From eaa65992c5968df1912db7f6183ba4ec9b6def70 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 15 Feb 2011 21:14:11 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5654 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_orient_fcc.html | 7 ++++++- doc/fix_orient_fcc.txt | 7 ++++++- doc/fix_rigid.html | 19 +++++++++++++------ doc/fix_rigid.txt | 19 +++++++++++++------ doc/set.html | 17 +++++++++-------- doc/set.txt | 17 +++++++++-------- 6 files changed, 56 insertions(+), 30 deletions(-) diff --git a/doc/fix_orient_fcc.html b/doc/fix_orient_fcc.html index a27d9a6811..99ab333eca 100644 --- a/doc/fix_orient_fcc.html +++ b/doc/fix_orient_fcc.html @@ -126,11 +126,16 @@ 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.

-

This fix computes a global scalar which can be accessed by various +

This fix calculates a global scalar which can be accessed by various output commands. The scalar is the potential energy change due to this fix. The scalar value calculated by this fix is "extensive".

+

This fix also calculates a per-atom array which can be accessed by +various output commands. The array stores +the order parameter Xi and normalized order parameter (0 to 1) for +each atom. The per-atom values can be accessed on any timestep. +

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. diff --git a/doc/fix_orient_fcc.txt b/doc/fix_orient_fcc.txt index 6918453b4f..4b634e8d5c 100644 --- a/doc/fix_orient_fcc.txt +++ b/doc/fix_orient_fcc.txt @@ -123,11 +123,16 @@ 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. -This fix computes a global scalar which can be accessed by various +This fix calculates a global scalar which can be accessed by various "output commands"_Section_howto.html#4_15. The scalar is the potential energy change due to this fix. The scalar value calculated by this fix is "extensive". +This fix also calculates a per-atom array which can be accessed by +various "output commands"_Section_howto.html#4_15. The array stores +the order parameter Xi and normalized order parameter (0 to 1) for +each atom. The per-atom values can be accessed on any timestep. + 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. diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index 13b63adb7f..30b76c1867 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -148,6 +148,18 @@ different molecule ID is treated as a rigid body. separate rigid body. Only atoms that are also in the fix group are included in each rigid body.

+

IMPORTANT NOTE: To compute the initial center-of-mass position and +other properties of each rigid body, the image flags for each atom in +the body are used to "unwrap" the atom coordinates. Thus you must +insure that these image flags are consistent so that the unwrapping +creates a valid rigid body (one where the atoms are close together), +particularly if the atoms in a single rigid body straddle a periodic +boundary. This means the input data file or restart file must define +the image flags for each atom consistently or that you have used the +set command to specify them correctly. If a dimension is +non-periodic then the image flag of each atom must be 0 in that +dimension, else an error is generated. +

By default, each rigid body is acted on by other atoms which induce an external force and torque on its center of mass, causing it to translate and rotate. Components of the external center-of-mass force @@ -285,7 +297,7 @@ cumulative energy change due to the thermostatting the fix performs.

All of these fixes compute a global array of values which can be accessed by various output commands. The number of rows in the array is equal to the number of rigid bodies. -The number of columns is 15. Thus for each rigid body, 12 values are +The number of columns is 15. Thus for each rigid body, 15 values are stored: the xyz coords of the center of mass (COM), the xyz components of the COM velocity, the xyz components of the force acting on the COM, the xyz components of the torque acting on the COM, and the xyz @@ -315,11 +327,6 @@ proportional in length to the number of rigid bodies. Hence they will not scale well in parallel if large numbers of rigid bodies are simulated.

-

If the atoms in a single rigid body initially straddle a periodic -boundary, the input data file must define the image flags for each -atom correctly, so that LAMMPS can "unwrap" the atoms into a valid -rigid body. -

