forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7781 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
parent
61dac0f38d
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860fbe49c1
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@ -68,9 +68,7 @@ for which terms to include in their calculation (pair, bond, etc).
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The heat flux calculation will thus include exactly the same terms.
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The heat flux calculation will thus include exactly the same terms.
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Normally you should use <A HREF = "compute_stress_atom.html">compute stress/atom
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Normally you should use <A HREF = "compute_stress_atom.html">compute stress/atom
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virial</A> so as not to include a kinetic energy
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virial</A> so as not to include a kinetic energy
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term in the heat flux. Note that neither of those computes is able to
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term in the heat flux.
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include a long-range Coulombic contribution to the per-atom energy or
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stress.
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</P>
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</P>
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<P>This compute calculates 6 quantities and stores them in a 6-component
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<P>This compute calculates 6 quantities and stores them in a 6-component
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vector. The first 3 components are the x, y, z components of the full
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vector. The first 3 components are the x, y, z components of the full
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@ -65,9 +65,7 @@ for which terms to include in their calculation (pair, bond, etc).
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The heat flux calculation will thus include exactly the same terms.
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The heat flux calculation will thus include exactly the same terms.
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Normally you should use "compute stress/atom
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Normally you should use "compute stress/atom
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virial"_compute_stress_atom.html so as not to include a kinetic energy
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virial"_compute_stress_atom.html so as not to include a kinetic energy
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term in the heat flux. Note that neither of those computes is able to
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term in the heat flux.
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include a long-range Coulombic contribution to the per-atom energy or
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stress.
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This compute calculates 6 quantities and stores them in a 6-component
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This compute calculates 6 quantities and stores them in a 6-component
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vector. The first 3 components are the x, y, z components of the full
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vector. The first 3 components are the x, y, z components of the full
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@ -41,6 +41,12 @@ potential energy is the sum of pair, bond, angle, dihedral, improper,
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and kspace (long-range) energy. If any extra keywords are listed,
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and kspace (long-range) energy. If any extra keywords are listed,
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then only those components are summed to compute the potential energy.
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then only those components are summed to compute the potential energy.
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</P>
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</P>
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<P>The KSpace contribution requires 1 extra FFT each timestep the
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per-atom energy is calculated, if using the PPPM solver via the
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<A HREF = "kspace_style.html">kspace_style pppm</A> command. Thus it can increase
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the cost of the PPPM calculation if it is needed on a large fraction
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of the simulation timesteps.
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</P>
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<P>Various fixes can contribute to the total potential energy of the
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<P>Various fixes can contribute to the total potential energy of the
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system. See the doc pages for <A HREF = "fix.html">individual fixes</A> for
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system. See the doc pages for <A HREF = "fix.html">individual fixes</A> for
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details. The <I>thermo</I> option of the
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details. The <I>thermo</I> option of the
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@ -37,6 +37,12 @@ potential energy is the sum of pair, bond, angle, dihedral, improper,
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and kspace (long-range) energy. If any extra keywords are listed,
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and kspace (long-range) energy. If any extra keywords are listed,
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then only those components are summed to compute the potential energy.
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then only those components are summed to compute the potential energy.
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The KSpace contribution requires 1 extra FFT each timestep the
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per-atom energy is calculated, if using the PPPM solver via the
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"kspace_style pppm"_kspace_style.html command. Thus it can increase
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the cost of the PPPM calculation if it is needed on a large fraction
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of the simulation timesteps.
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Various fixes can contribute to the total potential energy of the
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Various fixes can contribute to the total potential energy of the
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system. See the doc pages for "individual fixes"_fix.html for
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system. See the doc pages for "individual fixes"_fix.html for
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details. The {thermo} option of the
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details. The {thermo} option of the
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@ -18,7 +18,7 @@
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>pe/atom = style name of this compute command
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<LI>pe/atom = style name of this compute command
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<LI>zero or more keywords may be appended
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<LI>zero or more keywords may be appended
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<LI>keyword = <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
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<LI>keyword = <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I>
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</UL>
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</UL>
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<P><B>Examples:</B>
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<P><B>Examples:</B>
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</P>
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</P>
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@ -35,8 +35,9 @@ you want the potential energy of the entire system.
