = 1;
+  // need to first initialize compute flags to allow this input script command prior
+  //   to a first run/minimize.   this is b/c internal variables are evaulated which
+  //   invoke computes that will trigger an error unless they are initialized
 
+  frags->init_flags();
+  chunk->init_flags();
+  flags->init_flags();
+  ifmin->init_flags();
+  ifmax->init_flags();
+  cdist->init_flags();
   frags->compute_peratom();
   chunk->compute_peratom();
   flags->compute_peratom();
@@ -109,8 +110,6 @@ void ResetAtomsImage::command(int narg, char **arg)
   ifmax->compute_array();
   cdist->compute_peratom();
 
-  update->first_update = first_update_saved;
-
   // reset image flags for atoms in group
 
   const int *const mask = atom->mask;

From 0b57ea246c536e0d3594e5f2e526fefe876734ae Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 20 Jul 2023 21:48:51 -0400
Subject: [PATCH 394/396] update dump styles to use Compute::is_initialized()

---
 src/VTK/dump_vtk.cpp | 5 +++--
 src/dump_custom.cpp  | 5 +++--
 src/dump_grid.cpp    | 5 +++--
 src/dump_image.cpp   | 5 +++--
 src/dump_local.cpp   | 5 +++--
 5 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/src/VTK/dump_vtk.cpp b/src/VTK/dump_vtk.cpp
index a77f5b2e11..00bd451fb0 100644
--- a/src/VTK/dump_vtk.cpp
+++ b/src/VTK/dump_vtk.cpp
@@ -297,9 +297,10 @@ int DumpVTK::count()
   // cannot invoke before first run, otherwise invoke if necessary
 
   if (ncompute) {
-    if (update->first_update == 0)
-      error->all(FLERR,"Dump compute cannot be invoked before first run");
     for (i = 0; i < ncompute; i++) {
+      if (!compute[i]->is_initialized())
+        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialized by a run",
+          compute[i]->id);
       if (!(compute[i]->invoked_flag & Compute::INVOKED_PERATOM)) {
         compute[i]->compute_peratom();
         compute[i]->invoked_flag |= Compute::INVOKED_PERATOM;
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index dba72c7478..570ddd104f 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -562,9 +562,10 @@ int DumpCustom::count()
   // cannot invoke before first run, otherwise invoke if necessary
 
   if (ncompute) {
-    if (update->first_update == 0)
-      error->all(FLERR,"Dump compute cannot be invoked before first run");
     for (i = 0; i < ncompute; i++) {
+      if (!compute[i]->is_initialized())
+        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialized by a run",
+          compute[i]->id);
       if (!(compute[i]->invoked_flag & Compute::INVOKED_PERATOM)) {
         compute[i]->compute_peratom();
         compute[i]->invoked_flag |= Compute::INVOKED_PERATOM;
diff --git a/src/dump_grid.cpp b/src/dump_grid.cpp
index 39d80ade11..24f2586568 100644
--- a/src/dump_grid.cpp
+++ b/src/dump_grid.cpp
@@ -527,9 +527,10 @@ int DumpGrid::count()
   // cannot invoke before first run, otherwise invoke if necessary
 
   if (ncompute) {
-    if (update->first_update == 0)
-      error->all(FLERR,"Dump compute cannot be invoked before first run");
     for (i = 0; i < ncompute; i++) {
+      if (!compute[i]->is_initialized())
+        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialized by a run",
+          compute[i]->id);
       if (!(compute[i]->invoked_flag & Compute::INVOKED_PERGRID)) {
         compute[i]->compute_pergrid();
         compute[i]->invoked_flag |= Compute::INVOKED_PERGRID;
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index 0d54c60595..530e19a04c 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -667,8 +667,9 @@ void DumpImage::write()
     // cannot invoke before first run, otherwise invoke if necessary
 
     if (grid_compute) {
-      if (update->first_update == 0)
-        error->all(FLERR,"Grid compute used in dump image cannot be invoked before first run");
+      if (!grid_compute->is_initialized())
+        error->all(FLERR,"Grid compute ID {} used in dump image cannot be invoked "
+                   "before initialized by a run", grid_compute->id);
       if (!(grid_compute->invoked_flag & Compute::INVOKED_PERGRID)) {
         grid_compute->compute_pergrid();
         grid_compute->invoked_flag |= Compute::INVOKED_PERGRID;
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index 097589ea41..e81ab0590f 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -328,9 +328,10 @@ int DumpLocal::count()
   // cannot invoke before first run, otherwise invoke if necessary
 
   if (ncompute) {
-    if (update->first_update == 0)
-      error->all(FLERR,"Dump compute cannot be invoked before first run");
     for (i = 0; i < ncompute; i++) {
+      if (!compute[i]->is_initialized())
+        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialized by a run",
+          compute[i]->id);
       if (!(compute[i]->invoked_flag & Compute::INVOKED_LOCAL)) {
         compute[i]->compute_local();
         compute[i]->invoked_flag |= Compute::INVOKED_LOCAL;

