From a9b8a6521d15cbcf97fff4348ff15b1266f17178 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Tue, 25 Sep 2018 13:18:54 -0600
Subject: [PATCH] more mis-matches between doc pages and src files
---
doc/src/Commands_bond.txt | 2 +-
doc/src/Commands_fix.txt | 2 +-
doc/src/Commands_pair.txt | 2 +-
doc/src/angle_sdk.txt | 25 ++++++++++++++++++++++++
doc/src/fix_property_atom.txt | 24 +++++++++++++++++++++++
doc/src/fix_surface_global.txt | 19 ------------------
doc/src/fix_wall_gran.txt | 23 ++++++++++++++++++++++
doc/src/pair_born.txt | 19 ++----------------
doc/src/pair_buck.txt | 14 +++-----------
doc/src/pair_charmm.txt | 3 +++
doc/src/pair_cs.txt | 34 +++++++++++++++++++++++++++++++++
doc/src/pair_dipole.txt | 1 +
doc/src/pair_edip.txt | 1 +
doc/src/pair_gran.txt | 2 +-
doc/src/pair_gromacs.txt | 2 ++
doc/src/pair_hybrid.txt | 3 +--
doc/src/pair_lj.txt | 2 ++
doc/src/pair_lj_expand.txt | 1 +
doc/src/pair_lj_long.txt | 1 +
doc/src/pair_meam_sw_spline.txt | 1 -
doc/src/pair_tersoff.txt | 8 ++++----
21 files changed, 131 insertions(+), 58 deletions(-)
delete mode 100644 doc/src/fix_surface_global.txt
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
index 0cf433d53a..773202f126 100644
--- a/doc/src/Commands_bond.txt
+++ b/doc/src/Commands_bond.txt
@@ -70,7 +70,7 @@ OPT.
"fourier/simple (o)"_angle_fourier_simple.html,
"harmonic (iko)"_angle_harmonic.html,
"quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html,
+"sdk (o)"_angle_sdk.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
:line
diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt
index e002c11770..838bcbe7a6 100644
--- a/doc/src/Commands_fix.txt
+++ b/doc/src/Commands_fix.txt
@@ -216,7 +216,7 @@ OPT.
"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
"wall/colloid"_fix_wall.html,
"wall/ees"_fix_wall_ees.html,
-"wall/gran"_fix_wall_gran.html,
+"wall/gran (o)"_fix_wall_gran.html,
"wall/gran/region"_fix_wall_gran_region.html,
"wall/harmonic"_fix_wall.html,
"wall/lj1043"_fix_wall.html,
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index 33890df1fe..3b6a5f48fa 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -26,7 +26,7 @@ OPT.
"none"_pair_none.html,
"zero"_pair_zero.html,
-"hybrid"_pair_hybrid.html,
+"hybrid (k)"_pair_hybrid.html,
"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
"adp (o)"_pair_adp.html,
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
index 4de1a6755d..22238880fe 100644
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@@ -7,6 +7,7 @@
:line
angle_style sdk command :h3
+angle_style sdk/omp command :h3
[Syntax:]
@@ -43,6 +44,30 @@ internally; hence the units of K are in energy/radian^2.
The also required {lj/sdk} parameters will be extracted automatically
from the pair_style.
+: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:]
This angle style can only be used if LAMMPS was built with the
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index 8a70cd8213..19e3b0ca40 100644
--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@@ -7,6 +7,7 @@
:line
fix property/atom command :h3
+fix property/atom/kk command :h3
[Syntax:]
@@ -201,6 +202,7 @@ added classes.
:line
:link(isotopes)
+
Example for using per-atom masses with TIP4P water to
study isotope effects. When setting up simulations with the "TIP4P
pair styles"_Howto_tip4p.html for water, you have to provide exactly
@@ -238,6 +240,28 @@ set group hwat mass 2.0141018 :pre
: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
+
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the per-atom values it stores to "binary restart
diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt
deleted file mode 100644
index 2ee045141a..0000000000
--- a/doc/src/fix_surface_global.txt
+++ /dev/null
@@ -1,19 +0,0 @@
-"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 wall/surface/global command :h3
-
-[Description:]
-
-This feature is not yet implemented.
-
-[Related commands:]
-
-"dump image"_dump_image.html
-
-
diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt
index 0ea5b194eb..871ee2e5d1 100644
--- a/doc/src/fix_wall_gran.txt
+++ b/doc/src/fix_wall_gran.txt
@@ -7,6 +7,7 @@
:line
fix wall/gran command :h3
+fix wall/gran/omp command :h3
[Syntax:]
@@ -136,6 +137,28 @@ the clockwise direction for {vshear} > 0 or counter-clockwise for
{vshear} < 0. In this case, {vshear} is the tangential velocity of
the wall at whatever {radius} has been defined.
+: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.
