The forces due to this fix are also imposed during an energy -minimization, invoked by the minimize command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. +
+The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command.
Restrictions: none
diff --git a/doc/fix_addforce.txt b/doc/fix_addforce.txt index 85dc07926f..dde46e4e72 100644 --- a/doc/fix_addforce.txt +++ b/doc/fix_addforce.txt @@ -27,8 +27,17 @@ the group. This command can be used to give an additional push to atoms in a simulation, such as for a simulation of Poiseuille flow in a channel. -The forces due to this fix are also imposed during an energy -minimization, invoked by the "minimize"_minimize.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the "minimize"_minimize.html command. [Restrictions:] none diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html index a37b08c3a1..f34f1bec0f 100644 --- a/doc/fix_ave_spatial.html +++ b/doc/fix_ave_spatial.html @@ -143,6 +143,16 @@ the fix group and compute group do not match. or creation of neighbor lists. If the compute is invoked too often by fix ave/spatial, it can slow down a simulation. +Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_ave_spatial.txt b/doc/fix_ave_spatial.txt index ddaba0fe41..9b15930a0d 100644 --- a/doc/fix_ave_spatial.txt +++ b/doc/fix_ave_spatial.txt @@ -130,6 +130,16 @@ Note that some computes perform costly calculations, involving use of or creation of neighbor lists. If the compute is invoked too often by fix ave/spatial, it can slow down a simulation. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html index f7eef19644..35cdba8f4d 100644 --- a/doc/fix_ave_time.html +++ b/doc/fix_ave_time.html @@ -74,6 +74,16 @@ if a constant pressure simulation is being run (fix npt or fix nph), LAMMPS is already calculating virial terms for the pressure every timestep.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt index 3a716ab0a8..f951d804e1 100644 --- a/doc/fix_ave_time.txt +++ b/doc/fix_ave_time.txt @@ -71,6 +71,16 @@ if a constant pressure simulation is being run ("fix npt"_fix_npt.html or "fix nph"_fix_nph.html), LAMMPS is already calculating virial terms for the pressure every timestep. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_aveforce.html b/doc/fix_aveforce.html index 84efd0c528..29f57680b8 100644 --- a/doc/fix_aveforce.html +++ b/doc/fix_aveforce.html @@ -41,8 +41,17 @@ dimension are not changed. Note that this is not the same as specifying a 0.0 value, since that sets all forces to the same average value without adding in any additional force.
-The forces due to this fix are also imposed during an energy -minimization, invoked by the minimize command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. +
+The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command.
Restrictions: none
diff --git a/doc/fix_aveforce.txt b/doc/fix_aveforce.txt index 4968bb0c66..4d6a3ae0bc 100644 --- a/doc/fix_aveforce.txt +++ b/doc/fix_aveforce.txt @@ -38,8 +38,17 @@ dimension are not changed. Note that this is not the same as specifying a 0.0 value, since that sets all forces to the same average value without adding in any additional force. -The forces due to this fix are also imposed during an energy -minimization, invoked by the "minimize"_minimize.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the "minimize"_minimize.html command. [Restrictions:] none diff --git a/doc/fix_com.html b/doc/fix_com.html index ede1fefe45..e44fc277a8 100644 --- a/doc/fix_com.html +++ b/doc/fix_com.html @@ -30,6 +30,16 @@ including all effects due to atoms passing thru periodic boundaries. Write the results to the specified file. +Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: none diff --git a/doc/fix_com.txt b/doc/fix_com.txt index c5b5a71f8b..7d4305bcf1 100644 --- a/doc/fix_com.txt +++ b/doc/fix_com.txt @@ -27,6 +27,16 @@ Compute the center-of-mass of the group of atoms every N steps, including all effects due to atoms passing thru periodic boundaries. Write the results to the specified file. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] none diff --git a/doc/fix_deform.html b/doc/fix_deform.html index daf8ee6db7..fa827892f4 100644 --- a/doc/fix_deform.html +++ b/doc/fix_deform.html @@ -111,8 +111,7 @@ triclinic, even if its initial tilt factors are 0.0. end of the run are determined by the parameters of the fix deform command. Every Nth timestep during the run, the simulation box is expanded, contracted, or tilted to ramped values between the initial -and final values. The run command documents how to make -the ramping take place across multiple runs. +and final values.
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. +
+This fix can perform deformation over multiple runs, using the start +and stop keywords of the run command. See the +run command for details of how to do this. +
+This fix is not invoked during energy minimization. +
Restrictions:
Any box dimension varied by this fix must be periodic. diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt index ba195a261d..7b3d1f8ea7 100644 --- a/doc/fix_deform.txt +++ b/doc/fix_deform.txt @@ -50,7 +50,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz} zero or more keyword/value pairs may be appended to the args :l keyword = {remap} or {units} :l {remap} value = {x} or {v} or {none} - x = remap coords of atoms in group into deforming box (affine deformation) + x = remap coords of atoms in group into deforming box v = remap velocities of all atoms when they cross periodic boundaries none = no remapping of x or v {units} value = {lattice} or {box} @@ -100,8 +100,7 @@ As described below, the desired simulation box size and shape at the end of the run are determined by the parameters of the fix deform command. Every Nth timestep during the run, the simulation box is expanded, contracted, or tilted to ramped values between the initial -and final values. The "run"_run.html command documents how to make -the ramping take place across multiple runs. +and final values. :line @@ -313,18 +312,13 @@ remapped into the new box in the appropriate manner. Each time the box size or shape is changed, the {remap} keyword determines whether atom positions are re-mapped to the new box. If {remap} is set to {x} (the default), atoms in the fix group are -re-mapped; otherwise they are not. If all atoms are remapped, this is -effectively an "affine" deformation. - -If {remap} is set to {v}, then any atom in the fix group that crosses -a periodic boundary will have a delta added to its velocity equal to -the difference in velocities between the lo and hi boundaries. Note -that this velocity difference can include tilt components, e.g. a -delta in the x velocity when an atom crosses the y periodic boundary. -If {remap} is set to {none}, then neither of these remappings take -place. Note that unlike remap x which changes atom coords -continuously as the box deforms, this remapping of v is done ONLY when -an atom crosses a periodic boundary. +re-mapped; otherwise they are not. If {remap} is set to {v}, then any +atom in the fix group that crosses a periodic boundary will have a +delta added to its velocity equal to the difference in velocities +between the lo and hi boundaries. Note that this velocity difference +can include tilt components, e.g. a delta in the x velocity when an +atom crosses the y periodic boundary. If {remap} is set to {none}, +then neither of these remappings take place. IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are performed using this fix, the option "remap v" should normally be @@ -346,13 +340,26 @@ been previously used to define the lattice spacing. Note that the units choice also affects the {vel} style parameters since it is defined in terms of distance/time. -:line +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. + +This fix can perform deformation over multiple runs, using the {start} +and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] Any box dimension varied by this fix must be periodic. -[Related commands:] none +[Related commands:] + +"displace_box"_displace_box.html [Default:] diff --git a/doc/fix_deposit.html b/doc/fix_deposit.html index aa44589564..d305f68097 100644 --- a/doc/fix_deposit.html +++ b/doc/fix_deposit.html @@ -131,6 +131,30 @@ command must have been previously used to define the lattice spacing. Note that the units choice affects all the keyword values that have units of distance or velocity.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. This means you must be careful when restarting a +deposition simulation, when the restart file was written in the middle +of the deposition operation. Specifically, you should use a new fix +deposit command in the input script for the restarted simulation that +continues the operation. You will need to adjust the arguments of the +original fix deposit command to do this. +
+Also note that because the state of the random number generator is not +saved in restart files, you cannot do "exact" restarts with this fix, +where the simulation continues on the same as if no restart had taken +place. However, in a statistical sense, a restarted simulation should +produce the same behavior if you adjust the fix deposit parameters +appropriately. +
+None of the fix_modify options are relevant to this +fix. No quantities calculated by this fix can be output by the +thermo_style custom command. No parameter of this +fix can be used with the start/stop keywords of the run +command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_deposit.txt b/doc/fix_deposit.txt index ae2bf0f75b..524f147ea9 100644 --- a/doc/fix_deposit.txt +++ b/doc/fix_deposit.txt @@ -119,6 +119,30 @@ command must have been previously used to define the lattice spacing. Note that the units choice affects all the keyword values that have units of distance or velocity. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. This means you must be careful when restarting a +deposition simulation, when the restart file was written in the middle +of the deposition operation. Specifically, you should use a new fix +deposit command in the input script for the restarted simulation that +continues the operation. You will need to adjust the arguments of the +original fix deposit command to do this. + +Also note that because the state of the random number generator is not +saved in restart files, you cannot do "exact" restarts with this fix, +where the simulation continues on the same as if no restart had taken +place. However, in a statistical sense, a restarted simulation should +produce the same behavior if you adjust the fix deposit parameters +appropriately. + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No quantities calculated by this fix can be output by the +"thermo_style custom"_thermo_style.html command. No parameter of this +fix can be used with the {start/stop} keywords of the "run"_run.html +command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_drag.html b/doc/fix_drag.html index 48eebee2d8..aac8731c88 100644 --- a/doc/fix_drag.html +++ b/doc/fix_drag.html @@ -39,6 +39,16 @@ application.
This command can be used to steer one or more atoms to a new location in the simulation.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_drag.txt b/doc/fix_drag.txt index 45eabd6695..f360fb719a 100644 --- a/doc/fix_drag.txt +++ b/doc/fix_drag.txt @@ -37,6 +37,16 @@ application. This command can be used to steer one or more atoms to a new location in the simulation. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_efield.html b/doc/fix_efield.html index a74e9252ae..20f5204af5 100644 --- a/doc/fix_efield.html +++ b/doc/fix_efield.html @@ -28,6 +28,16 @@
Add a force F = qE to each charged atom in the group due to an external electric field being applied to the system.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_efield.txt b/doc/fix_efield.txt index f2c3b7fd2b..20aff825e2 100644 --- a/doc/fix_efield.txt +++ b/doc/fix_efield.txt @@ -25,6 +25,16 @@ fix kick external-field efield 1.0 0.0 0.0 :pre Add a force F = qE to each charged atom in the group due to an external electric field being applied to the system. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_enforce2d.html b/doc/fix_enforce2d.html index e209a91794..5d2bd86362 100644 --- a/doc/fix_enforce2d.html +++ b/doc/fix_enforce2d.html @@ -28,8 +28,17 @@ This is useful when running a 2d simulation to insure that atoms do not move from their initial z coordinate.
-The forces due to this fix are also imposed during an energy -minimization, invoked by the minimize command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. +
+The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command.
Restrictions: none
diff --git a/doc/fix_enforce2d.txt b/doc/fix_enforce2d.txt index 070cc627cb..29db81fb74 100644 --- a/doc/fix_enforce2d.txt +++ b/doc/fix_enforce2d.txt @@ -25,8 +25,17 @@ Zero out the z-dimension velocity and force on each atom in the group. This is useful when running a 2d simulation to insure that atoms do not move from their initial z coordinate. -The forces due to this fix are also imposed during an energy -minimization, invoked by the "minimize"_minimize.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the "minimize"_minimize.html command. [Restrictions:] none diff --git a/doc/fix_freeze.html b/doc/fix_freeze.html index c8e43efd9d..5ef6820fa3 100644 --- a/doc/fix_freeze.html +++ b/doc/fix_freeze.html @@ -27,9 +27,21 @@Zero out the force and torque on a granular particle. This is useful for preventing certain particles from moving in a simulation.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
-Can only be used if LAMMPS was built with the "granular" package. +
This fix is part of the "granular" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info.
There can only be a single freeze fix defined. This is because other parts of the code (pair potentials, thermodynamics, etc) treat frozen diff --git a/doc/fix_freeze.txt b/doc/fix_freeze.txt index c332647a06..46f9625b57 100644 --- a/doc/fix_freeze.txt +++ b/doc/fix_freeze.txt @@ -24,9 +24,21 @@ fix 2 bottom freeze :pre Zero out the force and torque on a granular particle. This is useful for preventing certain particles from moving in a simulation. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] -Can only be used if LAMMPS was built with the "granular" package. +This fix is part of the "granular" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. There can only be a single freeze fix defined. This is because other parts of the code (pair potentials, thermodynamics, etc) treat frozen diff --git a/doc/fix_gran_diag.html b/doc/fix_gran_diag.html index ec1f9f804f..d5df6ab372 100644 --- a/doc/fix_gran_diag.html +++ b/doc/fix_gran_diag.html @@ -34,9 +34,21 @@ and file.str. The z bins begin at the bottom of the system and extend upward with a thickness of zlayer for each bin. The quantities written to the file are averaged over all atoms in the bin.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
-Can only be used if LAMMPS was built with the "granular" package. +
This fix is part of the "granular" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info.
Related commands:
diff --git a/doc/fix_gran_diag.txt b/doc/fix_gran_diag.txt index 6818538098..e3f43133e2 100644 --- a/doc/fix_gran_diag.txt +++ b/doc/fix_gran_diag.txt @@ -31,9 +31,21 @@ and file.str. The z bins begin at the bottom of the system and extend upward with a thickness of {zlayer} for each bin. The quantities written to the file are averaged over all atoms in the bin. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] -Can only be used if LAMMPS was built with the "granular" package. +This fix is part of the "granular" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/fix_gravity.html b/doc/fix_gravity.html index b5d9783263..538bad27bd 100644 --- a/doc/fix_gravity.html +++ b/doc/fix_gravity.html @@ -80,6 +80,16 @@ vector direction given by (x,y,z).The strength of the acceleration due to gravity is 1.0 in LJ units, which are the only allowed units for granular systems.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
Styles chute, spherical, and gradient can only be used with diff --git a/doc/fix_gravity.txt b/doc/fix_gravity.txt index 70cc50e172..06b772a859 100644 --- a/doc/fix_gravity.txt +++ b/doc/fix_gravity.txt @@ -73,6 +73,16 @@ vector direction given by (x,y,z). The strength of the acceleration due to gravity is 1.0 in LJ units, which are the only allowed units for granular systems. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] Styles {chute}, {spherical}, and {gradient} can only be used with diff --git a/doc/fix_gyration.html b/doc/fix_gyration.html index 1110a35368..f2c498ddfd 100644 --- a/doc/fix_gyration.html +++ b/doc/fix_gyration.html @@ -38,6 +38,16 @@ this formula
where M is the total mass of the group and Rcm is the center-of-mass position of the group.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: none diff --git a/doc/fix_gyration.txt b/doc/fix_gyration.txt index 6f285842fe..911526a57e 100644 --- a/doc/fix_gyration.txt +++ b/doc/fix_gyration.txt @@ -35,6 +35,16 @@ this formula where M is the total mass of the group and Rcm is the center-of-mass position of the group. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] none diff --git a/doc/fix_heat.html b/doc/fix_heat.html index e1028c3360..93099a72c8 100644 --- a/doc/fix_heat.html +++ b/doc/fix_heat.html @@ -59,6 +59,16 @@ not normally be used on atoms that have their temperature controlled by another fix - e.g. fix nvt or fix langevin fix.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_heat.txt b/doc/fix_heat.txt index 03fb62a287..c0839e9370 100644 --- a/doc/fix_heat.txt +++ b/doc/fix_heat.txt @@ -56,6 +56,16 @@ not normally be used on atoms that have their temperature controlled by another fix - e.g. "fix nvt"_fix_nvt.html or "fix langevin"_fix_langevin.html fix. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_indent.html b/doc/fix_indent.html index 37f96f8f63..d66cd11c6a 100644 --- a/doc/fix_indent.html +++ b/doc/fix_indent.html @@ -80,15 +80,9 @@ specified velocity.
If the rstart keyword is specified, then the radius of the indenter is a time-dependent quantity. R0 is the value assigned at the start of the run; R is the value at the end. At intermediate times, the -radius is linearly interpolated between these two values. The -run command documents how to make the interpolation take -place across multiple runs. This option can be used, for example, to -grow/shrink a void within the simulation box. This option is not -relevant during an energy minimization; the indenter always has radius -R in that case. Note that if you do multiple runs, you may need to -re-specify the fix so that the indenter radius has the appropriate -value. If you do nothing, it will be reset to R0 at the beginning of -each run. +radius is linearly interpolated between these two values. This option +can be used, for example, to grow/shrink a void within the simulation +box.
The units keyword determines the meaning of the distance units used to define the indenter. A box value selects standard distance units @@ -100,18 +94,36 @@ choice affects not only the indenter's physical geometry, but also its velocity and force constant since they are defined in terms of distance as well.
-This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The energy of each -particle interacting with the indenter is K/3 (r - R)^3. The -contribution can also be printed by itself via the keyword f_fix-ID -in the thermo_style custom command. +
Restart, fix_modify, thermo output, run start/stop, minimize info:
-The forces due to this fix are also imposed during an energy -minimization, invoked by the minimize command. If you -want that energy to be included in the total potential energy of the -system (the quantity being minimized), you must enable the -fix_modify energy option for this fix. +
No information about this fix is written to binary restart +files. +
+The fix_modify energy option is supported by this +fix to add the energy of interaction between atoms and the indenter to +the system's potential energy as part of thermodynamic +output. The energy of each particle interacting +with the indenter is K/3 (r - R)^3. +
+The atom/indenter interaction energy can be printed as part of +thermodynamic output via the keyword f_ID, where ID is the fix-ID of +this fix. See the thermo_style custom command for +details. +
+This fix can adjust the indenter position and radius over multiple +runs, using the start and stop keywords of the run +command. See the run command for details of how to do +this. +
+The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command. The rstart keyword +does not change the indenter radius during an energy minimization; the +indenter always has a radius of its final value R in that case. +
+IMPORTANT NOTE: If you want the atom/indenter interaction energy to be +included in the total potential energy of the system (the quantity +being minimized), you MUST enable the fix_modify +energy option for this fix.
Restrictions: none
diff --git a/doc/fix_indent.txt b/doc/fix_indent.txt index ff045b9236..50947370e7 100644 --- a/doc/fix_indent.txt +++ b/doc/fix_indent.txt @@ -71,15 +71,9 @@ specified velocity. If the {rstart} keyword is specified, then the radius of the indenter is a time-dependent quantity. R0 is the value assigned at the start of the run; R is the value at the end. At intermediate times, the -radius is linearly interpolated between these two values. The -"run"_run.html command documents how to make the interpolation take -place across multiple runs. This option can be used, for example, to -grow/shrink a void within the simulation box. This option is not -relevant during an energy minimization; the indenter always has radius -R in that case. Note that if you do multiple runs, you may need to -re-specify the fix so that the indenter radius has the appropriate -value. If you do nothing, it will be reset to R0 at the beginning of -each run. +radius is linearly interpolated between these two values. This option +can be used, for example, to grow/shrink a void within the simulation +box. The {units} keyword determines the meaning of the distance units used to define the indenter. A {box} value selects standard distance units @@ -91,18 +85,36 @@ choice affects not only the indenter's physical geometry, but also its velocity and force constant since they are defined in terms of distance as well. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The energy of each -particle interacting with the indenter is K/3 (r - R)^3. The -contribution can also be printed by itself via the keyword {f_fix-ID} -in the "thermo_style custom"_thermo_style.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] -The forces due to this fix are also imposed during an energy -minimization, invoked by the "minimize"_minimize.html command. If you -want that energy to be included in the total potential energy of the -system (the quantity being minimized), you must enable the -"fix_modify"_fix_modify.html {energy} option for this fix. +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy of interaction between atoms and the indenter to +the system's potential energy as part of "thermodynamic +output"_thermo_style.html. The energy of each particle interacting +with the indenter is K/3 (r - R)^3. + +The atom/indenter interaction energy can be printed as part of +thermodynamic output via the keyword f_ID, where ID is the fix-ID of +this fix. See the "thermo_style custom"_thermo_style.html command for +details. + +This fix can adjust the indenter position and radius over multiple +runs, using the {start} and {stop} keywords of the "run"_run.html +command. See the "run"_run.html command for details of how to do +this. + +The forces due to this fix are imposed during an energy minimization, +invoked by the "minimize"_minimize.html command. The {rstart} keyword +does not change the indenter radius during an energy minimization; the +indenter always has a radius of its final value R in that case. + +IMPORTANT NOTE: If you want the atom/indenter interaction energy to be +included in the total potential energy of the system (the quantity +being minimized), you MUST enable the "fix_modify"_fix_modify.html +{energy} option for this fix. [Restrictions:] none diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html index 944d69b6ad..ba0ccdf5de 100644 --- a/doc/fix_langevin.html +++ b/doc/fix_langevin.html @@ -71,8 +71,7 @@ timestep size, and damp is the damping factor. Random numbers are used to randomize the direction and magnitude of this force.The desired temperature at each timestep is a ramped value during the -run from Tstart to Tstop. The run command documents -how to make the ramping take place across multiple runs. +run from Tstart to Tstop.