From 2da908190bd34dca2791e58e96bb2354c85f7484 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 21 Jul 2023 11:24:57 -0400
Subject: [PATCH 395/396] make error messages consistent and improve their
 grammar

---
 src/VTK/dump_vtk.cpp |  2 +-
 src/dump_custom.cpp  |  2 +-
 src/dump_grid.cpp    |  2 +-
 src/dump_image.cpp   |  2 +-
 src/dump_local.cpp   |  2 +-
 src/thermo.cpp       |  8 ++++----
 src/variable.cpp     | 33 ++++++++++++++++++++++-----------
 7 files changed, 31 insertions(+), 20 deletions(-)

diff --git a/src/VTK/dump_vtk.cpp b/src/VTK/dump_vtk.cpp
index 00bd451fb0..172a092629 100644
--- a/src/VTK/dump_vtk.cpp
+++ b/src/VTK/dump_vtk.cpp
@@ -299,7 +299,7 @@ int DumpVTK::count()
   if (ncompute) {
     for (i = 0; i < ncompute; i++) {
       if (!compute[i]->is_initialized())
-        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialized by a run",
+        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialization by a run",
           compute[i]->id);
       if (!(compute[i]->invoked_flag & Compute::INVOKED_PERATOM)) {
         compute[i]->compute_peratom();
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 570ddd104f..1e60295bbe 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -564,7 +564,7 @@ int DumpCustom::count()
   if (ncompute) {
     for (i = 0; i < ncompute; i++) {
       if (!compute[i]->is_initialized())
-        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialized by a run",
+        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialization by a run",
           compute[i]->id);
       if (!(compute[i]->invoked_flag & Compute::INVOKED_PERATOM)) {
         compute[i]->compute_peratom();
diff --git a/src/dump_grid.cpp b/src/dump_grid.cpp
index 24f2586568..3c10aa9083 100644
--- a/src/dump_grid.cpp
+++ b/src/dump_grid.cpp
@@ -529,7 +529,7 @@ int DumpGrid::count()
   if (ncompute) {
     for (i = 0; i < ncompute; i++) {
       if (!compute[i]->is_initialized())
-        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialized by a run",
+        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialization by a run",
           compute[i]->id);
       if (!(compute[i]->invoked_flag & Compute::INVOKED_PERGRID)) {
         compute[i]->compute_pergrid();
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index 530e19a04c..1ba433f93f 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -669,7 +669,7 @@ void DumpImage::write()
     if (grid_compute) {
       if (!grid_compute->is_initialized())
         error->all(FLERR,"Grid compute ID {} used in dump image cannot be invoked "
-                   "before initialized by a run", grid_compute->id);
+                   "before initialization by a run", grid_compute->id);
       if (!(grid_compute->invoked_flag & Compute::INVOKED_PERGRID)) {
         grid_compute->compute_pergrid();
         grid_compute->invoked_flag |= Compute::INVOKED_PERGRID;
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index e81ab0590f..9695e152b2 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -330,7 +330,7 @@ int DumpLocal::count()
   if (ncompute) {
     for (i = 0; i < ncompute; i++) {
       if (!compute[i]->is_initialized())
-        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialized by a run",
+        error->all(FLERR,"Dump compute ID {} cannot be invoked before initialization by a run",
           compute[i]->id);
       if (!(compute[i]->invoked_flag & Compute::INVOKED_LOCAL)) {
         compute[i]->compute_local();
diff --git a/src/thermo.cpp b/src/thermo.cpp
index bdf2b8cf7b..a8442d42db 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -1135,7 +1135,7 @@ void Thermo::check_temp(const std::string &keyword)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init temperature",
                keyword);
   if (!temperature->is_initialized())
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialized by run",keyword);
+    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
   if (!(temperature->invoked_flag & Compute::INVOKED_SCALAR)) {
     temperature->compute_scalar();
     temperature->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1154,7 +1154,7 @@ void Thermo::check_pe(const std::string &keyword)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init potential energy",
                keyword);
   if (!pe->is_initialized())
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialized by run",keyword);
+    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
   if (!(pe->invoked_flag & Compute::INVOKED_SCALAR)) {
     pe->compute_scalar();
     pe->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1170,7 +1170,7 @@ void Thermo::check_press_scalar(const std::string &keyword)
   if (!pressure)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init press", keyword);
   if (!pressure->is_initialized())
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialized by run",keyword);
+    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
   if (!(pressure->invoked_flag & Compute::INVOKED_SCALAR)) {
     pressure->compute_scalar();
     pressure->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1186,7 +1186,7 @@ void Thermo::check_press_vector(const std::string &keyword)
   if (!pressure)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init press", keyword);
   if (!pressure->is_initialized())
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialized by run",keyword);
+    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
   if (!(pressure->invoked_flag & Compute::INVOKED_VECTOR)) {
     pressure->compute_vector();
     pressure->invoked_flag |= Compute::INVOKED_VECTOR;
diff --git a/src/variable.cpp b/src/variable.cpp
index 7cbd43b7c6..cf2e5c3b6f 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -1506,7 +1506,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
         if (nbracket == 0 && compute->scalar_flag && lowercase) {
 
