git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@134 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/dump.html

@@ -33,7 +33,7 @@
     possible attributes = tag, mol, type, x, y, z, xs, ys, zs, xu, yu, zu,
                  ix, iy, iz, vx, vy, vz, fx, fy, fz,
                  q, mux, muy, muz, tqx, tqy, tqz,
-		 centro, eng, sxx, syy, szz, sxy, sxz, syz 
+		 etotal, ke, epair, centro, sxx, syy, szz, sxy, sxz, syz 
       tag = atom ID
       mol = molecule ID
       type = atom type
@@ -46,8 +46,10 @@
       q = atom charge
       mux,muy,muz = orientation of dipolar atom
       tqx,tqy,tqz = torque on dipolar atoms
+      etotal = per-atom total energy (ke + epair)
+      ke = per-atom kinetic energy
+      epair = per-atom pairwise energy
       centro = per-atom centro-symmetry parameter
-      eng = per-atom pairwise energy
       sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
   <I>dcd</I> args = none
   <I>xtc</I> args = precision (optional)
@@ -61,7 +63,7 @@
 <PRE>dump myDump all atom 100 dump.atom
 dump 2 subgroup atom 50 dump.run.bin
 dump 4a all custom 100 dump.myforce.* tag type x y vx fx
-dump 4b flow custom 100 dump.%.myforce tag type eng sxx syy szz
+dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz
 dump 1 all xtc 1000 file.xtc 100.0 
 </PRE>
 <P><B>Description:</B>
@@ -227,6 +229,25 @@ what is meant by scaled vs unscaled coordinates and the image flags.
 <P>The <I>mux</I>, <I>muy</I>, <I>muz</I>, <I>tqy</I>, <I>tqx</I>, <I>tqy</I> attributes are specific
 to dipolar systems defined with an atom style of <I>dipole</I>.
 </P>
+<P>The <I>etotal</I> attribute computes the total energy of each atom, which
+is the <I>ke</I> plus <I>epair</I> values.  Note that it does not include
+contributions due to bonds, angles, etc that the atom is part of.
+</P>
+<P>The <I>ke</I> attribute computes the kinetic energy of each atom
+which is simply 0.5 m v^2.
+</P>
+<P>The <I>epair</I> attribute computes the pairwise energy for each atom.
+This is its pairwise interaction with all of its neighbors (divided by
+2).  Summed over all atoms, this should equal the pairwise energy of
+the entire system (Van der Waals + Coulombic).  However, for force
+fields that include a contribution to the pairwise energy that is
+computed as part of dihedral terms (i.e. 1-4 interactions), this
+contribution is not included in the per-atom pairwise energy.
+Computation of the per-atom energy requires a loop thru the neighbor
+list and inter-processor communication, so it can be inefficient to
+dump this quantity too frequently or to have multiple dump commands,
+each with a <I>epair</I> attribute.
+</P>
 <P>The <I>centro</I> attribute causes the centro-symmetry parameter to be
 computed for each atom in the dump group using the following formula
 from <A HREF = "#Kelchner">(Kelchner)</A>
@@ -244,18 +265,6 @@ performed.  Thus it can be inefficient to dump this quantity too
 frequently or to have multiple dump commands, each with a <I>centro</I>
 attribute.
 </P>
-<P>The <I>eng</I> attribute computes the pairwise energy for each atom.  This
-is its pairwise interaction with all of its neighbors (divided by 2).
-Summed over all atoms, this should equal the pairwise energy of the
-entire system (Van der Waals + Coulombic).  However, for force fields
-that include a contribution to the pairwise energy that is computed as
-part of dihedral terms (i.e. 1-4 interactions), this contribution is
-not included in the per-atom pairwise energy.  Computation of the
-per-atom energy requires a loop thru the neighbor list and
-inter-processor communication, so it can be inefficient to dump this
-quantity too frequently or to have multiple dump commands, each with a
-<I>eng</I> attribute.
-</P>
 <P>The <I>sxx</I>, <I>syy</I>, <I>szz</I>, <I>sxy</I>, <I>sxz</I>, <I>syz</I> attributes compute the
 pairwise stress tensor for each atom where the <I>ab</I> component of the
 stress on atom <I>i</I> is given by

