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sjplimp 2010-08-17 21:58:29 +00:00
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20
doc/Section_commands.html
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@ -323,16 +323,16 @@ in the command's documentation.
of each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_nh.html">nph</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere</A></TD><TD ><A HREF = "fix_nh.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nh.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A>
<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_nh.html">nph</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere</A></TD><TD ><A HREF = "fix_nh.html">npt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nh.html">nvt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A>
</TD></TR></TABLE></DIV>
<P>These are fix styles contributed by users, which can be used if

1
doc/Section_commands.txt
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@ -386,6 +386,7 @@ of each style or click on the style itself for a full description:
"addforce"_fix_addforce.html,
"aveforce"_fix_aveforce.html,
"ave/atom"_fix_ave_atom.html,
"ave/correlate"_fix_ave_correlate.html,
"ave/histo"_fix_ave_histo.html,
"ave/spatial"_fix_ave_spatial.html,
"ave/time"_fix_ave_time.html,

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doc/Section_howto.html
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@ -1093,9 +1093,11 @@ command.
</P>
<H5><A NAME = "fixoutput"></A>Fixes that write output files
</H5>
<P>Three fixes take various quantities as input and can write output
<P>Sevarl fixes take various quantities as input and can write output
files: <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>.
ave/spatial</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,
<A HREF = "fix_ave_correlate.html">fix ave/correlate</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 direct output to
a file and/or time-averaging of global scalars or vectors. The user
@ -1126,6 +1128,11 @@ to a file of histogrammed quantities, which can be global or per-atom
or local quantities. The histogram output of this fix can also be
used as input to other output commands.
</P>
<P>The <A HREF = "fix_ave_histo.html">fix ave/correlate</A> command enables direct
output to a file of time-correlated quantities, which can be global
scalars. The correlation matrix output of this fix can also be used
as input to other output commands.
</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 or to a separate file, periodically
during a running simulation. The line can contain one or more
@ -1141,10 +1148,10 @@ from normal thermodynamic or dump file output.
<H5><A NAME = "computeoutput"></A>Computes that process output quantities
</H5>
<P>The <A HREF = "compute_reduce.html">compute reduce</A> and <A HREF = "compute_reduce.html">compute
reduce/region</A> commands take one or more vector
quantities as inputs and "reduce" them (sum, min, max, ave) to scalar
quantities. These are produced as output values which can be used as
input to other output commands.
reduce/region</A> commands take one or more per-atom
or local vector quantities as inputs and "reduce" them (sum, min, max,
ave) to scalar quantities. These are produced as output values which
can be used as input to other output commands.
</P>
<P>The <A HREF = "compute_property_atom.html">compute property/atom</A> command takes a
list of one or more pre-defined atom attributes (id, x, fx, etc) and
@ -1169,9 +1176,9 @@ quantities calculated by a <A HREF = "compute.html">compute</A>, by a
time-averaged per-atom output of this fix can be used as input to
other output commands.
</P>
<P>The <A HREF = "fix_ave_atom.html">fix store</A> command can archive one or more
per-atom attributes at a particular time, so that the old values can
be used in a future calculation or output. The list of atom
<P>The <A HREF = "fix_store_state.html">fix store/state</A> command can archive one or
more per-atom attributes at a particular time, so that the old values
can be used in a future calculation or output. The list of atom
attributes is the same as for the <A HREF = "dump.html">dump custom</A> command,
including 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>.
@ -1232,14 +1239,15 @@ vector input could be a column of an array.
<TR><TD ><A HREF = "compute.html">computes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix.html">fixes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "variable.html">variables</A></TD><TD > global scalars, per-atom vectors</TD><TD > global scalar, per-atom vector</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_reduce.html">compute reduce</A></TD><TD > global/per-atom/local vectors</TD><TD > global scalar/vector</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_reduce.html">compute reduce</A></TD><TD > per-atom/local vectors</TD><TD > global scalar/vector</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_property_atom.html">compute property/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "compute_property_local.html">compute property/local</A></TD><TD > local vectors</TD><TD > local vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_atom.html">fix ave/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_time.html">fix ave/time</A></TD><TD > global scalars/vectors</TD><TD > global scalar/vector/array, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_spatial.html">fix ave/spatial</A></TD><TD > per-atom vectors</TD><TD > global array, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_histo.html">fix ave/histo</A></TD><TD > global/per-atom/local scalars and vectors</TD><TD > global array, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_store.html">fix store</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_ave_correlate.html">fix ave/correlate</A></TD><TD > global scalars</TD><TD > global array, file</TD><TD ></TD></TR>
<TR><TD ><A HREF = "fix_store_state.html">fix store/state</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
<TR><TD >
</TD></TR></TABLE></DIV>

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@ -1084,9 +1084,11 @@ command.
Fixes that write output files :h5,link(fixoutput)
Three fixes take various quantities as input and can write output
Sevarl fixes take various quantities as input and can write output
files: "fix ave/time"_fix_ave_time.html, "fix
ave/spatial"_fix_ave_spatial.html, and "fix print"_fix_print.html.
ave/spatial"_fix_ave_spatial.html, "fix ave/histo"_fix_ave_histo.html,
"fix ave/correlate"_fix_ave_correlate.html, and "fix
print"_fix_print.html.
The "fix ave/time"_fix_ave_time.html command enables direct output to
a file and/or time-averaging of global scalars or vectors. The user
@ -1117,6 +1119,11 @@ to a file of histogrammed quantities, which can be global or per-atom
or local quantities. The histogram output of this fix can also be
used as input to other output commands.
The "fix ave/correlate"_fix_ave_histo.html command enables direct
output to a file of time-correlated quantities, which can be global
scalars. The correlation matrix output of this fix can also be used
as input to other output commands.
The "fix print"_fix_print.html command can generate a line of output
written to the screen and log file or to a separate file, periodically
during a running simulation. The line can contain one or more
@ -1132,10 +1139,10 @@ from normal thermodynamic or dump file output.
Computes that process output quantities :h5,link(computeoutput)
The "compute reduce"_compute_reduce.html and "compute
reduce/region"_compute_reduce.html commands take one or more vector
quantities as inputs and "reduce" them (sum, min, max, ave) to scalar
quantities. These are produced as output values which can be used as
input to other output commands.
reduce/region"_compute_reduce.html commands take one or more per-atom
or local vector quantities as inputs and "reduce" them (sum, min, max,
ave) to scalar quantities. These are produced as output values which
can be used as input to other output commands.
The "compute property/atom"_compute_property_atom.html command takes a
list of one or more pre-defined atom attributes (id, x, fx, etc) and
@ -1160,9 +1167,9 @@ quantities calculated by a "compute"_compute.html, by a
time-averaged per-atom output of this fix can be used as input to
other output commands.
The "fix store"_fix_ave_atom.html command can archive one or more
per-atom attributes at a particular time, so that the old values can
be used in a future calculation or output. The list of atom
The "fix store/state"_fix_store_state.html command can archive one or
more per-atom attributes at a particular time, so that the old values
can be used in a future calculation or output. The list of atom
attributes is the same as for the "dump custom"_dump.html command,
including per-atom quantities calculated by a "compute"_compute.html,
by a "fix"_fix.html, or by an atom-style "variable"_variable.html.
@ -1222,14 +1229,15 @@ Command: Input: Output:
"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array:
"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array:
"variables"_variable.html: global scalars, per-atom vectors: global scalar, per-atom vector:
"compute reduce"_compute_reduce.html: global/per-atom/local vectors: global scalar/vector:
"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector:
"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array:
"compute property/local"_compute_property_local.html: local vectors: local vector/array:
"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:
"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file:
"fix ave/spatial"_fix_ave_spatial.html: per-atom vectors: global array, file:
"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file:
"fix store"_fix_store.html: per-atom vectors: per-atom vector/array:
"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file:
"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array:
:tb(s=:)
:line

