forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3592 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
6b656f965e
commit
94fcde12ac
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@ -346,12 +346,13 @@ of each style or click on the style itself for a full description:
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each style or click on the style itself for a full description:
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each style or click on the style itself for a full description:
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</P>
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD></TR>
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<TR ALIGN="center"><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><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</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_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</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_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
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</TD></TR></TABLE></DIV>
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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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<P>These are compute styles contributed by users, which can be used if
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@ -171,6 +171,7 @@ available in LAMMPS:
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<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
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<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
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<LI><A HREF = "compute_cna_atom.html">cna/atom</A> - common neighbor analysis (CNA) for each atom
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<LI><A HREF = "compute_cna_atom.html">cna/atom</A> - common neighbor analysis (CNA) for each atom
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<LI><A HREF = "compute_com.html">com</A> - center-of-mass of group of atoms
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<LI><A HREF = "compute_com.html">com</A> - center-of-mass of group of atoms
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<LI><A HREF = "compute_com_molecule.html">com/molecule</A> - center-of-mass for each molecule
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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_coord_atom.html">coord/atom</A> - coordination number for each atom
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<LI><A HREF = "compute_damage_atom.html">damage/atom</A> - Peridynamic damage for each atom
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<LI><A HREF = "compute_damage_atom.html">damage/atom</A> - Peridynamic damage for each atom
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<LI><A HREF = "compute_dihedral_local.html">dihedral/local</A> - angle of each dihedral
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<LI><A HREF = "compute_dihedral_local.html">dihedral/local</A> - angle of each dihedral
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@ -180,11 +181,13 @@ available in LAMMPS:
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<LI><A HREF = "compute_event_displace.html">event/displace</A> - detect event on atom displacement
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<LI><A HREF = "compute_event_displace.html">event/displace</A> - detect event on atom displacement
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<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
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<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
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<LI><A HREF = "compute_gyration.html">gyration</A> - radius of gyration of group of atoms
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<LI><A HREF = "compute_gyration.html">gyration</A> - radius of gyration of group of atoms
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<LI><A HREF = "compute_gyration_molecule.html">gyration/molecule</A> - radius of gyration for each molecule
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<LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
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<LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
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<LI><A HREF = "compute_improper_local.html">improper/local</A> - angle of each improper
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<LI><A HREF = "compute_improper_local.html">improper/local</A> - angle of each improper
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<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
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<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
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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_ke_atom.html">ke/atom</A> - kinetic energy for each atom
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<LI><A HREF = "compute_msd.html">msd</A> - mean-squared displacement of group of atoms
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<LI><A HREF = "compute_msd.html">msd</A> - mean-squared displacement of group of atoms
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<LI><A HREF = "compute_msd_molecule.html">msd/molecule</A> - mean-squared displacement for each molecule
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<LI><A HREF = "compute_pe.html">pe</A> - potential energy
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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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<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
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<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
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<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
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@ -0,0 +1,80 @@
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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>compute com/molecule command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID com/molecule
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>com/molecule = style name of this compute command
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 fluid com/molecule
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that calculates the center-of-mass of individual
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molecules. The calculation includes all effects due to atoms passing
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thru periodic boundaries.
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</P>
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<P>The x,y,z coordinate of the center-of-mass for a particular molecule
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is only computed if one or more of its atoms are in the specified
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group. Normally all atoms in the molecule should be in the group,
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however this is not required. LAMMPS will warn you if this is not the
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case. Only atoms in the group contribute to the center-of-mass
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calculation for the molecule.
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</P>
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<P>Let Nmolecules be the number of molecules for which the center-of-mass
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is calculated. If not all molecules have atoms in the group, then the
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molecule with the lowest ID is the first of the Nmolecules. The next
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lowest ID is the second, etc, up to Nmolecules.
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</P>
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<P>IMPORTANT NOTE: The coordinates of an atom contribute to the
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molecule's center-of-mass in "unwrapped" form, by using the image
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flags associated with each atom. See the <A HREF = "dump.html">dump custom</A>
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command for a discussion of "unwrapped" coordinates. See the Atoms
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section of the <A HREF = "read_data.html">read_data</A> command for a discussion of
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image flags and how they are set for each atom. You can reset the
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image flags (e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
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image</A> command.
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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 contribution to the center-of-mass may not reflect its true
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contribution. See the <A HREF = "fix_rigid.html">fix rigid</A> command for details.
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Thus, to compute the center-of-mass of rigid bodies as they cross
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periodic boundaries, you will need to post-process a <A HREF = "dump.html">dump
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file</A> containing coordinates of the atoms in the bodies.
