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

1
doc/Section_commands.txt
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@ -382,6 +382,7 @@ Fix styles :h4
See the "fix"_fix.html command for one-line descriptions
of each style or click on the style itself for a full description:
"adapt"_fix_adapt.html,
"addforce"_fix_addforce.html,
"aveforce"_fix_aveforce.html,
"ave/atom"_fix_ave_atom.html,

3
doc/fix.html
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@ -160,7 +160,8 @@ for further info.
arguments and what it does, as listed below. Here is an alphabetic
list of fix styles available in LAMMPS:
</P>
<UL><LI><A HREF = "fix_addforce.html">addforce</A> - add a force to each atom
<UL><LI><A HREF = "fix_adapt.html">adapt</A> - change a simulation parameter over time
<LI><A HREF = "fix_addforce.html">addforce</A> - add a force to each atom
<LI><A HREF = "fix_aveforce.html">aveforce</A> - add an averaged force to each atom
<LI><A HREF = "fix_ave_atom.html">ave/atom</A> - compute per-atom time-averaged quantities
<LI><A HREF = "fix_ave_atom.html">ave/histo</A> - compute/output time-averaged histograms

1
doc/fix.txt
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@ -155,6 +155,7 @@ Each fix style has its own documentation page which describes its
arguments and what it does, as listed below. Here is an alphabetic
list of fix styles available in LAMMPS:
"adapt"_fix_adapt.html - change a simulation parameter over time
"addforce"_fix_addforce.html - add a force to each atom
"aveforce"_fix_aveforce.html - add an averaged force to each atom
"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities

50
doc/pair_soft.html
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@ -20,8 +20,8 @@
<P><B>Examples:</B>
</P>
<PRE>pair_style soft 2.5
pair_coeff * * 0.0 60.0
pair_coeff 1 1 0.0 60.0 3.0
pair_coeff * * 10.0
pair_coeff 1 1 10.0 3.0
</PRE>
<P><B>Description:</B>
</P>
@ -30,11 +30,12 @@ pair_coeff 1 1 0.0 60.0 3.0
<CENTER><IMG SRC = "Eqs/pair_soft.jpg">
</CENTER>
<P>It is useful for pushing apart overlapping atoms, since it does not
blow up as r goes to 0. A is a pre-factor that varies in time from
the start to the end of the run. The <A HREF = "run.html">run</A> command documents
how to make the ramping take place across multiple runs. Rc is the
cutoff. See the <A HREF = "fix_nve_limit.html">fix nve/limit</A> command for
another way to push apart overlapping atoms.
blow up as r goes to 0. A is a pre-factor that can be made to vary in
time from the start to the end of the run (see discussion below),
e.g. to start with a very soft potential and slowly harden the
interactions over time. Rc is the cutoff. See the <A HREF = "fix_nve_limit.html">fix
nve/limit</A> command for another way to push apart
overlapping atoms.
</P>
<P>The following coefficients must be defined for each pair of atom types
via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
@ -42,28 +43,34 @@ or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>Astart (energy units)
<LI>Astop (energy units)
<UL><LI>A (energy units)
<LI>cutoff (distance units)
</UL>
<P>Astart and Astop are the values of the prefactor at the start and end
of the next run. At intermediate times the value of A will be ramped
between these 2 values. Note that before performing a 2nd run, you
will want to adjust the values of Astart and Astop for all type pairs,
or switch to a new pair style.
</P>
<P>The last coefficient is optional. If not specified, the global soft
cutoff is used.
</P>
<P>The <A HREF = "fix_adapt.html">fix adapt</A> command can be used to vary A over the
course of a simulation. For example these commands will vary the
prefactor A for all pairwise interactions from 0.0 at the beginning to
30.0 at the end of a 10,000 step run:
</P>
<PRE>variable prefactor equal 30.0*elapsed/10000
fix 1 all adapt 1 pair soft a * * prefactor
</PRE>
<P>Note that a formula defined by an <A HREF = "variable.html">equal-style variable</A>
can use the current timestep, elapsed time in the current run, elapsed
time since the beginning of a series of runs, as well as access other
variables.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the Astart, Astop coefficients and
cutoff distance for this pair style can be mixed. Astart and Atop are
always mixed via a <I>geometric</I> rule. The cutoff is mixed according to
the pair_modify mix value. The default mix value is <I>geometric</I>. See
the "pair_modify" command for details.
<P>For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is always mixed via a
<I>geometric</I> rule. The cutoff is mixed according to the pair_modify
mix value. The default mix value is <I>geometric</I>. See the
"pair_modify" command for details.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option, since the pair interaction goes to 0.0 at the cutoff.
@ -85,7 +92,8 @@ to be specified in an input script that reads a restart file.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_limit.html">fix nve/limit</A>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_limit.html">fix nve/limit</A>, <A HREF = "fix_adapt.html">fix
adapt</A>
</P>
<P><B>Default:</B> none
</P>