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@ -32,10 +32,10 @@
<LI>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
<PRE> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
c_ID = vector calculated by a compute with ID
c_ID[I] = Ith column of array calculated by a compute with ID
f_ID = vector calculated by a fix with ID
f_ID[I] = Ith column of array calculated by a fix with ID
c_ID = per-atom or local vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
f_ID = per-atom or local vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
</PRE>
<LI>zero or more keyword/args pairs may be appended
@ -58,11 +58,14 @@ compute 3 fluid reduce max c_index<B>1</B> c_index<B>2</B> c_dist replace 1 3 re
<P><B>Description:</B>
</P>
<P>Define a calculation that "reduces" one or more vector inputs into
scalar values, one per listed input. The inputs can be global,
per-atom, or local quantities. Atom attributes are per-atom
quantities, <A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> may generate
any of the three kinds of quantities, and <A HREF = "variable.html">atom-style
variables</A> generate per-atom quantities.
scalar values, one per listed input. The inputs can be per-atom or
local quantities; they cannot be global quantities. Atom attributes
are per-atom quantities, <A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A>
may generate any of the three kinds of quantities, and <A HREF = "variable.html">atom-style
variables</A> generate per-atom quantities. See the
<A HREF = "variable">variable</A> command and its special functions which can
perform the same operations as the compute reduce command on global
vectors.
</P>
<P>The reduction operation is specified by the <I>mode</I> setting. The <I>sum</I>
option adds the values in the vector into a global total. The <I>min</I>
@ -92,8 +95,8 @@ property/atom</A> command and then specifying
an input value from that compute.
</P>
<P>If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. Computes can generate global,
per-atom, or local quantities. See the individual
previously defined in the input script. Computes can generate
per-atom or local quantities. See the individual
<A HREF = "compute.html">compute</A> doc page for details. If no bracketed integer
is appended, the vector calculated by the compute is used. If a
bracketed interger is appended, the Ith column of the array calculated
@ -101,10 +104,10 @@ by the compute is used. Users can also write code for their own
compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
</P>
<P>If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. Fixes can generate global,
per-atom, or local quantities. See the individual <A HREF = "fix.html">fix</A> doc
page for details. Note that some fixes only produce their values on
certain timesteps, which must be compatible with when compute reduce
previously defined in the input script. Fixes can generate per-atom
or local quantities. See the individual <A HREF = "fix.html">fix</A> doc page for
details. Note that some fixes only produce their values on certain
timesteps, which must be compatible with when compute reduce
references the values, else an error results. If no bracketed integer
is appended, the vector calculated by the fix is used. If a bracketed
integer is appended, the Ith column of the array calculated by the fix
@ -151,7 +154,7 @@ IDs and the bond stretch will be printed with thermodynamic output.
<P>If a single input is specified this compute produces a global scalar
value. If multiple inputs are specified, this compute produces a
vector of global values, the length of which is equal to the number of
global vector of values, the length of which is equal to the number of
inputs specified.
</P>
<P>As discussed below, for <I>sum</I> mode, the value(s) produced by this
@ -162,18 +165,20 @@ command with <A HREF = "thermo_modify.html">thermo_modify norm yes</A> set as an
option. Or it can be accessed by a <A HREF = "variable.html">variable</A> that
divides by the appropriate atom count.
</P>
<HR>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar or global vector of length N
where N is the number of inputs, and which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
or vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
<P>This compute calculates a global scalar if a single input value is
specified or a global vector of length N where N is the number of
inputs, and which can be accessed by indices 1 to N. These values can
be used by any command that uses global scalar or vector values from a
compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an
overview of LAMMPS output options.
</P>
<P>For <I>sum</I> mode, the scalar and vector values calculated by this
compute are "extensive". For <I>min</I> or <I>max</I> or <I>ave</I> modes, the
value(s) are "intensive".
<P>All the scalar or vector values calculated by this compute are
"intensive", except when the <I>sum</I> mode is used on per-atom or local
vectors, in which case the calculated values are "extensive".
</P>
<P>The scalar or vector values will be in whatever <A HREF = "units.html">units</A> the
quantities being reduced are in.

55
doc/compute_reduce.txt
View File

@ -22,10 +22,10 @@ mode = {sum} or {min} or {max} or {ave} :l
one or more inputs can be listed :l
input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
c_ID = vector calculated by a compute with ID
c_ID\[I\] = Ith column of array calculated by a compute with ID
f_ID = vector calculated by a fix with ID
f_ID\[I\] = Ith column of array calculated by a fix with ID
c_ID = per-atom or local vector calculated by a compute with ID
c_ID\[I\] = Ith column of per-atom or local array calculated by a compute with ID
f_ID = per-atom or local vector calculated by a fix with ID
f_ID\[I\] = Ith column of per-atom or local array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name :pre
zero or more keyword/args pairs may be appended :l
@ -45,11 +45,14 @@ compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
[Description:]
Define a calculation that "reduces" one or more vector inputs into
scalar values, one per listed input. The inputs can be global,
per-atom, or local quantities. Atom attributes are per-atom
quantities, "computes"_compute.html and "fixes"_fix.html may generate
any of the three kinds of quantities, and "atom-style
variables"_variable.html generate per-atom quantities.
scalar values, one per listed input. The inputs can be per-atom or
local quantities; they cannot be global quantities. Atom attributes
are per-atom quantities, "computes"_compute.html and "fixes"_fix.html
may generate any of the three kinds of quantities, and "atom-style
variables"_variable.html generate per-atom quantities. See the
"variable"_variable command and its special functions which can
perform the same operations as the compute reduce command on global
vectors.
The reduction operation is specified by the {mode} setting. The {sum}
option adds the values in the vector into a global total. The {min}
@ -79,8 +82,8 @@ property/atom"_compute_property_atom.html command and then specifying
an input value from that compute.
If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. Computes can generate global,
per-atom, or local quantities. See the individual
previously defined in the input script. Computes can generate
per-atom or local quantities. See the individual
"compute"_compute.html doc page for details. If no bracketed integer
is appended, the vector calculated by the compute is used. If a
bracketed interger is appended, the Ith column of the array calculated
@ -88,10 +91,10 @@ by the compute is used. Users can also write code for their own
compute styles and "add them to LAMMPS"_Section_modify.html.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. Fixes can generate global,
per-atom, or local quantities. See the individual "fix"_fix.html doc
page for details. Note that some fixes only produce their values on
certain timesteps, which must be compatible with when compute reduce
previously defined in the input script. Fixes can generate per-atom
or local quantities. See the individual "fix"_fix.html doc page for
details. Note that some fixes only produce their values on certain
timesteps, which must be compatible with when compute reduce
references the values, else an error results. If no bracketed integer
is appended, the vector calculated by the fix is used. If a bracketed
integer is appended, the Ith column of the array calculated by the fix
@ -138,7 +141,7 @@ IDs and the bond stretch will be printed with thermodynamic output.
If a single input is specified this compute produces a global scalar
value. If multiple inputs are specified, this compute produces a
vector of global values, the length of which is equal to the number of
global vector of values, the length of which is equal to the number of
inputs specified.
As discussed below, for {sum} mode, the value(s) produced by this
@ -149,18 +152,20 @@ command with "thermo_modify norm yes"_thermo_modify.html set as an
option. Or it can be accessed by a "variable"_variable.html that
divides by the appropriate atom count.
:line
[Output info:]
This compute calculates a global scalar or global vector of length N
where N is the number of inputs, and which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
or vector values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
options.
This compute calculates a global scalar if a single input value is
specified or a global vector of length N where N is the number of
inputs, and which can be accessed by indices 1 to N. These values can
be used by any command that uses global scalar or vector values from a
compute as input. See "this section"_Section_howto.html#4_15 for an
overview of LAMMPS output options.
For {sum} mode, the scalar and vector values calculated by this
compute are "extensive". For {min} or {max} or {ave} modes, the
value(s) are "intensive".
All the scalar or vector values calculated by this compute are
"intensive", except when the {sum} mode is used on per-atom or local
vectors, in which case the calculated values are "extensive".
The scalar or vector values will be in whatever "units"_units.html the
quantities being reduced are in.

