ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

new fix halt command, other sundry small bug fixes

Browse Source
This commit is contained in:
Steve Plimpton
2016-10-18 13:11:40 -06:00
parent 713b2af067
commit 2106dce2b3
41 changed files with 118040 additions and 110939 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
doc/src/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="12 Oct 2016 version">
<META NAME="docnumber" CONTENT="18 Oct 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
12 Oct 2016 version :c,h4
18 Oct 2016 version :c,h4
Version info: :h4

1
doc/src/Section_commands.txt
View File

@ -573,6 +573,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"gcmc"_fix_gcmc.html,
"gld"_fix_gld.html,
"gravity (o)"_fix_gravity.html,
"halt"_fix_halt.html,
"heat"_fix_heat.html,
"indent"_fix_indent.html,
"langevin (k)"_fix_langevin.html,

16
doc/src/dump_modify.txt
View File

@ -47,9 +47,9 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
id = sort per-atom lines by atom ID
N = sort per-atom lines in ascending order by the Nth column
-N = sort per-atom lines in descending order by the Nth column
{thresh} args = attribute operation value
{thresh} args = attribute operator value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
value = numeric value to compare to, or LAST
these 3 args can be replaced by the word "none" to turn off thresholding
{unwrap} arg = {yes} or {no} :pre
@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold.
If an atom-style variable is used as the attribute, then it can
produce continuous numeric values or effective Boolean 0/1 values
which may be useful for the comparision operation. Boolean values can
which may be useful for the comparision operator. Boolean values can
be generated by variable formulas that use comparison or Boolean math
operators or special functions like gmask() and rmask() and grmask().
See the "variable"_variable.html command doc page for details.
@ -503,11 +503,11 @@ less than 1/2 to greater than 1/2 (or vice versa) since the last dump.
E.g. due to reactions and subsequent charge equilibration in a
reactive force field.
The choice of operations are the usual comparison operators. The XOR
operation (exclusive or) is also included as "|^". In this context,
XOR means that if either the attribute or value is 0.0 and the other
is non-zero, then the result is "true" and the threshold criterion is
met. Otherwise it is not met.
The choice of operators listed above are the usual comparison
operators. The XOR operation (exclusive or) is also included as "|^".
In this context, XOR means that if either the attribute or value is
0.0 and the other is non-zero, then the result is "true" and the
threshold criterion is met. Otherwise it is not met.
:line

121
doc/src/fix_halt.txt Normal file
View File

@ -0,0 +1,121 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix halt command :h3
[Syntax:]
fix ID group-ID halt N attribute operator avalue keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
halt = style name of this fix command :l
N = check halt condition every N steps :l
attribute = hstyle or v_name :l
hstyle = {bondmax}
v_name = name of "equal-style variable"_variable.html :pre
operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l
avalue = numeric value to compare attribute to :l
string = text string to print with optional variable names :l
zero or more keyword/value pairs may be appended :l
keyword = {error} :l
{error} value = {hard} or {soft} or {continue} :pre
:ule
[Examples:]
fix 10 all halt 1 bondmax > 1.5
fix 10 all print 10 v_myCheck != 0 error soft :pre
[Description:]
Check a condition every N steps during a simulation run. N must be >=
1. If the condition is met, exit the run immediately. In this
context a "run" can be dynamics or minimization iterations, as
specified by the "run"_run.html or "minimize"_minimize.html command.
The specified group-ID is ignored by this fix.
The specified {attribute} can be one of the {hstyle} options listed
above, or an "equal-style variable"_variable.html referenced as
{v_name}, where "name" is the name of a variable that has been defined
previously in the input script.
The only {hstyle} option currently implemented is {bondmax}. This
will loop over all bonds in the system, compute their current
lengths, and set {attribute} to the longest bond distance.
Equal-style variables evaluate to a numeric value. See the
"variable"_variable.html command for a description. They calculate
formulas which can involve mathematical operations, atom properties,
group properties, thermodynamic properties, global values calculated
by a "compute"_compute.html or "fix"_fix.html, or references to other
"variables"_variable.html. Thus they are a very general means of
computing some attribute of the current system. For example, the
following "bondmax" variable will calculate the same quantity as the
hstyle = bondmax option.
compute bdist all bond/local dist
compute bmax all reduce max c_bdist
variable bondmax equal c_bmax :pre
Thus these two versions of a fix halt command will do the same thing:
fix 10 all halt 1 bondmax > 1.5
fix 10 all halt 1 v_bondmax > 1.5 :pre
The version with "bondmax" will just run somewhat faster, due to less
overhead in computing bond lengths and not storing them in a separate
compute.
The choice of operators listed above are the usual comparison
operators. The XOR operation (exclusive or) is also included as "|^".
In this context, XOR means that if either the attribute or avalue is
0.0 and the other is non-zero, then the result is "true". Otherwise
it is "false".
The specified {avalue} must be a numeric value.
:line
The optional {error} keyword determines how the current run is halted.
If its value is {hard}, then LAMMPS will stop with an error message.
If its value is {soft}, LAMMPS will exit the current run, but continue
to execute subsequent commands in the input script. However,
additional "run"_run.html or "minimize"_minimize.html commands will be
skipped. For example, this allows a script to output the current
state of the system, e.g. via a "write_dump"_write_dump.html or
"write_restart"_write_restart.html command.
If its value is {continue}, the behavior is the same as for {soft},
except subsequent subsequent "run"_run.html or
"minimize"_minimize.html commands are executed. This allows your
script to remedy the condition that triggered the halt, if necessary.
Note that you may wish use the "unfix"_unfix.html command on the fix
halt ID, so that the same condition is not immediately triggered in a
subsequent run.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"variable"_variable.html
[Default:]
The option defaults are error = hard.

5
doc/src/minimize.txt
View File

@ -103,6 +103,11 @@ the line search fails because the step distance backtracks to 0.0
the number of outer iterations or timesteps exceeds {maxiter}
the number of total force evaluations exceeds {maxeval} :ul
NOTE: You can also use the "fix halt"_fix_halt.html command to specify
a general criterion for exiting a minimization, that is a calculation
performed on the state of the current system, as defined by an
"equal-style variable"_variable.html.
For the first criterion, the specified energy tolerance {etol} is
unitless; it is met when the energy change between successive
iterations divided by the energy magnitude is less than or equal to

14
doc/src/run.txt
View File

@ -169,17 +169,17 @@ If the {pre} and {post} options are set to "no" when used with the
run will print the full timing summary, but these operations will be
skipped for intermediate runs.
NOTE: You might hope to specify a command that exits the run by
NOTE: You might wish to specify a command that exits the run by
jumping out of the loop, e.g.
variable t equal temp
run 10000 every 100 "if '$t < 300.0' then 'jump SELF afterrun'" :pre
Unfortunately this will not currently work. The run command simply
executes each command one at a time each time it pauses, then
continues the run. You can replace the jump command with a simple
"quit"_quit.html command and cause LAMMPS to exit during the
middle of a run when the condition is met.
However, this will not work. The run command simply executes each
command one at a time each time it pauses, then continues the run.
Instead, you should use the "fix halt"_fix_halt.html command, which
has additional options for how to exit the run.
[Restrictions:]
@ -198,7 +198,7 @@ successive runs to run a simulation for any number of steps (ok, up to
[Related commands:]
"minimize"_minimize.html, "run_style"_run_style.html,
"temper"_temper.html
"temper"_temper.html, "fix halt"_fix_halt.html
[Default:]