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Merge commit 'refs/pull/1903/head' of github.com:lammps/lammps into release-preparation

This commit is contained in:
Axel Kohlmeyer 2020-02-27 01:15:17 -05:00
parent 3563d2f10d 9ef5949798
commit 1bb38ed09b
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GPG Key ID: D9B44E93BF0C375A
132 changed files with 1664 additions and 1654 deletions
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22
doc/src/change_box.rst
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@ -1,13 +1,13 @@
.. index:: change\_box
.. index:: change_box
change\_box command
===================
change_box command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
change_box group-ID parameter args ... keyword args ...
@ -58,7 +58,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
change_box all x scale 1.1 y volume z volume remap
@ -114,7 +114,7 @@ new owning processors.
is non-periodic and atoms extend from 0 to 20 in all dimensions:
.. parsed-literal::
.. code-block:: LAMMPS
change_box all x final -10 20
create_atoms 1 single -5 5 5 # this will fail to insert an atom
@ -195,7 +195,7 @@ style, then both it and the current keyword apply to the keyword
preceding "key". I.e. this sequence of keywords is allowed:
.. parsed-literal::
.. code-block:: LAMMPS
change_box all x scale 1.1 y volume z volume
@ -207,7 +207,7 @@ If the following command is used, then the z box length will shrink by
the same 1.1 factor the x box length was increased by:
.. parsed-literal::
.. code-block:: LAMMPS
change_box all x scale 1.1 z volume
@ -217,16 +217,16 @@ y,z box lengths shrink so as to keep their relative aspect ratio
constant:
.. parsed-literal::
.. code-block:: LAMMPS
change_box all"x scale 1.1 y volume z volume
change_box all x scale 1.1 y volume z volume
If the following command is used, then the final box will be a factor
of 10% larger in x and y, and a factor of 21% smaller in z, so as to
keep the volume constant:
.. parsed-literal::
.. code-block:: LAMMPS
change_box all x scale 1.1 z volume y scale 1.1 z volume

14
doc/src/comm_modify.rst
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@ -1,13 +1,13 @@
.. index:: comm\_modify
.. index:: comm_modify
comm\_modify command
====================
comm_modify command
===================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
comm_modify keyword value ...
@ -30,14 +30,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
comm_modify mode multi
comm_modify mode multi group solvent
comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2\*4 15.0
comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
comm_modify vel yes
comm_modify mode single cutoff 5.0 vel yes
comm_modify cutoff/multi \* 0.0
comm_modify cutoff/multi * 0.0
Description
"""""""""""

10
doc/src/comm_style.rst
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@ -1,13 +1,13 @@
.. index:: comm\_style
.. index:: comm_style
comm\_style command
===================
comm_style command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
comm_style style
@ -17,7 +17,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
comm_style brick
comm_style tiled

10
doc/src/compute_modify.rst
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@ -1,13 +1,13 @@
.. index:: compute\_modify
.. index:: compute_modify
compute\_modify command
=======================
compute_modify command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute_modify compute-ID keyword value ...
@ -30,7 +30,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute_modify myTemp extra/dof 0
compute_modify newtemp dynamic/dof yes extra/dof 600

4
doc/src/compute_smd_ulsph_num_neighs.rst
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@ -7,7 +7,7 @@ Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/ulsph/num/neighs
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all smd/ulsph/num/neighs

4
doc/src/compute_smd_ulsph_strain.rst
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@ -7,7 +7,7 @@ Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/ulsph/strain
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all smd/ulsph/strain

4
doc/src/compute_smd_ulsph_strain_rate.rst
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@ -7,7 +7,7 @@ Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/ulsph/strain/rate
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all smd/ulsph/strain/rate

4
doc/src/compute_smd_ulsph_stress.rst
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@ -7,7 +7,7 @@ Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID smd/ulsph/stress
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all smd/ulsph/stress

14
doc/src/create_atoms.rst
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@ -1,13 +1,13 @@
.. index:: create\_atoms
.. index:: create_atoms
create\_atoms command
create_atoms command
=====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
create_atoms type style args keyword values ...
@ -29,7 +29,7 @@ Syntax
* zero or more keyword/value pairs may be appended
* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *units*
.. parsed-literal::
.. code-block:: LAMMPS
*mol* value = template-ID seed
template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
@ -61,7 +61,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
create_atoms 1 box
create_atoms 3 region regsphere basis 2 3
@ -269,7 +269,7 @@ converts lattice spacings to distance. Click on the image for a
larger version.
.. parsed-literal::
.. code-block:: LAMMPS
dimension 2
variable x equal 100
@ -280,7 +280,7 @@ larger version.
variable xx internal 0.0
variable yy internal 0.0
variable v equal "(0.2\*v_y\*ylat \* cos(v_xx/xlat \* 2.0\*PI\*4.0/v_x) + 0.5\*v_y\*ylat - v_yy) > 0.0"
variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
create_atoms 1 box var v set x xx set y yy
write_dump all atom sinusoid.lammpstrj