342
doc/fix_ave_correlate.html Normal file
View File

@ -0,0 +1,342 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix ave/correlate command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>ave/time = style name of this fix command
<LI>Nevery = use input values every this many timesteps
<LI>Nrepeat = # of correlation time windows to accumulate
<LI>Nfreq = calculate tine window averages every this many timesteps
<LI>one or more input values can be listed
<LI>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
<PRE> c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID
v_name = global value calculated by an equal-style variable with name
</PRE>
<LI>zero or more keyword/arg pairs may be appended
<LI>keyword = <I>type</I> or <I>ave</I> or <I>start</I> or <I>prefactor</I> or <I>file</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
<PRE> <I>type</I> arg = <I>auto</I> or <I>upper</I> or <I>lower</I> or <I>auto/upper</I> or <I>auto/lower</I> or <I>full</I>
auto = correlate each value with itself
upper = correlate each value with each succeeding value
lower = correlate each value with each preceding value
auto/upper = auto + upper
auto/lower = auto + lower
full = correlate each value with every other value, including itself = auto + upper + lower
<I>ave</I> args = <I>one</I> or <I>running</I>
one = zero the correlation accumulation every Nfreq steps
running = accumulate correlations continuously
<I>start</I> args = Nstart
Nstart = start accumulating correlations on this timestep
<I>prefactor</I> args = value
value = prefactor to scale all the correlation data by
<I>file</I> arg = filename
filename = name of file to output correlation data to
<I>title1</I> arg = string
string = text to print as 1st line of output file
<I>title2</I> arg = string
string = text to print as 2nd line of output file
<I>title3</I> arg = string
string = text to print as 3rd line of output file
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
fix 1 all ave/correlate 1 50 10000 &
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
type upper ave running title1 "My correlation data"
</PRE>
<P><B>Description:</B>
</P>
<P>Use one or more global scalar values as inputs every few timesteps,
calculate time correlations bewteen them at varying time intervals,
and average the correlation data over longer timescales. The
resulting correlation values can be time integrated by
<A HREF = "variable.html">variables</A> or used by other <A HREF = "Section_howto.html#4_15">output
commands</A> such as <A HREF = "thermo_style.html">thermo_style
custom</A>, and can also be written to a file.
</P>
<P>The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
</P>
<P>Each listed value can be the result of a <A HREF = "compute.html">compute</A> or
<A HREF = "fix.html">fix</A> or the evaluation of an equal-style
<A HREF = "variable.html">variable</A>. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
you wish to spatial- or time-average or histogram per-atom quantities
from a compute, fix, or variable, then see the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>,
or <A HREF = "fix_ave_histo.html">fix ave/histo</A> commands. If you wish to sum a
per-atom quantity into a single global quantity, see the <A HREF = "compute_reduce.html">compute
reduce</A> command.
</P>
<P><A HREF = "compute.html">Computes</A> that produce global quantities are those which
do not have the word <I>atom</I> in their style name. Only a few
<A HREF = "fix.html">fixes</A> produce global quantities. See the doc pages for
individual fixes for info on which ones produce such values.
<A HREF = "variable.html">Variables</A> of style <I>equal</I> are the only ones that can
be used with this fix. Variables of style <I>atom</I> cannot be used,
since they produce per-atom values.
</P>
<P>The input values must either be all scalars. What kinds of
correlations between input values are calculated is determined by the
<I>type</I> keyword as discussed below.
</P>
<HR>
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
timesteps the input values will be used to calculate correlation data.
The input values are sampled every <I>Nevery</I> timesteps. The
correlation data for the preceding samples is computed every <I>Nfreq</I>
timesteps. Consider a set of samples from some initial time up to an
output timestep. The initial time could be the beginning of the
simulation or the last output time; see the <I>ave</I> keyword for options.
For the set of samples, the correlation value Cij is calculated as:
</P>
<PRE>Cij(delta) = <Vi(t)*Vj(t+delta)>
</PRE>
<P>which is the correlation value between input values Vi and Vj,
separated by time delta. Note that the second value Vj in the pair is
always the one sampled at the later time. The <> brackets represent
an average over every pair of samples in the set that are separated by
time delta. The maximum delta used is of size (<I>Nrepeat</I>-1)*<I>Nevery</I>.
Thus the correlation between a pair of input values yields <I>Nrepeat</I>
correlation datums:
</P>
<PRE>Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery)
</PRE>
<P><I>Nfreq</I> must be a multiple of <I>Nevery</I>; <I>Nevery</I> and <I>Nrepeat</I> must be
non-zero. Also, <I>Nfreq</I> >= (<I>Nrepeat</I>-1)*<I>Nevery</I> is required.
</P>
<P>For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
timesteps 0,5,10,15,...,100 will be used to compute the final averages
on timestep 100. Six averages will be computed: Cij(0), Cij(5),
Cij(10), Cij(15), Cij(20), and Cij(25). Cij(10) on timestep 100 will
be the average of 19 samples, namely Vi(0)*Vj(10), Vi(5)*Vj(15),
Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100).
</P>
<HR>
<P>If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the compute is used.
</P>
<P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/correlate. Or it can be a compute
defined not in your input script, but by <A HREF = "thermo_style.html">thermodynamic
output</A> or other fixes such as <A HREF = "fix_nh.html">fix nvt</A>
or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>.
</P>
<P>If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the fix is used.
</P>
<P>Note that some fixes only produce their values on certain timesteps,
which must be compatible with <I>Nevery</I>, else an error will result.
Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>.
</P>
<P>If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. Only equal-style
variables can be referenced. See the <A HREF = "variable.html">variable</A> command
for details. Note that variables of style <I>equal</I> define a formula
which can reference individual atom properties or thermodynamic
keywords, or they can invoke other computes, fixes, or variables when
they are evaluated, so this is a very general means of specifying
quantities to time correlate.
</P>
<HR>
<P>Additional optional keywords also affect the operation of this fix.
</P>
<P>The <I>type</I> keyword determines which pairs of input values are
correlated with each other. For N input values Vi, for i = 1 to N,
let the number of pairs = Npair. Note that the second value in the
pair Vi(t)*Vj(t+delta) is always the one sampled at the later time.
</P>
<UL><LI>If <I>type</I> is set to <I>auto</I> then each input value is correlated with
itself. I.e. Cii = Vi*Vi, for i = 1 to N, so Npair = N.
<LI>If <I>type</I> is set
to <I>upper</I> then each input value is correlated with every succeeding
value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2.
<LI>If <I>type</I> is set
to <I>lower</I> then each input value is correlated with every preceeding
value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2.
<LI>If <I>type</I> is set to <I>auto/upper</I> then each input value is correlated
with itself and every succeeding value. I.e. Cij = Vi*Vj, for i >= j,
so Npair = N*(N+1)/2.
<LI>If <I>type</I> is set to <I>auto/lower</I> then each input value is correlated
with itself and every preceding value. I.e. Cij = Vi*Vj, for i <= j,
so Npair = N*(N+1)/2.
<LI>If <I>type</I> is set to <I>full</I> then each input value is correlated with
itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so
Npair = N^2.
</UL>
<P>The <I>ave</I> keyword determines what happens to the accumulation of
correlation samples every <I>Nfreq</I> timesteps. If the <I>ave</I> setting is
<I>one</I>, then the accumulation is restarted or zeroed every <I>Nfreq</I>
timesteps. Thus the outputs on successive <I>Nfreq</I> timesteps are
essentially independent of each other. The exception is that the
Cij(0) = Vi(T)*Vj(T) value at a timestep T, where T is a multiple of
<I>Nfreq</I>, contributes to the correlation output both at time T and at
time T+Nfreq.
</P>
<P>If the <I>ave</I> setting is <I>running</I>, then the accumulation is never
zeroed. Thus the output of correlation data at any timestep is the
average over samples accumulated every <I>Nevery</I> steps since the fix
was defined. it can only be restarted by deleting the fix via the
<A HREF = "unfix.html">unfix</A> command, or by re-defining the fix by re-specifying
it.
</P>
<P>The <I>start</I> keyword specifies what timestep the accumulation of
correlation samples will begin on. The default is step 0. Setting it
to a larger value can avoid adding non-equilibrated data to the
correlation averages.
</P>
<P>The <I>prefactor</I> keyword specifies a constant which will be used as a
multiplier on the correlation data after it is averaged. It is
effectively a scale factor on Vi*Vj, which can be used to account for
the size of the time window or other unit conversions.
</P>
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
steps, an array of correlation data is written to the file. The
number of rows is <I>Nrepeat</I>, as described above. The number of
columns is the Npair+2, also as described above. Thus the file ends
up to be a series of these array sections.
</P>
<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
the strings that will be printed as the first 3 lines of the output
file, assuming the <I>file</I> keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified.
</P>
<P>By default, these header lines are as follows:
</P>
<PRE># Time-correlated data for fix ID
# TimeStep Number-of-time-windows
# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...
</PRE>
<P>In the first line, ID is replaced with the fix-ID. The second line
describes the two values that are printed at the first of each section
of output. In the third line the value pairs are replaced with the
appropriate fields from the fix ave/correlate command.
</P>
<HR>
<P>Let Sij = a set of time correlation data for input values I and J,
namely the <I>Nrepeat</I> values:
</P>
<PRE>Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery)
</PRE>
<P>As explained below, these datums are output as one column of a global
array, which is effectively the correlation matrix.
</P>
<P>The <I>trap</I> function defined for <A HREF = "variable.html">equal-style variables</A>
can be used to perform a time integration of this vector of datums,
using a trapezoidal rule. This is useful for calculating various
quantities which can be derived from time correlation data. If a
normalization factor is needed for the time integration, it can be
included in the variable formula or via the <I>prefactor</I> keyword.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix computes a global array of values which can be accessed by
various <A HREF = "Section_howto.html#4_15">output commands</A>. The values can
only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
is when averaging is performed. The global array has # of rows =
<I>Nrepeat</I> and # of columns = Npair+2. The first column has the time
delta (in timesteps) between the pairs of input values used to
calculate the correlation, as described above. The 2nd column has the
number of samples contributing to the correlation average, as
described above. The remaining Npair columns are for I,J pairs of the
N input values, as determined by the <I>type</I> keyword, as described
above.
</P>
<UL><LI>For <I>type</I> = <I>auto</I>, the Npair = N columns are ordered: C11, C22, ...,
CNN.
<LI>For <I>type</I> = <I>upper</I>, the Npair = N*(N-1)/2 columns are ordered: C12,
C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N.
<LI>For <I>type</I> = <I>lower</I>, the Npair = N*(N-1)/2 columns are ordered: C21,
C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1.
<LI>For <I>type</I> = <I>auto/upper</I>, the Npair = N*(N+1)/2 columns are ordered:
C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N,
CNN.
<LI>For <I>type</I> = <I>auto/lower</I>, the Npair = N*(N+1)/2 columns are ordered:
C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1,
CNN.
<LI>For <I>type</I> = <I>full</I>, the Npair = N^2 columns are ordered: C11, C12,
..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
CNN.
</UL>
<P>The array values calculated by this fix are treated as "intensive".
If you need to divide them by the number of atoms, you must do this in
a later processing step, e.g. when using them in a
<A HREF = "variable.html">variable</A>.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_atom.html">fix
ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
<A HREF = "fix_ave_histo.html">fix ave/histo</A>, <A HREF = "variable.html">variable</A>
</P>
<P><B>Default:</B> none
</P>
<P>The option defaults are ave = one, type = auto, start = 0, no file
output, title 1,2,3 = strings as described above, and prefactor = 1.0.
</P>
</HTML>

