mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@134 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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@ -33,7 +33,7 @@
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possible attributes = tag, mol, type, x, y, z, xs, ys, zs, xu, yu, zu,
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ix, iy, iz, vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz, tqx, tqy, tqz,
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centro, eng, sxx, syy, szz, sxy, sxz, syz
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etotal, ke, epair, centro, sxx, syy, szz, sxy, sxz, syz
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tag = atom ID
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mol = molecule ID
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type = atom type
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@ -46,8 +46,10 @@
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q = atom charge
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mux,muy,muz = orientation of dipolar atom
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tqx,tqy,tqz = torque on dipolar atoms
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etotal = per-atom total energy (ke + epair)
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ke = per-atom kinetic energy
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epair = per-atom pairwise energy
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centro = per-atom centro-symmetry parameter
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eng = per-atom pairwise energy
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sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
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<I>dcd</I> args = none
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<I>xtc</I> args = precision (optional)
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@ -61,7 +63,7 @@
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<PRE>dump myDump all atom 100 dump.atom
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dump 2 subgroup atom 50 dump.run.bin
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dump 4a all custom 100 dump.myforce.* tag type x y vx fx
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dump 4b flow custom 100 dump.%.myforce tag type eng sxx syy szz
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dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz
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dump 1 all xtc 1000 file.xtc 100.0
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</PRE>
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<P><B>Description:</B>
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@ -227,6 +229,25 @@ what is meant by scaled vs unscaled coordinates and the image flags.
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<P>The <I>mux</I>, <I>muy</I>, <I>muz</I>, <I>tqy</I>, <I>tqx</I>, <I>tqy</I> attributes are specific
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to dipolar systems defined with an atom style of <I>dipole</I>.
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</P>
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<P>The <I>etotal</I> attribute computes the total energy of each atom, which
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is the <I>ke</I> plus <I>epair</I> values. Note that it does not include
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contributions due to bonds, angles, etc that the atom is part of.
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</P>
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<P>The <I>ke</I> attribute computes the kinetic energy of each atom
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which is simply 0.5 m v^2.
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</P>
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<P>The <I>epair</I> attribute computes the pairwise energy for each atom.
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This is its pairwise interaction with all of its neighbors (divided by
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2). Summed over all atoms, this should equal the pairwise energy of
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the entire system (Van der Waals + Coulombic). However, for force
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fields that include a contribution to the pairwise energy that is
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computed as part of dihedral terms (i.e. 1-4 interactions), this
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contribution is not included in the per-atom pairwise energy.
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Computation of the per-atom energy requires a loop thru the neighbor
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list and inter-processor communication, so it can be inefficient to
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dump this quantity too frequently or to have multiple dump commands,
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each with a <I>epair</I> attribute.
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</P>
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<P>The <I>centro</I> attribute causes the centro-symmetry parameter to be
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computed for each atom in the dump group using the following formula
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from <A HREF = "#Kelchner">(Kelchner)</A>
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@ -244,18 +265,6 @@ performed. Thus it can be inefficient to dump this quantity too
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frequently or to have multiple dump commands, each with a <I>centro</I>
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attribute.
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</P>
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<P>The <I>eng</I> attribute computes the pairwise energy for each atom. This
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is its pairwise interaction with all of its neighbors (divided by 2).
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Summed over all atoms, this should equal the pairwise energy of the
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entire system (Van der Waals + Coulombic). However, for force fields
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that include a contribution to the pairwise energy that is computed as
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part of dihedral terms (i.e. 1-4 interactions), this contribution is
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not included in the per-atom pairwise energy. Computation of the
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per-atom energy requires a loop thru the neighbor list and
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inter-processor communication, so it can be inefficient to dump this
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quantity too frequently or to have multiple dump commands, each with a
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<I>eng</I> attribute.
