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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4237 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-06-04 00:37:28 +00:00
parent eb80b6a17b
commit 0eeb48a7b3
14 changed files with 76 additions and 54 deletions
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2
doc/Section_commands.html
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@ -330,7 +330,7 @@ of each style or click on the style itself for a full description:
<TR ALIGN="center"><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><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</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_press_berendsen.html">press/berendsen</A></TD><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></TR>
<TR ALIGN="center"><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><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_store.html">store</A></TD><TD ><A HREF = "fix_store_force.html">store/force</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><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD></TR>
<TR ALIGN="center"><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><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>

2
doc/Section_commands.txt
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@ -438,8 +438,8 @@ of each style or click on the style itself for a full description:
"spring"_fix_spring.html,
"spring/rg"_fix_spring_rg.html,
"spring/self"_fix_spring_self.html,
"store"_fix_store.html,
"store/force"_fix_store_force.html,
"store/state"_fix_store_state.html,
"temp/berendsen"_fix_temp_berendsen.html,
"temp/rescale"_fix_temp_rescale.html,
"thermal/conductivity"_fix_thermal_conductivity.html,

9
doc/Section_howto.html
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@ -1153,6 +1153,14 @@ 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
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>.
The output of this fix can be used as input to other output commands.
</P>
<H5><A NAME = "compute"></A>Computes that generate values to output
</H5>
<P>Every <A HREF = "compute.html">compute</A> in LAMMPS produces either global or
@ -1215,6 +1223,7 @@ vector input could be a column of an array.
<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 >
</TD></TR></TABLE></DIV>

9
doc/Section_howto.txt
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@ -1144,6 +1144,14 @@ 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
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.
The output of this fix can be used as input to other output commands.
Computes that generate values to output :h5,link(compute)
Every "compute"_compute.html in LAMMPS produces either global or
@ -1205,6 +1213,7 @@ Command: Input: Output:
"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:
:tb(s=:)
:line

19
doc/compute_displace_atom.html
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@ -35,19 +35,20 @@ dz*dz).
</P>
<P>The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates,
the compute creates its own fix of style "store", as if this command
had been issued:
the compute creates its own fix of style "store/state", as if this
command had been issued:
</P>
<PRE>fix compute-ID_store group-ID store xu yu zu
<PRE>fix compute-ID_store_state group-ID store/state xu yu zu
</PRE>
<P>See the <A HREF = "fix_store.html">fix store</A> command for details. Note that the
ID of the new fix is the compute-ID + underscore + "store", and the
group for the new fix is the same as the compute group.
<P>See the <A HREF = "fix_store_state.html">fix store/state</A> command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store/state", and the group for the new fix is the same as the
compute group.
</P>
<P>The value of the displacement will be 0.0 for atoms not in the
specified compute group.
</P>
<P>IMPORTANT NOTE: Fix store stores the initial coordinates in
<P>IMPORTANT NOTE: Fix store/state stores the initial coordinates in
"unwrapped" form, by using the image flags associated with each atom.
See the <A HREF = "dump.html">dump custom</A> command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
@ -84,8 +85,8 @@ overview of LAMMPS output options.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_store.html">fix
store</A>
<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_store_state.html">fix
store/state</A>
</P>
<P><B>Default:</B> none
</P>

17
doc/compute_displace_atom.txt
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@ -32,19 +32,20 @@ dz*dz).
The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates,
the compute creates its own fix of style "store", as if this command
had been issued:
the compute creates its own fix of style "store/state", as if this
command had been issued:
fix compute-ID_store group-ID store xu yu zu :pre
fix compute-ID_store_state group-ID store/state xu yu zu :pre
See the "fix store"_fix_store.html command for details. Note that the
ID of the new fix is the compute-ID + underscore + "store", and the
group for the new fix is the same as the compute group.
See the "fix store/state"_fix_store_state.html command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store/state", and the group for the new fix is the same as the
compute group.
The value of the displacement will be 0.0 for atoms not in the
specified compute group.
IMPORTANT NOTE: Fix store stores the initial coordinates in
IMPORTANT NOTE: Fix store/state stores the initial coordinates in
"unwrapped" form, by using the image flags associated with each atom.
See the "dump custom"_dump.html command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
@ -82,6 +83,6 @@ The per-atom array values will be in distance "units"_units.html.
[Related commands:]
"compute msd"_compute_msd.html, "dump custom"_dump.html, "fix
store"_fix_store.html
store/state"_fix_store_state.html
[Default:] none

21
doc/compute_msd.html
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@ -49,21 +49,22 @@ proportional to the diffusion coefficient of the diffusing atoms.
</P>
<P>The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates,
the compute creates its own fix of style "store", as if this command
had been issued:
the compute creates its own fix of style "store/state", as if this
command had been issued:
</P>
<PRE>fix compute-ID_store group-ID store xu yu zu
<PRE>fix compute-ID_store_state group-ID store/state xu yu zu
</PRE>
<P>See the <A HREF = "fix_store.html">fix store</A> command for details. Note that the
ID of the new fix is the compute-ID + underscore + "store", and the
group for the new fix is the same as the compute group.
<P>See the <A HREF = "fix_store_state.html">fix store/state</A> command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store_state", and the group for the new fix is the same as the
compute group.
</P>
<P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calcluated. The <I>com</I> option is also
passed to the created fix store.
passed to the created fix store/state.
</P>
<P>IMPORTANT NOTE: Fix store stores the initial coordinates in
<P>IMPORTANT NOTE: Fix store/state stores the initial coordinates in
"unwrapped" form, by using the image flags associated with each atom.
See the <A HREF = "dump.html">dump custom</A> command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
@ -101,8 +102,8 @@ distance^2 <A HREF = "units.html">units</A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_store.html">fix
store</A>, <A HREF = "compute_msd_molecule.html">compute
<P><A HREF = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_store_state.html">fix
store/state</A>, <A HREF = "compute_msd_molecule.html">compute
msd/molecule</A>
</P>
<P><B>Default:</B>