327
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@ -0,0 +1,327 @@
"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 ave/correlate command :h3
[Syntax:]
fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
ave/time = style name of this fix command :l
Nevery = use input values every this many timesteps :l
Nrepeat = # of correlation time windows to accumulate :l
Nfreq = calculate tine window averages every this many timesteps :l
one or more input values can be listed :l
value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
c_ID = global scalar calculated by a compute with ID
c_ID\[I\] = Ith component of global vector calculated by a compute with ID
f_ID = global scalar calculated by a fix with ID
f_ID\[I\] = Ith component of global vector calculated by a fix with ID
v_name = global value calculated by an equal-style variable with name :pre
zero or more keyword/arg pairs may be appended :l
keyword = {type} or {ave} or {start} or {prefactor} or {file} or {title1} or {title2} or {title3} :l
{type} arg = {auto} or {upper} or {lower} or {auto/upper} or {auto/lower} or {full}
auto = correlate each value with itself
upper = correlate each value with each succeeding value
lower = correlate each value with each preceding value
auto/upper = auto + upper
auto/lower = auto + lower
full = correlate each value with every other value, including itself = auto + upper + lower
{ave} args = {one} or {running}
one = zero the correlation accumulation every Nfreq steps
running = accumulate correlations continuously
{start} args = Nstart
Nstart = start accumulating correlations on this timestep
{prefactor} args = value
value = prefactor to scale all the correlation data by
{file} arg = filename
filename = name of file to output correlation data to
{title1} arg = string
string = text to print as 1st line of output file
{title2} arg = string
string = text to print as 2nd line of output file
{title3} arg = string
string = text to print as 3rd line of output file :pre
:ule
[Examples:]
fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
fix 1 all ave/correlate 1 50 10000 &
c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
type upper ave running title1 "My correlation data" :pre
[Description:]
Use one or more global scalar values as inputs every few timesteps,
calculate time correlations bewteen them at varying time intervals,
and average the correlation data over longer timescales. The
resulting correlation values can be time integrated by
"variables"_variable.html or used by other "output
commands"_Section_howto.html#4_15 such as "thermo_style
custom"_thermo_style.html, and can also be written to a file.
The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each listed value can be the result of a "compute"_compute.html or
"fix"_fix.html or the evaluation of an equal-style
"variable"_variable.html. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
you wish to spatial- or time-average or histogram per-atom quantities
from a compute, fix, or variable, then see the "fix
ave/spatial"_fix_ave_spatial.html, "fix ave/atom"_fix_ave_atom.html,
or "fix ave/histo"_fix_ave_histo.html commands. If you wish to sum a
per-atom quantity into a single global quantity, see the "compute
reduce"_compute_reduce.html command.
"Computes"_compute.html that produce global quantities are those which
do not have the word {atom} in their style name. Only a few
"fixes"_fix.html produce global quantities. See the doc pages for
individual fixes for info on which ones produce such values.
"Variables"_variable.html of style {equal} are the only ones that can
be used with this fix. Variables of style {atom} cannot be used,
since they produce per-atom values.
The input values must either be all scalars. What kinds of
correlations between input values are calculated is determined by the
{type} keyword as discussed below.
:line
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
timesteps the input values will be used to calculate correlation data.
The input values are sampled every {Nevery} timesteps. The
correlation data for the preceding samples is computed every {Nfreq}
timesteps. Consider a set of samples from some initial time up to an
output timestep. The initial time could be the beginning of the
simulation or the last output time; see the {ave} keyword for options.
For the set of samples, the correlation value Cij is calculated as:
Cij(delta) = <Vi(t)*Vj(t+delta)> :pre
which is the correlation value between input values Vi and Vj,
separated by time delta. Note that the second value Vj in the pair is
always the one sampled at the later time. The <> brackets represent
an average over every pair of samples in the set that are separated by
time delta. The maximum delta used is of size ({Nrepeat}-1)*{Nevery}.
Thus the correlation between a pair of input values yields {Nrepeat}
correlation datums:
Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery) :pre
{Nfreq} must be a multiple of {Nevery}; {Nevery} and {Nrepeat} must be
non-zero. Also, {Nfreq} >= ({Nrepeat}-1)*{Nevery} is required.
For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
timesteps 0,5,10,15,...,100 will be used to compute the final averages
on timestep 100. Six averages will be computed: Cij(0), Cij(5),
Cij(10), Cij(15), Cij(20), and Cij(25). Cij(10) on timestep 100 will
be the average of 19 samples, namely Vi(0)*Vj(10), Vi(5)*Vj(15),
Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100).
:line
If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the compute is used.
Note that there is a "compute reduce"_compute_reduce.html command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/correlate. Or it can be a compute
defined not in your input script, but by "thermodynamic
output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html
or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and "add them to
LAMMPS"_Section_modify.html.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the fix is used.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with {Nevery}, else an error will result.
Users can also write code for their own fix styles and "add them to
LAMMPS"_Section_modify.html.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. Only equal-style
variables can be referenced. See the "variable"_variable.html command
for details. Note that variables of style {equal} define a formula
which can reference individual atom properties or thermodynamic
keywords, or they can invoke other computes, fixes, or variables when
they are evaluated, so this is a very general means of specifying
quantities to time correlate.
:line
Additional optional keywords also affect the operation of this fix.
The {type} keyword determines which pairs of input values are
correlated with each other. For N input values Vi, for i = 1 to N,
let the number of pairs = Npair. Note that the second value in the
pair Vi(t)*Vj(t+delta) is always the one sampled at the later time.
If {type} is set to {auto} then each input value is correlated with
itself. I.e. Cii = Vi*Vi, for i = 1 to N, so Npair = N. :ulb,l
If {type} is set
to {upper} then each input value is correlated with every succeeding
value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. :l
If {type} is set
to {lower} then each input value is correlated with every preceeding
value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. :l
If {type} is set to {auto/upper} then each input value is correlated
with itself and every succeeding value. I.e. Cij = Vi*Vj, for i >= j,
so Npair = N*(N+1)/2. :l
If {type} is set to {auto/lower} then each input value is correlated
with itself and every preceding value. I.e. Cij = Vi*Vj, for i <= j,
so Npair = N*(N+1)/2. :l
If {type} is set to {full} then each input value is correlated with
itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so
Npair = N^2. :l,ule
The {ave} keyword determines what happens to the accumulation of
correlation samples every {Nfreq} timesteps. If the {ave} setting is
{one}, then the accumulation is restarted or zeroed every {Nfreq}
timesteps. Thus the outputs on successive {Nfreq} timesteps are
essentially independent of each other. The exception is that the
Cij(0) = Vi(T)*Vj(T) value at a timestep T, where T is a multiple of
{Nfreq}, contributes to the correlation output both at time T and at
time T+Nfreq.
If the {ave} setting is {running}, then the accumulation is never
zeroed. Thus the output of correlation data at any timestep is the
average over samples accumulated every {Nevery} steps since the fix
was defined. it can only be restarted by deleting the fix via the
"unfix"_unfix.html command, or by re-defining the fix by re-specifying
it.
The {start} keyword specifies what timestep the accumulation of
correlation samples will begin on. The default is step 0. Setting it
to a larger value can avoid adding non-equilibrated data to the
correlation averages.
The {prefactor} keyword specifies a constant which will be used as a
multiplier on the correlation data after it is averaged. It is
effectively a scale factor on Vi*Vj, which can be used to account for
the size of the time window or other unit conversions.
The {file} keyword allows a filename to be specified. Every {Nfreq}
steps, an array of correlation data is written to the file. The
number of rows is {Nrepeat}, as described above. The number of
columns is the Npair+2, also as described above. Thus the file ends
up to be a series of these array sections.
The {title1} and {title2} and {title3} keywords allow specification of
the strings that will be printed as the first 3 lines of the output
file, assuming the {file} keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified.
By default, these header lines are as follows:
# Time-correlated data for fix ID
# TimeStep Number-of-time-windows
# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ... :pre
In the first line, ID is replaced with the fix-ID. The second line
describes the two values that are printed at the first of each section
of output. In the third line the value pairs are replaced with the
appropriate fields from the fix ave/correlate command.
:line
Let Sij = a set of time correlation data for input values I and J,
namely the {Nrepeat} values:
Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery) :pre
As explained below, these datums are output as one column of a global
array, which is effectively the correlation matrix.
The {trap} function defined for "equal-style variables"_variable.html
can be used to perform a time integration of this vector of datums,
using a trapezoidal rule. This is useful for calculating various
quantities which can be derived from time correlation data. If a
normalization factor is needed for the time integration, it can be
included in the variable formula or via the {prefactor} keyword.
:line
[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.
This fix computes a global array of values which can be accessed by
various "output commands"_Section_howto.html#4_15. The values can
only be accessed on timesteps that are multiples of {Nfreq} since that
is when averaging is performed. The global array has # of rows =
{Nrepeat} and # of columns = Npair+2. The first column has the time
delta (in timesteps) between the pairs of input values used to
calculate the correlation, as described above. The 2nd column has the
number of samples contributing to the correlation average, as
described above. The remaining Npair columns are for I,J pairs of the
N input values, as determined by the {type} keyword, as described
above.
For {type} = {auto}, the Npair = N columns are ordered: C11, C22, ...,
CNN. :ulb,l
For {type} = {upper}, the Npair = N*(N-1)/2 columns are ordered: C12,
C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N. :l
For {type} = {lower}, the Npair = N*(N-1)/2 columns are ordered: C21,
C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1. :l
For {type} = {auto/upper}, the Npair = N*(N+1)/2 columns are ordered:
C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N,
CNN. :l
For {type} = {auto/lower}, the Npair = N*(N+1)/2 columns are ordered:
C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1,
CNN. :l
For {type} = {full}, the Npair = N^2 columns are ordered: C11, C12,
..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
CNN. :l,ule
The array values calculated by this fix are treated as "intensive".
If you need to divide them by the number of atoms, you must do this in
a later processing step, e.g. when using them in a
"variable"_variable.html.
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:]
"compute"_compute.html, "fix ave/time"_fix_ave_time.html, "fix
ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html,
"fix ave/histo"_fix_ave_histo.html, "variable"_variable.html
[Default:] none
The option defaults are ave = one, type = auto, start = 0, no file
output, title 1,2,3 = strings as described above, and prefactor = 1.0.

