Loading doc/README +0 −3 Original line number Diff line number Diff line Loading @@ -91,6 +91,3 @@ This will install virtualenv from the Python Package Index. ---------------- Installing prerequisites for PDF build doc/src/compute_pe_atom.txt +4 −3 Original line number Diff line number Diff line Loading @@ -72,9 +72,10 @@ compute peratom all pe/atom compute pe all reduce sum c_peratom thermo_style custom step temp etotal press pe c_pe :pre NOTE: The per-atom energy does not any Lennard-Jones tail corrections invoked by the "pair_modify tail yes"_pair_modify.html command, since those are global contributions to the system energy. NOTE: The per-atom energy does not include any Lennard-Jones tail corrections to the energy added by the "pair_modify tail yes"_pair_modify.html command, since those are contributions to the global system energy. [Output info:] Loading doc/src/compute_stress_atom.txt +5 −0 Original line number Diff line number Diff line Loading @@ -133,6 +133,11 @@ compute p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\] variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol) thermo_style custom step temp etotal press v_press :pre NOTE: The per-atom stress does not include any Lennard-Jones tail corrections to the pressure added by the "pair_modify tail yes"_pair_modify.html command, since those are contributions to the global system pressure. [Output info:] This compute calculates a per-atom array with 6 columns, which can be Loading doc/src/fix_wall_gran_region.txt +13 −19 Original line number Diff line number Diff line Loading @@ -164,25 +164,19 @@ restart file, so that the operation of the fix continues in an uninterrupted fashion. NOTE: Information about region definitions is NOT included in restart files. This means that in a restart script you must re-define a region to associate with this fix in a consistent manner with how a region was used in the original script (same style, ID, geometric attributes). If it is a moving region, you should also define its motion attributes consistent with the original simulation that wrote the restart file. If you use a region that is a union or intersection of sub-regions, LAMMPS will do some limited checking that the new region is consistent with the one defined in the previous script before reassigning the motion attributes, but does not currently check recursively down a nested tree of union or intersection regions. Note that if you want to change the region's motion attributes in the restart run (e.g. its velocity), then you should insure the postition/orientation of the region at the initial restart timestep is the same as it was on the timestep the restart file was written. Otherwise the position of the region may make an instantanous jump when the restart simulation begins. If this is not easy or possible, then you can just ignore info in the restart file by defining a new fix wall/gran/region command in your restart script (e.g. with a different fix ID). files, as discussed on the "read_restart"_read_restart.html doc page. So you must re-define your region and if it is a moving region, define its motion attributes in a way that is consistent with the simulation that wrote the restart file. In particular, if you want to change the region motion attributes (e.g. its velocity), then you should ensure the postition/orientation of the region at the initial restart timestep is the same as it was on the timestep the restart file was written. If this is not possible, you may need to ignore info in the restart file by defining a new fix wall/gran/region command in your restart script, e.g. with a different fix ID. Or if you want to keep the shear history info but discard the region motion information, you can use the same fix ID for fix wall/gran/region, but assign it a region with a different region ID. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for Loading Loading
doc/README +0 −3 Original line number Diff line number Diff line Loading @@ -91,6 +91,3 @@ This will install virtualenv from the Python Package Index. ---------------- Installing prerequisites for PDF build
doc/src/compute_pe_atom.txt +4 −3 Original line number Diff line number Diff line Loading @@ -72,9 +72,10 @@ compute peratom all pe/atom compute pe all reduce sum c_peratom thermo_style custom step temp etotal press pe c_pe :pre NOTE: The per-atom energy does not any Lennard-Jones tail corrections invoked by the "pair_modify tail yes"_pair_modify.html command, since those are global contributions to the system energy. NOTE: The per-atom energy does not include any Lennard-Jones tail corrections to the energy added by the "pair_modify tail yes"_pair_modify.html command, since those are contributions to the global system energy. [Output info:] Loading
doc/src/compute_stress_atom.txt +5 −0 Original line number Diff line number Diff line Loading @@ -133,6 +133,11 @@ compute p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\] variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol) thermo_style custom step temp etotal press v_press :pre NOTE: The per-atom stress does not include any Lennard-Jones tail corrections to the pressure added by the "pair_modify tail yes"_pair_modify.html command, since those are contributions to the global system pressure. [Output info:] This compute calculates a per-atom array with 6 columns, which can be Loading
doc/src/fix_wall_gran_region.txt +13 −19 Original line number Diff line number Diff line Loading @@ -164,25 +164,19 @@ restart file, so that the operation of the fix continues in an uninterrupted fashion. NOTE: Information about region definitions is NOT included in restart files. This means that in a restart script you must re-define a region to associate with this fix in a consistent manner with how a region was used in the original script (same style, ID, geometric attributes). If it is a moving region, you should also define its motion attributes consistent with the original simulation that wrote the restart file. If you use a region that is a union or intersection of sub-regions, LAMMPS will do some limited checking that the new region is consistent with the one defined in the previous script before reassigning the motion attributes, but does not currently check recursively down a nested tree of union or intersection regions. Note that if you want to change the region's motion attributes in the restart run (e.g. its velocity), then you should insure the postition/orientation of the region at the initial restart timestep is the same as it was on the timestep the restart file was written. Otherwise the position of the region may make an instantanous jump when the restart simulation begins. If this is not easy or possible, then you can just ignore info in the restart file by defining a new fix wall/gran/region command in your restart script (e.g. with a different fix ID). files, as discussed on the "read_restart"_read_restart.html doc page. So you must re-define your region and if it is a moving region, define its motion attributes in a way that is consistent with the simulation that wrote the restart file. In particular, if you want to change the region motion attributes (e.g. its velocity), then you should ensure the postition/orientation of the region at the initial restart timestep is the same as it was on the timestep the restart file was written. If this is not possible, you may need to ignore info in the restart file by defining a new fix wall/gran/region command in your restart script, e.g. with a different fix ID. Or if you want to keep the shear history info but discard the region motion information, you can use the same fix ID for fix wall/gran/region, but assign it a region with a different region ID. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for Loading