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</P>
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<P>The <I>sxx</I>, <I>syy</I>, <I>szz</I>, <I>sxy</I>, <I>sxz</I>, <I>syz</I> attributes compute the
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pairwise stress tensor for each atom where the <I>ab</I> component of the
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stress on atom <I>i</I> is given by
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39
doc/dump.txt
39
doc/dump.txt
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@ -24,7 +24,7 @@ args = list of arguments for a particular style :l
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possible attributes = tag, mol, type, x, y, z, xs, ys, zs, xu, yu, zu,
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ix, iy, iz, vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz, tqx, tqy, tqz,
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centro, eng, sxx, syy, szz, sxy, sxz, syz
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etotal, ke, epair, centro, sxx, syy, szz, sxy, sxz, syz
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tag = atom ID
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mol = molecule ID
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type = atom type
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@ -37,8 +37,10 @@ args = list of arguments for a particular style :l
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q = atom charge
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mux,muy,muz = orientation of dipolar atom
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tqx,tqy,tqz = torque on dipolar atoms
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etotal = per-atom total energy (ke + epair)
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ke = per-atom kinetic energy
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epair = per-atom pairwise energy
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centro = per-atom centro-symmetry parameter
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eng = per-atom pairwise energy
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sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
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{dcd} args = none
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{xtc} args = precision (optional)
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@ -51,7 +53,7 @@ args = list of arguments for a particular style :l
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dump myDump all atom 100 dump.atom
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dump 2 subgroup atom 50 dump.run.bin
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dump 4a all custom 100 dump.myforce.* tag type x y vx fx
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dump 4b flow custom 100 dump.%.myforce tag type eng sxx syy szz
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dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz
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dump 1 all xtc 1000 file.xtc 100.0 :pre
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[Description:]
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@ -217,6 +219,25 @@ what is meant by scaled vs unscaled coordinates and the image flags.
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The {mux}, {muy}, {muz}, {tqy}, {tqx}, {tqy} attributes are specific
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to dipolar systems defined with an atom style of {dipole}.
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The {etotal} attribute computes the total energy of each atom, which
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is the {ke} plus {epair} values. Note that it does not include
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contributions due to bonds, angles, etc that the atom is part of.
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The {ke} attribute computes the kinetic energy of each atom
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which is simply 0.5 m v^2.
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The {epair} attribute computes the pairwise energy for each atom.
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This is its pairwise interaction with all of its neighbors (divided by
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2). Summed over all atoms, this should equal the pairwise energy of
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the entire system (Van der Waals + Coulombic). However, for force
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fields that include a contribution to the pairwise energy that is
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computed as part of dihedral terms (i.e. 1-4 interactions), this
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contribution is not included in the per-atom pairwise energy.
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Computation of the per-atom energy requires a loop thru the neighbor
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list and inter-processor communication, so it can be inefficient to
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dump this quantity too frequently or to have multiple dump commands,
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each with a {epair} attribute.
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The {centro} attribute causes the centro-symmetry parameter to be
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computed for each atom in the dump group using the following formula
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from "(Kelchner)"_#Kelchner
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@ -234,18 +255,6 @@ performed. Thus it can be inefficient to dump this quantity too
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frequently or to have multiple dump commands, each with a {centro}
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attribute.
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The {eng} attribute computes the pairwise energy for each atom. This
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is its pairwise interaction with all of its neighbors (divided by 2).
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Summed over all atoms, this should equal the pairwise energy of the
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entire system (Van der Waals + Coulombic). However, for force fields
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that include a contribution to the pairwise energy that is computed as
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part of dihedral terms (i.e. 1-4 interactions), this contribution is
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not included in the per-atom pairwise energy. Computation of the
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per-atom energy requires a loop thru the neighbor list and
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inter-processor communication, so it can be inefficient to dump this
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quantity too frequently or to have multiple dump commands, each with a
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{eng} attribute.
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The {sxx}, {syy}, {szz}, {sxy}, {sxz}, {syz} attributes compute the
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pairwise stress tensor for each atom where the {ab} component of the
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stress on atom {i} is given by
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<I>multi</I> args = none
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<I>granular</I> args = none
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<I>custom</I> args = list of attributes
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possible attributes = step, atoms, cpu, temp, press, pe, ke, eng,
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possible attributes = step, atoms, cpu, temp, press, pe, ke, etotal,
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evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail,
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vol, lx, ly, lz, pxx, pyy, pzz, pxy, pxz, pyz
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gke, grot, tave, pave, eave, peave, t_ID
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@ -34,7 +34,7 @@
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press = pressure
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pe = total potential energy
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ke = kinetic energy
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eng = total energy (pe + ke)
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etotal = total energy (pe + ke)
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evdwl = VanderWaal pairwise energy
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ecoul = Coulombic pairwise energy
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epair = pairwise (evdwl + ecoul)
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@ -58,8 +58,8 @@
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<P><B>Examples:</B>
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</P>
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<PRE>thermo_style multi
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thermo_style custom step temp pe eng press vol
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thermo_style custom step temp t_left t_right eng
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thermo_style custom step temp pe etotal press vol
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thermo_style custom step temp t_left t_right etotal
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</PRE>
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<P><B>Description:</B>
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</P>
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log file.