2
doc/fix_ave_histo.html
View File

@ -317,7 +317,7 @@ minimization</A>.
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
<A HREF = "variable.html">variable</A>,
<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
</P>
<P><B>Default:</B> none
</P>

2
doc/fix_ave_histo.txt
View File

@ -305,7 +305,7 @@ minimization"_minimize.html.
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
ave/spatial"_fix_ave_spatial.html, "fix ave/time"_fix_ave_time.html,
"variable"_variable.html,
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
[Default:] none

6
doc/fix_ave_spatial.html
View File

@ -49,12 +49,12 @@
<PRE> <I>units</I> arg = <I>box</I> or <I>lattice</I> or <I>reduced</I>
<I>norm</I> arg = <I>all</I> or <I>sample</I>
<I>file</I> arg = filename
filename = file to write results to
<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
one = output new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
<I>file</I> arg = filename
filename = file to write results to
<I>title1</I> arg = string
string = text to print as 1st line of output file
<I>title2</I> arg = string
@ -322,7 +322,7 @@ simulation box size doesn't change or if the <I>units</I> keyword is set to
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_histo.html">fix
ave/histo</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
<A HREF = "variable.html">variable</A>,
<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
</P>
<P><B>Default:</B>
</P>

6
doc/fix_ave_spatial.txt
View File

@ -34,12 +34,12 @@ zero or more keyword/arg pairs may be appended :l
keyword = {norm} or {units} or {file} or {ave} or {title1} or {title2} or {title3} :l
{units} arg = {box} or {lattice} or {reduced}
{norm} arg = {all} or {sample}
{file} arg = filename
filename = file to write results to
{ave} args = {one} or {running} or {window M}
one = output new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
{file} arg = filename
filename = file to write results to
{title1} arg = string
string = text to print as 1st line of output file
{title2} arg = string
@ -306,7 +306,7 @@ simulation box size doesn't change or if the {units} keyword is set to
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
ave/histo"_fix_ave_histo.html, "fix ave/time"_fix_ave_time.html,
"variable"_variable.html,
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
[Default:]

22
doc/fix_ave_time.html
View File

@ -42,8 +42,6 @@
<PRE> <I>mode</I> arg = <I>scalar</I> or <I>vector</I>
scalar = all input values are global scalars
vector = all input values are global vectors or global arrays
<I>file</I> arg = filename
filename = name of file to output time averages to
<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
one = output a new average value every Nfreq steps
running = output cummulative average of all previous Nfreq steps
@ -52,6 +50,8 @@
Nstart = start averaging on this timestep
<I>off</I> arg = M = do not average this value
M = value # from 1 to Nvalues
<I>file</I> arg = filename
filename = name of file to output time averages to
<I>title1</I> arg = string
string = text to print as 1st line of output file
<I>title2</I> arg = string
@ -82,7 +82,7 @@ a file.
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
</P>
<P>Each input value can be the result of a <A HREF = "compute.html">compute</A> or
<P>Each listed value can be the result of a <A HREF = "compute.html">compute</A> or
<A HREF = "fix.html">fix</A> or the evaluation of an equal-style
<A HREF = "variable.html">variable</A>. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
@ -298,13 +298,13 @@ of rows = length of the input vectors and # of columns = number of
inputs.
</P>
<P>If the fix prouduces a scalar or vector, then the scalar and each
element of the vector may be either "intensive" or "extensive". If
the fix produces an array, then all elements in the array will be
either "intensive" or "extensive". If a compute or fix provides the
value being time averaged, then the compute or fix determines whether
the value is intensive or extensive; see the doc page for that compute
or fix for further info. Values produced by a variable are whatever
the variable calculates.
element of the vector can be either "intensive" or "extensive". If
the fix produces an array, then all elements in the array must be the
same, either "intensive" or "extensive". If a compute or fix provides
the value being time averaged, then the compute or fix determines
whether the value is intensive or extensive; see the doc page for that
compute or fix for further info. Values produced by a variable are
treated as intensive.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
@ -316,7 +316,7 @@ minimization</A>.
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,
<A HREF = "variable.html">variable</A>
<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
</P>
<P><B>Default:</B> none
</P>

