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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2591 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2009-02-17 14:58:00 +00:00
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62
doc/variable.html
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@ -443,10 +443,11 @@ evaluated later.
evaluation is performed. Depending on what is included in the evaluation is performed. Depending on what is included in the
formula, this may require invoking a <A HREF = "compute.html">compute</A>, either formula, this may require invoking a <A HREF = "compute.html">compute</A>, either
directly or indirectly via a thermo keyword, or accessing a value directly or indirectly via a thermo keyword, or accessing a value
calculated and stored by a <A HREF = "fix.html">fix</A>. If the compute is one that previously calculated by a compute, or accessing a value calculated
calculates the pressure or energy of the system, then these quantities and stored by a <A HREF = "fix.html">fix</A>. If the compute is one that calculates
need to be tallied during the evaluation of the interatomic potentials the pressure or energy of the system, then these quantities need to be
(pair, bond, etc) on timesteps that the variable will need the values. tallied during the evaluation of the interatomic potentials (pair,
bond, etc) on timesteps that the variable will need the values.
</P> </P>
<P>LAMMPS keeps track of all of this during a <A HREF = "run.html">run</A> or <A HREF = "minimize.html">energy <P>LAMMPS keeps track of all of this during a <A HREF = "run.html">run</A> or <A HREF = "minimize.html">energy
minimization</A>. An error will be generated if you minimization</A>. An error will be generated if you
@ -455,29 +456,29 @@ accurate values. For example, if a <A HREF = "thermo_style.html">thermo_style
custom</A> command prints a variable which accesses custom</A> command prints a variable which accesses
values stored by a <A HREF = "fix_ave_time.html">fix ave/time</A> command and the values stored by a <A HREF = "fix_ave_time.html">fix ave/time</A> command and the
timesteps on which thermo output is generated are not multiples of the timesteps on which thermo output is generated are not multiples of the
averaging frequency used in the fix command, then it is an error. averaging frequency used in the fix command, then an error will occur.
</P> </P>
<P>However, your input script can also require variables to be evaluated <P>An input script can also request variables be evaluated before or
before or after or inbetween runs. In this case, one of three things after or in between runs, e.g. by including them in a
may happen. <A HREF = "print.html">print</A> command. In this case, if a compute is needed to
evaluate a variable (either directly or indirectly), LAMMPS will not
invoke the compute, but it will use a value previously calculated by
the compute if it is current. Fixes will always provide a quantity
needed by a variable, but the quantity may or may not be current.
This leads to one of three kinds of behavior:
</P> </P>
<P>(1) The variable may be evaluated accurately. If it contains <P>(1) The variable may be evaluated accurately. If it contains
references to a compute or fix, and these values were calculated and references to a compute or fix, and these values were calculated on
stored on the last timestep of a preceeding run, then they can be the last timestep of a preceeding run, then they will be accessed and
accessed and used by the variable. used by the variable and the result will be accurate.
</P> </P>
<P>(2) LAMMPS may not be able to evaluate the variable and generate an <P>(2) LAMMPS may not be able to evaluate the variable and generate an
error. For example, if the variable formula requires a error. For example, if the variable requires a quantity from a
<A HREF = "compute.html">compute</A> to be invoked, either directly or indirectly <A HREF = "compute.html">compute</A> that is not current, LAMMPS will not do it.
via a thermo keyword, then the variable cannot be evaluated before the This means, for example, that such a variable then the variable cannot
first run has occurred. The general rule is that if a variable uses a be evaluated before the first run has occurred.
value calculated by a compute, and the variable is not being evaluated
during a run, then the variable will not invoke the compute. Instead,
it can only use the value stored by the compute, which for accuracy
requires that the compute was already invoked on the same timestep
during a preceeding run.
</P> </P>
<P>Thus the way to get around this error is to perform a 0-timestep run <P>One way to get around this problem is to perform a 0-timestep run
before using the variable. For example, these commands before using the variable. For example, these commands
</P> </P>
<PRE>variable t equal temp <PRE>variable t equal temp
@ -500,21 +501,20 @@ the one for temperature, so that the value it stores is current and
can be accessed by the variable "t" after the run has completed. Note can be accessed by the variable "t" after the run has completed. Note
that a 0-timestep run does not alter the state of the system, so it that a 0-timestep run does not alter the state of the system, so it
does not change the input state for the 1000-timestep run that does not change the input state for the 1000-timestep run that
follows. Also note, that the 0-timestep run must actually use and follows. Also note that the 0-timestep run must actually use and
invoke the compute in question (e.g. via <A HREF = "thermo_style.html">thermo</A> or invoke the compute in question (e.g. via <A HREF = "thermo_style.html">thermo</A> or
<A HREF = "dump.html">dump</A> output) in order for it to enable the compute to be <A HREF = "dump.html">dump</A> output) in order for it to enable the compute to be
used in a variable after the run. used in a variable after the run.
</P> </P>
<P>Note that unlike computes, <A HREF = "fix.html">fixes</A> will never generate an <P>Unlike computes, <A HREF = "fix.html">fixes</A> will never generate an error if
error if their values are accessed by a variable in between runs. their values are accessed by a variable in between runs. They always
They always return some value to the variable. However, this value return some value to the variable. However, the value may not be what
may not be what you expect if the fix has not yet calculated the you expect if the fix has not yet calculated the quantity of interest
quantity of interest. For example, the <A HREF = "fix_indent.html">fix indent</A> or it is not current. For example, the <A HREF = "fix_indent.html">fix indent</A>
command stores the force on the indenter. But this is not computed command stores the force on the indenter. But this is not computed
until a run is performed. Thus if a variable attempts to print this until a run is performed. Thus if a variable attempts to print this
value before the first run, values of zero will be output. Again, value before the first run, zeroes will be output. Again, performing
performing a 0-timestep run before printing the variable has the a 0-timestep run before printing the variable has the desired effect.
desired effect.
</P> </P>
<P>(3) The variable may be evaluated incorrectly. And LAMMPS may have <P>(3) The variable may be evaluated incorrectly. And LAMMPS may have
no way to detect this has occurred. Consider the following sequence no way to detect this has occurred. Consider the following sequence
@ -540,7 +540,7 @@ could alter the state of the system between runs, causing a variable
to evaluate incorrectly. to evaluate incorrectly.
</P> </P>
<P>The solution to this issue is the same as for case (2) above, namely <P>The solution to this issue is the same as for case (2) above, namely
to perform a 0-timestep run before the variable is evaluated to insure perform a 0-timestep run before the variable is evaluated to insure
the system is up-to-date. For example, this sequence of commands the system is up-to-date. For example, this sequence of commands
would print a potential energy that reflected the changed pairwise would print a potential energy that reflected the changed pairwise
coefficient: coefficient:

62
doc/variable.txt
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@ -434,10 +434,11 @@ Obviously, LAMMPS attempts to evaluate variables containing formulas
evaluation is performed. Depending on what is included in the evaluation is performed. Depending on what is included in the
formula, this may require invoking a "compute"_compute.html, either formula, this may require invoking a "compute"_compute.html, either
directly or indirectly via a thermo keyword, or accessing a value directly or indirectly via a thermo keyword, or accessing a value
calculated and stored by a "fix"_fix.html. If the compute is one that previously calculated by a compute, or accessing a value calculated
calculates the pressure or energy of the system, then these quantities and stored by a "fix"_fix.html. If the compute is one that calculates
need to be tallied during the evaluation of the interatomic potentials the pressure or energy of the system, then these quantities need to be
(pair, bond, etc) on timesteps that the variable will need the values. tallied during the evaluation of the interatomic potentials (pair,
bond, etc) on timesteps that the variable will need the values.
LAMMPS keeps track of all of this during a "run"_run.html or "energy LAMMPS keeps track of all of this during a "run"_run.html or "energy
minimization"_minimize.html. An error will be generated if you minimization"_minimize.html. An error will be generated if you
@ -446,29 +447,29 @@ accurate values. For example, if a "thermo_style
custom"_thermo_style.html command prints a variable which accesses custom"_thermo_style.html command prints a variable which accesses
values stored by a "fix ave/time"_fix_ave_time.html command and the values stored by a "fix ave/time"_fix_ave_time.html command and the
timesteps on which thermo output is generated are not multiples of the timesteps on which thermo output is generated are not multiples of the
averaging frequency used in the fix command, then it is an error. averaging frequency used in the fix command, then an error will occur.