doc/dump.txt

@@ -24,7 +24,7 @@ args = list of arguments for a particular style :l
     possible attributes = tag, mol, type, x, y, z, xs, ys, zs, xu, yu, zu,
                  ix, iy, iz, vx, vy, vz, fx, fy, fz,
                  q, mux, muy, muz, tqx, tqy, tqz,
-		 centro, eng, sxx, syy, szz, sxy, sxz, syz 
+		 etotal, ke, epair, centro, sxx, syy, szz, sxy, sxz, syz 
       tag = atom ID
       mol = molecule ID
       type = atom type
@@ -37,8 +37,10 @@ args = list of arguments for a particular style :l
       q = atom charge
       mux,muy,muz = orientation of dipolar atom
       tqx,tqy,tqz = torque on dipolar atoms
+      etotal = per-atom total energy (ke + epair)
+      ke = per-atom kinetic energy
+      epair = per-atom pairwise energy
       centro = per-atom centro-symmetry parameter
-      eng = per-atom pairwise energy
       sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
   {dcd} args = none
   {xtc} args = precision (optional)
@@ -51,7 +53,7 @@ args = list of arguments for a particular style :l
 dump myDump all atom 100 dump.atom
 dump 2 subgroup atom 50 dump.run.bin
 dump 4a all custom 100 dump.myforce.* tag type x y vx fx
-dump 4b flow custom 100 dump.%.myforce tag type eng sxx syy szz
+dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz
 dump 1 all xtc 1000 file.xtc 100.0 :pre
 
 [Description:]
@@ -217,6 +219,25 @@ what is meant by scaled vs unscaled coordinates and the image flags.
 The {mux}, {muy}, {muz}, {tqy}, {tqx}, {tqy} attributes are specific
 to dipolar systems defined with an atom style of {dipole}.
 
+The {etotal} attribute computes the total energy of each atom, which
+is the {ke} plus {epair} values.  Note that it does not include
+contributions due to bonds, angles, etc that the atom is part of.
+
+The {ke} attribute computes the kinetic energy of each atom
+which is simply 0.5 m v^2.
+
+The {epair} attribute computes the pairwise energy for each atom.
+This is its pairwise interaction with all of its neighbors (divided by
+2).  Summed over all atoms, this should equal the pairwise energy of
+the entire system (Van der Waals + Coulombic).  However, for force
+fields that include a contribution to the pairwise energy that is
+computed as part of dihedral terms (i.e. 1-4 interactions), this
+contribution is not included in the per-atom pairwise energy.
+Computation of the per-atom energy requires a loop thru the neighbor
+list and inter-processor communication, so it can be inefficient to
+dump this quantity too frequently or to have multiple dump commands,
+each with a {epair} attribute.
+
 The {centro} attribute causes the centro-symmetry parameter to be
 computed for each atom in the dump group using the following formula
 from "(Kelchner)"_#Kelchner
@@ -234,18 +255,6 @@ performed.  Thus it can be inefficient to dump this quantity too
 frequently or to have multiple dump commands, each with a {centro}
 attribute.
 
-The {eng} attribute computes the pairwise energy for each atom.  This
-is its pairwise interaction with all of its neighbors (divided by 2).
-Summed over all atoms, this should equal the pairwise energy of the
-entire system (Van der Waals + Coulombic).  However, for force fields
-that include a contribution to the pairwise energy that is computed as
-part of dihedral terms (i.e. 1-4 interactions), this contribution is
-not included in the per-atom pairwise energy.  Computation of the
-per-atom energy requires a loop thru the neighbor list and
-inter-processor communication, so it can be inefficient to dump this
-quantity too frequently or to have multiple dump commands, each with a
-{eng} attribute.
-
 The {sxx}, {syy}, {szz}, {sxy}, {sxz}, {syz} attributes compute the
 pairwise stress tensor for each atom where the {ab} component of the
 stress on atom {i} is given by

