description:

</P>

<DIV ALIGN=center><TABLE  BORDER=1 >

<TR ALIGN="center"><TD ><A HREF = "compute_attribute_atom.html">attribute/atom</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>

<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum.html">sum</A></TD><TD ><A HREF = "compute_sum_atom.html">sum/atom</A></TD></TR>

<TR ALIGN="center"><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>

<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A> 

<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD></TR>

<TR ALIGN="center"><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum.html">sum</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD></TR>

<TR ALIGN="center"><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A> 

</TD></TR></TABLE></DIV>

<P>These are compute styles contributed by users, which can be used if

descriptions of each style or click on the style itself for a full

description:

"attribute/atom"_compute_attribute_atom.html,

"centro/atom"_compute_centro_atom.html,

"coord/atom"_compute_coord_atom.html,

"ke/atom"_compute_ke_atom.html,

"rotate/gran"_compute_rotate_gran.html,

"stress/atom"_compute_stress_atom.html,

"sum"_compute_sum.html,

"sum/atom"_compute_sum_atom.html,

"temp"_compute_temp.html,

"temp/asphere"_compute_temp_asphere.html,

"temp/deform"_compute_temp_deform.html,

"temp/dipole"_compute_temp_dipole.html,

"temp/partial"_compute_temp_partial.html,

"temp/ramp"_compute_temp_ramp.html,

"temp/region"_compute_temp_region.html,

"variable"_compute_variable.html,

"variable/atom"_compute_variable_atom.html :tb(c=6,ea=c)

"temp/region"_compute_temp_region.html :tb(c=6,ea=c)

These are compute styles contributed by users, which can be used if

"LAMMPS is built with the appropriate package"_Section_start.html#2_3.

screen and logfile.  The second is <A HREF = "dump.html">dump files</A>, which

contain snapshots of atoms and various per-atom values and are written

at a specified frequency.  A simulation prints one set of

thermodynamic output; it may generate zero, or one, or multiple dump

files.  LAMMPS gives you a variety of ways to determine what

thermodynamic output; it may generate any number of dump files.  As

discussed below, LAMMPS gives you a variety of ways to determine what

quantities are computed and printed when thermodynamic info or dump

files are output.  There are also three fixes which can do their own

output of user-defined quantities: <A HREF = "fix_ave_time.html">fix ave/time</A>

for time averaging, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> for spatial

averaging, and <A HREF = "fix_print.html">fix print</A>.  These are described below.

</P>

output of user-chosen quantities: <A HREF = "fix_ave_time.html">fix ave/time</A> for

time averaging, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> for spatial

averaging, and <A HREF = "fix_print.html">fix print</A>.  These are also described

below.  Throughout this discussion, note that users can <A HREF = "Section_modify.html">add their own

computes and fixes to LAMMPS</A> which can then

generate values that can be output with these commands.

</P>

<H5>Thermodynamic output 

</H5>

<P>The frequency and format of thermodynamic output is set by the

<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and

<A HREF = "thermo_modify.html">thermo_modify</A> commands.  The

<A HREF = "themo_style.html">thermo_style</A> command also specifies what values are

calculated and written out.  Pre-defined keywords can be specified

(e.g. press, etotal, etc) which include time-averaged versions of

temperature, pressure, and a few other variables (tave, pave, etc).

Three addtional kinds of keywords can also be specified (c_ID, f_ID,

v_name), where a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or

<A HREF = "variable.html">variable</A> provides the value(s) to be output.  Each of

these are described in turn.

(e.g. press, etotal, etc).  Three addtional kinds of keywords can also

be specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A> or

<A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the value to be

output.  Each of these are described in turn.

</P>

<P>In LAMMPS, a <A HREF = "compute.html">compute</A> comes in two flavors: ones that

compute one or more global values (e.g. temperature, kinetic energy

tensor) and ones that compute one or more per-atom values.  There is a

<A HREF = "compute_sum.html">compute sum</A> command which sums per-atom quantities

into a global scalar or vector.