12
doc/src/create_bonds.rst
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@ -1,13 +1,13 @@
.. index:: create\_bonds
.. index:: create_bonds
create\_bonds command
=====================
create_bonds command
====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
create_bonds style args ... keyword value ...
@ -48,7 +48,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
create_bonds many all all 1 1.0 1.2
create_bonds many surf solvent 3 2.0 2.4
@ -198,7 +198,7 @@ to only trigger the internal list to be created once, after the last
bond (or angle, or dihedral, or improper) is added:
.. parsed-literal::
.. code-block:: LAMMPS
create_bonds single/bond 5 52 98 special no
create_bonds single/bond 5 73 74 special no

10
doc/src/create_box.rst
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@ -1,13 +1,13 @@
.. index:: create\_box
.. index:: create_box
create\_box command
===================
create_box command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
create_box N region-ID keyword value ...
@ -34,7 +34,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
create_box 2 mybox
create_box 2 mybox bond/types 2 extra/bond/per/atom 1

10
doc/src/delete_atoms.rst
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@ -1,13 +1,13 @@
.. index:: delete\_atoms
.. index:: delete_atoms
delete\_atoms command
=====================
delete_atoms command
====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
delete_atoms style args keyword value ...
@ -41,7 +41,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
delete_atoms group edge
delete_atoms region sphere compress no

15
doc/src/delete_bonds.rst
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@ -1,19 +1,18 @@
.. index:: delete\_bonds
.. index:: delete_bonds
delete\_bonds command
=====================
delete_bonds command
====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
delete_bonds group-ID style arg keyword ...
* group-ID = group ID
* style = *multi* or *atom* or *bond* or *angle* or *dihedral* or
*improper* or *stats*
* style = *multi* or *atom* or *bond* or *angle* or *dihedral* or *improper* or *stats*
.. parsed-literal::
@ -33,11 +32,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
delete_bonds frozen multi remove
delete_bonds all atom 4 special
delete_bonds all bond 0\*3 special
delete_bonds all bond 0*3 special
delete_bonds all stats
Description

28
doc/src/dihedral_charmm.rst
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@ -1,25 +1,25 @@
.. index:: dihedral\_style charmm
.. index:: dihedral_style charmm
dihedral\_style charmm command
==============================
dihedral_style charmm command
=============================
dihedral\_style charmm/intel command
====================================
dihedral_style charmm/intel command
===================================
dihedral\_style charmm/kk command
dihedral_style charmm/kk command
================================
dihedral_style charmm/omp command
=================================
dihedral\_style charmm/omp command
==================================
dihedral\_style charmmfsw command
=================================
dihedral_style charmmfsw command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style style
@ -29,7 +29,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style charmm
dihedral_style charmmfsw
@ -44,7 +44,7 @@ The *charmm* and *charmmfsw* dihedral styles use the potential
.. math::
E = K [ 1 + \cos (n \phi - d) ]
E = K [ 1 + \cos (n \phi - d) ]
See :ref:`(MacKerell) <dihedral-MacKerell>` for a description of the CHARMM

44
doc/src/dihedral_class2.rst
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@ -1,19 +1,19 @@
.. index:: dihedral\_style class2
.. index:: dihedral_style class2
dihedral\_style class2 command
==============================
dihedral_style class2 command
=============================
dihedral\_style class2/omp command
==================================
dihedral\_style class2/kk command
dihedral_style class2/omp command
=================================
dihedral_style class2/kk command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style class2
@ -21,15 +21,15 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style class2
dihedral_coeff 1 100 75 100 70 80 60
dihedral_coeff \* mbt 3.5945 0.1704 -0.5490 1.5228
dihedral_coeff \* ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
dihedral_coeff \* aat -13.5271 110.2453 105.1270
dihedral_coeff \* bb13 0.0 1.0119 1.1010
dihedral_coeff * aat -13.5271 110.2453 105.1270
dihedral_coeff * bb13 0.0 1.0119 1.1010
Description
"""""""""""
@ -38,15 +38,15 @@ The *class2* dihedral style uses the potential
.. math::
E = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\
E_d = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\
E_{mbt} = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\
E_{ebt} = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\
& (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\
E_{at} = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\
& (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\
E_{aat} = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\
E_{bb13} = & N (r_{ij} - r_1) (r_{kl} - r_3)
E = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\
E_d = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\
E_{mbt} = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\
E_{ebt} = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\
& (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\
E_{at} = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\
& (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\
E_{aat} = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\
E_{bb13} = & N (r_{ij} - r_1) (r_{kl} - r_3)
where :math:`E_d` is the dihedral term, :math:`E_{mbt}` is a middle-bond-torsion term,