The damp parameter is specified in time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 @@ -88,10 +87,7 @@ viscous command for more details. A Marsaglia random number generator is used. Each processor uses the input seed to generate its own unique seed and its own stream of random numbers. Thus the dynamics of the system will not be identical -on two runs on different numbers of processors. Also, the state of -the random number generator is not saved in a restart file. This -means you cannot do exact restarts when a fix langevin command is -used. +on two runs on different numbers of processors.
The keyword axes can be used to specify which dimensions to add Ff and Fr to. A flag of 0 means skip that dimension; a flag of 1 means @@ -121,6 +117,25 @@ should not normally be used on atoms that also have their temperature controlled by another fix - e.g. a nvt or temp/rescale fix.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. Because the state of the random number generator +is not saved in restart files, this means you cannot do "exact" +restarts with this fix, where the simulation continues on the same as +if no restart had taken place. However, in a statistical sense, a +restarted simulation should produce the same behavior. +
+None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. +
+This fix can ramp its target temperature over multiple runs, using the +start and stop keywords of the run command. See the +run command for details of how to do this. +
+This fix is not invoked during energy minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt index 8d9bd8c683..869649c609 100644 --- a/doc/fix_langevin.txt +++ b/doc/fix_langevin.txt @@ -61,8 +61,7 @@ timestep size, and damp is the damping factor. Random numbers are used to randomize the direction and magnitude of this force. The desired temperature at each timestep is a ramped value during the -run from {Tstart} to {Tstop}. The "run"_run.html command documents -how to make the ramping take place across multiple runs. +run from {Tstart} to {Tstop}. The {damp} parameter is specified in time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 @@ -78,10 +77,7 @@ The random # {seed} should be a non-zero integer with 1 to 8 digits. A Marsaglia random number generator is used. Each processor uses the input seed to generate its own unique seed and its own stream of random numbers. Thus the dynamics of the system will not be identical -on two runs on different numbers of processors. Also, the state of -the random number generator is not saved in a restart file. This -means you cannot do exact restarts when a fix {langevin} command is -used. +on two runs on different numbers of processors. The keyword {axes} can be used to specify which dimensions to add Ff and Fr to. A flag of 0 means skip that dimension; a flag of 1 means @@ -111,6 +107,25 @@ should not normally be used on atoms that also have their temperature controlled by another fix - e.g. a "nvt"_fix_nvt.html or "temp/rescale"_fix_temp_rescale.html fix. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. Because the state of the random number generator +is not saved in restart files, this means you cannot do "exact" +restarts with this fix, where the simulation continues on the same as +if no restart had taken place. However, in a statistical sense, a +restarted simulation should produce the same behavior. + +None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. + +This fix can ramp its target temperature over multiple runs, using the +{start} and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +This fix is not invoked during "energy minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_lineforce.html b/doc/fix_lineforce.html index 930dd66836..208351bd76 100644 --- a/doc/fix_lineforce.html +++ b/doc/fix_lineforce.html @@ -33,8 +33,17 @@ line.
If the initial velocity of the atom is 0.0 (or along the line), then it should continue to move along the line thereafter.
-The forces due to this fix are also imposed during an energy -minimization, invoked by the minimize command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. +
+The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command.
Restrictions: none
diff --git a/doc/fix_lineforce.txt b/doc/fix_lineforce.txt index c053f00855..151f0b70dd 100644 --- a/doc/fix_lineforce.txt +++ b/doc/fix_lineforce.txt @@ -30,8 +30,17 @@ line. If the initial velocity of the atom is 0.0 (or along the line), then it should continue to move along the line thereafter. -The forces due to this fix are also imposed during an energy -minimization, invoked by the "minimize"_minimize.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the "minimize"_minimize.html command. [Restrictions:] none diff --git a/doc/fix_modify.html b/doc/fix_modify.html index 8069485042..362942c298 100644 --- a/doc/fix_modify.html +++ b/doc/fix_modify.html @@ -58,10 +58,10 @@ default method for computing P.For fixes that calculate a contribution to the potential energy of the system, the energy keyword will include that contribution in thermodyanmic output of potential energy. See the -thermo_style command for info on how to output -potential energy is printed. The contribution itself can also be -printed by using the keyword f_ID in the thermo_style custom command, -where ID is the fix-ID of the appropriate fix. +thermo_style command for info on how potential +energy is output. The contribution by itself can be printed by using +the keyword f_ID in the thermo_style custom command, where ID is the +fix-ID of the appropriate fix.
Restrictions: none
diff --git a/doc/fix_modify.txt b/doc/fix_modify.txt index 19812f4cac..a4699187a1 100644 --- a/doc/fix_modify.txt +++ b/doc/fix_modify.txt @@ -27,33 +27,34 @@ fix_modify 1 energy yes :pre [Description:] -Modify one or more parameters of a previously defined fix. Not all -fix styles support all parameters. +Modify one or more parameters of a previously defined fix. Only +specific fix styles support specific parameters. See the doc pages +for individual fix commands for info on which ones support which +fix_modify parameters. The {temp} keyword is used to determine how a fix computes temperature. The specified compute ID must have been previously defined by the user via the "compute"_compute.html command and it must be a style of compute that calculates a temperature. All fixes that -compute temperatures defined their own compute by default, as -described in their documentation. Thus this option allows the user to -override the default method for computing T. +compute temperatures define their own compute by default, as described +in their documentation. Thus this option allows the user to override +the default method for computing T. The {press} keyword is used to determine how a fix computes pressure. The specified compute ID must have been previously defined by the user via the "compute"_compute.html command and it must be a style of compute that calculates a pressure. All fixes that compute pressures -defined their own compute by default, as described in their +define their own compute by default, as described in their documentation. Thus this option allows the user to override the default method for computing P. -For fixes that calculates a contribution to the potential energy of -the system, the {energy} keyword will include that contribution in -thermodyanmic output of the potential energy, as invoked by the -"thermo_style"_thermo_style.html command. The value of the -contribution can also be printed by itself using the "thermo_style -custom"_thermo_style.html keywords. The documentation for individual -fix commands specifies whether they make a contribution to the -potential energy. +For fixes that calculate a contribution to the potential energy of the +system, the {energy} keyword will include that contribution in +thermodyanmic output of potential energy. See the +"thermo_style"_thermo_style.html command for info on how potential +energy is output. The contribution by itself can be printed by using +the keyword f_ID in the thermo_style custom command, where ID is the +fix-ID of the appropriate fix. [Restrictions:] none diff --git a/doc/fix_momentum.html b/doc/fix_momentum.html index c18b2d3547..89d7eb6f8a 100644 --- a/doc/fix_momentum.html +++ b/doc/fix_momentum.html @@ -58,6 +58,16 @@ thermostatting).Note that the velocity command can be used to create initial velocities with zero aggregate linear and/or angular momentum.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_momentum.txt b/doc/fix_momentum.txt index 8e55236025..8a1c3ed983 100644 --- a/doc/fix_momentum.txt +++ b/doc/fix_momentum.txt @@ -50,6 +50,16 @@ thermostatting). Note that the "velocity"_velocity.html command can be used to create initial velocities with zero aggregate linear and/or angular momentum. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_msd.html b/doc/fix_msd.html index f695940399..94ff529e7c 100644 --- a/doc/fix_msd.html +++ b/doc/fix_msd.html @@ -33,6 +33,22 @@ proportional to the diffusion coefficient of the diffusing atoms. The "origin" of the displacement for each atom is its position at the time the fix command was issued. Write the results to the specified file.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+This fix writes the original coordinates of diffusing atoms to binary +restart files, so that the mean-squared displacement +will be accurate in a restarted simulation. See the +read_restart command for 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. +
+None of the fix_modify options are relevant to this +fix. No quantities calculated by this fix can be output by the +thermo_style custom command. No parameter of this +fix can be used with the start/stop keywords of the run +command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: none diff --git a/doc/fix_msd.txt b/doc/fix_msd.txt index f808f14901..29657cfecf 100644 --- a/doc/fix_msd.txt +++ b/doc/fix_msd.txt @@ -30,6 +30,22 @@ proportional to the diffusion coefficient of the diffusing atoms. The "origin" of the displacement for each atom is its position at the time the fix command was issued. Write the results to the specified file. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +This fix writes the original coordinates of diffusing atoms to "binary +restart files"_restart.html, so that the mean-squared displacement +will be accurate in a restarted simulation. See the +"read_restart"_read_restart.html command for 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. + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No quantities calculated by this fix can be output by the +"thermo_style custom"_thermo_style.html command. No parameter of this +fix can be used with the {start/stop} keywords of the "run"_run.html +command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] none diff --git a/doc/fix_nph.html b/doc/fix_nph.html index a2b625fa04..4cb1ebbfa6 100644 --- a/doc/fix_nph.html +++ b/doc/fix_nph.html @@ -76,8 +76,7 @@ unchanged and controlling the pressure of a surrounding fluid.
The pressure can be controlled in one of several styles, as specified by the p-style argument. In each case, the desired pressure at each timestep is a ramped value during the run from the starting value to -the end value. The run command documents how to make the -ramping take place across multiple runs. +the end value.
Style xyz means couple all 3 dimensions together when pressure is computed (isotropic pressure), and dilate/contract the 3 dimensions @@ -142,19 +141,39 @@ this fix's temperature or pressure via the or pressure during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or -thermo_pressure will have no effect on this fix. Alternatively, you -can directly assign a new compute (for calculating temeperature or -pressure) that you have defined to this fix via the -fix_modify command. If you do this, note that the -kinetic energy derived from T should be consistent with the virial -term computed using all atoms. LAMMPS will warn you if you choose to -compute temperature on a subset of atoms. +thermo_pressure will have no effect on this fix.
-This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The contribution can -also be printed by itself via the keyword f_fix-ID in the -thermo_style custom command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+This fix writes the state of the Nose/Hoover barostat to binary +restart files. See the read_restart +command for 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. +
+The fix_modify temp and press options are +supported by this fix. You can use them to assign a +compute you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. +
+The fix_modify energy option is supported by this +fix to add the energy change induced by Nose/Hoover barostatting to +the system's potential energy as part of thermodynamic +output. +
+The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +thermo_style custom command for details. +
+This fix can ramp its target pressure over multiple runs, using the +start and stop keywords of the run command. See the +run command for details of how to do this. +
+This fix is not invoked during energy minimization.
Restrictions:
diff --git a/doc/fix_nph.txt b/doc/fix_nph.txt index be0939bec9..01a34c7fb2 100644 --- a/doc/fix_nph.txt +++ b/doc/fix_nph.txt @@ -67,8 +67,7 @@ unchanged and controlling the pressure of a surrounding fluid. The pressure can be controlled in one of several styles, as specified by the {p-style} argument. In each case, the desired pressure at each timestep is a ramped value during the run from the starting value to -the end value. The "run"_run.html command documents how to make the -ramping take place across multiple runs. +the end value. Style {xyz} means couple all 3 dimensions together when pressure is computed (isotropic pressure), and dilate/contract the 3 dimensions @@ -132,19 +131,39 @@ this fix's temperature or pressure via the or pressure during thermodyanmic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or -{thermo_pressure} will have no effect on this fix. Alternatively, you -can directly assign a new compute (for calculating temeperature or -pressure) that you have defined to this fix via the -"fix_modify"_fix_modify.html command. If you do this, note that the -kinetic energy derived from T should be consistent with the virial -term computed using all atoms. LAMMPS will warn you if you choose to -compute temperature on a subset of atoms. +{thermo_pressure} will have no effect on this fix. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The contribution can -also be printed by itself via the keyword {f_fix-ID} in the -"thermo_style custom"_thermo_style.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +This fix writes the state of the Nose/Hoover barostat to "binary +restart files"_restart.html. See the "read_restart"_read_restart.html +command for 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. + +The "fix_modify"_fix_modify.html {temp} and {press} options are +supported by this fix. You can use them to assign a +"compute"_compute.html you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy change induced by Nose/Hoover barostatting to +the system's potential energy as part of "thermodynamic +output"_thermo_style.html. + +The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +"thermo_style custom"_thermo_style.html command for details. + +This fix can ramp its target pressure over multiple runs, using the +{start} and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_npt.html b/doc/fix_npt.html index f4b7f55836..f765d33167 100644 --- a/doc/fix_npt.html +++ b/doc/fix_npt.html @@ -57,12 +57,11 @@ temperature. This creates a system trajectory consistent with the isothermal-isobaric ensemble.The desired temperature at each timestep is a ramped value during the -run from Tstart to Tstop. The run command documents -how to make the ramping take place across multiple runs. The Tdamp -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or -fmsec or psec - see the units command). +run from Tstart to Tstop. The Tdamp parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +units command).
The atoms in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -81,8 +80,7 @@ unchanged and controlling the pressure of a surrounding fluid.
The pressure can be controlled in one of several styles, as specified by the p-style argument. In each case, the desired pressure at each timestep is a ramped value during the run from the starting value to -the end value. The run command documents how to make the -ramping take place across multiple runs. +the end value.
Style xyz means couple all 3 dimensions together when pressure is computed (isotropic pressure), and dilate/contract the 3 dimensions @@ -146,19 +144,40 @@ this fix's temperature or pressure via the or pressure during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or -thermo_pressure will have no effect on this fix. Alternatively, you -can directly assign a new compute (for calculating temeperature or -pressure) that you have defined to this fix via the -fix_modify command. If you do this, note that the -kinetic energy derived from T should be consistent with the virial -term computed using all atoms. LAMMPS will warn you if you choose to -compute temperature on a subset of atoms. +thermo_pressure will have no effect on this fix.
-This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The contribution can -also be printed by itself via the keyword f_fix-ID in the -thermo_style custom command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+This fix writes the state of the Nose/Hoover thermostat and barostat +to binary restart files. See the +read_restart command for 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. +
+The fix_modify temp and press options are +supported by this fix. You can use them to assign a +compute you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. +
+The fix_modify energy option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting and +barostatting to the system's potential energy as part of +thermodynamic output. +
+The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +thermo_style custom command for details. +
+This fix can ramp its target temperature and pressure over multiple +runs, using the start and stop keywords of the run +command. See the run command for details of how to do +this. +
+This fix is not invoked during energy minimization.
Restrictions:
diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt index 793b190a93..00e4aa87b1 100644 --- a/doc/fix_npt.txt +++ b/doc/fix_npt.txt @@ -46,12 +46,11 @@ temperature. This creates a system trajectory consistent with the isothermal-isobaric ensemble. The desired temperature at each timestep is a ramped value during the -run from {Tstart} to {Tstop}. The "run"_run.html command documents -how to make the ramping take place across multiple runs. The {Tdamp} -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or -fmsec or psec - see the "units"_units.html command). +run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +"units"_units.html command). The atoms in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -70,8 +69,7 @@ unchanged and controlling the pressure of a surrounding fluid. The pressure can be controlled in one of several styles, as specified by the {p-style} argument. In each case, the desired pressure at each timestep is a ramped value during the run from the starting value to -the end value. The "run"_run.html command documents how to make the -ramping take place across multiple runs. +the end value. Style {xyz} means couple all 3 dimensions together when pressure is computed (isotropic pressure), and dilate/contract the 3 dimensions @@ -135,19 +133,40 @@ this fix's temperature or pressure via the or pressure during thermodyanmic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or -{thermo_pressure} will have no effect on this fix. Alternatively, you -can directly assign a new compute (for calculating temeperature or -pressure) that you have defined to this fix via the -"fix_modify"_fix_modify.html command. If you do this, note that the -kinetic energy derived from T should be consistent with the virial -term computed using all atoms. LAMMPS will warn you if you choose to -compute temperature on a subset of atoms. +{thermo_pressure} will have no effect on this fix. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The contribution can -also be printed by itself via the keyword {f_fix-ID} in the -"thermo_style custom"_thermo_style.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +This fix writes the state of the Nose/Hoover thermostat and barostat +to "binary restart files"_restart.html. See the +"read_restart"_read_restart.html command for 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. + +The "fix_modify"_fix_modify.html {temp} and {press} options are +supported by this fix. You can use them to assign a +"compute"_compute.html you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting and +barostatting to the system's potential energy as part of +"thermodynamic output"_thermo_style.html. + +The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +"thermo_style custom"_thermo_style.html command for details. + +This fix can ramp its target temperature and pressure over multiple +runs, using the {start} and {stop} keywords of the "run"_run.html +command. See the "run"_run.html command for details of how to do +this. + +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html index 8f0c15cb76..d91d02aa87 100644 --- a/doc/fix_npt_asphere.html +++ b/doc/fix_npt_asphere.html @@ -58,12 +58,11 @@ temperature. This creates a system trajectory consistent with the isothermal-isobaric ensemble.The desired temperature at each timestep is a ramped value during the -run from Tstart to Tstop. The run command documents -how to make the ramping take place across multiple runs. The Tdamp -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or -fmsec or psec - see the units command). +run from Tstart to Tstop. The Tdamp parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +units command).
The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -82,8 +81,7 @@ unchanged and controlling the pressure of a surrounding fluid.
The pressure can be controlled in one of several styles, as specified by the p-style argument. In each case, the desired pressure at each timestep is a ramped value during the run from the starting value to -the end value. The run command documents how to make the -ramping take place across multiple runs. +the end value.
Style xyz means couple all 3 dimensions together when pressure is computed (isotropic pressure), and dilate/contract the 3 dimensions @@ -115,7 +113,7 @@ is working. Typically a value between 0.2 to 2.0 is sufficient to damp oscillations after a few periods.
For all pressure styles, the simulation box stays rectangular in -shape. Parinello-Rahman boundary conditions (tilted box) are not +shape. Parinello-Rahman boundary conditions (tilted box) are not yet implemented in LAMMPS.
For all styles, the Pdamp parameter operates like the Tdamp @@ -147,23 +145,46 @@ fix's temperature or pressure via the or pressure during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or -thermo_press will have no effect on this fix. Alternatively, you -can directly assign a new compute (for calculating temeperature or -pressure) that you have defined to this fix via the -fix_modify command. If you do this, note that the -kinetic energy derived from T should be consistent with the virial -term computed using all particles. LAMMPS will warn you if you choose -to compute temperature on a subset of particles. +thermo_press will have no effect on this fix.
-This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The contribution can -also be printed by itself via the keyword f_fix-ID in the -thermo_style custom command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+This fix writes the state of the Nose/Hoover thermostat and barostat +to binary restart files. See the +read_restart command for 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. +
+The fix_modify temp and press options are +supported by this fix. You can use them to assign a +compute you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. +
+The fix_modify energy option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting and +barostatting to the system's potential energy as part of +thermodynamic output. +
+The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +thermo_style custom command for details. +
+This fix can ramp its target temperature and pressure over multiple +runs, using the start and stop keywords of the run +command. See the run command for details of how to do +this. +
+This fix is not invoked during energy minimization.
Restrictions:
-Can only be used if LAMMPS was built with the "asphere" package. +
This fix is part of the "asphere" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info.
