From 358134485ab44f6ac251fac0ef5617ab7b6a95ce Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 30 Nov 2007 21:58:15 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1194 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.txt | 4 +-- doc/compute.txt | 3 +- doc/compute_ebond_atom.html | 51 ------------------------------- doc/compute_ebond_atom.txt | 46 ---------------------------- doc/compute_epair_atom.html | 58 ----------------------------------- doc/compute_epair_atom.txt | 53 -------------------------------- doc/fix.txt | 1 - doc/fix_gran_diag.html | 61 ------------------------------------- doc/fix_gran_diag.txt | 56 ---------------------------------- 9 files changed, 2 insertions(+), 331 deletions(-) delete mode 100644 doc/compute_ebond_atom.html delete mode 100644 doc/compute_ebond_atom.txt delete mode 100644 doc/compute_epair_atom.html delete mode 100644 doc/compute_epair_atom.txt delete mode 100644 doc/fix_gran_diag.html delete mode 100644 doc/fix_gran_diag.txt diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 963f2df329..91b93d4ce9 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -388,7 +388,6 @@ of each style or click on the style itself for a full description: "efield"_fix_efield.html, "enforce2d"_fix_enforce2d.html, "freeze"_fix_freeze.html, -"gran/diag"_fix_gran_diag.html, "gravity"_fix_gravity.html, "gyration"_fix_gyration.html, "heat"_fix_heat.html, @@ -441,10 +440,9 @@ description: "attribute/atom"_compute_attribute_atom.html, "centro/atom"_compute_centro_atom.html, "coord/atom"_compute_coord_atom.html, -"ebond/atom"_compute_ebond_atom.html, -"epair/atom"_compute_epair_atom.html, "ke/atom"_compute_ke_atom.html, "pe"_compute_pe.html, +"pe/atom"_compute_pe_atom.html, "pressure"_compute_pressure.html, "rotate/dipole"_compute_rotate_dipole.html, "rotate/gran"_compute_rotate_gran.html, diff --git a/doc/compute.txt b/doc/compute.txt index 67c4799443..450da73f55 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -90,10 +90,9 @@ defined in LAMMPS: "attribute/atom"_compute_attribute_atom.html - attribute (x,v,f,etc) of each atom "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "coord/atom"_compute_coord_atom.html - coordination number for each atom -"ebond/atom"_compute_ebond_atom.html - bond energy for each atom -"epair/atom"_compute_epair_atom.html - pairwise energy for each atom "ke/atom"_compute_ke_atom.html - kinetic energy for each atom "pe"_compute_pe.html - potential energy +"pe"_compute_pe.html - potential energy for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor "rotate/dipole"_compute_rotate_dipole.html - rotational energy of dipolar atoms "rotate/gran"_compute_rotate_gran.html - rotational energy of granular atoms diff --git a/doc/compute_ebond_atom.html b/doc/compute_ebond_atom.html deleted file mode 100644 index d39417d97c..0000000000 --- a/doc/compute_ebond_atom.html +++ /dev/null @@ -1,51 +0,0 @@ - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
- - - - - - -
- -

compute ebond/atom command -

-

Syntax: -

-
compute ID group-ID ebond/atom 
-
- -

Examples: -

-
compute 1 all ebond/atom 
-
-

Description: -

-

Define a computation that computes the per-atom bond energy for each -atom in a group. -

-

The bond energy for each atom is computed by looping over the atoms it -is bonded to and computing the bond energy associated with the defined -bond_style command for each I-J bond (divided by 2). -Thus the sum of per-atom bond energy for all atoms should give the -total bond energy of the system. -

-

If two atoms are bonded and only one of them is in the compute group, -the energy of the bond is included in the per-atom energy of the atom -in the group. -

-

Computation of per-atom bond energy requires a loop thru the bond list -and inter-processor communication, so it can be inefficient to -compute/dump this quantity too frequently or to have multiple -compute/dump commands, each of a ebond/atom style. -

-

Restrictions: none -

-

Related commands: none -

-

Default: none -

- diff --git a/doc/compute_ebond_atom.txt b/doc/compute_ebond_atom.txt deleted file mode 100644 index 5f7710dfd1..0000000000 --- a/doc/compute_ebond_atom.txt +++ /dev/null @@ -1,46 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute ebond/atom command :h3 - -[Syntax:] - -compute ID group-ID ebond/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -ebond/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all ebond/atom :pre - -[Description:] - -Define a computation that computes the per-atom bond energy for each -atom in a group. - -The bond energy for each atom is computed by looping over the atoms it -is bonded to and computing the bond energy associated with the defined -"bond_style"_bond_style.html command for each I-J bond (divided by 2). -Thus the sum of per-atom bond energy for all atoms should give the -total bond energy of the system. - -If two atoms are bonded and only one of them is in the compute group, -the energy of the bond is included in the per-atom energy of the atom -in the group. - -Computation of per-atom bond energy requires a loop thru the bond list -and inter-processor communication, so it can be inefficient to -compute/dump this quantity too frequently or to have multiple -compute/dump commands, each of a {ebond/atom} style. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none diff --git a/doc/compute_epair_atom.html b/doc/compute_epair_atom.html deleted file mode 100644 index eabdf3131e..0000000000 --- a/doc/compute_epair_atom.html +++ /dev/null @@ -1,58 +0,0 @@ - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
- - - - - - -
- -

compute epair/atom command -

-

Syntax: -

-
compute ID group-ID epair/atom 
-
- -

Examples: -

-
compute 1 all epair/atom 
-
-

Description: -

-

Define a computation that computes the per-atom pairwise energy for -each atom in a group. -

