Commit e790a0e9 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1609 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 892fb116

doc/thermo_modify.html

+6 −28
Original line number Diff line number Diff line
@@ -17,9 +17,8 @@ 
</PRE>

<UL><LI>one or more keyword/value pairs may be listed 



<LI>keyword = <I>lost</I> or <I>norm</I> or <I>flush</I> or <I>line</I> or <I>format</I> or <I>temp</I> or <I>press</I> or <I>drot</I> or <I>grot</I> 



<PRE>  <I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>

keyword = <I>lost</I> or <I>norm</I> or <I>flush</I> or <I>line</I> or <I>format</I> or <I>temp</I> or <I>press</I>:l

  <I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>

  <I>norm</I> value = <I>yes</I> or <I>no</I>

  <I>flush</I> value = <I>yes</I> or <I>no</I>

  <I>line</I> value = <I>one</I> or <I>multi</I>
@@ -28,9 +27,6 @@ 
    string = C-style format string

  <I>temp</I> value = compute ID that calculates a temperature

  <I>press</I> value = compute ID that calculates a pressure

  <I>drot</I> value = compute ID that calculates rotational energy for dipolar atoms

  <I>grot</I> value = compute ID that calculates rotational energy for granular atoms 

</PRE>



</UL>

<P><B>Examples:</B>
@@ -113,24 +109,6 @@ the <I>temp</I> keyword comes before the <I>press</I> keyword, then the new 
pressure compute specified by the <I>press</I> keyword will be unaffected

by the <I>temp</I> setting.

</P>

<P>The <I>drot</I> keyword is used to determine how rotational energy is

calculated for dipolar atoms, which is used by the thermo_style

keyword <I>drot</I>.  The specified compute ID must have been previously

defined by the user via the <A HREF = "compute.html">compute</A> command.  As

described in the <A HREF = "thermo_style.html">thermo_style</A> command, thermo

output has a default compute for this calculation with ID =

<I>thermo_rotate_dipole</I>.  This option allows the user to override the

default.

</P>

<P>The <I>grot</I> keyword is used to determine how rotational energy is

calculated for granular atoms, which is used by the thermo_style

keyword <I>grot</I>.  The specified compute ID must have been previously

defined by the user via the <A HREF = "compute.html">compute</A> command.  As

described in the <A HREF = "thermo_style.html">thermo_style</A> command, thermo

output has a default compute for this calculation with ID =

<I>thermo_rotate_gran</I>.  This option allows the user to override the

default.

</P>

<P><B>Restrictions:</B> none

</P>

<P><B>Related commands:</B>
@@ -141,11 +119,11 @@ default. 
</P>

<P>The option defaults are lost = error, norm = yes for unit style of

<I>lj</I>, norm = no for unit style of <I>real</I> and <I>metal</I>, flush = no,

temp/press/drot/grot = compute IDs defined by thermo_style.

temp/press = compute IDs defined by thermo_style.

</P>

<P>The defaults for the line and format options depend on the thermo

style.  For styles "one", "granular", and "custom" the line and format

defaults are "one", "%8d", and "%12.8g".  For style "multi", the line

and format defaults are "multi", "%8d", and "%14.4f".

style.  For styles "one" and and "custom" the line and format defaults

are "one", "%8d", and "%12.8g".  For style "multi", the line and

format defaults are "multi", "%8d", and "%14.4f".

</P>

</HTML>

doc/thermo_modify.txt

+5 −25
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ thermo_modify command :h3 
thermo_modify keyword value ... :pre



one or more keyword/value pairs may be listed :ulb,l

keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press} or {drot} or {grot} :l

keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press}:l

  {lost} value = {error} or {warn} or {ignore}

  {norm} value = {yes} or {no}

  {flush} value = {yes} or {no}
@@ -23,8 +23,6 @@ keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press} 
    string = C-style format string

  {temp} value = compute ID that calculates a temperature

  {press} value = compute ID that calculates a pressure

  {drot} value = compute ID that calculates rotational energy for dipolar atoms

  {grot} value = compute ID that calculates rotational energy for granular atoms :pre

:ule



[Examples:]
@@ -107,24 +105,6 @@ the {temp} keyword comes before the {press} keyword, then the new 
pressure compute specified by the {press} keyword will be unaffected

by the {temp} setting.



The {drot} keyword is used to determine how rotational energy is

calculated for dipolar atoms, which is used by the thermo_style

keyword {drot}.  The specified compute ID must have been previously

defined by the user via the "compute"_compute.html command.  As

described in the "thermo_style"_thermo_style.html command, thermo

output has a default compute for this calculation with ID =

{thermo_rotate_dipole}.  This option allows the user to override the

default.