</P>

<P>Only global quantities from a compute can be used for thermodynamic

output.  The user-defined ID of the compute is used along with an

optional subscript as part of the <A HREF = "thermo_style.html">thermo_style</A>

command.  E.g. c_myTemp outputs the single scalar value generated by

the compute; c_myTemp[2] would output the 2nd vector value.

</P>

<P><A HREF = "fix.html">Fixes</A> can also generate global scalar or vector values

which can be output with thermodynamic output, e.g. the energy of an

indenter's interaction with the simulation atoms.  These values are

accessed via the same format as a compute's values, as f_ID or

f_ID[N].  See the doc pages for individual fix commands to see which

ones generate global values that can be output with thermodynamic

info.  The <A HREF = "fix_ave_time.html">fix ave/time</A> command generates

time-averaged global quantities which can be accessed for

thermodynamic output.

</P>

<P>Input script variables of various kinds are defined by the

<A HREF = "variable.html">variable</A> command.  All kinds except the atom-style

variable can be used for thermodynamic output.  A variable with name

compute global values (e.g. temperature, pressure tensor) and ones

that compute per-atom values.  Only global quantities from a compute

can be used for thermodynamic output.  The user-defined ID of the

compute is used along with an optional subscript as part of the

<A HREF = "thermo_style.html">thermo_style</A> command.  E.g. c_myTemp outputs the

single scalar value generated by the compute; c_myTemp[2] outputs

the 2nd vector value.  Note that there is a <A HREF = "compute_sum.html">compute

sum</A> command which sums per-atom quantities into a

global scalar or vector.

</P>

<P><A HREF = "fix.html">Fixes</A> can generate global scalar or vector values which can

be output with thermodynamic output, e.g. the energy of an indenter's

interaction with the simulation atoms.  These values are accessed via

the same format as a compute's values, as f_ID or f_ID[N].  See the

doc pages for individual fix commands to see which ones generate

global values that can be output with thermodynamic info.  The <A HREF = "fix_ave_time.html">fix

ave/time</A> command generates time-averaged global

quantities which can be accessed for thermodynamic output, e.g. a

time-averaged pressure.

</P>

<P><A HREF = "variable.html">Variables</A> can be defined in the input script.  All

styles except the atom-style variable can be used for thermodynamic

output, since it generates per-atom values.  A variable with the name

"abc" is referenced in a thermo_style command as v_abc.

</P>

<P>The variable formula defined in the input script can contain math

functions (add, exp, etc), atom values (x[N], fx[N]), groups

quantities (mass(), vcm(), etc), references to thermodynamic

quantities (e.g. temp, volume, etc), or references to other variables

or <A HREF = "compute.html">computes</A> or <A HREF = "fix.html">fixes</A>.  Thus a variable is

the most general way to define some quantity you want calculated and

output with thermodynamic info.

<P>The formula associated with equal-style variables can contain math

operations and functions (x+y,x*y,(),sqrt,exp,etc), atom values

(x[N],fx[N],etc), group functions (mass(),vcm(),etc), references

to thermodynamic quantities (temp,press,vol,etc), references to

<A HREF = "compute.html">computes</A> that generate global values, references to

<A HREF = "fix.html">fixes</A> that generate global values, or references to other

<A HREF = "variable.html">variables</A>.  Thus an equal-style variable is the most

general way to define some quantity to calculate and include with

thermodynamic output.

</P>

<H5>Dump file output 

</H5>

<P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and

<A HREF = "dump_modify.html">dump_modify</A> commands.  There are several

pre-defined formats (dump atom, dump xtc, etc).  There is also a <A HREF = "dump.html">dump

custom</A> format where you specify what values are output with

each atom.  Pre-defined keywords can be specified (e.g. tag, type, x,

etc).  Two additional kinds of keywords can also be specified (c_ID,

f_ID), where a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> provides the

values to be output.

