new neigh_modify exclude option, other SNAP changes

doc/src/compute_voronoi_atom.txt

@@ -217,6 +217,10 @@ This compute is part of the VORONOI package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
+It also requiers you have a copy of the Voro++ library built and
+installed on your system.  See instructions on obtaining and
+installing the Voro++ software in the src/VORONOI/README file.
+
 [Related commands:]
 
 "dump custom"_dump.html, "dump local"_dump.html

doc/src/neigh_modify.txt

@@ -34,8 +34,10 @@ keyword = {delay} or {every} or {check} or {once} or {cluster} or {include} or {
       M,N = exclude if one atom in pair is type M, other is type N
     group group1-ID group2-ID
       group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd
-    molecule group-ID
+    molecule/intra group-ID
-      groupname = exclude if both atoms are in the same molecule and in the same group
+      group-ID = exclude if both atoms are in the same molecule and in group
+    molecule/inter group-ID
+      group-ID = exclude if both atoms are in different molecules and in group
     none
       delete all exclude settings
   {page} value = N
@@ -52,7 +54,7 @@ neigh_modify every 2 delay 10 check yes page 100000
 neigh_modify exclude type 2 3
 neigh_modify exclude group frozen frozen check no
 neigh_modify exclude group residue1 chain3
-neigh_modify exclude molecule rigid :pre
+neigh_modify exclude molecule/intra rigid :pre
 
 [Description:]
 
@@ -130,9 +132,11 @@ The {exclude type} option turns off the pairwise interaction if one
 atom is of type M and the other of type N.  M can equal N.  The
 {exclude group} option turns off the interaction if one atom is in the
 first group and the other is the second.  Group1-ID can equal
-group2-ID.  The {exclude molecule} option turns off the interaction if
+group2-ID.  The {exclude molecule/intra} option turns off the
-both atoms are in the specified group and in the same molecule, as
+interaction if both atoms are in the specified group and in the same
-determined by their molecule ID.
+molecule, as determined by their molecule ID.  The {exclude
+molecule/inter} turns off the interaction between pairs of atoms that
+have different molecule IDs and are both in the specified group.
 
 Each of the exclude options can be specified multiple times.  The
 {exclude type} option is the most efficient option to use; it requires
@@ -195,8 +199,8 @@ binsize of 1/2 the cutoff.
 If the "delay" setting is non-zero, then it must be a multiple of the
 "every" setting.
 
-The exclude molecule option can only be used with atom styles that
+The molecule/intra and molecule/inter exclude options can only be used
-define molecule IDs.
+with atom styles that define molecule IDs.
 
 The value of the {page} setting must be at least 10x larger than the
 {one} setting.  This insures neighbor pages are not mostly empty

examples/USER/misc/gauss-diel/in.gauss-diel

@@ -81,7 +81,7 @@ group           sds subtract all cions
 velocity        all create 1. 87287 dist gaussian
 
 neighbor        1.5 multi
-neigh_modify    exclude molecule sds
+neigh_modify    exclude molecule/intra sds
 neigh_modify    every 5 delay 0 check yes
 
 fix             1 all nve/limit 0.2

examples/USER/misc/gauss-diel/in.gauss-diel-cg

@@ -81,7 +81,7 @@ group           sds subtract all cions
 velocity        all create 1. 87287 dist gaussian
 
 neighbor        1.5 multi
-neigh_modify    exclude molecule sds
+neigh_modify    exclude molecule/intra sds
 neigh_modify    every 5 delay 0 check yes
 
 fix             1 all nve/limit 0.2

examples/USER/misc/gauss-diel/in.gauss-diel-split

@@ -84,7 +84,7 @@ group           sds subtract all cions
 velocity        all create 1. 87287 dist gaussian
 
 neighbor        1.5 multi
-neigh_modify    exclude molecule sds
+neigh_modify    exclude molecule/intra sds
 neigh_modify    every 5 delay 0 check yes
 
 fix             1 all nve/limit 0.2

examples/rigid/in.rigid.tnr

@@ -20,7 +20,7 @@ velocity	all create 1.4 109345
 group		rods type 2	
 group		tethers	subtract all rods
 
-neigh_modify 	exclude	molecule rods delay 0 every 1
+neigh_modify 	exclude	molecule/intra rods delay 0 every 1
 
