From 2366287df6e7d26c9fad7db453da0babb8d0cd6e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 5 Sep 2013 22:59:35 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10723 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 15 ++++---- doc/Section_commands.txt | 2 ++ doc/compute.html | 2 ++ doc/compute.txt | 2 ++ doc/compute_erotate_rigid.html | 62 ++++++++++++++++++++++++++++++++++ doc/compute_erotate_rigid.txt | 57 +++++++++++++++++++++++++++++++ doc/compute_ke_rigid.html | 61 +++++++++++++++++++++++++++++++++ doc/compute_ke_rigid.txt | 56 ++++++++++++++++++++++++++++++ doc/fix.html | 2 ++ doc/fix.txt | 3 ++ 10 files changed, 255 insertions(+), 7 deletions(-) create mode 100644 doc/compute_erotate_rigid.html create mode 100644 doc/compute_erotate_rigid.txt create mode 100644 doc/compute_ke_rigid.html create mode 100644 doc/compute_ke_rigid.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 08d8a462d8..bbaf357629 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -427,13 +427,14 @@ each style or click on the style itself for a full description:
- - - - - - - + + + + + + +
angle/localatom/moleculebody/localbond/localcentro/atomcluster/atom
cna/atomcomcom/moleculecontact/atomcoord/atomdamage/atom
dihedral/localdisplace/atomerotate/asphereerotate/sphereerotate/sphere/atomevent/displace
group/groupgyrationgyration/moleculeheat/fluximproper/localinertia/molecule
keke/atommsdmsd/moleculemsd/nongausspair
pair/localpepe/atompressureproperty/atomproperty/local
property/moleculerdfreducereduce/regionslicestress/atom
temptemp/aspheretemp/comtemp/deformtemp/partialtemp/profile
temp/ramptemp/regiontemp/spheretivoronoi/atom +
dihedral/localdisplace/atomerotate/asphereerotate/rigiderotate/sphereerotate/sphere/atom
event/displacegroup/groupgyrationgyration/moleculeheat/fluximproper/local
inertia/moleculekeke/atomke/rigidmsdmsd/molecule
msd/nongausspairpair/localpepe/atompressure
property/atomproperty/localproperty/moleculerdfreducereduce/region
slicestress/atomtemptemp/aspheretemp/comtemp/deform
temp/partialtemp/profiletemp/ramptemp/regiontemp/sphereti
voronoi/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 341c90c1e4..f3979f7a72 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -625,6 +625,7 @@ each style or click on the style itself for a full description: "dihedral/local"_compute_dihedral_local.html, "displace/atom"_compute_displace_atom.html, "erotate/asphere"_compute_erotate_asphere.html, +"erotate/rigid"_compute_erotate_rigid.html, "erotate/sphere"_compute_erotate_sphere.html, "erotate/sphere/atom"_compute_erotate_sphere_atom.html, "event/displace"_compute_event_displace.html, @@ -636,6 +637,7 @@ each style or click on the style itself for a full description: "inertia/molecule"_compute_inertia_molecule.html, "ke"_compute_ke.html, "ke/atom"_compute_ke_atom.html, +"ke/rigid"_compute_ke_rigid.html, "msd"_compute_msd.html, "msd/molecule"_compute_msd_molecule.html, "msd/nongauss"_compute_msd_nongauss.html, diff --git a/doc/compute.html b/doc/compute.html index a7272cdfb7..53079c391e 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -182,6 +182,7 @@ available in LAMMPS:

  • dihedral/local - angle of each dihedral
  • displace/atom - displacement of each atom
  • erotate/asphere - rotational energy of aspherical particles +
  • erotate/rigid - rotational energy of rigid bodies
  • erotate/sphere - rotational energy of spherical particles
  • erotate/sphere/atom - rotational energy for each spherical particle
  • event/displace - detect event on atom displacement @@ -193,6 +194,7 @@ available in LAMMPS:
  • inertia/molecule - inertia tensor for each molecule
  • ke - translational kinetic energy
  • ke/atom - kinetic energy for each atom +
  • ke/rigid - translational kinetic energy of rigid bodies
  • msd - mean-squared displacement of group of atoms
  • msd/molecule - mean-squared displacement for each molecule
  • pair - values computed by a pair style diff --git a/doc/compute.txt b/doc/compute.txt index cc64d107ce..30be93b472 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -177,6 +177,7 @@ available in LAMMPS: "dihedral/local"_compute_dihedral_local.html - angle of each dihedral "displace/atom"_compute_displace_atom.html - displacement of each atom "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles +"erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle "event/displace"_compute_event_displace.html - detect event on atom displacement @@ -188,6 +189,7 @@ available in LAMMPS: "inertia/molecule"_compute_inertia_molecule.html - inertia tensor for each molecule "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom +"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/molecule"_compute_msd_molecule.html - mean-squared displacement for each molecule "pair"_compute_pair.html - values computed by a pair style diff --git a/doc/compute_erotate_rigid.html b/doc/compute_erotate_rigid.html new file mode 100644 index 0000000000..395b05bc29 --- /dev/null +++ b/doc/compute_erotate_rigid.html @@ -0,0 +1,62 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    compute erotate/rigid command +

    +

    Syntax: +

    +
    compute ID group-ID erotate/rigid fix-ID 
+
    + +

    Examples: +

    +
    compute 1 all erotate/rigid myRigid 
+
    +

    Description: +

    +

    Define a computation that calculates the rotational kinetic energy of +a collection of rigid bodies, as defined by one of the fix +rigid command variants. +

    +

    The rotational energy of each rigid body is computed as 1/2 I Wbody^2, +where I is the inertia tensor for the rigid body, and Wbody is its +angular velocity vector. Both I and Wbody are in the frame of +reference of the rigid body, i.e. I is diagonalized. +

    +

    The fix-ID should be the ID of one of the fix rigid +commands which defines the rigid bodies. The group specified in the +compute command is ignored. The rotational energy of all the rigid +bodies defined by the fix rigid command in included in the +calculation. +

    +

    Output info: +

    +

    This compute calculates a global scalar (the summed rotational energy +of all the rigid bodies). This value can be used by any command that +uses a global scalar value from a compute as input. See +Section_howto 15 for an overview of +LAMMPS output options. +

    +

    The scalar value calculated by this compute is "extensive". The +scalar value will be in energy units. +

    +

    Restrictions: none +

    +

    Related commands: +

    +

    compute ke/rigid +

    +

    Default: none +

    + diff --git a/doc/compute_erotate_rigid.txt b/doc/compute_erotate_rigid.txt new file mode 100644 index 0000000000..df64dd6f01 --- /dev/null +++ b/doc/compute_erotate_rigid.txt @@ -0,0 +1,57 @@ +"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 erotate/rigid command :h3 + +[Syntax:] + +compute ID group-ID erotate/rigid fix-ID :pre + +ID, group-ID are documented in "compute"_compute.html command +erotate/rigid = style name of this compute command +fix-ID = ID of rigid body fix :ul + +[Examples:] + +compute 1 all erotate/rigid myRigid :pre + +[Description:] + +Define a computation that calculates the rotational kinetic energy of +a collection of rigid bodies, as defined by one of the "fix +rigid"_fix_rigid.html command variants. + +The rotational energy of each rigid body is computed as 1/2 I Wbody^2, +where I is the inertia tensor for the rigid body, and Wbody is its +angular velocity vector. Both I and Wbody are in the frame of +reference of the rigid body, i.e. I is diagonalized. + +The {fix-ID} should be the ID of one of the "fix rigid"_fix_rigid.html +commands which defines the rigid bodies. The group specified in the +compute command is ignored. The rotational energy of all the rigid +bodies defined by the fix rigid command in included in the +calculation. + +[Output info:] + +This compute calculates a global scalar (the summed rotational energy +of all the rigid bodies). This value can be used by any command that +uses a global scalar value from a compute as input. See +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The scalar value calculated by this compute is "extensive". The +scalar value will be in energy "units"_units.html. + +[Restrictions:] none + +[Related commands:] + +"compute ke/rigid"_compute_erotate_ke_rigid.html + +[Default:] none diff --git a/doc/compute_ke_rigid.html b/doc/compute_ke_rigid.html new file mode 100644 index 0000000000..8767e75b4f --- /dev/null +++ b/doc/compute_ke_rigid.html @@ -0,0 +1,61 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    compute ke/rigid command +

    +

    Syntax: +

    +
    compute ID group-ID ke/rigid fix-ID 
+
    + +

    Examples: +

    +
    compute 1 all ke/rigid myRigid 
+
    +

    Description: +

    +

    Define a computation that calculates the translational kinetic energy +of a collection of rigid bodies, as defined by one of the fix +rigid command variants. +

    +

    The kinetic energy of each rigid body is computed as 1/2 M Vcm^2, +where M is the total mass of the rigid body, and Vcm is its +center-of-mass velocity. +

    +

    The fix-ID should be the ID of one of the fix rigid +commands which defines the rigid bodies. The group specified in the +compute command is ignored. The kinetic energy of all the rigid +bodies defined by the fix rigid command in included in the +calculation. +

    +

    Output info: +

    +

    This compute calculates a global scalar (the summed KE of all the +rigid bodies). This value can be used by any command that uses a +global scalar value from a compute as input. See Section_howto +15 for an overview of LAMMPS output +options. +

    +

    The scalar value calculated by this compute is "extensive". The +scalar value will be in energy units. +

    +

    Restrictions: none +

    +

    Related commands: +

    +

    compute erotate/rigid +

    +

    Default: none +

    + diff --git a/doc/compute_ke_rigid.txt b/doc/compute_ke_rigid.txt new file mode 100644 index 0000000000..c6deb9a6be --- /dev/null +++ b/doc/compute_ke_rigid.txt @@ -0,0 +1,56 @@ +"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 ke/rigid command :h3 + +[Syntax:] + +compute ID group-ID ke/rigid fix-ID :pre + +ID, group-ID are documented in "compute"_compute.html command +ke = style name of this compute command +fix-ID = ID of rigid body fix :ul + +[Examples:] + +compute 1 all ke/rigid myRigid :pre + +[Description:] + +Define a computation that calculates the translational kinetic energy +of a collection of rigid bodies, as defined by one of the "fix +rigid"_fix_rigid.html command variants. + +The kinetic energy of each rigid body is computed as 1/2 M Vcm^2, +where M is the total mass of the rigid body, and Vcm is its +center-of-mass velocity. + +The {fix-ID} should be the ID of one of the "fix rigid"_fix_rigid.html +commands which defines the rigid bodies. The group specified in the +compute command is ignored. The kinetic energy of all the rigid +bodies defined by the fix rigid command in included in the +calculation. + +[Output info:] + +This compute calculates a global scalar (the summed KE of all the +rigid bodies). This value can be used by any command that uses a +global scalar value from a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "extensive". The +scalar value will be in energy "units"_units.html. + +[Restrictions:] none + +[Related commands:] + +"compute erotate/rigid"_compute_erotate_rigid.html + +[Default:] none diff --git a/doc/fix.html b/doc/fix.html index a621c3eb2e..0f3c4118e6 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -217,6 +217,7 @@ list of fix styles available in LAMMPS:
  • pour - pour new atoms into a granular simulation domain
  • press/berendsen - pressure control by Berendsen barostat
  • print - print text and variables during a simulation +
  • property/atom - add customized per-atom values
  • reax/bonds - write out ReaxFF bond information recenter - constrain the center-of-mass position of a group of atoms
  • restrain - constrain a bond, angle, dihedral
  • rigid - constrain one or more clusters of atoms to move as a rigid body with NVE integration @@ -224,6 +225,7 @@ list of fix styles available in LAMMPS:
  • rigid/npt - constrain one or more clusters of atoms to move as a rigid body with NPT integration
  • rigid/nve - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
  • rigid/nvt - constrain one or more clusters of atoms to move as a rigid body with NVT integration +
  • rigid - constrain many small clusters of atoms to move as a rigid body with NVE integration
  • setforce - set the force on each atom
  • shake - SHAKE constraints on bonds and/or angles
  • spring - apply harmonic spring force to group of atoms diff --git a/doc/fix.txt b/doc/fix.txt index a077122c72..76b190048b 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -214,6 +214,7 @@ list of fix styles available in LAMMPS: "press/berendsen"_fix_press_berendsen.html - pressure control by \ Berendsen barostat "print"_fix_print.html - print text and variables during a simulation +"property/atom"_fix_property_atom.html - add customized per-atom values "reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \ "recenter"_fix_recenter.html - constrain the center-of-mass position \ of a group of atoms @@ -228,6 +229,8 @@ list of fix styles available in LAMMPS: move as a rigid body with alternate NVE integration "rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to \ move as a rigid body with NVT integration +"rigid"_fix_rigid.html - constrain many small clusters of atoms to \ + move as a rigid body with NVE integration "setforce"_fix_setforce.html - set the force on each atom "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles "spring"_fix_spring.html - apply harmonic spring force to group of atoms