50
doc/pair_soft.txt
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@ -17,8 +17,8 @@ cutoff = global cutoff for soft interactions (distance units) :ul
[Examples:]
pair_style soft 2.5
pair_coeff * * 0.0 60.0
pair_coeff 1 1 0.0 60.0 3.0 :pre
pair_coeff * * 10.0
pair_coeff 1 1 10.0 3.0 :pre
[Description:]
@ -27,11 +27,12 @@ Style {soft} computes pairwise interactions with the formula
:c,image(Eqs/pair_soft.jpg)
It is useful for pushing apart overlapping atoms, since it does not
blow up as r goes to 0. A is a pre-factor that varies in time from
the start to the end of the run. The "run"_run.html command documents
how to make the ramping take place across multiple runs. Rc is the
cutoff. See the "fix nve/limit"_fix_nve_limit.html command for
another way to push apart overlapping atoms.
blow up as r goes to 0. A is a pre-factor that can be made to vary in
time from the start to the end of the run (see discussion below),
e.g. to start with a very soft potential and slowly harden the
interactions over time. Rc is the cutoff. See the "fix
nve/limit"_fix_nve_limit.html command for another way to push apart
overlapping atoms.
The following coefficients must be defined for each pair of atom types
via the "pair_coeff"_pair_coeff.html command as in the examples above,
@ -39,28 +40,34 @@ or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
Astart (energy units)
Astop (energy units)
A (energy units)
cutoff (distance units) :ul
Astart and Astop are the values of the prefactor at the start and end
of the next run. At intermediate times the value of A will be ramped
between these 2 values. Note that before performing a 2nd run, you
will want to adjust the values of Astart and Astop for all type pairs,
or switch to a new pair style.
The last coefficient is optional. If not specified, the global soft
cutoff is used.
The "fix adapt"_fix_adapt.html command can be used to vary A over the
course of a simulation. For example these commands will vary the
prefactor A for all pairwise interactions from 0.0 at the beginning to
30.0 at the end of a 10,000 step run:
variable prefactor equal 30.0*elapsed/10000
fix 1 all adapt 1 pair soft a * * prefactor :pre
Note that a formula defined by an "equal-style variable"_variable.html
can use the current timestep, elapsed time in the current run, elapsed
time since the beginning of a series of runs, as well as access other
variables.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the Astart, Astop coefficients and
cutoff distance for this pair style can be mixed. Astart and Atop are
always mixed via a {geometric} rule. The cutoff is mixed according to
the pair_modify mix value. The default mix value is {geometric}. See
the "pair_modify" command for details.
For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is always mixed via a
{geometric} rule. The cutoff is mixed according to the pair_modify
mix value. The default mix value is {geometric}. See the
"pair_modify" command for details.
This pair style does not support the "pair_modify"_pair_modify.html
shift option, since the pair interaction goes to 0.0 at the cutoff.
@ -82,6 +89,7 @@ This pair style can only be used via the {pair} keyword of the
[Related commands:]
"pair_coeff"_pair_coeff.html, "fix nve/limit"_fix_nve_limit.html
"pair_coeff"_pair_coeff.html, "fix nve/limit"_fix_nve_limit.html, "fix
adapt"_fix_adapt.html
[Default:] none

3
doc/run.html
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@ -69,8 +69,7 @@ performed and you want a <A HREF = "fix.html">fix</A> command that changes some
value over time (e.g. temperature) to make the change across the
entire set of runs and not just a single run. See the doc page for
individual fixes to see which ones can be used with the <I>start/stop</I>
keywords. The <A HREF = "pair_style.html">pair_style soft</A> potential also
changes its pair potential coefficients in this manner.
keywords.
</P>
<P>For example, consider this fix followed by 10 run commands:
</P>

3
doc/run.txt
View File

@ -62,8 +62,7 @@ performed and you want a "fix"_fix.html command that changes some
value over time (e.g. temperature) to make the change across the
entire set of runs and not just a single run. See the doc page for
individual fixes to see which ones can be used with the {start/stop}
keywords. The "pair_style soft"_pair_style.html potential also
changes its pair potential coefficients in this manner.
keywords.
For example, consider this fix followed by 10 run commands: