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gatherv fix, doc updates

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This commit is contained in:
jrgissing
2018-02-24 22:49:28 -07:00
parent d5e43a9ab1
commit 7d1de34533
4 changed files with 13 additions and 4 deletions
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4
doc/src/fix_bond_react.txt
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@ -252,7 +252,7 @@ Equivalences :pre
6 6
7 7 :pre
:line
:line
Once a reaction site has been successfully identified, data structures
within LAMMPS that store bond topology are updated to reflect the
@ -338,7 +338,7 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
This fix is part of the USER-MISC package. It is only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.

4
examples/USER/misc/bond_react/nylon,6-6_melt/infromdata.class2
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@ -40,7 +40,9 @@ fix myrxns all bond/react stabilization yes statted_grp .03 &
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
fix 4 bond_react_MASTER_group temp/rescale 1 800 800 10 1
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts

1
src/USER-MISC/README
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@ -39,6 +39,7 @@ dihedral_style spherical, Andrew Jewett, jewett.aij@gmail.com, 15 Jul 16
dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
fix bond/react, Jacob Gissinger (CU Boulder), info at disarmmd.org, 24 Feb 2018
fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017
fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016
fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014

8
src/USER-MISC/fix_bond_react.cpp
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@ -1751,9 +1751,15 @@ void FixBondReact::ghost_glovecast()
}
}
// let's send to root, dedup, then broadcast
MPI_Gatherv(&(global_mega_glove[0][start]), ghostly_num_mega, column,
if (me == 0) {
MPI_Gatherv(MPI_IN_PLACE, ghostly_num_mega, column, // Note: some values ignored for MPI_IN_PLACE
&(global_mega_glove[0][0]), allncols, allstarts,
column, 0, world);
} else {
MPI_Gatherv(&(global_mega_glove[0][start]), ghostly_num_mega, column,
&(global_mega_glove[0][0]), allncols, allstarts,
column, 0, world);
}
if (me == 0) dedup_mega_gloves(1); // global_mega_glove mode
MPI_Bcast(&global_megasize,1,MPI_INT,0,world);