forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1609 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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@ -17,9 +17,8 @@
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</PRE>
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<UL><LI>one or more keyword/value pairs may be listed
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<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>
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<PRE> <I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
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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
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<I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
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<I>norm</I> value = <I>yes</I> or <I>no</I>
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<I>flush</I> value = <I>yes</I> or <I>no</I>
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<I>line</I> value = <I>one</I> or <I>multi</I>
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@ -28,9 +27,6 @@
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string = C-style format string
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<I>temp</I> value = compute ID that calculates a temperature
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<I>press</I> value = compute ID that calculates a pressure
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<I>drot</I> value = compute ID that calculates rotational energy for dipolar atoms
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<I>grot</I> value = compute ID that calculates rotational energy for granular atoms
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</PRE>
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</UL>
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<P><B>Examples:</B>
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@ -113,24 +109,6 @@ the <I>temp</I> keyword comes before the <I>press</I> keyword, then the new
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pressure compute specified by the <I>press</I> keyword will be unaffected
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by the <I>temp</I> setting.
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</P>
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<P>The <I>drot</I> keyword is used to determine how rotational energy is
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calculated for dipolar atoms, which is used by the thermo_style
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keyword <I>drot</I>. The specified compute ID must have been previously
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defined by the user via the <A HREF = "compute.html">compute</A> command. As
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described in the <A HREF = "thermo_style.html">thermo_style</A> command, thermo
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output has a default compute for this calculation with ID =
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<I>thermo_rotate_dipole</I>. This option allows the user to override the
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default.
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</P>
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<P>The <I>grot</I> keyword is used to determine how rotational energy is
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calculated for granular atoms, which is used by the thermo_style
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keyword <I>grot</I>. The specified compute ID must have been previously
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defined by the user via the <A HREF = "compute.html">compute</A> command. As
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described in the <A HREF = "thermo_style.html">thermo_style</A> command, thermo
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output has a default compute for this calculation with ID =
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<I>thermo_rotate_gran</I>. This option allows the user to override the
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default.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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@ -141,11 +119,11 @@ default.
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</P>
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<P>The option defaults are lost = error, norm = yes for unit style of
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<I>lj</I>, norm = no for unit style of <I>real</I> and <I>metal</I>, flush = no,
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temp/press/drot/grot = compute IDs defined by thermo_style.
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temp/press = compute IDs defined by thermo_style.
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</P>
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<P>The defaults for the line and format options depend on the thermo
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style. For styles "one", "granular", and "custom" the line and format
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defaults are "one", "%8d", and "%12.8g". For style "multi", the line
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and format defaults are "multi", "%8d", and "%14.4f".
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style. For styles "one" and and "custom" the line and format defaults
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are "one", "%8d", and "%12.8g". For style "multi", the line and
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format defaults are "multi", "%8d", and "%14.4f".
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</P>
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</HTML>
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@ -13,7 +13,7 @@ thermo_modify command :h3
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thermo_modify keyword value ... :pre
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one or more keyword/value pairs may be listed :ulb,l
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keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press} or {drot} or {grot} :l
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keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press}:l
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{lost} value = {error} or {warn} or {ignore}
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{norm} value = {yes} or {no}
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{flush} value = {yes} or {no}
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@ -23,8 +23,6 @@ keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press}
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string = C-style format string
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{temp} value = compute ID that calculates a temperature
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{press} value = compute ID that calculates a pressure
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{drot} value = compute ID that calculates rotational energy for dipolar atoms
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{grot} value = compute ID that calculates rotational energy for granular atoms :pre
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:ule
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[Examples:]
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@ -107,24 +105,6 @@ the {temp} keyword comes before the {press} keyword, then the new
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pressure compute specified by the {press} keyword will be unaffected
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by the {temp} setting.
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The {drot} keyword is used to determine how rotational energy is
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calculated for dipolar atoms, which is used by the thermo_style
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keyword {drot}. The specified compute ID must have been previously
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defined by the user via the "compute"_compute.html command. As
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described in the "thermo_style"_thermo_style.html command, thermo
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output has a default compute for this calculation with ID =
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{thermo_rotate_dipole}. This option allows the user to override the
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default.
