ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

jive src headers with doc page entries and example scripts

Browse Source
This commit is contained in:
Steve Plimpton
2018-09-25 10:50:43 -06:00
parent de010551cf
commit 5a6226caa5
29 changed files with 140 additions and 71 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
doc/src/compute_smd_triangle_mesh_vertices.txt → doc/src/compute_smd_triangle_vertices.txt
View File

@ -6,14 +6,14 @@
:line
compute smd/triangle/mesh/vertices :h3
compute smd/triangle/vertices command :h3
[Syntax:]
compute ID group-ID smd/triangle/mesh/vertices :pre
compute ID group-ID smd/triangle/vertices :pre
ID, group-ID are documented in "compute"_compute.html command
smd/triangle/mesh/vertices = style name of this compute command :ul
smd/triangle/vertices = style name of this compute command :ul
[Examples:]

13
doc/src/compute_spin.txt
View File

@ -10,14 +10,14 @@ compute spin command :h3
[Syntax:]
compute ID group-ID compute/spin :pre
compute ID group-ID spin :pre
ID, group-ID are documented in "compute"_compute.html command
compute/spin = style name of this compute command :ul
spin = style name of this compute command :ul
[Examples:]
compute out_mag all compute/spin :pre
compute out_mag all spin :pre
[Description:]
@ -26,7 +26,8 @@ of atoms having spins.
This compute calculates 6 magnetic quantities.
The three first quantities are the x,y and z coordinates of the total magnetization.
The three first quantities are the x,y and z coordinates of the total
magnetization.
The fourth quantity is the norm of the total magnetization.
@ -39,7 +40,7 @@ The simplest way to output the results of the compute spin calculation
is to define some of the quantities as variables, and to use the thermo and
thermo_style commands, for example:
compute out_mag all compute/spin :pre
compute out_mag all spin :pre
variable mag_z equal c_out_mag\[3\]
variable mag_norm equal c_out_mag\[4\]
@ -53,7 +54,6 @@ the total magnetization, and the magnetic temperature. Three variables are
assigned to those quantities. The thermo and thermo_style commands print them
every 10 timesteps.
[Output info:]
The array values are "intensive". The array values will be in
@ -68,7 +68,6 @@ has to be "spin" for this compute to be valid.
[Related commands:] none
[Default:] none
:line

2
doc/src/fix_msst.txt
View File

@ -6,7 +6,7 @@
:line
fix msst command :h3
fix msst command :h3
[Syntax:]

56
doc/src/fix_nve_awpmd.txt Normal file
View File

@ -0,0 +1,56 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix nve/awpmd command :h3
[Syntax:]
fix ID group-ID nve/awpmd :pre
ID, group-ID are documented in "fix"_fix.html command
nve/awpmd = style name of this fix command :ul
[Examples:]
fix 1 all nve/awpmd :pre
[Description:]
Perform constant NVE integration to update position and velocity for
nuclei and electrons in the group for the "Antisymmetrized Wave Packet
Molecular Dynamics"_pair_awpmd.html model. V is volume; E is energy.
This creates a system trajectory consistent with the microcanonical
ensemble.
The operation of this fix is exactly like that described by the "fix
nve"_fix_nve.html command, except that the width and width-velocity of
the electron wavefunctions are also updated.
:line
[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 or per-atom quantities are stored
by this fix for access by various "output commands"_Howto_output.html.
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 USER-AWPMD package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]
"fix nve"_fix_nve.html
[Default:] none

2
doc/src/fix_poems.txt
View File

@ -6,7 +6,7 @@
:line
fix poems :h3
fix poems command :h3
Syntax:

2
doc/src/pair_body_nparticle.txt
View File

@ -6,7 +6,7 @@
:line
pair_style body command :h3
pair_style body/nparticle command :h3
[Syntax:]

4
doc/src/pair_buck6d_coul_gauss.txt
View File

@ -6,8 +6,8 @@
:line
pair_style buck6d/coul/gauss/dsf :h3
pair_style buck6d/coul/gauss/long :h3
pair_style buck6d/coul/gauss/dsf command :h3
pair_style buck6d/coul/gauss/long command :h3
[Syntax:]

23
doc/src/pair_lj_expand.txt
View File

@ -9,6 +9,8 @@
pair_style lj/expand command :h3
pair_style lj/expand/gpu command :h3
pair_style lj/expand/omp command :h3
pair_style lj/expand/coul/long command :h3
pair_style lj/expand/coul/long/gpu command :h3
[Syntax:]
@ -22,6 +24,11 @@ pair_style lj/expand 2.5
pair_coeff * * 1.0 1.0 0.5
pair_coeff 1 1 1.0 1.0 -0.2 2.0 :pre
pair_style lj/expand/coul/long 2.5
pair_style lj/expand/coul/long 2.5 4.0
pair_coeff * * 1.0 1.0 0.5
pair_coeff 1 1 1.0 1.0 -0.2 3.0 :pre
[Description:]
Style {lj/expand} computes a LJ interaction with a distance shifted by
@ -34,11 +41,12 @@ formula:
Rc is the cutoff which does not include the delta distance. I.e. the
actual force cutoff is the sum of cutoff + delta.
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, or by mixing as described below:
For all of the {lj/expand} pair styles, 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, or by mixing as
described below:
epsilon (energy units)
sigma (distance units)
@ -48,6 +56,11 @@ 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.
For {lj/expand/coul/long} only the LJ cutoff 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
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are

