diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html index 3b0a13f751..3b01d0ede2 100644 --- a/doc/html/Section_commands.html +++ b/doc/html/Section_commands.html @@ -619,13 +619,13 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

+--++- @@ -696,72 +696,72 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

- + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + -
adapt nvt/sllod (io) nvt/sphere (o) onewayorient/fccorient/bccorient/fcc planeforcepoems
pour
poemspour press/berendsen print property/atom qeq/comb (o) qeq/dynamic qeq/fireqeq/point
qeq/shielded
qeq/pointqeq/shielded qeq/slater rattle reax/bonds recenter restrain rigid (o)rigid/nph (o)
rigid/npt (o)
rigid/nph (o)rigid/npt (o) rigid/nve (o) rigid/nvt (o) rigid/small (o) rigid/small/nph rigid/small/npt rigid/small/nverigid/small/nvt
setforce (k)
rigid/small/nvtsetforce (k) shake spring spring/chunk spring/rg spring/self srdstore/force
store/state
store/forcestore/state temp/berendsen temp/csld temp/csvr temp/rescale tfmc thermal/conductivitytmd
ttm
tmdttm tune/kspace vector viscosity viscous wall/colloid wall/granwall/harmonic
wall/lj1043
wall/harmonicwall/lj1043 wall/lj126 wall/lj93 wall/piston wall/reflect (k) wall/region wall/srd 
diff --git a/doc/html/_sources/Section_commands.txt b/doc/html/_sources/Section_commands.txt index 2fbb8287b8..958b72d815 100644 --- a/doc/html/_sources/Section_commands.txt +++ b/doc/html/_sources/Section_commands.txt @@ -457,37 +457,37 @@ with the :doc:`appropriate accelerated package `. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`adapt ` | :doc:`addforce ` | :doc:`append/atoms ` | :doc:`atom/swap ` | :doc:`aveforce ` | :doc:`ave/atom ` | :doc:`ave/chunk ` | :doc:`ave/correlate ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`ave/histo ` | :doc:`ave/histo/weight ` | :doc:`ave/time ` | :doc:`balance ` | :doc:`bond/break ` | :doc:`bond/create ` | :doc:`bond/swap ` | :doc:`box/relax ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`deform (k) ` | :doc:`deposit ` | :doc:`drag ` | :doc:`dt/reset ` | :doc:`efield ` | :doc:`ehex ` | :doc:`enforce2d ` | :doc:`evaporate ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`external ` | :doc:`freeze ` | :doc:`gcmc ` | :doc:`gld ` | :doc:`gravity (o) ` | :doc:`heat ` | :doc:`indent ` | :doc:`langevin (k) ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`lineforce ` | :doc:`momentum ` | :doc:`move ` | :doc:`msst ` | :doc:`neb ` | :doc:`nph (ko) ` | :doc:`nphug (o) ` | :doc:`nph/asphere (o) ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`nph/body ` | :doc:`nph/sphere (o) ` | :doc:`npt (kio) ` | :doc:`npt/asphere (o) ` | :doc:`npt/body ` | :doc:`npt/sphere (o) ` | :doc:`nve (kio) ` | :doc:`nve/asphere (i) ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`nve/asphere/noforce ` | :doc:`nve/body ` | :doc:`nve/limit ` | :doc:`nve/line ` | :doc:`nve/noforce ` | :doc:`nve/sphere (o) ` | :doc:`nve/tri ` | :doc:`nvt (iko) ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`nvt/asphere (o) ` | :doc:`nvt/body ` | :doc:`nvt/sllod (io) ` | :doc:`nvt/sphere (o) ` | :doc:`oneway ` | :doc:`orient/fcc ` | :doc:`planeforce ` | :doc:`poems ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`pour ` | :doc:`press/berendsen ` | :doc:`print ` | :doc:`property/atom ` | :doc:`qeq/comb (o) ` | :doc:`qeq/dynamic ` | :doc:`qeq/fire ` | :doc:`qeq/point ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`qeq/shielded ` | :doc:`qeq/slater ` | :doc:`rattle ` | :doc:`reax/bonds ` | :doc:`recenter ` | :doc:`restrain ` | :doc:`rigid (o) ` | :doc:`rigid/nph (o) ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`rigid/npt (o) ` | :doc:`rigid/nve (o) ` | :doc:`rigid/nvt (o) ` | :doc:`rigid/small (o) ` | :doc:`rigid/small/nph ` | :doc:`rigid/small/npt ` | :doc:`rigid/small/nve ` | :doc:`rigid/small/nvt ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`setforce (k) ` | :doc:`shake ` | :doc:`spring ` | :doc:`spring/chunk ` | :doc:`spring/rg ` | :doc:`spring/self ` | :doc:`srd ` | :doc:`store/force ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`store/state ` | :doc:`temp/berendsen ` | :doc:`temp/csld ` | :doc:`temp/csvr ` | :doc:`temp/rescale ` | :doc:`tfmc ` | :doc:`thermal/conductivity ` | :doc:`tmd ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`ttm ` | :doc:`tune/kspace ` | :doc:`vector ` | :doc:`viscosity ` | :doc:`viscous ` | :doc:`wall/colloid ` | :doc:`wall/gran ` | :doc:`wall/harmonic ` | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ -| :doc:`wall/lj1043 ` | :doc:`wall/lj126 ` | :doc:`wall/lj93 ` | :doc:`wall/piston ` | :doc:`wall/reflect (k) ` | :doc:`wall/region ` | :doc:`wall/srd ` | | -+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+ ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`adapt ` | :doc:`addforce ` | :doc:`append/atoms ` | :doc:`atom/swap ` | :doc:`aveforce ` | :doc:`ave/atom ` | :doc:`ave/chunk ` | :doc:`ave/correlate ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`ave/histo ` | :doc:`ave/histo/weight ` | :doc:`ave/time ` | :doc:`balance ` | :doc:`bond/break ` | :doc:`bond/create ` | :doc:`bond/swap ` | :doc:`box/relax ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`deform (k) ` | :doc:`deposit ` | :doc:`drag ` | :doc:`dt/reset ` | :doc:`efield ` | :doc:`ehex ` | :doc:`enforce2d ` | :doc:`evaporate ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`external ` | :doc:`freeze ` | :doc:`gcmc ` | :doc:`gld ` | :doc:`gravity (o) ` | :doc:`heat ` | :doc:`indent ` | :doc:`langevin (k) ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`lineforce ` | :doc:`momentum ` | :doc:`move ` | :doc:`msst ` | :doc:`neb ` | :doc:`nph (ko) ` | :doc:`nphug (o) ` | :doc:`nph/asphere (o) ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`nph/body ` | :doc:`nph/sphere (o) ` | :doc:`npt (kio) ` | :doc:`npt/asphere (o) ` | :doc:`npt/body ` | :doc:`npt/sphere (o) ` | :doc:`nve (kio) ` | :doc:`nve/asphere (i) ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`nve/asphere/noforce ` | :doc:`nve/body ` | :doc:`nve/limit ` | :doc:`nve/line ` | :doc:`nve/noforce ` | :doc:`nve/sphere (o) ` | :doc:`nve/tri ` | :doc:`nvt (iko) ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`nvt/asphere (o) ` | :doc:`nvt/body ` | :doc:`nvt/sllod (io) ` | :doc:`nvt/sphere (o) ` | :doc:`oneway ` | :doc:`orient/bcc ` | :doc:`orient/fcc ` | :doc:`planeforce ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`poems ` | :doc:`pour ` | :doc:`press/berendsen ` | :doc:`print ` | :doc:`property/atom ` | :doc:`qeq/comb (o) ` | :doc:`qeq/dynamic ` | :doc:`qeq/fire ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`qeq/point ` | :doc:`qeq/shielded ` | :doc:`qeq/slater ` | :doc:`rattle ` | :doc:`reax/bonds ` | :doc:`recenter ` | :doc:`restrain ` | :doc:`rigid (o) ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`rigid/nph (o) ` | :doc:`rigid/npt (o) ` | :doc:`rigid/nve (o) ` | :doc:`rigid/nvt (o) ` | :doc:`rigid/small (o) ` | :doc:`rigid/small/nph ` | :doc:`rigid/small/npt ` | :doc:`rigid/small/nve ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`rigid/small/nvt ` | :doc:`setforce (k) ` | :doc:`shake ` | :doc:`spring ` | :doc:`spring/chunk ` | :doc:`spring/rg ` | :doc:`spring/self ` | :doc:`srd ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`store/force ` | :doc:`store/state ` | :doc:`temp/berendsen ` | :doc:`temp/csld ` | :doc:`temp/csvr ` | :doc:`temp/rescale ` | :doc:`tfmc ` | :doc:`thermal/conductivity ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`tmd ` | :doc:`ttm ` | :doc:`tune/kspace ` | :doc:`vector ` | :doc:`viscosity ` | :doc:`viscous ` | :doc:`wall/colloid ` | :doc:`wall/gran ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ +| :doc:`wall/harmonic ` | :doc:`wall/lj1043 ` | :doc:`wall/lj126 ` | :doc:`wall/lj93 ` | :doc:`wall/piston ` | :doc:`wall/reflect (k) ` | :doc:`wall/region ` | :doc:`wall/srd ` | ++------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+ These are additional fix styles in USER packages, which can be used if :ref:`LAMMPS is built with the appropriate package `. diff --git a/doc/html/_sources/fix.txt b/doc/html/_sources/fix.txt index 2914668e6a..1a94179199 100644 --- a/doc/html/_sources/fix.txt +++ b/doc/html/_sources/fix.txt @@ -226,7 +226,8 @@ of :ref:`this page `. * :doc:`nvt/sllod ` - NVT for NEMD with SLLOD equations * :doc:`nvt/sphere ` - NVT for spherical particles * :doc:`oneway ` - constrain particles on move in one direction -* :doc:`orient/fcc ` - add grain boundary migration force +* :doc:`orient/bcc ` - add grain boundary migration force for BCC +* :doc:`orient/fcc ` - add grain boundary migration force for FCC * :doc:`planeforce ` - constrain atoms to move in a plane * :doc:`poems ` - constrain clusters of atoms to move as coupled rigid bodies * :doc:`pour ` - pour new atoms/molecules into a granular simulation domain diff --git a/doc/html/_sources/fix_orient.txt b/doc/html/_sources/fix_orient.txt index e7fa7c23fc..c7418d470f 100644 --- a/doc/html/_sources/fix_orient.txt +++ b/doc/html/_sources/fix_orient.txt @@ -3,14 +3,18 @@ fix orient/fcc command ====================== +fix orient/bcc command +====================== + .. parsed-literal:: fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1 + fix ID group-ID orient/bcc nstats dir alat dE cutlo cuthi file0 file1 * ID, group-ID are documented in :doc:`fix ` command * nstats = print stats every this many steps, 0 = never * dir = 0/1 for which crystal is used as reference -* alat = fcc cubic lattice constant (distance units) +* alat = fcc/bcc cubic lattice constant (distance units) * dE = energy added to each atom (energy units) * cutlo,cuthi = values between 0.0 and 1.0, cutlo < cuthi * file0,file1 = files that specify orientation of each grain @@ -21,6 +25,7 @@ Examples .. parsed-literal:: fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec + fix gb all orient/bcc 0 1 2.882 0.001 0.25 0.75 ngb.left ngb.right Description """"""""""" @@ -29,8 +34,9 @@ The fix applies an orientation-dependent force to atoms near a planar grain boundary which can be used to induce grain boundary migration (in the direction perpendicular to the grain boundary plane). The motivation and explanation of this force and its application are -described in :ref:`(Janssens) `. The force is only applied to -atoms in the fix group. +described in :ref:`(Janssens) `. The adaptiation to bcc crystals +is described in :ref:`(Wicaksono1) `. The computed force is only +applied to atoms in the fix group. The basic idea is that atoms in one grain (on one side of the boundary) have a potential energy dE added to them. Atoms in the @@ -53,19 +59,21 @@ The potential energy added to atom I is given by these formulas .. image:: Eqs/fix_orient_fcc.jpg :align: center -which are fully explained in :ref:`(Janssens) `. The order -parameter Xi for atom I in equation (1) is a sum over the 12 nearest -neighbors of atom I. Rj is the vector from atom I to its neighbor J, -and RIj is a vector in the reference (perfect) crystal. That is, if -dir = 0/1, then RIj is a vector to an atom coord from file 0/1. -Equation (2) gives the expected value of the order parameter XiIJ in -the other grain. Hi and lo cutoffs are defined in equations (3) and -(4), using the input parameters *cutlo* and *cuthi* as thresholds to -avoid adding grain boundary energy when the deviation in the order -parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a -perfect crystal). The added potential energy Ui for atom I is given -in equation (6) where it is interpolated between 0 and dE using the -two threshold Xi values and the Wi value of equation (5). +which are fully explained in :ref:`(Janssens) `. For fcc