+
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the shear friction state of atoms interacting with the
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index 195d3e6669..9cbfcffea0 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -11,19 +11,14 @@ pair_style born command :h3
pair_style born/omp command :h3
pair_style born/gpu command :h3
pair_style born/coul/long command :h3
-pair_style born/coul/long/cs command :h3
-pair_style born/coul/long/cs/gpu command :h3
pair_style born/coul/long/gpu command :h3
pair_style born/coul/long/omp command :h3
pair_style born/coul/msm command :h3
pair_style born/coul/msm/omp command :h3
pair_style born/coul/wolf command :h3
-pair_style born/coul/wolf/cs command :h3
-pair_style born/coul/wolf/cs/gpu command :h3
pair_style born/coul/wolf/gpu command :h3
pair_style born/coul/wolf/omp command :h3
pair_style born/coul/dsf command :h3
-pair_style born/coul/dsf/cs command :h3
[Syntax:]
@@ -55,9 +50,7 @@ pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/long 10.0
-pair_style born/coul/long/cs 10.0
-pair_style born/coul/long 10.0 8.0
-pair_style born/coul/long/cs 10.0 8.0
+pair_style born/coul/long 10.0 8.
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
@@ -68,7 +61,6 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/wolf 0.25 10.0
pair_style born/coul/wolf 0.25 10.0 9.0
-pair_style born/coul/wolf/cs 0.25 10.0 9.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
@@ -107,13 +99,6 @@ Wolf potential in the "coul/wolf"_pair_coul.html pair style.
The {born/coul/dsf} style computes the Coulomb contribution with the
damped shifted force model as in the "coul/dsf"_pair_coul.html style.
-Style {born/coul/long/cs} is identical to {born/coul/long} except that
-a term is added for the "core/shell model"_Howto_coreshell.html to
-allow charges on core and shell particles to be separated by r = 0.0.
-The same correction is introduced for the {born/coul/dsf/cs} style
-which is identical to {born/coul/dsf}. And likewise for
-{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.
-
Note that these potentials are related to the "Buckingham
potential"_pair_buck.html.
@@ -174,7 +159,7 @@ for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
interaction.
The {born/coul/long} pair style supports the
-"pair_modify"_pair_modify.html table option ti tabulate the
+"pair_modify"_pair_modify.html table option to tabulate the
short-range portion of the long-range Coulombic interaction.
These styles support the pair_modify tail option for adding long-range
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index 5b1688e868..ec83e6b339 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -17,7 +17,6 @@ pair_style buck/coul/cut/intel command :h3
pair_style buck/coul/cut/kk command :h3
pair_style buck/coul/cut/omp command :h3
pair_style buck/coul/long command :h3
-pair_style buck/coul/long/cs command :h3
pair_style buck/coul/long/gpu command :h3
pair_style buck/coul/long/intel command :h3
pair_style buck/coul/long/kk command :h3
@@ -29,14 +28,14 @@ pair_style buck/coul/msm/omp command :h3
pair_style style args :pre
-style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/long/cs} or {buck/coul/msm}
+style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/msm}
args = list of arguments for a particular style :ul
{buck} args = cutoff
cutoff = global cutoff for Buckingham interactions (distance units)
{buck/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
- {buck/coul/long} or {buck/coul/long/cs} args = cutoff (cutoff2)
+ {buck/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{buck/coul/msm} args = cutoff (cutoff2)
@@ -56,9 +55,7 @@ pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 :pre
pair_style buck/coul/long 10.0
-pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long 10.0 8.0
-pair_style buck/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre
@@ -92,10 +89,6 @@ A,C and Coulombic terms. If two cutoffs are specified, the first is
used as the cutoff for the A,C terms, and the second is the cutoff for
the Coulombic term.
-Style {buck/coul/long/cs} is identical to {buck/coul/long} except that
-a term is added for the "core/shell model"_Howto_coreshell.html to
-allow charges on core and shell particles to be separated by r = 0.0.
-
Note that these potentials are related to the "Born-Mayer-Huggins
potential"_pair_born.html.
@@ -184,8 +177,7 @@ respa"_run_style.html command. They do not support the {inner},
[Restrictions:]
-The {buck/coul/long} style is part of the KSPACE package. The
-{buck/coul/long/cs} style is part of the CORESHELL package. They are
+The {buck/coul/long} style is part of the KSPACE package. They are
only enabled if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index dfc87e1bce..131e289227 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -8,12 +8,15 @@
pair_style lj/charmm/coul/charmm command :h3
pair_style lj/charmm/coul/charmm/intel command :h3
+pair_style lj/charmm/coul/charmm/kk command :h3
pair_style lj/charmm/coul/charmm/omp command :h3
pair_style lj/charmm/coul/charmm/implicit command :h3
+pair_style lj/charmm/coul/charmm/implicit/kk command :h3
pair_style lj/charmm/coul/charmm/implicit/omp command :h3
pair_style lj/charmm/coul/long command :h3
pair_style lj/charmm/coul/long/gpu command :h3
pair_style lj/charmm/coul/long/intel command :h3
+pair_style lj/charmm/coul/long/kk command :h3
pair_style lj/charmm/coul/long/opt command :h3
pair_style lj/charmm/coul/long/omp command :h3
pair_style lj/charmm/coul/msm command :h3
diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt
index 8bd4abed68..faaea42f15 100644
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@@ -7,9 +7,11 @@
:line
pair_style born/coul/long/cs command :h3
+pair_style born/coul/long/cs/gpu command :h3
pair_style buck/coul/long/cs command :h3
pair_style born/coul/dsf/cs command :h3
pair_style born/coul/wolf/cs command :h3
+pair_style born/coul/wolf/cs/gpu command :h3
[Syntax:]
@@ -97,6 +99,38 @@ a long-range solver, thus the only correction is the addition of a
minimal distance to avoid the possible r = 0.0 case for a
core/shell pair.
