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sjplimp 2010-06-04 00:14:14 +00:00
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commit 6ddb0f6af1
22 changed files with 579 additions and 332 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_coord.html">store/coord</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.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_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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@ -438,7 +438,7 @@ 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/coord"_fix_store_coord.html,
"store"_fix_store.html,
"store/force"_fix_store_force.html,
"temp/berendsen"_fix_temp_berendsen.html,
"temp/rescale"_fix_temp_rescale.html,

19
doc/compute_displace_atom.html
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@ -35,20 +35,19 @@ 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/coord", as if this
command had been issued:
the compute creates its own fix of style "store", as if this command
had been issued:
</P>
<PRE>fix compute-ID_store_coord group-ID store/coord
<PRE>fix compute-ID_store group-ID store xu yu zu
</PRE>
<P>See the <A HREF = "fix_store_coord.html">fix store/coord</A> command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store_coord", and the group for the new fix is the same as the
compute group.
<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>
<P>The value of the displacement will be 0.0 for atoms not in the
specified compute group.
</P>
<P>IMPORTANT NOTE: Fix store/coord stores the initial coordinates in
<P>IMPORTANT NOTE: Fix store 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
@ -85,8 +84,8 @@ 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_coord.html">fix
store/coord</A>
<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>
<P><B>Default:</B> none
</P>

17
doc/compute_displace_atom.txt
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@ -32,20 +32,19 @@ 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/coord", as if this
command had been issued:
the compute creates its own fix of style "store", as if this command
had been issued:
fix compute-ID_store_coord group-ID store/coord :pre
fix compute-ID_store group-ID store xu yu zu :pre
See the "fix store/coord"_fix_store_coord.html command for details.
Note that the ID of the new fix is the compute-ID + underscore +
"store_coord", and the group for the new fix is the same as the
compute group.
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.
The value of the displacement will be 0.0 for atoms not in the
specified compute group.
IMPORTANT NOTE: Fix store/coord stores the initial coordinates in
IMPORTANT NOTE: Fix store 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
@ -83,6 +82,6 @@ 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/coord"_fix_store_coord.html
store"_fix_store.html
[Default:] none

27
doc/compute_msd.html
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@ -49,22 +49,21 @@ 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/coord", as if this
command had been issued:
the compute creates its own fix of style "store", as if this command
had been issued:
</P>
<PRE>fix compute-ID_store_coord group-ID store/coord
<PRE>fix compute-ID_store group-ID store xu yu zu
</PRE>
<P>See the <A HREF = "fix_store_coord.html">fix store/coord</A> command for
details. Note that the ID of the new fix is the compute-ID +
underscore + "store_coord", and the group for the new fix is
the same as the compute group.
<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>
<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/coord.
<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.
</P>
<P>IMPORTANT NOTE: Fix store/coord stores the initial coordinates in
<P>IMPORTANT NOTE: Fix store 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
@ -102,8 +101,8 @@ 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_coord.html">fix
store/coord</A>, <A HREF = "compute_msd_molecule.html">compute
<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
msd/molecule</A>
</P>
<P><B>Default:</B>

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@ -41,22 +41,21 @@ 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/coord", as if this
command had been issued:
the compute creates its own fix of style "store", as if this command
had been issued:
fix compute-ID_store_coord group-ID store/coord :pre
fix compute-ID_store group-ID store xu yu zu :pre
See the "fix store/coord"_fix_store_coord.html command for
details. Note that the ID of the new fix is the compute-ID +
underscore + "store_coord", and the group for the new fix is
the same as the compute group.
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.
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/coord.
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.
IMPORTANT NOTE: Fix store/coord stores the initial coordinates in
IMPORTANT NOTE: Fix store 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
@ -95,7 +94,7 @@ distance^2 "units"_units.html.
[Related commands:]
"compute displace_atom"_compute_displace_atom.html, "fix
store/coord"_fix_store_coord.html, "compute
store"_fix_store.html, "compute
msd/molecule"_compute_msd_molecule.html
[Default:]

2
doc/fix.html
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@ -215,7 +215,7 @@ 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_coord.html">store/coord</A> - store coords of each atom
<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_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

2
doc/fix.txt
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@ -218,7 +218,7 @@ 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/coord"_fix_store_coord.html - store coords of each atom
"store"_fix_store.html - store attributes for each atom
"store/force"_fix_store_force.html - store force on each atom
"temp/berendsen"_fix_temp_berendsen.html - temperature control by \
Berendsen thermostat