22
doc/fix_ave_time.txt
View File

@ -30,8 +30,6 @@ keyword = {mode} or {file} or {ave} or {start} or {off} or {title1} or {title2}
{mode} arg = {scalar} or {vector}
scalar = all input values are global scalars
vector = all input values are global vectors or global arrays
{file} arg = filename
filename = name of file to output time averages to
{ave} args = {one} or {running} or {window M}
one = output a new average value every Nfreq steps
running = output cummulative average of all previous Nfreq steps
@ -40,6 +38,8 @@ keyword = {mode} or {file} or {ave} or {start} or {off} or {title1} or {title2}
Nstart = start averaging on this timestep
{off} arg = M = do not average this value
M = value # from 1 to Nvalues
{file} arg = filename
filename = name of file to output time averages to
{title1} arg = string
string = text to print as 1st line of output file
{title2} arg = string
@ -69,7 +69,7 @@ The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each input value can be the result of a "compute"_compute.html or
Each listed value can be the result of a "compute"_compute.html or
"fix"_fix.html or the evaluation of an equal-style
"variable"_variable.html. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
@ -285,13 +285,13 @@ of rows = length of the input vectors and # of columns = number of
inputs.
If the fix prouduces a scalar or vector, then the scalar and each
element of the vector may be either "intensive" or "extensive". If
the fix produces an array, then all elements in the array will be
either "intensive" or "extensive". If a compute or fix provides the
value being time averaged, then the compute or fix determines whether
the value is intensive or extensive; see the doc page for that compute
or fix for further info. Values produced by a variable are whatever
the variable calculates.
element of the vector can be either "intensive" or "extensive". If
the fix produces an array, then all elements in the array must be the
same, either "intensive" or "extensive". If a compute or fix provides
the value being time averaged, then the compute or fix determines
whether the value is intensive or extensive; see the doc page for that
compute or fix for further info. Values produced by a variable are
treated as intensive.
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
@ -303,7 +303,7 @@ minimization"_minimize.html.
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
ave/spatial"_fix_ave_spatial.html, "fix ave/histo"_fix_ave_histo.html,
"variable"_variable.html
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
[Default:] none