</P>

<P><A HREF = "compute.html">Computes</A> that generate per-atom values can be accessed

by the dump custom command.  These are computes that have the word

"atom" in their style name, e.g. ke/atom, stress/atom, etc.  The

values are accessed as c_myKE for a scalar per-atom quantity or as

c_myStress[2] for a component of a vector per-atom quantity.  The

<A HREF = "compute_variable_atom.html">compute variable/atom</A> command takes a

user-defined atom-style <A HREF = "variable.html">variable</A> as input and

calculates its value for each atom.  Since this compute can be

accessed by the dump custom command, this is a general way to define

some quantity you want calculated and output in a dump file.

</P>

<P><A HREF = "fix.html">Fixes</A> can also generate per-atom values to output to dump

files.  For example, the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command

calculates time-averages of compute quantities.  As indicated in the

preceeding paragraph, a <A HREF = "compute.html">compute quantity</A> can be a

calculated value such as <A HREF = "compute_epair_atom.html">energy</A> or

<A HREF = "compute_stress_atom.html">stress</A> or it can be a value calculated by

an atom-style <A HREF = "variable.html">variable</A>, or it can be an <A HREF = "compute_attribute_atom.html">atom

attribute</A> such as velocity or force.

These per-atom fix values are accessed by the <A HREF = "dump.html">dump custom</A>

command as f_myKE for a scalar per-atom quantity or as f_myStress[2]

for a component of a vector per-atom quantity.

custom</A> format where the user specifies what values are

output with each atom.  Pre-defined keywords can be specified (tag, x,

fx, etc).  Three additional kinds of keywords can also be specified

(c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A>

or <A HREF = "variable.html">variable</A> provides the value to be output.  Each of

these are described in turn.

</P>

<P><A HREF = "compute.html">Computes</A> that generate one or more per-atom values can

be accessed by the dump custom command.  These are computes that have

the word "atom" in their style name, e.g. ke/atom, stress/atom, etc.

The values are accessed as c_myKE for a scalar per-atom quantity or as

c_myStress[2] for a component of a vector per-atom quantity.

</P>

<P><A HREF = "fix.html">Fixes</A> can generate per-atom values to output to dump files.

For example, the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command calculates

time-averages of per-atom quantities, such as per-atom

<A HREF = "compute.html">computes</A> and atom-style <A HREF = "variable.html">variables</A>.

These per-atom fix values are accessed by the <A HREF = "dump.html">dump custom</A>

command via the same format as a compute's values, as f_myKE or

f_myStress[2].

</P>

<P><A HREF = "variable.html">Variables</A> can be defined in the input script.  Only

atom-style variables can be used for dump custom output, since only

they produce per-atom values.  A variable with the name "abc" is

referenced in a dump custom command as v_abc.

</P>

<P>Just like equal-style variables, the formula associated with

atom-style variables can contain math operations and functions

(x+y,x*y,(),sqrt,exp,etc), atom values (x[N],fx[N],etc), group

functions (mass(),vcm(),etc), references to thermodynamic quantities

(temp,press,vol,etc), references to <A HREF = "compute.html">computes</A> that

generate global values, references to <A HREF = "fix.html">fixes</A> that generate

global values, or references to non atom-style variables that generate

global values.  In addition, an atom-style variable can reference

vectors of atom values (x[],fx[],etc), <A HREF = "compute.html">computes</A>

that generate per-atom values, <A HREF = "fix.html">fixes</A> that generate per-atom

values, or other atom-style variables.  Thus an atom-style variable is

the most general way to define some quantity to calculate and output

to a dump file.

</P>

<H5>Fix output 

</H5>

<P>Three other fixes are of particular note for output: <A HREF = "fix_ave_time.html">fix

ave/time</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,

and <A HREF = "fix_print.html">fix print</A>.

