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2016-05-31 16:50:06 +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/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>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
| :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:`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>` | |
+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
----------

63
doc/html/_sources/dihedral_charmm.txt
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@ -25,7 +25,9 @@ Examples
.. parsed-literal::
dihedral_style charmm
dihedral_coeff 1 120.0 1 60 0.5
dihedral_coeff 1 0.2 1 180 1.0
dihedral_coeff 2 1.8 1 0 1.0
dihedral_coeff 1 3.1 2 180 0.5
Description
"""""""""""
@ -49,33 +51,44 @@ or :doc:`read_restart <read_restart>` commands:
* K (energy)
* n (integer >= 0)
* d (integer value of degrees)
* weighting factor (0.0 to 1.0)
* weighting factor (1.0, 0.5, or 0.0)
The weighting factor is applied to pairwise interaction between the
1st and 4th atoms in the dihedral, which are computed by a CHARMM
:doc:`pair_style <pair_charmm>` with epsilon and sigma values specified
with a :doc:`pair_coeff <pair_charmm>` command. Note that this
weighting factor is unrelated to the weighting factor specified by the
:doc:`special bonds <special_bonds>` command which applies to all 1-4
interactions in the system.
The weighting factor is required to correct for double counting
pairwise non-bonded Lennard-Jones interactions in cyclic systems or
when using the CHARMM dihedral style with non-CHARMM force fields.
With the CHARMM dihedral style, interactions between the 1st and 4th
atoms in a dihedral are skipped during the normal non-bonded force
computation and instead evaluated as part of the dihedral using
special epsilon and sigma values specified with the
:doc:`pair_coeff <pair_charmm>` command of pair styles that contain
"lj/charmm" (e.g. :doc:`pair_style lj/charmm/coul/long <pair_charmm>`)
In 6-membered rings, the same 1-4 interaction would be computed twice
(once for the clockwise 1-4 pair in dihedral 1-2-3-4 and once in the
counterclockwise dihedral 1-6-5-4) and thus the weighting factor has
to be 0.5 in this case. In 4-membered or 5-membered rings, the 1-4
dihedral also is counted as a 1-2 or 1-3 interaction when going around
the ring in the opposite direction and thus the weighting factor is
0.0, as the 1-2 and 1-3 exclusions take precedence.
For CHARMM force fields, the special_bonds 1-4 weighting factor should
be set to 0.0. This is because the pair styles that contain "charmm"
(e.g. :doc:`pair_style lj/charmm/coul/long <pair_charmm>`) define extra
1-4 interaction coefficients that are used by this dihedral style to
compute those interactions explicitly. This means that if any of the
weighting factors defined as dihedral coefficients (4th coeff above)
are non-zero, then you must use a charmm pair style. Note that if you
do not set the special_bonds 1-4 weighting factor to 0.0 (which is the
default) then 1-4 interactions in dihedrals will be computed twice,
once by the pair routine and once by the dihedral routine, which is
probably not what you want.
Note that this dihedral weighting factor is unrelated to the scaling
factor specified by the :doc:`special bonds <special_bonds>` command
which applies to all 1-4 interactions in the system. For CHARMM force
fields, the special_bonds 1-4 interaction scaling factor should be set
to 0.0. Since the corresponding 1-4 non-bonded interactions are
computed with the dihedral. This means that if any of the weighting
factors defined as dihedral coefficients (4th coeff above) are
non-zero, then you must use a pair style with "lj/charmm" and set the
special_bonds 1-4 scaling factor to 0.0 (which is the
default). Otherwise 1-4 non-bonded interactions in dihedrals will be
computed twice.
For AMBER force fields, the special_bonds 1-4 weighting factor should
be set to the AMBER defaults (1/2 and 5/6) and all the dihedral
weighting factors (4th coeff above) should be set to 0.0. In this
case, you can use any pair style you wish, since the dihedral does not
need any 1-4 information.
Also note that for AMBER force fields, which use pair styles with
"lj/cut", the special_bonds 1-4 scaling factor should be set to the
AMBER defaults (1/2 and 5/6) and all the dihedral weighting factors
(4th coeff above) must be set to 0.0. In this case, you can use any
pair style you wish, since the dihedral does not need any
Lennard-Jones parameter information and will not compute any 1-4
non-bonded interactions.
----------

19
doc/html/_sources/pair_airebo.txt
View File

@ -164,6 +164,25 @@ it was fit, so modifying the file should be done cautiously. The
AIREBO-M Morse potentials were parameterized using a cutoff of
3.0 (sigma). Modifying this cutoff may impact simulation accuracy.
This pair style tallies a breakdown of the total AIREBO potential
energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 3.
The 3 values correspond to the following sub-categories:
1. *E_REBO* = REBO energy
2. *E_LJ* = Lennard-Jones energy
3. *E_TORSION* = Torsion energy
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
.. parsed-literal::
compute 0 all pair airebo
variable REBO equal c_0[1]
variable LJ equal c_0[2]
variable TORSION equal c_0[3]
thermo_style custom step temp epair v_REBO v_LJ v_TORSION
----------