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<P>The per-atom energy is calculated by the various pair, bond, etc
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<P>The per-atom energy is calculated by the various pair, bond, etc
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potentials defined for the simulation. If no extra keywords are
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potentials defined for the simulation. If no extra keywords are
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listed, then the potential energy is the sum of pair, bond, angle,
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listed, then the potential energy is the sum of pair, bond, angle,
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dihedral, and improper energy. If any extra keywords are listed, then
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dihedral,improper, and kspace energy. If any extra keywords are
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only those components are summed to compute the potential energy.
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listed, then only those components are summed to compute the potential
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energy.
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</P>
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</P>
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<P>Note that the energy of each atom is due to its interaction with all
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<P>Note that the energy of each atom is due to its interaction with all
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other atoms in the simulation, not just with other atoms in the group.
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other atoms in the simulation, not just with other atoms in the group.
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@ -58,13 +59,9 @@ in the last 2 columns of thermo output:
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compute pe all reduce sum c_peratom
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compute pe all reduce sum c_peratom
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thermo_style custom step temp etotal press pe c_pe
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thermo_style custom step temp etotal press pe c_pe
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</PRE>
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</PRE>
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<P>IMPORTANT NOTE: The per-atom energy does NOT include contributions due
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<P>IMPORTANT NOTE: The per-atom energy does not any Lennard-Jones tail
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to long-range Coulombic interactions (via the
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corrections invoked by the <A HREF = "pair_modify.html">pair_modify tail yes</A>
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<A HREF = "kspace_style.html">kspace_style</A> command). It's not clear this
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command, since those are global contributions to the system energy.
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contribution can easily be computed. It also does not include any
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Lennard-Jones tail corrections invoked by the <A HREF = "pair_modify.html">pair_modify tail
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yes</A> command, since those are global contributions to
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the system energy.
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</P>
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</P>
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<P><B>Output info:</B>
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<P><B>Output info:</B>
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</P>
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</P>
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@ -15,7 +15,7 @@ compute ID group-ID pe/atom keyword ... :pre
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ID, group-ID are documented in "compute"_compute.html command
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ID, group-ID are documented in "compute"_compute.html command
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pe/atom = style name of this compute command
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pe/atom = style name of this compute command
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zero or more keywords may be appended
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zero or more keywords may be appended
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keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} :ul
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keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} :ul
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[Examples:]
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[Examples:]
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@ -32,8 +32,9 @@ you want the potential energy of the entire system.
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The per-atom energy is calculated by the various pair, bond, etc
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The per-atom energy is calculated by the various pair, bond, etc
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potentials defined for the simulation. If no extra keywords are
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potentials defined for the simulation. If no extra keywords are
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listed, then the potential energy is the sum of pair, bond, angle,
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listed, then the potential energy is the sum of pair, bond, angle,
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dihedral, and improper energy. If any extra keywords are listed, then
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dihedral,improper, and kspace energy. If any extra keywords are
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only those components are summed to compute the potential energy.
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listed, then only those components are summed to compute the potential
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energy.
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Note that the energy of each atom is due to its interaction with all
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Note that the energy of each atom is due to its interaction with all
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other atoms in the simulation, not just with other atoms in the group.
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other atoms in the simulation, not just with other atoms in the group.
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@ -55,13 +56,9 @@ compute peratom all pe/atom
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compute pe all reduce sum c_peratom
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compute pe all reduce sum c_peratom
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thermo_style custom step temp etotal press pe c_pe :pre
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thermo_style custom step temp etotal press pe c_pe :pre
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IMPORTANT NOTE: The per-atom energy does NOT include contributions due
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IMPORTANT NOTE: The per-atom energy does not any Lennard-Jones tail
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to long-range Coulombic interactions (via the
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corrections invoked by the "pair_modify tail yes"_pair_modify.html
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"kspace_style"_kspace_style.html command). It's not clear this
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command, since those are global contributions to the system energy.