140
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@ -0,0 +1,140 @@
<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 store command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID store 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>N = store atom attributes every N steps, N = 0 for initial store only
<LI>input = one or more atom attributes
<PRE> possible attributes = id, mol, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
radius, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk, tqx, tqy, tqz
c_ID, c_ID[N], f_ID, f_ID[N], v_name
</PRE>
<PRE> id = atom ID
mol = molecule ID
type = atom type
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
ix,iy,iz = box image that the atom is in
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
radius = radius of extended spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom 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/value pairs may be appended
<LI>keyword = <I>com</I>
<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
</PRE>
</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>
<P><B>Description:</B>
</P>
<P>Define a fix that stores attributes for each atom in the group at the
time the fix is defined. If <I>N</I> is 0, then the values are never
updated, so this is a way of archiving an atom attribute at a given
time for future use in a calculation or output. See the discussion of
<A HREF = "Section_howto.html#4_15">output commands</A> that take fixes as inputs.
And see for example, the <A HREF = "compute_reduce.html">compute reduce</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_spatial.html">fix
ave/spatial</A>, and <A HREF = "variable.html">atom-style
variable</A> commands.
</P>
<P>If <I>N</I> is not zero, then the attributes will be updated every <I>N</I>
steps.
</P>
<P>IMPORTANT NOTE: Actually, only atom attributes specified by keywords
like <I>xu</I> or <I>vy</I> are initially stored immediately at the point in
your input script when the fix is defined. Attributes specified by a
compute, fix, or variable are not initially stored until the first run
following the fix definition begins. This is because calculating
those attributes may require quantities that are not defined in
between runs.
</P>
<P>The list of possible attributes is the same as that used by the <A HREF = "dump.html">dump
custom</A> command, which describes their meaning.
</P>
<P>If the <I>com</I> keyword is set to <I>yes</I> then the <I>xu</I>, <I>yu</I>, and <I>zu</I>
inputs store the position of each atom relative to the center-of-mass
of the group of atoms, instead of storing the absolute position. This
option is used by the <A HREF = "compute_msd.html">compute msd</A> command.
</P>
<P>The requested values are stored in a per-atom vector or array as
discussed below. Zeroes are stored for atoms not in the specified
group.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the per-atom values it stores to <A HREF = "restart.html">binary restart
files</A>, so that the values can be restored when a
simulation is restarted. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix.
</P>
<P>If a single input is specified, this fix produces a per-atom vector.
If multiple inputs are specified, a per-atom array is produced where
the number of columns for each atom is the number of inputs. These
can be accessed by various <A HREF = "Section_howto.html#4_15">output commands</A>.
The per-atom values be accessed on any timestep.
</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 = "dump.html">dump custom</A>, <A HREF = "compute_property_atom.html">compute
property/atom</A>, <A HREF = "variable.html">variable</A>
</P>
<P><B>Default:</B>
</P>
<P>The option default is com = no.
</P>
</HTML>

128
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@ -0,0 +1,128 @@
"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 store command :h3
[Syntax:]
fix ID group-ID store 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
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,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
radius, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk, tqx, tqy, tqz
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
id = atom ID
mol = molecule ID
type = atom type
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
ix,iy,iz = box image that the atom is in
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
radius = radius of extended spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
c_ID = per-atom vector calculated by a compute with ID
c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID\[I\] = Ith column of per-atom 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/value pairs may be appended :l
keyword = {com} :l
{com} value = {yes} or {no} :pre
:ule
[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
[Description:]
Define a fix that stores attributes for each atom in the group at the
time the fix is defined. If {N} is 0, then the values are never
updated, so this is a way of archiving an atom attribute at a given
time for future use in a calculation or output. See the discussion of
"output commands"_Section_howto.html#4_15 that take fixes as inputs.
And see for example, the "compute reduce"_compute_reduce.html, "fix
ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, "fix
ave/spatial"_fix_ave_spatial.html, and "atom-style
variable"_variable.html commands.
If {N} is not zero, then the attributes will be updated every {N}
steps.
IMPORTANT NOTE: Actually, only atom attributes specified by keywords
like {xu} or {vy} are initially stored immediately at the point in
your input script when the fix is defined. Attributes specified by a
compute, fix, or variable are not initially stored until the first run
following the fix definition begins. This is because calculating
those attributes may require quantities that are not defined in
between runs.
The list of possible attributes is the same as that used by the "dump
custom"_dump.html command, which describes their meaning.
If the {com} keyword is set to {yes} then the {xu}, {yu}, and {zu}
inputs store the position of each atom relative to the center-of-mass
of the group of atoms, instead of storing the absolute position. This
option is used by the "compute msd"_compute_msd.html command.
The requested values are stored in a per-atom vector or array as
discussed below. Zeroes are stored for atoms not in the specified
group.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the per-atom values it stores to "binary restart
files"_restart.html, so that the values can be restored when a
simulation is restarted. See the "read_restart"_read_restart.html
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
If a single input is specified, this fix produces a per-atom vector.
If multiple inputs are specified, a per-atom array is produced where
the number of columns for each atom is the number of inputs. These
can be accessed by various "output commands"_Section_howto.html#4_15.
The per-atom values be accessed on any timestep.
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:]
"dump custom"_dump.html, "compute
property/atom"_compute_property_atom.html, "variable"_variable.html
[Default:]
The option default is com = no.

