From 7baaf2dfe2103cf573d3a76afe3b1538a2466be8 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 9 May 2016 20:20:41 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14970 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/compute_dpd.html | 2 +- doc/html/compute_gyration.html | 2 +- doc/html/compute_gyration_chunk.html | 2 +- doc/html/compute_heat_flux.html | 4 ++-- doc/html/compute_msd_nongauss.html | 2 +- doc/html/compute_pressure.html | 2 +- doc/html/compute_stress_atom.html | 2 +- doc/html/create_atoms.html | 2 +- doc/html/dump_image.html | 6 +++--- doc/html/fix_nh.html | 18 +++++++++--------- doc/html/fix_wall.html | 2 +- doc/html/genindex.html | 4 ++++ doc/html/pair_airebo.html | 2 +- doc/html/pair_bop.html | 2 +- doc/html/pair_comb.html | 2 +- doc/html/pair_dipole.html | 2 +- doc/html/pair_eam.html | 6 +++--- doc/html/pair_edip.html | 2 +- doc/html/pair_eff.html | 2 +- doc/html/pair_eim.html | 2 +- doc/html/pair_meam.html | 2 +- doc/html/pair_meam_spline.html | 2 +- doc/html/pair_meam_sw_spline.html | 2 +- doc/html/pair_mgpt.html | 2 +- doc/html/pair_polymorphic.html | 2 +- doc/html/pair_sw.html | 2 +- doc/html/pair_tersoff.html | 2 +- doc/html/pair_tersoff_mod.html | 2 +- doc/html/pair_tersoff_zbl.html | 2 +- doc/html/pair_vashishta.html | 2 +- doc/html/pair_zbl.html | 2 +- 31 files changed, 47 insertions(+), 43 deletions(-) diff --git a/doc/html/compute_dpd.html b/doc/html/compute_dpd.html index 12e58daa9f..ddab1ca7a8 100644 --- a/doc/html/compute_dpd.html +++ b/doc/html/compute_dpd.html @@ -160,7 +160,7 @@ relations:

U, dpdTheta, N_particles), which can be accessed by indices 1-5. See this section for an overview of LAMMPS output options.

-

The vector values will be in energy and temperature units.

+

The vector values will be in energy and temperature units.

Restrictions

diff --git a/doc/html/compute_gyration.html b/doc/html/compute_gyration.html index 5958bda2d9..9d92b09b0d 100644 --- a/doc/html/compute_gyration.html +++ b/doc/html/compute_gyration.html @@ -177,7 +177,7 @@ vector values from a compute as input. See units respectively.

+distance^2 units respectively.

Restrictions

diff --git a/doc/html/compute_gyration_chunk.html b/doc/html/compute_gyration_chunk.html index 4105254e76..388ee64c04 100644 --- a/doc/html/compute_gyration_chunk.html +++ b/doc/html/compute_gyration_chunk.html @@ -209,7 +209,7 @@ input. See

All the vector or array values calculated by this compute are “intensive”. The vector or array values will be in distance -units, since they are the square root of values +units, since they are the square root of values represented by the formula above.

diff --git a/doc/html/compute_heat_flux.html b/doc/html/compute_heat_flux.html index 5af22ca900..6357ed4531 100644 --- a/doc/html/compute_heat_flux.html +++ b/doc/html/compute_heat_flux.html @@ -212,9 +212,9 @@ the simulation. Note that if the compute is “all”, then the appropriate volume to divide by is the simulation box volume. However, if a sub-group is used, it should be the volume containing those atoms.

-

The vector values will be in energy*velocity units. Once +

The vector values will be in energy*velocity units. Once divided by a volume the units will be that of flux, namely -energy/area/time units

+energy/area/time units

Restrictions

diff --git a/doc/html/compute_msd_nongauss.html b/doc/html/compute_msd_nongauss.html index 056dd59073..a185b2a470 100644 --- a/doc/html/compute_msd_nongauss.html +++ b/doc/html/compute_msd_nongauss.html @@ -177,7 +177,7 @@ accessed by indices 1-3 by any command that uses global vector values from a compute as input. See this section for an overview of LAMMPS output options.

The vector values are “intensive”. The first vector value will be in -distance^2 units, the second is in distance^4 units, and +distance^2 units, the second is in distance^4 units, and the 3rd is dimensionless.

diff --git a/doc/html/compute_pressure.html b/doc/html/compute_pressure.html index 62864812f2..cdee346c85 100644 --- a/doc/html/compute_pressure.html +++ b/doc/html/compute_pressure.html @@ -229,7 +229,7 @@ or vector values from a compute as input. See

The scalar and vector values calculated by this compute are “intensive”. The scalar and vector values will be in pressure -units.

