From 05ccdfc1510c25a17698fe6a602d35fd6e74eeaf Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 1 Nov 2007 16:46:50 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1111 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 6 ++-- doc/Section_commands.txt | 1 + doc/compute.html | 11 ++++--- doc/compute.txt | 11 ++++--- doc/compute_modify.html | 14 +++++++-- doc/compute_modify.txt | 14 +++++++-- doc/compute_pe.html | 64 +++++++++++++++++++++++++++++++++++++++ doc/compute_pe.txt | 59 ++++++++++++++++++++++++++++++++++++ doc/compute_pressure.html | 20 ++++++++---- doc/compute_pressure.txt | 20 ++++++++---- doc/compute_temp.html | 7 +++++ doc/compute_temp.txt | 7 +++++ doc/thermo_style.html | 28 ++++++++++++----- doc/thermo_style.txt | 28 ++++++++++++----- 14 files changed, 249 insertions(+), 41 deletions(-) create mode 100644 doc/compute_pe.html create mode 100644 doc/compute_pe.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 8955246e6a..36193c7fab 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -334,9 +334,9 @@ description:

- - - + +
attribute/atomcentro/atomcoord/atomebond/atomepair/atomke/atom
pressurerotate/dipolerotate/granstress/atomsumsum/atom
temptemp/aspheretemp/deformtemp/dipoletemp/partialtemp/ramp
temp/regionvariablevariable/atom +
pepressurerotate/dipolerotate/granstress/atomsum
sum/atomtemptemp/aspheretemp/deformtemp/dipoletemp/partial
temp/ramptemp/regionvariablevariable/atom

These are compute styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index db4578bf83..292f723959 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -444,6 +444,7 @@ description: "ebond/atom"_compute_ebond_atom.html, "epair/atom"_compute_epair_atom.html, "ke/atom"_compute_ke_atom.html, +"pe"_compute_pe.html, "pressure"_compute_pressure.html, "rotate/dipole"_compute_rotate_dipole.html, "rotate/gran"_compute_rotate_gran.html, diff --git a/doc/compute.html b/doc/compute.html index 8453388b5c..7bd256009b 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -53,12 +53,14 @@ ave/spatial commands.

See this howto section for a summary of various LAMMPS output options.

-

LAMMPS creates its own global computes for thermodynamic output. Two -computes are always created, named "thermo_temp" and -"thermo_pressure", as if these commands had been invoked: +

LAMMPS creates its own global computes for thermodynamic output. +Three computes are always created, named "thermo_temp", +"thermo_pressure", and"thermo_pe", as if these commands had been +invoked in the input script: 

compute thermo_temp all temp
-compute thermo_pressure all pressure thermo_temp 
+compute thermo_pressure all pressure thermo_temp
+compute thermo_pe all pe

Additional computes are created if the thermo style requires it. See the documentation for the thermo_style command. @@ -92,6 +94,7 @@ defined in LAMMPS:

  • ebond/atom - bond energy for each atom
  • epair/atom - pairwise energy for each atom
  • ke/atom - kinetic energy for each atom +
  • pe - potential energy
  • pressure - total pressure and pressure tensor
  • rotate/dipole - rotational energy of dipolar atoms
  • rotate/gran - rotational energy of granular atoms diff --git a/doc/compute.txt b/doc/compute.txt index 01092a0876..d324e12cda 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -50,12 +50,14 @@ ave/spatial"_fix_ave_spatial.html commands. See this "howto section"_Section_howto.html#4_15 for a summary of various LAMMPS output options. -LAMMPS creates its own global computes for thermodynamic output. Two -computes are always created, named "thermo_temp" and -"thermo_pressure", as if these commands had been invoked: +LAMMPS creates its own global computes for thermodynamic output. +Three computes are always created, named "thermo_temp", +"thermo_pressure", and"thermo_pe", as if these commands had been +invoked in the input script: compute thermo_temp all temp -compute thermo_pressure all pressure thermo_temp :pre +compute thermo_pressure all pressure thermo_temp +compute thermo_pe all pe :pre Additional computes are created if the thermo style requires it. See the documentation for the "thermo_style"_thermo_style.html command. @@ -89,6 +91,7 @@ defined in LAMMPS: "ebond/atom"_compute_ebond_atom.html - bond energy for each atom "epair/atom"_compute_epair_atom.html - pairwise energy for each atom "ke/atom"_compute_ke_atom.html - kinetic energy for each atom +"pe"_compute_pe.html - potential energy "pressure"_compute_pressure.html - total pressure and pressure tensor "rotate/dipole"_compute_rotate_dipole.html - rotational energy of dipolar atoms "rotate/gran"_compute_rotate_gran.html - rotational energy of granular atoms diff --git a/doc/compute_modify.html b/doc/compute_modify.html index 176b74e1fb..8ca891cc89 100644 --- a/doc/compute_modify.html +++ b/doc/compute_modify.html @@ -24,7 +24,9 @@ 
      extra value = N
     N = # of extra degrees of freedom to subtract
   dynamic value = yes or no
-    yes/no = do or do not recompute the number of atoms contributing to the temperature 
+    yes/no = do or do not recompute the number of atoms contributing to the temperature
+  thermo value = yes or no
+    yes/no = do or do not add contributions from fixes to the potential energy
    @@ -53,6 +55,12 @@ deposit commands) or expect atoms to be lost (e.g. due to evaporation), then this option can be used to insure the temperature is correctly normalized.