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@ -1,97 +0,0 @@
<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 store/coord command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID store/coord keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>store/coord = style name of this fix command
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>com</I>
<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all store/coord
fix 1 upper store/coord com yes
</PRE>
<P><B>Description:</B>
</P>
<P>Store the original coordinates of atoms in the group at the time the
fix command is issued. This is used for computing a displacement of
the atoms at later times, via the <A HREF = "compute_displace_atom.html">compute
displace/atom</A> command. Or the original
coordinates can be accessed by other <A HREF = "Section_howto.html#4_15">output
commands</A> that use per-atom quantities such as
the <A HREF = "dump.html">dump custom</A> command.
</P>
<P>IMPORTANT NOTE: The original coordinates are stored 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 <A HREF = "read_data.html">read_data</A>
command for a discussion of image flags and how they are set for each
atom. You can reset the image flags (e.g. to 0) before invoking this
fix by using the <A HREF = "set.html">set image</A> command.
</P>
<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
rigid</A> command), it's periodic image flags are altered,
and its original coordinates may not be what you expect. See the
<A HREF = "fix_rigid.html">fix rigid</A> command for details.
</P>
<P>If the <I>com</I> keyword is set to <I>yes</I> then the position
of each atom relative to the center-of-mass of the group of
atoms is stored, instead of the absolute position. This option
is used by the <A HREF = "compute_msd.html">compute msd</A> command.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the original coordinates of the atoms to <A HREF = "restart.html">binary
restart files</A>, so that the values can be restored when a
simulation is restarted. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix.
</P>
<P>This fix produces a per-atom array which can be accessed by various
<A HREF = "Section_howto.html#4_15">output commands</A>. The number of columns
for each atom is 3, and the columns store the original unwrapped
x,y,z coords of each atom. The per-atom values be accessed on any
timestep.
</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_msd.html">compute msd</A>, <A HREF = "compute_displace_atom.html">compute
displace/atom</A>, <A HREF = "fix_store_force.html">fix
store/force</A>
</P>
<P><B>Default:</B>
</P>
<P>The option default is com = no.
</P>
</HTML>

87
doc/fix_store_coord.txt
View File

@ -1,87 +0,0 @@
"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 store/coord command :h3
[Syntax:]
fix ID group-ID store/coord keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
store/coord = style name of this fix command :l
zero or more keyword/value pairs may be appended :l
keyword = {com} :l
{com} value = {yes} or {no} :pre
:ule
[Examples:]
fix 1 all store/coord
fix 1 upper store/coord com yes :pre
[Description:]
Store the original coordinates of atoms in the group at the time the
fix command is issued. This is used for computing a displacement of
the atoms at later times, via the "compute
displace/atom"_compute_displace_atom.html command. Or the original
coordinates can be accessed by other "output
commands"_Section_howto.html#4_15 that use per-atom quantities such as
the "dump custom"_dump.html command.
IMPORTANT NOTE: The original coordinates are stored 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 "read_data"_read_data.html
command for a discussion of image flags and how they are set for each
atom. You can reset the image flags (e.g. to 0) before invoking this
fix by using the "set image"_set.html command.
IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
rigid"_fix_rigid.html command), it's periodic image flags are altered,
and its original coordinates may not be what you expect. See the
"fix rigid"_fix_rigid.html command for details.
If the {com} keyword is set to {yes} then the position
of each atom relative to the center-of-mass of the group of
atoms is stored, instead of the absolute position. This option
is used by the "compute msd"_compute_msd.html command.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the original coordinates of the atoms to "binary
restart files"_restart.html, so that the values can be restored when a
simulation is restarted. See the "read_restart"_read_restart.html
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix produces a per-atom array which can be accessed by various
"output commands"_Section_howto.html#4_15. The number of columns
for each atom is 3, and the columns store the original unwrapped
x,y,z coords of each atom. The per-atom values be accessed on any
timestep.
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 msd"_compute_msd.html, "compute
displace/atom"_compute_displace_atom.html, "fix
store/force"_fix_store_force.html
[Default:]
The option default is com = no.