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</P>
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<P>Style <I>one</I> prints a one-line summary of thermodynamic info that is
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the equivalent of "thermo_style custom step temp epair emol eng
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the equivalent of "thermo_style custom step temp epair emol etotal
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press". The line contains only numeric values.
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</P>
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<P>Style <I>multi</I> prints a multiple-line listing of thermodynamic info
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that is the equivalent of "thermo_style custom eng ke temp pe ebond
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that is the equivalent of "thermo_style custom etotal ke temp pe ebond
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eangle edihed eimp evdwl ecoul elong press". The listing contains
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numeric values and a string ID for each quantity.
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</P>
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@ -88,7 +88,7 @@ outputs as a final printed quantity when the simulation box volume
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changes during the simulation.
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</P>
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<P>All thermodynamic quantities which require a temperature (<I>temp, press,
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ke, eng, tave, eave</I>) use the temperature with ID = <I>default</I> that is
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ke, etotal, tave, eave</I>) use the temperature with ID = <I>default</I> that is
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defined by LAMMPS (see the <A HREF = "temperature.html">temperature</A> command)
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that performs an average over all atoms. This can be changed via the
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<A HREF = "thermo_modify.html">thermo_modify</A> command. The exception is the
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@ -98,7 +98,7 @@ and print out.
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<P>A long-range tail correction <I>etail</I> for the VanderWaal pairwise
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energy will be non-zero only if the <A HREF = "pair_modify.html">pair_modify
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tail</A> option is turned on. The <I>etail</I> contribution
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is included in <I>evdwl</I>, <I>pe</I>, and <I>eng</I>, and the corresponding tail
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is included in <I>evdwl</I>, <I>pe</I>, and <I>etotal</I>, and the corresponding tail
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correction to the pressure is included in <I>press</I> and <I>pxx</I>, <I>pyy</I>,
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etc.
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</P>
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@ -18,7 +18,7 @@ args = list of arguments for a particular style :l
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{multi} args = none
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{granular} args = none
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{custom} args = list of attributes
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possible attributes = step, atoms, cpu, temp, press, pe, ke, eng,
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possible attributes = step, atoms, cpu, temp, press, pe, ke, etotal,
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evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail,
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vol, lx, ly, lz, pxx, pyy, pzz, pxy, pxz, pyz
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gke, grot, tave, pave, eave, peave, t_ID
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@ -29,7 +29,7 @@ args = list of arguments for a particular style :l
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press = pressure
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pe = total potential energy
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ke = kinetic energy
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eng = total energy (pe + ke)
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etotal = total energy (pe + ke)
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evdwl = VanderWaal pairwise energy
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ecoul = Coulombic pairwise energy
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epair = pairwise (evdwl + ecoul)
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[Examples:]
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thermo_style multi
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thermo_style custom step temp pe eng press vol
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thermo_style custom step temp t_left t_right eng :pre
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thermo_style custom step temp pe etotal press vol
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thermo_style custom step temp t_left t_right etotal :pre
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[Description:]
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@ -61,11 +61,11 @@ Set the style in which thermodynamic data is printed to the screen and
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log file.
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Style {one} prints a one-line summary of thermodynamic info that is
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the equivalent of "thermo_style custom step temp epair emol eng
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the equivalent of "thermo_style custom step temp epair emol etotal
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press". The line contains only numeric values.
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Style {multi} prints a multiple-line listing of thermodynamic info
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that is the equivalent of "thermo_style custom eng ke temp pe ebond
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that is the equivalent of "thermo_style custom etotal ke temp pe ebond
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eangle edihed eimp evdwl ecoul elong press". The listing contains
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numeric values and a string ID for each quantity.
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@ -82,7 +82,7 @@ outputs as a final printed quantity when the simulation box volume
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changes during the simulation.
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All thermodynamic quantities which require a temperature ({temp, press,
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ke, eng, tave, eave}) use the temperature with ID = {default} that is
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ke, etotal, tave, eave}) use the temperature with ID = {default} that is
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defined by LAMMPS (see the "temperature"_temperature.html command)
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that performs an average over all atoms. This can be changed via the
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"thermo_modify"_thermo_modify.html command. The exception is the
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@ -92,7 +92,7 @@ and print out.
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A long-range tail correction {etail} for the VanderWaal pairwise
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energy will be non-zero only if the "pair_modify
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tail"_pair_modify.html option is turned on. The {etail} contribution
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is included in {evdwl}, {pe}, and {eng}, and the corresponding tail
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is included in {evdwl}, {pe}, and {etotal}, and the corresponding tail
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correction to the pressure is included in {press} and {pxx}, {pyy},
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etc.
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