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more tweaks

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This commit is contained in:
Steve Plimpton
2024-04-08 16:25:17 -06:00
parent e40a1527d3
commit f1c2a22e2d
5 changed files with 36 additions and 39 deletions
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36
doc/src/dump_modify.rst
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@ -80,7 +80,7 @@ Syntax
value = numeric value to compare to, or LAST
these 3 args can be replaced by the word "none" to turn off thresholding
*time* arg = *yes* or *no*
*triclinic/general* arg = none
*triclinic/general* arg = *yes* or *no*
*units* arg = *yes* or *no*
*unwrap* arg = *yes* or *no*
@ -815,7 +815,7 @@ threshold criterion is met. Otherwise it is not met.
.. note::
For style *custom*, the *triclinic/general* keyword alters dump
For style *custom*, the *triclinic/general* keyword can alter dump
output for general triclinic simulation boxes and their atoms. See
the :doc:`dump <dump>` command for details of how this changes the
format of dump file snapshots. The thresh keyword may access
@ -850,23 +850,25 @@ The default setting is *no*\ .
----------
The *triclinic/general* keyword only applies to the dump *atom* and
*custom* styles. It can only be used if the simulation box was
created as a general triclinic box. See the :doc:`Howto_triclinic
<Howto_triclinic>` doc page for a detailed explanation of orthogonal,
restricted triclinic, and general triclinic simulation boxes.
*custom* styles. It can only be used with a value of *yes* if the
simulation box was created as a general triclinic box. See the
:doc:`Howto_triclinic <Howto_triclinic>` doc page for a detailed
explanation of orthogonal, restricted triclinic, and general triclinic
simulation boxes.
If this keyword is used, the box information at the beginning of each
snapshot will include information about the 3 arbitrary edge vectors
**A**, **B**, **C** that define the general triclinic box as well as
their origin. The format is described on the :doc:`dump <dump>` doc
page.
If this keyword is used with a value of *yes*, the box information at
the beginning of each snapshot will include information about the 3
arbitrary edge vectors **A**, **B**, **C** that define the general
triclinic box as well as their origin. The format is described on the
:doc:`dump <dump>` doc page.
The coordinates of each atom will be output as values in (or near) the
general triclinic box. Likewise, per-atom vector quantities such as
velocity, omega, dipole moment, etc will have orientations consistent
with the general triclinic box, meaning they will be rotated relative
to the standard xyz coordinate axes. See the :doc:`dump <dump>` doc
page for a full list of which dump attributes this affects.
The coordinates of each atom will likewise be output as values in (or
near) the general triclinic box. Likewise, per-atom vector quantities
such as velocity, omega, dipole moment, etc will have orientations
consistent with the general triclinic box, meaning they will be
rotated relative to the standard xyz coordinate axes. See the
:doc:`dump <dump>` doc page for a full list of which dump attributes
this affects.
----------

27
doc/src/thermo_modify.rst
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@ -32,7 +32,7 @@ Syntax
*or* a thermo keyword or reference to compute, fix, property or variable.
*temp* value = compute ID that calculates a temperature
*press* value = compute ID that calculates a pressure
*triclinic/general* arg = none
*triclinic/general* arg = *yes* or *no*
Examples
@ -242,16 +242,18 @@ command, thermo output uses a default compute for pressure with ID =
keyword, then the new pressure compute specified by the *press*
keyword will be unaffected by the *temp* setting.
The *triclinic/general* keyword can only be used if the simulation box
was created as a general triclinic box. See the :doc:`Howto_triclinic
<Howto_triclinic>` doc page for a detailed explanation of orthogonal,
restricted triclinic, and general triclinic simulation boxes.
The *triclinic/general* keyword can only be used with a value of *yes*
if the simulation box was created as a general triclinic box. See the
:doc:`Howto_triclinic <Howto_triclinic>` doc page for a detailed
explanation of orthogonal, restricted triclinic, and general triclinic
simulation boxes.
If this keyword is used, the output of the simulation box edge vectors
and the pressure tensor components for the system are affected. These
are specified by the *avec,bvec,cvec* and *pxx,pyy,pzz,pxy,pxz,pyz*
keywords of the :doc:`thermo_style <thermo_style>` command. See the
:doc:`thermo_style <thermo_style>` doc page for details.
If this keyword is *yes*, the output of the simulation box edge
vectors and the pressure tensor components for the system are
affected. These are specified by the *avec,bvec,cvec* and
*pxx,pyy,pzz,pxy,pxz,pyz* keywords of the :doc:`thermo_style
<thermo_style>` command. See the :doc:`thermo_style <thermo_style>`
doc page for details.
Restrictions
""""""""""""
@ -266,8 +268,9 @@ Default
"""""""
The option defaults are lost = error, warn = 100, norm = yes for unit
style of *lj*, norm = no for unit style of *real* and *metal*,
flush = no, and temp/press = compute IDs defined by thermo_style.
style of *lj*, norm = no for unit style of *real* and *metal*, flush =
no, temp/press = compute IDs defined by thermo_style, and
triclinic/general = no.
The defaults for the line and format options depend on the thermo style.
For styles "one" and "custom", the line and format defaults are "one",

2
examples/README
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@ -115,7 +115,7 @@ tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
template: examples for using atom_style template and comparing to atom style molecular
tersoff: regression test input for Tersoff variants
threebody: regression test input for a variety of threebody potentials
triclinic: general and restricted triclinic examples
triclinic: general triclinic simulation box examples
ttm: two-temeperature model examples
vashishta: models using the Vashishta potential
voronoi: Voronoi tesselation via compute voronoi/atom command

8
src/dump_custom.cpp
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@ -1762,14 +1762,6 @@ int DumpCustom::modify_param(int narg, char **arg)
return 2;
}
if (strcmp(arg[0],"triclinic/general") == 0) {
triclinic_general = 1;
if (triclinic_general && !domain->triclinic_general)
error->all(FLERR,"Dump_modify triclinic/general cannot be used "
"if simulation box is not general triclinic");
return 1;
}
if (strcmp(arg[0],"triclinic/general") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
triclinic_general = utils::logical(FLERR,arg[1],false,lmp);

2
src/write_data.cpp
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@ -338,7 +338,7 @@ void WriteData::header()
domain->bvec[0],domain->bvec[1],domain->bvec[2],
domain->cvec[0],domain->cvec[1],domain->cvec[2]);
fmt::print(fp,"{} {} {} abc origin\n",
domain->boxlo[0],domain->boxlo[1],domain->boxhi[2]);
domain->boxlo[0],domain->boxlo[1],domain->boxlo[2]);
}
}