+: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
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+See the corresponding doc pages for pair styles without the "cs"
+suffix to see how mixing, shifting, tabulation, tail correction,
+restarting, and rRESPA are handled by theses pair styles.
+
+:line
+
[Restrictions:]
These pair styles are part of the CORESHELL package. They are only
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index dcb2448949..bdf37983b6 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -13,6 +13,7 @@ pair_style lj/sf/dipole/sf command :h3
pair_style lj/sf/dipole/sf/gpu command :h3
pair_style lj/sf/dipole/sf/omp command :h3
pair_style lj/cut/dipole/long command :h3
+pair_style lj/cut/dipole/long/gpu command :h3
pair_style lj/long/dipole/long command :h3
[Syntax:]
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index 053d43b2ba..e0e8fbb27e 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -7,6 +7,7 @@
:line
pair_style edip command :h3
+pair_style edip/omp command :h3
pair_style edip/multi command :h3
[Syntax:]
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index e06d410084..5beaf30e06 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -7,7 +7,7 @@
:line
pair_style gran/hooke command :h3
-pair_style gran/omp command :h3
+pair_style gran/hooke/omp command :h3
pair_style gran/hooke/history command :h3
pair_style gran/hooke/history/omp command :h3
pair_style gran/hertz/history command :h3
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index 6a36a036c9..e50a21588c 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -8,8 +8,10 @@
pair_style lj/gromacs command :h3
pair_style lj/gromacs/gpu command :h3
+pair_style lj/gromacs/kk command :h3
pair_style lj/gromacs/omp command :h3
pair_style lj/gromacs/coul/gromacs command :h3
+pair_style lj/gromacs/coul/gromacs/kk command :h3
pair_style lj/gromacs/coul/gromacs/omp command :h3
[Syntax:]
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 6e68e820a8..97a5972bfb 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -7,9 +7,8 @@
:line
pair_style hybrid command :h3
-pair_style hybrid/omp command :h3
+pair_style hybrid/kk command :h3
pair_style hybrid/overlay command :h3
-pair_style hybrid/overlay/omp command :h3
pair_style hybrid/overlay/kk command :h3
[Syntax:]
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index b5a5726182..4939f505bb 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -14,6 +14,7 @@ pair_style lj/cut/opt command :h3
pair_style lj/cut/omp command :h3
pair_style lj/cut/coul/cut command :h3
pair_style lj/cut/coul/cut/gpu command :h3
+pair_style lj/cut/coul/cut/kk command :h3
pair_style lj/cut/coul/cut/omp command :h3
pair_style lj/cut/coul/debye command :h3
pair_style lj/cut/coul/debye/gpu command :h3
@@ -26,6 +27,7 @@ pair_style lj/cut/coul/dsf/omp command :h3
pair_style lj/cut/coul/long command :h3
pair_style lj/cut/coul/long/cs command :h3
pair_style lj/cut/coul/long/gpu command :h3
+pair_style lj/cut/coul/long/kk command :h3
pair_style lj/cut/coul/long/intel command :h3
pair_style lj/cut/coul/long/opt command :h3
pair_style lj/cut/coul/long/omp command :h3
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index f37cb0fb83..178ba8d1a8 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -8,6 +8,7 @@
pair_style lj/expand command :h3
pair_style lj/expand/gpu command :h3
+pair_style lj/expand/kk 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
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 2bc2b656ac..47a554ef4f 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -11,6 +11,7 @@ pair_style lj/long/coul/long/intel command :h3
pair_style lj/long/coul/long/omp command :h3
pair_style lj/long/coul/long/opt command :h3
pair_style lj/long/tip4p/long command :h3
+pair_style lj/long/tip4p/long/omp command :h3
[Syntax:]
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index 8281315031..77322953cf 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -7,7 +7,6 @@
:line
pair_style meam/sw/spline command :h3
-pair_style meam/sw/spline/omp command :h3
[Syntax:]
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 20744bc2a9..4b7bb0d93d 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -8,10 +8,10 @@
pair_style tersoff command :h3
pair_style tersoff/table command :h3
-pair_style tersoff/gpu :h3
-pair_style tersoff/intel :h3
-pair_style tersoff/kk :h3
-pair_style tersoff/omp :h3
+pair_style tersoff/gpu command :h3
+pair_style tersoff/intel command :h3
+pair_style tersoff/kk command :h3
+pair_style tersoff/omp command :h3
pair_style tersoff/table/omp command :h3
[Syntax:]
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