136
doc/variable.html
View File

@ -34,8 +34,7 @@
x==y, x!=y, x<y, x<=y, x>y, x>=y, x&&y, x||y
math functions = sqrt(x), exp(x), ln(x), log(x),
sin(x), cos(x), tan(x), asin(x), acos(x), atan(x),
ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y),
logfreq(x,y,z)
ceil(x), floor(x), round(x)
group functions = count(group), mass(group), charge(group),
xcm(group,dim), vcm(group,dim), fcm(group,dim),
bound(group,xmin), gyration(group), ke(group),
@ -44,6 +43,7 @@
xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
bound(group,xmin,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), inertia(group,dimdim,region),omega(group,dim,region)
special functions = ramp(x,y), stagger(x,y), logfreq(x,y,z), sum(x), min(x), max(x), ave(x), trap(x)
atom value = mass[i], type[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i]
atom vector = mass, type, x, y, z, vx, vy, vz, fx, fy, fz
compute references = c_ID, c_ID[i], c_ID[i][j]
@ -258,9 +258,10 @@ references to other variables.
<TR><TD >Number</TD><TD > 0.2, 100, 1.0e20, -15.4, etc</TD></TR>
<TR><TD >Thermo keywords</TD><TD > vol, pe, ebond, etc</TD></TR>
<TR><TD >Math operators</TD><TD > (), -x, x+y, x-y, x*y, x/y, x^y, x==y, x!=y, x<y, x<=y, x>y, x>=y, x&&y, x||y</TD></TR>
<TR><TD >Math functions</TD><TD > sqrt(x), exp(x), ln(x), log(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z)</TD></TR>
<TR><TD >Math functions</TD><TD > sqrt(x), exp(x), ln(x), log(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), ceil(x), floor(x), round(x)</TD></TR>
<TR><TD >Group functions</TD><TD > count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), inertia(ID,dimdim), omega(ID,dim)</TD></TR>
<TR><TD >Region functions</TD><TD > count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)</TD></TR>
<TR><TD >Special functions</TD><TD > ramp(x,y), stagger(x,y), logfreq(x,y,z), sum(x), min(x), max(x), ave(x), trap(x)</TD></TR>
<TR><TD >Atom values</TD><TD > mass[i], type[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i]</TD></TR>
<TR><TD >Atom vectors</TD><TD > mass, type, x, y, z, vx, vy, vz, fx, fy, fz</TD></TR>
<TR><TD >Compute references</TD><TD > c_ID, c_ID[i], c_ID[i][j]</TD></TR>
@ -268,13 +269,15 @@ references to other variables.
<TR><TD >Other variables</TD><TD > v_name, v_name[i]
</TD></TR></TABLE></DIV>
<HR>
<P>Most of the formula elements produce a scalar value. A few produce a
per-atom vector of values. These are the atom vectors, compute
references that represent a per-atom vector, fix references that
represent a per-atom vector, and variables that are atom-style
variables. Math functions that operate on scalar values produce a
scalar value; math function that operate on per-atom vectors produce a
per-atom vector.
scalar value; math function that operate on per-atom vectors do so
element-by-element and produce a per-atom vector.
</P>
<P>A formula for equal-style variables cannot use any formula element
that produces a per-atom vector. A formula for an atom-style variable
@ -295,12 +298,14 @@ evaluated directly in an input script (not during a run), then the
values accessed by the thermo keyword must be current. See the
discussion below about "Variable Accuracy".
</P>
<HR>
<P>Math operators are written in the usual way, where the "x" and "y" in
the examples can themselves be arbitrarily complex formulas, as in the
examples above. In this syntax, "x" and "y" can be scalar values or
per-atom vectors. For example, "ke/natoms" is the division of two
scalars, where "y+z" is the sum of two per-atom vectors of y- and
z-coordinates.
scalars, where "y+z" is the element-by-element sum of two per-atom
vectors of y- and z-coordinates.
</P>
<P>Operators are evaluated left to right and have the usual C-style
precedence: unary minus before exponentiation ("^"); exponentiation
@ -330,10 +335,11 @@ to the <A HREF = "compute_reduce.html">compute reduce</A> command.
<P>Math functions are specified as keywords followed by one or more
parenthesized arguments "x", "y", etc, each of which can themselves be
arbitrarily complex formulas. In this syntax, the arguments can
represent scalar values or per-atom vectors. For example,
"sqrt(natoms)" is the sqrt() of a scalar, where "sqrt(y*z)" is a
per-atom vector with each element being the sqrt() of the product of
two atom coordinates.
represent scalar values or per-atom vectors. In the latter case, the
math operation is performed on each element of the vector. For
example, "sqrt(natoms)" is the sqrt() of a scalar, where "sqrt(y*z)"
yields a per-atom vector with each element being the sqrt() of the
product of one atom's y and z coordinates.
</P>
<P>Most of the math functions perform obvious operations. The ln() is
the natural log; log() is the base 10 log. The ceil(), floor(), and
@ -342,35 +348,8 @@ smallest integer not less than its argument. Floor() if the largest
integer not greater than its argument. Round() is the nearest integer
to its argument.
</P>
<P>Ramp(x,y) uses the current timestep to generate a scalar value:
</P>
<PRE>value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)
</PRE>
<P>which is a value that ramps linear between x and y over the course of
a run. The run begins on startstep and ends on stopstep. Startstep
and stopstep can span multiple runs, using the <I>start</I> and <I>stop</I>
keywords of the <A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A>
command for details of how to do this.
</P>
<P>Stagger(x,y) requires x,y > 0 and x > y and uses the current timestep
to generate a new timestep, in a staggered fashion, as the sequence
x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next
timestep in the sequence is returned. Thus if stagger(1000,100) is
used in a variable by the <A HREF = "dump_modify.html">dump_modify every</A>
command, it will generate the sequence of output timesteps:
</P>
<PRE>100,1000,1100,2000,2100,3000,etc
</PRE>
<P>Logfreq(x,y,z) requires x,y,z > 0 and y < z and uses the current
timestep to generate a new timestep, in a logarithmic fashion, as the
sequence x,2x,3x,...y*x,z*x,2*z*x,3*z*x,...y*z*x,z*z*x,2*z*x*x,etc.
For any current timestep, the next timestep in the sequence is
returned. Thus if logfreq(100,4,10) is used in a variable by the
<A HREF = "dump_modify.html">dump_modify every</A> command, it will generate the
sequence of output timesteps:
</P>
<PRE>100,200,300,400,1000,2000,3000,4000,10000,20000,etc
</PRE>
<HR>
<P>Group functions are specified as keywords followed by one or two
parenthesized arguments. The first argument is the group-ID. The
<I>dim</I> argument, if it exists, is <I>x</I> or <I>y</I> or <I>z</I>. The <I>dir</I>
@ -398,6 +377,77 @@ function is computed for all atoms that are in both the group and the
region. If the group is "all", then the only criteria for atom
inclusion is that it be in the region.
</P>
<HR>
<P>Special functions take specific kinds of arguments, meaning their
arguments cannot be formulas themselves. For example ramp(10.0,100.0)
is valid, but ramp(2*5,sqrt(10000)) is not.
</P>
<P>Ramp(x,y) takes two integer or floating point values and uses the
current timestep to generate a scalar value:
</P>
<PRE>value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)
</PRE>
<P>which is a value that ramps linearly between x and y over the course of
a run. The run begins on startstep and ends on stopstep. Startstep
and stopstep can span multiple runs, using the <I>start</I> and <I>stop</I>
keywords of the <A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A>
command for details of how to do this.
</P>
<P>Stagger(x,y) takes two integer values and uses the current timestep to
generate a new timestep. X,y > 0 and x > y is required. The
generated timesteps increase in a staggered fashion, as the sequence
x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next
timestep in the sequence is returned. Thus if stagger(1000,100) is
used in a variable by the <A HREF = "dump_modify.html">dump_modify every</A>
command, it will generate the sequence of output timesteps:
</P>
<PRE>100,1000,1100,2000,2100,3000,etc
</PRE>
<P>Logfreq(x,y,z) takes 3 integer values and uses the current timestep to
generate a new timestep. X,y,z > 0 and y < z is required. The
generated timesteps increase in a logarithmic fashion, as the sequence
x,2x,3x,...y*x,z*x,2*z*x,3*z*x,...y*z*x,z*z*x,2*z*x*x,etc. For any
current timestep, the next timestep in the sequence is returned. Thus
if logfreq(100,4,10) is used in a variable by the <A HREF = "dump_modify.html">dump_modify
every</A> command, it will generate the sequence of
output timesteps:
</P>
<PRE>100,200,300,400,1000,2000,3000,4000,10000,20000,etc
</PRE>
<P>The sum(x), min(x), max(x), ave(x), and trap(x) functions each take 1
argument which is of the form "c_ID" or "c_ID[N]" or "f_ID" or
"f_ID[N]". The first two are computes and the second two are fixes;
the ID in the reference should be replaced by the ID of a compute or
fix defined elsewhere in the input script. The compute or fix must
produce either a global vector or array. If it produces a global
vector, then the notation without "[N]" should be used. If it
produces a global array, then the notation with "[N]" should be
used, when N is an integer, to specify which column of the global
array is being referenced.
</P>
<P>All of these functions operate on the global vector of inputs and
reduce it to a single scalar value. This is analagous to the
operation of the <A HREF = "compute_reduce.html">compute reduce</A> command, which
invokes the same functions on per-atom and local vectors.
</P>
<P>The sum() function calculates the sum of all the vector elements. The
min() and max() functions find the minimum and maximum element
respectively. The ave() function is the same as sum() except that it
divides the result by the length of the vector. The trap() function
is the same as sum() except the first and last elements are multiplied
by a weighting factor of 1/2 when performing the sum. This
effectively implements an integratiion via the trapezoidal rule on the
global vector of data. I.e. consider a set of points, equally spaced
by 1 in their x coordinate: (1,V1), (2,V2), ..., (N,VN), where the Vi
are the values in the global vector of length N. The integral from 1
to N of these points is trap(). When appropriately normalized by the
timestep size, this function is useful for calculating integrals of
time-series data, like that generated by the <A HREF = "fix_ave_correlate.html">fix
ave/correlate</A> command.
</P>
<HR>
<P>Atom values take a single integer argument I from 1 to N, where I is
the an atom-ID, e.g. x[243], which means use the x coordinate of the
atom with ID = 243.
@ -409,6 +459,8 @@ as inputs to a variable by using the <A HREF = "compute_property_atom.html">comp
property/atom</A> command and then specifying
a quantity from that compute.
</P>
<HR>
<P>Compute references access quantities calculated by a
<A HREF = "compute.html">compute</A>. The ID in the reference should be replaced by
the ID of a compute defined elsewhere in the input script. As
@ -438,6 +490,8 @@ directly in an input script (not during a run), then the values
accessed by the compute must be current. See the discussion below
about "Variable Accuracy".
</P>
<HR>
<P>Fix references access quantities calculated by a <A HREF = "compute.html">fix</A>.
The ID in the reference should be replaced by the ID of a fix defined
elsewhere in the input script. As discussed in the doc page for the
@ -472,6 +526,8 @@ error is generated. For example, the <A HREF = "fix_ave_time.html">fix ave/time
command may only generate averaged quantities every 100 steps. See
the doc pages for individual fix commands for details.
</P>
<HR>
<P>Variable references access quantities calulated by other variables,
which will cause those variables to be evaluated. The name in the
reference should be replaced by the name of a variable defined

