Merge branch 'master' into kk_ports

Ng = 1 and Ns is not set.

Depending on which flavor of MPI you are running, LAMMPS will look for

one of these 3 environment variables

one of these 4 environment variables

SLURM_LOCALID (various MPI variants compiled with SLURM support)

MPT_LRANK (HPE MPI)

MV2_COMM_WORLD_LOCAL_RANK (Mvapich)

OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre

processors and stored as properties of ghost atoms.

NOTE: These options apply to the currently defined comm style.  When

you specify a "comm_style"_comm_style.html command, all communication

settings are restored to their default values, including those

you specify a "comm_style"_comm_style.html or

"read_restart"_read_restart.html command, all communication settings

are restored to their default or stored values, including those

previously reset by a comm_modify command.  Thus if your input script

specifies a comm_style command, you should use the comm_modify command

after it.

specifies a comm_style or read_restart command, you should use the

comm_modify command after it.

The {mode} keyword determines whether a single or multiple cutoff

distances are used to determine which atoms to communicate.

ID, group-ID are documented in "compute"_compute.html command :ulb,l

bond/local = style name of this compute command :l

one or more values may be appended :l

value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l

value = {dist} or {engpot} or {force} or {fx} or {fy} or {fz} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l

  {dist} = bond distance

  {engpot} = bond potential energy

  {force} = bond force :pre

  {fx},{fy},{fz} = components of bond force

  {engvib} = bond kinetic energy of vibration

  {engrot} = bond kinetic energy of rotation

  {engtrans} = bond kinetic energy of translation

compute 1 all bond/local engpot

compute 1 all bond/local dist engpot force :pre

compute 1 all bond/local dist fx fy fz :pre

compute 1 all angle/local dist v_distsq set dist d :pre

[Description:]

The value {force} is the magnitude of the force acting between the

pair of atoms in the bond.

The values {fx}, {fy}, and {fz} are the xyz components of

{force} between the pair of atoms in the bond.

The remaining properties are all computed for motion of the two atoms

relative to the center of mass (COM) velocity of the 2 atoms in the

bond.

  {cutoff} value = distance cutoff

  {nnn} value = number of nearest neighbors

  {degrees} values = nlvalues, l1, l2,...

  {wl} value = yes or no

  {wl/hat} value = yes or no

  {components} value = ldegree  :pre

:ule

compute 1 all orientorder/atom

compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5

compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre

compute 1 all orientorder/atom wl/hat yes

compute 1 all orientorder/atom components 6 :pre

[Description:]

The angles theta and phi are the standard spherical polar angles

defining the direction of the bond vector {rij}.

The second equation defines {Ql}, which is a

rotationally invariant scalar quantity obtained by summing

rotationally invariant non-negative amplitude obtained by summing

over all the components of degree {l}.

The optional keyword {cutoff} defines the distance cutoff

The optional keyword {degrees} defines the list of order parameters to

be computed.  The first argument {nlvalues} is the number of order

parameters. This is followed by that number of integers giving the

parameters. This is followed by that number of non-negative integers giving the

degree of each order parameter. Because {Q}2 and all odd-degree order

parameters are zero for atoms in cubic crystals (see

"Steinhardt"_#Steinhardt), the default order parameters are {Q}4,

= sqrt(7/3)/8 = 0.19094....  The numerical values of all order

parameters up to {Q}12 for a range of commonly encountered

high-symmetry structures are given in Table I of "Mickel et

al."_#Mickel.

al."_#Mickel, and these can be reproduced with this compute

The optional keyword {wl} will output the third-order invariants {Wl} 

(see Eq. 1.4 in "Steinhardt"_#Steinhardt) for the same degrees as

for the {Ql} parameters. For the FCC crystal with {nnn} =12,

{W}4 = -sqrt(14/143).(49/4096)/Pi^1.5 = -0.0006722136...

The optional keyword {wl/hat} will output the normalized third-order 

invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt) 

for the same degrees as for the {Ql} parameters. For the FCC crystal 

with {nnn} =12, {W}4hat = -7/3*sqrt(2/429) = -0.159317...The numerical

values of {Wlhat} for a range of commonly encountered high-symmetry

structures are given in Table I of "Steinhardt"_#Steinhardt, and these

can be reproduced with this keyword.

The optional keyword {components} will output the components of the

normalized complex vector {Ybar_lm} of degree {ldegree}, which must be

The value of {Ql} is set to zero for atoms not in the

specified compute group, as well as for atoms that have less than

{nnn} neighbors within the distance cutoff.

{nnn} neighbors within the distance cutoff, unless {nnn} is NULL.

The neighbor list needed to compute this quantity is constructed each

time the calculation is performed (i.e. each time a snapshot of atoms

giving the {Ql} values for each atom, which are real numbers on the

range 0 <= {Ql} <= 1.

If the keyword {wl} is set to yes, then the {Wl} values for each

atom will be added to the output array, which are real numbers.

If the keyword {wl/hat} is set to yes, then the {Wl_hat} 

values for each atom will be added to the output array, which are real numbers.

If the keyword {components} is set, then the real and imaginary parts

of each component of (normalized) {Ybar_lm} will be added to the

output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})

[Default:]

The option defaults are {cutoff} = pair style cutoff, {nnn} = 12,

{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.

{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12,

{wl} = no, {wl/hat} = no, and {components} off

:line

min_style style :pre

style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul

style = {cg} or {cg/kk} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul

[Examples:]

converge more quickly if you use a timestep about 10x larger than you

would normally use for dynamics simulations.

NOTE: The {quickmin}, {fire}, and {hftn} styles do not yet support the

use of the "fix box/relax"_fix_box_relax.html command or minimizations

involving the electron radius in "eFF"_pair_eff.html models.

NOTE: The {quickmin}, {fire}, {hftn}, and {cg/kk} styles do not yet 

support the use of the "fix box/relax"_fix_box_relax.html command or 

minimizations involving the electron radius in "eFF"_pair_eff.html 

models. 

:line

Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are

functionally the same as the corresponding style without the suffix.

They have been optimized to run faster, depending on your available

hardware, as discussed on the "Speed packages"_Speed_packages.html doc

page.  The accelerated styles take the same arguments and should

produce the same results, except for round-off and precision issues.

These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,

USER-OMP and OPT packages, respectively.  They are only enabled if

LAMMPS was built with those packages.  See the "Build

package"_Build_package.html doc page for more info.

You can specify the accelerated styles explicitly in your input script

by including their suffix, or you can use the "-suffix command-line

switch"_Run_options.html when you invoke LAMMPS, or you can use the

"suffix"_suffix.html command in your input script.

See the "Speed packages"_Speed_packages.html doc page for more

instructions on how to use the accelerated styles effectively.

:line

[Restrictions:] none