    +

    The thermo keyword determines whether the potential energy +contribution calculated by some fixes is added to the +potential energy calculated by the compute. Only the compute of style +pe uses this option. See the doc pages for individual +fixes for details. +

    Restrictions: none

    Related commands: @@ -61,6 +69,8 @@ temperature is correctly normalized.

    Default:

    -

    The option defaults are extra = 3 and dynamic = no. +

    The option defaults are extra = 3 and dynamic = no. Thermo is yes if +the compute of style pe was defined with no extra keywords; otherwise +it is no.

    diff --git a/doc/compute_modify.txt b/doc/compute_modify.txt index 795c28cda2..293eef16d3 100644 --- a/doc/compute_modify.txt +++ b/doc/compute_modify.txt @@ -18,7 +18,9 @@ keyword = {extra} or {dynamic} :l {extra} value = N N = # of extra degrees of freedom to subtract {dynamic} value = {yes} or {no} - yes/no = do or do not recompute the number of atoms contributing to the temperature :pre + yes/no = do or do not recompute the number of atoms contributing to the temperature + {thermo} value = {yes} or {no} + yes/no = do or do not add contributions from fixes to the potential energy :pre :ule [Examples:] @@ -46,6 +48,12 @@ deposit"_fix_deposit.html commands) or expect atoms to be lost (e.g. due to evaporation), then this option can be used to insure the temperature is correctly normalized. +The {thermo} keyword determines whether the potential energy +contribution calculated by some "fixes"_fix.html is added to the +potential energy calculated by the compute. Only the compute of style +{pe} uses this option. See the doc pages for "individual +fixes"_fix.html for details. + [Restrictions:] none [Related commands:] @@ -54,4 +62,6 @@ temperature is correctly normalized. [Default:] -The option defaults are extra = 3 and dynamic = no. +The option defaults are extra = 3 and dynamic = no. Thermo is {yes} if +the compute of style {pe} was defined with no extra keywords; otherwise +it is {no}. diff --git a/doc/compute_pe.html b/doc/compute_pe.html new file mode 100644 index 0000000000..cf2033800d --- /dev/null +++ b/doc/compute_pe.html @@ -0,0 +1,64 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    compute pe command +

    +

    Syntax: +

    +
    compute ID group-ID pe keyword ... 
+
    + +

    Examples: +

    +
    compute 1 all pe
+compute molPE all bond angle dihedral improper 
+
    +

    Description: +

    +

    Define a computation that calculates the potential energy of the +entire system of atoms. The specified group must be "all". See the +compute epair/atom compute +ebond/atom or commands if you want per-atom +energies. These per-atom values could be summed for a group of atoms +via the compute sum command. +

    +

    The energy is calulated by the various pair, bond, etc potentials +defined for the simulation. If no extra keywords are listed, then the +potential energy is the sum of pair, bond, angle, dihedral, improper, +and kspace (long-range) energy. If any extra keywords are listed, +then only those components are summed to compute the potential energy. +

    +

    Various fixes can contribute to the total potential energy of the +system. See the doc pages for individual fixes for +details. The thermo option of the +compute_modify command determines whether these +contributions are added into the computed potential energy. If no +keywords are specified the default is yes. If any keywords are +specified, the default is no. +

    +

    A compute of this style with the ID of "thermo_pe" is created when +LAMMPS starts up, as if this command were in the input script: +

    +
    compute thermo_pe all pe 
+
    +

    See the "thermo_style" command for more details. +

    +

    Restrictions: none +

    +

    Related commands: none +

    +

    Default: none +

    + diff --git a/doc/compute_pe.txt b/doc/compute_pe.txt new file mode 100644 index 0000000000..e5f77a8b1f --- /dev/null +++ b/doc/compute_pe.txt @@ -0,0 +1,59 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute pe command :h3 + +[Syntax:] + +compute ID group-ID pe keyword ... :pre + +ID, group-ID are documented in "compute"_compute.html command +pe = style name of this compute command +zero of more keywords may be appended +keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} :ul + +[Examples:] + +compute 1 all pe +compute molPE all bond angle dihedral improper :pre + +[Description:] + +Define a computation that calculates the potential energy of the +entire system of atoms. The specified group must be "all". See the +"compute epair/atom"_compute_epair_atom.html "compute +ebond/atom"_compute_ebond_atom.html or commands if you want per-atom +energies. These per-atom values could be summed for a group of atoms +via the "compute sum"_compute_sum.html command. + +The energy is calulated by the various pair, bond, etc potentials +defined for the simulation. If no extra keywords are listed, then the +potential energy is the sum of pair, bond, angle, dihedral, improper, +and kspace (long-range) energy. If any extra keywords are listed, +then only those components are summed to compute the potential energy. + +Various fixes can contribute to the total potential energy of the +system. See the doc pages for "individual fixes"_fix.html for +details. The {thermo} option of the +"compute_modify"_compute_modify.html command determines whether these +contributions are added into the computed potential energy. If no +keywords are specified the default is {yes}. If any keywords are +specified, the default is {no}. + +A compute of this style with the ID of "thermo_pe" is created when +LAMMPS starts up, as if this command were in the input script: + +compute thermo_pe all pe :pre + +See the "thermo_style" command for more details. + +[Restrictions:] none + +[Related commands:] none + +[Default:] none diff --git a/doc/compute_pressure.html b/doc/compute_pressure.html index 5c68cec50f..af675c03ae 100644 --- a/doc/compute_pressure.html +++ b/doc/compute_pressure.html @@ -25,13 +25,13 @@

    Description:

    -

    Define a computation that calculates the pressure of atoms averaged -over the entire system. The specified group must be "all". See the -dump custom command for how to dump the per-atom stress -tensor if you want more localized information about pressure (stress) -in your system. +

    Define a computation that calculates the pressure of the entire system +of atoms. The specified group must be "all". See the compute +stress/atom command if you want per-atom +pressure (stress). These per-atom values could be summed for a group +of atoms via the compute sum command.

    -

    The pressure is computed by the standard formula +

    The pressure is computed by the formula

    @@ -62,6 +62,14 @@ excludes frozen atoms or other degrees of freedom. where the DOF is specified by the temperature compute. See the various compute temperature styles for details.

    +

    A compute of this style with the ID of "thermo_press" is created when +LAMMPS starts up, as if this command were in the input script: +

    +
    compute thermo_press all pressure thermo_temp 
+
    +

    where "thermo_temp" is the ID of a similarly defined compute of style +"temp". See the "thermo_style" command for more details. +

    Restrictions: none

    Related commands: diff --git a/doc/compute_pressure.txt b/doc/compute_pressure.txt index 726f658a31..830359bcd0 100644 --- a/doc/compute_pressure.txt +++ b/doc/compute_pressure.txt @@ -22,13 +22,13 @@ compute 1 all pressure myTemp :pre [Description:] -Define a computation that calculates the pressure of atoms averaged -over the entire system. The specified group must be "all". See the -"dump custom"_dump.html command for how to dump the per-atom stress -tensor if you want more localized information about pressure (stress) -in your system. +Define a computation that calculates the pressure of the entire system +of atoms. The specified group must be "all". See the "compute +stress/atom"_compute_stress_atom.html command if you want per-atom +pressure (stress). These per-atom values could be summed for a group +of atoms via the "compute sum"_compute_sum.html command. -The pressure is computed by the standard formula +The pressure is computed by the formula :c,image(Eqs/pressure.jpg) @@ -59,6 +59,14 @@ Note that the N is the above formula is really degrees-of-freedom/d where the DOF is specified by the temperature compute. See the various "compute temperature"_compute.html styles for details. +A compute of this style with the ID of "thermo_press" is created when +LAMMPS starts up, as if this command were in the input script: + +compute thermo_press all pressure thermo_temp :pre + +where "thermo_temp" is the ID of a similarly defined compute of style +"temp". See the "thermo_style" command for more details. + [Restrictions:] none [Related commands:] diff --git a/doc/compute_temp.html b/doc/compute_temp.html index cdad72776e..8e466ef4ae 100644 --- a/doc/compute_temp.html +++ b/doc/compute_temp.html @@ -51,6 +51,13 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    +

    A compute of this style with the ID of "thermo_temp" is created when +LAMMPS starts up, as if this command were in the input script: +

    +
    compute thermo_temp all temp 
+
    +

    See the "thermo_style" command for more details. +

    Restrictions: none

    Related commands: diff --git a/doc/compute_temp.txt b/doc/compute_temp.txt index 2bbe0bd249..a21c85cc4f 100644 --- a/doc/compute_temp.txt +++ b/doc/compute_temp.txt @@ -48,6 +48,13 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. +A compute of this style with the ID of "thermo_temp" is created when +LAMMPS starts up, as if this command were in the input script: + +compute thermo_temp all temp :pre + +See the "thermo_style" command for more details. + [Restrictions:] none [Related commands:] diff --git a/doc/thermo_style.html b/doc/thermo_style.html index 542d12bb92..82cae6b80c 100644 --- a/doc/thermo_style.html +++ b/doc/thermo_style.html @@ -123,7 +123,7 @@ use the thermo_modify command after it.

    Several of the thermodynamic quantities require a temperature to be computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc". By default this is done by using the "thermo_temp" compute which is -created by LAMMPS as if this command had been issued: +created when LAMMPS starts up, as if this command had been issued: 

    compute thermo_temp all temp
    @@ -137,9 +137,9 @@ calculating any thermodynamic quantity that requires a temperature. This is done via the thermo_modify command.

    Several of the thermodynamic quantities require a pressure to be -computed: "press", "enthalpy", "pxx etc", "pave". By default this is -done by using the "thermo_pressure" compute which is created by LAMMPS -as if this command had been issued: +computed: "press", "enthalpy", "pxx", etc. By default this is done by +using the "thermo_pressure" compute which is created when LAMMPS +starts up, as if this command had been issued: 

    compute thermo_pressure all pressure thermo_temp
    @@ -152,6 +152,18 @@ have defined, to be used for calculating any thermodynamic quantity that requires a pressure. This is done via the thermo_modify command.

    +

    Several of the thermodynamic quantities require a potential energy to +be computed: "pe", "etotal", "ebond", etc. This is done by using the +"thermo_pe" compute which is created when LAMMPS starts up, as if this +command had been issued: +

    +
    compute thermo_pe all pe 
+
    +

    See the compute pe command for details. Note that +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 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: @@ -186,9 +198,11 @@ be useful if you wish to exclude frozen particles from the compuation.

    The potential energy of the system pe will include contributions -from fixes if the fix_modify thermo option was set -for each fix. For example, the fix wall/lj93 fix will -contribute the energy of atoms interacting with the wall. +from fixes if the fix_modify thermo option is set +for a fix that calculates such a contribution. For example, the fix +wall/lj93 fix calculates the energy of atoms +interacting with the wall. See the doc pages for "individual fixes" +to see which ones contribute.

    A long-range tail correction etail for the VanderWaal pairwise energy will be non-zero only if the pair_modify diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt index fefecdd4e6..e131594f66 100644 --- a/doc/thermo_style.txt +++ b/doc/thermo_style.txt @@ -117,7 +117,7 @@ use the thermo_modify command after it. Several of the thermodynamic quantities require a temperature to be computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc". By default this is done by using the "thermo_temp" compute which is -created by LAMMPS as if this command had been issued: +created when LAMMPS starts up, as if this command had been issued: compute thermo_temp all temp :pre @@ -131,9 +131,9 @@ calculating any thermodynamic quantity that requires a temperature. This is done via the "thermo_modify"_thermo_modify.html command. Several of the thermodynamic quantities require a pressure to be -computed: "press", "enthalpy", "pxx etc", "pave". By default this is -done by using the "thermo_pressure" compute which is created by LAMMPS -as if this command had been issued: +computed: "press", "enthalpy", "pxx", etc. By default this is done by +using the "thermo_pressure" compute which is created when LAMMPS +starts up, as if this command had been issued: compute thermo_pressure all pressure thermo_temp :pre @@ -146,6 +146,18 @@ have defined, to be used for calculating any thermodynamic quantity that requires a pressure. This is done via the "thermo_modify"_thermo_modify.html command. +Several of the thermodynamic quantities require a potential energy to +be computed: "pe", "etotal", "ebond", etc. This is done by using the +"thermo_pe" compute which is created when LAMMPS starts up, as if this +command had been issued: + +compute thermo_pe all pe :pre + +See the "compute pe"_compute_pe.html command for details. Note that +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: @@ -180,9 +192,11 @@ be useful if you wish to exclude frozen particles from the compuation. :line The potential energy of the system {pe} will include contributions -from fixes if the "fix_modify thermo"_fix_modify.html option was set -for each fix. For example, the "fix wall/lj93"_fix_wall_lj93 fix will -contribute the energy of atoms interacting with the wall. +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 +wall/lj93"_fix_wall_lj93 fix calculates the energy of atoms +interacting with the wall. See the doc pages for "individual fixes" +to see which ones contribute. A long-range tail correction {etail} for the VanderWaal pairwise energy will be non-zero only if the "pair_modify