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</P>
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<P><B>Output info:</B>
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</P>
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<P>This compute calculates a global array with the number of rows =
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Nmolecules and the number of columns = 3 for the x,y,z center-of-mass
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coordinates of each molecule. These values can be accessed by any
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command that uses global array values from a compute as input. See
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<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
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output options.
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</P>
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<P>The array values are "intensive", meaning they are independent of the
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number of atoms in the simulation.
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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 = "compute_com.html">compute com</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>
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@ -0,0 +1,75 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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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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:line
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compute com/molecule command :h3
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[Syntax:]
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compute ID group-ID com/molecule :pre
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ID, group-ID are documented in "compute"_compute.html command
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com/molecule = style name of this compute command :ul
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[Examples:]
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compute 1 fluid com/molecule :pre
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[Description:]
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Define a computation that calculates the center-of-mass of individual
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molecules. The calculation includes all effects due to atoms passing
|
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|
thru periodic boundaries.
|
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|
|
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The x,y,z coordinate of the center-of-mass for a particular molecule
|
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|
is only computed if one or more of its atoms are in the specified
|
||||||
|
group. Normally all atoms in the molecule should be in the group,
|
||||||
|
however this is not required. LAMMPS will warn you if this is not the
|
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|
case. Only atoms in the group contribute to the center-of-mass
|
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|
calculation for the molecule.
|
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|
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Let Nmolecules be the number of molecules for which the center-of-mass
|
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is calculated. If not all molecules have atoms in the group, then the
|
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molecule with the lowest ID is the first of the Nmolecules. The next
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lowest ID is the second, etc, up to Nmolecules.
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|
|
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IMPORTANT NOTE: The coordinates of an atom contribute to the
|
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|
molecule's center-of-mass in "unwrapped" form, by using the image
|
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|
flags associated with each atom. See the "dump custom"_dump.html
|
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|
command for a discussion of "unwrapped" coordinates. See the Atoms
|
||||||
|
section of the "read_data"_read_data.html command for a discussion of
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|
image flags and how they are set for each atom. You can reset the
|
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image flags (e.g. to 0) before invoking this compute by using the "set
|
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image"_set.html command.
|
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|
|
||||||
|
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 contribution to the center-of-mass may not reflect its true
|
||||||
|
contribution. See the "fix rigid"_fix_rigid.html command for details.
|
||||||
|
Thus, to compute the center-of-mass of rigid bodies as they cross
|
||||||
|
periodic boundaries, you will need to post-process a "dump
|
||||||
|
file"_dump.html containing coordinates of the atoms in the bodies.
|
||||||
|
|
||||||
|
[Output info:]
|
||||||
|
|
||||||
|
This compute calculates a global array with the number of rows =
|
||||||
|
Nmolecules and the number of columns = 3 for the x,y,z center-of-mass
|
||||||
|
coordinates of each molecule. These values can be accessed by any
|
||||||
|
command that uses global array values from a compute as input. See
|
||||||
|
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
|
||||||
|
output options.
|
||||||
|
|
||||||
|
The array values are "intensive", meaning they are independent of the
|
||||||
|
number of atoms in the simulation.
|
||||||
|
|
||||||
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[Restrictions:] none
|
||||||
|
|
||||||
|
[Related commands:]
|
||||||
|
|
||||||
|
"compute com"_compute_com.html
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|
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[Default:] none
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@ -0,0 +1,78 @@
|
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|
<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>
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|
</CENTER>
|
||||||
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|
||||||
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|
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|
||||||
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|
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|
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|
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|
<HR>
|
||||||
|
|
||||||
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<H3>compute gyration/molecule command
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</H3>
|
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<P><B>Syntax:</B>
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|
</P>
|
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<PRE>compute ID group-ID gyration/molecule
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
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|
<LI>gyration/molecule = style name of this compute command
|
||||||
|
</UL>
|
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|
<P><B>Examples:</B>
|
||||||
|
</P>
|
||||||
|
<PRE>compute 1 molecule gyration/molecule
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|
</PRE>
|
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|
<P><B>Description:</B>
|
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|
</P>
|
||||||
|
<P>Define a computation that calculates the radius of gyration Rg of
|
||||||
|
individual molecules. The calculation includes all effects due to
|
||||||
|
atoms passing thru periodic boundaries.
|
||||||
|
</P>
|
||||||
|
<P>Rg is a measure of the size of a molecule, and is computed by this
|
||||||
|
formula
|
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|
</P>
|
||||||
|
<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
|
||||||
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</CENTER>
|
||||||
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<P>where M is the total mass of the molecule and Rcm is the center-of-mass
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|
position of the molecule.
