Loading doc/src/Developer/developer.tex +16 −15 Original line number Diff line number Diff line Loading @@ -609,8 +609,9 @@ this situation there are several methods which should be implemented: \item \verb|double memory_usage| - return how much memory fix uses \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} Loading Loading @@ -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); } Loading doc/src/compute_heat_flux.txt +10 −8 Original line number Diff line number Diff line Loading @@ -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 Loading Loading
doc/src/Developer/developer.tex +16 −15 Original line number Diff line number Diff line Loading @@ -609,8 +609,9 @@ this situation there are several methods which should be implemented: \item \verb|double memory_usage| - return how much memory fix uses \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} Loading Loading @@ -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); } Loading
doc/src/compute_heat_flux.txt +10 −8 Original line number Diff line number Diff line Loading @@ -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 Loading