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The {grot} keyword is used to determine how rotational energy is
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calculated for granular atoms, which is used by the thermo_style
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keyword {grot}. The specified compute ID must have been previously
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defined by the user via the "compute"_compute.html command. As
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described in the "thermo_style"_thermo_style.html command, thermo
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output has a default compute for this calculation with ID =
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{thermo_rotate_gran}. This option allows the user to override the
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default.
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[Restrictions:] none
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[Related commands:]
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@ -135,9 +115,9 @@ default.
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The option defaults are lost = error, norm = yes for unit style of
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{lj}, norm = no for unit style of {real} and {metal}, flush = no,
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temp/press/drot/grot = compute IDs defined by thermo_style.
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temp/press = compute IDs defined by thermo_style.
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The defaults for the line and format options depend on the thermo
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style. For styles "one", "granular", and "custom" the line and format
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defaults are "one", "%8d", and "%12.8g". For style "multi", the line
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and format defaults are "multi", "%8d", and "%14.4f".
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style. For styles "one" and and "custom" the line and format defaults
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are "one", "%8d", and "%12.8g". For style "multi", the line and
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format defaults are "multi", "%8d", and "%14.4f".
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@ -15,13 +15,12 @@
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</P>
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<PRE>thermo_style style args
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</PRE>
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<UL><LI>style = <I>one</I> or <I>multi</I> or <I>granular</I> or <I>custom</I>
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<UL><LI>style = <I>one</I> or <I>multi</I> or <I>custom</I>
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<LI>args = list of arguments for a particular style
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<PRE> <I>one</I> args = none
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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,
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pe, ke, etotal, enthalpy,
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emol, elong, etail,
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vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
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pxx, pyy, pzz, pxy, pxz, pyz
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drot, grot,
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c_ID, c_ID[n], f_ID, f_ID[n], v_name
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step = timestep
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atoms = # of atoms
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@ -54,8 +52,6 @@
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lx,ly,lz = box lengths in x,y,z
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xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
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pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
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drot = rotational energy of dipolar atoms
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grot = rotational energy of granular atoms
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c_ID = global scalar value calculated by a compute with ID
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c_ID[N] = Nth component of global vector calculated by a compute with ID
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f_ID = global scalar value calculated by a fix with ID
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@ -84,10 +80,6 @@ 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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<P>Style <I>granular</I> is used with <A HREF = "atom_style.html">atom style</A> granular
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and prints a one-line numeric summary that is the equivalent of
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"thermo_style custom step atoms ke grot".
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</P>
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<P>Style <I>custom</I> is the most general setting and allows you to specify
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which of the keywords listed above you want printed on each
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thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are
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@ -165,39 +157,14 @@ the ID of this compute is <I>thermo_pe</I> and the group is <I>all</I>. You can
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change the attributes of this potential energy via the
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<A HREF = "compute_modify.html">compute_modify</A> command.
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</P>
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<P>The <I>drot</I> keyword requires a rotational energy to be computed for
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point dipole particles. To do this, a compute of style
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"rotate/dipole" is created, as if this command had been issued:
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</P>
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<PRE>compute thermo_rotate_dipole all rotate/dipole
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</PRE>
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<P>See the <A HREF = "compute_rotate_dipole.html">compute rotate/dipole</A> command for
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details. Note that the ID of the new compute is
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<I>thermo_rotate_dipole</I> and the group is <I>all</I>. You can change the
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attributes of this computation via the
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<A HREF = "compute_modify.html">compute_modify</A> command. Alternatively, you can
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directly assign a new compute which you have defined, to be used for
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<I>drot</I>. This is done via the <A HREF = "thermo_modify.html">thermo_modify</A>
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command. For example, this could be useful if you wish to exclude
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certain particles from the computation.
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</P>
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<P>The <I>grot</I> keyword requires a rotational energy to be computed for
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granular particles. To do this, a compute of style "rotate/gran" is
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created, as if this command had been issued:
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</P>
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<PRE>compute thermo_rotate_gran all rotate/gran
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</PRE>
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<P>See the <A HREF = "compute_rotate_gran.html">compute rotate/gran</A> command for
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details. Note that the ID of the new compute is <I>thermo_rotate_gran</I>
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and the group is <I>all</I>. You can change the attributes of this
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computation via the <A HREF = "compute_modify.html">compute_modify</A> command.