           if (!compute->is_initialized())
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                            "initialization by a run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_SCALAR)) {
             compute->compute_scalar();
             compute->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1528,7 +1529,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
               compute->size_vector_variable == 0)
             print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range",ivar,0);
           if (!compute->is_initialized())
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                            "initialization by a run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
             compute->compute_vector();
             compute->invoked_flag |= Compute::INVOKED_VECTOR;
@@ -1554,7 +1556,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
           if (index2 > compute->size_array_cols)
             print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
           if (!compute->is_initialized())
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                            "initialization by a run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
             compute->compute_array();
             compute->invoked_flag |= Compute::INVOKED_ARRAY;
@@ -1581,7 +1584,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
           if (compute->size_vector == 0)
             print_var_error(FLERR,"Variable formula compute vector is zero length",ivar);
           if (!compute->is_initialized())
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                            "initialization by a run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
             compute->compute_vector();
             compute->invoked_flag |= Compute::INVOKED_VECTOR;
@@ -1605,7 +1609,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
           if (compute->size_array_rows == 0)
             print_var_error(FLERR,"Variable formula compute array is zero length",ivar);
           if (!compute->is_initialized())
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                            "initialization by a run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
             compute->compute_array();
             compute->invoked_flag |= Compute::INVOKED_ARRAY;
@@ -1624,7 +1629,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
                    compute->size_peratom_cols == 0) {
 
           if (!compute->is_initialized())
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                            "initialization by a run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
             compute->compute_peratom();
             compute->invoked_flag |= Compute::INVOKED_PERATOM;
@@ -1641,7 +1647,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
           if (index2 > compute->size_peratom_cols)
             print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
           if (!compute->is_initialized())
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                            "initialization by a run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
             compute->compute_peratom();
             compute->invoked_flag |= Compute::INVOKED_PERATOM;
@@ -1664,7 +1671,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
           if (treetype == VECTOR)
             print_var_error(FLERR,"Per-atom compute in vector-style variable formula",ivar);
           if (!compute->is_initialized())
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                            "initialization by a run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
             compute->compute_peratom();
             compute->invoked_flag |= Compute::INVOKED_PERATOM;
@@ -1688,7 +1696,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
           if (index1 > compute->size_peratom_cols)
             print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
           if (!compute->is_initialized())
-            print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+            print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                            "initialization by a run",ivar);
           if (!(compute->invoked_flag & Compute::INVOKED_PERATOM)) {
             compute->compute_peratom();
             compute->invoked_flag |= Compute::INVOKED_PERATOM;
@@ -4164,7 +4173,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
       }
       if (index == 0 && compute->vector_flag) {
         if (!compute->is_initialized())
-          print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+          print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                          "initialization by a run",ivar);
         if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
           compute->compute_vector();
           compute->invoked_flag |= Compute::INVOKED_VECTOR;
@@ -4175,7 +4185,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
         if (index > compute->size_array_cols)
           print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0);
         if (!compute->is_initialized())
-          print_var_error(FLERR,"Variable formula compute cannot be invoked before initialized by run",ivar);
+          print_var_error(FLERR,"Variable formula compute cannot be invoked before "
+                          "initialization by a run",ivar);
         if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
           compute->compute_array();
           compute->invoked_flag |= Compute::INVOKED_ARRAY;