However, your input script can also require variables to be evaluated An input script can also request variables be evaluated before or
before or after or inbetween runs. In this case, one of three things after or in between runs, e.g. by including them in a
may happen. "print"_print.html command. In this case, if a compute is needed to
evaluate a variable (either directly or indirectly), LAMMPS will not
invoke the compute, but it will use a value previously calculated by
the compute if it is current. Fixes will always provide a quantity
needed by a variable, but the quantity may or may not be current.
This leads to one of three kinds of behavior:
(1) The variable may be evaluated accurately. If it contains (1) The variable may be evaluated accurately. If it contains
references to a compute or fix, and these values were calculated and references to a compute or fix, and these values were calculated on
stored on the last timestep of a preceeding run, then they can be the last timestep of a preceeding run, then they will be accessed and
accessed and used by the variable. used by the variable and the result will be accurate.
(2) LAMMPS may not be able to evaluate the variable and generate an (2) LAMMPS may not be able to evaluate the variable and generate an
error. For example, if the variable formula requires a error. For example, if the variable requires a quantity from a
"compute"_compute.html to be invoked, either directly or indirectly "compute"_compute.html that is not current, LAMMPS will not do it.
via a thermo keyword, then the variable cannot be evaluated before the This means, for example, that such a variable then the variable cannot
first run has occurred. The general rule is that if a variable uses a be evaluated before the first run has occurred.
value calculated by a compute, and the variable is not being evaluated
during a run, then the variable will not invoke the compute. Instead,
it can only use the value stored by the compute, which for accuracy
requires that the compute was already invoked on the same timestep
during a preceeding run.
Thus the way to get around this error is to perform a 0-timestep run One way to get around this problem is to perform a 0-timestep run
before using the variable. For example, these commands before using the variable. For example, these commands
variable t equal temp variable t equal temp
@ -491,21 +492,20 @@ the one for temperature, so that the value it stores is current and
can be accessed by the variable "t" after the run has completed. Note can be accessed by the variable "t" after the run has completed. Note
that a 0-timestep run does not alter the state of the system, so it that a 0-timestep run does not alter the state of the system, so it
does not change the input state for the 1000-timestep run that does not change the input state for the 1000-timestep run that
follows. Also note, that the 0-timestep run must actually use and follows. Also note that the 0-timestep run must actually use and
invoke the compute in question (e.g. via "thermo"_thermo_style.html or invoke the compute in question (e.g. via "thermo"_thermo_style.html or
"dump"_dump.html output) in order for it to enable the compute to be "dump"_dump.html output) in order for it to enable the compute to be
used in a variable after the run. used in a variable after the run.
Note that unlike computes, "fixes"_fix.html will never generate an Unlike computes, "fixes"_fix.html will never generate an error if
error if their values are accessed by a variable in between runs. their values are accessed by a variable in between runs. They always
They always return some value to the variable. However, this value return some value to the variable. However, the value may not be what
may not be what you expect if the fix has not yet calculated the you expect if the fix has not yet calculated the quantity of interest
quantity of interest. For example, the "fix indent"_fix_indent.html or it is not current. For example, the "fix indent"_fix_indent.html
command stores the force on the indenter. But this is not computed command stores the force on the indenter. But this is not computed
until a run is performed. Thus if a variable attempts to print this until a run is performed. Thus if a variable attempts to print this
value before the first run, values of zero will be output. Again, value before the first run, zeroes will be output. Again, performing
performing a 0-timestep run before printing the variable has the a 0-timestep run before printing the variable has the desired effect.
desired effect.
(3) The variable may be evaluated incorrectly. And LAMMPS may have (3) The variable may be evaluated incorrectly. And LAMMPS may have
no way to detect this has occurred. Consider the following sequence no way to detect this has occurred. Consider the following sequence
@ -531,7 +531,7 @@ could alter the state of the system between runs, causing a variable
to evaluate incorrectly. to evaluate incorrectly.
The solution to this issue is the same as for case (2) above, namely The solution to this issue is the same as for case (2) above, namely
to perform a 0-timestep run before the variable is evaluated to insure perform a 0-timestep run before the variable is evaluated to insure
the system is up-to-date. For example, this sequence of commands the system is up-to-date. For example, this sequence of commands
would print a potential energy that reflected the changed pairwise would print a potential energy that reflected the changed pairwise
coefficient: coefficient: