forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@324 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
5f537d7841
commit
2dabff1657
|
|
@ -94,12 +94,12 @@ across two or more lines.
|
|||
comment and discarded.
|
||||
</P>
|
||||
<P>(3) The line is searched repeatedly for $ characters which indicate
|
||||
variables that are replaced with text. If the $ is followed by curly
|
||||
brackets, then the variable name is the text inside the curly
|
||||
variables that are replaced with a text string. If the $ is followed
|
||||
by curly brackets, then the variable name is the text inside the curly
|
||||
brackets. If no curly brackets follow the $, then the variable name
|
||||
is the character immediately following the $. Thus ${myTemp} and $x
|
||||
refer to variable names "myTemp" and "x". See the
|
||||
<A HREF = "variable.html">variable</A> command for details of how values are
|
||||
<A HREF = "variable.html">variable</A> command for details of how strings are
|
||||
assigned to variables and how they are substituted for in input
|
||||
scripts.
|
||||
</P>
|
||||
|
|
@ -315,12 +315,12 @@ descriptions of each style or click on the style itself for a full
|
|||
description:
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</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><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nvt.html">nvt</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></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</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_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">uniaxial</A></TD><TD ><A HREF = "fix_vcm.html">vcm</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">volume/rescale</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</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_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</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_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</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_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD></TR>
|
||||
<TR ALIGN="center"><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_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
|
||||
<TR ALIGN="center"><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><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_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">uniaxial</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_vcm.html">vcm</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<HR>
|
||||
|
|
@ -331,7 +331,7 @@ description:
|
|||
</P>
|
||||
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_epair_atom.html">epair/atom</A></TD><TD ><A HREF = "compute_etotal_atom.html">etotal/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A><A HREF = "compute_variable_atom.html">variable/atom</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<HR>
|
||||
|
|
|
|||
|
|
@ -91,12 +91,12 @@ across two or more lines.
|
|||
comment and discarded.
|
||||
|
||||
(3) The line is searched repeatedly for $ characters which indicate
|
||||
variables that are replaced with text. If the $ is followed by curly
|
||||
brackets, then the variable name is the text inside the curly
|
||||
variables that are replaced with a text string. If the $ is followed
|
||||
by curly brackets, then the variable name is the text inside the curly
|
||||
brackets. If no curly brackets follow the $, then the variable name
|
||||
is the character immediately following the $. Thus $\{myTemp\} and $x
|
||||
refer to variable names "myTemp" and "x". See the
|
||||
"variable"_variable.html command for details of how values are
|
||||
"variable"_variable.html command for details of how strings are
|
||||
assigned to variables and how they are substituted for in input
|
||||
scripts.
|
||||
|
||||
|
|
@ -371,6 +371,9 @@ description:
|
|||
|
||||
"addforce"_fix_addforce.html,
|
||||
"aveforce"_fix_aveforce.html,
|
||||
"ave/spatial"_fix_ave_spatial.html,
|
||||
"ave/time"_fix_ave_time.html,
|
||||
"box/relax"_fix_box_relax.html,
|
||||
"com"_fix_com.html,
|
||||
"deposit"_fix_deposit.html,
|
||||
"drag"_fix_drag.html,
|
||||
|
|
@ -432,7 +435,8 @@ description:
|
|||
"temp"_compute_temp.html,
|
||||
"temp/partial"_compute_temp_partial.html,
|
||||
"temp/ramp"_compute_temp_ramp.html,
|
||||
"temp/region"_compute_temp_region.html :tb(c=6,ea=c)
|
||||
"temp/region"_compute_temp_region.html
|
||||
"variable/atom"_compute_variable_atom.html :tb(c=6,ea=c)
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -513,10 +513,10 @@ the input script is read. "Name" is the variable name which can be a
|
|||
single character (referenced as $x in the input script) or a full
|
||||
string (referenced as ${abc}). The value can be any string. Using
|
||||
this command-line option is equivalent to putting the line "variable
|
||||
name index value" at the beginning of the input script. See the
|
||||
name equal value" at the beginning of the input script. See the
|
||||
<A HREF = "variable.html">variable</A> command for more info on defining variables
|
||||
and <A HREF = "Section_commands.html#3_2">this section</A> for more info on using
|
||||
variables in scripts.
|
||||
variables in input scripts.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
|
|||
|
|
@ -506,10 +506,10 @@ the input script is read. "Name" is the variable name which can be a
|
|||
single character (referenced as $x in the input script) or a full
|
||||
string (referenced as $\{abc\}). The value can be any string. Using
|
||||
this command-line option is equivalent to putting the line "variable
|
||||
name index value" at the beginning of the input script. See the
|
||||
name equal value" at the beginning of the input script. See the
|
||||
"variable"_variable.html command for more info on defining variables
|
||||
and "this section"_Section_commands.html#3_2 for more info on using
|
||||
variables in scripts.
|
||||
variables in input scripts.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -32,13 +32,14 @@ compute 3 all ke/atom
|
|||
</P>
|
||||
<P>In LAMMPS, a "compute" is used in several ways. Computes that
|
||||
calculate one or more values for the entire group of atoms can output
|
||||
those values via the <A HREF = "thermo_style.html">thermo_style custom</A> command.
|
||||
Or the values can be referenced in a <A HREF = "variable.html">variable equal</A>
|
||||
command. Computes that calculate a temperature or pressure are used
|
||||
by fixes that do thermostatting or barostatting and when atom
|
||||
velocities are created. Computes that calculate one or more values
|
||||
for each atom in the group can output those values via the <A HREF = "dump.html">dump
|
||||
custom</A> command.
|
||||
those values via the <A HREF = "thermo_style.html">thermo_style custom</A> or <A HREF = "fix_ave_time.html">fix
|
||||
ave/time</A> command. Or the values can be referenced
|
||||
in a <A HREF = "variable.html">variable equal</A> command. Computes that calculate
|
||||
a temperature or pressure are used by fixes that do thermostatting or
|
||||
barostatting and when atom velocities are created. Computes that
|
||||
calculate one or more values for each atom in the group can output
|
||||
those values via the <A HREF = "dump.html">dump custom</A> command or the <A HREF = "fix_ave_spatial.html">fix
|
||||
ave/spatial</A> command.
|
||||
</P>
|
||||
<P>LAMMPS creates its own computes for thermodynamic output and dumping
|
||||
atom snapshots. Likewise fixes that compute temperature or pressure
|
||||
|
|
@ -73,7 +74,8 @@ defined in LAMMPS:
|
|||
<LI><A HREF = "compute_temp.html">temp</A> - temperature of group of atoms
|
||||
<LI><A HREF = "compute_temp_partial.html">temp/partial</A> - temperature excluding one or more dimensions of velocity
|
||||
<LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature after subtracting a ramped velocity component
|
||||
<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
|
||||
<LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
|
||||
<LI><A HREF = "compute_variable_atom.html">variable/atom</A> - calculate a formula for each atom
|
||||
</UL>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -29,13 +29,14 @@ Create a computation that will be performed on a group of atoms.
|
|||
|
||||
In LAMMPS, a "compute" is used in several ways. Computes that
|
||||
calculate one or more values for the entire group of atoms can output
|
||||
those values via the "thermo_style custom"_thermo_style.html command.
|
||||
Or the values can be referenced in a "variable equal"_variable.html
|
||||
command. Computes that calculate a temperature or pressure are used
|
||||
by fixes that do thermostatting or barostatting and when atom
|
||||
velocities are created. Computes that calculate one or more values
|
||||
for each atom in the group can output those values via the "dump
|
||||
custom"_dump.html command.
|
||||
those values via the "thermo_style custom"_thermo_style.html or "fix
|
||||
ave/time"_fix_ave_time.html command. Or the values can be referenced
|
||||
in a "variable equal"_variable.html command. Computes that calculate
|
||||
a temperature or pressure are used by fixes that do thermostatting or
|
||||
barostatting and when atom velocities are created. Computes that
|
||||
calculate one or more values for each atom in the group can output
|
||||
those values via the "dump custom"_dump.html command or the "fix
|
||||
ave/spatial"_fix_ave_spatial.html command.
|
||||
|
||||
LAMMPS creates its own computes for thermodynamic output and dumping
|
||||
atom snapshots. Likewise fixes that compute temperature or pressure
|
||||
|
|
@ -70,7 +71,8 @@ defined in LAMMPS:
|
|||
"temp"_compute_temp.html - temperature of group of atoms
|
||||
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
|
||||
"temp/ramp"_compute_temp_ramp.html - temperature after subtracting a ramped velocity component
|
||||
"temp/region"_compute_temp_region.html - temperature of a region of atoms :ul
|
||||
"temp/region"_compute_temp_region.html - temperature of a region of atoms
|
||||
"variable/atom"_compute_variable_atom.html - calculate a formula for each atom :ul
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -9,18 +9,18 @@
|
|||
|
||||
<HR>
|
||||
|
||||
<H3>compute ke/atom command
|
||||
<H3>compute centro/atom command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID ke/atom
|
||||
<PRE>compute ID group-ID centro/atom
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>ke/atom = style name of this compute command
|
||||
<LI>centro/atom = style name of this compute command
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all ke/atom
|
||||
<PRE>compute 1 all centro/atom
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -6,18 +6,18 @@
|
|||
|
||||
:line
|
||||
|
||||
compute ke/atom command :h3
|
||||
compute centro/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID ke/atom :pre
|
||||
compute ID group-ID centro/atom :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
ke/atom = style name of this compute command :ul
|
||||
centro/atom = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all ke/atom :pre
|
||||
compute 1 all centro/atom :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
|
|||
|
|
@ -263,16 +263,15 @@ quantities calculated by a compute to be output. The ID in the
|
|||
keyword should be replaced by the actual ID of the compute that has
|
||||
been defined elsewhere in the input script. See the
|
||||
<A HREF = "compute.html">compute</A> command for details. Note that scalar and
|
||||
vector quantities that are not calculated on a per-atoms basis
|
||||
vector quantities that are not calculated on a per-atom basis
|
||||
(e.g. global temperature or pressure) cannot be output in a dump.
|
||||
Rather, these quantities are output by the <A HREF = "thermo_style.html">thermo_style
|
||||
custom</A> command.
|
||||
</P>
|
||||
<P>If <I>c_ID</I> is used as a keyword, then the a single per-atom quantity
|
||||
calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N in
|
||||
the range from 1-M will print a specific component of the per-atom
|
||||
vector calculated by the compute. A value of N=0 will output the
|
||||
single per-atom quantity.
|
||||
<P>If <I>c_ID</I> is used as a keyword, then the scalar per-atom quantity
|
||||
calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N
|
||||
in the range from 1-M will print the Nth component of the M-length
|
||||
per-atom vector calculated by the compute.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_modify.html">this section</A> for information on how to add
|
||||
new compute styles to LAMMPS that calculate per-atom quantities which
|
||||
|
|
|
|||
11
doc/dump.txt
11
doc/dump.txt
|
|
@ -253,16 +253,15 @@ quantities calculated by a compute to be output. The ID in the
|
|||
keyword should be replaced by the actual ID of the compute that has
|
||||
been defined elsewhere in the input script. See the
|
||||
"compute"_compute.html command for details. Note that scalar and
|
||||
vector quantities that are not calculated on a per-atoms basis
|
||||
vector quantities that are not calculated on a per-atom basis
|
||||
(e.g. global temperature or pressure) cannot be output in a dump.
|
||||
Rather, these quantities are output by the "thermo_style
|
||||
custom"_thermo_style.html command.
|
||||
|
||||
If {c_ID} is used as a keyword, then the a single per-atom quantity
|
||||
calculated by the compute is printed. If {c_ID\[N\]} is used, then N in
|
||||
the range from 1-M will print a specific component of the per-atom
|
||||
vector calculated by the compute. A value of N=0 will output the
|
||||
single per-atom quantity.
|
||||
If {c_ID} is used as a keyword, then the scalar per-atom quantity
|
||||
calculated by the compute is printed. If {c_ID\[N\]} is used, then N
|
||||
in the range from 1-M will print the Nth component of the M-length
|
||||
per-atom vector calculated by the compute.