Any dimension being adjusted by this fix must be periodic. A dimension whose target pressures are specified as NULL can be diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt index 654d3de662..0661677692 100755 --- a/doc/fix_npt_asphere.txt +++ b/doc/fix_npt_asphere.txt @@ -47,12 +47,11 @@ temperature. This creates a system trajectory consistent with the isothermal-isobaric ensemble. The desired temperature at each timestep is a ramped value during the -run from {Tstart} to {Tstop}. The "run"_run.html command documents -how to make the ramping take place across multiple runs. The {Tdamp} -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or -fmsec or psec - see the "units"_units.html command). +run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +"units"_units.html command). The particles in the fix group are the only ones whose velocities and positions are updated by the velocity/position update portion of the @@ -71,8 +70,7 @@ unchanged and controlling the pressure of a surrounding fluid. The pressure can be controlled in one of several styles, as specified by the {p-style} argument. In each case, the desired pressure at each timestep is a ramped value during the run from the starting value to -the end value. The "run"_run.html command documents how to make the -ramping take place across multiple runs. +the end value. Style {xyz} means couple all 3 dimensions together when pressure is computed (isotropic pressure), and dilate/contract the 3 dimensions @@ -104,7 +102,7 @@ is working. Typically a value between 0.2 to 2.0 is sufficient to damp oscillations after a few periods. For all pressure styles, the simulation box stays rectangular in -shape. Parinello-Rahman boundary conditions (tilted box) are not +shape. Parinello-Rahman boundary conditions (tilted box) are not yet implemented in LAMMPS. For all styles, the {Pdamp} parameter operates like the {Tdamp} @@ -136,23 +134,46 @@ fix's temperature or pressure via the or pressure during thermodyanmic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or -{thermo_press} will have no effect on this fix. Alternatively, you -can directly assign a new compute (for calculating temeperature or -pressure) that you have defined to this fix via the -"fix_modify"_fix_modify.html command. If you do this, note that the -kinetic energy derived from T should be consistent with the virial -term computed using all particles. LAMMPS will warn you if you choose -to compute temperature on a subset of particles. +{thermo_press} will have no effect on this fix. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The contribution can -also be printed by itself via the keyword {f_fix-ID} in the -"thermo_style custom"_thermo_style.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +This fix writes the state of the Nose/Hoover thermostat and barostat +to "binary restart files"_restart.html. See the +"read_restart"_read_restart.html command for 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. + +The "fix_modify"_fix_modify.html {temp} and {press} options are +supported by this fix. You can use them to assign a +"compute"_compute.html you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting and +barostatting to the system's potential energy as part of +"thermodynamic output"_thermo_style.html. + +The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +"thermo_style custom"_thermo_style.html command for details. + +This fix can ramp its target temperature and pressure over multiple +runs, using the {start} and {stop} keywords of the "run"_run.html +command. See the "run"_run.html command for details of how to do +this. + +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] -Can only be used if LAMMPS was built with the "asphere" package. +This fix is part of the "asphere" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. Any dimension being adjusted by this fix must be periodic. A dimension whose target pressures are specified as NULL can be diff --git a/doc/fix_nve.html b/doc/fix_nve.html index 61b962a032..ab42591788 100644 --- a/doc/fix_nve.html +++ b/doc/fix_nve.html @@ -28,6 +28,16 @@ group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_nve.txt b/doc/fix_nve.txt index cd3f90937b..2ff28977e4 100644 --- a/doc/fix_nve.txt +++ b/doc/fix_nve.txt @@ -25,6 +25,16 @@ Perform constant NVE updates of position and velocity for atoms in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_nve_asphere.html b/doc/fix_nve_asphere.html index 054b2c63c2..3f670bf0e5 100644 --- a/doc/fix_nve_asphere.html +++ b/doc/fix_nve_asphere.html @@ -29,9 +29,21 @@ angular velocity for aspherical or ellipsoidal particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
-Can only be used if LAMMPS was built with the "asphere" package. +
This fix is part of the "asphere" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info.
Related commands:
diff --git a/doc/fix_nve_asphere.txt b/doc/fix_nve_asphere.txt index 90f4ace9fc..b40be7224f 100755 --- a/doc/fix_nve_asphere.txt +++ b/doc/fix_nve_asphere.txt @@ -26,9 +26,21 @@ angular velocity for aspherical or ellipsoidal particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] -Can only be used if LAMMPS was built with the "asphere" package. +This fix is part of the "asphere" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/fix_nve_dipole.html b/doc/fix_nve_dipole.html index aa1fa9d9d2..4c90f1e613 100644 --- a/doc/fix_nve_dipole.html +++ b/doc/fix_nve_dipole.html @@ -29,9 +29,21 @@ angular velocity for particles with point dipole moments in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. +Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
-Can only be used if LAMMPS was built with the "dipole" package. +
This fix is part of the "dipole" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info.
Related commands:
diff --git a/doc/fix_nve_dipole.txt b/doc/fix_nve_dipole.txt index b78f4c2383..ce54074c83 100755 --- a/doc/fix_nve_dipole.txt +++ b/doc/fix_nve_dipole.txt @@ -26,9 +26,21 @@ angular velocity for particles with point dipole moments in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] -Can only be used if LAMMPS was built with the "dipole" package. +This fix is part of the "dipole" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/fix_nve_gran.html b/doc/fix_nve_gran.html index 21d9c1ec24..1fae9ed3cc 100644 --- a/doc/fix_nve_gran.html +++ b/doc/fix_nve_gran.html @@ -30,9 +30,21 @@ rotational information as well as position and velocity, so this integrator updates translational and rotational degrees of freedom due to forces and torques. +Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
-Can only be used if LAMMPS was built with the "granular" package. +
This fix is part of the "granular" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info.
Related commands:
diff --git a/doc/fix_nve_gran.txt b/doc/fix_nve_gran.txt index 22caaf49ea..4423733b90 100644 --- a/doc/fix_nve_gran.txt +++ b/doc/fix_nve_gran.txt @@ -27,9 +27,21 @@ rotational information as well as position and velocity, so this integrator updates translational and rotational degrees of freedom due to forces and torques. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none -Can only be used if LAMMPS was built with the "granular" package. +This fix is part of the "granular" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/fix_nve_noforce.html b/doc/fix_nve_noforce.html index c6dab7199f..bac32dc510 100644 --- a/doc/fix_nve_noforce.html +++ b/doc/fix_nve_noforce.html @@ -38,6 +38,16 @@ unchanged, and can thus be printed by the dump command queried with an equal-style variable that uses the fcm() group function to compute the total force on the group of atoms. +Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_nve_noforce.txt b/doc/fix_nve_noforce.txt index 627dc686f9..12716b6be4 100644 --- a/doc/fix_nve_noforce.txt +++ b/doc/fix_nve_noforce.txt @@ -35,6 +35,16 @@ unchanged, and can thus be printed by the "dump"_dump.html command or queried with an equal-style "variable"_variable.html that uses the fcm() group function to compute the total force on the group of atoms. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_nvt.html b/doc/fix_nvt.html index 0f89ae6c61..a1939a03d7 100644 --- a/doc/fix_nvt.html +++ b/doc/fix_nvt.html @@ -44,12 +44,11 @@ thermostat. V is volume; T is temperature. This creates a system trajectory consistent with the canonical ensemble.
The desired temperature at each timestep is a ramped value during the -run from Tstart to Tstop. The run command documents -how to make the ramping take place across multiple runs. The Tdamp -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or -fmsec or psec - see the units command). +run from Tstart to Tstop. The Tdamp parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +units command).
In some cases (e.g. for solids) the temperature of the system can oscillate undesirably when a Nose/Hoover thermostat is applied. The @@ -80,15 +79,35 @@ This means you can change the attributes of this fix's temperature during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no -effect on this fix. Alternatively, you can directly assign a new -compute (for calculating temeperature) that you have defined to this -fix via the fix_modify command. +effect on this fix.
-This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The contribution can -also be printed by itself via the keyword f_fix-ID in the -thermo_style custom command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+This fix writes the state of the Nose/Hoover thermostat to binary +restart files. See the read_restart +command for 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. +
+The fix_modify temp option is supported by this +fix. You can use it to assign a compute you have +defined to this fix which will be used in its thermostatting +procedure. +
+The fix_modify energy option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of thermodynamic +output. +
+The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +thermo_style custom command for details. +
+This fix can ramp its target temperature over multiple runs, using the +start and stop keywords of the run command. See the +run command for details of how to do this. +
+This fix is not invoked during energy minimization.
Restrictions:
diff --git a/doc/fix_nvt.txt b/doc/fix_nvt.txt index 58e8a3da03..b50df05e0c 100644 --- a/doc/fix_nvt.txt +++ b/doc/fix_nvt.txt @@ -35,12 +35,11 @@ thermostat. V is volume; T is temperature. This creates a system trajectory consistent with the canonical ensemble. The desired temperature at each timestep is a ramped value during the -run from {Tstart} to {Tstop}. The "run"_run.html command documents -how to make the ramping take place across multiple runs. The {Tdamp} -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or -fmsec or psec - see the "units"_units.html command). +run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +"units"_units.html command). In some cases (e.g. for solids) the temperature of the system can oscillate undesirably when a Nose/Hoover thermostat is applied. The @@ -71,15 +70,35 @@ This means you can change the attributes of this fix's temperature during thermodyanmic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no -effect on this fix. Alternatively, you can directly assign a new -compute (for calculating temeperature) that you have defined to this -fix via the "fix_modify"_fix_modify.html command. +effect on this fix. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The contribution can -also be printed by itself via the keyword {f_fix-ID} in the -"thermo_style custom"_thermo_style.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +This fix writes the state of the Nose/Hoover thermostat to "binary +restart files"_restart.html. See the "read_restart"_read_restart.html +command for 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. + +The "fix_modify"_fix_modify.html {temp} option is supported by this +fix. You can use it to assign a "compute"_compute.html you have +defined to this fix which will be used in its thermostatting +procedure. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of "thermodynamic +output"_thermo_style.html. + +The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +"thermo_style custom"_thermo_style.html command for details. + +This fix can ramp its target temperature over multiple runs, using the +{start} and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html index c8bbee14b2..cdffdedb76 100644 --- a/doc/fix_nvt_asphere.html +++ b/doc/fix_nvt_asphere.html @@ -45,12 +45,11 @@ V is volume; T is temperature. This creates a system trajectory consistent with the canonical ensemble.The desired temperature at each timestep is a ramped value during the -run from Tstart to Tstop. The run command documents -how to make the ramping take place across multiple runs. The Tdamp -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or -fmsec or psec - see the units command). +run from Tstart to Tstop. The Tdamp parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +units command).
In some cases (e.g. for solids) the temperature of the system can oscillate undesirably when a Nose/Hoover thermostat is applied. The @@ -81,19 +80,41 @@ This means you can change the attributes of this fix's temperature during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no -effect on this fix. Alternatively, you can directly assign a new -compute (for calculating temeperature) that you have defined to this -fix via the fix_modify command. +effect on this fix.
-This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The contribution can -also be printed by itself via the keyword f_fix-ID in the -thermo_style custom command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+This fix writes the state of the Nose/Hoover thermostat to binary +restart files. See the read_restart +command for 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. +
+The fix_modify temp option is supported by this +fix. You can use it to assign a compute you have +defined to this fix which will be used in its thermostatting +procedure. +
+The fix_modify energy option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of thermodynamic +output. +
+The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +thermo_style custom command for details. +
+This fix can ramp its target temperature over multiple runs, using the +start and stop keywords of the run command. See the +run command for details of how to do this. +
+This fix is not invoked during energy minimization.
Restrictions:
-Can only be used if LAMMPS was built with the "asphere" package. +
This fix is part of the "asphere" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info.
The final Tstop cannot be 0.0 since it would make the target T = 0.0 at some timestep during the simulation which is not allowed in diff --git a/doc/fix_nvt_asphere.txt b/doc/fix_nvt_asphere.txt index 7909fee987..e38b3ba717 100755 --- a/doc/fix_nvt_asphere.txt +++ b/doc/fix_nvt_asphere.txt @@ -36,12 +36,11 @@ V is volume; T is temperature. This creates a system trajectory consistent with the canonical ensemble. The desired temperature at each timestep is a ramped value during the -run from {Tstart} to {Tstop}. The "run"_run.html command documents -how to make the ramping take place across multiple runs. The {Tdamp} -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or -fmsec or psec - see the "units"_units.html command). +run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +"units"_units.html command). In some cases (e.g. for solids) the temperature of the system can oscillate undesirably when a Nose/Hoover thermostat is applied. The @@ -72,19 +71,41 @@ This means you can change the attributes of this fix's temperature during thermodyanmic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no -effect on this fix. Alternatively, you can directly assign a new -compute (for calculating temeperature) that you have defined to this -fix via the "fix_modify"_fix_modify.html command. +effect on this fix. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The contribution can -also be printed by itself via the keyword {f_fix-ID} in the -"thermo_style custom"_thermo_style.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +This fix writes the state of the Nose/Hoover thermostat to "binary +restart files"_restart.html. See the "read_restart"_read_restart.html +command for 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. + +The "fix_modify"_fix_modify.html {temp} option is supported by this +fix. You can use it to assign a "compute"_compute.html you have +defined to this fix which will be used in its thermostatting +procedure. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of "thermodynamic +output"_thermo_style.html. + +The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +"thermo_style custom"_thermo_style.html command for details. + +This fix can ramp its target temperature over multiple runs, using the +{start} and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] -Can only be used if LAMMPS was built with the "asphere" package. +This fix is part of the "asphere" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. The final Tstop cannot be 0.0 since it would make the target T = 0.0 at some timestep during the simulation which is not allowed in diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html index 61dc955787..1ee4502548 100644 --- a/doc/fix_nvt_sllod.html +++ b/doc/fix_nvt_sllod.html @@ -71,12 +71,11 @@ discussed in (Tuckerman) (eqs 4 and 5), which is what implemented in LAMMPS in a velocity Verlet formulation.
The desired temperature at each timestep is a ramped value during the -run from Tstart to Tstop. The run command documents -how to make the ramping take place across multiple runs. The Tdamp -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or -fmsec or psec - see the units command). +run from Tstart to Tstop. The Tdamp parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +units command).
In some cases (e.g. for solids) the temperature of the system can oscillate undesirably when a Nose/Hoover thermostat is applied. The @@ -107,15 +106,35 @@ This means you can change the attributes of this fix's temperature during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no -effect on this fix. Alternatively, you can directly assign a new -compute (for calculating temeperature) that you have defined to this -fix via the fix_modify command. +effect on this fix.
-This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The contribution can -also be printed by itself via the keyword f_fix-ID in the -thermo_style custom command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+This fix writes the state of the Nose/Hoover thermostat to binary +restart files. See the read_restart +command for 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. +
+The fix_modify temp option is supported by this +fix. You can use it to assign a compute you have +defined to this fix which will be used in its thermostatting +procedure. +
+The fix_modify energy option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of thermodynamic +output. +
+The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +thermo_style custom command for details. +
+This fix can ramp its target temperature over multiple runs, using the +start and stop keywords of the run command. See the +run command for details of how to do this. +
+This fix is not invoked during energy minimization.
Restrictions:
diff --git a/doc/fix_nvt_sllod.txt b/doc/fix_nvt_sllod.txt index d4896d9537..f951f8c112 100644 --- a/doc/fix_nvt_sllod.txt +++ b/doc/fix_nvt_sllod.txt @@ -62,12 +62,11 @@ discussed in "(Tuckerman)"_#Tuckerman (eqs 4 and 5), which is what is implemented in LAMMPS in a velocity Verlet formulation. The desired temperature at each timestep is a ramped value during the -run from {Tstart} to {Tstop}. The "run"_run.html command documents -how to make the ramping take place across multiple runs. The {Tdamp} -parameter is specified in time units and determines how rapidly the -temperature is relaxed. For example, a value of 100.0 means to relax -the temperature in a timespan of (roughly) 100 time units (tau or -fmsec or psec - see the "units"_units.html command). +run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +"units"_units.html command). In some cases (e.g. for solids) the temperature of the system can oscillate undesirably when a Nose/Hoover thermostat is applied. The @@ -98,15 +97,35 @@ This means you can change the attributes of this fix's temperature during thermodyanmic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no -effect on this fix. Alternatively, you can directly assign a new -compute (for calculating temeperature) that you have defined to this -fix via the "fix_modify"_fix_modify.html command. +effect on this fix. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The contribution can -also be printed by itself via the keyword {f_fix-ID} in the -"thermo_style custom"_thermo_style.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +This fix writes the state of the Nose/Hoover thermostat to "binary +restart files"_restart.html. See the "read_restart"_read_restart.html +command for 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. + +The "fix_modify"_fix_modify.html {temp} option is supported by this +fix. You can use it to assign a "compute"_compute.html you have +defined to this fix which will be used in its thermostatting +procedure. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of "thermodynamic +output"_thermo_style.html. + +The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +"thermo_style custom"_thermo_style.html command for details. + +This fix can ramp its target temperature over multiple runs, using the +{start} and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_orient_fcc.html b/doc/fix_orient_fcc.html index 36ed72e7ac..66fc8f7856 100644 --- a/doc/fix_orient_fcc.html +++ b/doc/fix_orient_fcc.html @@ -116,11 +116,24 @@ symmetry, so the list must include one from each pair of equal-and-opposite neighbors. A pair of orientation files for a Sigma=5 tilt boundary are show below. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The contribution can -also be printed by itself via the keyword f_fix-ID in the -thermo_style custom command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. +
+The fix_modify energy option is supported by this +fix to add the potential energy of atom interactions with the grain +boundary driving force to the system's potential energy as part of +thermodynamic output. +
+The atom/grain-boundary interaction energy can be printed as part of +thermodynamic output via the keyword f_ID, where ID is the fix-ID of +this fix. See the thermo_style custom command for +details. +
+No parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization.
Restrictions:
diff --git a/doc/fix_orient_fcc.txt b/doc/fix_orient_fcc.txt index 44cfd3045a..2f586125c5 100644 --- a/doc/fix_orient_fcc.txt +++ b/doc/fix_orient_fcc.txt @@ -113,11 +113,24 @@ symmetry, so the list must include one from each pair of equal-and-opposite neighbors. A pair of orientation files for a Sigma=5 tilt boundary are show below. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The contribution can -also be printed by itself via the keyword {f_fix-ID} in the -"thermo_style custom"_thermo_style.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the potential energy of atom interactions with the grain +boundary driving force to the system's potential energy as part of +"thermodynamic output"_thermo_style.html. + +The atom/grain-boundary interaction energy can be printed as part of +thermodynamic output via the keyword f_ID, where ID is the fix-ID of +this fix. See the "thermo_style custom"_thermo_style.html command for +details. + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_planeforce.html b/doc/fix_planeforce.html index 438f75572f..6560681e1a 100644 --- a/doc/fix_planeforce.html +++ b/doc/fix_planeforce.html @@ -32,8 +32,17 @@ by subtracting out components of force perpendicular to the plane.If the initial velocity of the atom is 0.0 (or in the plane), then it should continue to move in the plane thereafter.
-The forces due to this fix are also imposed during an energy -minimization, invoked by the minimize command. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. +
+The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command.
Restrictions: none
diff --git a/doc/fix_planeforce.txt b/doc/fix_planeforce.txt index e584faec52..134d3c6d50 100644 --- a/doc/fix_planeforce.txt +++ b/doc/fix_planeforce.txt @@ -29,8 +29,17 @@ by subtracting out components of force perpendicular to the plane. If the initial velocity of the atom is 0.0 (or in the plane), then it should continue to move in the plane thereafter. -The forces due to this fix are also imposed during an energy -minimization, invoked by the "minimize"_minimize.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the "minimize"_minimize.html command. [Restrictions:] none diff --git a/doc/fix_poems.html b/doc/fix_poems.html index c6bc552108..b1e7c52173 100644 --- a/doc/fix_poems.html +++ b/doc/fix_poems.html @@ -110,9 +110,22 @@ body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined. +Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
-Can only be used if LAMMPS was built with the "poems" package. +
This fix is part of the "poems" package. It is only enabled if LAMMPS +was built with that package, which also requires the POEMS library be +built and linked with LAMMPS. See the Making +LAMMPS section for more info.
Related commands:
diff --git a/doc/fix_poems.txt b/doc/fix_poems.txt index a814985d1e..3b0634dc52 100644 --- a/doc/fix_poems.txt +++ b/doc/fix_poems.txt @@ -103,9 +103,22 @@ body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] -Can only be used if LAMMPS was built with the "poems" package. +This fix is part of the "poems" package. It is only enabled if LAMMPS +was built with that package, which also requires the POEMS library be +built and linked with LAMMPS. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/fix_pour.html b/doc/fix_pour.html index 422a340b08..55bf544245 100644 --- a/doc/fix_pour.html +++ b/doc/fix_pour.html @@ -101,9 +101,35 @@ completing all insertions, it prints a warning. or y direction (2d). This enables pouring particles from a successively higher height over time. +Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. This means you must be careful when restarting a +pouring simulation, when the restart file was written in the middle of +the pouring operation. Specifically, you should use a new fix pour +command in the input script for the restarted simulation that +continues the operation. You will need to adjust the arguments of the +original fix pour command to do this. +
+Also note that because the state of the random number generator is not +saved in restart files, you cannot do "exact" restarts with this fix, +where the simulation continues on the same as if no restart had taken +place. However, in a statistical sense, a restarted simulation should +produce the same behavior if you adjust the fix pour parameters +appropriately. +
+None of the fix_modify options are relevant to this +fix. No quantities calculated by this fix can be output by the +thermo_style custom command. No parameter of this +fix can be used with the start/stop keywords of the run +command. This fix is not invoked during energy +minimization. +
Restrictions:
-Can only be used if LAMMPS was built with the "granular" package. +
This fix is part of the "granular" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info.