+units.

Restrictions

diff --git a/doc/html/compute_stress_atom.html b/doc/html/compute_stress_atom.html index d55fe581dc..e99ece1705 100644 --- a/doc/html/compute_stress_atom.html +++ b/doc/html/compute_stress_atom.html @@ -246,7 +246,7 @@ accessed by indices 1-6 by any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.

The per-atom array values will be in pressure*volume -units as discussed above.

+units as discussed above.

Restrictions

diff --git a/doc/html/create_atoms.html b/doc/html/create_atoms.html index d2b1b65049..e7b3d635fd 100644 --- a/doc/html/create_atoms.html +++ b/doc/html/create_atoms.html @@ -363,7 +363,7 @@ rotation.

The units keyword determines the meaning of the distance units used to specify the coordinates of the one particle created by the single style. A box value selects standard distance units as defined by -the units command, e.g. Angstroms for units = real or +the units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings.

diff --git a/doc/html/dump_image.html b/doc/html/dump_image.html index 04e766fde9..d87a864619 100644 --- a/doc/html/dump_image.html +++ b/doc/html/dump_image.html @@ -364,7 +364,7 @@ bodies, as discussed below. These particles can be drawn separately if the line, tri, or body keywords are used.

The adiam keyword allows you to override the diameter setting to set a single numeric size. All atoms will be drawn with that -diameter, e.g. 1.5, which is in whatever distance units +diameter, e.g. 1.5, which is in whatever distance units the input script defines, e.g. Angstroms.

The bond keyword allows to you to alter how bonds are drawn. A bond is only drawn if both atoms in the bond are being drawn due to being @@ -394,7 +394,7 @@ the dump none as indicated above).

If a numeric value is specified, then all bonds will be drawn as cylinders with that diameter, e.g. 1.0, which is in whatever distance -units the input script defines, e.g. Angstroms.

+units the input script defines, e.g. Angstroms.

If atom is specified for the width value, then each bond will be drawn with a width corresponding to the minimum diameter of the 2 atoms in the bond.

@@ -420,7 +420,7 @@ mapping of types to colors is as follows:

change this via the dump_modify command.

The line width can only be a numeric value, which specifies that all lines will be drawn as cylinders with that diameter, e.g. 1.0, which -is in whatever distance units the input script defines, +is in whatever distance units the input script defines, e.g. Angstroms.

The tri keyword can be used when atom_style tri is used to define particles as triangles, and will draw them as triangles diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html index bc140c13ff..bdf5b051b7 100644 --- a/doc/html/fix_nh.html +++ b/doc/html/fix_nh.html @@ -240,11 +240,11 @@ particles will match the target values specified by Tstart/Tstop and Pstart/Pstop.

The equations of motion used are those of Shinoda et al in (Shinoda), which combine the hydrostatic equations of -Martyna, Tobias and Klein in (Martyna) with the strain +Martyna, Tobias and Klein in (Martyna) with the strain energy proposed by Parrinello and Rahman in -(Parrinello). The time integration schemes closely +(Parrinello). The time integration schemes closely follow the time-reversible measure-preserving Verlet and rRESPA -integrators derived by Tuckerman et al in (Tuckerman).

+integrators derived by Tuckerman et al in (Tuckerman).

The thermostat parameters for fix styles nvt and npt is specified using the temp keyword. Other thermostat-related keywords are @@ -257,7 +257,7 @@ ramped value during the run from Tstart to Tstop. The Tda parameter is specified in time units and determines how rapidly the temperature is relaxed. For example, a value of 10.0 means to relax the temperature in a timespan of (roughly) 10 time units (e.g. tau or -fmsec or psec - see the units command). The atoms in the +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 integration.

@@ -267,7 +267,7 @@ of Tdamp. If Tdamp is too small, the temperature can fluctuat wildly; if it is too large, the temperature will take a very long time to equilibrate. A good choice for many models is a Tdamp of around 100 timesteps. Note that this is NOT the same as 100 time units for -most units settings.

+most units settings.

The barostat parameters for fix styles npt and nph is specified @@ -302,7 +302,7 @@ simulation box must be triclinic, even if its initial tilt factors are Tdamp parameter, determining the time scale on which pressure is relaxed. For example, a value of 10.0 means to relax the pressure in a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see -the units command).

