mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2610 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
99f2b70e24
commit
af35857d8b
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@ -318,13 +318,13 @@ of each style or click on the style itself for a full description:
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</P>
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<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_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><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD></TR>
|
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<TR ALIGN="center"><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_coord_original.html">coord/original</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>
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||||
<TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</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_msd.html">msd</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD></TR>
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||||
<TR ALIGN="center"><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_nvt.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><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD></TR>
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||||
<TR ALIGN="center"><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_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_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>
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<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_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
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<TR ALIGN="center"><TD ><A HREF = "fix_box_relax.html">box</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_coord_original.html">coord/original</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>
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<TR ALIGN="center"><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</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>
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<TR ALIGN="center"><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD></TR>
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<TR ALIGN="center"><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_nvt.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><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD></TR>
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<TR ALIGN="center"><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_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</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_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
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</TD></TR></TABLE></DIV>
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<P>These are fix styles contributed by users, which can be used if
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|
|
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@ -383,6 +383,7 @@ of each style or click on the style itself for a full description:
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"bond/break"_fix_bond_break.html,
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"bond/create"_fix_bond_create.html,
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"bond/swap"_fix_bond_swap.html,
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"box"_fix_box_relax.html,
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"com"_fix_com.html,
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"coord/original"_fix_coord_original.html,
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"deform"_fix_deform.html,
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@ -111,6 +111,7 @@ list of fix styles available in LAMMPS:
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<LI><A HREF = "fix_bond_break.html">bond/break</A> - break bonds on the fly
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<LI><A HREF = "fix_bond_create.html">bond/create</A> - create bonds on the fly
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<LI><A HREF = "fix_bond_swap.html">bond/swap</A> - Monte Carlo bond swapping
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<LI><A HREF = "fix_box_relax.html">box/relax</A> - relax box size during energy minimization
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<LI><A HREF = "fix_com.html">com</A> - compute a center-of-mass
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<LI><A HREF = "fix_coord_original.html">coord/original</A> - store original coords of each atom
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<LI><A HREF = "fix_deform.html">deform</A> - change the simulation box size/shape
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|
|
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@ -108,6 +108,7 @@ list of fix styles available in LAMMPS:
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"bond/break"_fix_bond_break.html - break bonds on the fly
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"bond/create"_fix_bond_create.html - create bonds on the fly
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"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
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"box/relax"_fix_box_relax.html - relax box size during energy minimization
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"com"_fix_com.html - compute a center-of-mass
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"coord/original"_fix_coord_original.html - store original coords of each atom
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"deform"_fix_deform.html - change the simulation box size/shape
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@ -0,0 +1,176 @@
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<HTML>
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<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>
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</CENTER>
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<HR>
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<H3>fix box/relax command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID box/relax style args keyword value ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>box/relax = style name of this fix command
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<LI>style = <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I>
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<PRE> <I>xyz</I> arg = P = desired pressure (pressure units)
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<I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I> args = Px Py Pz
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Px,Py,Pz = desired pressure in x,y,z (pressure units)
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</PRE>
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<LI>zero or more keyword/value pairs may be appended to the args
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<LI>keyword = <I>dilate</I>
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<PRE> <I>dilate</I> value = <I>all</I> or <I>partial</I>
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all box/relax xyz 0.0
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fix 2 water box/relax aniso 0.0 0.0 1000.0 dilate partial
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Apply a pressure to the simulation box during an <A HREF = "minimize.html">energy
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minimization</A>. This allows the box dimensions to vary
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during the iterations of the minimizer so that the final configuration
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will be both an energy minimum for the potential energy of the atoms
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and the system pressure will be close to the desired pressure.
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Conceptually, specifying a positive pressure is like squeezing on the
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simulation box; a negative pressure typically allows the box to
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expand.
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</P>
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<P>The pressure can be specified in one of several styles, as determined
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by the <I>style</I> argument.