|
||||||
|
</P>
|
||||||
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<P>Rg for a particular molecule is only computed if one or more of its
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|
atoms are in the specified group. Normally all atoms in the molecule
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||||||
|
should be in the group, however this is not required. LAMMPS will
|
||||||
|
warn you if this is not the case. Only atoms in the group contribute
|
||||||
|
to the Rg calculation for the molecule.
|
||||||
|
</P>
|
||||||
|
<P>Let Nmolecules be the number of molecules for which Rg is calculated.
|
||||||
|
If not all molecules have atoms in the group, then the molecule with
|
||||||
|
the lowest ID is the first of the Nmolecules. The next lowest ID is
|
||||||
|
the second, etc, up to Nmolecules.
|
||||||
|
</P>
|
||||||
|
<P>IMPORTANT NOTE: The coordinates of an atom contribute to Rg 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 compute by using the <A HREF = "set.html">set
|
||||||
|
image</A> command.
|
||||||
|
</P>
|
||||||
|
<P><B>Output info:</B>
|
||||||
|
</P>
|
||||||
|
<P>This compute calculates a global vector of Rg values with the number
|
||||||
|
of elements = Nmolecules. These values can be used by any command
|
||||||
|
that uses a global vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
|
||||||
|
section</A> for an overview of LAMMPS output
|
||||||
|
options.
|
||||||
|
</P>
|
||||||
|
<P>The vector values calculated by this compute are "intensive", meaning
|
||||||
|
it is independent of the number of atoms in the simulation.
|
||||||
|
</P>
|
||||||
|
<P><B>Restrictions:</B> none
|
||||||
|
</P>
|
||||||
|
<P><B>Related commands:</B> none
|
||||||
|
</P>
|
||||||
|
<P><A HREF = "compute_gyration.html">compute gyration</A>
|
||||||
|
</P>
|
||||||
|
<P><B>Default:</B> none
|
||||||
|
</P>
|
||||||
|
</HTML>
|
||||||
|
|
@ -0,0 +1,73 @@
|
||||||
|
"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
|
||||||
|
|
||||||
|
compute gyration/molecule command :h3
|
||||||
|
|
||||||
|
[Syntax:]
|
||||||
|
|
||||||
|
compute ID group-ID gyration/molecule :pre
|
||||||
|
|
||||||
|
ID, group-ID are documented in "compute"_compute.html command
|
||||||
|
gyration/molecule = style name of this compute command :ul
|
||||||
|
|
||||||
|
[Examples:]
|
||||||
|
|
||||||
|
compute 1 molecule gyration/molecule :pre
|
||||||
|
|
||||||
|
[Description:]
|
||||||
|
|
||||||
|
Define a computation that calculates the radius of gyration Rg of
|
||||||
|
individual molecules. The calculation includes all effects due to
|
||||||
|
atoms passing thru periodic boundaries.
|
||||||
|
|
||||||
|
Rg is a measure of the size of a molecule, and is computed by this
|
||||||
|
formula
|
||||||
|
|
||||||
|
:c,image(Eqs/compute_gyration.jpg)
|
||||||
|
|
||||||
|
where M is the total mass of the molecule and Rcm is the center-of-mass
|
||||||
|
position of the molecule.
|
||||||
|
|
||||||
|
Rg for a particular molecule is only computed if one or more of its
|
||||||
|
atoms are in the specified group. Normally all atoms in the molecule
|
||||||
|
should be in the group, however this is not required. LAMMPS will
|
||||||
|
warn you if this is not the case. Only atoms in the group contribute
|
||||||
|
to the Rg calculation for the molecule.
|
||||||
|
|
||||||
|
Let Nmolecules be the number of molecules for which Rg is calculated.
|
||||||
|
If not all molecules have atoms in the group, then the molecule with
|
||||||
|
the lowest ID is the first of the Nmolecules. The next lowest ID is
|
||||||
|
the second, etc, up to Nmolecules.
|
||||||
|
|
||||||
|
IMPORTANT NOTE: The coordinates of an atom contribute to Rg 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 compute by using the "set
|
||||||
|
image"_set.html command.
|
||||||
|
|
||||||
|
[Output info:]
|
||||||
|
|
||||||
|
This compute calculates a global vector of Rg values with the number
|
||||||
|
of elements = Nmolecules. These values can be used by any command
|
||||||
|
that uses a global vector values from a compute as input. See "this
|
||||||
|
section"_Section_howto.html#4_15 for an overview of LAMMPS output
|
||||||
|
options.