14
doc/fix_store_force.html
View File

@ -24,12 +24,12 @@
</PRE>
<P><B>Description:</B>
</P>
<P>Store the forces on atoms in the group at the point in time during
timestepping when the fix is invoked, as described below. This is
useful for storing forces before constraints or other boundary
conditions are computed which modify the forces, so that the original
forces can be <A HREF = "dump.html">written to a dump file</A> or accessed by other
<A HREF = "Section_howto.html#4_15">output commands</A> that use per-atom quantities.
<P>Store the forces on atoms in the group at the point during each
timestep when the fix is invoked, as described below. This is useful
for storing forces before constraints or other boundary conditions are
computed which modify the forces, so that unmodified forces can be
<A HREF = "dump.html">written to a dump file</A> or accessed by other <A HREF = "Section_howto.html#4_15">output
commands</A> that use per-atom quantities.
</P>
<P>This fix is invoked at the point in the velocity-Verlet timestepping
immediately after <A HREF = "pair_style.html">pair</A>, <A HREF = "bond_style.html">bond</A>,
@ -70,7 +70,7 @@ minimization</A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_store_coord.html">fix store/coord</A>
<P><A HREF = "fix_store.html">fix store</A>
</P>
<P><B>Default:</B> none
</P>

14
doc/fix_store_force.txt
View File

@ -21,12 +21,12 @@ fix 1 all store/force :pre
[Description:]
Store the forces on atoms in the group at the point in time during
timestepping when the fix is invoked, as described below. This is
useful for storing forces before constraints or other boundary
conditions are computed which modify the forces, so that the original
forces can be "written to a dump file"_dump.html or accessed by other
"output commands"_Section_howto.html#4_15 that use per-atom quantities.
Store the forces on atoms in the group at the point during each
timestep when the fix is invoked, as described below. This is useful
for storing forces before constraints or other boundary conditions are
computed which modify the forces, so that unmodified forces can be
"written to a dump file"_dump.html or accessed by other "output
commands"_Section_howto.html#4_15 that use per-atom quantities.
This fix is invoked at the point in the velocity-Verlet timestepping
immediately after "pair"_pair_style.html, "bond"_bond_style.html,
@ -67,6 +67,6 @@ minimization"_minimize.html.
[Related commands:]
"fix store/coord"_fix_store_coord.html
"fix store"_fix_store.html
[Default:] none

7
doc/fix_viscous.html
View File

@ -92,7 +92,12 @@ are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. 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>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command. This fix should only
be used with damped dynamics minimizers that allow for
non-conservative forces. See the <A HREF = "min_style.html">min_style</A> command
for details.
</P>
<P><B>Restrictions:</B> none
</P>

7
doc/fix_viscous.txt
View File

@ -82,7 +82,12 @@ are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#4_15. 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.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. This fix should only
be used with damped dynamics minimizers that allow for
non-conservative forces. See the "min_style"_min_style.html command
for details.
[Restrictions:] none

34
doc/min_modify.html
View File

@ -37,24 +37,28 @@ various settings may affect the convergence rate and overall number of
force evaluations required by a minimization, so users can experiment
with these parameters to tune their minimizations.
</P>
<P>The <I>cg</I> and <I>sd</I> minimization styles have an outer iteration and an
inner iteration which is steps along a one-dimensional line search in
a particular search direction. The <I>dmax</I> parameter is how far any
atom can move in a single line search in any dimension (x, y, or z).
<P>The <I>dmax</I> parameter is a bound on how far any atom can move in a
single dimension (x, y, or z) in a single iteration of the minimizer.
Thus a value of 0.1 in real <A HREF = "units.html">units</A> means no atom will move
further than 0.1 Angstroms in a single outer iteration. This prevents
highly overlapped atoms from being moved long distances (e.g. through
another atom) due to large forces.
further than 0.1 Angstroms in a single iteration. This prevents
highly overlapped atoms from being moved long distances (e.g. passing
through another atom) due to large forces. Note that for the <I>cg</I> and
<I>sd</I> style miminizers (see the <A HREF = "min_style.html">min_style</A> command),
<I>dmax</I> is a bound on the outer iteration or step along a search
direction, not a bound on the inner iteration of steps within a single
line search.
</P>
<P>The choice of line search algorithm for the <I>cg</I> and <I>sd</I> minimization
styles can be selected via the <I>line</I> keyword. The default
backtracking search is robust and should always find a local energy
minimum. However, it will "converge" when it can no longer reduce the
energy of the system. Individual atom forces may still be larger than
desired at this point, because the energy change is measured as the
difference of two large values (energy before and energy after) and
that difference may be smaller than machine epsilon even if atoms
could move in the gradient direction to reduce forces further.
styles can be selected via the <I>line</I> keyword. Other minimizer styles
do not perform line searches, so they ignore this setting. The
default <I>backtrack</I> search is robust and should always find a local
energy minimum. However, it will "converge" when it can no longer
reduce the energy of the system. Individual atom forces may still be
larger than desired at this point, because the energy change is
measured as the difference of two large values (energy before and
energy after) and that difference may be smaller than machine epsilon
even if atoms could move in the gradient direction to reduce forces
further.
</P>
<P>By contast, the <I>quadratic</I> line search algorithm is often able to
reduce forces closer to 0.0. It may also be more efficient than the