For 3d simulations, a gravity fix in the -z direction must be defined for use in conjunction with this fix. For 2d simulations, gravity diff --git a/doc/fix_pour.txt b/doc/fix_pour.txt index 499ba8aa4c..fd1044fbd4 100644 --- a/doc/fix_pour.txt +++ b/doc/fix_pour.txt @@ -90,9 +90,35 @@ The {rate} option moves the insertion volume in the z direction (3d) or y direction (2d). This enables pouring particles from a successively higher height over time. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. This means you must be careful when restarting a +pouring simulation, when the restart file was written in the middle of +the pouring operation. Specifically, you should use a new fix pour +command in the input script for the restarted simulation that +continues the operation. You will need to adjust the arguments of the +original fix pour command to do this. + +Also note that because the state of the random number generator is not +saved in restart files, you cannot do "exact" restarts with this fix, +where the simulation continues on the same as if no restart had taken +place. However, in a statistical sense, a restarted simulation should +produce the same behavior if you adjust the fix pour parameters +appropriately. + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No quantities calculated by this fix can be output by the +"thermo_style custom"_thermo_style.html command. No parameter of this +fix can be used with the {start/stop} keywords of the "run"_run.html +command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] -Can only be used if LAMMPS was built with the "granular" package. +This fix is part of the "granular" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. For 3d simulations, a gravity fix in the -z direction must be defined for use in conjunction with this fix. For 2d simulations, gravity diff --git a/doc/fix_print.html b/doc/fix_print.html index 6376baae68..faec35aa71 100644 --- a/doc/fix_print.html +++ b/doc/fix_print.html @@ -42,6 +42,16 @@ fix print line is output. Equal-style variables can calculate complex formulas involving atom and group properties, mathematical operations, other variables, etc.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
If equal-style variables are used which contain diff --git a/doc/fix_print.txt b/doc/fix_print.txt index f6bcfe1bb0..d9f5f5e39b 100644 --- a/doc/fix_print.txt +++ b/doc/fix_print.txt @@ -39,6 +39,16 @@ fix print line is output. Equal-style variables can calculate complex formulas involving atom and group properties, mathematical operations, other variables, etc. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] If {equal}-style variables are used which contain diff --git a/doc/fix_rdf.html b/doc/fix_rdf.html index 53897154f5..71c25a4268 100644 --- a/doc/fix_rdf.html +++ b/doc/fix_rdf.html @@ -48,6 +48,16 @@ factor is set by the special_bonds command.
The RDF statistics for each timestep are written to the specified file, as are the RDF values averaged over all timesteps.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
The RDF is not computed for distances longer than the force cutoff, diff --git a/doc/fix_rdf.txt b/doc/fix_rdf.txt index 9716efadad..e4b52a59ba 100644 --- a/doc/fix_rdf.txt +++ b/doc/fix_rdf.txt @@ -45,6 +45,16 @@ factor is set by the "special_bonds"_special_bonds.html command. The RDF statistics for each timestep are written to the specified file, as are the RDF values averaged over all timesteps. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] The RDF is not computed for distances longer than the force cutoff, diff --git a/doc/fix_recenter.html b/doc/fix_recenter.html index f6b1a05df5..c467b29207 100644 --- a/doc/fix_recenter.html +++ b/doc/fix_recenter.html @@ -82,6 +82,16 @@ the input script, since the adjustments it makes to atom coordinates should come after the changes made by time integration. LAMMPS will warn you if your fixes are not ordered this way.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
This fix should not be used with an x,y,z setting that causes a large diff --git a/doc/fix_recenter.txt b/doc/fix_recenter.txt index cc8bdf7a2e..a9d7809208 100644 --- a/doc/fix_recenter.txt +++ b/doc/fix_recenter.txt @@ -74,6 +74,16 @@ the input script, since the adjustments it makes to atom coordinates should come after the changes made by time integration. LAMMPS will warn you if your fixes are not ordered this way. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] This fix should not be used with an x,y,z setting that causes a large diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index 8f9de65346..e6a4d232a4 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -87,6 +87,16 @@ effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
This fix performs an MPI_Allreduce each timestep that is proportional diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt index 34a7fba925..468114d81f 100644 --- a/doc/fix_rigid.txt +++ b/doc/fix_rigid.txt @@ -80,6 +80,16 @@ effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] This fix performs an MPI_Allreduce each timestep that is proportional diff --git a/doc/fix_setforce.html b/doc/fix_setforce.html index 77083a54a9..1d68b32c0e 100644 --- a/doc/fix_setforce.html +++ b/doc/fix_setforce.html @@ -35,17 +35,27 @@ force, assuming their initial velocity zero.
Any of the fx,fy,fz values can be specified as NULL which means do not alter the force component in that dimension.
-The forces due to this fix are also imposed during an energy -minimization, invoked by the minimize command. +
Restart, fix_modify, thermo output, run start/stop, minimize info:
-The total force on the group of atoms before it is reset is stored by -the fix and its components can be accessed during thermodynamic -print-out by using f_ID[N] where ID = he fix-ID and N = 1,2,3. See -the thermo_style custom command for details. Note -that the fix stores the total force on the group of atoms, but the -printed value may be normalized by the total number of atoms in the -simulation depending on the thermo_modify norm -option you are using. +
No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. +
+The total vector force on the group of atoms before it is reset is +stored by the fix and its components can be printed as part of +thermodynamic output via the keywords f_ID[N] where ID is the fix-ID +of this fix and N = 1,2,3. See the thermo_style +custom command for details. Note that the fix +stores the total force on the group of atoms, but the printed value +may be normalized by the total number of atoms in the simulation +depending on the thermo_modify norm option being +used. +
+No parameter of this fix can be used with the start/stop keywords of +the run command. +
+The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command.
Restrictions: none
diff --git a/doc/fix_setforce.txt b/doc/fix_setforce.txt index 5cef6a4ceb..6c2180792a 100644 --- a/doc/fix_setforce.txt +++ b/doc/fix_setforce.txt @@ -32,17 +32,27 @@ force, assuming their initial velocity zero. Any of the fx,fy,fz values can be specified as NULL which means do not alter the force component in that dimension. -The forces due to this fix are also imposed during an energy -minimization, invoked by the "minimize"_minimize.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] -The total force on the group of atoms before it is reset is stored by -the fix and its components can be accessed during thermodynamic -print-out by using f_ID\[N\] where ID = he fix-ID and N = 1,2,3. See -the "thermo_style custom"_thermo_style.html command for details. Note -that the fix stores the total force on the group of atoms, but the -printed value may be normalized by the total number of atoms in the -simulation depending on the "thermo_modify norm"_thermo_modify.html -option you are using. +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. + +The total vector force on the group of atoms before it is reset is +stored by the fix and its components can be printed as part of +thermodynamic output via the keywords f_ID\[N\] where ID is the fix-ID +of this fix and N = 1,2,3. See the "thermo_style +custom"_thermo_style.html command for details. Note that the fix +stores the total force on the group of atoms, but the printed value +may be normalized by the total number of atoms in the simulation +depending on the "thermo_modify norm"_thermo_modify.html option being +used. + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the "minimize"_minimize.html command. [Restrictions:] none diff --git a/doc/fix_shake.html b/doc/fix_shake.html index 1315ddbc55..c1e8870d41 100644 --- a/doc/fix_shake.html +++ b/doc/fix_shake.html @@ -85,6 +85,16 @@ in the bond are in the group specified with the SHAKE fix. for in temperature and pressure computations. Similarly, the SHAKE contribution to the pressure virial is also accounted for. +Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
For computational efficiency, there can only be one shake fix defined diff --git a/doc/fix_shake.txt b/doc/fix_shake.txt index 86f32d1588..3ce8e1f8b2 100644 --- a/doc/fix_shake.txt +++ b/doc/fix_shake.txt @@ -74,6 +74,16 @@ The degrees-of-freedom removed by SHAKE bonds and angles are accounted for in temperature and pressure computations. Similarly, the SHAKE contribution to the pressure virial is also accounted for. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] For computational efficiency, there can only be one shake fix defined diff --git a/doc/fix_spring.html b/doc/fix_spring.html index 1016420171..689ead3fca 100644 --- a/doc/fix_spring.html +++ b/doc/fix_spring.html @@ -91,6 +91,16 @@ below the z = 0 center plane of the pore (umbrella sampling). The last example holds the ion a distance 5 away from the pore axis (assuming the center-of-mass of the pore in x,y is the pore axis).
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_spring.txt b/doc/fix_spring.txt index e05af0e1fd..cfe2c6c00c 100644 --- a/doc/fix_spring.txt +++ b/doc/fix_spring.txt @@ -84,6 +84,16 @@ below the z = 0 center plane of the pore (umbrella sampling). The last example holds the ion a distance 5 away from the pore axis (assuming the center-of-mass of the pore in x,y is the pore axis). +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_spring_rg.html b/doc/fix_spring_rg.html index 13f51832d3..d42648e5e2 100644 --- a/doc/fix_spring_rg.html +++ b/doc/fix_spring_rg.html @@ -50,6 +50,16 @@ for the aggregate force on the group of atoms, not a per-atom force.
If RG0 is specified as NULL, then the RG of the group is computed at the time the fix is specified, and that value is used as the target.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_spring_rg.txt b/doc/fix_spring_rg.txt index e8561b260c..5dafee6f98 100644 --- a/doc/fix_spring_rg.txt +++ b/doc/fix_spring_rg.txt @@ -46,6 +46,16 @@ for the aggregate force on the group of atoms, not a per-atom force. If RG0 is specified as NULL, then the RG of the group is computed at the time the fix is specified, and that value is used as the target. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_spring_self.html b/doc/fix_spring_self.html index 1028781c82..9f0c1d4f4c 100644 --- a/doc/fix_spring_self.html +++ b/doc/fix_spring_self.html @@ -32,6 +32,22 @@ the magnitude of the force on each atom is -Kr, where r is the displacement of the atom from its current position to its initial position.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+This fix writes the original coordinates of tethered atoms to binary +restart files, so that the spring effect will be the +same in a restarted simulation. See the +read_restart command for 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. +
+None of the fix_modify options are relevant to this +fix. No quantities calculated by this fix can be output by the +thermo_style custom command. No parameter of this +fix can be used with the start/stop keywords of the run +command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_spring_self.txt b/doc/fix_spring_self.txt index b221e7f81b..466525d5ed 100644 --- a/doc/fix_spring_self.txt +++ b/doc/fix_spring_self.txt @@ -29,6 +29,22 @@ the magnitude of the force on each atom is -Kr, where r is the displacement of the atom from its current position to its initial position. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +This fix writes the original coordinates of tethered atoms to "binary +restart files"_restart.html, so that the spring effect will be the +same in a restarted simulation. See the +"read_restart"_read_restart.html command for 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. + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No quantities calculated by this fix can be output by the +"thermo_style custom"_thermo_style.html command. No parameter of this +fix can be used with the {start/stop} keywords of the "run"_run.html +command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html index d5531cfb12..7f84d702fe 100644 --- a/doc/fix_temp_rescale.html +++ b/doc/fix_temp_rescale.html @@ -38,8 +38,7 @@ their velocities.
Rescaling is performed every N timesteps. The target temperature is a ramped value between the Tstart and Tstop temperatures at the -beginning and end of the run. The run command documents -how to make the ramping take place across multiple runs. +beginning and end of the run.
Rescaling is only performed if the difference between the current and desired temperatures is greater than the window value. The amount @@ -80,20 +79,37 @@ This means you can change the attributes of this fix's temperature during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no -effect on this fix. Alternatively, you can directly assign a new -compute (for calculating temeperature) that you have defined to this -fix via the fix_modify command. For consistency, if -using the keyword region, the compute you assign should also be of -style temp/region. +effect on this fix.
-This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The contribution can -also be printed by itself via the keyword f_fix-ID in the -thermo_style custom command. Note that because -this fix is invoked every N steps and thermodynamic info may be -printed every M steps, that unless M is a multiple of N, the energy -info accessed will not be for the current timestep. +
Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. +
+The fix_modify temp option is supported by this +fix. You can use it to assign a compute you have +defined to this fix which will be used in its thermostatting +procedure. For consistency, if using the keyword region, the +compute you assign should also be of style +temp/region. +
+The fix_modify energy option is supported by this +fix to add the energy change implied by a velocity rescaling to the +system's potential energy as part of thermodynamic +output. Note that because this fix is invoked +every N steps and thermodynamic info is printed every M steps, that +unless M is a multiple of N, the energy contribution will not be for +the current timestep. +
+The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +thermo_style custom command for details. +
+This fix can ramp its target temperature over multiple runs, using the +start and stop keywords of the run command. See the +run command for details of how to do this. +
+This fix is not invoked during energy minimization.
Restrictions: none
diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt index 871ad50cee..9ae3d08d62 100644 --- a/doc/fix_temp_rescale.txt +++ b/doc/fix_temp_rescale.txt @@ -34,8 +34,7 @@ their velocities. Rescaling is performed every N timesteps. The target temperature is a ramped value between the {Tstart} and {Tstop} temperatures at the -beginning and end of the run. The "run"_run.html command documents -how to make the ramping take place across multiple runs. +beginning and end of the run. Rescaling is only performed if the difference between the current and desired temperatures is greater than the {window} value. The amount @@ -76,20 +75,37 @@ This means you can change the attributes of this fix's temperature during thermodyanmic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no -effect on this fix. Alternatively, you can directly assign a new -compute (for calculating temeperature) that you have defined to this -fix via the "fix_modify"_fix_modify.html command. For consistency, if -using the keyword {region}, the compute you assign should also be of -style {temp/region}. +effect on this fix. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The contribution can -also be printed by itself via the keyword {f_fix-ID} in the -"thermo_style custom"_thermo_style.html command. Note that because -this fix is invoked every N steps and thermodynamic info may be -printed every M steps, that unless M is a multiple of N, the energy -info accessed will not be for the current timestep. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {temp} option is supported by this +fix. You can use it to assign a "compute"_compute.html you have +defined to this fix which will be used in its thermostatting +procedure. For consistency, if using the keyword {region}, the +compute you assign should also be of style +"temp/region"_compute_temp_region.html. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy change implied by a velocity rescaling to the +system's potential energy as part of "thermodynamic +output"_thermo_style.html. Note that because this fix is invoked +every N steps and thermodynamic info is printed every M steps, that +unless M is a multiple of N, the energy contribution will not be for +the current timestep. + +The energy change can be printed as part of thermodynamic output via +the keyword f_ID, where ID is the fix-ID of this fix. See the +"thermo_style custom"_thermo_style.html command for details. + +This fix can ramp its target temperature over multiple runs, using the +{start} and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_tmd.html b/doc/fix_tmd.html index 7df6e41b6f..c5ddf6755d 100644 --- a/doc/fix_tmd.html +++ b/doc/fix_tmd.html @@ -33,8 +33,7 @@ fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file holonomic constraint is used to force the atoms to move towards (or away from) the target configuration. The parameter "rho" is monotonically decreased (or increased) from its initial value to -rho_final at the end of the run. The run command documents -how to make the ramping take place across multiple runs. +rho_final at the end of the run.Rho has distance units and is a measure of the root-mean-squared distance (RMSD) between the current configuration of the atoms in the @@ -88,6 +87,19 @@ to prevent it being overwritten.
For more information about TMD, see (Schlitter1) and (Schlitter2).
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. +
+This fix can ramp its rho parameter over multiple runs, using the +start and stop keywords of the run command. See the +run command for details of how to do this. +
+This fix is not invoked during energy minimization. +
Restrictions:
All TMD fixes must be listed in the input script after all integrator diff --git a/doc/fix_tmd.txt b/doc/fix_tmd.txt index 6f51d792dc..bd7096f506 100644 --- a/doc/fix_tmd.txt +++ b/doc/fix_tmd.txt @@ -30,8 +30,7 @@ Perform targeted molecular dynamics (TMD) on a group of atoms. A holonomic constraint is used to force the atoms to move towards (or away from) the target configuration. The parameter "rho" is monotonically decreased (or increased) from its initial value to -rho_final at the end of the run. The "run"_run.html command documents -how to make the ramping take place across multiple runs. +rho_final at the end of the run. Rho has distance units and is a measure of the root-mean-squared distance (RMSD) between the current configuration of the atoms in the @@ -85,6 +84,19 @@ to prevent it being overwritten. For more information about TMD, see "(Schlitter1)"_#Schlitter1 and "(Schlitter2)"_#Schlitter2. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. + +This fix can ramp its rho parameter over multiple runs, using the +{start} and {stop} keywords of the "run"_run.html command. See the +"run"_run.html command for details of how to do this. + +This fix is not invoked during "energy minimization"_minimize.html. + [Restrictions:] All TMD fixes must be listed in the input script after all integrator diff --git a/doc/fix_viscous.html b/doc/fix_viscous.html index 81efb9797d..c536a974e9 100644 --- a/doc/fix_viscous.html +++ b/doc/fix_viscous.html @@ -75,6 +75,16 @@ langevin command adds both a viscous damping term and this random force to each atom; hence if using fix langevin you do not typically need to use fix viscous.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: diff --git a/doc/fix_viscous.txt b/doc/fix_viscous.txt index f9b96826cd..bec27a7054 100644 --- a/doc/fix_viscous.txt +++ b/doc/fix_viscous.txt @@ -65,6 +65,16 @@ langevin"_fix_langevin.html command adds both a viscous damping term and this random force to each atom; hence if using fix {langevin} you do not typically need to use fix {viscous}. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] diff --git a/doc/fix_wall_gran.html b/doc/fix_wall_gran.html index 482e163906..a57b6e4c2a 100644 --- a/doc/fix_wall_gran.html +++ b/doc/fix_wall_gran.html @@ -77,13 +77,32 @@ the amplitude, omega is 2 PI / period, and delta is elapsed time since the fix was specified. The velocity of the wall is also set to the derivative of this expression.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+This fix writes the shear friction state of atoms interacting with the +wall to binary restart files, so that a simulation can +continue correctly if granular potentials with shear "history" effects +are being used. See the read_restart command for +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. +
+None of the fix_modify options are relevant to this +fix. No quantities calculated by this fix can be output by the +thermo_style custom command. No parameter of this +fix can be used with the start/stop keywords of the run +command. This fix is not invoked during energy +minimization. +
Restrictions:
+This fix is part of the "granular" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info. +
Any dimension (xyz) that has a granular wall must be non-periodic.
-This fix can only be used if LAMMPS was built with the "granular" -package and with atom_style granular. A zcylinder wall can only be -oscillated in the z dimension. +
A zcylinder wall can only be oscillated in the z dimension.
Related commands:
diff --git a/doc/fix_wall_gran.txt b/doc/fix_wall_gran.txt index c5b36bd8b3..2f6c31ff14 100644 --- a/doc/fix_wall_gran.txt +++ b/doc/fix_wall_gran.txt @@ -67,13 +67,32 @@ the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the elapsed time since the fix was specified. The velocity of the wall is also set to the derivative of this expression. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +This fix writes the shear friction state of atoms interacting with the +wall to "binary restart files"_restart.html, so that a simulation can +continue correctly if granular potentials with shear "history" effects +are being used. See the "read_restart"_read_restart.html command for +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. + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No quantities calculated by this fix can be output by the +"thermo_style custom"_thermo_style.html command. No parameter of this +fix can be used with the {start/stop} keywords of the "run"_run.html +command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] +This fix is part of the "granular" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. + Any dimension (xyz) that has a granular wall must be non-periodic. -This fix can only be used if LAMMPS was built with the "granular" -package and with atom_style granular. A zcylinder wall can only be -oscillated in the z dimension. +A zcylinder wall can only be oscillated in the z dimension. [Related commands:] diff --git a/doc/fix_wall_lj126.html b/doc/fix_wall_lj126.html index 512552fc0c..46dae8478f 100644 --- a/doc/fix_wall_lj126.html +++ b/doc/fix_wall_lj126.html @@ -44,17 +44,31 @@ provided by the fix wall/lj93 command.The wall potential is shifted so that the energy of a wall-particle interaction is 0.0 at the cutoff distance.
