Merge pull request #870 from lammps/doc-tweak

add info to compute heat/flux doc page and a small update to the developer's guide

doc/src/Developer/developer.tex

@@ -449,15 +449,15 @@ Writing fixes is a flexible way of extending LAMMPS.  Users can
 implement many things using fixes:
 
 \begin{itemize}
-\item changing particles attributes (positions, velocities, forces, etc.). 
+\item changing particles attributes (positions, velocities, forces, etc.).
 Example: FixFreeze.
 \item reading/writing data. Example: FixRestart.
 \item implementing boundary conditions. Example: FixWall.
-\item saving information about particles for future use (previous positions, 
+\item saving information about particles for future use (previous positions,
 for instance). Example: FixStoreState.
 \end{itemize}
 
-All fixes are derived from class Fix and must have constructor with the 
+All fixes are derived from class Fix and must have constructor with the
 signature: FixMine(class LAMMPS *, int, char **).
 
 Every fix must be registered in LAMMPS by writing the following lines
@@ -478,7 +478,7 @@ included in the file "style\_fix.h". In case if you use LAMMPS make,
 this file is generated automatically - all files starting with prefix
 fix\_ are included, so call your header the same way. Otherwise, donÕt
 forget to add your include into "style\_fix.h".
- 
+
 Let's write a simple fix which will print average velocity at the end
 of each timestep. First of all, implement a constructor:
 
@@ -487,11 +487,11 @@ of each timestep. First of all, implement a constructor:
 FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
 : Fix(lmp, narg, arg)
 {
-  if (narg < 4) 
+  if (narg < 4)
       error->all(FLERR,"Illegal fix print command");
- 
+
   nevery = atoi(arg[3]);
-  if (nevery <= 0) 
+  if (nevery <= 0)
       error->all(FLERR,"Illegal fix print command");
 }
   \end{verbatim}
@@ -545,7 +545,7 @@ void FixPrintVel::end_of_step()
 {
   // for add3, scale3
   using namespace MathExtra;
-  
+
   double** v = atom->v;
   int nlocal = atom->nlocal;
   double localAvgVel[4]; // 4th element for particles count
@@ -559,7 +559,7 @@ void FixPrintVel::end_of_step()
   MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
   scale3(1.0 / globalAvgVel[3], globalAvgVel);
   if (comm->me == 0) {
-    printf("\%e, \%e, \%e\n", 
+    printf("\%e, \%e, \%e\n",
       globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
   }
 }
@@ -607,14 +607,15 @@ this situation there are several methods which should be implemented:
 
 \begin{itemize}
 \item \verb|double memory_usage| - return how much memory fix uses
-\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays 
+\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays
   in your fix
-\item \verb|void copy_arrays(int i, int j)| - copy i-th per-particle information 
-  to j-th. Used when atoms sorting is performed
+\item \verb|void copy_arrays(int i, int j, int delflag)| - copy i-th per-particle
+  information to j-th. Used when atoms sorting is performed. if delflag is set
+  and atom j owns a body, move the body information to atom i.
 \item \verb|void set_arrays(int i)| - sets i-th particle related information to zero
 \end{itemize}
 
-Note, that if your class implements these methods, it must call add calls of 
+Note, that if your class implements these methods, it must call add calls of
 add\_callback and delete\_callback to constructor and destructor:
 
 \begin{center}
@@ -654,7 +655,7 @@ void FixSavePos::grow_arrays(int nmax)
     memory->grow(this->x, nmax, 3, "FixSavePos:x");
 }
 
-void FixSavePos::copy_arrays(int i, int j)
+void FixSavePos::copy_arrays(int i, int j, int delflag)
 {
     memcpy(this->x[j], this->x[i], sizeof(double) * 3);
 }
@@ -670,7 +671,7 @@ int FixSavePos::pack_exchange(int i, double *buf)
   buf[m++] = x[i][0];
   buf[m++] = x[i][1];
   buf[m++] = x[i][2];
-  
+
   return m;
 }
 

doc/src/compute_heat_flux.txt

@@ -26,14 +26,16 @@ compute myFlux all heat/flux myKE myPE myStress :pre
 
 Define a computation that calculates the heat flux vector based on
 contributions from atoms in the specified group.  This can be used by
-itself to measure the heat flux into or out of a reservoir of atoms,
-or to calculate a thermal conductivity using the Green-Kubo formalism.
-
-See the "fix thermal/conductivity"_fix_thermal_conductivity.html
-command for details on how to compute thermal conductivity in an
-alternate way, via the Muller-Plathe method.  See the "fix
-heat"_fix_heat.html command for a way to control the heat added or
-subtracted to a group of atoms.
+itself to measure the heat flux through a set of atoms (e.g. a region
+between two thermostatted reservoirs held at different temperatures),
+or to calculate a thermal conductivity using the equilibrium
+Green-Kubo formalism.
+
+For other non-equilibrium ways to compute a thermal conductivity, see
+"this section"_Section_howto.html#howto_20.  These include use of the
+"fix thermal/conductivity"_fix_thermal_conductivity.html command for
+the Muller-Plathe method.  Or the "fix heat"_fix_heat.html command
+which can add or subtract heat from groups of atoms.
 
 The compute takes three arguments which are IDs of other
 "computes"_compute.html.  One calculates per-atom kinetic energy