 # Specify the pair potentials
 

examples/snap/W_2940_2017_2.snap

@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL potential.
 variable zblcutinner equal 4

examples/snap/W_2940_2017_2.snapcoeff

@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 # 
 # LAMMPS SNAP coefficients for W
 

examples/snap/W_2940_2017_2.snapparam

@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 # 
 # required
 rcutfac 4.73442

examples/snap/W_2940_2017_2_He_JW2013.snap

@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL+Tabulated potential.
 variable zblcutinner equal 4

examples/snap/in.snap.Ta06A

@@ -24,7 +24,7 @@ mass 1 180.88
 
 # choose potential
 
-include Ta06A_pot.snap
+include Ta06A.snap
 
 # Setup output
 

examples/snap/in.snap.W.2940

@@ -24,7 +24,7 @@ mass 1 183.84
 
 # choose potential
 
-include W_2940_2017_2.pot.snap
+include W_2940_2017_2.snap
 
 # Setup output
 

examples/snap/in.snap.hybrid.WSNAP.HePair

@@ -27,7 +27,7 @@ group	tungsten type 1
 group	helium	type 2
 # choose potential
 
-include W.SNAP_HePair.pot
+include W_2940_2017_2_He_JW2013.snap
 
 # Setup output
 

potentials/Ta06A.snap

@@ -9,9 +9,9 @@ variable zblz equal 73
 
 # Specify hybrid with SNAP, ZBL
 
-pair_style hybrid/overlay snap &
+pair_style hybrid/overlay &
-zbl ${zblcutinner} ${zblcutouter}
+zbl ${zblcutinner} ${zblcutouter} &
-
+snap
 pair_coeff 1 1 zbl ${zblz} ${zblz}
 pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
 

potentials/W_2940_2017_2.snap

@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL potential.
 variable zblcutinner equal 4

potentials/W_2940_2017_2.snapcoeff

@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 # 
 # LAMMPS SNAP coefficients for W
 

potentials/W_2940_2017_2.snapparam

@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 # 
 # required
 rcutfac 4.73442

potentials/W_2940_2017_2_He_JW2013.snap

@@ -1,4 +1,4 @@
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL+Tabulated potential.
 variable zblcutinner equal 4

src/GPU/README

@@ -1,11 +1,16 @@
 This package implements GPU optimizations of various LAMMPS styles.
 
-This package uses an external library in lib/gpu which must be
+Section 5.3.1 on the manual gives details of what hardware and Cuda
-compiled before making LAMMPS.  See the lib/gpu/README file and the
+software is required on your system, and full details on how to build
+and use this package.  See the KOKKOS package, which also has
+GPU-enabled styles.
+
+This package uses an external library provided in lib/gpu which must
+be compiled before making LAMMPS.  See the lib/gpu/README file and the
 LAMMPS manual for information on building LAMMPS with external
 libraries.  The settings in the Makefile.lammps file in that directory
 must be correct for LAMMPS to build correctly with this package
 installed.
 
-The people who created this package are Mike Brown (while at Sandia
+The GPU package and its associated library was created by Mike Brown
-and ORNL) and Trung Nguyen (while at ORNL).
+while at Sandia and ORNL, and by Trung Nguyen while at ORNL.

src/KIM/README

@@ -1,5 +1,3 @@
--*- fill-column: 70; -*-
-
 This package provides a pair_style kim command which is a wrapper on
 the Knowledge Base for Interatomic Models (KIM) repository of
 interatomic potentials, so that they can be used by LAMMPS scripts.

src/KOKKOS/neighbor_kokkos.cpp

@@ -64,6 +64,7 @@ NeighborKokkos::~NeighborKokkos()
     memory->destroy_kokkos(k_ex1_bit,ex1_bit);
     memory->destroy_kokkos(k_ex2_bit,ex2_bit);
     memory->destroy_kokkos(k_ex_mol_bit,ex_mol_bit);
+    memory->destroy_kokkos(k_ex_mol_intra,ex_mol_intra);
 
     memory->destroy_kokkos(k_bondlist,bondlist);
     memory->destroy_kokkos(k_anglelist,anglelist);
@@ -133,6 +134,14 @@ void NeighborKokkos::init_ex_mol_bit_kokkos()
   k_ex_mol_bit.modify<LMPHostType>();
 }
 
+/* ---------------------------------------------------------------------- */
+
+void NeighborKokkos::grow_ex_mol_intra_kokkos()
+{
+  memory->grow_kokkos(k_ex_mol_intra, ex_mol_intra, maxex_mol, "neigh:ex_mol_intra");
+  k_ex_mol_intra.modify<LMPHostType>();
+}
+
 /* ----------------------------------------------------------------------
    if any atom moved trigger distance (half of neighbor skin) return 1
    shrink trigger distance if box size has changed
@@ -348,6 +357,12 @@ void NeighborKokkos::modify_mol_group_grow_kokkos(){
   k_ex_mol_group.modify<LMPHostType>();
 }
 
+/* ---------------------------------------------------------------------- */
+void NeighborKokkos::modify_mol_intra_grow_kokkos(){
+  memory->grow_kokkos(k_ex_mol_intra,ex_mol_intra,maxex_mol,"neigh:ex_mol_intra");
+  k_ex_mol_intra.modify<LMPHostType>();
+}
+
 /* ---------------------------------------------------------------------- */
 
 void NeighborKokkos::init_topology() {

src/KOKKOS/neighbor_kokkos.h

@@ -54,6 +54,7 @@ class NeighborKokkos : public Neighbor {
   DAT::tdual_int_1d k_ex1_bit,k_ex2_bit;
   DAT::tdual_int_1d k_ex_mol_group;
   DAT::tdual_int_1d k_ex_mol_bit;
+  DAT::tdual_int_1d k_ex_mol_intra;
 
   NeighBondKokkos<LMPHostType> neighbond_host;
   NeighBondKokkos<LMPDeviceType> neighbond_device;
@@ -76,6 +77,7 @@ class NeighborKokkos : public Neighbor {
   void init_ex_type_kokkos(int);
   void init_ex_bit_kokkos();
   void init_ex_mol_bit_kokkos();
+  void grow_ex_mol_intra_kokkos();
   virtual int check_distance();
   template<class DeviceType> int check_distance_kokkos();
   virtual void build(int);
@@ -84,6 +86,7 @@ class NeighborKokkos : public Neighbor {
   void modify_ex_type_grow_kokkos();
   void modify_ex_group_grow_kokkos();
   void modify_mol_group_grow_kokkos();
+  void modify_mol_intra_grow_kokkos();
 };
 
 }

src/KOKKOS/npair_kokkos.cpp

@@ -56,6 +56,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::copy_neighbor_info()
   k_ex2_bit = neighborKK->k_ex2_bit;
   k_ex_mol_group = neighborKK->k_ex_mol_group;
   k_ex_mol_bit = neighborKK->k_ex_mol_bit;
+  k_ex_mol_intra = neighborKK->k_ex_mol_intra;
 }
 
 /* ----------------------------------------------------------------------
@@ -147,6 +148,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::build(NeighList *list_)
          nex_mol,
          k_ex_mol_group.view<DeviceType>(),
          k_ex_mol_bit.view<DeviceType>(),
+         k_ex_mol_intra.view<DeviceType>(),
          bboxhi,bboxlo,
          domain->xperiodic,domain->yperiodic,domain->zperiodic,
          domain->xprd_half,domain->yprd_half,domain->zprd_half);
@@ -161,6 +163,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::build(NeighList *list_)
   k_ex2_bit.sync<DeviceType>();
   k_ex_mol_group.sync<DeviceType>();
   k_ex_mol_bit.sync<DeviceType>();
+  k_ex_mol_intra.sync<DeviceType>();
   k_bincount.sync<DeviceType>(),
   k_bins.sync<DeviceType>(),
   atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK);
@@ -284,8 +287,12 @@ int NeighborKokkosExecute<DeviceType>::exclusion(const int &i,const int &j,
 
   if (nex_mol) {
     for (m = 0; m < nex_mol; m++)
-      if (mask(i) & ex_mol_bit(m) && mask(j) & ex_mol_bit(m) &&
+      if (ex_mol_intra[m]) { // intra-chain: exclude i-j pair if on same molecule 
-          molecule(i) == molecule(j)) return 1;
+        if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
+	    molecule[i] == molecule[j]) return 1;
+      } else                 // exclude i-j pair if on different molecules 
+	if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
+	    molecule[i] != molecule[j]) return 1;
   }
 
   return 0;

src/KOKKOS/npair_kokkos.h

@@ -98,6 +98,7 @@ class NPairKokkos : public NPair {
   DAT::tdual_int_1d k_ex1_bit,k_ex2_bit;
   DAT::tdual_int_1d k_ex_mol_group;
   DAT::tdual_int_1d k_ex_mol_bit;
+  DAT::tdual_int_1d k_ex_mol_intra;
 