-

The pairwise energy for each atom is computed by looping over its -neighbors and computing the energy associated with the defined -pair_style command for each I,J pair (divided by 2). -Thus the sum of per-atom energy for all atoms should give the total -pairwise energy of the system. -

-

If two atoms interact and only one of them is in the compute group, -the energy of the pairwise interaction is included in the per-atom -energy of the atom in the group. -

-

For force fields that include a contribution to the pairwise energy -that is computed as part of dihedral terms (i.e. 1-4 interactions), -this contribution is NOT included in the per-atom pairwise energy. -

-

Computation of per-atom pairwise energy requires a loop thru the -neighbor list and inter-processor communication, so it can be -inefficient to compute/dump this quantity too frequently or to have -multiple compute/dump commands, each of a epair/atom style. -

-

Restrictions: -

-

Some pair potentials do not allow the calculation of per-atom energy -via this command. An error will be generated if this is the case. -

-

Related commands: none -

-

Default: none -

- diff --git a/doc/compute_epair_atom.txt b/doc/compute_epair_atom.txt deleted file mode 100644 index 14dea3b9bc..0000000000 --- a/doc/compute_epair_atom.txt +++ /dev/null @@ -1,53 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -compute epair/atom command :h3 - -[Syntax:] - -compute ID group-ID epair/atom :pre - -ID, group-ID are documented in "compute"_compute.html command -epair/atom = style name of this compute command :ul - -[Examples:] - -compute 1 all epair/atom :pre - -[Description:] - -Define a computation that computes the per-atom pairwise energy for -each atom in a group. - -The pairwise energy for each atom is computed by looping over its -neighbors and computing the energy associated with the defined -"pair_style"_pair_style.html command for each I,J pair (divided by 2). -Thus the sum of per-atom energy for all atoms should give the total -pairwise energy of the system. - -If two atoms interact and only one of them is in the compute group, -the energy of the pairwise interaction is included in the per-atom -energy of the atom in the group. - -For force fields that include a contribution to the pairwise energy -that is computed as part of dihedral terms (i.e. 1-4 interactions), -this contribution is NOT included in the per-atom pairwise energy. - -Computation of per-atom pairwise energy requires a loop thru the -neighbor list and inter-processor communication, so it can be -inefficient to compute/dump this quantity too frequently or to have -multiple compute/dump commands, each of a {epair/atom} style. - -[Restrictions:] - -Some pair potentials do not allow the calculation of per-atom energy -via this command. An error will be generated if this is the case. - -[Related commands:] none - -[Default:] none diff --git a/doc/fix.txt b/doc/fix.txt index 15f1a70249..88ece7afac 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -91,7 +91,6 @@ Here is an alphabetic list of fix styles available in LAMMPS: "efield"_fix_efield.html - impose electric field on system "enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force "freeze"_fix_freeze.html - freeze atoms in a granular simulation -"gran/diag"_fix_gran_diag.html - compute granular diagnostics "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation "gyration"_fix_gyration.html - compute radius of gyration "heat"_fix_heat.html - add/subtract momentum-conserving heat diff --git a/doc/fix_gran_diag.html b/doc/fix_gran_diag.html deleted file mode 100644 index 83b3ed602e..0000000000 --- a/doc/fix_gran_diag.html +++ /dev/null @@ -1,61 +0,0 @@ - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
- - - - - - -
- -

fix gran/diag command -

-

Syntax: -

-
fix ID group-ID gran/diag nevery file layer 
-
- -

Examples: -

-
fix 1 all gran/diag 1000 tmp 0.9 
-
-

Description: -

-

Compute aggregate density, velocity, and stress diagnostics for a -group of granular atoms as a function of depth in the granular system. -"Depth" means the z-dimension for a 3d simulation, and the y-dimension -for a 2d simulation. The results are written to 3 files named -file.den, file.vel, and file.str. The bins begin at the bottom of the -system and extend upward with a thickness of layer for each bin. -The quantities written to the file are averaged over all atoms in the -bin. -

-

Restart, fix_modify, 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 global scalar or vector or per-atom -quantities are stored by this fix for access by various output -commands. 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. -

-

Related commands: -

-

atom_style granular -

-

Default: none -

- diff --git a/doc/fix_gran_diag.txt b/doc/fix_gran_diag.txt deleted file mode 100644 index cd4976ab5b..0000000000 --- a/doc/fix_gran_diag.txt +++ /dev/null @@ -1,56 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -fix gran/diag command :h3 - -[Syntax:] - -fix ID group-ID gran/diag nevery file layer :pre - -ID, group-ID are documented in "fix"_fix.html command -gran/diag = style name of this fix command -nevery = compute diagnostics every this many timesteps -file = filename to store diagnostic info in -layer = bin size in z-dimension (3d) or y-dimension (2d) :ul - -[Examples:] - -fix 1 all gran/diag 1000 tmp 0.9 :pre - -[Description:] - -Compute aggregate density, velocity, and stress diagnostics for a -group of granular atoms as a function of depth in the granular system. -"Depth" means the z-dimension for a 3d simulation, and the y-dimension -for a 2d simulation. The results are written to 3 files named -file.den, file.vel, and file.str. The bins begin at the bottom of the -system and extend upward with a thickness of {layer} for each bin. -The quantities written to the file are averaged over all atoms in the -bin. - -[Restart, fix_modify, 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 global scalar or vector or per-atom -quantities are stored by this fix for access by various "output -commands"_Section_howto.html#4_15. 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. - -[Related commands:] - -"atom_style granular"_atom_style.html - -[Default:] none