(94fcde12) · Commits · 郑智淋 / lammps

doc/Section_commands.html

+7 −6

Original line number	Diff line number	Diff line
		@@ -346,12 +346,13 @@ of each style or click on the style itself for a full description:
		each style or click on the style itself for a full description:
		</P>
		<DIV ALIGN=center><TABLE BORDER=1 >
		<TR ALIGN="center"><TD ><A HREF = "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>
		<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>
		<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>
		<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>
		<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>
		<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>
		<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>
		<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>
		<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>
		<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>
		<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>
		<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>
		<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>
		</TD></TR></TABLE></DIV>

		<P>These are compute styles contributed by users, which can be used if

doc/compute.html

+3 −0

Original line number	Diff line number	Diff line
		@@ -171,6 +171,7 @@ available in LAMMPS:
		<LI><A HREF = "compute_centro_atom.html">centro/atom</A> - centro-symmetry parameter for each atom
		<LI><A HREF = "compute_cna_atom.html">cna/atom</A> - common neighbor analysis (CNA) for each atom
		<LI><A HREF = "compute_com.html">com</A> - center-of-mass of group of atoms
		<LI><A HREF = "compute_com_molecule.html">com/molecule</A> - center-of-mass for each molecule
		<LI><A HREF = "compute_coord_atom.html">coord/atom</A> - coordination number for each atom
		<LI><A HREF = "compute_damage_atom.html">damage/atom</A> - Peridynamic damage for each atom
		<LI><A HREF = "compute_dihedral_local.html">dihedral/local</A> - angle of each dihedral
		@@ -180,11 +181,13 @@ available in LAMMPS:
		<LI><A HREF = "compute_event_displace.html">event/displace</A> - detect event on atom displacement
		<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
		<LI><A HREF = "compute_gyration.html">gyration</A> - radius of gyration of group of atoms
		<LI><A HREF = "compute_gyration_molecule.html">gyration/molecule</A> - radius of gyration for each molecule
		<LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
		<LI><A HREF = "compute_improper_local.html">improper/local</A> - angle of each improper
		<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
		<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
		<LI><A HREF = "compute_msd.html">msd</A> - mean-squared displacement of group of atoms
		<LI><A HREF = "compute_msd_molecule.html">msd/molecule</A> - mean-squared displacement for each molecule
		<LI><A HREF = "compute_pe.html">pe</A> - potential energy
		<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
		<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor

doc/compute_com_molecule.html

0 → 100644

+80 −0

Original line number	Diff line number	Diff line
		<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 com/molecule command
		</H3>
		<P><B>Syntax:</B>
		</P>
		<PRE>compute ID group-ID com/molecule
		</PRE>
		<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
		<LI>com/molecule = style name of this compute command
		</UL>
		<P><B>Examples:</B>
		</P>
		<PRE>compute 1 fluid com/molecule
		</PRE>
		<P><B>Description:</B>
		</P>
		<P>Define a computation that calculates the center-of-mass of individual
		molecules. The calculation includes all effects due to atoms passing
		thru periodic boundaries.
		</P>
		<P>The x,y,z coordinate of the center-of-mass 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.
		</P>
		<P>Let Nmolecules be the number of molecules for which the center-of-mass
		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 the
		molecule's center-of-mass 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 center-of-mass may not reflect its true
		contribution. See the <A HREF = "fix_rigid.html">fix rigid</A> 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 <A HREF = "dump.html">dump
		file</A> containing coordinates of the atoms in the bodies.
		</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 = 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
		<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_com.html">compute com</A>
		</P>
		<P><B>Default:</B> none
		</P>
		</HTML>

doc/compute_com_molecule.txt

0 → 100644

+75 −0

Original line number	Diff line number	Diff line
		"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 com/molecule command :h3

		[Syntax:]

		compute ID group-ID com/molecule :pre

		ID, group-ID are documented in "compute"_compute.html command
		com/molecule = style name of this compute command :ul

		[Examples:]

		compute 1 fluid com/molecule :pre

		[Description:]

		Define a computation that calculates the center-of-mass of individual
		molecules. The calculation includes all effects due to atoms passing
		thru periodic boundaries.

		The x,y,z coordinate of the center-of-mass 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.

		Let Nmolecules be the number of molecules for which the center-of-mass
		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 the
		molecule's center-of-mass 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 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.

		[Restrictions:] none

		[Related commands:]

		"compute com"_compute_com.html

		[Default:] none

doc/compute_gyration_molecule.html

0 → 100644

+78 −0

Original line number	Diff line number	Diff line
		<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 gyration/molecule command
		</H3>
		<P><B>Syntax:</B>
		</P>
		<PRE>compute ID group-ID gyration/molecule
		</PRE>
		<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
		<LI>gyration/molecule = style name of this compute command
		</UL>
		<P><B>Examples:</B>
		</P>
		<PRE>compute 1 molecule gyration/molecule
		</PRE>
		<P><B>Description:</B>
		</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
		</P>
		<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
		</CENTER>
		<P>where M is the total mass of the molecule and Rcm is the center-of-mass
		position of the molecule.
		</P>
		<P>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.
		</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>

Admin message