git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1470 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/fix_npt_asphere.cpp

@@ -21,6 +21,7 @@
 #include "fix_npt_asphere.h"
 #include "math_extra.h"
 #include "atom.h"
+#include "atom_vec.h"
 #include "force.h"
 #include "compute.h"
 #include "kspace.h"
@@ -34,9 +35,10 @@ using namespace LAMMPS_NS;
 FixNPTASphere::FixNPTASphere(LAMMPS *lmp, int narg, char **arg) :
   FixNPT(lmp, narg, arg)
 {
-  if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag)
+  if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
+      !atom->avec->shape_type)
     error->all("Fix npt/asphere requires atom attributes "
-	       "quat, angmom, torque");
+	       "quat, angmom, torque, shape");
 }
 
 /* ----------------------------------------------------------------------

src/ASPHERE/fix_nve_asphere.cpp

@@ -21,6 +21,7 @@
 #include "fix_nve_asphere.h"
 #include "math_extra.h"
 #include "atom.h"
+#include "atom_vec.h"
 #include "force.h"
 #include "update.h"
 #include "memory.h"
@@ -36,9 +37,10 @@ using namespace LAMMPS_NS;
 FixNVEASphere::FixNVEASphere(LAMMPS *lmp, int narg, char **arg) : 
   FixNVE(lmp, narg, arg)
 {
-  if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag)
+  if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
+      !atom->avec->shape_type)
     error->all("Fix nve/asphere requires atom attributes "
-	       "quat, angmom, torque");
+	       "quat, angmom, torque, shape");
   inertia = 
     memory->create_2d_double_array(atom->ntypes+1,3,"fix_temp_sphere:inertia");
 }

src/ASPHERE/fix_nvt_asphere.cpp

@@ -21,6 +21,7 @@
 #include "fix_nvt_asphere.h"
 #include "math_extra.h"
 #include "atom.h"
+#include "atom_vec.h"
 #include "force.h"
 #include "comm.h"
 #include "group.h"
@@ -36,9 +37,10 @@ using namespace LAMMPS_NS;
 FixNVTASphere::FixNVTASphere(LAMMPS *lmp, int narg, char **arg) :
   FixNVT(lmp, narg, arg)
 {
-  if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag)
+  if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
+      !atom->avec->shape_type)
     error->all("Fix nvt/asphere requires atom attributes "
-	       "quat, angmom, torque");
+	       "quat, angmom, torque, shape");
 }
 
 /* ---------------------------------------------------------------------- */

src/DIPOLE/fix_nve_dipole.cpp

@@ -15,6 +15,7 @@
 #include "string.h"
 #include "fix_nve_dipole.h"
 #include "atom.h"
+#include "atom_vec.h"
 #include "force.h"
 #include "update.h"
 #include "respa.h"
@@ -33,7 +34,7 @@ FixNVEDipole::FixNVEDipole(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 3) error->all("Illegal fix nve/dipole command");
   if (!atom->mu_flag || !atom->omega_flag || 
-      !atom->torque_flag || atom->shape == NULL)
+      !atom->torque_flag || !atom->avec->shape_type)
     error->all("Fix nve/dipole requires atom attributes "
 	       "mu, omega, torque, shape");
   inertia = new double[atom->ntypes+1];

src/DPD/atom_vec_dpd.cpp

@@ -31,6 +31,7 @@ AtomVecDPD::AtomVecDPD(LAMMPS *lmp, int narg, char **arg) :
 {
   mass_type = 1;
   comm_x_only = 0;
+  ghost_velocity = 1;
   size_comm = 6;
   size_reverse = 3;
   size_border = 9;

src/DPD/pair_dpd.cpp

@@ -20,6 +20,7 @@
 #include "stdlib.h"
 #include "pair_dpd.h"
 #include "atom.h"
+#include "atom_vec.h"
 #include "comm.h"
 #include "update.h"
 #include "force.h"
@@ -250,17 +251,14 @@ void PairDPD::coeff(int narg, char **arg)
 
 void PairDPD::init_style()
 {
-  // check that atom style is dpd or hybrid with dpd
+  if (atom->avec->ghost_velocity == 0)
-  // else compute() will not have ghost atom velocities
+    error->all("Pair dpd requires ghost atoms store velocity");
-
-  if (atom->style_match("dpd") == 0)
-    error->all("Pair style dpd requires atom style dpd");
 