crystals +this order parameter Xi for atom I in equation (1) is a sum over the +12 nearest neighbors of atom I. For bcc crystals it is the +corresponding sum of the 8 nearest neighbors. Rj is the vector from +atom I to its neighbor J, and RIj is a vector in the reference +(perfect) crystal. That is, if dir = 0/1, then RIj is a vector to an +atom coord from file 0/1. Equation (2) gives the expected value of +the order parameter XiIJ in the other grain. Hi and lo cutoffs are +defined in equations (3) and (4), using the input parameters *cutlo* +and *cuthi* as thresholds to avoid adding grain boundary energy when +the deviation in the order parameter from 0 or 1 is small (e.g. due to +thermal fluctuations in a perfect crystal). The added potential +energy Ui for atom I is given in equation (6) where it is interpolated +between 0 and dE using the two threshold Xi values and the Wi value of +equation (5). The derivative of this energy expression gives the force on each atom which thus depends on the orientation of its neighbors relative to the @@ -84,14 +92,14 @@ expense of the other. A value of 0 means the first grain will shrink; a value of 1 means it will grow. This assumes that *dE* is positive. The reverse will be true if *dE* is negative. -The *alat* parameter is the cubic lattice constant for the fcc +The *alat* parameter is the cubic lattice constant for the fcc or bcc material and is only used to compute a cutoff distance of 1.57 * alat -/ sqrt(2) for finding the 12 nearest neighbors of each atom (which -should be valid for an fcc crystal). A longer/shorter cutoff can be -imposed by adjusting *alat*\ . If a particular atom has less than 12 -neighbors within the cutoff, the order parameter of equation (1) is -effectively multiplied by 12 divided by the actual number of neighbors -within the cutoff. +/ sqrt(2) for finding the 12 or 8 nearest neighbors of each atom +(which should be valid for an fcc or bcc crystal). A longer/shorter +cutoff can be imposed by adjusting *alat*\ . If a particular atom has +less than 12 or 8 neighbors within the cutoff, the order parameter of +equation (1) is effectively multiplied by 12 or 8 divided by the +actual number of neighbors within the cutoff. The *dE* parameter is the maximum amount of additional energy added to each atom in the grain which wants to shrink. @@ -113,7 +121,8 @@ orientation. The vector lengths should all be identical since an fcc lattice has a coordination number of 12. Only 6 are listed due to symmetry, so the list must include one from each pair of equal-and-opposite neighbors. A pair of orientation files for a -Sigma=5 tilt boundary are show below. +Sigma=5 tilt boundary are shown below. A tutorial that can help for +writing the orientation files is given in :ref:`(Wicaksono2) ` Restart, fix_modify, output, run start/stop, minimize info """""""""""""""""""""""""""""""""""""""""""""""""""""""""" @@ -145,7 +154,7 @@ Restrictions This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. -This fix should only be used with fcc lattices. +This fix should only be used with fcc or bcc lattices. Related commands """""""""""""""" @@ -165,6 +174,20 @@ Related commands **(Janssens)** Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature Materials, 5, 124-127 (2006). +.. _Wicaksono1: + + + +**(Wicaksono1)** Wicaksono, Sinclair, Militzer, Computational Materials +Science, 117, 397-405 (2016). + +.. _Wicaksono2: + + + +**(Wicaksono2)** Wicaksono, figshare, +https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (2015). + ---------- diff --git a/doc/html/_sources/kspace_modify.txt b/doc/html/_sources/kspace_modify.txt index c2c406b144..f340182943 100644 --- a/doc/html/_sources/kspace_modify.txt +++ b/doc/html/_sources/kspace_modify.txt @@ -189,6 +189,15 @@ supported by Ewald or PPPM when using a triclinic simulation cell. The slab correction has also been extended to point dipole interactions :ref:`(Klapp) ` in :doc:`kspace_style ` *ewald/disp*\ . +.. note:: + + If you wish to apply an electric field in the Z-direction, in + conjunction with the *slab* keyword, you should do it by adding + explicit charged particles to the +/- Z surfaces. If you do it via + the :doc:`fix efield ` command, it will not give the correct + dielectric constant due to the Yeh/Berkowitz :ref:`(Yeh) ` correction + not being compatible with how :doc:`fix efield ` works. + The *compute* keyword allows Kspace computations to be turned off, even though a :doc:`kspace_style ` is defined. This is not useful for running a real simulation, but can be useful for diff --git a/doc/html/_sources/read_data.txt b/doc/html/_sources/read_data.txt index 4f179e0646..2f03a1aa8f 100644 --- a/doc/html/_sources/read_data.txt +++ b/doc/html/_sources/read_data.txt @@ -1239,7 +1239,7 @@ script. *Triangles* section: * one line per triangle -* line syntax: atom-ID x1 y1 x2 y2 +* line syntax: atom-ID x1 y1 z1 x2 y2 z2 x3 y3 z3 .. parsed-literal:: atom-ID = ID of atom which is a line segment diff --git a/doc/html/_sources/read_restart.txt b/doc/html/_sources/read_restart.txt index 7eb2a4b629..632a90d3a8 100644 --- a/doc/html/_sources/read_restart.txt +++ b/doc/html/_sources/read_restart.txt @@ -147,6 +147,7 @@ script that reads the restart file, though you can redefine many of these settings after the restart file is read. * :doc:`units ` +* :doc:`newton bond ` (see discussion of newton command below) * :doc:`atom style ` and :doc:`atom_modify ` settings id, map, sort * :doc:`comm style ` and `comm_modify `_ settings mode, cutoff, vel * :doc:`timestep ` @@ -163,6 +164,7 @@ Here is a list of information not stored in a restart file, which means you must re-issue these commands in your input script, after reading the restart file. +* :doc:`newton pair ` (see discussion of newton command below) * :doc:`fix ` commands (see below) * :doc:`compute ` commands (see below) * :doc:`variable ` commands @@ -171,6 +173,16 @@ reading the restart file. * :doc:`kspace_style ` and :doc:`kspace_modify ` settings * info for :doc:`thermodynamic `, :doc:`dump `, or :doc:`restart ` output +The :doc:`newton ` command has two settings, one for pairwise +interactions, the other for bonded. Both settings are stored in the +restart file. For the bond setting, the value in the file will +overwrite the current value (at the time the read_restart command is +issued) and warn if the two values are not the same and the current +value is not the default. For the pair setting, the value in the file +will not overwrite the current value (so that you can override the +previous run's value), but a warning is issued if the two values are +not the same and the current value is not the default. + Note that some force field styles (pair, bond, angle, etc) do not store their coefficient info in restart files. Typically these are many-body or tabulated potentials which read their parameters from diff --git a/doc/html/fix.html b/doc/html/fix.html index 2acaed8ca4..885ad1653b 100644 --- a/doc/html/fix.html +++ b/doc/html/fix.html @@ -332,7 +332,8 @@ of nvt/sllod - NVT for NEMD with SLLOD equations
  • nvt/sphere - NVT for spherical particles
  • oneway - constrain particles on move in one direction
    • -
  • orient/fcc - add grain boundary migration force
    • +
  • orient/bcc - add grain boundary migration force for BCC
    • +
  • orient/fcc - add grain boundary migration force for FCC
  • planeforce - constrain atoms to move in a plane
  • poems - constrain clusters of atoms to move as coupled rigid bodies
  • pour - pour new atoms/molecules into a granular simulation domain
    • diff --git a/doc/html/fix_orient.html b/doc/html/fix_orient.html index 0515bceeba..ee3d207258 100644 --- a/doc/html/fix_orient.html +++ b/doc/html/fix_orient.html @@ -126,14 +126,18 @@