|
||||
|
||||
See "this section"_Section_modify.html for information on how to add
|
||||
new compute styles to LAMMPS that calculate per-atom quantities which
|
||||
|
|
|
|||
|
|
@ -65,6 +65,9 @@ made to the old fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
|
|||
</P>
|
||||
<UL><LI><A HREF = "fix_addforce.html">fix addforce</A> - add a force to each atom
|
||||
<LI><A HREF = "fix_aveforce.html">fix aveforce</A> - add an averaged force to each atom
|
||||
<LI><A HREF = "fix_ave_spatial.html">fix ave/spatial</A> - output per-atom quantities by layer
|
||||
<LI><A HREF = "fix_ave_time.html">fix ave/time</A> - output time-averaged compute quantities
|
||||
<LI><A HREF = "fix_box_relax.html">fix box/relax</A> - relax box size during a minimization
|
||||
<LI><A HREF = "fix_com.html">fix com</A> - compute a center-of-mass
|
||||
<LI><A HREF = "fix_desosit.html">fix deposit</A> - add new atoms above a surface
|
||||
<LI><A HREF = "fix_drag.html">fix drag</A> - drag atoms towards a defined coordinate
|
||||
|
|
|
|||
|
|
@ -62,6 +62,9 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
|
|||
|
||||
"fix addforce"_fix_addforce.html - add a force to each atom
|
||||
"fix aveforce"_fix_aveforce.html - add an averaged force to each atom
|
||||
"fix ave/spatial"_fix_ave_spatial.html - output per-atom quantities by layer
|
||||
"fix ave/time"_fix_ave_time.html - output time-averaged compute quantities
|
||||
"fix box/relax"_fix_box_relax.html - relax box size during a minimization
|
||||
"fix com"_fix_com.html - compute a center-of-mass
|
||||
"fix deposit"_fix_desosit.html - add new atoms above a surface
|
||||
"fix drag"_fix_drag.html - drag atoms towards a defined coordinate
|
||||
|
|
|
|||
|
|
@ -204,8 +204,8 @@ are output by the <A HREF = "dump.html">dump custom</A> command.
|
|||
</P>
|
||||
<P>If <I>c_ID</I> is used as a keyword, then the scalar quantity calculated by
|
||||
the compute is printed. If <I>c_ID[N]</I> is used, then N in the range
|
||||
from 1-M will print a specific component of the vector calculated by
|
||||
the compute. A value of N=0 will output the scalar quantity.
|
||||
from 1-M will print the Nth component of the M-length vector
|
||||
calculated by the compute.
|
||||
</P>
|
||||
<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow scalar or vector quantities
|
||||
calculated by a fix to be output. The ID in the keyword should be
|
||||
|
|
@ -214,8 +214,8 @@ in the input script. See the <A HREF = "fix.html">fix</A> command for details.
|
|||
</P>
|
||||
<P>If <I>f_ID</I> is used as a keyword, then the scalar quantity calculated by
|
||||
the fix is printed. If <I>f_ID[N]</I> is used, then N in the range from
|
||||
1-M will print a specific component of the vector calculated by the
|
||||
fix. A value of N=0 will output the scalar quantity.
|
||||
1-M will print the Nth component of the M-length vector calculated by
|
||||
the fix.
|
||||
</P>
|
||||
<P>The <I>v_name</I> keyword allow the current value of a variable to be
|
||||
output. The name in the keyword should be replaced by the actual namd
|
||||
|
|
|
|||
|
|
@ -198,8 +198,8 @@ are output by the "dump custom"_dump.html command.
|
|||
|
||||
If {c_ID} is used as a keyword, then the scalar quantity calculated by
|
||||
the compute is printed. If {c_ID\[N\]} is used, then N in the range
|
||||
from 1-M will print a specific component of the vector calculated by
|
||||
the compute. A value of N=0 will output the scalar quantity.
|
||||
from 1-M will print the Nth component of the M-length vector
|
||||
calculated by the compute.
|
||||
|
||||
The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector quantities
|
||||
calculated by a fix to be output. The ID in the keyword should be
|
||||
|
|
@ -208,8 +208,8 @@ in the input script. See the "fix"_fix.html command for details.
|
|||
|
||||
If {f_ID} is used as a keyword, then the scalar quantity calculated by
|
||||
the fix is printed. If {f_ID\[N\]} is used, then N in the range from
|
||||
1-M will print a specific component of the vector calculated by the
|
||||
fix. A value of N=0 will output the scalar quantity.
|
||||
1-M will print the Nth component of the M-length vector calculated by
|
||||
the fix.
|
||||
|
||||
The {v_name} keyword allow the current value of a variable to be
|
||||
output. The name in the keyword should be replaced by the actual namd
|
||||
|
|
|
|||
|
|
@ -17,22 +17,26 @@
|
|||
</PRE>
|
||||
<UL><LI>name = name of variable to define
|
||||
|
||||
<LI>style = <I>index</I> or <I>loop</I> or <I>world</I> or <I>universe</I> or <I>uloop</I> or <I>equal</I>
|
||||
<LI>style = <I>index</I> or <I>loop</I> or <I>world</I> or <I>universe</I> or <I>uloop</I> or <I>equal</I> or <I>atom</I>
|
||||
|
||||
<PRE> <I>index</I> args = one or more strings
|
||||
<I>loop</I> args = N = integer size of loop
|
||||
<I>world</I> args = one string for each partition of processors
|
||||
<I>universe</I> args = one or more strings
|
||||
<I>uloop</I> args = N = integer size of loop
|
||||
<I>equal</I> args = one equation containing numbers, thermo keywords, math functions, group functions, atom vectors, compute references, other variables
|
||||
<I>equal</I> or <I>atom</I> args = one equation containing numbers, thermo keywords, math functions, group functions, atom vectors, compute references, other variables
|
||||
numbers = 0.0, -5.4, 2.8e-4, etc
|
||||
thermo keywords = vol, ke, press, etc from <A HREF = "thermo_style.html">thermo_style</A>
|
||||
math functions = add(x,y), sub(x,y), mult(x,y), div(x,y),
|
||||
neg(x), pow(x,y), exp(x), ln(x), sqrt(x)
|
||||
group functions = mass(group), charge(group), xcm(group,dim),
|
||||
vcm(group,dim), bound(group,xmin), gyration(group)
|
||||
atom vectors = x[N], y[N], z[N], vx[N], vy[N], vz[N],
|
||||
fx[N], fy[N], fz[N]
|
||||
atom vectors for <I>equal</I> = mass[N], x[N], y[N], z[N],
|
||||
vx[N], vy[N], vz[N],
|
||||
fx[N], fy[N], fz[N]
|
||||
atom vectors for <I>atom</I> = mass[], x[], y[], z[],
|
||||
vx[], vy[], vz[],
|
||||
fx[], fy[], fz[]
|
||||
compute references = c_ID[0], c_ID[N]
|
||||
other variables = v_abc, v_x, etc
|
||||
</PRE>
|
||||
|
|
@ -43,68 +47,78 @@
|
|||
<PRE>variable x index run1 run2 run3 run4 run5 run6 run7 run8
|
||||
variable LoopVar loop 20
|
||||
variable beta equal div(temp,3.0)
|
||||
variable b1 equal add(x[234],mult(0.5,col))
|
||||
variable b1 equal add(x[234],mult(0.5,vol))
|
||||
variable b equal div(xcm(mol1,x),2.0)
|
||||
variable b equal c_myTemp[0]
|
||||
variable b atom div(mult(x<B></B>,y<B></B>),vol)
|
||||
variable temp world 300.0 310.0 320.0 330.0
|
||||
variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
|
||||
variable x uloop 15
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>This command assigns one or more values to a variable name so that the
|
||||
variable can be used in subsequent input script commands or its value
|
||||
output during a simulation. The "name" of the variable is an
|
||||
arbitrary string. Each "value" is a string which could be text or
|
||||
numbers, as in the examples above.
