forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1293 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
parent
0808bd4c86
commit
b06573d3fb
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@ -317,13 +317,13 @@ in the command's documentation.
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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 >
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<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_com.html">com</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
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<TR ALIGN="center"><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><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></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><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></TR>
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<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_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</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_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</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_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD></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_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_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></TR>
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<TR ALIGN="center"><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><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></TR>
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<TR ALIGN="center"><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><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></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</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_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</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_nvt.html">nvt</A></TD></TR>
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<TR ALIGN="center"><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_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD></TR>
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<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_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></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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<HR>
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@ -333,9 +333,9 @@ descriptions of each style or click on the style itself for a full
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description:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum.html">sum</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A>
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<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_sum.html">sum</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A>
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</TD></TR></TABLE></DIV>
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<P>These are compute styles contributed by users, which can be used if
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|
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@ -381,6 +381,7 @@ of each style or click on the style itself for a full description:
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"ave/spatial"_fix_ave_spatial.html,
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"ave/time"_fix_ave_time.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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"deposit"_fix_deposit.html,
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"drag"_fix_drag.html,
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@ -439,6 +440,7 @@ description:
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"centro/atom"_compute_centro_atom.html,
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"coord/atom"_compute_coord_atom.html,
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"displace/atom"_compute_displace_atom.html,
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"ke/atom"_compute_ke_atom.html,
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"pe"_compute_pe.html,
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"pe/atom"_compute_pe_atom.html,
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|
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@ -111,6 +111,7 @@ available in LAMMPS:
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</P>
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<UL><LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
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<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
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<LI><A HREF = "compute_displace_atom.html">displace/atom</A> - displacement of each atom
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<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
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<LI><A HREF = "compute_pe.html">pe</A> - potential energy
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<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
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|
|
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@ -108,6 +108,7 @@ available in LAMMPS:
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"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
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"coord/atom"_compute_coord_atom.html - coordination number for each atom
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"displace/atom"_compute_displace_atom.html - displacement of each atom
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"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
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"pe"_compute_pe.html - potential energy
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"pe/atom"_compute_pe_atom.html - potential energy for each atom
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|
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@ -109,6 +109,7 @@ list of fix styles available in LAMMPS:
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<LI><A HREF = "fix_ave_spatial.html">ave/spatial</A> - output per-atom quantities by layer
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<LI><A HREF = "fix_ave_time.html">ave/time</A> - output time-averaged compute quantities
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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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<LI><A HREF = "fix_deposit.html">deposit</A> - add new atoms above a surface
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<LI><A HREF = "fix_drag.html">drag</A> - drag atoms towards a defined coordinate
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|
|
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@ -106,6 +106,7 @@ list of fix styles available in LAMMPS:
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"ave/spatial"_fix_ave_spatial.html - output per-atom quantities by layer
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"ave/time"_fix_ave_time.html - output time-averaged compute quantities
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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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"deposit"_fix_deposit.html - add new atoms above a surface
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"drag"_fix_drag.html - drag atoms towards a defined coordinate
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|
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@ -0,0 +1,77 @@
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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 coord/original 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 coord/original
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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>coord/original = style name of this fix command
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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 coord/original
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Store the original coordinates of atoms in the group at the time the
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fix command is issued. This is useful for computing a displacement of
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the atoms at later times, via the <A HREF = "compute_displace_atom.html">compute
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displace/atom</A> command. Or the original
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coordinates can be accessed by other <A HREF = "Section_howto.html#4_15">output
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commands</A> that use per-atom quantities such as
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the <A HREF = "dump.html">dump custom</A> command.
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</P>
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<P>IMPORTANT NOTE: To enable displacements to be calculated which include
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the effects of atoms passing through periodic boundaries, the original
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coordinates are stored in "unwrapped" form, by using the image flags
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associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
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for a discussion of "unwrapped" coordinates. See the Atoms section of
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the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
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and how they are set for each atom.
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</P>
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<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
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rigid</A> command), it's periodic image flags are altered,
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and its original coordinates may not be what you expect. See the
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<A HREF = "fix_rigid.html">fix rigid</A> command for details.
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</P>
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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>This fix writes the original coordinates of the atoms to <A HREF = "restart.html">binary
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restart files</A>, so that the values can be restored when a
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simulation is restarted. See the <A HREF = "read_restart.html">read_restart</A>
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command for info on how to re-specify a fix in an input script that
|
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reads a restart file, so that the operation of the fix continues in an
|
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uninterrupted fashion.
|
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</P>
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<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
|
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fix.
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</P>
|
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<P>This fix produces a per-atom vector which can be accessed by various
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<A HREF = "Section_howto.html#4_15">output commands</A>. The length of the vector
|
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for each atom is 3, and the components store the x,y,z coords of each
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atom. The per-atom values be accessed on any timestep.
|
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B> none
|
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</P>
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<P><B>Related commands:</B>
|
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</P>
|
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<P><A HREF = "fix_msd.html">fix msd</A>
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</P>
|
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<P><B>Default:</B> none
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</P>
|
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</HTML>
|
|
@ -0,0 +1,72 @@
|
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
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|
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:link(lws,http://lammps.sandia.gov)
|
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:link(ld,Manual.html)
|
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:link(lc,Section_commands.html#comm)
|
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|
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:line
|
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|
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fix coord/original command :h3
|
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|
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[Syntax:]
|
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|
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fix ID group-ID coord/original :pre
|
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|
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ID, group-ID are documented in "fix"_fix.html command
|
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coord/original = style name of this fix command :ul
|
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|
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[Examples:]
|
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|
||||
fix 1 all coord/original :pre
|
||||
|
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[Description:]
|
||||
|
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Store the original coordinates of atoms in the group at the time the
|
||||
fix command is issued. This is useful 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: To enable displacements to be calculated which include
|
||||
the effects of atoms passing through periodic boundaries, 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.
|
||||
|
||||
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.
|
||||
|
||||
[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 vector which can be accessed by various
|
||||
"output commands"_Section_howto.html#4_15. The length of the vector
|
||||
for each atom is 3, and the components store the 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:]
|
||||
|
||||
"fix msd"_fix_msd.html
|
||||
|
||||
[Default:] none
|
|
@ -60,7 +60,9 @@ 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> none
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_coord_original.html">fix coord/original</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
|
|
|
@ -57,12 +57,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
|
|||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
[Related commands:]
|
||||
|
||||
"fix coord/original"_fix_coord_original.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
Loading…
Reference in New Issue