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contribution can easily be computed. It also does not include any
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Lennard-Jones tail corrections invoked by the "pair_modify tail
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yes"_pair_modify.html command, since those are global contributions to
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the system energy.
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[Output info:]
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[Output info:]
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@ -18,7 +18,7 @@
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>stress/atom = style name of this compute command
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<LI>stress/atom = style name of this compute command
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<LI>zero or more keywords may be appended
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<LI>zero or more keywords may be appended
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<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>fix</I> or <I>virial</I>
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<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I> or <I>fix</I> or <I>virial</I>
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</UL>
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</UL>
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<P><B>Examples:</B>
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<P><B>Examples:</B>
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</P>
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</P>
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@ -47,11 +47,12 @@ atoms in the pairwise interaction, and <I>F1</I> and <I>F2</I> are the forces on
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the 2 atoms resulting from the pairwise interaction. The third term
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the 2 atoms resulting from the pairwise interaction. The third term
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is a bond contribution of similar form for the <I>Nb</I> bonds which atom
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is a bond contribution of similar form for the <I>Nb</I> bonds which atom
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<I>I</I> is part of. There are similar terms for the <I>Na</I> angle, <I>Nd</I>
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<I>I</I> is part of. There are similar terms for the <I>Na</I> angle, <I>Nd</I>
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dihedral, and <I>Ni</I> improper interactions atom <I>I</I> is part of.
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dihedral, and <I>Ni</I> improper interactions atom <I>I</I> is part of. There
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Finally, there is a term for the <I>Nf</I> <A HREF = "fix.html">fixes</A> that apply
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is also a term for the KSpace contribution from long-range Coulombic
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internal constraint forces to atom <I>I</I>. Currently, only the <A HREF = "fix_shake.html">fix
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interactions, if defined. Finally, there is a term for the <I>Nf</I>
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shake</A> and <A HREF = "fix_rigid.html">fix rigid</A> commands
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<A HREF = "fix.html">fixes</A> that apply internal constraint forces to atom <I>I</I>.
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contribute to this term.
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Currently, only the <A HREF = "fix_shake.html">fix shake</A> and <A HREF = "fix_rigid.html">fix
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rigid</A> commands contribute to this term.
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</P>
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</P>
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<P>As the coefficients in the formula imply, a virial contribution
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<P>As the coefficients in the formula imply, a virial contribution
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produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
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produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
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@ -74,6 +75,12 @@ other atoms in the simulation, not just with other atoms in the group.
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pairwise interactions between 1-4 atoms. The virial contribution of
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pairwise interactions between 1-4 atoms. The virial contribution of
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these terms is included in the pair virial, not the dihedral virial.
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these terms is included in the pair virial, not the dihedral virial.
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</P>
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</P>
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<P>The KSpace contribution to the per-atom stress requires 6 extra FFTs
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each timestep that per-atom stress is calculated, if using the PPPM
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solver via the <A HREF = "kspace_style.html">kspace_style pppm</A> command. Thus it
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can significantly increase the cost of the PPPM calculation if it is
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needed on a large fraction of the simulation timesteps.
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</P>
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<P>Note that as defined in the formula, per-atom stress is the negative
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<P>Note that as defined in the formula, per-atom stress is the negative
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of the per-atom pressure tensor. It is also really a stress*volume
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of the per-atom pressure tensor. It is also really a stress*volume
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formulation, meaning the computed quantity is in units of
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formulation, meaning the computed quantity is in units of
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@ -93,11 +100,6 @@ compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
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variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
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variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
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thermo_style custom step temp etotal press v_press
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thermo_style custom step temp etotal press v_press
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</PRE>
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</PRE>
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<P>IMPORTANT NOTE: The per-atom stress does NOT include contributions due
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to long-range Coulombic interactions (via the
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<A HREF = "kspace_style.html">kspace_style</A> command). It's not clear this
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contribution can easily be computed.
