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Merge remote-tracking branch 'origin/master' into lammps_gjf

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charlie sievers
2019-09-17 12:08:12 -07:00
parent 971f4763e3 d357259cc4
commit eba10b10e8
51 changed files with 3356 additions and 225 deletions
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2
doc/src/Commands_bond.txt
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@ -108,7 +108,7 @@ OPT.
"class2 (ko)"_dihedral_class2.html,
"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
"fourier (io)"_dihedral_fourier.html,
"harmonic (io)"_dihedral_harmonic.html,
"harmonic (iko)"_dihedral_harmonic.html,
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"nharmonic (o)"_dihedral_nharmonic.html,

3
doc/src/Run_options.txt
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@ -126,9 +126,10 @@ are intended for computational work like running LAMMPS. By default
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

9
doc/src/comm_modify.txt
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@ -40,11 +40,12 @@ coordinates and other properties are exchanged between neighboring
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.

7
doc/src/compute_bond_local.txt
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@ -15,10 +15,11 @@ compute ID group-ID bond/local value1 value2 ... keyword args ... :pre
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
@ -38,6 +39,7 @@ keyword = {set} :l
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:]
@ -59,6 +61,9 @@ based on the current separation of the pair of atoms in the bond.
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.

35
doc/src/compute_orientorder_atom.txt
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@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
{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
@ -27,7 +29,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
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:]
@ -48,7 +51,7 @@ neighbors of the central atom.
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
@ -63,7 +66,7 @@ specified distance cutoff are used.
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,
@ -71,7 +74,20 @@ parameters are zero for atoms in cubic crystals (see
= 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
@ -82,7 +98,7 @@ particles, as discussed in "ten Wolde"_#tenWolde2.
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
@ -108,6 +124,12 @@ This compute calculates a per-atom array with {nlvalues} columns,
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})
@ -130,7 +152,8 @@ hexorder/atom"_compute_hexorder_atom.html
[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

1
doc/src/dihedral_harmonic.txt
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@ -8,6 +8,7 @@
dihedral_style harmonic command :h3
dihedral_style harmonic/intel command :h3
dihedral_style harmonic/kk command :h3
dihedral_style harmonic/omp command :h3
[Syntax:]

33
doc/src/min_style.txt
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@ -11,7 +11,7 @@ min_style command :h3
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:]
@ -74,9 +74,34 @@ defined via the "timestep"_timestep.html command. Often they will
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

23
doc/src/minimize.txt
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@ -7,6 +7,7 @@
:line
minimize command :h3
minimize/kk command :h3
[Syntax:]
@ -256,6 +257,28 @@ info in the Restrictions section below.
: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:]
Features that are not yet implemented are listed here, in case someone