-This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The contribution can -also be printed by itself via the keyword f_fix-ID in the -thermo_style custom command. +
Restart, fix_modify, thermo output, run start/stop, minimize info:
-The forces due to this fix are also imposed during an energy -minimization, invoked by the minimize command. If you -want that energy to be included in the total potential energy of the -system (the quantity being minimized), you must enable the -fix_modify energy option for this fix. +
No information about this fix is written to binary restart +files. +
+The fix_modify energy option is supported by this +fix to add the energy of interaction between atoms and the wall to the +system's potential energy as part of thermodynamic +output. +
+The atom/wall interaction energy can be printed as part of +thermodynamic output via the keyword f_ID, where ID is the fix-ID of +this fix. See the thermo_style custom command for +details. +
+No parameter of this fix can be used with the start/stop keywords of +the run command. +
+The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command. +
+IMPORTANT NOTE: If you want the atom/wall interaction energy to be +included in the total potential energy of the system (the quantity +being minimized), you MUST enable the fix_modify +energy option for this fix.
Restrictions:
diff --git a/doc/fix_wall_lj126.txt b/doc/fix_wall_lj126.txt index 23a269298b..3bb4f10337 100644 --- a/doc/fix_wall_lj126.txt +++ b/doc/fix_wall_lj126.txt @@ -41,17 +41,31 @@ provided by the "fix wall/lj93"_fix_wall_lj93.html command. The wall potential is shifted so that the energy of a wall-particle interaction is 0.0 at the cutoff distance. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The contribution can -also be printed by itself via the keyword {f_fix-ID} in the -"thermo_style custom"_thermo_style.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] -The forces due to this fix are also imposed during an energy -minimization, invoked by the "minimize"_minimize.html command. If you -want that energy to be included in the total potential energy of the -system (the quantity being minimized), you must enable the -"fix_modify"_fix_modify.html {energy} option for this fix. +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy of interaction between atoms and the wall to the +system's potential energy as part of "thermodynamic +output"_thermo_style.html. + +The atom/wall interaction energy can be printed as part of +thermodynamic output via the keyword f_ID, where ID is the fix-ID of +this fix. See the "thermo_style custom"_thermo_style.html command for +details. + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the "minimize"_minimize.html command. + +IMPORTANT NOTE: If you want the atom/wall interaction energy to be +included in the total potential energy of the system (the quantity +being minimized), you MUST enable the "fix_modify"_fix_modify.html +{energy} option for this fix. [Restrictions:] diff --git a/doc/fix_wall_lj93.html b/doc/fix_wall_lj93.html index d60ecc30bc..116fa5ddef 100644 --- a/doc/fix_wall_lj93.html +++ b/doc/fix_wall_lj93.html @@ -45,17 +45,31 @@ wall/lj126 command.The wall potential is shifted so that the energy of a wall-particle interaction is 0.0 at the cutoff distance.
-This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the fix_modify energy option. The contribution can -also be printed by itself via the keyword f_fix-ID in the -thermo_style custom command. +
Restart, fix_modify, thermo output, run start/stop, minimize info:
-The forces due to this fix are also imposed during an energy -minimization, invoked by the minimize command. If you -want that energy to be included in the total potential energy of the -system (the quantity being minimized), you must enable the -fix_modify energy option for this fix. +
No information about this fix is written to binary restart +files. +
+The fix_modify energy option is supported by this +fix to add the energy of interaction between atoms and the wall to the +system's potential energy as part of thermodynamic +output. +
+The atom/wall interaction energy can be printed as part of +thermodynamic output via the keyword f_ID, where ID is the fix-ID of +this fix. See the thermo_style custom command for +details. +
+No parameter of this fix can be used with the start/stop keywords of +the run command. +
+The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command. +
+IMPORTANT NOTE: If you want the atom/wall interaction energy to be +included in the total potential energy of the system (the quantity +being minimized), you MUST enable the fix_modify +energy option for this fix.
Restrictions:
diff --git a/doc/fix_wall_lj93.txt b/doc/fix_wall_lj93.txt index a859c86688..49fb34872a 100644 --- a/doc/fix_wall_lj93.txt +++ b/doc/fix_wall_lj93.txt @@ -42,17 +42,31 @@ wall/lj126"_fix_wall_lj126.html command. The wall potential is shifted so that the energy of a wall-particle interaction is 0.0 at the cutoff distance. -This fix makes a contribution to the potential energy of the system -that can be included in thermodynamic output of potential energy using -the "fix_modify energy"_fix_modify.html option. The contribution can -also be printed by itself via the keyword {f_fix-ID} in the -"thermo_style custom"_thermo_style.html command. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] -The forces due to this fix are also imposed during an energy -minimization, invoked by the "minimize"_minimize.html command. If you -want that energy to be included in the total potential energy of the -system (the quantity being minimized), you must enable the -"fix_modify"_fix_modify.html {energy} option for this fix. +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy of interaction between atoms and the wall to the +system's potential energy as part of "thermodynamic +output"_thermo_style.html. + +The atom/wall interaction energy can be printed as part of +thermodynamic output via the keyword f_ID, where ID is the fix-ID of +this fix. See the "thermo_style custom"_thermo_style.html command for +details. + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the "minimize"_minimize.html command. + +IMPORTANT NOTE: If you want the atom/wall interaction energy to be +included in the total potential energy of the system (the quantity +being minimized), you MUST enable the "fix_modify"_fix_modify.html +{energy} option for this fix. [Restrictions:] diff --git a/doc/fix_wall_reflect.html b/doc/fix_wall_reflect.html index d592c7691a..85c644b02c 100644 --- a/doc/fix_wall_reflect.html +++ b/doc/fix_wall_reflect.html @@ -43,6 +43,16 @@ in the input script, since the adjustments it makes to atom coordinates should come after the changes made by time integration. LAMMPS will warn you if your fixes are not ordered this way. +Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions:
Any dimension (xyz) that has a reflecting wall must be non-periodic. diff --git a/doc/fix_wall_reflect.txt b/doc/fix_wall_reflect.txt index 330b172f67..334a3229ea 100644 --- a/doc/fix_wall_reflect.txt +++ b/doc/fix_wall_reflect.txt @@ -40,6 +40,16 @@ in the input script, since the adjustments it makes to atom coordinates should come after the changes made by time integration. LAMMPS will warn you if your fixes are not ordered this way. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] Any dimension (xyz) that has a reflecting wall must be non-periodic. diff --git a/doc/fix_wiggle.html b/doc/fix_wiggle.html index aefff2ec10..422b63a3cd 100644 --- a/doc/fix_wiggle.html +++ b/doc/fix_wiggle.html @@ -40,6 +40,16 @@ the dim coordinate of each atom is set to elapsed time since the fix was specified. The velocity of the atom is set to the derivative of this expression.
+Restart, fix_modify, thermo output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No quantities calculated by this fix can be +output by the thermo_style custom command. No +parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
Restrictions: none
Related commands: none diff --git a/doc/fix_wiggle.txt b/doc/fix_wiggle.txt index 6f82cd7b22..a4f9dcdd5d 100644 --- a/doc/fix_wiggle.txt +++ b/doc/fix_wiggle.txt @@ -37,6 +37,16 @@ where {coord0} is the coordinate at the time the fix was specified, elapsed time since the fix was specified. The velocity of the atom is set to the derivative of this expression. +[Restart, fix_modify, thermo output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No quantities calculated by this fix can be +output by the "thermo_style custom"_thermo_style.html command. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + [Restrictions:] none [Related commands:] none diff --git a/doc/improper_class2.txt b/doc/improper_class2.txt index f5390e56a2..5e27bb6aa2 100644 --- a/doc/improper_class2.txt +++ b/doc/improper_class2.txt @@ -36,8 +36,8 @@ The following coefficients must be defined for each improper type via the the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands: -For this style, only coefficients for the Ei formula can be specified -in the input script. These are the 2 coefficients: +For this style, coefficients for the Ei formula can be specified in +eiher the input script or data file. These are the 2 coefficients: K (energy/radian^2) X0 (degrees) :ul @@ -45,8 +45,8 @@ X0 (degrees) :ul X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2. -Coefficients for the Eaa formula must be specified in the data file. -For the Eaa formula, the coefficients are listed under a +Coefficients for the Eaa formula can only be specified in the data +file. For the Eaa formula, the coefficients are listed under a "AngleAngle Coeffs" heading and each line lists 6 coefficients: M1 (energy/distance) @@ -61,9 +61,9 @@ radians internally; hence the units of M are in energy/radian^2. [Restrictions:] -This improper style is part of the "class2" package. It is only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. +This improper style can only be used if LAMMPS was built with the +"class2" package. See the "Making LAMMPS"_Section_start.html#2_3 +section for more info on packages. [Related commands:] diff --git a/doc/improper_cvff.txt b/doc/improper_cvff.txt index d47660d79f..ddec5bcfe7 100644 --- a/doc/improper_cvff.txt +++ b/doc/improper_cvff.txt @@ -34,7 +34,11 @@ K (energy) d (+1 or -1) n (0,1,2,3,4,6) :ul -[Restrictions:] none +[Restrictions:] + +This improper style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info on packages. [Related commands:] diff --git a/doc/improper_harmonic.txt b/doc/improper_harmonic.txt index a5567428e1..9b66c35ec7 100644 --- a/doc/improper_harmonic.txt +++ b/doc/improper_harmonic.txt @@ -37,7 +37,11 @@ X0 (degrees) :ul X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2. -[Restrictions:] none +[Restrictions:] + +This improper style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info on packages. [Related commands:] diff --git a/doc/improper_hybrid.txt b/doc/improper_hybrid.txt index 3bed0c6c34..b6f2e92a93 100644 --- a/doc/improper_hybrid.txt +++ b/doc/improper_hybrid.txt @@ -50,7 +50,11 @@ An improper style of {none} can be specified as an argument to improper_style hybrid and the corresponding improper_coeff commands, if you desire to turn off certain improper types. -[Restrictions:] none +[Restrictions:] + +This improper style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info on packages. [Related commands:] diff --git a/doc/improper_style.txt b/doc/improper_style.txt index 85fbc69183..420bbc0e75 100644 --- a/doc/improper_style.txt +++ b/doc/improper_style.txt @@ -31,13 +31,23 @@ from a data or restart file. Hybrid models where impropers are computed using different improper potentials can be setup using the {hybrid} improper style. -The coefficients associated with an improper style can be specified in a -data or restart file or via the "improper_coeff"_improper_coeff.html command. +The coefficients associated with an improper style can be specified in +a data or restart file or via the "improper_coeff"_improper_coeff.html +command. -Note that when both an improper and pair style is defined, the -"special_bond"_special_bond.html command often needs to be used to -turn off (or weight) the pairwise interactions that would otherwise -exist between the 4 bonded atoms. +All improper potentials store their coefficient data in binary restart +files which means improper_style and +"improper_coeff"_improper_coeff.html commands do not need to be +re-specified in an input script that restarts a simulation. See the +"read_restart"_read_restart.html command for details on how to do +this. The one exception is that improper_style {hybrid} only stores +the list of sub-styles in the restart file; improper coefficients need +to be re-specified. + +IMPORTANT NOTE: When both an improper and pair style is defined, the +"special_bonds"_special_bonds.html command often needs to be used to +turn off (or weight) the pairwise interaction that would otherwise +exist between 4 bonded atoms. :line @@ -59,10 +69,11 @@ specified by the associated "improper_coeff"_improper_coeff.html command: Improper styles can only be set for atom_style choices that allow impropers to be defined. -Improper styles are part of the "molecular" package or other packages -as noted in their documentation. They are only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. +Most improper styles are part of the "molecular" package. They are +only enabled if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info on packages. The +doc pages for individual improper potentials tell if it is part of a +package. [Related commands:] diff --git a/doc/kspace_style.txt b/doc/kspace_style.txt index 3a8bd6d8cd..e7e5e24479 100644 --- a/doc/kspace_style.txt +++ b/doc/kspace_style.txt @@ -73,7 +73,7 @@ must be periodic and the z dimension must be non-periodic. Kspace styles are part of the "kspace" package. They are only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. +LAMMPS"_Section_start.html#2_3 section for more info. When using a long-range pairwise TIP4P potential, you must use kspace style {pppm/tip4p} and vice versa. diff --git a/doc/minimize.html b/doc/minimize.html index 64c251b2bd..7f1550b278 100644 --- a/doc/minimize.html +++ b/doc/minimize.html @@ -34,6 +34,9 @@ fashion that should allow for systems with highly overlapped atoms (large energies and forces) to still be minimized by pushing the atoms off of each other.
+Following the minimization a statistical summary is printed that +includes the energy change and convergence criteria information. +
A minimization involves an outer iteration loop which sets the search direction along which coordinates are changed. An inner iteration is then performed using a line search algorithm. The line search @@ -61,21 +64,20 @@ include pair/lj/charmm/coul/charmm and pair/lj/charmm/coul/long. If a soft potential is used the Astop value is used for the prefactor (no time dependence).
-Only fixes that apply force constraints are invoked during -minimization. The list of the currently implemented ones include fix -addforce, aveforce, enforce2d, indent, lineforce, -planeforce, setforce, and wall/lj93. Note that indent, -wall/lj93 have an associated potential energy. If you want that -energy to be included in the total potential energy of the system (the -quantity being minimized), you must enable the -fix_modify energy option for that fix. +
Only some fixes (typically those that apply force constraints) are +invoked during minimization. See the doc pages for individual +fix commands to see which ones are relevant.
-Following the minimization a statistical summary is printed that -includes the energy change and convergence criteria information. +
IMPORTANT NOTE: Some fixes which are invoked during minimization have +an associated potential energy. For that energy to be included in the +total potential energy of the system (the quantity being minimized), +you MUST enable the fix_modify energy option for +that fix. The doc pages for individual fix commands +specify if this should be done.
Restrictions:
-Features that are not yet implemented listed here, in case someone +
Features that are not yet implemented are listed here, in case someone knows how they could be coded:
It is an error to use fix shake with minimization diff --git a/doc/minimize.txt b/doc/minimize.txt index 0b3459a076..30a7609a58 100644 --- a/doc/minimize.txt +++ b/doc/minimize.txt @@ -31,6 +31,9 @@ fashion that should allow for systems with highly overlapped atoms (large energies and forces) to still be minimized by pushing the atoms off of each other. +Following the minimization a statistical summary is printed that +includes the energy change and convergence criteria information. + A minimization involves an outer iteration loop which sets the search direction along which coordinates are changed. An inner iteration is then performed using a line search algorithm. The line search @@ -58,21 +61,20 @@ include {pair/lj/charmm/coul/charmm} and {pair/lj/charmm/coul/long}. If a {soft} potential is used the Astop value is used for the prefactor (no time dependence). -Only fixes that apply force constraints are invoked during -minimization. The list of the currently implemented ones include fix -{addforce}, {aveforce}, {enforce2d}, {indent}, {lineforce}, -{planeforce}, {setforce}, and {wall/lj93}. Note that {indent}, -{wall/lj93} have an associated potential energy. If you want that -energy to be included in the total potential energy of the system (the -quantity being minimized), you must enable the -"fix_modify"_fix_modify.html {energy} option for that fix. +Only some fixes (typically those that apply force constraints) are +invoked during minimization. See the doc pages for individual +"fix"_fix.html commands to see which ones are relevant. -Following the minimization a statistical summary is printed that -includes the energy change and convergence criteria information. +IMPORTANT NOTE: Some fixes which are invoked during minimization have +an associated potential energy. For that energy to be included in the +total potential energy of the system (the quantity being minimized), +you MUST enable the "fix_modify"_fix_modify.html {energy} option for +that fix. The doc pages for individual "fix"_fix.html commands +specify if this should be done. [Restrictions:] -Features that are not yet implemented listed here, in case someone +Features that are not yet implemented are listed here, in case someone knows how they could be coded: It is an error to use "fix shake"_fix_shake.html with minimization diff --git a/doc/pair_buck.txt b/doc/pair_buck.txt index 9d23621c2a..e485597434 100644 --- a/doc/pair_buck.txt +++ b/doc/pair_buck.txt @@ -80,20 +80,41 @@ Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +None of the Buckingham pair styles support mixing. Thus, coefficients +for all I,J pairs must be specified explicitly. + +All of the Buckingham pair styles support the +"pair_modify"_pair_modify.html shift option for the energy of the +exp() and 1/r^6 portion of the pair interaction. + +The {buck/coul/long} pair style does not support the +"pair_modify"_pair_modify.html table option since a tabulation +capability has not yet been added to this potential. + +None of the Buckingham pair styles support the +"pair_modify"_pair_modify.html tail option for adding long-range tail +corrections to energy and pressure. + +All of the Buckinham pair styles can calculate per-atom energy and +stress, as used by the "compute epair/atom"_compute_epair_atom.html, +"compute stress/atom"_compute_stress_atom.html, and "dump +custom"_dump.html commands. + +All of the Buckinham pair styles write their information to "binary +restart files"_restart.html, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + [Restrictions:] -The {buck} potentials do not support the -"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j -pairs must be specified explicitly. - The {buck/coul/long} style is part of the "kspace" package. It is -only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. - -On some 64-bit machines, compiling with -O3 appears to break the -Coulombic tabling option used by the {buck/coul/long} style. See -the "Additional build tips" section of the Making LAMMPS documentation -pages for workarounds on this issue. +only enabled if LAMMPS was built with that package (which it is by +default). See the "Making LAMMPS"_Section_start.html#2_3 section for +more info. [Related commands:] diff --git a/doc/pair_charmm.txt b/doc/pair_charmm.txt index abc291acae..312ac09deb 100644 --- a/doc/pair_charmm.txt +++ b/doc/pair_charmm.txt @@ -88,7 +88,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: epsilon (energy units) sigma (distance units) @@ -106,11 +106,40 @@ because this CHARMM force field does not allow varying cutoffs for individual atom pairs; all pairs use the global cutoff(s) specified in the pair_style command. -If the pair_coeff command is not used to define coefficients for a -particular I != J type pair, the mixing rule for epsilon and sigma for -all CHARMM potentials is to use the {arithmetic} formulas documented -by the "pair_modify"_pair_modify.html command. The "pair_modify -mix"_pair_modify.html setting is thus ignored for CHARMM potentials. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14, +and sigma_14 coefficients for all of the lj/charmm pair styles can be +mixed. They are always mixed with the value {arithmetic}. See the +"pair_modify" command for details. + +None of the lj/charmm pair styles support the +"pair_modify"_pair_modify.html shift option, since the Lennard-Jones +portion of the pair interaction is smoothed to 0.0 at the cutoff. + +The {lj/charmm/coul/long} and {lj/charmm/coul/long/opt} pair styles +support the "pair_modify"_pair_modify.html table option since they can +tabulate the short-range portion of the long-range Coulombic +interaction. + +None of the lj/charmm pair styles support the +"pair_modify"_pair_modify.html tail option for adding long-range tail +corrections to energy and pressure, since the Lennard-Jones portion of +the pair interaction is smoothed to 0.0 at the cutoff. + +All of the lj/charmm pair styles can calculate per-atom energy and +stress, as used by the "compute epair/atom"_compute_epair_atom.html, +"compute stress/atom"_compute_stress_atom.html, and "dump +custom"_dump.html commands. + +All of the lj/charmm pair styles write their information to "binary +restart files"_restart.html, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + +:line [Restrictions:] @@ -119,8 +148,8 @@ styles are part of the "molecule" package. The {lj/charmm/coul/long} style is part of the "kspace" package. The {lj/charmm/coul/long/opt} style is part of the "opt" package and also requires the "kspace" package. They are only enabled if LAMMPS was built with those -package(s). See the "Making LAMMPS"_Section_start.html#2_3 section -for more info. +package(s) (molecule and kspace are by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. On some 64-bit machines, compiling with -O3 appears to break the Coulombic tabling option used by the {lj/charmm/coul/long} style. See diff --git a/doc/pair_class2.txt b/doc/pair_class2.txt index 10deb96488..ed29ceaff3 100644 --- a/doc/pair_class2.txt +++ b/doc/pair_class2.txt @@ -60,7 +60,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: epsilon (energy units) sigma (distance units) @@ -80,6 +80,8 @@ since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command. +: line + If the pair_coeff command is not used to define coefficients for a particular I != J type pair, the mixing rule for epsilon and sigma for all class2 potentials is to use the {sixthpower} formulas documented @@ -88,16 +90,43 @@ mix"_pair_modify.html setting is thus ignored for class2 potentials for epsilon and sigma. However it is still followed for mixing the cutoff distance. +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of the lj/class2 pair styles can be mixed. +Epsilon and sigma are always mixed with the value {sixthpower}. The +cutoff distance is mixed by whatever option is set by the pair_modify +command (default = geometric). See the "pair_modify" command for +details. + +All of the lj/class2 pair styles support the +"pair_modify"_pair_modify.html shift option for the energy of the +Lennard-Jones portion of the pair interaction. + +The {lj/class2/coul/long} pair style does not support the +"pair_modify"_pair_modify.html table option since a tabulation +capability has not yet been added to this potential. + +All of the lj/class2 pair styles support the +"pair_modify"_pair_modify.html tail option for adding a long-range +tail correction to the energy and pressure of the Lennard-Jones +portion of the pair interaction. + +All of the lj/class2 pair styles can calculate per-atom energy and +stress, as used by the "compute epair/atom"_compute_epair_atom.html, +"compute stress/atom"_compute_stress_atom.html, and "dump +custom"_dump.html commands. + +All of the lj/class2 pair styles write their information to "binary +restart files"_restart.html, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + [Restrictions:] -These styles are part of the "class2" package. They are only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. - -On some 64-bit machines, compiling with -O3 appears to break the -Coulombic tabling option used by the {lj/class2/coul/long} style. See -the "Additional build tips" section of the Making LAMMPS documentation -pages for workarounds on this issue. +All of these pair styles are part of the "class2" package. They are +only enabled if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/pair_coeff.txt b/doc/pair_coeff.txt index 040236aa0b..acaeafab1c 100644 --- a/doc/pair_coeff.txt +++ b/doc/pair_coeff.txt @@ -37,7 +37,7 @@ can be used for each, as in the 1st example above. I <= J is required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same values. -A wild-card asterik can be used in place of in conjunction with the +A wild-card asterik can be used in place of or in conjunction with the I,J arguments to set the coefficients for multiple pairs of atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of atom types, then an asterik with no numeric values means all @@ -70,8 +70,9 @@ as For many potentials, if coefficients for type pairs with I != J are not set explicity by a pair_coeff command, the values are inferred from the I,I and J,J settings by mixing rules; see the -"pair_modify"_pair_modify.html command for a discussion. Exceptions -to the mixing rules are discussed with the individual pair styles. +"pair_modify"_pair_modify.html command for a discussion. Details on +this option as it pertains to individual potentials are described on +the doc page for the potential. :line @@ -80,20 +81,15 @@ the style to display the formula it computes, arguments specified in the pair_style command, and coefficients specified by the associated "pair_coeff"_pair_coeff.html command: -"pair_style none"_pair_none.html - turn off pairwise interactions -"pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul +"pair_style airebo"_pair_airebo.html - AI-REBO potential "pair_style buck"_pair_buck.html - Buckingham potential "pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb "pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb "pair_style colloid"_pair_colloid.html - integrated colloidal potential -"pair_style dipole/cut"_pair_dpd.html - point dipole potential "pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD) "pair_style eam"_pair_eam.html - embedded atom method (EAM) -"pair_style eam/opt"_pair_eam.html - optimized embedded atom method (EAM) "pair_style eam/alloy"_pair_eam.html - alloy EAM -"pair_style eam/alloy/opt"_pair_eam.html - optimized alloy EAM "pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM -"pair_style eam/fs/opt"_pair_eam.html - optimized Finnis-Sinclair EAM "pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential "pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions "pair_style gran/history"_pair_gran.html - granular potential with history effects @@ -101,12 +97,10 @@ the pair_style command, and coefficients specified by the associated "pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb "pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent "pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb -"pair_style lj/charmm/coul/long/opt"_pair_charmm.html - optimized CHARMM with long-range Coulomb "pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb "pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb "pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb "pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb -"pair_style lj/cut/opt"_pair_lj.html - optimized cutoff Lennard-Jones potential with no Coulomb "pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb "pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye damping added to Coulomb "pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb @@ -115,7 +109,6 @@ the pair_style command, and coefficients specified by the associated "pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM) "pair_style morse"_pair_morse.html - Morse potential -"pair_style morse/opt"_pair_morse.html - optimized Morse potential "pair_style soft"_pair_soft.html - Soft (cosine) potential "pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential "pair_style table"_pair_table.html - tabulated pair potential diff --git a/doc/pair_colloid.txt b/doc/pair_colloid.txt index d7a263069a..72832c6646 100644 --- a/doc/pair_colloid.txt +++ b/doc/pair_colloid.txt @@ -59,7 +59,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: A (energy units) sigma (distance units) @@ -107,16 +107,42 @@ rule-of-thumb is to use a colloid-solvent cutoff that is half the big diamter + 4 times the small diamter. I.e. 9 = 5 + 4 for the colloid-solvent cutoff in this case. -If a pair_coeff command is not specified for I != J, then the -coefficients are mixed according the mixing rules defined by the -"pair_modify"_pair_modify.html command. The prefactor A is mixed like -the Lennard-Jones epsilon; sigma,d1,d2 are all mixed like the -Lennard-Jones sigma. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the A, sigma, d1, and d2 +coefficients and cutoff distance for this pair style can be mixed. A +is an energy value mixed like a LJ epsilon. D1 and d2 are distance +values and are mixed like sigma. The default mix value is +{geometric}. See the "pair_modify" command for details. + +This pair style supports the "pair_modify"_pair_modify.html shift +option for the energy of the pair interaction. + +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. + +This pair style does not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style can calculate per-atom energy and stress, as used by +the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +:line [Restrictions:] -The {colloid} style is part of the "colloid" package. It is only -enabled if LAMMPS was built with that package. See the "Making +This style is part of the "colloid" package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/pair_dipole.txt b/doc/pair_dipole.txt index 5d6662902c..cea8a63e82 100755 --- a/doc/pair_dipole.txt +++ b/doc/pair_dipole.txt @@ -59,7 +59,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: epsilon (energy units) sigma (distance units) @@ -73,12 +73,46 @@ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this type pair. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distances for this pair style can be mixed. The default +mix value is {geometric}. See the "pair_modify" command for details. + +For atom type pairs I,J and I != J, the A, sigma, d1, and d2 +coefficients and cutoff distance for this pair style can be mixed. A +is an energy value mixed like a LJ epsilon. D1 and d2 are distance +values and are mixed like sigma. The default mix value is +{geometric}. See the "pair_modify" command for details. + +This pair style supports the "pair_modify"_pair_modify.html shift +option for the energy of the Lennard-Jones portion of the pair +interaction. + +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. + +This pair style does not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style can calculate per-atom energy and stress, as used by +the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + [Restrictions:] -Can only be used if LAMMPS was built with the "dipole" package. - -The use of this potential requires additional fixes as described -above. +This style is part of the "dipole" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/pair_dpd.txt b/doc/pair_dpd.txt index cfd8c5f565..95dc12146a 100644 --- a/doc/pair_dpd.txt +++ b/doc/pair_dpd.txt @@ -53,15 +53,48 @@ cutoff is used. Note that sigma is set equal to sqrt(2 T gamma), where T is the temperature set by the "pair_style"_pair_style.html command so it does not need to be specified. -[Restrictions:] none +:line -This style is part of the "dpd" package. It is only enabled if LAMMPS -was built with those package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: -The {dpd} potential does not support the -"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j -pairs must be specified explicitly. +Thsi pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. + +This pair style does not support the "pair_modify"_pair_modify.html +shift option for the energy of the pair interaction. + +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. + +This pair style does not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style can calculate per-atom energy and stress, as used by +the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. However, only the first term with the A coefficienct +(conservative force) is used for these computations. The drag force +and random force terms are not. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. Note +that the user-specifice random number seed is stored in the restart +file, so when a simulation is restarted, each processor will +re-initialize its random number generator the same way it did +intially. This means the random forces will be random, but will not +be the same as they would have been if the original simulation had +continued past the restart time. + +:line + +[Restrictions:] + +This style is part of the "dpd" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. The default frequency for rebuilding neighbor lists is every 10 steps (see the "neigh_modify"_neigh_modify.html command). This may be too diff --git a/doc/pair_eam.html b/doc/pair_eam.html index 5b07c4cc6f..826d478ba3 100644 --- a/doc/pair_eam.html +++ b/doc/pair_eam.html @@ -325,21 +325,13 @@ are listed.
Mixing, shift, table, tail correction, per-atom energy/stress, and restart info:
-For atom type pairs I,J and I != J, mixing is performed by LAMMPS as +
For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS as described above with the individual styles. You never need to specify a pair_coeff command with I != J arguments for the eam styles.
This pair style does not support the pair_modify -shift option for the energy of the pair interaction. -
-The pair_modify shift option is not relevant -for this pair style. -
-The pair_modify table option is not relevant -for this pair style. -
-The pair_modify tail option is not relevant -for this pair style. +shift, table, and tail options.
All of the eam pair styles can calculate per-atom energy and stress, as used by the compute epair/atom, compute @@ -347,10 +339,10 @@ stress/atom, and dump custom commands. These quantities include the contribution from the embedding term in the EAM formulas.
-None of the eam pair styles write their information to binary restart -files, since the info is tabulated in potential files. -Thus, you need to re-specify the pair style and coefficient commands -in an input script that reads a restart file. +
The eam pair styles do not write their information to binary restart +files, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file.
For granular styles there are no individual atom type coefficients -that can be set. All global settings are made via the pair_style -command. +that can be set via the pair_coeff command. All +global settings are made via the pair_style command.
-See the citation for more discussion of the granular potentials. +
See the citation below for more discussion of granular potentials.
+Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+The pair_modify mix, shift, table, and tail options +are not relevant for granular pair styles. +
+This pair style does not calculate per-atom energy and stress, as used +by the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style writes its information to binary restart +files, so a pair_style commands does not need to be +specified in an input script that reads a restart file. +
+Restrictions: none
-All of these styles are part of the "granular" package. It is only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -
-You must use atom style granular with these pair -styles. +
All the granular pair styles are part of the "granular" package. It +is only enabled if LAMMPS was built with that package. See the +Making LAMMPS section for more info.
Related commands:
diff --git a/doc/pair_gran.txt b/doc/pair_gran.txt index 15d2ca24ea..43fee9582b 100644 --- a/doc/pair_gran.txt +++ b/doc/pair_gran.txt @@ -58,19 +58,35 @@ spring and dash-pot model until Ft/Fn = xmu and then is held at Ft = Fn*xmu until the particles lose contact. For granular styles there are no individual atom type coefficients -that can be set. All global settings are made via the pair_style -command. +that can be set via the "pair_coeff"_pair_coeff.html command. All +global settings are made via the pair_style command. -See the citation for more discussion of the granular potentials. +See the citation below for more discussion of granular potentials. + +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +The "pair_modify"_pair_modify.html mix, shift, table, and tail options +are not relevant for granular pair styles. + +This pair style does not calculate per-atom energy and stress, as used +by the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes its information to "binary restart +files"_restart.html, so a pair_style commands does not need to be +specified in an input script that reads a restart file. + +:line [Restrictions:] none -All of these styles are part of the "granular" package. It is only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. - -You must use "atom style"_atom_style.html {granular} with these pair -styles. +All the granular pair styles are part of the "granular" package. It +is only enabled if LAMMPS was built with that package. See the +"Making LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/pair_hybrid.html b/doc/pair_hybrid.html index 05f66c2ed5..3a389128fa 100644 --- a/doc/pair_hybrid.html +++ b/doc/pair_hybrid.html @@ -50,14 +50,6 @@ pair_coeff * * eam/alloy nialhjea 1 1 0 pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0 pair_coeff 1*2 3 lj/cut 0.8 1.1 -Note that as with any pair_style, coeffs must be defined for all I,J -interactions. If the sub-style allows for mixing (see the -pair_modify command), then I,J interactions between -atom types which both are assigned to that sub-style do not need to be -specified. I.e. if atom types 1 and 2 are both computed with lj/cut -and coeffs for 1,1 and 2,2 interactions are specified, then coeffs for -1,2 interactions will be generated automatically via mixing. -
If the pair_coeff command for a sub-style requires the use of * * as atom type arguments (e.g. the eam/alloy example above), then it will also include trailing arguments which map atom types to elements in @@ -69,8 +61,43 @@ hybrid command in your input script, if atoms in the simulation will have attributes from several atom styles, due to using multiple pair potentials.
+Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+Any pair potential settings made via the +pair_modify command are passed along to all +sub-styles of the hybrid potential. +
+For atom type pairs I,J and I != J, if the sub-style assigned to I,I +and J,J is the same, and if the sub-style allows for mixing, then the +coefficients for I,J can be mixed. The default mix value is +geometric. See the "pair_modify" command for details. See the +See the doc page for the sub-style to see if allows for mixing. +
+The hybrid pair style supports the pair_modify +shift, table, and tail options for an I,J pair interaction, if the +associated sub-style supports it. +
+The hybrid pair style can calculate per-atom energy and stress, as +used by the compute epair/atom, compute +stress/atom, and dump custom +commands, if all its sub-styles can perform per-atom calculations. +
+For the hybrid pair style, the list of sub-styles and their respective +settings are written to binary restart files, so a +pair_style command does not need to specified in an input script that +reads a restart file. However, the coefficient information is not +stored in the restart file. Thus, pair_coeff commands do need to be +specified in the restart input script. +
Restrictions:
+A pair style of none can be specified as an argument to pair_style +hybrid and the corresponding pair_coeff commands, if you desire to +turn off pairwise interactions between certain pairs of atom types. +
When using a long-range Coulomic solver (via the kspace_style command) with pair_style hybrid, one or more sub-styles will be of the "long" variety. @@ -79,17 +106,6 @@ than one sub-style with a "long" component, but you must insure that the short-range Coulombic cutoff used by each of these pair styles is consistent. Else the long-range Coulombic solve will be inconsistent.
-A pair style of none can be specified as an argument to pair_style -hybrid and the corresponding pair_coeff commands, if you desire to -turn off pairwise interactions between certain pairs of atom types. -
-The hybrid style cannot include any of the granular styles in its -list of styles to use. -
-If you use multiple coul/long pair styles along with a kspace -style, then you should make sure the pairwise -Coulombic cutoff is the same for all the pair styles. -
Related commands:
pair_coeff diff --git a/doc/pair_hybrid.txt b/doc/pair_hybrid.txt index 37ad495cd5..ff27251384 100644 --- a/doc/pair_hybrid.txt +++ b/doc/pair_hybrid.txt @@ -47,14 +47,6 @@ pair_coeff * * eam/alloy nialhjea 1 1 0 pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0 pair_coeff 1*2 3 lj/cut 0.8 1.1 :pre -Note that as with any pair_style, coeffs must be defined for all I,J -interactions. If the sub-style allows for mixing (see the -"pair_modify"_pair_modify.html command), then I,J interactions between -atom types which both are assigned to that sub-style do not need to be -specified. I.e. if atom types 1 and 2 are both computed with {lj/cut} -and coeffs for 1,1 and 2,2 interactions are specified, then coeffs for -1,2 interactions will be generated automatically via mixing. - If the pair_coeff command for a sub-style requires the use of * * as atom type arguments (e.g. the {eam/alloy} example above), then it will also include trailing arguments which map atom types to elements in @@ -66,8 +58,43 @@ hybrid command in your input script, if atoms in the simulation will have attributes from several atom styles, due to using multiple pair potentials. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +Any pair potential settings made via the +"pair_modify"_pair_modify.html command are passed along to all +sub-styles of the hybrid potential. + +For atom type pairs I,J and I != J, if the sub-style assigned to I,I +and J,J is the same, and if the sub-style allows for mixing, then the +coefficients for I,J can be mixed. The default mix value is +{geometric}. See the "pair_modify" command for details. See the +See the doc page for the sub-style to see if allows for mixing. + +The hybrid pair style supports the "pair_modify"_pair_modify.html +shift, table, and tail options for an I,J pair interaction, if the +associated sub-style supports it. + +The hybrid pair style can calculate per-atom energy and stress, as +used by the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands, if all its sub-styles can perform per-atom calculations. + +For the hybrid pair style, the list of sub-styles and their respective +settings are written to "binary restart files"_restart.html, so a +pair_style command does not need to specified in an input script that +reads a restart file. However, the coefficient information is not +stored in the restart file. Thus, pair_coeff commands do need to be +specified in the restart input script. + [Restrictions:] +A pair style of {none} can be specified as an argument to pair_style +hybrid and the corresponding pair_coeff commands, if you desire to +turn off pairwise interactions between certain pairs of atom types. + When using a long-range Coulomic solver (via the "kspace_style"_kspace_style command) with pair_style hybrid, one or more sub-styles will be of the "long" variety. @@ -76,17 +103,6 @@ than one sub-style with a "long" component, but you must insure that the short-range Coulombic cutoff used by each of these pair styles is consistent. Else the long-range Coulombic solve will be inconsistent. -A pair style of {none} can be specified as an argument to pair_style -hybrid and the corresponding pair_coeff commands, if you desire to -turn off pairwise interactions between certain pairs of atom types. - -The hybrid style cannot include any of the {granular} styles in its -list of styles to use. - -If you use multiple {coul/long} pair styles along with a "kspace -style"_kspace_style.html, then you should make sure the pairwise -Coulombic cutoff is the same for all the pair styles. - [Related commands:] "pair_coeff"_pair_coeff.html diff --git a/doc/pair_lj.txt b/doc/pair_lj.txt index 5730d0a91c..154045a722 100644 --- a/doc/pair_lj.txt +++ b/doc/pair_lj.txt @@ -131,7 +131,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: epsilon (energy units) sigma (distance units) @@ -155,13 +155,49 @@ can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of the lj/cut pair styles can be mixed. +The default mix value is {geometric}. See the "pair_modify" command +for details. + +All of the lj/cut pair styles support the +"pair_modify"_pair_modify.html shift option for the energy of the +Lennard-Jones portion of the pair interaction. + +The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} pair styles +support the "pair_modify"_pair_modify.html table option since they can +tabulate the short-range portion of the long-range Coulombic +interaction. + +All of the lj/cut pair styles support the +"pair_modify"_pair_modify.html tail option for adding a long-range +tail correction to the energy and pressure of the Lennard-Jones +portion of the pair interaction. + +All of the lj/cut pair styles can calculate per-atom energy and +stress, as used by the "compute epair/atom"_compute_epair_atom.html, +"compute stress/atom"_compute_stress_atom.html, and "dump +custom"_dump.html commands. + +All of the lj/cut pair styles write their information to "binary +restart files"_restart.html, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + +:line + [Restrictions:] -The {lj/cut/coul/long} style is part of the "kspace" package. It is -only enabled if LAMMPS was built with that package. The {lj/cut/opt} -style is part of the "opt" package. It is only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. +The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} styles are part of +the "kspace" package. They are only enabled if LAMMPS was built with +that package (which it is by default). The {lj/cut/opt} style is part +of the "opt" package. It is only enabled if LAMMPS was built with +that package. See the "Making LAMMPS"_Section_start.html#2_3 section +for more info. On some 64-bit machines, compiling with -O3 appears to break the Coulombic tabling option used by the {lj/cut/coul/long} style. See diff --git a/doc/pair_lj_expand.html b/doc/pair_lj_expand.html index 89604c17de..09082f4ff7 100644 --- a/doc/pair_lj_expand.html +++ b/doc/pair_lj_expand.html @@ -39,7 +39,7 @@ actual force cutoff is the sum of cutoff + delta. types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart -commands: +commands, or by mixing as described below:
The delta values can be positive or negative. The last coefficient is optional. If not specified, the global LJ cutoff is used.