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</P>
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<P>Style <I>xyz</I> means couple all 3 dimensions together when pressure is
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computed (isotropic pressure), and dilate/contract the 3 dimensions
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together. Styles <I>xy</I> or <I>yz</I> or <I>xz</I> means that the 2 specified
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dimensions are coupled together, both for pressure computation and for
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dilation/contraction. The 3rd dimension dilates/contracts
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independently according to its specified pressure. For style <I>aniso</I>,
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all 3 dimensions dilate/contract independently according to the 3
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specified pressure values.
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</P>
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<P>For any of the styles except <I>xyz</I>, the target pressure for any
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independent components (e.g. z in <I>xy</I>, or any dimension in <I>aniso</I>)
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can be specified as NULL. This means that no pressure is applied to
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that dimension so that the box dimension remains unchanged during the
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minimization.
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</P>
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<P>For styles <I>xy</I> and <I>yz</I> and <I>xz</I>, the target pressures must be the
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same for the two coupled dimensions and cannot be specified as NULL.
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</P>
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<P>For all pressure styles, the simulation box stays rectangular in
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shape. Tilted boxes (triclinic symmetry) are supported by other
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LAMMPS commands (see <A HREF = "Section_howto.html#4_12">this section</A> of the
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manual), but not yet by this command.
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</P>
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<P>When the size of the simulation box changes, all atoms are re-scaled
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to new positions, unless the keyword <I>dilate</I> is specified with a
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value of <I>partial</I>, in which case only the atoms in the fix group are
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re-scaled. This can be useful for leaving the coordinates of atoms in
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a solid substrate unchanged and controlling the pressure of a
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surrounding fluid.
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</P>
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<HR>
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<P>This fix computes a temperature and pressure each timestep. The
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temperature is used to compute the kinetic contribution to the
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pressure. Since atom velocities do not change during minimization,
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that contribution will depend on what atom velocities are at the
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beginning of the minimization procedure, and will remain constant. To
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do this, the fix creates its own computes of style "temp" and
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"pressure", as if these commands had been issued:
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</P>
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<PRE>compute fix-ID_temp group-ID temp
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compute fix-ID_press group-ID pressure fix-ID_temp
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</PRE>
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<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
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pressure</A> commands for details. Note that the
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IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
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+ underscore + "press", and the group for the new computes is the same
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as the fix group.
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</P>
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<P>Note that these are NOT the computes used by thermodynamic output (see
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the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
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and <I>thermo_press</I>. This means you can change the attributes of this
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fix's temperature or pressure via the
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<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
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or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
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custom</A> command using the appropriate compute-ID.
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It also means that changing attributes of <I>thermo_temp</I> or
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<I>thermo_press</I> will have no effect on this fix.
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</P>
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<P>Like other fixes that perform thermostatting, this fix can be used
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with <A HREF = "compute.html">compute commands</A> that calculate a temperature
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after removing a "bias" from the atom velocities. E.g. removing the
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center-of-mass velocity from a group of atoms or only calculating
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temperature on the x-component of velocity or only calculating
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temperature for atoms in a geometric region. This is not done by
|
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default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
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to assign a temperature compute to this fix that includes such a bias
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term. See the doc pages for individual <A HREF = "compute.html">compute
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commands</A> to determine which ones include a bias.
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</P>
|
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<HR>
|
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
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</P>
|
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>.
|
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</P>
|
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
|
||||
supported by this fix. You can use them to assign a
|
||||
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
|
||||
in its temperature and pressure calculation, as described above. If
|
||||
you do this, note that the kinetic energy derived from the compute
|
||||
temperature should be consistent with the virial term computed using
|
||||
all atoms for the pressure. LAMMPS will warn you if you choose to
|
||||
compute temperature on a subset of atoms.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
|
||||
single thermo_modify command (or in two separate commands), then the
|
||||
order in which the keywords are specified is important. Note that a
|
||||
<A HREF = "compute_pressure.html">pressure compute</A> defines its own temperature
|
||||
compute as an argument when it is specified. The <I>temp</I> keyword will
|
||||
override this (for the pressure compute being used by fix npt), but
|
||||
only if the <I>temp</I> keyword comes after the <I>press</I> keyword. If the
|
||||
<I>temp</I> keyword comes before the <I>press</I> keyword, then the new pressure
|
||||
compute specified by the <I>press</I> keyword will be unaffected by the
|
||||
<I>temp</I> setting.