|
||||
<P>This command assigns one or more strings to a variable name.
|
||||
Variables can be used in several ways in LAMMPS. A variable can be
|
||||
referenced elsewhere in an input script. For variable styles that
|
||||
store multiple strings, the <A HREF = "next.html">next</A> command can be used to
|
||||
increment which string is assigned to the variable. Variables can be
|
||||
evaluated to produce a numeric value which can be output either
|
||||
directly (see the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix print</A>, and
|
||||
<A HREF = "run.html">run every</A> commands) or as part of thermodynamic output (see
|
||||
the <A HREF = "thermo_style.html">thermo_style</A> command), fix output (see the
|
||||
<A HREF = "fix_ave_spatial.html">fix ave/spatial</A> and <A HREF = "compute_variable_atom.html">compute
|
||||
variable/atom</A> commands), or dump output
|
||||
(see the <A HREF = "dump.html">dump custom</A> and <A HREF = "compute_variable_atom.html">compute
|
||||
variable/atom</A> commands).
|
||||
</P>
|
||||
<P>As explained in <A HREF = "Section_commands.html#3_2">this section</A>, occurrences
|
||||
of the variable name in an input script line are replaced by the
|
||||
variable's value. The variable name can be referenced in the input
|
||||
script as $x if the name "x" is a single character, or as ${LoopVar}
|
||||
if the name "LoopVar" is one or more characters.
|
||||
<P>In the discussion that follows, the "name" of the variable is the
|
||||
arbitrary string that is the 1st argument in the variable command.
|
||||
The "string" is one of the subsequent arguments. The "value" is the
|
||||
numeric quantity resulting from evaluation of the string. Note that
|
||||
the same string can generate different values when it is evaluated at
|
||||
different times during a simulation.
|
||||
</P>
|
||||
<P>Variable values can also be accessed for output once or periodically
|
||||
during a simulation by the <A HREF = "print.html">print</A> command, <A HREF = "fix_print.html">fix
|
||||
print</A> command, <A HREF = "run.html">run every</A> command, and the
|
||||
<A HREF = "thermo_style.html">thermo_style</A> command.
|
||||
<P>IMPORTANT NOTE: When a variable command is encountered in the input
|
||||
script and the variable name has already been specified, the command
|
||||
is ignored. This means variables can NOT be re-defined in an input
|
||||
script. This is to allow an input script with variable commands to be
|
||||
processed multiple times without resetting the variables; see the
|
||||
<A HREF = "jump.html">jump</A> or <A HREF = "include.html">include</A> commands. It also means
|
||||
that using a command-line switch -var will override a corresponding
|
||||
variable setting in the input script.
|
||||
</P>
|
||||
<P>There is one exception to this rule. As described below, if a
|
||||
variable is iterated on to the end of its list of strings via the
|
||||
<A HREF = "next.html">next</A> command, it is available to be re-defined in a
|
||||
subsequent variable command.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><A HREF = "Section_commands.html#3_2">This section</A> explains how occurrences of a
|
||||
variable name in an input script line are replaced by the variable's
|
||||
string. The variable name can be referenced as $x if the name "x" is
|
||||
a single character, or as ${LoopVar} if the name "LoopVar" is one or
|
||||
more characters.
|
||||
</P>
|
||||
<P>As described below, for variable styles <I>index</I>, <I>loop</I>, <I>universe</I>,
|
||||
and <I>uloop</I>, the value assigned to a variable can be incremented via
|
||||
the <A HREF = "next.html">next</A> command. When there are no more values to
|
||||
and <I>uloop</I>, the string assigned to a variable can be incremented via
|
||||
the <A HREF = "next.html">next</A> command. When there are no more strings to
|
||||
assign, the variable is "exhausted" and a flag is set that causes the
|
||||
next <A HREF = "jump.html">jump</A> command encountered in the input script to be
|
||||
skipped. This enables the construction of simple loops in the input
|
||||
script that are iterated over and exited from.
|
||||
</P>
|
||||
<P>When a variable command is encountered for a variable that has already
|
||||
been specified, the command is ignored. This allows an input script
|
||||
with a variable command to be processed multiple times; see the
|
||||
<A HREF = "jump.html">jump</A> or <A HREF = "include.html">include</A> commands. It also means
|
||||
that the use of the command-line switch -var will override a
|
||||
corresponding variable setting in the input script.
|
||||
</P>
|
||||
<P>There are two exceptions to this rule. The first is for <I>equal</I> style
|
||||
variables. They are re-defined each time a variable command using an
|
||||
equal-style variable is encountered. Also, if a variable is iterated
|
||||
on to the end of its list via the <A HREF = "next.html">next</A> command, it is
|
||||
available to be re-defined in a subsequent variable command.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>For the <I>index</I> style, one or more strings are specified. Initially,
|
||||
the 1st string is assigned to the variable. Each time a
|
||||
<A HREF = "next.html">next</A> command is used with the variable name, the next
|
||||
string is assigned. All processors assign the same string to the
|
||||
variable. <I>Index</I>-style variables can also be set (with a single
|
||||
value) by using the command-line switch -var; see <A HREF = "Section_start.html#2_6">this
|
||||
section</A> for details.
|
||||
variable.
|
||||
</P>
|
||||
<P>The <I>loop</I> style is identical to the <I>index</I> style except that the
|
||||
strings are the integers from 1 to N. This allows you to generate a
|
||||
long list of runs (e.g. 1000) without having to list N values in your
|
||||
strings are the integers from 1 to N. This allows generation of a
|
||||
long list of runs (e.g. 1000) without having to list N strings in the
|
||||
input script. Initially, the string "1" is assigned to the variable.