|
||||||
|
|
||||||
|
The vector values calculated by this compute are "intensive", meaning
|
||||||
|
it is independent of the number of atoms in the simulation.
|
||||||
|
|
||||||
|
[Restrictions:] none
|
||||||
|
|
||||||
|
[Related commands:] none
|
||||||
|
|
||||||
|
"compute gyration"_compute_gyration.html
|
||||||
|
|
||||||
|
[Default:] none
|
||||||
|
|
@ -0,0 +1,98 @@
|
||||||
|
<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>compute msd/molecule command
|
||||||
|
</H3>
|
||||||
|
<P><B>Syntax:</B>
|
||||||
|
</P>
|
||||||
|
<PRE>compute ID group-ID msd/molecule
|
||||||
|
</PRE>
|
||||||
|
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||||
|
<LI>msd/molecule = style name of this compute command
|
||||||
|
</UL>
|
||||||
|
<P><B>Examples:</B>
|
||||||
|
</P>
|
||||||
|
<PRE>compute 1 all msd/molecule
|
||||||
|
</PRE>
|
||||||
|
<P><B>Description:</B>
|
||||||
|
</P>
|
||||||
|
<P>Define a computation that calculates the mean-squared displacement
|
||||||
|
(MSD) of individual molecules. The calculation includes all effects
|
||||||
|
due to atoms passing thru periodic boundaries.
|
||||||
|
</P>
|
||||||
|
<P>Four quantites are calculated by this compute for each molecule. The
|
||||||
|
first 3 quantities are the squared dx,dy,dz displacements of the
|
||||||
|
center-of-mass. The 4th component is the total squared displacement,
|
||||||
|
i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass.
|
||||||
|
</P>
|
||||||
|
<P>The slope of the mean-squared displacement (MSD) versus time is
|
||||||
|
proportional to the diffusion coefficient of the diffusing molecules.
|
||||||
|
</P>
|
||||||
|
<P>The displacement of the center-of-mass of the molecule is from its
|
||||||
|
original center-of-mass position at the time the compute command was
|
||||||
|
issued.
|
||||||
|
</P>
|
||||||
|
<P>The MSD for a particular molecule is only computed if one or more of
|
||||||
|
its atoms are in the specified group. Normally all atoms in the
|
||||||
|
molecule should be in the group, however this is not required. LAMMPS
|
||||||
|
will warn you if this is not the case. Only atoms in the group
|
||||||
|
contribute to the center-of-mass calculation for the molecule, which
|
||||||
|
is used to caculate its initial and current position.
|
||||||
|
</P>
|
||||||
|
<P>Let Nmolecules be the number of molecules for which the MSD is
|
||||||
|
calculated. If not all molecules have atoms in the group, then the
|
||||||
|
molecule with the lowest ID is the first of the Nmolecules. The next
|
||||||
|
lowest ID is the second, etc, up to Nmolecules.
|
||||||
|
</P>
|
||||||
|
<P>IMPORTANT NOTE: The initial coordinates of each molecule 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 compute 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 contribution to the MSD may not reflect its true contribution.
|
||||||
|
See the <A HREF = "fix_rigid.html">fix rigid</A> command for details. Thus, to
|
||||||
|
compute the MSD of rigid bodies as they cross periodic boundaries, you
|
||||||
|
will need to post-process a <A HREF = "dump.html">dump file</A> containing
|
||||||
|
coordinates of the atoms in the bodies.
|
||||||
|
</P>
|
||||||
|
<P>IMPORTANT NOTE: Unlike the <A HREF = "compute_msd.html">compute msd</A> command,
|
||||||
|
this compute does not store the initial center-of-mass coorindates of
|
||||||
|
its molecules in a restart file. Thus you cannot continue the MSD per
|
||||||
|
molecule calculation when running from a <A HREF = "read_restart.html">restart
|
||||||
|
file</A>.
|
||||||
|
</P>
|
||||||
|
<P><B>Output info:</B>
|
||||||
|
</P>
|
||||||
|
<P>This compute calculates a global array with the number of rows =
|
||||||
|
Nmolecules and the number of columns = 4 for dx,dy,dz and the total
|
||||||
|
displacement. These values can be accessed by any command that uses
|
||||||
|
global array values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
|
||||||
|
section</A> for an overview of LAMMPS output
|
||||||
|
options.
|
||||||
|
</P>
|
||||||
|
<P>The array values are "intensive", meaning they are independent of the
|
||||||
|
number of atoms in the simulation.