|
||||
</P>
|
||||
<P>No global scalar or vector 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.
|
||||
</P>
|
||||
<P>This fix is invoked during <A HREF = "minimize.html">energy minimization</A>, but
|
||||
not for the purpose of adding a contribution to the energy or forces
|
||||
being minimized. Instead it alters the box geometry as described
|
||||
above.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>Any box dimension adjusted by this fix must be periodic. A dimension
|
||||
whose target pressure is specified as NULL can be non-periodic or
|
||||
periodic.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_nph.html">fix npt</A>, <A HREF = "minimize.html">minimize</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The keyword default is dilate = all.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,165 @@
|
|||
"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 box/relax command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID box/relax style args keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
box/relax = style name of this fix command :l
|
||||
style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
|
||||
{xyz} arg = P = desired pressure (pressure units)
|
||||
{xy} or {yz} or {xz} or {aniso} args = Px Py Pz
|
||||
Px,Py,Pz = desired pressure in x,y,z (pressure units) :pre
|
||||
|
||||
zero or more keyword/value pairs may be appended to the args :l
|
||||
keyword = {dilate} :l
|
||||
{dilate} value = {all} or {partial} :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all box/relax xyz 0.0
|
||||
fix 2 water box/relax aniso 0.0 0.0 1000.0 dilate partial :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Apply a pressure to the simulation box during an "energy
|
||||
minimization"_minimize.html. This allows the box dimensions to vary
|
||||
during the iterations of the minimizer so that the final configuration
|
||||
will be both an energy minimum for the potential energy of the atoms
|
||||
and the system pressure will be close to the desired pressure.
|
||||
Conceptually, specifying a positive pressure is like squeezing on the
|
||||
simulation box; a negative pressure typically allows the box to
|
||||
expand.
|
||||
|
||||
The pressure can be specified in one of several styles, as determined
|
||||
by the {style} argument.
|
||||
|
||||
Style {xyz} means couple all 3 dimensions together when pressure is
|
||||
computed (isotropic pressure), and dilate/contract the 3 dimensions
|
||||
together. Styles {xy} or {yz} or {xz} means that the 2 specified
|
||||
dimensions are coupled together, both for pressure computation and for
|
||||
dilation/contraction. The 3rd dimension dilates/contracts
|
||||
independently according to its specified pressure. For style {aniso},
|
||||
all 3 dimensions dilate/contract independently according to the 3
|
||||
specified pressure values.
|
||||
|
||||
For any of the styles except {xyz}, the target pressure for any
|
||||
independent components (e.g. z in {xy}, or any dimension in {aniso})
|
||||
can be specified as NULL. This means that no pressure is applied to
|
||||
that dimension so that the box dimension remains unchanged during the
|
||||
minimization.
|
||||
|
||||
For styles {xy} and {yz} and {xz}, the target pressures must be the
|
||||
same for the two coupled dimensions and cannot be specified as NULL.
|
||||
|
||||
For all pressure styles, the simulation box stays rectangular in
|
||||
shape. Tilted boxes (triclinic symmetry) are supported by other
|
||||
LAMMPS commands (see "this section"_Section_howto.html#4_12 of the
|
||||
manual), but not yet by this command.
|
||||
|
||||
When the size of the simulation box changes, all atoms are re-scaled
|
||||
to new positions, unless the keyword {dilate} is specified with a
|
||||
value of {partial}, in which case only the atoms in the fix group are
|
||||
re-scaled. This can be useful for leaving the coordinates of atoms in
|
||||
a solid substrate unchanged and controlling the pressure of a
|
||||
surrounding fluid.