135
doc/variable.txt
View File

@ -29,8 +29,7 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
x==y, x!=y, x<y, x<=y, x>y, x>=y, x&&y, x||y
math functions = sqrt(x), exp(x), ln(x), log(x),
sin(x), cos(x), tan(x), asin(x), acos(x), atan(x),
ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y),
logfreq(x,y,z)
ceil(x), floor(x), round(x)
group functions = count(group), mass(group), charge(group),
xcm(group,dim), vcm(group,dim), fcm(group,dim),
bound(group,xmin), gyration(group), ke(group),
@ -39,6 +38,7 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
bound(group,xmin,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), inertia(group,dimdim,region),omega(group,dim,region)
special functions = ramp(x,y), stagger(x,y), logfreq(x,y,z), sum(x), min(x), max(x), ave(x), trap(x)
atom value = mass\[i\], type\[i\], x\[i\], y\[i\], z\[i\], vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\]
atom vector = mass, type, x, y, z, vx, vy, vz, fx, fy, fz
compute references = c_ID, c_ID\[i\], c_ID\[i\]\[j\]
@ -251,7 +251,7 @@ references to other variables.
Number: 0.2, 100, 1.0e20, -15.4, etc
Thermo keywords: vol, pe, ebond, etc
Math operators: (), -x, x+y, x-y, x*y, x/y, x^y, x==y, x!=y, x<y, x<=y, x>y, x>=y, x&&y, x||y
Math functions: sqrt(x), exp(x), ln(x), log(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z)
Math functions: sqrt(x), exp(x), ln(x), log(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), ceil(x), floor(x), round(x)
Group functions: count(ID), mass(ID), charge(ID), xcm(ID,dim), \
vcm(ID,dim), fcm(ID,dim), bound(ID,dir), \
gyration(ID), ke(ID), angmom(ID,dim), \
@ -260,6 +260,8 @@ Region functions: count(ID,IDR), mass(ID,IDR), charge(ID,IDR), \
xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), \
bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), \
angmom(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)
Special functions: ramp(x,y), stagger(x,y), logfreq(x,y,z), \
sum(x), min(x), max(x), ave(x), trap(x)
Atom values: mass\[i\], type\[i\], x\[i\], y\[i\], z\[i\], \
vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\]
Atom vectors: mass, type, x, y, z, vx, vy, vz, fx, fy, fz
@ -267,13 +269,15 @@ Compute references: c_ID, c_ID\[i\], c_ID\[i\]\[j\]
Fix references: f_ID, f_ID\[i\], f_ID\[i\]\[j\]
Other variables: v_name, v_name\[i\] :tb(s=:)
:line
Most of the formula elements produce a scalar value. A few produce a
per-atom vector of values. These are the atom vectors, compute
references that represent a per-atom vector, fix references that
represent a per-atom vector, and variables that are atom-style
variables. Math functions that operate on scalar values produce a
scalar value; math function that operate on per-atom vectors produce a
per-atom vector.
scalar value; math function that operate on per-atom vectors do so
element-by-element and produce a per-atom vector.
A formula for equal-style variables cannot use any formula element
that produces a per-atom vector. A formula for an atom-style variable
@ -294,12 +298,14 @@ evaluated directly in an input script (not during a run), then the
values accessed by the thermo keyword must be current. See the
discussion below about "Variable Accuracy".
:line
Math operators are written in the usual way, where the "x" and "y" in
the examples can themselves be arbitrarily complex formulas, as in the
examples above. In this syntax, "x" and "y" can be scalar values or
per-atom vectors. For example, "ke/natoms" is the division of two
scalars, where "y+z" is the sum of two per-atom vectors of y- and
z-coordinates.
scalars, where "y+z" is the element-by-element sum of two per-atom
vectors of y- and z-coordinates.
Operators are evaluated left to right and have the usual C-style
precedence: unary minus before exponentiation ("^"); exponentiation
@ -329,10 +335,11 @@ to the "compute reduce"_compute_reduce.html command.
Math functions are specified as keywords followed by one or more
parenthesized arguments "x", "y", etc, each of which can themselves be
arbitrarily complex formulas. In this syntax, the arguments can
represent scalar values or per-atom vectors. For example,
"sqrt(natoms)" is the sqrt() of a scalar, where "sqrt(y*z)" is a
per-atom vector with each element being the sqrt() of the product of
two atom coordinates.
represent scalar values or per-atom vectors. In the latter case, the
math operation is performed on each element of the vector. For
example, "sqrt(natoms)" is the sqrt() of a scalar, where "sqrt(y*z)"
yields a per-atom vector with each element being the sqrt() of the
product of one atom's y and z coordinates.
Most of the math functions perform obvious operations. The ln() is
the natural log; log() is the base 10 log. The ceil(), floor(), and
@ -341,34 +348,7 @@ smallest integer not less than its argument. Floor() if the largest
integer not greater than its argument. Round() is the nearest integer
to its argument.
Ramp(x,y) uses the current timestep to generate a scalar value:
value = x + (y-x) * (timestep-startstep) / (stopstep-startstep) :pre
which is a value that ramps linear between x and y over the course of
a run. The run begins on startstep and ends on stopstep. Startstep
and stopstep can span multiple runs, using the {start} and {stop}
keywords of the "run"_run.html command. See the "run"_run.html
command for details of how to do this.
Stagger(x,y) requires x,y > 0 and x > y and uses the current timestep
to generate a new timestep, in a staggered fashion, as the sequence
x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next
timestep in the sequence is returned. Thus if stagger(1000,100) is
used in a variable by the "dump_modify every"_dump_modify.html
command, it will generate the sequence of output timesteps:
100,1000,1100,2000,2100,3000,etc :pre
Logfreq(x,y,z) requires x,y,z > 0 and y < z and uses the current
timestep to generate a new timestep, in a logarithmic fashion, as the
sequence x,2x,3x,...y*x,z*x,2*z*x,3*z*x,...y*z*x,z*z*x,2*z*x*x,etc.
For any current timestep, the next timestep in the sequence is
returned. Thus if logfreq(100,4,10) is used in a variable by the
"dump_modify every"_dump_modify.html command, it will generate the
sequence of output timesteps:
100,200,300,400,1000,2000,3000,4000,10000,20000,etc :pre
:line
Group functions are specified as keywords followed by one or two
parenthesized arguments. The first argument is the group-ID. The
@ -397,6 +377,77 @@ function is computed for all atoms that are in both the group and the
region. If the group is "all", then the only criteria for atom
inclusion is that it be in the region.
:line
Special functions take specific kinds of arguments, meaning their
arguments cannot be formulas themselves. For example ramp(10.0,100.0)
is valid, but ramp(2*5,sqrt(10000)) is not.
Ramp(x,y) takes two integer or floating point values and uses the
current timestep to generate a scalar value:
value = x + (y-x) * (timestep-startstep) / (stopstep-startstep) :pre
which is a value that ramps linearly between x and y over the course of
a run. The run begins on startstep and ends on stopstep. Startstep
and stopstep can span multiple runs, using the {start} and {stop}
keywords of the "run"_run.html command. See the "run"_run.html
command for details of how to do this.
Stagger(x,y) takes two integer values and uses the current timestep to
generate a new timestep. X,y > 0 and x > y is required. The
generated timesteps increase in a staggered fashion, as the sequence
x,x+y,2x,2x+y,3x,3x+y,etc. For any current timestep, the next
timestep in the sequence is returned. Thus if stagger(1000,100) is
used in a variable by the "dump_modify every"_dump_modify.html
command, it will generate the sequence of output timesteps:
100,1000,1100,2000,2100,3000,etc :pre
Logfreq(x,y,z) takes 3 integer values and uses the current timestep to
generate a new timestep. X,y,z > 0 and y < z is required. The
generated timesteps increase in a logarithmic fashion, as the sequence
x,2x,3x,...y*x,z*x,2*z*x,3*z*x,...y*z*x,z*z*x,2*z*x*x,etc. For any
current timestep, the next timestep in the sequence is returned. Thus
if logfreq(100,4,10) is used in a variable by the "dump_modify
every"_dump_modify.html command, it will generate the sequence of
output timesteps:
100,200,300,400,1000,2000,3000,4000,10000,20000,etc :pre
The sum(x), min(x), max(x), ave(x), and trap(x) functions each take 1
argument which is of the form "c_ID" or "c_ID\[N\]" or "f_ID" or
"f_ID\[N\]". The first two are computes and the second two are fixes;
the ID in the reference should be replaced by the ID of a compute or
fix defined elsewhere in the input script. The compute or fix must
produce either a global vector or array. If it produces a global
vector, then the notation without "\[N\]" should be used. If it
produces a global array, then the notation with "\[N\]" should be
used, when N is an integer, to specify which column of the global
array is being referenced.
All of these functions operate on the global vector of inputs and
reduce it to a single scalar value. This is analagous to the
operation of the "compute reduce"_compute_reduce.html command, which
invokes the same functions on per-atom and local vectors.
The sum() function calculates the sum of all the vector elements. The
min() and max() functions find the minimum and maximum element
respectively. The ave() function is the same as sum() except that it
divides the result by the length of the vector. The trap() function
is the same as sum() except the first and last elements are multiplied
by a weighting factor of 1/2 when performing the sum. This
effectively implements an integratiion via the trapezoidal rule on the
global vector of data. I.e. consider a set of points, equally spaced
by 1 in their x coordinate: (1,V1), (2,V2), ..., (N,VN), where the Vi
are the values in the global vector of length N. The integral from 1
to N of these points is trap(). When appropriately normalized by the
timestep size, this function is useful for calculating integrals of
time-series data, like that generated by the "fix
ave/correlate"_fix_ave_correlate.html command.
:line
Atom values take a single integer argument I from 1 to N, where I is
the an atom-ID, e.g. x\[243\], which means use the x coordinate of the
atom with ID = 243.
@ -408,6 +459,8 @@ as inputs to a variable by using the "compute
property/atom"_compute_property_atom.html command and then specifying
a quantity from that compute.
:line
Compute references access quantities calculated by a
"compute"_compute.html. The ID in the reference should be replaced by
the ID of a compute defined elsewhere in the input script. As
@ -435,6 +488,8 @@ directly in an input script (not during a run), then the values
accessed by the compute must be current. See the discussion below
about "Variable Accuracy".
:line
Fix references access quantities calculated by a "fix"_compute.html.
The ID in the reference should be replaced by the ID of a fix defined
elsewhere in the input script. As discussed in the doc page for the
@ -467,6 +522,8 @@ error is generated. For example, the "fix ave/time"_fix_ave_time.html
command may only generate averaged quantities every 100 steps. See
the doc pages for individual fix commands for details.
:line
Variable references access quantities calulated by other variables,
which will cause those variables to be evaluated. The name in the
reference should be replaced by the name of a variable defined