|
||||
Each time a <A HREF = "next.html">next</A> command is used with the variable name,
|
||||
the next string ("2", "3", etc) is assigned. All processors assign
|
||||
|
|
@ -116,7 +130,7 @@ section</A> of the manual for information on
|
|||
running LAMMPS with multiple partitions via the "-partition"
|
||||
command-line switch. This variable command assigns one string to each
|
||||
world. All processors in the world are assigned the same string. The
|
||||
next command cannot be used with <I>equal</I>-style variables, since there
|
||||
next command cannot be used with <I>equal</I> style variables, since there
|
||||
is only one value per world. This style of variable is useful when
|
||||
you wish to run different simulations on different partitions, or when
|
||||
performing a parallel tempering simulation (see the
|
||||
|
|
@ -130,31 +144,43 @@ running LAMMPS with multiple partitions via the "-partition"
|
|||
command-line switch. This variable command initially assigns one
|
||||
string to each world. When a <A HREF = "next.html">next</A> command is encountered
|
||||
using this variable, the first processor partition to encounter it, is
|
||||
assigned the next available value. This continues until all the
|
||||
variable values are consumed. Thus, this command can be used to run
|
||||
assigned the next available string. This continues until all the
|
||||
variable strings are consumed. Thus, this command can be used to run
|
||||
50 simulations on 8 processor partitions. The simulations will be run
|
||||
one after the other on whatever partition becomes available, until
|
||||
they are all finished. <I>Universe</I>-style variables are incremented
|
||||
they are all finished. <I>Universe</I> style variables are incremented
|
||||
using the files "tmp.lammps.variable" and "tmp.lammps.variable.lock"
|
||||
which you will see in your directory during such a LAMMPS run.
|
||||
</P>
|
||||
<P>The <I>uloop</I> style is identical to the <I>universe</I> style except that the
|
||||
strings are the integers from 1 to N. This allows you to generate a
|
||||
long list of runs (e.g. 1000) without having to list N values in your
|
||||
input script.
|
||||
strings are the integers from 1 to N. This allows generation of long
|
||||
list of runs (e.g. 1000) without having to list N strings in the input
|
||||
script.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>For the <I>equal</I> style, a single string is specified which represents
|
||||
an equation that will be evaluated afresh each time the variable is
|
||||
used. Thus the variable can take on different values at different
|
||||
stages of the input script. For example, if the variable is used in a
|
||||
<A HREF = "fix_print.html">fix print</A> command, different values could be printed
|
||||
each timestep it was invoked. The next command cannot be used with
|
||||
<I>equal</I>-style variables, since there is only one value.
|
||||
<P>For the <I>equal</I> and <I>atom</I> styles, a single string is specified which
|
||||
represents an equation that will be evaluated afresh each time the
|
||||
variable is used. For <I>equal</I> style variables this equation computes
|
||||
a scalar quantity, which becomes the value of the variable whenever it
|
||||
is evaluated. For <I>atom</I> style variables it computes a quantity for
|
||||
each atom, which is used by the "compute variable/atom" command and
|
||||
its associated output.
|
||||
</P>
|
||||
<P>The equation for an <I>equal</I>-style variable can contain a variety of
|
||||
quantities. The syntax for each kind of quantity is simple, but
|
||||
<P>Note that <I>equal</I> and <I>atom</I> variables can produce different values at
|
||||
different stages of the input script or at different times during a
|
||||
run. For example, if an <I>equal</I> variable is used in a <A HREF = "fix_print.html">fix
|
||||
print</A> command, different values could be printed each
|
||||
timestep it was invoked.
|
||||
</P>
|
||||
<P><I>Equal</I> style variables can also be set by using the command-line
|
||||
switch -var; see <A HREF = "Section_start.html#2_6">this section</A> for details.
|
||||
</P>
|
||||
<P>The next command cannot be used with <I>equal</I> or <I>atom</I> style
|
||||
variables, since there is only one string.
|
||||
</P>
|
||||
<P>The equation for an <I>equal</I> or <I>atom</I> variable can contain a variety
|
||||
of quantities. The syntax for each kind of quantity is simple, but
|
||||
multiple quantities can be nested and combined in various ways to
|
||||
build up formulas of arbitrary complexity. For example, this is a
|
||||
valid (though strange) variable equation:
|
||||
|
|
@ -163,14 +189,16 @@ valid (though strange) variable equation:
|
|||
</PRE>
|
||||
<P>Specifically, an equation can contain numbers, thermo keywords, math
|
||||
functions, group functions, atom vectors, compute references, and
|
||||
other variables:
|
||||
other variables. There is one difference between <I>equal</I> and <I>atom</I>
|
||||
variables; the syntax of Atom vector references is different.
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
||||
<TR><TD >Number</TD><TD > 0.2, 1.0e20, -15.4, etc</TD></TR>
|
||||
<TR><TD >Thermo keywords</TD><TD > vol, pe, ebond, etc</TD></TR>
|
||||
<TR><TD >Math functions</TD><TD > add(x,y), sub(x,y), mult(x,y), div(x,y), neg(x), pow(x,y), exp(x), ln(x), sqrt(x)</TD></TR>
|
||||
<TR><TD >Group functions</TD><TD > mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), bound(ID,dir), gyration(ID)</TD></TR>
|
||||
<TR><TD >Atom vectors</TD><TD > x[N], y[N], z[N], vx[N], vy[N], vz[N], fx[N], fy[N], fz[N]</TD></TR>
|
||||
<TR><TD >Atom vectors for <I>equal</I></TD><TD > mass[N], x[N], y[N], z[N], vx[N], vy[N], vz[N], fx[N], fy[N], fz[N]</TD></TR>
|
||||
<TR><TD >Atom vectors for <I>atom</I></TD><TD > mass[], x[], y[], z[], vx[], vy[], vz[], fx[], fy[], fz[]</TD></TR>
|
||||
<TR><TD >Compute references</TD><TD > c_ID[0], c_ID[N]</TD></TR>
|
||||
<TR><TD >Other variables</TD><TD > v_abc, v_x, etc
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
|
@ -197,20 +225,24 @@ min/max of a particular coordinate for all atoms in the group.
|
|||
Gyration() computes the radius-of-gyration of the group of atoms. See
|
||||
the <A HREF = "fix_gyration.html">fix gyration</A> command for the formula.
|
||||
</P>
|
||||
<P>The atom vectors take a single integer argument from 1-N, which
|
||||
is the desired atom-ID, e.g. x[243].
|
||||
<P>For <I>equal</I> style variables, atom vectors take a single integer
|
||||
argument from 1-N, which is the desired atom-ID, e.g. x[243]. For
|
||||
<I>atom</I> style variables, atom vectors take no argument. Since <I>atom</I>
|
||||
style variables compute one value per atom, a reference like x[]
|
||||
means the x-coord of each atom will be used when evaluating the
|
||||
variable.