</P>

<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables time-averaging of

global quantities like temperature or pressure.  The global quantities

are calculated by a <A HREF = "compute.html">compute</A> or a <A HREF = "fix.html">fix</A>.  The

compute or fix must generate global scalar or vector quantities.  Note

that this includes the "compute sum" command which computes global

values by summing per-atom quantities.  The time-averaged values

generated by <A HREF = "fix_ave_time.html">fix ave/time</A> can be written directly

to a file and/or accessed by any output command that uses fixes as a

source of input, e.g. the <A HREF = "thermo_style.html">thermo_style custom</A>

command.  Fix ave/time options allow for running cummulative averages

or moving time-windowed averages to be output.

any global quantity, like those output with thermodynamic info.  The

user specifies one or more quantities to time average.  These can be

global <A HREF = "compute.html">compute</A> values, global <A HREF = "fix.html">fix</A> values, or

<A HREF = "variable.html">variables</A> of any style except the atom style which

produces per-atom values.  Since a variable can refer to keywords used

by the <A HREF = "thermo_style.html">thermo_style custom</A> command (like temp or

press), any thermodynamic quantity can be time averaged in this way.

</P>

<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command offers several options

for how it performs time averaging.  The results it produces can be

used in two ways.  First, they can be written directly to a file, one

line per timestamp.  Note that the averaging parameters can be

specified in such a way that averaging is not done at all, in which

case this is simply a convenient means of outputting desired

quantities directly to a separate file.  Like other fixes that produce

global quantities, the results of this fix can also be used as input

to any command that accesses global quantities, e.g. by the

<A HREF = "thermo_style.html">thermo_style custom</A> command, by a variable, etc.

</P>

<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables

spatial-averaging of per-atom quantities like per-atom energy or

stress.  The per-atom quantities can be atom density (mass or number)

or be calculated by a <A HREF = "compute.html">compute</A> or a <A HREF = "fix.html">fix</A>.  The

compute or fix must generate per-atom scalar or vector quantities.

Note that if you use the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command with

fix ave/spatial, it means you are effectively calculating a time

average of a spatial average of a time-averaged per-atom quantity.

The time-averaged values generated by <A HREF = "fix_ave_spatial.html">fix

ave/spatial</A> can be written directly to a file

and/or accessed by any output command that uses fixes as a source of

input, e.g. the <A HREF = "thermo_style.html">thermo_style custom</A> command.  Fix

ave/spatial options allow for running cummulative averages or moving

time-windowed averages to be output.

spatial-averaging of per-atom quantities like those output in dump

files, within 1d layers of the simulation box.  The per-atom

quantities can be atom density (mass or number) or atom attributes

such as position, velocity, force.  They can also be per-atom

quantities calculated by a <A HREF = "compute.html">compute</A>, by a

<A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>.

</P>

<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command offers several

options for how it performs time averaging.  The per-layer values it

produces can be used in two ways.  First, they can be written directly

to a file.  Note that the averaging parameters can be specified in

such a way that time averaging is not done, in which case this is a

convenient means of simply outputting desired quanitities (summed over

atoms within a 1d layer) directly to a separate file.  Like other

fixes that produce global quantities, the results of this fix can also

be used as input by any command that accesses global quantities,

e.g. by the <A HREF = "thermo_style.html">thermo_style custom</A> command, by a

variable, etc.  See the doc page for <A HREF = "fix_ave_spatial.html">fix

ave/spatial</A> for a description of how these

values are indexed.

</P>

<P>The <A HREF = "fix_print.html">fix print</A> command can generate a line of output

written to the screen and log file periodically during a running

simulation.  Since the line can contain one or more

<A HREF = "variable.html">variable</A> quantities, this command is a means to output

desired calculated quantities that are not part of thermodynamic or

dump file output.

</P>

written to the screen and log file or to a separate file, periodically

during a running simulation.  The line can contain one or more

<A HREF = "variable.html">variable</A> values (for any style variable except the

atom style), and as explained above, variables themselves can contain

references to global values generated by <A HREF = "thermo_style.html">thermodynamic

keywords</A>, <A HREF = "compute.html">computes</A>,

<A HREF = "fix.html">fixes</A>, or other <A HREF = "variable.html">variables</A>.  Thus the <A HREF = "fix_print.html">fix

print</A> command is a means to output any desired

calculated quantity separate from normal thermodynamic or dump file

output.