34
doc/min_modify.txt
View File

@ -32,24 +32,28 @@ various settings may affect the convergence rate and overall number of
force evaluations required by a minimization, so users can experiment
with these parameters to tune their minimizations.
The {cg} and {sd} minimization styles have an outer iteration and an
inner iteration which is steps along a one-dimensional line search in
a particular search direction. The {dmax} parameter is how far any
atom can move in a single line search in any dimension (x, y, or z).
The {dmax} parameter is a bound on how far any atom can move in a
single dimension (x, y, or z) in a single iteration of the minimizer.
Thus a value of 0.1 in real "units"_units.html means no atom will move
further than 0.1 Angstroms in a single outer iteration. This prevents
highly overlapped atoms from being moved long distances (e.g. through
another atom) due to large forces.
further than 0.1 Angstroms in a single iteration. This prevents
highly overlapped atoms from being moved long distances (e.g. passing
through another atom) due to large forces. Note that for the {cg} and
{sd} style miminizers (see the "min_style"_min_style.html command),
{dmax} is a bound on the outer iteration or step along a search
direction, not a bound on the inner iteration of steps within a single
line search.
The choice of line search algorithm for the {cg} and {sd} minimization
styles can be selected via the {line} keyword. The default
backtracking search is robust and should always find a local energy
minimum. However, it will "converge" when it can no longer reduce the
energy of the system. Individual atom forces may still be larger than
desired at this point, because the energy change is measured as the
difference of two large values (energy before and energy after) and
that difference may be smaller than machine epsilon even if atoms
could move in the gradient direction to reduce forces further.
styles can be selected via the {line} keyword. Other minimizer styles
do not perform line searches, so they ignore this setting. The
default {backtrack} search is robust and should always find a local
energy minimum. However, it will "converge" when it can no longer
reduce the energy of the system. Individual atom forces may still be
larger than desired at this point, because the energy change is
measured as the difference of two large values (energy before and
energy after) and that difference may be smaller than machine epsilon
even if atoms could move in the gradient direction to reduce forces
further.
By contast, the {quadratic} line search algorithm is often able to
reduce forces closer to 0.0. It may also be more efficient than the