|
||||
</P>
|
||||
<P>Compute references access allow access to scalar or vector quantities
|
||||
calculated by a compute. The ID in the reference should be replaced
|
||||
by the actual ID of the compute that has been defined elsewhere in the
|
||||
input script. See the <A HREF = "compute.html">compute</A> command for details.
|
||||
Note that per-atom quantities calcalated by a compute cannot be
|
||||
accessed this way, but only global scalar or vector quantities.
|
||||
<P>Compute references access scalar or vector quantities calculated by a
|
||||
<A HREF = "compute.html">compute</A>. The ID in the reference should be replaced by
|
||||
the actual ID of the compute defined elsewhere in the input script.
|
||||
See the <A HREF = "compute.html">compute</A> command for details. Note that
|
||||
per-atom quantities calculated by a compute cannot be accessed this
|
||||
way, but only global scalar or vector quantities.
|
||||
</P>
|
||||
<P>If <I>c_ID[0]</I> is used as a keyword, then the scalar quantity
|
||||
calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N
|
||||
in the range from 1-M will print a specific component of the vector
|
||||
calculated by the compute.
|
||||
in the range from 1-M will print the Mth component of the N-length
|
||||
vector calculated by the compute.
|
||||
</P>
|
||||
<P>The current values of other variables can be accessed by prepending a
|
||||
"v_" to the variable name. This will cause the other variable to be
|
||||
|
|
@ -222,8 +254,8 @@ print $a
|
|||
</PRE>
|
||||
<P>then LAMMPS will run for a while when the print statement is invoked.
|
||||
</P>
|
||||
<P>Note that there is a subtle difference between using a variable
|
||||
in a <I>equal</I>-style equation in the form $x versus v_x.
|
||||
<P>Note that there is a subtle difference between using a variable in a
|
||||
<I>equal</I> or <I>atom</I> style equation in the form $x versus v_x.
|
||||
</P>
|
||||
<P>In the former case, as with any other input script command, the
|
||||
variable's value is substituted for immediately when the line is read
|
||||
|
|
@ -243,7 +275,7 @@ variable y equal mult(v_x,2)
|
|||
<P>would associate the equation string "mult(v_x,2)" with variable y.
|
||||
</P>
|
||||
<P>Thus if the variable y were evaluated periodically during a run where
|
||||
the box volume changed, the resulting value would always be 500.0 for
|
||||
the box volume changed, the resulting value would always be 2000.0 for
|
||||
the first case, but would change dynamically for the second case.
|
||||
</P>
|
||||
<HR>
|
||||
|
|
|
|||
177
doc/variable.txt
177
doc/variable.txt
|
|
@ -13,21 +13,25 @@ variable command :h3
|
|||
variable name style args ... :pre
|
||||
|
||||
name = name of variable to define :ulb,l
|
||||
style = {index} or {loop} or {world} or {universe} or {uloop} or {equal} :l
|
||||
style = {index} or {loop} or {world} or {universe} or {uloop} or {equal} or {atom} :l
|
||||
{index} args = one or more strings
|
||||
{loop} args = N = integer size of loop
|
||||
{world} args = one string for each partition of processors
|
||||
{universe} args = one or more strings
|
||||
{uloop} args = N = integer size of loop
|
||||
{equal} args = one equation containing numbers, thermo keywords, math functions, group functions, atom vectors, compute references, other variables
|
||||
{equal} or {atom} args = one equation containing numbers, thermo keywords, math functions, group functions, atom vectors, compute references, other variables
|
||||
numbers = 0.0, -5.4, 2.8e-4, etc
|
||||
thermo keywords = vol, ke, press, etc from "thermo_style"_thermo_style.html
|
||||
math functions = add(x,y), sub(x,y), mult(x,y), div(x,y),
|
||||
neg(x), pow(x,y), exp(x), ln(x), sqrt(x)
|
||||
group functions = mass(group), charge(group), xcm(group,dim),
|
||||
vcm(group,dim), bound(group,xmin), gyration(group)
|
||||
atom vectors = x\[N\], y\[N\], z\[N\], vx\[N\], vy\[N\], vz\[N\],
|
||||
fx\[N\], fy\[N\], fz\[N\]
|
||||
atom vectors for {equal} = mass\[N\], x\[N\], y\[N\], z\[N\],
|
||||
vx\[N\], vy\[N\], vz\[N\],
|
||||
fx\[N\], fy\[N\], fz\[N\]
|
||||
atom vectors for {atom} = mass\[\], x\[\], y\[\], z\[\],
|
||||
vx\[\], vy\[\], vz\[\],
|
||||
fx\[\], fy\[\], fz\[\]
|
||||
compute references = c_ID\[0\], c_ID\[N\]
|
||||
other variables = v_abc, v_x, etc :pre
|
||||
:ule
|
||||
|
|
@ -37,68 +41,78 @@ style = {index} or {loop} or {world} or {universe} or {uloop} or {equal} :l
|
|||
variable x index run1 run2 run3 run4 run5 run6 run7 run8
|
||||
variable LoopVar loop 20
|
||||
variable beta equal div(temp,3.0)
|
||||
variable b1 equal add(x\[234\],mult(0.5,col))
|
||||
variable b1 equal add(x\[234\],mult(0.5,vol))
|
||||
variable b equal div(xcm(mol1,x),2.0)
|
||||
variable b equal c_myTemp\[0\]
|
||||
variable b atom div(mult(x[],y[]),vol)
|
||||
variable temp world 300.0 310.0 320.0 330.0
|
||||
variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
|
||||
variable x uloop 15 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This command assigns one or more values to a variable name so that the
|
||||
variable can be used in subsequent input script commands or its value
|
||||
output during a simulation. The "name" of the variable is an
|
||||
arbitrary string. Each "value" is a string which could be text or
|
||||
numbers, as in the examples above.
|
||||
This command assigns one or more strings to a variable name.
|
||||
Variables can be used in several ways in LAMMPS. A variable can be
|
||||
referenced elsewhere in an input script. For variable styles that
|
||||
store multiple strings, the "next"_next.html command can be used to
|
||||
increment which string is assigned to the variable. Variables can be
|
||||
evaluated to produce a numeric value which can be output either
|
||||
directly (see the "print"_print.html, "fix print"_fix_print.html, and
|
||||
"run every"_run.html commands) or as part of thermodynamic output (see
|
||||
the "thermo_style"_thermo_style.html command), fix output (see the
|
||||
"fix ave/spatial"_fix_ave_spatial.html and "compute
|
||||
variable/atom"_compute_variable_atom.html commands), or dump output
|
||||
(see the "dump custom"_dump.html and "compute
|
||||
variable/atom"_compute_variable_atom.html commands).