The {grot} keyword is used to determine how rotational energy is

calculated for granular atoms, which is used by the thermo_style

keyword {grot}.  The specified compute ID must have been previously

defined by the user via the "compute"_compute.html command.  As

described in the "thermo_style"_thermo_style.html command, thermo

output has a default compute for this calculation with ID =

{thermo_rotate_gran}.  This option allows the user to override the

default.



[Restrictions:] none



[Related commands:]
@@ -135,9 +115,9 @@ default. 


The option defaults are lost = error, norm = yes for unit style of

{lj}, norm = no for unit style of {real} and {metal}, flush = no,

temp/press/drot/grot = compute IDs defined by thermo_style.

temp/press = compute IDs defined by thermo_style.



The defaults for the line and format options depend on the thermo

style.  For styles "one", "granular", and "custom" the line and format

defaults are "one", "%8d", and "%12.8g".  For style "multi", the line

and format defaults are "multi", "%8d", and "%14.4f".
 
style.  For styles "one" and and "custom" the line and format defaults

are "one", "%8d", and "%12.8g".  For style "multi", the line and

format defaults are "multi", "%8d", and "%14.4f".

doc/thermo_style.html

+7 −40
Original line number Diff line number Diff line
@@ -15,13 +15,12 @@ 
</P>

<PRE>thermo_style style args 

</PRE>

<UL><LI>style = <I>one</I> or <I>multi</I> or <I>granular</I> or <I>custom</I> 

<UL><LI>style = <I>one</I> or <I>multi</I> or <I>custom</I> 



<LI>args = list of arguments for a particular style 



<PRE>  <I>one</I> args = none

  <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, etotal, enthalpy,
@@ -29,7 +28,6 @@ 
                          emol, elong, etail,

                          vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,

			  pxx, pyy, pzz, pxy, pxz, pyz

                          drot, grot,

			  c_ID, c_ID[n], f_ID, f_ID[n], v_name

      step = timestep

      atoms = # of atoms
@@ -54,8 +52,6 @@ 
      lx,ly,lz = box lengths in x,y,z

      xlo,xhi,ylo,yhi,zlo,zhi = box boundaries

      pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor

      drot = rotational energy of dipolar atoms

      grot = rotational energy of granular atoms

      c_ID = global scalar value calculated by a compute with ID

      c_ID[N] = Nth component of global vector calculated by a compute with ID

      f_ID = global scalar value calculated by a fix with ID
@@ -84,10 +80,6 @@ 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>

<P>Style <I>granular</I> is used with <A HREF = "atom_style.html">atom style</A> granular

and prints a one-line numeric summary that is the equivalent of

"thermo_style custom step atoms ke grot".

</P>

<P>Style <I>custom</I> is the most general setting and allows you to specify

which of the keywords listed above you want printed on each

thermodynamic timestep.  Note that the keywords c_ID, f_ID, v_name are
@@ -165,39 +157,14 @@ the ID of this compute is <I>thermo_pe</I> and the group is <I>all</I>. You can 
change the attributes of this potential energy via the

<A HREF = "compute_modify.html">compute_modify</A> command.

</P>

<P>The <I>drot</I> keyword requires a rotational energy to be computed for

point dipole particles.  To do this, a compute of style

"rotate/dipole" is created, as if this command had been issued:

</P>

<PRE>compute thermo_rotate_dipole all rotate/dipole 

</PRE>

<P>See the <A HREF = "compute_rotate_dipole.html">compute rotate/dipole</A> command for

details.  Note that the ID of the new compute is

<I>thermo_rotate_dipole</I> and the group is <I>all</I>.  You can change the

attributes of this computation via the

<A HREF = "compute_modify.html">compute_modify</A> command.  Alternatively, you can

directly assign a new compute which you have defined, to be used for

<I>drot</I>.  This is done via the <A HREF = "thermo_modify.html">thermo_modify</A>

command.  For example, this could be useful if you wish to exclude

certain particles from the computation.

</P>

<P>The <I>grot</I> keyword requires a rotational energy to be computed for

granular particles.  To do this, a compute of style "rotate/gran" is

created, as if this command had been issued:

</P>

<PRE>compute thermo_rotate_gran all rotate/gran 

</PRE>

<P>See the <A HREF = "compute_rotate_gran.html">compute rotate/gran</A> command for

details.  Note that the ID of the new compute is <I>thermo_rotate_gran</I>

and the group is <I>all</I>.  You can change the attributes of this

computation via the <A HREF = "compute_modify.html">compute_modify</A> command.

