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Commit2 JT 072319

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- corrected some mistakes in doc files
- modified oso examples to match new line options
This commit is contained in:
julient31
2019-07-23 11:24:52 -06:00
parent f0679cff6d
commit f1c3b9d0bf
6 changed files with 13 additions and 12 deletions
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10
doc/src/min_modify.txt
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@ -13,7 +13,7 @@ min_modify command :h3
min_modify keyword values ... :pre min_modify keyword values ... :pre
one or more keyword/value pairs may be listed :ulb,l one or more keyword/value pairs may be listed :ulb,l
keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor} or {spin_cubic} or {spin_none} keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor}
{dmax} value = max {dmax} value = max
max = maximum distance for line search to move (distance units) max = maximum distance for line search to move (distance units)
{line} value = {backtrack} or {quadratic} or {forcezero} or {spin_cubic} or {spin_none} {line} value = {backtrack} or {quadratic} or {forcezero} or {spin_cubic} or {spin_none}
@ -81,9 +81,9 @@ quantities.
Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0. Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
The choice of a line search algorithm for the {spin_oso_cg} and The choice of a line search algorithm for the {spin_oso_cg} and
{spin_oso_lbfgs} can be specified via the {line} keyword. {spin_oso_lbfgs} styles can be specified via the {line} keyword.
The {spin_cubic} and {spin_none} only make sense when those two The {spin_cubic} and {spin_none} only make sense when one of those
when one of those two minimization styles is declared. two minimization styles is declared.
The {spin_cubic} keyword activates the line search procedure when The {spin_cubic} keyword activates the line search procedure when
the {spin_oso_cg} algorithm is used. the {spin_oso_cg} algorithm is used.
@ -93,7 +93,7 @@ the {spin_oso_lbfgs} algorithm is used.
[Restrictions:] The line search procedure of styles [Restrictions:] The line search procedure of styles
{spin_oso_cg} and {spin_oso_lbfgs} cannot be used for magnetic {spin_oso_cg} and {spin_oso_lbfgs} cannot be used for magnetic
NEB calculations. See "neb/spin"_neb_spin.html for more GNEB calculations. See "neb/spin"_neb_spin.html for more
explanation. explanation.
[Related commands:] [Related commands:]

5
doc/src/min_spin.txt
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@ -18,7 +18,7 @@ min_style spin_oso_lbfgs :pre
[Examples:] [Examples:]
min_style spin_oso_lbfgs min_style spin_oso_lbfgs
min_modify discrete_factor 10.0 line_search 0 :pre min_modify discrete_factor 10.0 line spin_none :pre
[Description:] [Description:]
@ -62,7 +62,8 @@ Style {spin_oso_lbfgs} defines an orthogonal spin optimization
(LBFGS) algorithm. (LBFGS) algorithm.
By default, style {spin_oso_lbfgs} uses a line search procedure. By default, style {spin_oso_lbfgs} uses a line search procedure.
The "min_modify"_min_modify.html command can be used to The "min_modify"_min_modify.html command can be used to
deactivate the line search procedure. deactivate the line search procedure, and to modify the
discretization factor {discrete_factor}.
For more information about styles {spin_oso_cg} and {spin_oso_lbfgs}, For more information about styles {spin_oso_cg} and {spin_oso_lbfgs},
see their implementation reported in "(Ivanov)"_#Ivanov1. see their implementation reported in "(Ivanov)"_#Ivanov1.

4
doc/src/neb_spin.txt
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@ -60,8 +60,8 @@ processors per replica. See the "Howto replica"_Howto_replica.html
doc page for further discussion. doc page for further discussion.
NOTE: As explained below, a GNEB calculation performs a damped dynamics NOTE: As explained below, a GNEB calculation performs a damped dynamics
minimization across all the replicas. The "spin"_min_spin.html minimization across all the replicas. One of the "spin"_min_spin.html
style minimizer has to be defined in your input script. style minimizers has to be defined in your input script.
When a GNEB calculation is performed, it is assumed that each replica When a GNEB calculation is performed, it is assumed that each replica
is running the same system, though LAMMPS does not check for this. is running the same system, though LAMMPS does not check for this.

2
examples/SPIN/spinmin/in.spinmin_cg.bfo
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@ -50,5 +50,5 @@ compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
min_style spin/oso_cg min_style spin/oso_cg
min_modify discrete_factor 10.0 line_search 0 min_modify discrete_factor 10.0 line spin_cubic
minimize 1.0e-10 1.0e-10 10000 1000 minimize 1.0e-10 1.0e-10 10000 1000

2
examples/SPIN/spinmin/in.spinmin_lbfgs.bfo
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@ -50,5 +50,5 @@ compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
min_style spin/oso_lbfgs min_style spin/oso_lbfgs
min_modify discrete_factor 10.0 line_search 1 min_modify discrete_factor 10.0 line spin_none
minimize 1.0e-15 1.0e-10 10000 1000 minimize 1.0e-15 1.0e-10 10000 1000

2
src/SPIN/neb_spin.cpp
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@ -650,7 +650,7 @@ int NEBSpin::initial_rotation(double *spi, double *sploc, double fraction)
kcrossy = kz*spix - kx*spiz; kcrossy = kz*spix - kx*spiz;
kcrossz = kx*spiy - ky*spix; kcrossz = kx*spiy - ky*spix;
kdots = kx*spix + ky*spiz + kz*spiz; kdots = kx*spix + ky*spiy + kz*spiz;
omega = acos(sidotsf); omega = acos(sidotsf);
omega *= fraction; omega *= fraction;