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Alternatively, you can directly assign a new compute which you have
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defined, to be used for <I>grot</I>. This is done via the
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<A HREF = "thermo_modify.html">thermo_modify</A> command. For example, this could
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be useful if you wish to exclude frozen particles from the computation.
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</P>
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<HR>
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<P>The kinetic energy of the system <I>ke</I> is inferred from the temperature
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of the system with 1/2 Kb T of energy for each degree of freedom.
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Thus using different <A HREF = "compute.html">compute commands</A> for calculating
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temperature, via the <A HREF = "thermo_modify.html">thermo_modify temp</A> command,
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may yield different kinetic energies.
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</P>
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<P>The potential energy of the system <I>pe</I> will include contributions
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from fixes if the <A HREF = "fix_modify.html">fix_modify thermo</A> option is set
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for a fix that calculates such a contribution. For example, the <A HREF = "fix_wall_lj93">fix
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@ -12,11 +12,10 @@ thermo_style command :h3
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thermo_style style args :pre
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style = {one} or {multi} or {granular} or {custom} :ulb,l
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style = {one} or {multi} or {custom} :ulb,l
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args = list of arguments for a particular style :l
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{one} args = none
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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,
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pe, ke, etotal, enthalpy,
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@ -24,7 +23,6 @@ args = list of arguments for a particular style :l
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emol, elong, etail,
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vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
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pxx, pyy, pzz, pxy, pxz, pyz
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drot, grot,
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c_ID, c_ID\[n\], f_ID, f_ID\[n\], v_name
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step = timestep
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atoms = # of atoms
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@ -49,8 +47,6 @@ args = list of arguments for a particular style :l
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lx,ly,lz = box lengths in x,y,z
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xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
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pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
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drot = rotational energy of dipolar atoms
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grot = rotational energy of granular atoms
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c_ID = global scalar value calculated by a compute with ID
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c_ID\[N\] = Nth component of global vector calculated by a compute with ID
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f_ID = global scalar value calculated by a fix with ID
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@ -78,10 +74,6 @@ 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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Style {granular} is used with "atom style"_atom_style.html granular
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and prints a one-line numeric summary that is the equivalent of
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"thermo_style custom step atoms ke grot".
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Style {custom} is the most general setting and allows you to specify
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which of the keywords listed above you want printed on each
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thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are
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@ -159,39 +151,14 @@ the ID of this compute is {thermo_pe} and the group is {all}. You can
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change the attributes of this potential energy via the
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"compute_modify"_compute_modify.html command.
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The {drot} keyword requires a rotational energy to be computed for
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point dipole particles. To do this, a compute of style
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"rotate/dipole" is created, as if this command had been issued:
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compute thermo_rotate_dipole all rotate/dipole :pre
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See the "compute rotate/dipole"_compute_rotate_dipole.html command for
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details. Note that the ID of the new compute is
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{thermo_rotate_dipole} and the group is {all}. You can change the
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attributes of this computation via the
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"compute_modify"_compute_modify.html command. Alternatively, you can
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directly assign a new compute which you have defined, to be used for
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{drot}. This is done via the "thermo_modify"_thermo_modify.html
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command. For example, this could be useful if you wish to exclude
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certain particles from the computation.
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The {grot} keyword requires a rotational energy to be computed for
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granular particles. To do this, a compute of style "rotate/gran" is
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created, as if this command had been issued:
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compute thermo_rotate_gran all rotate/gran :pre
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See the "compute rotate/gran"_compute_rotate_gran.html command for
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details. Note that the ID of the new compute is {thermo_rotate_gran}
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and the group is {all}. You can change the attributes of this
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computation via the "compute_modify"_compute_modify.html command.
|
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Alternatively, you can directly assign a new compute which you have
|
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defined, to be used for {grot}. This is done via the
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"thermo_modify"_thermo_modify.html command. For example, this could
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be useful if you wish to exclude frozen particles from the computation.
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|
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:line
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The kinetic energy of the system {ke} is inferred from the temperature
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of the system with 1/2 Kb T of energy for each degree of freedom.
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Thus using different "compute commands"_compute.html for calculating
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temperature, via the "thermo_modify temp"_thermo_modify.html command,
|
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may yield different kinetic energies.
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The potential energy of the system {pe} will include contributions
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from fixes if the "fix_modify thermo"_fix_modify.html option is set
|
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for a fix that calculates such a contribution. For example, the "fix
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|
|
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Reference in New Issue