    fix orient/fcc command

    +
    +
    +

    fix orient/bcc command

    fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1
+fix ID group-ID orient/bcc nstats dir alat dE cutlo cuthi file0 file1
    • ID, group-ID are documented in fix command
    • nstats = print stats every this many steps, 0 = never
    • dir = 0/1 for which crystal is used as reference
      • -
    • alat = fcc cubic lattice constant (distance units)
      • +
    • alat = fcc/bcc cubic lattice constant (distance units)
    • dE = energy added to each atom (energy units)
    • cutlo,cuthi = values between 0.0 and 1.0, cutlo < cuthi
    • file0,file1 = files that specify orientation of each grain
      • @@ -141,6 +145,7 @@

      Examples

      fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec
+fix gb all orient/bcc 0 1 2.882 0.001 0.25 0.75 ngb.left ngb.right
      @@ -150,8 +155,9 @@ grain boundary which can be used to induce grain boundary migration (in the direction perpendicular to the grain boundary plane). The motivation and explanation of this force and its application are -described in (Janssens). The force is only applied to -atoms in the fix group.

      +described in (Janssens). The adaptiation to bcc crystals +is described in (Wicaksono1). The computed force is only +applied to atoms in the fix group.

      The basic idea is that atoms in one grain (on one side of the boundary) have a potential energy dE added to them. Atoms in the other grain have 0.0 potential energy added. Atoms near the boundary @@ -169,19 +175,21 @@ system can displace during the simulation, and such motion should be accounted for in measuring the grain boundary velocity.

      The potential energy added to atom I is given by these formulas

      _images/fix_orient_fcc.jpg -

      which are fully explained in (Janssens). The order -parameter Xi for atom I in equation (1) is a sum over the 12 nearest -neighbors of atom I. Rj is the vector from atom I to its neighbor J, -and RIj is a vector in the reference (perfect) crystal. That is, if -dir = 0/1, then RIj is a vector to an atom coord from file 0/1. -Equation (2) gives the expected value of the order parameter XiIJ in -the other grain. Hi and lo cutoffs are defined in equations (3) and -(4), using the input parameters cutlo and cuthi as thresholds to -avoid adding grain boundary energy when the deviation in the order -parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a -perfect crystal). The added potential energy Ui for atom I is given -in equation (6) where it is interpolated between 0 and dE using the -two threshold Xi values and the Wi value of equation (5).

      +

      which are fully explained in (Janssens). For fcc crystals +this order parameter Xi for atom I in equation (1) is a sum over the +12 nearest neighbors of atom I. For bcc crystals it is the +corresponding sum of the 8 nearest neighbors. Rj is the vector from +atom I to its neighbor J, and RIj is a vector in the reference +(perfect) crystal. That is, if dir = 0/1, then RIj is a vector to an +atom coord from file 0/1. Equation (2) gives the expected value of +the order parameter XiIJ in the other grain. Hi and lo cutoffs are +defined in equations (3) and (4), using the input parameters cutlo +and cuthi as thresholds to avoid adding grain boundary energy when +the deviation in the order parameter from 0 or 1 is small (e.g. due to +thermal fluctuations in a perfect crystal). The added potential +energy Ui for atom I is given in equation (6) where it is interpolated +between 0 and dE using the two threshold Xi values and the Wi value of +equation (5).

      The derivative of this energy expression gives the force on each atom which thus depends on the orientation of its neighbors relative to the 2 grain orientations. Only atoms near the grain boundary feel a net @@ -196,14 +204,14 @@ effect of duplicate reference vector usage is small.

      expense of the other. A value of 0 means the first grain will shrink; a value of 1 means it will grow. This assumes that dE is positive. The reverse will be true if dE is negative.

      -

      The alat parameter is the cubic lattice constant for the fcc +

      The alat parameter is the cubic lattice constant for the fcc or bcc material and is only used to compute a cutoff distance of 1.57 * alat -/ sqrt(2) for finding the 12 nearest neighbors of each atom (which -should be valid for an fcc crystal). A longer/shorter cutoff can be -imposed by adjusting alat. If a particular atom has less than 12 -neighbors within the cutoff, the order parameter of equation (1) is -effectively multiplied by 12 divided by the actual number of neighbors -within the cutoff.

      +/ sqrt(2) for finding the 12 or 8 nearest neighbors of each atom +(which should be valid for an fcc or bcc crystal). A longer/shorter +cutoff can be imposed by adjusting alat. If a particular atom has +less than 12 or 8 neighbors within the cutoff, the order parameter of +equation (1) is effectively multiplied by 12 or 8 divided by the +actual number of neighbors within the cutoff.

      The dE parameter is the maximum amount of additional energy added to each atom in the grain which wants to shrink.

      The cutlo and cuthi parameters are used to reduce the force added @@ -222,7 +230,8 @@ orientation. The vector lengths should all be identical since an fcc lattice has a coordination number of 12. Only 6 are listed due to symmetry, so the list must include one from each pair of equal-and-opposite neighbors. A pair of orientation files for a -Sigma=5 tilt boundary are show below.

      +Sigma=5 tilt boundary are shown below. A tutorial that can help for +writing the orientation files is given in (Wicaksono2)

    Restart, fix_modify, output, run start/stop, minimize info

    @@ -246,7 +255,7 @@ the runRestrictions

    This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

    -

    This fix should only be used with fcc lattices.

    +

    This fix should only be used with fcc or bcc lattices.