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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15031 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2016-05-11 20:36:18 +00:00
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50
doc/html/_sources/Section_commands.txt
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@ -648,31 +648,31 @@ KOKKOS, o = USER-OMP, t = OPT.
These are additional pair styles in USER packages, which can be used
if :ref:`LAMMPS is built with the appropriate package <start_3>`.
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`awpmd/cut <pair_awpmd>` | :doc:`buck/mdf <pair_mdf>` | :doc:`coul/cut/soft (o) <pair_lj_soft>` | :doc:`coul/diel (o) <pair_coul_diel>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`coul/long/soft (o) <pair_lj_soft>` | :doc:`dpd/conservative <pair_dpd_conservative>` | :doc:`dpd/fdt <pair_dpd_fdt>` | :doc:`dpd/fdt/energy <pair_dpd_fdt>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`eam/cd (o) <pair_eam>` | :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lennard/mdf <pair_mdf>` | :doc:`list <pair_list>` | :doc:`lj/charmm/coul/long/soft (o) <pair_charmm>` | :doc:`lj/cut/coul/cut/soft (o) <pair_lj_soft>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/cut/coul/long/soft (o) <pair_lj_soft>` | :doc:`lj/cut/dipole/sf (go) <pair_dipole>` | :doc:`lj/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/thole/long (o) <pair_thole>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/cut/tip4p/long/soft (o) <pair_lj_soft>` | :doc:`lj/mdf <pair_mdf>` | :doc:`lj/sdk (gko) <pair_sdk>` | :doc:`lj/sdk/coul/long (go) <pair_sdk>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/sdk/coul/msm (o) <pair_sdk>` | :doc:`lj/sf (o) <pair_lj_sf>` | :doc:`meam/spline <pair_meam_spline>` | :doc:`meam/sw/spline <pair_meam_sw_spline>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`mgpt <pair_mgpt>` | :doc:`morse/smooth/linear <pair_morse>` | :doc:`morse/soft <pair_morse>` | :doc:`quip <pair_quip>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`reax/c <pair_reax_c>` | :doc:`smd/hertz <pair_smd_hertz>` | :doc:`smd/tlsph <pair_smd_tlsph>` | :doc:`smd/triangulated/surface <pair_smd_triangulated_surface>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`smd/ulsph <pair_smd_ulsph>` | :doc:`smtbq <pair_smtbq>` | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`sph/lj <pair_sph_lj>` | :doc:`sph/rhosum <pair_sph_rhosum>` | :doc:`sph/taitwater <pair_sph_taitwater>` | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`srp <pair_srp>` | :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`thole <pair_thole>` | :doc:`tip4p/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------------+-------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`awpmd/cut <pair_awpmd>` | :doc:`buck/mdf <pair_mdf>` | :doc:`coul/cut/soft (o) <pair_lj_soft>` | :doc:`coul/diel (o) <pair_coul_diel>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`coul/long/soft (o) <pair_lj_soft>` | :doc:`dpd/fdt <pair_dpd_fdt>` | :doc:`dpd/fdt/energy <pair_dpd_fdt>` | :doc:`eam/cd (o) <pair_eam>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` | :doc:`lennard/mdf <pair_mdf>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`list <pair_list>` | :doc:`lj/charmm/coul/long/soft (o) <pair_charmm>` | :doc:`lj/cut/coul/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/coul/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/cut/dipole/sf (go) <pair_dipole>` | :doc:`lj/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/thole/long (o) <pair_thole>` | :doc:`lj/cut/tip4p/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/mdf <pair_mdf>` | :doc:`lj/sdk (gko) <pair_sdk>` | :doc:`lj/sdk/coul/long (go) <pair_sdk>` | :doc:`lj/sdk/coul/msm (o) <pair_sdk>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/sf (o) <pair_lj_sf>` | :doc:`meam/spline <pair_meam_spline>` | :doc:`meam/sw/spline <pair_meam_sw_spline>` | :doc:`mgpt <pair_mgpt>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`morse/smooth/linear <pair_morse>` | :doc:`morse/soft <pair_morse>` | :doc:`multi/lucy <pair_multi_lucy>` | :doc:`quip <pair_quip>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`reax/c <pair_reax_c>` | :doc:`smd/hertz <pair_smd_hertz>` | :doc:`smd/tlsph <pair_smd_tlsph>` | :doc:`smd/triangulated/surface <pair_smd_triangulated_surface>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`smd/ulsph <pair_smd_ulsph>` | :doc:`smtbq <pair_smtbq>` | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`sph/lj <pair_sph_lj>` | :doc:`sph/rhosum <pair_sph_rhosum>` | :doc:`sph/taitwater <pair_sph_taitwater>` | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`srp <pair_srp>` | :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`thole <pair_thole>` | :doc:`tip4p/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
----------

26
doc/html/_sources/dump.txt
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@ -542,17 +542,21 @@ There are several options for outputting atom coordinates. The *x*\ ,
appropriate distance :doc:`units <units>` (Angstroms, sigma, etc). Use
*xs*\ , *ys*\ , *zs* if you want the coordinates "scaled" to the box size,
so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. Use
*xu*\ , *yu*\ , *zu* if you want the coordinates "unwrapped" by the image
flags for each atom. Unwrapped means that if the atom has passed thru
a periodic boundary one or more times, the value is printed for what
the coordinate would be if it had not been wrapped back into the
periodic box. Note that using *xu*\ , *yu*\ , *zu* means that the
coordinate values may be far outside the box bounds printed with the
snapshot. Using *xsu*\ , *ysu*\ , *zsu* is similar to using *xu*\ , *yu*\ , *zu*\ ,
except that the unwrapped coordinates are scaled by the box size. Atoms
that have passed through a periodic boundary will have the corresponding
cooordinate increased or decreased by 1.0.
(tilted), then all atom coords will still be between 0.0 and 1.0.
I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
the non-orthogonal vectors of the simulation box edges, as discussed
in :ref:`Section howto 6.12 <howto_12>`.
Use *xu*\ , *yu*\ , *zu* if you want the coordinates "unwrapped" by the
image flags for each atom. Unwrapped means that if the atom has
passed thru a periodic boundary one or more times, the value is
printed for what the coordinate would be if it had not been wrapped
back into the periodic box. Note that using *xu*\ , *yu*\ , *zu* means
that the coordinate values may be far outside the box bounds printed
with the snapshot. Using *xsu*\ , *ysu*\ , *zsu* is similar to using
*xu*\ , *yu*\ , *zu*\ , except that the unwrapped coordinates are scaled by
the box size. Atoms that have passed through a periodic boundary will
have the corresponding cooordinate increased or decreased by 1.0.
The image flags can be printed directly using the *ix*\ , *iy*\ , *iz*
attributes. For periodic dimensions, they specify which image of the