doc/thermo_style.html

@@ -23,7 +23,7 @@
   <I>multi</I> args = none
   <I>granular</I> args = none
   <I>custom</I> args = list of attributes
-    possible attributes = step, atoms, cpu, temp, press, pe, ke, eng,
+    possible attributes = step, atoms, cpu, temp, press, pe, ke, etotal,
              evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail,
              vol, lx, ly, lz, pxx, pyy, pzz, pxy, pxz, pyz
              gke, grot, tave, pave, eave, peave, t_ID
@@ -34,7 +34,7 @@
       press = pressure
       pe = total potential energy
       ke = kinetic energy
-      eng = total energy (pe + ke)
+      etotal = total energy (pe + ke)
       evdwl = VanderWaal pairwise energy
       ecoul = Coulombic pairwise energy
       epair = pairwise (evdwl + ecoul)
@@ -58,8 +58,8 @@
 <P><B>Examples:</B>
 </P>
 <PRE>thermo_style multi
-thermo_style custom step temp pe eng press vol
+thermo_style custom step temp pe etotal press vol
-thermo_style custom step temp t_left t_right eng 
+thermo_style custom step temp t_left t_right etotal 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -67,11 +67,11 @@ thermo_style custom step temp t_left t_right eng
 log file.
 </P>
 <P>Style <I>one</I> prints a one-line summary of thermodynamic info that is
-the equivalent of "thermo_style custom step temp epair emol eng
+the equivalent of "thermo_style custom step temp epair emol etotal
 press".  The line contains only numeric values.
 </P>
 <P>Style <I>multi</I> prints a multiple-line listing of thermodynamic info
-that is the equivalent of "thermo_style custom eng ke temp pe ebond
+that is the equivalent of "thermo_style custom etotal ke temp pe ebond
 eangle edihed eimp evdwl ecoul elong press".  The listing contains
 numeric values and a string ID for each quantity.
 </P>
@@ -88,7 +88,7 @@ outputs as a final printed quantity when the simulation box volume
 changes during the simulation.
 </P>
 <P>All thermodynamic quantities which require a temperature (<I>temp, press,
-ke, eng, tave, eave</I>) use the temperature with ID = <I>default</I> that is
+ke, etotal, tave, eave</I>) use the temperature with ID = <I>default</I> that is
 defined by LAMMPS (see the <A HREF = "temperature.html">temperature</A> command)
 that performs an average over all atoms.  This can be changed via the
 <A HREF = "thermo_modify.html">thermo_modify</A> command.  The exception is the
@@ -98,7 +98,7 @@ and print out.
 <P>A long-range tail correction <I>etail</I> for the VanderWaal pairwise
 energy will be non-zero only if the <A HREF = "pair_modify.html">pair_modify
 tail</A> option is turned on.  The <I>etail</I> contribution
-is included in <I>evdwl</I>, <I>pe</I>, and <I>eng</I>, and the corresponding tail
+is included in <I>evdwl</I>, <I>pe</I>, and <I>etotal</I>, and the corresponding tail
 correction to the pressure is included in <I>press</I> and <I>pxx</I>, <I>pyy</I>,
 etc.
 </P>

doc/thermo_style.txt

@@ -18,7 +18,7 @@ args = list of arguments for a particular style :l
   {multi} args = none
   {granular} args = none
   {custom} args = list of attributes
-    possible attributes = step, atoms, cpu, temp, press, pe, ke, eng,
+    possible attributes = step, atoms, cpu, temp, press, pe, ke, etotal,
              evdwl, ecoul, epair, ebond, eangle, edihed, eimp, emol, elong, etail,
              vol, lx, ly, lz, pxx, pyy, pzz, pxy, pxz, pyz
              gke, grot, tave, pave, eave, peave, t_ID
@@ -29,7 +29,7 @@ args = list of arguments for a particular style :l
       press = pressure
       pe = total potential energy
       ke = kinetic energy
-      eng = total energy (pe + ke)
+      etotal = total energy (pe + ke)
       evdwl = VanderWaal pairwise energy
       ecoul = Coulombic pairwise energy
       epair = pairwise (evdwl + ecoul)
@@ -52,8 +52,8 @@ args = list of arguments for a particular style :l
 [Examples:]
 
 thermo_style multi
-thermo_style custom step temp pe eng press vol
+thermo_style custom step temp pe etotal press vol
-thermo_style custom step temp t_left t_right eng :pre
+thermo_style custom step temp t_left t_right etotal :pre
 
 [Description:]
 
@@ -61,11 +61,11 @@ Set the style in which thermodynamic data is printed to the screen and
 log file.
 
 Style {one} prints a one-line summary of thermodynamic info that is
-the equivalent of "thermo_style custom step temp epair emol eng
+the equivalent of "thermo_style custom step temp epair emol etotal
 press".  The line contains only numeric values.
 
 Style {multi} prints a multiple-line listing of thermodynamic info
-that is the equivalent of "thermo_style custom eng ke temp pe ebond
+that is the equivalent of "thermo_style custom etotal ke temp pe ebond
 eangle edihed eimp evdwl ecoul elong press".  The listing contains
 numeric values and a string ID for each quantity.
 
@@ -82,7 +82,7 @@ outputs as a final printed quantity when the simulation box volume
 changes during the simulation.
 
 All thermodynamic quantities which require a temperature ({temp, press,
-ke, eng, tave, eave}) use the temperature with ID = {default} that is
+ke, etotal, tave, eave}) use the temperature with ID = {default} that is
 defined by LAMMPS (see the "temperature"_temperature.html command)
 that performs an average over all atoms.  This can be changed via the
 "thermo_modify"_thermo_modify.html command.  The exception is the
@@ -92,7 +92,7 @@ and print out.
 A long-range tail correction {etail} for the VanderWaal pairwise
 energy will be non-zero only if the "pair_modify
 tail"_pair_modify.html option is turned on.  The {etail} contribution
-is included in {evdwl}, {pe}, and {eng}, and the corresponding tail
+is included in {evdwl}, {pe}, and {etotal}, and the corresponding tail
 correction to the pressure is included in {press} and {pxx}, {pyy},
 etc.