104
doc/min_style.html
View File

@ -15,25 +15,49 @@
</P>
<PRE>min_style style
</PRE>
<UL><LI>style = <I>cg</I> or <I>hftn</I> or <I>sd</I>
<UL><LI>style = <I>cg</I> or <I>hftn</I> or <I>sd</I> or <I>downhill</I> or <I>quickmin</I> or <I>fire</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>min_style cg
min_style hftn
min_style hftn
min_style fire
</PRE>
<P><B>Description:</B>
</P>
<P>Choose a minimization algorithm to use when a <A HREF = "minimize.html">minimize</A>
command is performed.
</P>
<P>Style <I>cg</I> is the Polak-Ribiere version of the conjugate gradient (CG)
algorithm. At each iteration the force gradient is combined with the
previous iteration information to compute a new search direction
perpendicular (conjugate) to the previous search direction. The PR
variant affects how the direction is chosen and how the CG method is
restarted when it ceases to make progress. The PR variant is thought
to be the most effective CG choice.
<P>The <I>cg</I>, <I>htfn</I>. and <I>sd</I> styles are traditional minimizers, which
relax the potential energy of the system to a local minimum. As a
by-product they also relax the force on each atom towards 0.0. To
work effectively these minimizers require the negative gradient of the
energy of the system (the objective function) be equivalent to the
force on the atoms. None of these styles use the
<A HREF = "timestep.html">timestep</A> setting.
</P>
<P>The <I>downhill</I>, <I>quickmin</I>, and <I>fire</I> styles are damped-dynamics
minimizers which are less mathematically rigorous, but tend to work
well in practice. They perform calculations only using the forces on
atoms which they relax towards 0.0. As a by-product they also
typically relax the energy towards a local minimum. However, because
they ignore the energy of the system, they can work with
non-conservative interactions, e.g. dynamics that includes damping
terms, or with a coupled system, like for nudged elastic band (NEB)
calculations, where inter-replica forces are not an analytic
derivative of an energy objective function. Since they are performing
a damped form of dynamics, all of these minimizers update atom
positions based on the <A HREF = "timestep.html">timestep</A> setting.
</P>
<P>Style <I>cg</I> is the Polak-Ribiere (PR) version of the conjugate gradient
(CG) algorithm. At each iteration, the force gradient is combined
with the previous iteration information to compute a new search
direction perpendicular (conjugate) to the previous search direction.
A linesearch is performed along the search direction to determine the
distance to move atoms. The PR variant affects how the direction is
chosen and how the CG method is restarted when it ceases to make
progress. The PR variant is thought to be the most effective CG
choice.
</P>
<P>Style <I>hftn</I> is a Hessian-free truncated Newton algorithm. At each
iteration a quadratic model of the energy potential is solved by a
@ -42,16 +66,50 @@ of the energy is not formed directly, but approximated in each
conjugate search direction by a finite difference directional
derivative. When close to an energy minimum, the algorithm behaves
like a Newton method and exhibits a quadratic convergence rate to high
accuracy. In most cases the behavior of <I>hftn</I> is similar to <I>cg</I>,
accuracy. In many cases the behavior of <I>hftn</I> is similar to <I>cg</I>,
but it offers another minimizer alternative if <I>cg</I> seems to perform
poorly. This style is not affected by the
<A HREF = "min_modify.html">min_modify</A> command.
poorly.
</P>
<P>Style <I>sd</I> is a steepest descent algorithm. At each iteration, the
search direction is set to the downhill direction corresponding to the
force vector (negative gradient of energy). Typically, steepest
descent will not converge as quickly as CG, but may be more robust in
some situations.
force vector (negative gradient of energy). A linesearch is performed
along the search direction to determine the distance to move atoms.
Typically, steepest descent will not converge as quickly as CG, but
may be more robust in some situations.
</P>
<P>Style <I>downhill</I> is a simple damped-dynamics minimizer which is
conceptually similar to steepest descent. At each iteration, forces
are computed and the each atom's position is updated by an Euler
step:
</P>
<PRE>Xnew = X + dt*dt * F/m
</PRE>
<P>where X is the old position, dt is the timestep, m is the atom mass,
and F is the force on the atom. This is effectively an Euler time
integration step with the velocity set to 0.0. The timestep used is
set by the <A HREF = "timestep.html">timestep</A> command, except that if any forces
are too large, the timestep is limited so that no atoms displaces more
than <I>dmax</I>, as set by the <A HREF = "min_modify.html">min_modify</A> command.
</P>
<P>Style <I>quickmin</I> is a damped-dynamics minimizer based on the Quickmin
algorithm of <A HREF = "#Jonsson">(Jonsson)</A> as described in
<A HREF = "#Sheppard">(Sheppard)</A>. It performs an Euler update of the position
and velocity each iteration as follows:
</P>
<PRE>Xnew = X + dt V
Vnew = V + dt F/m
</PRE>
<P>where V is the velocity of each atom, which is intially set to 0.0 by
the minimizer. Quickmin also projects the velocity onto the force
direction (steepest descent) and zeroes the velocity whenever it
becomes anti-parallel to the force (moving uphill).
</P>
<P>Style <I>fire</I> is a damped-dynamics minimizer based on the FIRE
algorithm <A HREF = "#Bitzek">(Bitzek)</A>. It is an enhancement to the Quickmin
algorithm which adds an effective intertia term to the equations of
motion and adapts the timestep and degree of projection of the
velocity onto the force direction, in an attempt to converge more
quickly.
</P>
<P><B>Restrictions:</B> none
</P>
@ -63,4 +121,20 @@ some situations.
</P>
<PRE>min_style cg
</PRE>
<HR>
<A NAME = "Bitzek"></A>
<P><B>(Bitzek)</B> Bitzek, Koskinen, Gahler, Moseler, Gumbsch,
Phys Rev Lett, 97, 170201 (2006).
</P>
<A NAME = "Sheppard"></A>
<P><B>(Sheppard)</B> Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 (2008).
</P>
<A NAME = "Jonsson"></A>
<P><B>(Jonsson)</B> Jonsson, Mills, Jacobson, Classical and Quantum
Dynamics in Condensed Phase Simulations, J Chem Phys, 128, 134106 (2008).
</P>
</HTML>

