Merge branch 'master' of https://github.com/charlessievers/lammps into fix_numerical_differentiation

src/REPLICA/temper.cpp

@@ -219,7 +219,17 @@ void Temper::command(int narg, char **arg)
 
     timer->init_timeout();
     update->integrate->run(nevery);
-    if (timer->is_timeout()) break;
+
+    // check for timeout across all procs
+
+    int my_timeout=0;
+    int any_timeout=0;
+    if (timer->is_timeout()) my_timeout=1;
+    MPI_Allreduce(&my_timeout, &any_timeout, 1, MPI_INT, MPI_SUM, universe->uworld);
+    if (any_timeout) {
+      timer->force_timeout();
+      break;
+    }
 
     // compute PE
     // notify compute it will be called at next swap

src/USER-MISC/temper_grem.cpp

@@ -241,7 +241,17 @@ void TemperGrem::command(int narg, char **arg)
 
     timer->init_timeout();
     update->integrate->run(nevery);
-    if (timer->is_timeout()) break;
+
+    // check for timeout across all procs
+
+    int my_timeout=0;
+    int any_timeout=0;
+    if (timer->is_timeout()) my_timeout=1;
+    MPI_Allreduce(&my_timeout, &any_timeout, 1, MPI_INT, MPI_SUM, universe->uworld);
+    if (any_timeout) {
+      timer->force_timeout();
+      break;
+    }
 
     // compute PE
     // notify compute it will be called at next swap

src/USER-MISC/temper_npt.cpp

@@ -220,7 +220,17 @@ void TemperNPT::command(int narg, char **arg)
 
     timer->init_timeout();
     update->integrate->run(nevery);
-    if (timer->is_timeout()) break;
+
+    // check for timeout across all procs
+
+    int my_timeout=0;
+    int any_timeout=0;
+    if (timer->is_timeout()) my_timeout=1;
+    MPI_Allreduce(&my_timeout, &any_timeout, 1, MPI_INT, MPI_SUM, universe->uworld);
+    if (any_timeout) {
+      timer->force_timeout();
+      break;
+    }
 
     // compute PE
     // notify compute it will be called at next swap

src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp

@@ -23,7 +23,9 @@
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
+#include "neighbor.h"
 #include "neigh_list.h"
+#include "neigh_request.h"
 #include "memory.h"
 #include "error.h"
 #include "domain.h"
@@ -238,7 +240,7 @@ void PairSDPDTaitwaterIsothermal::allocate () {
 void PairSDPDTaitwaterIsothermal::settings (int narg, char **arg) {
   if (narg != 2 && narg != 3)
     error->all (FLERR, "Illegal number of arguments for "
-                "pair_style sdpd/taitwater/morris/isothermal");
+                "pair_style sdpd/taitwater/isothermal");
 
   temperature = force->numeric (FLERR, arg[0]);
   viscosity = force->numeric (FLERR, arg[1]);
@@ -297,13 +299,26 @@ void PairSDPDTaitwaterIsothermal::coeff (int narg, char **arg) {
     error->all(FLERR,"Incorrect args for pair coefficients");
 }
 
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairSDPDTaitwaterIsothermal::init_style()
+{
+  if ((!atom->rho_flag) || (atom->drho == NULL))
+    error->all(FLERR,"Pair style dpd/taitwater/isothermal requires atom "
+               "attributes rho and drho");
+
+  neighbor->request(this,instance_me);
+}
+
 /* ----------------------------------------------------------------------
  init for one type pair i,j and corresponding j,i
  ------------------------------------------------------------------------- */
 
 double PairSDPDTaitwaterIsothermal::init_one (int i, int j) {
   if (setflag[i][j] == 0)
-    error->all(FLERR,"Not all pair sph/taitwater/morris coeffs are set");
+    error->all(FLERR,"Not all pair sdpd/taitwater/isothermal coeffs are set");
 
   cut[j][i] = cut[i][j];
 

src/USER-SDPD/pair_sdpd_taitwater_isothermal.h

@@ -36,6 +36,7 @@ class PairSDPDTaitwaterIsothermal : public Pair {
   void settings (int, char **);
   void coeff (int, char **);
   virtual double init_one (int, int);
+  virtual void init_style();
 
  protected:
   double viscosity, temperature;

src/atom.cpp

@@ -175,6 +175,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
   spin_flag = eradius_flag = ervel_flag = erforce_flag = ervelforce_flag = 0;
   cs_flag = csforce_flag = vforce_flag = etag_flag = 0;
 
+  // USER-SPH, USER-MESO, and USER-DPD flags
+
   rho_flag = e_flag = cv_flag = vest_flag = 0;
   dpd_flag = edpd_flag = tdpd_flag = 0;