From 9669bf3d3b3d57286469ba9dc6f48e9b29e35787 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 21 Jul 2023 11:25:44 -0400
Subject: [PATCH 396/396] move creation of internal computes and variables
 before lmp->init() so they are initialized

---
 src/reset_atoms_image.cpp | 40 ++++++++++++++++-----------------------
 1 file changed, 16 insertions(+), 24 deletions(-)

diff --git a/src/reset_atoms_image.cpp b/src/reset_atoms_image.cpp
index 7e9dd45a17..84df5bf746 100644
--- a/src/reset_atoms_image.cpp
+++ b/src/reset_atoms_image.cpp
@@ -61,6 +61,22 @@ void ResetAtomsImage::command(int narg, char **arg)
   MPI_Barrier(world);
   double time1 = platform::walltime();
 
+  // create computes and variables
+  // must come before lmp->init so the computes are properly initialized
+
+  auto frags = modify->add_compute("frags_r_i_f all fragment/atom single yes");
+  auto chunk = modify->add_compute("chunk_r_i_f all chunk/atom c_frags_r_i_f compress yes");
+  auto flags = modify->add_compute("flags_r_i_f all property/atom ix iy iz");
+  input->variable->set("ix_r_i_f atom c_flags_r_i_f[1]");
+  input->variable->set("iy_r_i_f atom c_flags_r_i_f[2]");
+  input->variable->set("iz_r_i_f atom c_flags_r_i_f[3]");
+  auto ifmin = modify->add_compute("ifmin_r_i_f all reduce/chunk chunk_r_i_f min "
+                                   "v_ix_r_i_f v_iy_r_i_f v_iz_r_i_f");
+  auto ifmax = modify->add_compute("ifmax_r_i_f all reduce/chunk chunk_r_i_f max "
+                                   "v_ix_r_i_f v_iy_r_i_f v_iz_r_i_f");
+  auto cdist = modify->add_compute("cdist_r_i_f all chunk/spread/atom chunk_r_i_f "
+                                   "c_ifmax_r_i_f[*] c_ifmin_r_i_f[*]");
+
   // initialize system since comm->borders() will be invoked
 
   lmp->init();
@@ -77,32 +93,8 @@ void ResetAtomsImage::command(int narg, char **arg)
   comm->borders();
   if (domain->triclinic) domain->lamda2x(atom->nlocal + atom->nghost);
 
-  // create computes and variables
-
-  auto frags = modify->add_compute("frags_r_i_f all fragment/atom single yes");
-  auto chunk = modify->add_compute("chunk_r_i_f all chunk/atom c_frags_r_i_f compress yes");
-  auto flags = modify->add_compute("flags_r_i_f all property/atom ix iy iz");
-  input->variable->set("ix_r_i_f atom c_flags_r_i_f[1]");
-  input->variable->set("iy_r_i_f atom c_flags_r_i_f[2]");
-  input->variable->set("iz_r_i_f atom c_flags_r_i_f[3]");
-  auto ifmin = modify->add_compute("ifmin_r_i_f all reduce/chunk chunk_r_i_f min "
-                                   "v_ix_r_i_f v_iy_r_i_f v_iz_r_i_f");
-  auto ifmax = modify->add_compute("ifmax_r_i_f all reduce/chunk chunk_r_i_f max "
-                                   "v_ix_r_i_f v_iy_r_i_f v_iz_r_i_f");
-  auto cdist = modify->add_compute("cdist_r_i_f all chunk/spread/atom chunk_r_i_f "
-                                   "c_ifmax_r_i_f[*] c_ifmin_r_i_f[*]");
-
   // trigger computes
-  // need to first initialize compute flags to allow this input script command prior
-  //   to a first run/minimize.   this is b/c internal variables are evaulated which
-  //   invoke computes that will trigger an error unless they are initialized
 
-  frags->init_flags();
-  chunk->init_flags();
-  flags->init_flags();
-  ifmin->init_flags();
-  ifmax->init_flags();
-  cdist->init_flags();
   frags->compute_peratom();
   chunk->compute_peratom();
   flags->compute_peratom();