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Merge branch 'master' into user-intel-update

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Axel Kohlmeyer
2017-10-06 10:18:38 -04:00
committed by GitHub
parent 9dc42fd4db 439c2fd980
commit 05847a0e87
86 changed files with 2368 additions and 2628 deletions
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3
doc/src/Section_packages.txt
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@ -705,7 +705,7 @@ dynamics can be run with LAMMPS using density-functional tight-binding
quantum forces calculated by LATTE.
More information on LATTE can be found at this web site:
"https://github.com/lanl/LATTE"_#latte_home. A brief technical
"https://github.com/lanl/LATTE"_latte_home. A brief technical
description is given with the "fix latte"_fix_latte.html command.
:link(latte_home,https://github.com/lanl/LATTE)
@ -728,6 +728,7 @@ make lib-latte args="-b" # download and build in lib/latte/LATTE-
make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
:pre
Note that 3 symbolic (soft) links, "includelink" and "liblink" and
"filelink", are created in lib/latte to point into the LATTE home dir.

10
doc/src/fix_latte.txt
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@ -66,7 +66,7 @@ reference charge of overlapping atom-centered densities and bond
integrals are parameterized using a Slater-Koster tight-binding
approach. This procedure, which usually is referred to as the DFTB
method has been described in detail by ("Elstner"_#Elstner) and
("Finnis"_#Finnis) and coworkers.
("Finnis"_#Finnis2) and coworkers.
The work of the LATTE developers follows that of Elstner closely with
respect to the physical model. However, the development of LATTE is
@ -173,7 +173,7 @@ M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
7260 (1998).
:link(Finnis)
:link(Finnis2)
[(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van
Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).
@ -197,11 +197,11 @@ J. Sci. Comput. 36 (2), 147-170, (2014).
[(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys.,
141, 164123, (2014).
:link(Niklasson2014)
:link(Niklasson2017)
[(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
:link(Niklasson2012)
[(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
:link(Cawkwell2012)
[(Cawkwell2012)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
(17), 174308 (2012).
:link(Negre2016)

4
doc/src/fix_neb.txt
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@ -93,7 +93,7 @@ intermediate replica with the previous and the next image:
Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
Note that in this case the specified {Kspring) is in force/distance
Note that in this case the specified {Kspring} is in force/distance
units.
With a value of {ideal}, the spring force is computed as suggested in
@ -105,7 +105,7 @@ where RD is the "reaction coordinate" see "neb"_neb.html section, and
RDideal is the ideal RD for which all the images are equally spaced.
I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
I is the replica number). The meanDist is the average distance
between replicas. Note that in this case the specified {Kspring) is
between replicas. Note that in this case the specified {Kspring} is
in force units.
Note that the {ideal} form of nudging can often be more effective at

1
doc/src/fixes.txt
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@ -59,6 +59,7 @@ Fixes :h1
fix_langevin
fix_langevin_drude
fix_langevin_eff
fix_latte
fix_lb_fluid
fix_lb_momentum
fix_lb_pc

1
doc/src/lammps.book
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@ -187,6 +187,7 @@ fix_ipi.html
fix_langevin.html
fix_langevin_drude.html
fix_langevin_eff.html
fix_latte.html
fix_lb_fluid.html
fix_lb_momentum.html
fix_lb_pc.html

12
doc/src/package.txt
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@ -62,7 +62,7 @@ args = arguments specific to the style :l
{no_affinity} values = none
{kokkos} args = keyword value ...
zero or more keyword/value pairs may be appended
keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward}
keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse}
{neigh} value = {full} or {half}
full = full neighbor list
half = half neighbor list built in thread-safe manner
@ -75,9 +75,10 @@ args = arguments specific to the style :l
{binsize} value = size
size = bin size for neighbor list construction (distance units)
{comm} value = {no} or {host} or {device}
use value for both comm/exchange and comm/forward
use value for comm/exchange and comm/forward and comm/reverse
{comm/exchange} value = {no} or {host} or {device}
{comm/forward} value = {no} or {host} or {device}
{comm/reverse} value = {no} or {host} or {device}
no = perform communication pack/unpack in non-KOKKOS mode
host = perform pack/unpack on host (e.g. with OpenMP threading)
device = perform pack/unpack on device (e.g. on GPU)
@ -429,17 +430,18 @@ Coulombic solver"_kspace_style.html because the GPU is faster at
performing pairwise interactions, then this rule of thumb may give too
large a binsize.
The {comm} and {comm/exchange} and {comm/forward} keywords determine
The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} keywords determine
whether the host or device performs the packing and unpacking of data
when communicating per-atom data between processors. "Exchange"
communication happens only on timesteps that neighbor lists are
rebuilt. The data is only for atoms that migrate to new processors.
"Forward" communication happens every timestep. The data is for atom
"Forward" communication happens every timestep. "Reverse" communication
happens every timestep if the {newton} option is on. The data is for atom
coordinates and any other atom properties that needs to be updated for
ghost atoms owned by each processor.
The {comm} keyword is simply a short-cut to set the same value
for both the {comm/exchange} and {comm/forward} keywords.
for both the {comm/exchange} and {comm/forward} and {comm/reverse} keywords.
The value options for all 3 keywords are {no} or {host} or {device}.
A value of {no} means to use the standard non-KOKKOS method of

4
doc/src/pair_eam.txt
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@ -294,7 +294,7 @@ distribution have a ".cdeam" suffix.
Style {eam/fs} computes pairwise interactions for metals and metal
alloys using a generalized form of EAM potentials due to Finnis and
Sinclair "(Finnis)"_#Finnis. The total energy Ei of an atom I is
Sinclair "(Finnis)"_#Finnis1. The total energy Ei of an atom I is
given by
:c,image(Eqs/pair_eam_fs.jpg)
@ -442,7 +442,7 @@ of Physics: Condensed Matter, 16, S2629 (2004).
[(Daw)] Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
Daw, Baskes, Phys Rev B, 29, 6443 (1984).
:link(Finnis)
:link(Finnis1)
[(Finnis)] Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
:link(Stukowski)