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 +14 −10 Original line number Diff line number Diff line Loading @@ -163,16 +163,20 @@ info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. Note that info about region definitions is NOT included in restart files. 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 its motion attributes (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. If this is not possible, then 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). NOTE: Information about region definitions is NOT included in restart 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 doc/src/read_restart.txt +17 −12 Original line number Diff line number Diff line Loading @@ -197,12 +197,13 @@ was used in the input script that wrote the restart file. If a match is found, LAMMPS prints a message indicating that the fix is being re-enabled. If no match is found before the first run or minimization is performed by the new script, the "state" information for the saved fix is discarded. LAMMPS will also print a list of fixes for which the information is being discarded. See the doc pages for individual fixes for info on which ones can be restarted in this manner. Note that fixes which are created internally by other LAMMPS commands (computes, fixes, etc) will have style names which are all-capitalized, and IDs which are generated internally. for the saved fix is discarded. At the time the discard occurs, LAMMPS will also print a list of fixes for which the information is being discarded. See the doc pages for individual fixes for info on which ones can be restarted in this manner. Note that fixes which are created internally by other LAMMPS commands (computes, fixes, etc) will have style names which are all-capitalized, and IDs which are generated internally. Likewise, the "computes"_fix.html used for a simulation are not stored in the restart file. This means the new input script should specify Loading @@ -219,12 +220,16 @@ described in the previous paragraph, so that the compute can continue its calculations in a consistent manner. NOTE: There are a handful of commands which can be used before or between runs which require a system initialization. Examples include the "balance", "displace_atoms", and "delete_atoms" commands. This is because they may migrate atoms to new processors. Thus they will also discard unused "state" information from fixes. This means that, if desired, you must re-specify the relevant fixes and computes (which create fixes) before those commands are used. between runs which may require a system initialization. Examples include the "balance", "displace_atoms", "delete_atoms", "set" (some options), and "velocity" (some options) commands. This is because they can migrate atoms to new processors. Thus they will also discard unused "state" information from fixes. You will know the discard has occurred because a list of discarded fixes will be printed to the screen and log file, as explained above. This means that if you wish to retain that info in a restarted run, you must re-specify the relevant fixes and computes (which create fixes) before those commands are used. Some pair styles, like the "granular pair styles"_pair_gran.html, also use a fix to store "state" information that persists from timestep to 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 +14 −10 Original line number Diff line number Diff line Loading @@ -163,16 +163,20 @@ info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. Note that info about region definitions is NOT included in restart files. 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 its motion attributes (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. If this is not possible, then 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). NOTE: Information about region definitions is NOT included in restart 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
doc/src/read_restart.txt +17 −12 Original line number Diff line number Diff line Loading @@ -197,12 +197,13 @@ was used in the input script that wrote the restart file. If a match is found, LAMMPS prints a message indicating that the fix is being re-enabled. If no match is found before the first run or minimization is performed by the new script, the "state" information for the saved fix is discarded. LAMMPS will also print a list of fixes for which the information is being discarded. See the doc pages for individual fixes for info on which ones can be restarted in this manner. Note that fixes which are created internally by other LAMMPS commands (computes, fixes, etc) will have style names which are all-capitalized, and IDs which are generated internally. for the saved fix is discarded. At the time the discard occurs, LAMMPS will also print a list of fixes for which the information is being discarded. See the doc pages for individual fixes for info on which ones can be restarted in this manner. Note that fixes which are created internally by other LAMMPS commands (computes, fixes, etc) will have style names which are all-capitalized, and IDs which are generated internally. Likewise, the "computes"_fix.html used for a simulation are not stored in the restart file. This means the new input script should specify Loading @@ -219,12 +220,16 @@ described in the previous paragraph, so that the compute can continue its calculations in a consistent manner. NOTE: There are a handful of commands which can be used before or between runs which require a system initialization. Examples include the "balance", "displace_atoms", and "delete_atoms" commands. This is because they may migrate atoms to new processors. Thus they will also discard unused "state" information from fixes. This means that, if desired, you must re-specify the relevant fixes and computes (which create fixes) before those commands are used. between runs which may require a system initialization. Examples include the "balance", "displace_atoms", "delete_atoms", "set" (some options), and "velocity" (some options) commands. This is because they can migrate atoms to new processors. Thus they will also discard unused "state" information from fixes. You will know the discard has occurred because a list of discarded fixes will be printed to the screen and log file, as explained above. This means that if you wish to retain that info in a restarted run, you must re-specify the relevant fixes and computes (which create fixes) before those commands are used. Some pair styles, like the "granular pair styles"_pair_gran.html, also use a fix to store "state" information that persists from timestep to Loading