101
doc/min_style.txt
View File

@ -11,25 +11,49 @@ min_style command :h3
min_style style :pre
style = {cg} or {hftn} or {sd} :ul
style = {cg} or {hftn} or {sd} or {downhill} or {quickmin} or {fire} :ul
[Examples:]
min_style cg
min_style hftn :pre
min_style hftn
min_style fire :pre
[Description:]
Choose a minimization algorithm to use when a "minimize"_minimize.html
command is performed.
Style {cg} is the Polak-Ribiere version of the conjugate gradient (CG)
algorithm. At each iteration the force gradient is combined with the
previous iteration information to compute a new search direction
perpendicular (conjugate) to the previous search direction. The PR
variant affects how the direction is chosen and how the CG method is
restarted when it ceases to make progress. The PR variant is thought
to be the most effective CG choice.
The {cg}, {htfn}. and {sd} styles are traditional minimizers, which
relax the potential energy of the system to a local minimum. As a
by-product they also relax the force on each atom towards 0.0. To
work effectively these minimizers require the negative gradient of the
energy of the system (the objective function) be equivalent to the
force on the atoms. None of these styles use the
"timestep"_timestep.html setting.
The {downhill}, {quickmin}, and {fire} styles are damped-dynamics
minimizers which are less mathematically rigorous, but tend to work
well in practice. They perform calculations only using the forces on
atoms which they relax towards 0.0. As a by-product they also
typically relax the energy towards a local minimum. However, because
they ignore the energy of the system, they can work with
non-conservative interactions, e.g. dynamics that includes damping
terms, or with a coupled system, like for nudged elastic band (NEB)
calculations, where inter-replica forces are not an analytic
derivative of an energy objective function. Since they are performing
a damped form of dynamics, all of these minimizers update atom
positions based on the "timestep"_timestep.html setting.
Style {cg} is the Polak-Ribiere (PR) version of the conjugate gradient
(CG) algorithm. At each iteration, the force gradient is combined
with the previous iteration information to compute a new search
direction perpendicular (conjugate) to the previous search direction.
A linesearch is performed along the search direction to determine the
distance to move atoms. The PR variant affects how the direction is
chosen and how the CG method is restarted when it ceases to make
progress. The PR variant is thought to be the most effective CG
choice.
Style {hftn} is a Hessian-free truncated Newton algorithm. At each
iteration a quadratic model of the energy potential is solved by a
@ -38,16 +62,50 @@ of the energy is not formed directly, but approximated in each
conjugate search direction by a finite difference directional
derivative. When close to an energy minimum, the algorithm behaves
like a Newton method and exhibits a quadratic convergence rate to high
accuracy. In most cases the behavior of {hftn} is similar to {cg},
accuracy. In many cases the behavior of {hftn} is similar to {cg},
but it offers another minimizer alternative if {cg} seems to perform
poorly. This style is not affected by the
"min_modify"_min_modify.html command.
poorly.
Style {sd} is a steepest descent algorithm. At each iteration, the
search direction is set to the downhill direction corresponding to the
force vector (negative gradient of energy). Typically, steepest
descent will not converge as quickly as CG, but may be more robust in
some situations.
force vector (negative gradient of energy). A linesearch is performed
along the search direction to determine the distance to move atoms.
Typically, steepest descent will not converge as quickly as CG, but
may be more robust in some situations.
Style {downhill} is a simple damped-dynamics minimizer which is
conceptually similar to steepest descent. At each iteration, forces
are computed and the each atom's position is updated by an Euler
step:
Xnew = X + dt*dt * F/m :pre
where X is the old position, dt is the timestep, m is the atom mass,
and F is the force on the atom. This is effectively an Euler time
integration step with the velocity set to 0.0. The timestep used is
set by the "timestep"_timestep.html command, except that if any forces
are too large, the timestep is limited so that no atoms displaces more
than {dmax}, as set by the "min_modify"_min_modify.html command.
Style {quickmin} is a damped-dynamics minimizer based on the Quickmin
algorithm of "(Jonsson)"_#Jonsson as described in
"(Sheppard)"_#Sheppard. It performs an Euler update of the position
and velocity each iteration as follows:
Xnew = X + dt V
Vnew = V + dt F/m :pre
where V is the velocity of each atom, which is intially set to 0.0 by
the minimizer. Quickmin also projects the velocity onto the force
direction (steepest descent) and zeroes the velocity whenever it
becomes anti-parallel to the force (moving uphill).
Style {fire} is a damped-dynamics minimizer based on the FIRE
algorithm "(Bitzek)"_#Bitzek. It is an enhancement to the Quickmin
algorithm which adds an effective intertia term to the equations of
motion and adapts the timestep and degree of projection of the
velocity onto the force direction, in an attempt to converge more
quickly.
[Restrictions:] none
@ -58,3 +116,16 @@ some situations.
[Default:]
min_style cg :pre
:line
:link(Bitzek)
[(Bitzek)] Bitzek, Koskinen, Gahler, Moseler, Gumbsch,
Phys Rev Lett, 97, 170201 (2006).
:link(Sheppard)
[(Sheppard)] Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 (2008).
:link(Jonsson)
[(Jonsson)] Jonsson, Mills, Jacobson, Classical and Quantum
Dynamics in Condensed Phase Simulations, J Chem Phys, 128, 134106 (2008).