4
doc/src/pair_meam_spline.txt
View File

@ -6,8 +6,8 @@
:line
pair_style meam/spline :h3
pair_style meam/spline/omp :h3
pair_style meam/spline command :h3
pair_style meam/spline/omp command :h3
[Syntax:]

4
doc/src/pair_meam_sw_spline.txt
View File

@ -6,8 +6,8 @@
:line
pair_style meam/sw/spline :h3
pair_style meam/sw/spline/omp :h3
pair_style meam/sw/spline command :h3
pair_style meam/sw/spline/omp command :h3
[Syntax:]

14
doc/src/pair_sdk.txt
View File

@ -13,6 +13,8 @@ pair_style lj/sdk/omp command :h3
pair_style lj/sdk/coul/long command :h3
pair_style lj/sdk/coul/long/gpu command :h3
pair_style lj/sdk/coul/long/omp command :h3
pair_style lj/sdk/coul/msm command :h3
pair_style lj/sdk/coul/msm/omp command :h3
[Syntax:]
@ -35,6 +37,10 @@ pair_style lj/sdk/coul/long 10.0
pair_style lj/sdk/coul/long 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre
pair_style lj/sdk/coul/msm 10.0
pair_style lj/sdk/coul/msm 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre
[Description:]
The {lj/sdk} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
@ -75,10 +81,10 @@ 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.
For {lj/sdk/coul/long} only the LJ cutoff 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.
For {lj/sdk/coul/long} and {lj/sdk/coul/msm} only the LJ cutoff 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

8
doc/src/pair_spin_magelec.txt
View File

@ -6,11 +6,11 @@
:line
pair_style spin/me command :h3
pair_style spin/magelec command :h3
[Syntax:]
pair_style spin/me cutoff :pre
pair_style spin/magelec cutoff :pre
cutoff = global cutoff pair (distance in metal units) :ulb,l
@ -18,8 +18,8 @@ cutoff = global cutoff pair (distance in metal units) :ulb,l
[Examples:]
pair_style spin/me 4.5
pair_coeff * * me 4.5 0.00109 1.0 1.0 1.0 :pre
pair_style spin/magelec 4.5
pair_coeff * * magelec 4.5 0.00109 1.0 1.0 1.0 :pre
[Description:]

36
doc/src/pair_spin_neel.txt
View File

@ -29,34 +29,36 @@ between pairs of magnetic spins:
:c,image(Eqs/pair_spin_neel_interaction.jpg)
where si and sj are two neighboring magnetic spins of two particles,
where si and sj are two neighboring magnetic spins of two particles,
rij = ri - rj is the inter-atomic distance between the two particles,
eij = (ri - rj)/|ri-rj| is their normalized separation vector
and g1, q1 and q2 are three functions defining the intensity of the
dipolar and quadrupolar contributions, with:
eij = (ri - rj)/|ri-rj| is their normalized separation vector and g1,
q1 and q2 are three functions defining the intensity of the dipolar
and quadrupolar contributions, with:
:c,image(Eqs/pair_spin_neel_functions.jpg)
With the functions g(rij) and q(rij) defined and fitted according to the same
Bethe-Slater function used to fit the exchange interaction:
With the functions g(rij) and q(rij) defined and fitted according to
the same Bethe-Slater function used to fit the exchange interaction:
:c,image(Eqs/pair_spin_exchange_function.jpg)
where a, b and d are the three constant coefficients defined in the associated
"pair_coeff" command.
where a, b and d are the three constant coefficients defined in the
associated "pair_coeff" command.
The coefficients a, b, and d need to be fitted so that the function above matches with
the values of the magneto-elastic constant of the materials at stake.
The coefficients a, b, and d need to be fitted so that the function
above matches with the values of the magneto-elastic constant of the
materials at stake.
Examples and more explanations about this function and its parametrization are reported
in "(Tranchida)"_#Tranchida6. More examples of parametrization will be provided in
future work.
Examples and more explanations about this function and its
parametrization are reported in "(Tranchida)"_#Tranchida6. More
examples of parametrization will be provided in future work.
From this DM interaction, each spin i will be submitted to a magnetic torque
omega and its associated atom to a force F (for spin-lattice calculations only).
From this DM interaction, each spin i will be submitted to a magnetic
torque omega and its associated atom to a force F (for spin-lattice
calculations only).
More details about the derivation of these torques/forces are reported in
"(Tranchida)"_#Tranchida6.
More details about the derivation of these torques/forces are reported
in "(Tranchida)"_#Tranchida6.
:line