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</P>
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<P><B>Output info:</B>
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<P><B>Output info:</B>
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</P>
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</P>
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<P>This compute calculates a per-atom array with 6 columns, which can be
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<P>This compute calculates a per-atom array with 6 columns, which can be
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@ -15,7 +15,7 @@ compute ID group-ID stress/atom keyword ... :pre
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ID, group-ID are documented in "compute"_compute.html command
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ID, group-ID are documented in "compute"_compute.html command
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stress/atom = style name of this compute command
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stress/atom = style name of this compute command
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zero or more keywords may be appended
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zero or more keywords may be appended
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keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {fix} or {virial} :ul
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keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
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[Examples:]
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[Examples:]
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@ -44,11 +44,12 @@ atoms in the pairwise interaction, and {F1} and {F2} are the forces on
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the 2 atoms resulting from the pairwise interaction. The third term
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the 2 atoms resulting from the pairwise interaction. The third term
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is a bond contribution of similar form for the {Nb} bonds which atom
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is a bond contribution of similar form for the {Nb} bonds which atom
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{I} is part of. There are similar terms for the {Na} angle, {Nd}
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{I} is part of. There are similar terms for the {Na} angle, {Nd}
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dihedral, and {Ni} improper interactions atom {I} is part of.
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dihedral, and {Ni} improper interactions atom {I} is part of. There
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Finally, there is a term for the {Nf} "fixes"_fix.html that apply
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is also a term for the KSpace contribution from long-range Coulombic
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internal constraint forces to atom {I}. Currently, only the "fix
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interactions, if defined. Finally, there is a term for the {Nf}
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shake"_fix_shake.html and "fix rigid"_fix_rigid.html commands
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"fixes"_fix.html that apply internal constraint forces to atom {I}.
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contribute to this term.
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Currently, only the "fix shake"_fix_shake.html and "fix
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rigid"_fix_rigid.html commands contribute to this term.
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As the coefficients in the formula imply, a virial contribution
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As the coefficients in the formula imply, a virial contribution
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produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
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produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
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@ -71,6 +72,12 @@ The "dihedral_style charmm"_dihedral_charmm.html style calculates
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pairwise interactions between 1-4 atoms. The virial contribution of
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pairwise interactions between 1-4 atoms. The virial contribution of
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these terms is included in the pair virial, not the dihedral virial.
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these terms is included in the pair virial, not the dihedral virial.
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The KSpace contribution to the per-atom stress requires 6 extra FFTs
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each timestep that per-atom stress is calculated, if using the PPPM
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solver via the "kspace_style pppm"_kspace_style.html command. Thus it
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can significantly increase the cost of the PPPM calculation if it is
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needed on a large fraction of the simulation timesteps.
|
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Note that as defined in the formula, per-atom stress is the negative
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Note that as defined in the formula, per-atom stress is the negative
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of the per-atom pressure tensor. It is also really a stress*volume
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of the per-atom pressure tensor. It is also really a stress*volume
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formulation, meaning the computed quantity is in units of
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formulation, meaning the computed quantity is in units of
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@ -90,11 +97,6 @@ compute p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
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variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
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variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
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thermo_style custom step temp etotal press v_press :pre
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thermo_style custom step temp etotal press v_press :pre
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IMPORTANT NOTE: The per-atom stress does NOT include contributions due
|
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to long-range Coulombic interactions (via the
|
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"kspace_style"_kspace_style.html command). It's not clear this
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contribution can easily be computed.
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|
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[Output info:]
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[Output info:]
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This compute calculates a per-atom array with 6 columns, which can be
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This compute calculates a per-atom array with 6 columns, which can be
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