Related commands:

delete_bonds, neigh_modify diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt index f224b605fa..f304e6083c 100644 --- a/doc/fix_rigid.txt +++ b/doc/fix_rigid.txt @@ -137,6 +137,18 @@ For bodystyle {group}, each of the listed groups is treated as a separate rigid body. Only atoms that are also in the fix group are included in each rigid body. +IMPORTANT NOTE: To compute the initial center-of-mass position and +other properties of each rigid body, the image flags for each atom in +the body are used to "unwrap" the atom coordinates. Thus you must +insure that these image flags are consistent so that the unwrapping +creates a valid rigid body (one where the atoms are close together), +particularly if the atoms in a single rigid body straddle a periodic +boundary. This means the input data file or restart file must define +the image flags for each atom consistently or that you have used the +"set"_set.html command to specify them correctly. If a dimension is +non-periodic then the image flag of each atom must be 0 in that +dimension, else an error is generated. + By default, each rigid body is acted on by other atoms which induce an external force and torque on its center of mass, causing it to translate and rotate. Components of the external center-of-mass force @@ -274,7 +286,7 @@ cumulative energy change due to the thermostatting the fix performs. All of these fixes compute a global array of values which can be accessed by various "output commands"_Section_howto.html#4_15. The number of rows in the array is equal to the number of rigid bodies. -The number of columns is 15. Thus for each rigid body, 12 values are +The number of columns is 15. Thus for each rigid body, 15 values are stored: the xyz coords of the center of mass (COM), the xyz components of the COM velocity, the xyz components of the force acting on the COM, the xyz components of the torque acting on the COM, and the xyz @@ -304,11 +316,6 @@ proportional in length to the number of rigid bodies. Hence they will not scale well in parallel if large numbers of rigid bodies are simulated. -If the atoms in a single rigid body initially straddle a periodic -boundary, the input data file must define the image flags for each -atom correctly, so that LAMMPS can "unwrap" the atoms into a valid -rigid body. - [Related commands:] "delete_bonds"_delete_bonds.html, "neigh_modify"_neigh_modify.html diff --git a/doc/set.html b/doc/set.html index a9a00467b4..aa6cd5054c 100644 --- a/doc/set.html +++ b/doc/set.html @@ -156,14 +156,15 @@ PeriDynamics), then it also sets their mass. by PeriDynamics.

Keyword image sets which image of the simulation box the atom is -considered to be in. It is only applied to periodic dimensions. An -image of 0 means it is inside the box as defined. A value of 2 means -add 2 box lengths to get the true value. A value of -1 means subtract -1 box length to get the true value. LAMMPS updates these flags as -atoms cross periodic boundaries during the simulation. The flags can -be output with atom snapshots via the dump command. If a -value of NULL is specified for any of nx,ny,nz, then the current image -value for that dimension is unchanged. +considered to be in. An image of 0 means it is inside the box as +defined. A value of 2 means add 2 box lengths to get the true value. +A value of -1 means subtract 1 box length to get the true value. +LAMMPS updates these flags as atoms cross periodic boundaries during +the simulation. The flags can be output with atom snapshots via the +dump command. If a value of NULL is specified for any of +nx,ny,nz, then the current image value for that dimension is +unchanged. For non-periodic dimensions only a value of 0 is allowed +to be specified.

This command can be useful after a system has been equilibrated and atoms have diffused one or more box lengths in various directions. diff --git a/doc/set.txt b/doc/set.txt index fb95462190..99fb89344f 100644 --- a/doc/set.txt +++ b/doc/set.txt @@ -150,14 +150,15 @@ Keyword {volume} sets the volume of all selected particles, as defined by PeriDynamics. Keyword {image} sets which image of the simulation box the atom is -considered to be in. It is only applied to periodic dimensions. An -image of 0 means it is inside the box as defined. A value of 2 means -add 2 box lengths to get the true value. A value of -1 means subtract -1 box length to get the true value. LAMMPS updates these flags as -atoms cross periodic boundaries during the simulation. The flags can -be output with atom snapshots via the "dump"_dump.html command. If a -value of NULL is specified for any of nx,ny,nz, then the current image -value for that dimension is unchanged. +considered to be in. An image of 0 means it is inside the box as +defined. A value of 2 means add 2 box lengths to get the true value. +A value of -1 means subtract 1 box length to get the true value. +LAMMPS updates these flags as atoms cross periodic boundaries during +the simulation. The flags can be output with atom snapshots via the +"dump"_dump.html command. If a value of NULL is specified for any of +nx,ny,nz, then the current image value for that dimension is +unchanged. For non-periodic dimensions only a value of 0 is allowed +to be specified. This command can be useful after a system has been equilibrated and atoms have diffused one or more box lengths in various directions.