19
doc/compute_msd.txt
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@ -41,21 +41,22 @@ proportional to the diffusion coefficient of the diffusing atoms.
The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates,
the compute creates its own fix of style "store", as if this command
had been issued:
the compute creates its own fix of style "store/state", as if this
command had been issued:
fix compute-ID_store group-ID store xu yu zu :pre
fix compute-ID_store_state group-ID store/state xu yu zu :pre
See the "fix store"_fix_store.html command for details. Note that the
ID of the new fix is the compute-ID + underscore + "store", and the
group for the new fix is the same as the compute group.
See the "fix store/state"_fix_store_state.html command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store_state", and the group for the new fix is the same as the
compute group.
If the {com} option is set to {yes} then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calcluated. The {com} option is also
passed to the created fix store.
passed to the created fix store/state.
IMPORTANT NOTE: Fix store stores the initial coordinates in
IMPORTANT NOTE: Fix store/state stores the initial coordinates in
"unwrapped" form, by using the image flags associated with each atom.
See the "dump custom"_dump.html command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
@ -94,7 +95,7 @@ distance^2 "units"_units.html.
[Related commands:]
"compute displace_atom"_compute_displace_atom.html, "fix
store"_fix_store.html, "compute
store/state"_fix_store_state.html, "compute
msd/molecule"_compute_msd_molecule.html
[Default:]

2
doc/fix.html
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@ -215,8 +215,8 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_spring.html">spring</A> - apply harmonic spring force to group of atoms
<LI><A HREF = "fix_spring_rg.html">spring/rg</A> - spring on radius of gyration of group of atoms
<LI><A HREF = "fix_spring_self.html">spring/self</A> - spring from each atom to its origin
<LI><A HREF = "fix_store.html">store</A> - store attributes for each atom
<LI><A HREF = "fix_store_force.html">store/force</A> - store force on each atom
<LI><A HREF = "fix_store_state.html">store/state</A> - store attributes for each atom
<LI><A HREF = "fix_temp_berendsen.html">temp/berendsen</A> - temperature control by Berendsen thermostat
<LI><A HREF = "fix_temp_rescale.html">temp/rescale</A> - temperature control by velocity rescaling
<LI><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A> - Muller-Plathe kinetic energy exchange for thermal conductivity calculation

2
doc/fix.txt
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@ -218,8 +218,8 @@ list of fix styles available in LAMMPS:
"spring/rg"_fix_spring_rg.html - spring on radius of gyration of \
group of atoms
"spring/self"_fix_spring_self.html - spring from each atom to its origin
"store"_fix_store.html - store attributes for each atom
"store/force"_fix_store_force.html - store force on each atom
"store/state"_fix_store_state.html - store attributes for each atom
"temp/berendsen"_fix_temp_berendsen.html - temperature control by \
Berendsen thermostat
"temp/rescale"_fix_temp_rescale.html - temperature control by \

2
doc/fix_store_force.html
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@ -70,7 +70,7 @@ minimization</A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_store.html">fix store</A>
<P><A HREF = "fix_store_state.html">fix store_state</A>
</P>
<P><B>Default:</B> none
</P>

2
doc/fix_store_force.txt
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@ -67,6 +67,6 @@ minimization"_minimize.html.
[Related commands:]
"fix store"_fix_store.html
"fix store_state"_fix_store_state.html
[Default:] none

12
doc/fix_store.html → doc/fix_store_state.html
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@ -9,15 +9,15 @@
<HR>
<H3>fix store command
<H3>fix store/state command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID store N input1 input2 ... keyword value ...
<PRE>fix ID group-ID store/state N input1 input2 ... keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>store= style name of this fix command
<LI>store/state = style name of this fix command
<LI>N = store atom attributes every N steps, N = 0 for initial store only
@ -65,9 +65,9 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all store 0 x y z
fix 1 all store 0 xu yu zu com yes
fix 2 all store 1000 vx vy vz
<PRE>fix 1 all store/state 0 x y z
fix 1 all store/state 0 xu yu zu com yes
fix 2 all store/state 1000 vx vy vz
</PRE>
<P><B>Description:</B>
</P>

12
doc/fix_store.txt → doc/fix_store_state.txt
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@ -6,14 +6,14 @@
:line
fix store command :h3
fix store/state command :h3
[Syntax:]
fix ID group-ID store N input1 input2 ... keyword value ... :pre
fix ID group-ID store/state N input1 input2 ... keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
store= style name of this fix command :l
store/state = style name of this fix command :l
N = store atom attributes every N steps, N = 0 for initial store only :l
input = one or more atom attributes :l
possible attributes = id, mol, type, mass,
@ -55,9 +55,9 @@ keyword = {com} :l
[Examples:]
fix 1 all store 0 x y z
fix 1 all store 0 xu yu zu com yes
fix 2 all store 1000 vx vy vz :pre
fix 1 all store/state 0 x y z
fix 1 all store/state 0 xu yu zu com yes
fix 2 all store/state 1000 vx vy vz :pre
[Description:]