|
||||
|
||||
As explained in "this section"_Section_commands.html#3_2, occurrences
|
||||
of the variable name in an input script line are replaced by the
|
||||
variable's value. The variable name can be referenced in the input
|
||||
script as $x if the name "x" is a single character, or as $\{LoopVar\}
|
||||
if the name "LoopVar" is one or more characters.
|
||||
In the discussion that follows, the "name" of the variable is the
|
||||
arbitrary string that is the 1st argument in the variable command.
|
||||
The "string" is one of the subsequent arguments. The "value" is the
|
||||
numeric quantity resulting from evaluation of the string. Note that
|
||||
the same string can generate different values when it is evaluated at
|
||||
different times during a simulation.
|
||||
|
||||
Variable values can also be accessed for output once or periodically
|
||||
during a simulation by the "print"_print.html command, "fix
|
||||
print"_fix_print.html command, "run every"_run.html command, and the
|
||||
"thermo_style"_thermo_style.html command.
|
||||
IMPORTANT NOTE: When a variable command is encountered in the input
|
||||
script and the variable name has already been specified, the command
|
||||
is ignored. This means variables can NOT be re-defined in an input
|
||||
script. This is to allow an input script with variable commands to be
|
||||
processed multiple times without resetting the variables; see the
|
||||
"jump"_jump.html or "include"_include.html commands. It also means
|
||||
that using a command-line switch -var will override a corresponding
|
||||
variable setting in the input script.
|
||||
|
||||
There is one exception to this rule. As described below, if a
|
||||
variable is iterated on to the end of its list of strings via the
|
||||
"next"_next.html command, it is available to be re-defined in a
|
||||
subsequent variable command.
|
||||
|
||||
:line
|
||||
|
||||
"This section"_Section_commands.html#3_2 explains how occurrences of a
|
||||
variable name in an input script line are replaced by the variable's
|
||||
string. The variable name can be referenced as $x if the name "x" is
|
||||
a single character, or as $\{LoopVar\} if the name "LoopVar" is one or
|
||||
more characters.
|
||||
|
||||
As described below, for variable styles {index}, {loop}, {universe},
|
||||
and {uloop}, the value assigned to a variable can be incremented via
|
||||
the "next"_next.html command. When there are no more values to
|
||||
and {uloop}, the string assigned to a variable can be incremented via
|
||||
the "next"_next.html command. When there are no more strings to
|
||||
assign, the variable is "exhausted" and a flag is set that causes the
|
||||
next "jump"_jump.html command encountered in the input script to be
|
||||
skipped. This enables the construction of simple loops in the input
|
||||
script that are iterated over and exited from.
|
||||
|
||||
When a variable command is encountered for a variable that has already
|
||||
been specified, the command is ignored. This allows an input script
|
||||
with a variable command to be processed multiple times; see the
|
||||
"jump"_jump.html or "include"_include.html commands. It also means
|
||||
that the use of the command-line switch -var will override a
|
||||
corresponding variable setting in the input script.
|
||||
|
||||
There are two exceptions to this rule. The first is for {equal} style
|
||||
variables. They are re-defined each time a variable command using an
|
||||
equal-style variable is encountered. Also, if a variable is iterated
|
||||
on to the end of its list via the "next"_next.html command, it is
|
||||
available to be re-defined in a subsequent variable command.
|
||||
|
||||
:line
|
||||
|
||||
For the {index} style, one or more strings are specified. Initially,
|
||||
the 1st string is assigned to the variable. Each time a
|
||||
"next"_next.html command is used with the variable name, the next
|
||||
string is assigned. All processors assign the same string to the
|
||||
variable. {Index}-style variables can also be set (with a single
|
||||
value) by using the command-line switch -var; see "this
|
||||
section"_Section_start.html#2_6 for details.
|
||||
variable.
|
||||
|
||||
The {loop} style is identical to the {index} style except that the
|
||||
strings are the integers from 1 to N. This allows you to generate a
|
||||
long list of runs (e.g. 1000) without having to list N values in your
|
||||
strings are the integers from 1 to N. This allows generation of a
|
||||
long list of runs (e.g. 1000) without having to list N strings in the
|
||||
input script. Initially, the string "1" is assigned to the variable.
|
||||
Each time a "next"_next.html command is used with the variable name,
|
||||
the next string ("2", "3", etc) is assigned. All processors assign
|
||||
|
|
@ -110,7 +124,7 @@ section"_Section_start.html#2_6 of the manual for information on
|
|||
running LAMMPS with multiple partitions via the "-partition"
|
||||
command-line switch. This variable command assigns one string to each
|
||||
world. All processors in the world are assigned the same string. The
|
||||
next command cannot be used with {equal}-style variables, since there
|
||||
next command cannot be used with {equal} style variables, since there
|
||||
is only one value per world. This style of variable is useful when
|
||||
you wish to run different simulations on different partitions, or when
|
||||
performing a parallel tempering simulation (see the
|
||||
|
|
@ -124,31 +138,43 @@ running LAMMPS with multiple partitions via the "-partition"
|
|||
command-line switch. This variable command initially assigns one
|
||||
string to each world. When a "next"_next.html command is encountered
|
||||
using this variable, the first processor partition to encounter it, is
|
||||
assigned the next available value. This continues until all the
|
||||
variable values are consumed. Thus, this command can be used to run
|
||||
assigned the next available string. This continues until all the
|
||||
variable strings are consumed. Thus, this command can be used to run
|
||||
50 simulations on 8 processor partitions. The simulations will be run
|
||||
one after the other on whatever partition becomes available, until
|
||||
they are all finished. {Universe}-style variables are incremented
|
||||
they are all finished. {Universe} style variables are incremented
|
||||
using the files "tmp.lammps.variable" and "tmp.lammps.variable.lock"
|
||||
which you will see in your directory during such a LAMMPS run.
|
||||
|
||||
The {uloop} style is identical to the {universe} style except that the
|
||||
strings are the integers from 1 to N. This allows you to generate a
|
||||
long list of runs (e.g. 1000) without having to list N values in your
|
||||
input script.
|
||||
strings are the integers from 1 to N. This allows generation of long
|
||||
list of runs (e.g. 1000) without having to list N strings in the input
|
||||
script.
|
||||
|
||||
:line
|
||||
|
||||
For the {equal} style, a single string is specified which represents
|
||||
an equation that will be evaluated afresh each time the variable is
|
||||
used. Thus the variable can take on different values at different
|
||||
stages of the input script. For example, if the variable is used in a
|
||||
"fix print"_fix_print.html command, different values could be printed
|
||||
each timestep it was invoked. The next command cannot be used with
|
||||
{equal}-style variables, since there is only one value.