-If the pair_coeff command is not used to define coefficients for a -particular I != J type pair, the mixing rule is set by the -pair_modify command. Additionally, the delta -coefficient is always mixed by the rule +
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info:
-delta_ij = (delta_i + delta_j) / 2 -+
For atom type pairs I,J and I != J, the epsilon, sigma, and shift +coefficients and cutoff distance for this pair style can be mixed. +Shift is always mixed via an arithmetic rule. The other +coefficients are mixed according to the pair_modify mix value. The +default mix value is geometric. See the "pair_modify" command for +details. +
+This pair style supports the pair_modify shift +option for the energy of the pair interaction. +
+The pair_modify table option is not relevant +for this pair style. +
+This pair style supports the pair_modify tail +option for adding a long-range tail correction to the energy and +pressure of the pair interaction. +
+This pair style can calculate per-atom energy and stress, as used by +the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style writes its information to binary restart +files, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. +
+Restrictions: none
Related commands: diff --git a/doc/pair_lj_expand.txt b/doc/pair_lj_expand.txt index ed8885294a..221f8e0bae 100644 --- a/doc/pair_lj_expand.txt +++ b/doc/pair_lj_expand.txt @@ -36,7 +36,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: epsilon (energy units) sigma (distance units) @@ -46,12 +46,38 @@ cutoff (distance units) :ul The delta values can be positive or negative. The last coefficient is optional. If not specified, the global LJ cutoff is used. -If the pair_coeff command is not used to define coefficients for a -particular I != J type pair, the mixing rule is set by the -"pair_modify"_pair_modify.html command. Additionally, the delta -coefficient is always mixed by the rule +:line -delta_ij = (delta_i + delta_j) / 2 :pre +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the epsilon, sigma, and shift +coefficients and cutoff distance for this pair style can be mixed. +Shift is always mixed via an {arithmetic} rule. The other +coefficients are mixed according to the pair_modify mix value. The +default mix value is {geometric}. See the "pair_modify" command for +details. + +This pair style supports the "pair_modify"_pair_modify.html shift +option for the energy of the pair interaction. + +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. + +This pair style supports the "pair_modify"_pair_modify.html tail +option for adding a long-range tail correction to the energy and +pressure of the pair interaction. + +This pair style can calculate per-atom energy and stress, as used by +the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +:line [Restrictions:] none diff --git a/doc/pair_lj_smooth.html b/doc/pair_lj_smooth.html index 085ae8fd20..544cc11bd7 100644 --- a/doc/pair_lj_smooth.html +++ b/doc/pair_lj_smooth.html @@ -46,7 +46,7 @@ Plot the energy and force resulting from this formula via the types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart -commands: +commands, or by mixing as described below:
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+For atom type pairs I,J and I != J, the epsilon, sigma, Rin +coefficients and the cutoff distance for this pair style can be mixed. +Rin is a cutoff value and is mixed like the cutoff. The other +coefficients are mixed according to the pair_modify mix option. The +default mix value is geometric. See the "pair_modify" command for +details. +
+This pair style supports the pair_modify shift +option for the energy of the pair interaction. +
+The pair_modify table option is not relevant +for this pair style. +
+This pair style does not support the pair_modify +tail option for adding long-range tail corrections to energy and +pressure, since the energy of the pair interaction is smoothed to 0.0 +at the cutoff. +
+This pair style can calculate per-atom energy and stress, as used by +the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style writes its information to binary restart +files, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. +
+Restrictions: none
Related commands: diff --git a/doc/pair_lj_smooth.txt b/doc/pair_lj_smooth.txt index 3e678f4567..db6fa7cc14 100644 --- a/doc/pair_lj_smooth.txt +++ b/doc/pair_lj_smooth.txt @@ -43,7 +43,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: epsilon (energy units) sigma (distance units) @@ -55,6 +55,41 @@ Rin and cutoff are used. Rin cannot be 0.0. If Rin = cutoff, then no force smoothing is performed for this type pair; the standard LJ formula is used. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the epsilon, sigma, Rin +coefficients and the cutoff distance for this pair style can be mixed. +Rin is a cutoff value and is mixed like the cutoff. The other +coefficients are mixed according to the pair_modify mix option. The +default mix value is {geometric}. See the "pair_modify" command for +details. + +This pair style supports the "pair_modify"_pair_modify.html shift +option for the energy of the pair interaction. + +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. + +This pair style does not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and +pressure, since the energy of the pair interaction is smoothed to 0.0 +at the cutoff. + +This pair style can calculate per-atom energy and stress, as used by +the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +:line + + [Restrictions:] none [Related commands:] diff --git a/doc/pair_meam.html b/doc/pair_meam.html index c04ad14c42..103f200093 100644 --- a/doc/pair_meam.html +++ b/doc/pair_meam.html @@ -187,7 +187,35 @@ alloy interaction between elements 1 and 2 to 4.37.
Restrictions: none +
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS with +user-specifiable parameters as described above. You never need to +specify a pair_coeff command with I != J arguments for this style. +
+This pair style does not support the pair_modify +shift, table, and tail options. +
+This pair style does not calculate per-atom energy and stress, as used +by the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style does not write its information to binary restart +files, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. +
+Restrictions: +
+This style is part of the "meam" package. It is only enabled if +LAMMPS was built with that package, which also requires the MEAM +library be built and linked with LAMMPS. See the Making +LAMMPS section for more info.
Related commands:
diff --git a/doc/pair_meam.txt b/doc/pair_meam.txt index 49bed99bac..af15b3e860 100644 --- a/doc/pair_meam.txt +++ b/doc/pair_meam.txt @@ -184,7 +184,35 @@ alloy interaction between elements 1 and 2 to 4.37. :line -[Restrictions:] none +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS with +user-specifiable parameters as described above. You never need to +specify a pair_coeff command with I != J arguments for this style. + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This pair style does not calculate per-atom energy and stress, as used +by the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style does not write its information to "binary restart +files"_restart.html, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +:line + +[Restrictions:] + +This style is part of the "meam" package. It is only enabled if +LAMMPS was built with that package, which also requires the MEAM +library be built and linked with LAMMPS. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/pair_modify.txt b/doc/pair_modify.txt index 71ad1a4834..ddde445e8e 100644 --- a/doc/pair_modify.txt +++ b/doc/pair_modify.txt @@ -14,8 +14,8 @@ pair_modify keyword value ... :pre one or more keyword/value pairs may be listed :ulb,l keyword = {shift} or {mix} or {table} or {tabinner} or {tail} :l - {shift} value = {yes} or {no} {mix} value = {geometric} or {arithmetic} or {sixthpower} + {shift} value = {yes} or {no} {table} value = N 2^N = # of values in table {tabinner} value = cutoff @@ -34,51 +34,56 @@ pair_modify table 12 :pre Modify the parameters of the currently defined pair style. Not all parameters are relevant to all pair styles. -The {shift} keyword determines whether the Lennard-Jones potential is -shifted at its cutoff to 0.0. If so, this adds an energy term to each -pairwise interaction which will be printed in the thermodynamic -output, but does not affect atom dynamics (forces). Pair styles that -are already 0.0 at their cutoff such as {lj/charmm/coul/charmm} are -not affected by this setting. +The {mix} keyword affects pair coefficients for interactions between +atoms of type I and J, when I != J and the coefficients are not +explicity set in the input script. Note that coefficients for I = J +must be set explicitly, either in the input script via the +"pair_coeff" command or in the "Pair Coeffs" section of the "data +file"_read_data.html. For some pair styles is is not necessary to +specify coefficients when I != J, since a "mixing" rule will create +them from the I,I and J,J settings. The pair_modify {mix} value +determines what formulas are used to compute the mixed coefficients. +In each case, the cutoff distance is mixed the same way as sigma. -The {mix} keyword affects how Lennard-Jones coefficients for epsilon, -sigma, and the cutoff are generated for interactions between atoms of -type I and J, when I != J. Coefficients for I = J are set explicitly -in the data file or input script. The "pair_coeff"_pair_coeff.html -command can be used in the input script to specify epilon/sigma for a -specific I != J pairing, which overrides the setting of the {mix} -keyword. +Note that not all pair styles support mixing. Also, some mix options +are not available for certain pair styles. See the doc page for +individual pair styles for those restrictions. Note also that the +"pair_coeff"_pair_coeff.html command also can be to directly set +coefficients for a specific I != J pairing, in which case no mixing is +performed. -These are the formulas used by the 3 {mix} options. In each case, the -LJ cutoff is mixed the same way as sigma. Note that some of these -options are not available for certain pair styles. See the doc page -for individual pair styles for those restrictions. - -{geometric} +mix {geometric} epsilon_ij = sqrt(epsilon_i * epsilon_j) sigma_ij = sqrt(sigma_i * sigma_j) :pre -{arithmetic} +mix {arithmetic} epsilon_ij = sqrt(epsilon_i * epsilon_j) sigma_ij = (sigma_i + sigma_j) / 2 :pre -{sixthpower} +mix {sixthpower} epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) / (sigma_i^6 + sigma_j^6) sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre +The {shift} keyword determines whether a Lennard-Jones potential is +shifted at its cutoff to 0.0. If so, this adds an energy term to each +pairwise interaction which will be included in the thermodynamic +output, but does not affect pair forces or atom trajectories. See the +doc page for individual pair styles to see which ones support this +option. + The {table} keyword applies to pair styles with a long-range Coulombic -term (lj/cut/coul/long and lj/charmm/coul/long). If N is non-zero, a -table of length 2^N is pre-computed for forces and energies, which can -shrink their computational cost by up to a factor of 2. The table is -indexed via a bit-mapping technique "(Wolff)"_#Wolff and a linear -interpolation is performed between adjacent table values. In our -experiments with different table styles (lookup, linear, spline), this -method typically gave the best performance in terms of speed and -accuracy. +term; see the doc page for individual styles to see which potentials +support this option. If N is non-zero, a table of length 2^N is +pre-computed for forces and energies, which can shrink their +computational cost by up to a factor of 2. The table is indexed via a +bit-mapping technique "(Wolff)"_#Wolff and a linear interpolation is +performed between adjacent table values. In our experiments with +different table styles (lookup, linear, spline), this method typically +gave the best performance in terms of speed and accuracy. The choice of table length is a tradeoff in accuracy versus speed. A larger N yields more accurate force computations, but requires more @@ -100,19 +105,16 @@ nearly all pairwise interactions are computed via table lookup for simulations with "real" units, but some close pairs may be computed directly (non-table) for simulations with "lj" units. -When the {tail} keyword is set to {yes}, long-range VanderWaals tail -"corrections" are added to the energy and pressure. These are -included in the calculation and printing of thermodynamic quantities -(see the "thermo_style"_thermo_style.html command). Their effect will -also be included in constant NPT or NPH simulations where the pressure -influences the simulation box dimensions (see the "fix -npt"_fix_npt.html and "fix nph"_fix_nph.html commands). - -The {tail} keyword is only supported by "pair_style"_pair_style.html -pairwise potentials which include Lennard-Jones interactions which are -cutoff at a non-zero energy. This does not include the LJ CHARMM -potentials or {lj/smooth} since they go to zero at the cutoff. The -formulas used for the long-range corrections come from equation 5 of +When the {tail} keyword is set to {yes}, certain pair styles will add +a long-range VanderWaals tail "correction" to the energy and pressure. +See the doc page for individual styles to see which support this +option. These corrections are included in the calculation and +printing of thermodynamic quantities (see the +"thermo_style"_thermo_style.html command). Their effect will also be +included in constant NPT or NPH simulations where the pressure +influences the simulation box dimensions (e.g. the "fix +npt"_fix_npt.html and "fix nph"_fix_nph.html commands). The formulas +used for the long-range corrections come from equation 5 of "(Sun)"_#Sun. Several assumptions are inherent in using tail corrections, including @@ -138,13 +140,8 @@ those interactions. :l,ule [Restrictions:] none -Not all pair styles support mixing. See the doc page for individual -pair styles for details. - You cannot use {shift} yes with {tail} yes, since those are -conflicting options. - -You cannot use {tail} yes with 2d simulations. +conflicting options. You cannot use {tail} yes with 2d simulations. [Related commands:] @@ -153,9 +150,11 @@ You cannot use {tail} yes with 2d simulations. [Default:] -The option defaults are shift = no, mix = arithmetic (for lj/charmm -pair styles), mix = geometric (for other pair styles), table = 12, -and tabinner = sqrt(2.0), tail = no. +The option defaults are mix = geometric, shift = no, table = 12, +tabinner = sqrt(2.0), tail = no. + +Note that some pair styles perform mixing, but only a certain style of +mixing. See the doc pages for individual pair styles for details. :line diff --git a/doc/pair_morse.html b/doc/pair_morse.html index a489fae1e8..0bc9956c01 100644 --- a/doc/pair_morse.html +++ b/doc/pair_morse.html @@ -53,11 +53,37 @@ give identical answers. Depending on system size and the processor you are running on, it may be 5-25% faster (for the pairwise portion of the run time). -Restrictions: +
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info:
-The morse potential does not support the -pair_modify mix option. Coefficients for all i,j -pairs must be specified explicitly. +
None of the Morse pair styles support mixing. Thus, coefficients for +all I,J pairs must be specified explicitly. +
+All of the Morse pair styles support the +pair_modify shift option for the energy of the pair +interaction. +
+The pair_modify table options is not relevant for +the Morse pair styles. +
+None of the Morse pair styles support the +pair_modify tail option for adding long-range tail +corrections to energy and pressure. +
+All of the Morse pair styles can calculate per-atom energy and +stress, as used by the compute epair/atom, +compute stress/atom, and dump +custom commands. +
+All of the Morse pair styles write their information to binary +restart files, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. +
+Restrictions:
The morse/opt style is part of the "opt" package. It is only enabled if LAMMPS was built with that package. See the Making diff --git a/doc/pair_morse.txt b/doc/pair_morse.txt index f673db8a9f..4849968d88 100644 --- a/doc/pair_morse.txt +++ b/doc/pair_morse.txt @@ -49,11 +49,37 @@ give identical answers. Depending on system size and the processor you are running on, it may be 5-25% faster (for the pairwise portion of the run time). -[Restrictions:] +:line -The {morse} potential does not support the -"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j -pairs must be specified explicitly. +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +None of the Morse pair styles support mixing. Thus, coefficients for +all I,J pairs must be specified explicitly. + +All of the Morse pair styles support the +"pair_modify"_pair_modify.html shift option for the energy of the pair +interaction. + +The "pair_modify"_pair_modify.html table options is not relevant for +the Morse pair styles. + +None of the Morse pair styles support the +"pair_modify"_pair_modify.html tail option for adding long-range tail +corrections to energy and pressure. + +All of the Morse pair styles can calculate per-atom energy and +stress, as used by the "compute epair/atom"_compute_epair_atom.html, +"compute stress/atom"_compute_stress_atom.html, and "dump +custom"_dump.html commands. + +All of the Morse pair styles write their information to "binary +restart files"_restart.html, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + +:line + +[Restrictions:] The {morse/opt} style is part of the "opt" package. It is only enabled if LAMMPS was built with that package. See the "Making diff --git a/doc/pair_soft.html b/doc/pair_soft.html index 92a970717e..098d2de85b 100644 --- a/doc/pair_soft.html +++ b/doc/pair_soft.html @@ -39,7 +39,7 @@ cutoff. types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart -commands: +commands, or by mixing as described below:
The last coefficient is optional. If not specified, the global soft cutoff is used.
-If the pair_coeff command is not used to define coefficients for a -particular I != J type pair, the mixing rule for Astart and Astop is -as follows: +
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info:
-A_ij = sqrt(A_i * A_j) -+
For atom type pairs I,J and I != J, the Astart, Astop coefficients and +cutoff distance for this pair style can be mixed. Astart and Atop are +always mixed via a geometric rule. The cutoff is mixed according to +the pair_modify mix value. The default mix value is geometric. See +the "pair_modify" command for details. +
+This pair styles does not support the pair_modify +shift option, since the pair interaction is goes to 0.0 at the cutoff. +
+The pair_modify table and tail options are not +relevant for this pair style. +
+This pair style can calculate per-atom energy and stress, as used by +the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style writes its information to binary restart +files, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. +
+Restrictions: none
Related commands: diff --git a/doc/pair_soft.txt b/doc/pair_soft.txt index 5f1f21b895..6894ced294 100644 --- a/doc/pair_soft.txt +++ b/doc/pair_soft.txt @@ -36,7 +36,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: Astart (energy units) Astop (energy units) @@ -51,11 +51,33 @@ or switch to a new pair style. The last coefficient is optional. If not specified, the global soft cutoff is used. -If the pair_coeff command is not used to define coefficients for a -particular I != J type pair, the mixing rule for Astart and Astop is -as follows: +:line -A_ij = sqrt(A_i * A_j) :pre +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the Astart, Astop coefficients and +cutoff distance for this pair style can be mixed. Astart and Atop are +always mixed via a {geometric} rule. The cutoff is mixed according to +the pair_modify mix value. The default mix value is {geometric}. See +the "pair_modify" command for details. + +This pair styles does not support the "pair_modify"_pair_modify.html +shift option, since the pair interaction is goes to 0.0 at the cutoff. + +The "pair_modify"_pair_modify.html table and tail options are not +relevant for this pair style. + +This pair style can calculate per-atom energy and stress, as used by +the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +:line [Restrictions:] none diff --git a/doc/pair_style.txt b/doc/pair_style.txt index d546574415..9a6384a8a1 100644 --- a/doc/pair_style.txt +++ b/doc/pair_style.txt @@ -14,17 +14,14 @@ pair_style style args :pre style = one of the following :ulb,l -{none}, {hybrid}, {buck}, {buck/coul/cut}, {buck/coul/long}, -{colloid}, {dipole/cut}, {dpd}, {eam}, {eam/opt}, {eam/alloy}, -{eam/alloy/opt}, {eam/fs}, {eam/fs/opt}, {gayberne}, -{gran/hertzian}, {gran/history}, {gran/no_history}, -{lj/charmm/coul/charmm}, {lj/charmm/coul/charmm/opt}, -{lj/charmm/coul/charmm/implicit}, {lj/charmm/coul/long}, -{lj/class2}, {lj/class2/coul/cut}, {lj/class2/coul/long}, -{lj/cut}, {lj/cut/opt}, {lj/cut/coul/cut}, -{lj/cut/coul/debye}, {lj/cut/coul/long}, {lj/cut/coul/long/tip4p}, -{lj/expand}, {lj/smooth}, {meam}, {morse}, {morse/opt}, {soft}, {sw}, {table}, -{tersoff}, {yukawa} :ul +{none}, {hybrid}, {airebo}, {buck}, {buck/coul/cut}, {buck/coul/long}, +{dpd}, {eam}, {eam/alloy} or {eam/fs}, {gran/hertzian}, +{gran/history}, {gran/no_history}, {lj/charmm/coul/charmm}, +{lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long}, +{lj/class2}, {lj/class2/coul/cut} or {lj/class2/coul/long}, {lj/cut}, +{lj/cut/coul/cut} or {lj/cut/coul/debye}, {lj/cut/coul/long}, +{lj/cut/coul/long/tip4p}, {lj/expand}, {lj/smooth}, {meam}, {morse}, +{soft}, {sw}, {table}, {tersoff}, {yukawa} :ul args = arguments used by a particular style :l,ule @@ -49,7 +46,7 @@ In LAMMPS, pairwise force fields encompass a variety of interactions, some of which include many-body effects, e.g. EAM, Stillinger-Weber, Tersoff, REBO potentials. They are still classified as "pairwise" potentials because the set of interacting atoms changes with time -(unlike a bonded system) and thus a neighbor list is used to find +(unlike molecular bonds) and thus a neighbor list is used to find nearby interacting atoms. Hybrid models where specified pairs of atom types interact via @@ -59,9 +56,18 @@ The coefficients associated with a pair style are typically set for each pair of atom types, and are specified by the "pair_coeff"_pair_coeff.html command or read from a file by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands. Mixing, shifting, and tail corrections for the potentials -is discussed is the documentation for the -"pair_modify"_pair_modify.html command. +commands. + +The "pair_modify"_pair_modify.html command sets options for mixing of +type I-J interaction coefficients and adding energy offsets or tail +corrections to Lennard-Jones potentials. Details on these options as +they pertain to individual potentials are described on the doc page +for the potential. Likewise, info on whether the potential +information is stored in a "restart file"_write_restart.html or +whether the potential supports calculation of per-atom energy and +stress by the "compute epair/atom"_compute_epair_atom.html and +"compute stress/atom"_compute_stress_atom.html commands is given on +the potential doc page. In the formulas listed for each pair style, {E} is the energy of a pairwise interaction between two atoms separated by a distance {r}. @@ -92,18 +98,15 @@ the pair_style command, and coefficients specified by the associated "pair_style none"_pair_none.html - turn off pairwise interactions "pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul +"pair_style airebo"_pair_airebo.html - AI-REBO potential "pair_style buck"_pair_buck.html - Buckingham potential "pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb "pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb "pair_style colloid"_pair_colloid.html - integrated colloidal potential -"pair_style dipole/cut"_pair_dpd.html - point dipole potential "pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD) "pair_style eam"_pair_eam.html - embedded atom method (EAM) -"pair_style eam/opt"_pair_eam.html - optimized embedded atom method (EAM) "pair_style eam/alloy"_pair_eam.html - alloy EAM -"pair_style eam/alloy/opt"_pair_eam.html - optimized alloy EAM "pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM -"pair_style eam/fs/opt"_pair_eam.html - optimized Finnis-Sinclair EAM "pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential "pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions "pair_style gran/history"_pair_gran.html - granular potential with history effects @@ -111,12 +114,10 @@ the pair_style command, and coefficients specified by the associated "pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb "pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent "pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb -"pair_style lj/charmm/coul/long/opt"_pair_charmm.html - optimized CHARMM with long-range Coulomb "pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb "pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb "pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb "pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb -"pair_style lj/cut/opt"_pair_lj.html - optimized cutoff Lennard-Jones potential with no Coulomb "pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb "pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye damping added to Coulomb "pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb @@ -125,7 +126,6 @@ the pair_style command, and coefficients specified by the associated "pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM) "pair_style morse"_pair_morse.html - Morse potential -"pair_style morse/opt"_pair_morse.html - optimized Morse potential "pair_style soft"_pair_soft.html - Soft (cosine) potential "pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential "pair_style table"_pair_table.html - tabulated pair potential @@ -142,7 +142,9 @@ This command must be used before any coefficients are set by the Some pair styles are part of specific packages. They are only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. +LAMMPS"_Section_start.html#2_3 section for more info on packages. The +doc pages for individual pair potentials tell if it is part of a +package. [Related commands:] diff --git a/doc/pair_sw.html b/doc/pair_sw.html index 9f3bad4b1b..b33623832b 100644 --- a/doc/pair_sw.html +++ b/doc/pair_sw.html @@ -110,16 +110,44 @@ The parameters used only for two-body interactions (A, B, p, and q) in entries whose 2nd and 3rd element are different (e.g. SiCSi) are not used for anything and can be set to 0.0 if desired.
+Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS as +described above from values in the potential file. +
+This pair style does not support the pair_modify +shift, table, and tail options. +
+This pair style does not calculate per-atom energy and stress, as used +by the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style does not write its information to binary restart +files, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. +
+Restrictions:
-This pair potential requires the newton setting to be -"on" for pair interactions. +
This pair style is part of the "manybody" package. It is only enabled +if LAMMPS was built with that package (which it is by default). See +the Making LAMMPS section for more info. +
+This pair style requires the newton setting to be "on" +for pair interactions.
The Stillinger-Weber potential files provided with LAMMPS (see the potentials directory) are parameterized for metal units. -You can use the SW potential with any LAMMPS units, but you need to -create your own SW potential file if your simulation doesn't use -"metal" units. +You can use the SW potential with any LAMMPS units, but you would need +to create your own SW potential file with coefficients listed in the +appropriate units if your simulation doesn't use "metal" units.
Related commands:
diff --git a/doc/pair_sw.txt b/doc/pair_sw.txt index d2f7c4625c..3797815995 100644 --- a/doc/pair_sw.txt +++ b/doc/pair_sw.txt @@ -107,16 +107,44 @@ The parameters used only for two-body interactions (A, B, p, and q) in entries whose 2nd and 3rd element are different (e.g. SiCSi) are not used for anything and can be set to 0.0 if desired. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS as +described above from values in the potential file. + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This pair style does not calculate per-atom energy and stress, as used +by the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style does not write its information to "binary restart +files"_restart.html, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +:line + [Restrictions:] -This pair potential requires the "newton"_newton.html setting to be -"on" for pair interactions. +This pair style is part of the "manybody" package. It is only enabled +if LAMMPS was built with that package (which it is by default). See +the "Making LAMMPS"_Section_start.html#2_3 section for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. The Stillinger-Weber potential files provided with LAMMPS (see the potentials directory) are parameterized for metal "units"_units.html. -You can use the SW potential with any LAMMPS units, but you need to -create your own SW potential file if your simulation doesn't use -"metal" units. +You can use the SW potential with any LAMMPS units, but you would need +to create your own SW potential file with coefficients listed in the +appropriate units if your simulation doesn't use "metal" units. [Related commands:] diff --git a/doc/pair_table.html b/doc/pair_table.html index 34c78e993f..db24c18de0 100644 --- a/doc/pair_table.html +++ b/doc/pair_table.html @@ -140,11 +140,32 @@ from one line to the next (unless the BITMAP parameter is specified). potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. -Restrictions: +
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info:
-The table potential does not support the -pair_modify mix option. Coefficients for all i,j -pairs must be specified explicitly. +
This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. +
+The pair_modify shift, table, and tail options are +not relevant for this pair style. +
+This pair style can calculate per-atom energy and stress, as used by +the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style writes the settings for the "pair_style table" command +to binary restart files, so a pair_style command does +not need to specified in an input script that reads a restart file. +However, the coefficient information is not stored in the restart +file, since it is tabulated in the potential files. Thus, pair_coeff +commands do need to be specified in the restart input script. +
+Restrictions: none
Related commands:
diff --git a/doc/pair_table.txt b/doc/pair_table.txt index d362690a4b..96c7c15cd2 100644 --- a/doc/pair_table.txt +++ b/doc/pair_table.txt @@ -137,11 +137,32 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. -[Restrictions:] +:line -The {table} potential does not support the -"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j -pairs must be specified explicitly. +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +This pair style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. + +The "pair_modify"_pair_modify.html shift, table, and tail options are +not relevant for this pair style. + +This pair style can calculate per-atom energy and stress, as used by +the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes the settings for the "pair_style table" command +to "binary restart files"_restart.html, so a pair_style command does +not need to specified in an input script that reads a restart file. +However, the coefficient information is not stored in the restart +file, since it is tabulated in the potential files. Thus, pair_coeff +commands do need to be specified in the restart input script. + +:line + +[Restrictions:] none [Related commands:] diff --git a/doc/pair_tersoff.html b/doc/pair_tersoff.html index b60f359447..4a8bf839b3 100644 --- a/doc/pair_tersoff.html +++ b/doc/pair_tersoff.html @@ -113,16 +113,44 @@ The parameters used only for two-body interactions in entries whose 2nd and 3rd element are different (e.g. SiCSi) are not used for anything and can be set to 0.0 if desired. +Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS as +described above from values in the potential file. +
+This pair style does not support the pair_modify +shift, table, and tail options. +
+This pair style does not calculate per-atom energy and stress, as used +by the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style does not write its information to binary restart +files, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. +
+Restrictions:
-This pair potential requires the newton setting to be -"on" for pair interactions. +
This pair style is part of the "manybody" package. It is only enabled +if LAMMPS was built with that package (which it is by default). See +the Making LAMMPS section for more info. +
+This pair style requires the newton setting to be "on" +for pair interactions.
The Tersoff potential files provided with LAMMPS (see the potentials directory) are parameterized for metal units. You can -use the Tersoff potential with any LAMMPS units, but you need to -create your own Tersoff potential file if your simulation doesn't use -"metal" units. +use the Tersoff potential with any LAMMPS units, but you would need to +create your own Tersoff potential file with coefficients listed in the +appropriate units if your simulation doesn't use "metal" units.
Related commands:
diff --git a/doc/pair_tersoff.txt b/doc/pair_tersoff.txt index ad6328498a..6542bf30ed 100644 --- a/doc/pair_tersoff.txt +++ b/doc/pair_tersoff.txt @@ -110,16 +110,44 @@ The parameters used only for two-body interactions in entries whose 2nd and 3rd element are different (e.g. SiCSi) are not used for anything and can be set to 0.0 if desired. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS as +described above from values in the potential file. + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This pair style does not calculate per-atom energy and stress, as used +by the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style does not write its information to "binary restart +files"_restart.html, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +:line + [Restrictions:] -This pair potential requires the "newton"_newton.html setting to be -"on" for pair interactions. +This pair style is part of the "manybody" package. It is only enabled +if LAMMPS was built with that package (which it is by default). See +the "Making LAMMPS"_Section_start.html#2_3 section for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. The Tersoff potential files provided with LAMMPS (see the potentials directory) are parameterized for metal "units"_units.html. You can -use the Tersoff potential with any LAMMPS units, but you need to -create your own Tersoff potential file if your simulation doesn't use -"metal" units. +use the Tersoff potential with any LAMMPS units, but you would need to +create your own Tersoff potential file with coefficients listed in the +appropriate units if your simulation doesn't use "metal" units. [Related commands:] diff --git a/doc/pair_yukawa.html b/doc/pair_yukawa.html index fec92cab22..9f00f84951 100644 --- a/doc/pair_yukawa.html +++ b/doc/pair_yukawa.html @@ -36,7 +36,7 @@ pair_coeff * * 100.0 types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart -commands: +commands, or by mixing as described below:The last coefficient is optional. If not specified, the global yukawa cutoff is used.
+Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+For atom type pairs I,J and I != J, the A coefficient and cutoff +distance for this pair style can be mixed. A is an energy value mixed +like a LJ epsilon. The default mix value is geometric. See the +"pair_modify" command for details. +
+This pair style supports the pair_modify shift +option for the energy of the pair interaction. +
+The pair_modify table option is not relevant +for this pair style. +
+This pair style does not support the pair_modify +tail option for adding long-range tail corrections to energy and +pressure. +
+This pair style can calculate per-atom energy and stress, as used by +the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style writes its information to binary restart +files, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. +
+Restrictions: none
Related commands: diff --git a/doc/pair_yukawa.txt b/doc/pair_yukawa.txt index 1e692b1cb3..7c72ccbb5d 100644 --- a/doc/pair_yukawa.txt +++ b/doc/pair_yukawa.txt @@ -33,7 +33,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: A (energy units) cutoff (distance units) :ul @@ -41,6 +41,37 @@ cutoff (distance units) :ul The last coefficient is optional. If not specified, the global yukawa cutoff is used. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the A coefficient and cutoff +distance for this pair style can be mixed. A is an energy value mixed +like a LJ epsilon. The default mix value is {geometric}. See the +"pair_modify" command for details. + +This pair style supports the "pair_modify"_pair_modify.html shift +option for the energy of the pair interaction. + +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. + +This pair style does not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style can calculate per-atom energy and stress, as used by +the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +:line + [Restrictions:] none [Related commands:] diff --git a/doc/read_restart.txt b/doc/read_restart.txt index 48a94a6950..04a4e8d795 100644 --- a/doc/read_restart.txt +++ b/doc/read_restart.txt @@ -24,8 +24,9 @@ read_restart poly.*.% :pre [Description:] -Read in a previously saved problem from a restart file. This allows -continuation of a previous run. +Read in a previously saved simulation from a restart file. This +allows continuation of a previous run. Information about what is +stored in a restart file is given below. Restart files are saved in binary format to enable exact restarts, meaning that the trajectories of a restarted run will precisely match @@ -36,11 +37,11 @@ include running on a different number of processors or changing certain settings such as those set by the "newton"_newton.html or "processors"_processors.html commands. LAMMPS will issue a WARNING in these cases. Certain fixes will also not restart exactly, though they -should provide statistically similar results. These include the shake -and langevin styles. If a restarted run is immediately different than -the run which produced the restart file, it could be a LAMMPS bug, so -consider "reporting it"_Section_errors.html#9_2 if you think the -behavior is wrong. +should provide statistically similar results. These include "fix +shake"_fix_shake.html and "fix langevin"_fix_langevin.html. If a +restarted run is immediately different than the run which produced the +restart file, it could be a LAMMPS bug, so consider "reporting +it"_Section_errors.html#9_2 if you think the behavior is wrong. Because restart files are binary, they may not be portable to other machines. They can be converted to ASCII data files using the @@ -74,36 +75,39 @@ current LAMMPS simulation. :line -A restart file stores the units and atom style, simulation box -attibutes (including whether it is an orthogonal box or a -non-orthogonal parallelepiped with triclinic symmetry), individual -atoms and their attributes including molecular topology, force field -styles and coefficients, "special_bonds"_special_bonds.html settings, -and atom group definitions. This means that commands for these -quantities do not need to be specified in your input script that reads -the restart file. The exceptions to this are listed below in the -Restrictions section. +A restart file stores the following information about a simulation: +units and atom style, simulation box size and shape and boundary +settings, group definitions, atom type settings such as mass and +particle shape, individual atoms and their group assignments and +molecular topology attributes, force field styles and coefficients, +and "special_bonds"_special_bonds.html settings. This means that +commands for these quantities do not need to be re-specified in the +input script that reads the restart file, though you can redefine +settings after the restart file is read. -Information about the "kspace_style"_kspace_style.html settings are -not stored in the restart file. Hence if you wish to invoke an Ewald -or PPPM solver, this command must be re-issued after the restart file -is read. +One exception is that some pair styles do not store their info in +restart files. The doc pages for individual pair styles note if this +is the case. This is also true of bond_style hybrid (and angle_style, +dihedral_style, improper_style hybrid). -The restart file also stores values for any fixes that require state -information to enable restarting where they left off. These include -the {nvt} and {npt} styles that have a global state, as well as the -{msd} and {wall/gran} styles that store information about each atom. +Information about "kspace_style"_kspace_style.html settings are not +stored in the restart file. Hence if you wish to use an Ewald or PPPM +solver, these commands must be re-issued after the restart file is +read. -"Fix"_fix.html commands are not stored in the restart file which means -they must be specified in the input script that reads the restart -file. To re-enable a fix whose state was stored in the restart file, -the fix command in the new input script must use the same fix-ID and -group-ID as the input script that wrote the restart file. LAMMPS will -print a message indicating that the fix is being re-enabled. - -Note that no other information is stored in the restart file. This -means that your new input script should specify settings for -quantities like timestep size, thermodynamic and dump output, etc. +The list of "fixes"_fix.html used for a simulation is not stored in +the restart file. This means the new input script should specify all +fixes it will use. Note that some fixes store an internal "state" +which is written to the restart file. This allows the fix to continue +on with its calculations in a restarted simulation. To re-enable such +a fix, the fix command in the new input script must use the same +fix-ID and group-ID as 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. See the doc pages for +individual fixes for info on which ones can be restarted in this +manner. Bond interactions (angle, etc) that have been turned off by the "fix shake"_fix_shake.html or "delete_bonds"_delete_bonds.html command will @@ -115,15 +119,13 @@ Bonds that are broken (e.g. by a bond-breaking potential) are written to the restart file as broken bonds with a type of 0. Thus these bonds will still be broken when the restart file is read. -[Restrictions:] +IMPORTANT NOTE: No other information is stored in the restart file. +This means that an input script that reads a restart file should +specify settings for quantities like "timestep size"_timestep.html, +"thermodynamic"_thermo_style.html and "dump"_dump.html output, +"geometric regions"_region.html, etc. -The "pair_style"_pair_style.html {eam}, {table}, and {hybrid} styles -do not store coefficient data for individual atom type pairs in the -restart file. Nor does the "bond_style hybrid"_bond_style.html style -(angle, dihedral hybrid, etc). Thus for these styles you must use new -"pair_coeff"_pair_coeff.html and "bond_coeff"_bond_coeff.html (angle, -dihedral, etc) commands to read the appropriate tabulated files or -reset the coefficients after the restart file is read. +[Restrictions:] none [Related commands:] diff --git a/doc/run.html b/doc/run.html index 202b0dafde..1d48c29962 100644 --- a/doc/run.html +++ b/doc/run.html @@ -65,14 +65,12 @@ script with the same run command until the simulation finally completes.
The start or stop keywords can be used if multiple runs are being -performed and you want a fix command that ramps some value -(e.g. a temperature) over time to do its ramping across the entire set -of runs and not just a single run. Fixes in this category include -fix nvt, fix npt, fix -langevin, fix temp/rescale, -fix deform, and fix indent. The -pair_style soft potential also ramps its -coefficients in a similar way. +performed and you want a fix command that changes some +value over time (e.g. temperature) to make the change across the +entire set of runs and not just a single run. See the doc page for +individual fixes to see which ones can be used with the start/stop +keywords. The pair_style soft potential also +changes its pair potential coefficients in this manner.
For example, consider this fix followed by 10 run commands:
diff --git a/doc/run.txt b/doc/run.txt index 8568ad401d..a53cdc34d3 100644 --- a/doc/run.txt +++ b/doc/run.txt @@ -58,14 +58,12 @@ script with the same run command until the simulation finally completes. The {start} or {stop} keywords can be used if multiple runs are being -performed and you want a "fix"_fix.html command that ramps some value -(e.g. a temperature) over time to do its ramping across the entire set -of runs and not just a single run. Fixes in this category include -"fix nvt"_fix_nvt.html, "fix npt"_fix_npt.html, "fix -langevin"_fix_langevin.html, "fix temp/rescale"_fix_temp_rescale.html, -"fix deform"_fix_deform.html, and "fix indent"_fix_indent.html. The -"pair_style soft"_pair_style.html potential also ramps its -coefficients in a similar way. +performed and you want a "fix"_fix.html command that changes some +value over time (e.g. temperature) to make the change across the +entire set of runs and not just a single run. See the doc page for +individual fixes to see which ones can be used with the {start/stop} +keywords. The "pair_style soft"_pair_style.html potential also +changes its pair potential coefficients in this manner. For example, consider this fix followed by 10 run commands: diff --git a/doc/thermo_modify.txt b/doc/thermo_modify.txt index 67e60be88e..432b3a4137 100644 --- a/doc/thermo_modify.txt +++ b/doc/thermo_modify.txt @@ -41,11 +41,11 @@ Set options for how thermodynamic information is computed and printed by LAMMPS. IMPORTANT NOTE: These options apply to the currently defined thermo -style (thermo_style {one} by default). When you specify a -"thermo_style"_thermo_style.html command, all thermodynamic settings -are restored to their default values. Thus a thermo_style command -will wipe out any options previously specified by the -"thermo_modify"_thermo_modify.html command. +style. When you specify a "thermo_style"_thermo_style.html command, +all thermodynamic settings are restored to their default values, +including those previously set by a thermo_modify command. Thus if +your input script specifies a thermo_style command, you should use the +thermo_modify command after it. The {lost} keyword determines whether LAMMPS checks for lost atoms each time it computes thermodynamics and what it does if atoms are diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt index b309594c4f..8a5c4efc2f 100644 --- a/doc/thermo_style.txt +++ b/doc/thermo_style.txt @@ -102,11 +102,11 @@ be used to set the one- or multi-line format of the print-out, the normalization of energy quantities (total or per-atom), and the numeric precision of each printed value. -IMPORTANT NOTE: When you specify a "thermo_style"_thermo_style.html -command, all thermodynamic settings are restored to their default -values. Thus a thermo_style command will wipe out any options -previously specified by the "thermo_modify"_thermo_modify.html -command. +IMPORTANT NOTE: When you specify a "thermo_style" command, all +thermodynamic settings are restored to their default values, including +those previously set by a :thermo_modify"_thermo_modify.html command. +Thus if your input script specifies a thermo_style command, you should +use the thermo_modify command after it. :line @@ -198,24 +198,29 @@ The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector quantities calculated by a compute to be output. The ID in the keyword should be replaced by the actual ID of the compute that has been defined elsewhere in the input script. See the "compute"_compute.html command -for details. Note that per-atom quantities calcalated by a compute -cannot be output as part of thermodynamics. Rather, these quantities -are output by the "dump custom"_dump.html command. +for details. Note that only global scalar or vector quantites +calculated by a compute can be output as thermodynamic data; per-atom +quantities calcalated by a compute are output by the "dump +custom"_dump.html command. If {c_ID} is used as a keyword, then the scalar quantity calculated by the compute is printed. If {c_ID\[N\]} is used, then N in the range from 1-M will print the Nth component of the M-length vector -calculated by the compute. +calculated by the compute. See the doc pages for individual compute +styles for info on what these quantities are. The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector quantities calculated by a fix to be output. The ID in the keyword should be replaced by the actual ID of the fix that has been defined elsewhere -in the input script. See the "fix"_fix.html command for details. +in the input script. If {f_ID} is used as a keyword, then the scalar quantity calculated by the fix is printed. If {f_ID\[N\]} is used, then N in the range from 1-M will print the Nth component of the M-length vector calculated by -the fix. +the fix. See the doc pages for individual fix styles for info on what +these quantities are. For fixes that compute a contribution to the +potential energy of the system, the scalar quantity f_ID is typically +that quantity. The {v_name} keyword allow the current value of a variable to be output. The name in the keyword should be replaced by the actual namd @@ -228,7 +233,8 @@ periodically during a simulation. See "this section"_Section_modify.html for information on how to add new compute and fix styles as well as variable options to LAMMPS that -calculate quantities that could then be output with these keywords. +calculate quantities that could then be output with these keywords as +part of thermodyanmic information. :line