+the units command).

Note

A Nose-Hoover barostat will not work well for arbitrary values @@ -311,7 +311,7 @@ fluctuate wildly; if it is too large, the pressure will take a very long time to equilibrate. A good choice for many models is a Pdamp of around 1000 timesteps. However, note that Pdamp is specified in time units, and that timesteps are NOT the same as time units for most -units settings.

+units settings.

Regardless of what atoms are in the fix group (the only atoms which are time integrated), a global pressure or stress tensor is computed @@ -402,7 +402,7 @@ freedom. A value of 0 corresponds to no thermostatting of the barostat variables.

The mtk keyword controls whether or not the correction terms due to Martyna, Tuckerman, and Klein are included in the equations of motion -(Martyna). Specifying no reproduces the original +(Martyna). Specifying no reproduces the original Hoover barostat, whose volume probability distribution function differs from the true NPT and NPH ensembles by a factor of 1/V. Hence using yes is more correct, but in many cases the difference is @@ -411,7 +411,7 @@ negligible.

scheme at little extra cost. The initial and final updates of the thermostat variables are broken up into tloop substeps, each of length dt/tloop. This corresponds to using a first-order -Suzuki-Yoshida scheme (Tuckerman). The keyword ploop +Suzuki-Yoshida scheme (Tuckerman). The keyword ploop does the same thing for the barostat thermostat.

The keyword nreset controls how often the reference dimensions used to define the strain energy are reset. If this keyword is not used, diff --git a/doc/html/fix_wall.html b/doc/html/fix_wall.html index 0931658a23..2c601bc4a5 100644 --- a/doc/html/fix_wall.html +++ b/doc/html/fix_wall.html @@ -294,7 +294,7 @@ variable is used. It is not relevant when EDGE is used to specify a face position. In the variable case, the variable is assumed to produce a value compatible with the units setting you specify.

A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. +units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacings.

diff --git a/doc/html/genindex.html b/doc/html/genindex.html index f2a539cec8..cda2a3aa6c 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -2235,6 +2235,10 @@
unfix
+ +
units +
+ diff --git a/doc/html/pair_airebo.html b/doc/html/pair_airebo.html index 0055388538..75cc429e45 100644 --- a/doc/html/pair_airebo.html +++ b/doc/html/pair_airebo.html @@ -299,7 +299,7 @@ for more info.

These pair potentials require the newton setting to be “on” for pair interactions.

The CH.airebo and CH.airebo-m potential files provided with LAMMPS -(see the potentials directory) are parameterized for metal units. +(see the potentials directory) are parameterized for metal units. You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units, but you would need to create your own AIREBO or AIREBO-M potential file with coefficients listed in the appropriate units, if your simulation diff --git a/doc/html/pair_bop.html b/doc/html/pair_bop.html index e52f3f13e0..1b07d82d76 100644 --- a/doc/html/pair_bop.html +++ b/doc/html/pair_bop.html @@ -470,7 +470,7 @@ info.

These pair potentials require the newtion setting to be “on” for pair interactions.

The CdTe.bop and GaAs.bop potential files provided with LAMMPS (see the -potentials directory) are parameterized for metal units. +potentials directory) are parameterized for metal units. You can use the BOP potential with any LAMMPS units, but you would need to create your own BOP potential file with coefficients listed in the appropriate units if your simulation does not use “metal” units.

diff --git a/doc/html/pair_comb.html b/doc/html/pair_comb.html index e4e5b1371d..2c1cd6006e 100644 --- a/doc/html/pair_comb.html +++ b/doc/html/pair_comb.html @@ -266,7 +266,7 @@ the

The COMB potentials in the ffield.comb and ffield.comb3 files provided with LAMMPS (see the potentials directory) are parameterized for metal -units. You can use the COMB potential with any LAMMPS +units. You can use the COMB potential with any LAMMPS units, but you would need to create your own COMB potential file with coefficients listed in the appropriate units if your simulation doesn’t use “metal” units.

diff --git a/doc/html/pair_dipole.html b/doc/html/pair_dipole.html index 823c52dbdd..02978c0f02 100644 --- a/doc/html/pair_dipole.html +++ b/doc/html/pair_dipole.html @@ -343,7 +343,7 @@ to be specified in an input script that reads a restart file.

only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

The lj/sf/dipole/sf style is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

-

Using dipole pair styles with electron units is not +

Using dipole pair styles with electron units is not currently supported.