Alternatively, you can directly assign a new compute which you have

defined, to be used for <I>grot</I>.  This is done via the

<A HREF = "thermo_modify.html">thermo_modify</A> command.  For example, this could

be useful if you wish to exclude frozen particles from the computation.

</P>

<HR>



<P>The kinetic energy of the system <I>ke</I> is inferred from the temperature

of the system with 1/2 Kb T of energy for each degree of freedom.

Thus using different <A HREF = "compute.html">compute commands</A> for calculating

temperature, via the <A HREF = "thermo_modify.html">thermo_modify temp</A> command,

may yield different kinetic energies.

</P>

<P>The potential energy of the system <I>pe</I> will include contributions

from fixes if the <A HREF = "fix_modify.html">fix_modify thermo</A> option is set

for a fix that calculates such a contribution.  For example, the <A HREF = "fix_wall_lj93">fix

doc/thermo_style.txt

+7 −40
Original line number Diff line number Diff line
@@ -12,11 +12,10 @@ thermo_style command :h3 


thermo_style style args :pre



style = {one} or {multi} or {granular} or {custom} :ulb,l

style = {one} or {multi} or {custom} :ulb,l

args = list of arguments for a particular style :l

  {one} args = none

  {multi} args = none

  {granular} args = none

  {custom} args = list of attributes

    possible attributes = step, atoms, cpu, temp, press,

                          pe, ke, etotal, enthalpy,
@@ -24,7 +23,6 @@ args = list of arguments for a particular style :l 
                          emol, elong, etail,

                          vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,

			  pxx, pyy, pzz, pxy, pxz, pyz

                          drot, grot,

			  c_ID, c_ID\[n\], f_ID, f_ID\[n\], v_name

      step = timestep

      atoms = # of atoms
@@ -49,8 +47,6 @@ args = list of arguments for a particular style :l 
      lx,ly,lz = box lengths in x,y,z

      xlo,xhi,ylo,yhi,zlo,zhi = box boundaries

      pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor

      drot = rotational energy of dipolar atoms

      grot = rotational energy of granular atoms

      c_ID = global scalar value calculated by a compute with ID

      c_ID\[N\] = Nth component of global vector calculated by a compute with ID

      f_ID = global scalar value calculated by a fix with ID
@@ -78,10 +74,6 @@ 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.



Style {granular} is used with "atom style"_atom_style.html granular

and prints a one-line numeric summary that is the equivalent of

"thermo_style custom step atoms ke grot".



Style {custom} is the most general setting and allows you to specify

which of the keywords listed above you want printed on each

thermodynamic timestep.  Note that the keywords c_ID, f_ID, v_name are
@@ -159,39 +151,14 @@ the ID of this compute is {thermo_pe} and the group is {all}. You can 
change the attributes of this potential energy via the

"compute_modify"_compute_modify.html command.



The {drot} keyword requires a rotational energy to be computed for

point dipole particles.  To do this, a compute of style

"rotate/dipole" is created, as if this command had been issued:



compute thermo_rotate_dipole all rotate/dipole :pre



See the "compute rotate/dipole"_compute_rotate_dipole.html command for

details.  Note that the ID of the new compute is

{thermo_rotate_dipole} and the group is {all}.  You can change the

attributes of this computation via the

"compute_modify"_compute_modify.html command.  Alternatively, you can

directly assign a new compute which you have defined, to be used for

{drot}.  This is done via the "thermo_modify"_thermo_modify.html

command.  For example, this could be useful if you wish to exclude

certain particles from the computation.



The {grot} keyword requires a rotational energy to be computed for

granular particles.  To do this, a compute of style "rotate/gran" is

created, as if this command had been issued:



compute thermo_rotate_gran all rotate/gran :pre



See the "compute rotate/gran"_compute_rotate_gran.html command for

details.  Note that the ID of the new compute is {thermo_rotate_gran}

and the group is {all}.  You can change the attributes of this

computation via the "compute_modify"_compute_modify.html command.

Alternatively, you can directly assign a new compute which you have

defined, to be used for {grot}.  This is done via the

"thermo_modify"_thermo_modify.html command.  For example, this could

be useful if you wish to exclude frozen particles from the computation.



:line



The kinetic energy of the system {ke} is inferred from the temperature

of the system with 1/2 Kb T of energy for each degree of freedom.

Thus using different "compute commands"_compute.html for calculating

temperature, via the "thermo_modify temp"_thermo_modify.html command,

may yield different kinetic energies.



The potential energy of the system {pe} will include contributions

from fixes if the "fix_modify thermo"_fix_modify.html option is set

for a fix that calculates such a contribution.  For example, the "fix

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