|
||||
|
||||
:line
|
||||
|
||||
This fix computes a temperature and pressure each timestep. The
|
||||
temperature is used to compute the kinetic contribution to the
|
||||
pressure. Since atom velocities do not change during minimization,
|
||||
that contribution will depend on what atom velocities are at the
|
||||
beginning of the minimization procedure, and will remain constant. To
|
||||
do this, the fix creates its own computes of style "temp" and
|
||||
"pressure", as if these commands had been issued:
|
||||
|
||||
compute fix-ID_temp group-ID temp
|
||||
compute fix-ID_press group-ID pressure fix-ID_temp :pre
|
||||
|
||||
See the "compute temp"_compute_temp.html and "compute
|
||||
pressure"_compute_pressure.html commands for details. Note that the
|
||||
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
|
||||
+ underscore + "press", and the group for the new computes is the same
|
||||
as the fix group.
|
||||
|
||||
Note that these are NOT the computes used by thermodynamic output (see
|
||||
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
|
||||
and {thermo_press}. This means you can change the attributes of this
|
||||
fix's temperature or pressure via the
|
||||
"compute_modify"_compute_modify.html command or print this temperature
|
||||
or pressure during thermodynamic output via the "thermo_style
|
||||
custom"_thermo_style.html command using the appropriate compute-ID.
|
||||
It also means that changing attributes of {thermo_temp} or
|
||||
{thermo_press} will have no effect on this fix.
|
||||
|
||||
Like other fixes that perform thermostatting, this fix can be used
|
||||
with "compute commands"_compute.html that calculate a temperature
|
||||
after removing a "bias" from the atom velocities. E.g. removing the
|
||||
center-of-mass velocity from a group of atoms or only calculating
|
||||
temperature on the x-component of velocity or only calculating
|
||||
temperature for atoms in a geometric region. This is not done by
|
||||
default, but only if the "fix_modify"_fix_modify.html command is used
|
||||
to assign a temperature compute to this fix that includes such a bias
|
||||
term. See the doc pages for individual "compute
|
||||
commands"_compute.html to determine which ones include a bias.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {temp} and {press} options are
|
||||
supported by this fix. You can use them to assign a
|
||||
"compute"_compute.html you have defined to this fix which will be used
|
||||
in its temperature and pressure calculation, as described above. If
|
||||
you do this, note that the kinetic energy derived from the compute
|
||||
temperature should be consistent with the virial term computed using
|
||||
all atoms for the pressure. LAMMPS will warn you if you choose to
|
||||
compute temperature on a subset of atoms.
|
||||
|
||||
IMPORTANT NOTE: If both the {temp} and {press} keywords are used in a
|
||||
single thermo_modify command (or in two separate commands), then the
|
||||
order in which the keywords are specified is important. Note that a
|
||||
"pressure compute"_compute_pressure.html defines its own temperature
|
||||
compute as an argument when it is specified. The {temp} keyword will
|
||||
override this (for the pressure compute being used by fix npt), but
|
||||
only if the {temp} keyword comes after the {press} keyword. If the
|
||||
{temp} keyword comes before the {press} keyword, then the new pressure
|
||||
compute specified by the {press} keyword will be unaffected by the
|
||||
{temp} setting.
|
||||
|
||||
No global scalar or vector 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 invoked during "energy minimization"_minimize.html, but
|
||||
not for the purpose of adding a contribution to the energy or forces
|
||||
being minimized. Instead it alters the box geometry as described
|
||||
above.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Any box dimension adjusted by this fix must be periodic. A dimension
|
||||
whose target pressure is specified as NULL can be non-periodic or
|
||||
periodic.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix npt"_fix_nph.html, "minimize"_minimize.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The keyword default is dilate = all.
|
||||
Loading…
Reference in New Issue