   // if newton off, forces between atoms ij will be double computed
   // using different random numbers
 
   if (force->newton_pair == 0 && comm->me == 0) error->warning(
-      "Pair style dpd needs newton pair on for momentum conservation");
+      "Pair dpd needs newton pair on for momentum conservation");
 
   int irequest = neighbor->request(this);
 }

src/GRANULAR/atom_vec_granular.cpp

@@ -32,6 +32,7 @@ AtomVecGranular::AtomVecGranular(LAMMPS *lmp, int narg, char **arg) :
   AtomVec(lmp, narg, arg)
 {
   comm_x_only = comm_f_only = 0;
+  ghost_velocity = 1;
   size_comm = 9;
   size_reverse = 6;
   size_border = 14;

src/GRANULAR/pair_gran_history.cpp

@@ -21,6 +21,7 @@
 #include "string.h"
 #include "pair_gran_history.h"
 #include "atom.h"
+#include "atom_vec.h"
 #include "domain.h"
 #include "force.h"
 #include "update.h"
@@ -326,6 +327,8 @@ void PairGranHistory::init_style()
 
   if (!atom->radius_flag || !atom->omega_flag || !atom->torque_flag)
     error->all("Pair granular requires atom attributes radius, omega, torque");
+  if (atom->avec->ghost_velocity == 0)
+    error->all("Pair granular requires ghost atoms store velocity");
 
   // need a half neigh list and optionally a granular history neigh list
 

src/MOLECULE/dihedral_charmm.cpp

@@ -32,7 +32,6 @@
 using namespace LAMMPS_NS;
 
 #define TOLERANCE 0.05
-#define SMALL     0.001
 
 /* ---------------------------------------------------------------------- */
 

src/atom_vec.cpp

@@ -26,6 +26,7 @@ AtomVec::AtomVec(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 0;
   mass_type = shape_type = dipole_type = 0;
   comm_x_only = comm_f_only = 1;
+  ghost_velocity = 0;
   size_comm = size_reverse = size_border = 0;
 }
 

src/atom_vec.h

@@ -28,6 +28,8 @@ class AtomVec : protected Pointers {
   int dipole_type;                     // 1 if per-type dipole moments
   int comm_x_only;                     // 1 if only exchange x in forward comm
   int comm_f_only;                     // 1 if only exchange f in reverse comm
+  int ghost_velocity;                  // 1 if ghost atoms store velocity
+
   int size_comm;                       // # of values per atom in comm       
   int size_reverse;                    // # in reverse comm
   int size_border;                     // # in border comm

src/atom_vec_hybrid.cpp

@@ -75,6 +75,8 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
     dipole_type = MAX(dipole_type,styles[k]->dipole_type);
     comm_x_only = MIN(comm_x_only,styles[k]->comm_x_only);
     comm_f_only = MIN(comm_f_only,styles[k]->comm_f_only);
+    ghost_velocity = MAX(ghost_velocity,styles[k]->ghost_velocity);
+
     size_comm += styles[k]->size_comm - 3;
     size_reverse += styles[k]->size_reverse - 3;
     size_border += styles[k]->size_border - 6;

src/pair_lj_cut.cpp

@@ -712,3 +712,11 @@ double PairLJCut::single(int i, int j, int itype, int jtype, double rsq,
     offset[itype][jtype];
   return factor_lj*philj;
 }
+
+/* ---------------------------------------------------------------------- */
+
+void *PairLJCut::extract(char *str)
+{
+  if (strcmp(str,"sigma") == 0) return (void *) sigma;
+  return NULL;
+}

src/pair_lj_cut.h

@@ -37,6 +37,7 @@ class PairLJCut : public Pair {
   void compute_inner();
   void compute_middle();
   void compute_outer(int, int);
+  void *extract(char *);
 
  protected:
   double cut_global;