</P>

<P>This table summarizes the various output options, specifying what

their inputs and outputs are.  The frequency with which they are

invoked and produce output is also listed.  Basically, any two

commands can be hooked together so long as one produces output that

matches the input needs of the other.  A "match" means that the

frequencies and global vs per-atom attributes are the same.

</P>

<DIV ALIGN=center><TABLE  BORDER=1 >

<TR><TD >Command</TD><TD > Input</TD><TD > Input Freq</TD><TD > Output</TD><TD > Output Freq</TD></TR>

<TR><TD >thermo_style custom</TD><TD > thermo keyword, global scalar/vector compute, global scalar/vector fix, equal variable</TD><TD > nthermo</TD><TD > screen, log</TD><TD > nthermo</TD></TR>

<TR><TD >dump custom</TD><TD > keyword, peratom scalar/vector compute, peratom scalar/vector fix, atom variable</TD><TD > dump freq</TD><TD > file</TD><TD > dump freq</TD></TR>

<TR><TD >global fixes</TD><TD > N/A</TD><TD > N/A</TD><TD >	global scalar/vector</TD><TD > 1 or nevery</TD></TR>

<TR><TD >peratom fixes</TD><TD > N/A</TD><TD > N/A</TD><TD > peratom scalar/vector</TD><TD > 1 or nevery</TD></TR>

<TR><TD >fix ave/time</TD><TD > global scalar/vector fix, global scalar/vector compute, equal variable</TD><TD > nevery</TD><TD > global scalar/vector, file</TD><TD > nfreq</TD></TR>

<TR><TD >fix ave/spatial</TD><TD > peratom scalar/vector fix, peratom scalar/vector compute, atom vector, atom variable, density mass/number</TD><TD > nevery</TD><TD > global vector</TD><TD > nfreq, file</TD></TR>

<TR><TD >fix ave/atom</TD><TD > peratom scalar/vector compute, peratom scalar/vector fix, atom variable, atom vector</TD><TD > nevery</TD><TD > peratom scalar/vector</TD><TD > nfreq</TD></TR>

<TR><TD >fix print</TD><TD > any variable</TD><TD > nevery</TD><TD > screen, file</TD><TD > nevery</TD></TR>

<TR><TD >global computes</TD><TD > N/A</TD><TD > N/A</TD><TD > global scalar/vector</TD><TD > N/A</TD></TR>

<TR><TD >peratom computes</TD><TD > N/A</TD><TD > N/A</TD><TD > peratom scalar/vector</TD><TD > N/A</TD></TR>

<TR><TD >compute sum</TD><TD > peratom scalar/vector compute, peratom scalar/vector fix, atom variable</TD><TD > N/A</TD><TD > global scalar/vector</TD><TD > N/A</TD></TR>

<TR><TD >variable equal</TD><TD > thermo keywords, atom value vx[123], global scalar/vector compute, global scalar/vector fix, non-atom variable</TD><TD > N/A</TD><TD > global scalar</TD><TD > N/A</TD></TR>

<TR><TD >variable atom</TD><TD > thermo keywords, atom value vx[123], atom vector vx[], global scalar/vector compute, peratom scalar/vector compute, global scalar/vector fix, peratom scalar/vector fix, any variable</TD><TD > N/A</TD><TD > peratom scalar</TD><TD > N/A</TD></TR>

<TR><TD >print</TD><TD > any variable</TD><TD > N/A</TD><TD > screen, log</TD><TD > between runs</TD></TR>

<TR><TD >run every</TD><TD > any variable</TD><TD > nevery</TD><TD > screen, log</TD><TD > nevery 

</TD></TR></TABLE></DIV>

<HR>

<HR>

<A NAME = "Cornell"></A>