23
doc/minimize.html
View File

@ -27,28 +27,29 @@ minimize 0.0 1.0e-8 1000 100000
</PRE>
<P><B>Description:</B>
</P>
<P>Perform an energy minimization of the system, by iteratively adjusting
atom coordinates. Iterations are terminated when one of the stopping
criteria is satisfied. At that point the configuration will hopefully
be in local potential energy minimum. More precisely, the
configuration should approximate a critical point for the objective
function (see below), which may or may not be a local minimum.
<P>Perform an energy minimization or force zeroing of the system, by
iteratively adjusting atom coordinates. Iterations are terminated
when one of the stopping criteria is satisfied. At that point the
configuration will hopefully be in local potential energy minimum.
More precisely, the configuration should approximate a critical point
for the objective function (see below), which may or may not be a
local minimum.
</P>
<P>The minimization algorithm used is set by the
<A HREF = "min_style.html">min_style</A> command. Other options are set by the
<A HREF = "min_modify.html">min_modify</A> command. Minimize commands can be
interspersed with <A HREF = "run.html">run</A> commands to alternate between
relaxation and dynamics. The minimizers bound the distance atoms move
in one iteration, so that you can relax systems with highly overlapped
atoms (large energies and forces) by pushing the atoms off of each
other.
in one iteration (via the <A HREF = "min_modify.html">min_modify dmax</A> setting),
so that you can relax systems with highly overlapped atoms (large
energies and forces) by pushing the atoms off of each other.
</P>
<P>Alternate means of relaxing a system are to run dynamics with a small
or <A HREF = "fix_nve_limit.html">limited timestep</A>. Or dynamics can be run
using <A HREF = "fix_viscous.html">fix viscous</A> to impose a damping force that
slowly drains all kinetic energy from the system. The <A HREF = "pair_soft.html">pair_style
soft</A> potential can be used to un-overlap atoms while
running dynamics.
soft</A> potential can be used to un-overlap atoms
gradually while running dynamics.
</P>
<P>A minimization involves an outer iteration loop which sets the search
direction along which atom coordinates are changed. An inner

25
doc/minimize.txt
View File

@ -24,28 +24,31 @@ minimize 0.0 1.0e-8 1000 100000 :pre
[Description:]
Perform an energy minimization of the system, by iteratively adjusting
atom coordinates. Iterations are terminated when one of the stopping
criteria is satisfied. At that point the configuration will hopefully
be in local potential energy minimum. More precisely, the
configuration should approximate a critical point for the objective
function (see below), which may or may not be a local minimum.
Perform an energy minimization or force zeroing of the system, by
iteratively adjusting atom coordinates. Iterations are terminated
when one of the stopping criteria is satisfied. At that point the
configuration will hopefully be in local potential energy minimum.
More precisely, the configuration should approximate a critical point
for the objective function (see below), which may or may not be a
local minimum.
The minimization algorithm used is set by the
"min_style"_min_style.html command. Other options are set by the
"min_modify"_min_modify.html command. Minimize commands can be
interspersed with "run"_run.html commands to alternate between
relaxation and dynamics. The minimizers bound the distance atoms move
in one iteration, so that you can relax systems with highly overlapped
atoms (large energies and forces) by pushing the atoms off of each
other.
in one iteration (via the "min_modify dmax"_min_modify.html setting),
so that you can relax systems with highly overlapped atoms (large
energies and forces) by pushing the atoms off of each other.
Alternate means of relaxing a system are to run dynamics with a small
or "limited timestep"_fix_nve_limit.html. Or dynamics can be run
using "fix viscous"_fix_viscous.html to impose a damping force that
slowly drains all kinetic energy from the system. The "pair_style
soft"_pair_soft.html potential can be used to un-overlap atoms while
running dynamics.
soft"_pair_soft.html potential can be used to un-overlap atoms
gradually while running dynamics.
A minimization involves an outer iteration loop which sets the search
direction along which atom coordinates are changed. An inner