   // data from NBin class
 
@@ -139,6 +140,7 @@ class NeighborKokkosExecute
   const int nex_mol;
   const typename AT::t_int_1d_const ex_mol_group;
   const typename AT::t_int_1d_const ex_mol_bit;
+  const typename AT::t_int_1d_const ex_mol_intra;
 
   // data from NBin class
 
@@ -216,6 +218,7 @@ class NeighborKokkosExecute
                         const int & _nex_mol,
                         const typename AT::t_int_1d_const & _ex_mol_group,
                         const typename AT::t_int_1d_const & _ex_mol_bit,
+                        const typename AT::t_int_1d_const & _ex_mol_intra,
                         const X_FLOAT *_bboxhi, const X_FLOAT* _bboxlo,
                         const int & _xperiodic, const int & _yperiodic, const int & _zperiodic,
                         const int & _xprd_half, const int & _yprd_half, const int & _zprd_half):
@@ -235,6 +238,7 @@ class NeighborKokkosExecute
     ex1_group(_ex1_group),ex2_group(_ex2_group),
     ex1_bit(_ex1_bit),ex2_bit(_ex2_bit),nex_mol(_nex_mol),
     ex_mol_group(_ex_mol_group),ex_mol_bit(_ex_mol_bit),
+    ex_mol_intra(_ex_mol_intra),
     xperiodic(_xperiodic),yperiodic(_yperiodic),zperiodic(_zperiodic),
     xprd_half(_xprd_half),yprd_half(_yprd_half),zprd_half(_zprd_half) {
 

src/MAKE/OPTIONS/Makefile.omp

@@ -7,7 +7,7 @@ SHELL = /bin/sh
 # specify flags and libraries needed for your compiler
 
 CC =		mpicxx
-CCFLAGS =	-g -O3 -fopenmp
+CCFLAGS =	-g -O3 -restrict -fopenmp
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 

src/RIGID/fix_shake.cpp

@@ -447,7 +447,6 @@ void FixShake::setup(int vflag)
       next_output = (ntimestep/output_every)*output_every + output_every;
   } else next_output = -1;
 
-
   // set respa to 0 if verlet is used and to 1 otherwise
 
   if (strstr(update->integrate_style,"verlet")) 
@@ -476,7 +475,6 @@ void FixShake::setup(int vflag)
   // precalculate constraining forces for first integration step
 
   shake_end_of_step(vflag);
-
 }
 
 /* ----------------------------------------------------------------------
@@ -592,6 +590,7 @@ void FixShake::post_force(int vflag)
   }
   
   // store vflag for coordinate_constraints_end_of_step()
+
   vflag_post_force = vflag;
 }
 

src/SNAP/sna.cpp

@@ -815,7 +815,7 @@ void SNA::compute_dbidrj()
   //        for mb1 = 0,...,j1mid
   //          for ma1 = 0,...,j1
   //            zdb +=
-  //              Conj(dudr(j1,ma1,mb1))*z(j1,j2,j,ma1,mb1)
+  //              Conj(dudr(j1,ma1,mb1))*z(j,j2,j1,ma1,mb1)
   //        dbdr(j1,j2,j) += 2*zdb*(j+1)/(j1+1)
   //        zdb = 0
   //        for mb2 = 0,...,j2mid

src/neighbor.cpp

@@ -166,7 +166,7 @@ pairclass(NULL), pairnames(NULL), pairmasks(NULL)
   ex1_group = ex2_group = ex1_bit = ex2_bit = NULL;
 
   nex_mol = maxex_mol = 0;
-  ex_mol_group = ex_mol_bit = NULL;
+  ex_mol_group = ex_mol_bit = ex_mol_intra = NULL;
 