|
||||
For the {equal} and {atom} styles, a single string is specified which
|
||||
represents an equation that will be evaluated afresh each time the
|
||||
variable is used. For {equal} style variables this equation computes
|
||||
a scalar quantity, which becomes the value of the variable whenever it
|
||||
is evaluated. For {atom} style variables it computes a quantity for
|
||||
each atom, which is used by the "compute variable/atom" command and
|
||||
its associated output.
|
||||
|
||||
The equation for an {equal}-style variable can contain a variety of
|
||||
quantities. The syntax for each kind of quantity is simple, but
|
||||
Note that {equal} and {atom} variables can produce different values at
|
||||
different stages of the input script or at different times during a
|
||||
run. For example, if an {equal} variable is used in a "fix
|
||||
print"_fix_print.html command, different values could be printed each
|
||||
timestep it was invoked.
|
||||
|
||||
{Equal} style variables can also be set by using the command-line
|
||||
switch -var; see "this section"_Section_start.html#2_6 for details.
|
||||
|
||||
The next command cannot be used with {equal} or {atom} style
|
||||
variables, since there is only one string.
|
||||
|
||||
The equation for an {equal} or {atom} variable can contain a variety
|
||||
of quantities. The syntax for each kind of quantity is simple, but
|
||||
multiple quantities can be nested and combined in various ways to
|
||||
build up formulas of arbitrary complexity. For example, this is a
|
||||
valid (though strange) variable equation:
|
||||
|
|
@ -157,7 +183,8 @@ variable x equal div(add(pe,c_MyTemp\[0\]),pow(vol,div(1,3))) :pre
|
|||
|
||||
Specifically, an equation can contain numbers, thermo keywords, math
|
||||
functions, group functions, atom vectors, compute references, and
|
||||
other variables:
|
||||
other variables. There is one difference between {equal} and {atom}
|
||||
variables; the syntax of Atom vector references is different.
|
||||
|
||||
Number: 0.2, 1.0e20, -15.4, etc
|
||||
Thermo keywords: vol, pe, ebond, etc
|
||||
|
|
@ -165,8 +192,12 @@ Math functions: add(x,y), sub(x,y), mult(x,y), div(x,y), \
|
|||
neg(x), pow(x,y), exp(x), ln(x), sqrt(x)
|
||||
Group functions: mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), \
|
||||
bound(ID,dir), gyration(ID)
|
||||
Atom vectors: x\[N\], y\[N\], z\[N\], vx\[N\], vy\[N\], vz\[N\], \
|
||||
fx\[N\], fy\[N\], fz\[N\]
|
||||
Atom vectors for {equal}: mass\[N\], x\[N\], y\[N\], z\[N\], \
|
||||
vx\[N\], vy\[N\], vz\[N\], \
|
||||
fx\[N\], fy\[N\], fz\[N\]
|
||||
Atom vectors for {atom}: mass\[\], x\[\], y\[\], z\[\], \
|
||||
vx\[\], vy\[\], vz\[\], \
|
||||
fx\[\], fy\[\], fz\[\]
|
||||
Compute references: c_ID\[0\], c_ID\[N\]
|
||||
Other variables: v_abc, v_x, etc :tb(s=:)
|
||||
|
||||
|
|
@ -192,20 +223,24 @@ min/max of a particular coordinate for all atoms in the group.
|
|||
Gyration() computes the radius-of-gyration of the group of atoms. See
|
||||
the "fix gyration"_fix_gyration.html command for the formula.
|
||||
|
||||
The atom vectors take a single integer argument from 1-N, which
|
||||
is the desired atom-ID, e.g. x\[243\].
|
||||
For {equal} style variables, atom vectors take a single integer
|
||||
argument from 1-N, which is the desired atom-ID, e.g. x\[243\]. For
|
||||
{atom} style variables, atom vectors take no argument. Since {atom}
|
||||
style variables compute one value per atom, a reference like x\[\]
|
||||
means the x-coord of each atom will be used when evaluating the
|
||||
variable.
|
||||
|
||||
Compute references access allow access to scalar or vector quantities
|
||||
calculated by a compute. The ID in the reference should be replaced
|
||||
by the actual ID of the compute that has been defined elsewhere in the
|
||||
input script. See the "compute"_compute.html command for details.
|
||||
Note that per-atom quantities calcalated by a compute cannot be
|
||||
accessed this way, but only global scalar or vector quantities.
|
||||
Compute references access scalar or vector quantities calculated by a
|
||||
"compute"_compute.html. The ID in the reference should be replaced by
|
||||
the actual ID of the compute defined elsewhere in the input script.
|
||||
See the "compute"_compute.html command for details. Note that
|
||||
per-atom quantities calculated by a compute cannot be accessed this
|
||||
way, but only global scalar or vector quantities.
|
||||
|
||||
If {c_ID\[0\]} is used as a keyword, then the scalar quantity
|
||||
calculated by the compute is printed. If {c_ID\[N\]} is used, then N
|
||||
in the range from 1-M will print a specific component of the vector
|
||||
calculated by the compute.
|
||||
in the range from 1-M will print the Mth component of the N-length
|
||||
vector calculated by the compute.
|
||||
|
||||
The current values of other variables can be accessed by prepending a
|
||||
"v_" to the variable name. This will cause the other variable to be
|
||||
|
|
@ -217,8 +252,8 @@ print $a :pre
|
|||
|
||||
then LAMMPS will run for a while when the print statement is invoked.
|
||||
|
||||
Note that there is a subtle difference between using a variable
|
||||
in a {equal}-style equation in the form $x versus v_x.
|
||||
Note that there is a subtle difference between using a variable in a
|
||||
{equal} or {atom} style equation in the form $x versus v_x.
|
||||
|
||||
In the former case, as with any other input script command, the
|
||||
variable's value is substituted for immediately when the line is read
|
||||
|
|
@ -238,7 +273,7 @@ variable y equal mult(v_x,2) :pre
|
|||
would associate the equation string "mult(v_x,2)" with variable y.
|
||||
|
||||
Thus if the variable y were evaluated periodically during a run where
|
||||
the box volume changed, the resulting value would always be 500.0 for
|
||||
the box volume changed, the resulting value would always be 2000.0 for
|
||||
the first case, but would change dynamically for the second case.
|
||||
|
||||
:line
|
||||
|
|
|
|||
Loading…
Reference in New Issue