|
||||||
|
</P>
|
||||||
|
<P><B>Restrictions:</B> none
|
||||||
|
</P>
|
||||||
|
<P><B>Related commands:</B>
|
||||||
|
</P>
|
||||||
|
<P><A HREF = "compute_msd.html">compute msd</A>
|
||||||
|
</P>
|
||||||
|
<P><B>Default:</B> none
|
||||||
|
</P>
|
||||||
|
</HTML>
|
||||||
|
|
@ -0,0 +1,93 @@
|
||||||
|
"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
|
||||||
|
|
||||||
|
compute msd/molecule command :h3
|
||||||
|
|
||||||
|
[Syntax:]
|
||||||
|
|
||||||
|
compute ID group-ID msd/molecule :pre
|
||||||
|
|
||||||
|
ID, group-ID are documented in "compute"_compute.html command
|
||||||
|
msd/molecule = style name of this compute command :ul
|
||||||
|
|
||||||
|
[Examples:]
|
||||||
|
|
||||||
|
compute 1 all msd/molecule :pre
|
||||||
|
|
||||||
|
[Description:]
|
||||||
|
|
||||||
|
Define a computation that calculates the mean-squared displacement
|
||||||
|
(MSD) of individual molecules. The calculation includes all effects
|
||||||
|
due to atoms passing thru periodic boundaries.
|
||||||
|
|
||||||
|
Four quantites are calculated by this compute for each molecule. The
|
||||||
|
first 3 quantities are the squared dx,dy,dz displacements of the
|
||||||
|
center-of-mass. The 4th component is the total squared displacement,
|
||||||
|
i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass.
|
||||||
|
|
||||||
|
The slope of the mean-squared displacement (MSD) versus time is
|
||||||
|
proportional to the diffusion coefficient of the diffusing molecules.
|
||||||
|
|
||||||
|
The displacement of the center-of-mass of the molecule is from its
|
||||||
|
original center-of-mass position at the time the compute command was
|
||||||
|
issued.
|
||||||
|
|
||||||
|
The MSD for a particular molecule is only computed if one or more of
|
||||||
|
its atoms are in the specified group. Normally all atoms in the
|
||||||
|
molecule should be in the group, however this is not required. LAMMPS
|
||||||
|
will warn you if this is not the case. Only atoms in the group
|
||||||
|
contribute to the center-of-mass calculation for the molecule, which
|
||||||
|
is used to caculate its initial and current position.
|
||||||
|
|
||||||
|
Let Nmolecules be the number of molecules for which the MSD is
|
||||||
|
calculated. If not all molecules have atoms in the group, then the
|
||||||
|
molecule with the lowest ID is the first of the Nmolecules. The next
|
||||||
|
lowest ID is the second, etc, up to Nmolecules.
|
||||||
|
|
||||||
|
IMPORTANT NOTE: The initial coordinates of each molecule 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 compute 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 contribution to the MSD may not reflect its true contribution.
|
||||||
|
See the "fix rigid"_fix_rigid.html command for details. Thus, to
|
||||||
|
compute the MSD of rigid bodies as they cross periodic boundaries, you
|
||||||
|
will need to post-process a "dump file"_dump.html containing
|
||||||
|
coordinates of the atoms in the bodies.
|
||||||
|
|
||||||
|
IMPORTANT NOTE: Unlike the "compute msd"_compute_msd.html command,
|
||||||
|
this compute does not store the initial center-of-mass coorindates of
|
||||||
|
its molecules in a restart file. Thus you cannot continue the MSD per
|
||||||
|
molecule calculation when running from a "restart
|
||||||
|
file"_read_restart.html.
|
||||||
|
|
||||||
|
[Output info:]
|
||||||
|
|
||||||
|
This compute calculates a global array with the number of rows =
|
||||||
|
Nmolecules and the number of columns = 4 for dx,dy,dz and the total
|
||||||
|
displacement. These values can be accessed by any command that uses
|
||||||
|
global array values from a compute as input. See "this
|
||||||
|
section"_Section_howto.html#4_15 for an overview of LAMMPS output
|
||||||
|
options.
|
||||||
|
|
||||||
|
The array values are "intensive", meaning they are independent of the
|
||||||
|
number of atoms in the simulation.
|
||||||
|
|
||||||
|
[Restrictions:] none
|
||||||
|
|
||||||
|
[Related commands:]
|
||||||
|
|
||||||
|
"compute msd"_compute_msd.html
|
||||||
|
|
||||||
|
[Default:] none
|
||||||
Loading…
Reference in New Issue