   // Kokkos setting
 
@@ -234,6 +234,7 @@ Neighbor::~Neighbor()
 
   memory->destroy(ex_mol_group);
   delete [] ex_mol_bit;
+  memory->destroy(ex_mol_intra);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -2323,7 +2324,8 @@ void Neighbor::modify_params(int narg, char **arg)
         nex_group++;
         iarg += 4;
 
-      } else if (strcmp(arg[iarg+1],"molecule") == 0) {
+      } else if (strcmp(arg[iarg+1],"molecule/inter") == 0 ||
+		 strcmp(arg[iarg+1],"molecule/intra") == 0) {
         if (iarg+3 > narg) error->all(FLERR,"Illegal neigh_modify command");
         if (atom->molecule_flag == 0)
           error->all(FLERR,"Neigh_modify exclude molecule "
@@ -2331,10 +2333,18 @@ void Neighbor::modify_params(int narg, char **arg)
         if (nex_mol == maxex_mol) {
           maxex_mol += EXDELTA;
           memory->grow(ex_mol_group,maxex_mol,"neigh:ex_mol_group");
+          if (lmp->kokkos)
+            grow_ex_mol_intra_kokkos();
+          else
+            memory->grow(ex_mol_intra,maxex_mol,"neigh:ex_mol_intra");
         }
         ex_mol_group[nex_mol] = group->find(arg[iarg+2]);
         if (ex_mol_group[nex_mol] == -1)
           error->all(FLERR,"Invalid group ID in neigh_modify command");
+	if (strcmp(arg[iarg+1],"molecule/intra") == 0)
+	  ex_mol_intra[nex_mol] = 1;
+	else
+	  ex_mol_intra[nex_mol] = 0;
         nex_mol++;
         iarg += 3;
 	

src/neighbor.h

@@ -71,6 +71,8 @@ class Neighbor : protected Pointers {
   int nex_mol;                     // # of entries in molecule exclusion list
   int *ex_mol_group;               // molecule group #'s to exclude
   int *ex_mol_bit;                 // molecule group bits to exclude
+  int *ex_mol_intra;               // 0 = exclude if in 2 molecules (inter)
+                                   // 1 = exclude if in same molecule (intra)
 
   // special info, used by NeighPair
 
@@ -229,6 +231,7 @@ class Neighbor : protected Pointers {
   virtual void init_ex_type_kokkos(int) {}
   virtual void init_ex_bit_kokkos() {}
   virtual void init_ex_mol_bit_kokkos() {}
+  virtual void grow_ex_mol_intra_kokkos() {}
 };
 
 namespace NeighConst {

src/npair.cpp

@@ -86,6 +86,7 @@ void NPair::copy_neighbor_info()
   nex_mol = neighbor->nex_mol;
   ex_mol_group = neighbor->ex_mol_group;
   ex_mol_bit = neighbor->ex_mol_bit;
+  ex_mol_intra = neighbor->ex_mol_intra;
 
   // special info
 
@@ -180,8 +181,17 @@ int NPair::exclusion(int i, int j, int itype, int jtype,
 
   if (nex_mol) {
     for (m = 0; m < nex_mol; m++)
-      if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
+
-          molecule[i] == molecule[j]) return 1;
+      // intra-chain: exclude i-j pair if in same molecule 
+      // inter-chain: exclude i-j pair if in different molecules 
+
+      if (ex_mol_intra[m]) {
+        if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
+	    molecule[i] == molecule[j]) return 1;
+      } else {
+	if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
+	    molecule[i] != molecule[j]) return 1;
+      }
   }
 
   return 0;

src/npair.h

@@ -61,8 +61,10 @@ class NPair : protected Pointers {
   int *ex1_bit,*ex2_bit;           // pairs of group bits to exclude
 
   int nex_mol;                     // # of entries in molecule exclusion list
-  int *ex_mol_group;               // molecule group #'s to exclude
   int *ex_mol_bit;                 // molecule group bits to exclude
+  int *ex_mol_group;               // molecule group #'s to exclude
+  int *ex_mol_intra;               // 0 = exclude if in 2 molecules (inter)
+                                   // 1 = exclude if in same molecule (intra)
 
   // special data from Neighbor class