18
doc/src/dihedral_coeff.rst
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@ -1,13 +1,13 @@
.. index:: dihedral\_coeff
.. index:: dihedral_coeff
dihedral\_coeff command
=======================
dihedral_coeff command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_coeff N args
@ -18,11 +18,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_coeff 1 80.0 1 3
dihedral_coeff \* 80.0 1 3 0.5
dihedral_coeff 2\* 80.0 1 3 0.5
dihedral_coeff * 80.0 1 3 0.5
dihedral_coeff 2* 80.0 1 3 0.5
Description
"""""""""""
@ -46,9 +46,9 @@ for the same dihedral type. For example, these commands set the coeffs
for all dihedral types, then overwrite the coeffs for just dihedral type 2:
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_coeff \* 80.0 1 3
dihedral_coeff * 80.0 1 3
dihedral_coeff 2 200.0 1 3
A line in a data file that specifies dihedral coefficients uses the exact

16
doc/src/dihedral_cosine_shift_exp.rst
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@ -1,16 +1,16 @@
.. index:: dihedral\_style cosine/shift/exp
.. index:: dihedral_style cosine/shift/exp
dihedral\_style cosine/shift/exp command
========================================
dihedral_style cosine/shift/exp command
=======================================
dihedral\_style cosine/shift/exp/omp command
============================================
dihedral_style cosine/shift/exp/omp command
===========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style cosine/shift/exp
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style cosine/shift/exp
dihedral_coeff 1 10.0 45.0 2.0
@ -30,7 +30,7 @@ The *cosine/shift/exp* dihedral style uses the potential
.. math::
E = -U_{min}\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad\mbox{with}\quad U(\theta,\theta_0)=-0.5 \left(1+\cos(\theta-\theta_0) \right)
E = -U_{min}\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad\mbox{with}\quad U(\theta,\theta_0)=-0.5 \left(1+\cos(\theta-\theta_0) \right)
where :math:`U_{min}`, :math:`\theta`, and :math:`a` are defined for

20
doc/src/dihedral_fourier.rst
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@ -1,19 +1,19 @@
.. index:: dihedral\_style fourier
.. index:: dihedral_style fourier
dihedral\_style fourier command
===============================
dihedral_style fourier command
==============================
dihedral\_style fourier/intel command
=====================================
dihedral_style fourier/intel command
====================================
dihedral\_style fourier/omp command
===================================
dihedral_style fourier/omp command
==================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style fourier
@ -21,7 +21,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style fourier
dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
@ -33,7 +33,7 @@ The *fourier* dihedral style uses the potential:
.. math::
E = \sum_{i=1,m} K_i [ 1.0 + \cos ( n_i \phi - d_i ) ]
E = \sum_{i=1,m} K_i [ 1.0 + \cos ( n_i \phi - d_i ) ]
The following coefficients must be defined for each dihedral type via the

24
doc/src/dihedral_harmonic.rst
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@ -1,22 +1,22 @@
.. index:: dihedral\_style harmonic
.. index:: dihedral_style harmonic
dihedral\_style harmonic command
================================
dihedral_style harmonic command
===============================
dihedral\_style harmonic/intel command
======================================
dihedral_style harmonic/intel command
=====================================
dihedral\_style harmonic/kk command
dihedral_style harmonic/kk command
==================================
dihedral_style harmonic/omp command
===================================
dihedral\_style harmonic/omp command
====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style harmonic
@ -24,7 +24,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style harmonic
dihedral_coeff 1 80.0 1 2
@ -36,7 +36,7 @@ The *harmonic* dihedral style uses the potential
.. math::
E = K [ 1 + d \cos (n \phi) ]
E = K [ 1 + d \cos (n \phi) ]
The following coefficients must be defined for each dihedral type via the

18
doc/src/dihedral_helix.rst
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@ -1,16 +1,16 @@
.. index:: dihedral\_style helix
.. index:: dihedral_style helix
dihedral\_style helix command
=============================
dihedral_style helix command
============================
dihedral\_style helix/omp command
=================================
dihedral_style helix/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style helix
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style helix
dihedral_coeff 1 80.0 100.0 40.0
@ -30,8 +30,8 @@ The *helix* dihedral style uses the potential
.. math::
E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] +
C [1 + \cos(\theta + \frac{\pi}{4})]
E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] +
C [1 + \cos(\theta + \frac{\pi}{4})]
This coarse-grain dihedral potential is described in :ref:`(Guo) <Guo>`.

12
doc/src/dihedral_hybrid.rst
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@ -1,13 +1,13 @@
.. index:: dihedral\_style hybrid
.. index:: dihedral_style hybrid
dihedral\_style hybrid command
==============================
dihedral_style hybrid command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style hybrid style1 style2 ...
@ -17,11 +17,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style hybrid harmonic helix
dihedral_coeff 1 harmonic 6.0 1 3
dihedral_coeff 2\* helix 10 10 10
dihedral_coeff 2* helix 10 10 10
Description
"""""""""""

16
doc/src/dihedral_multi_harmonic.rst
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@ -1,16 +1,16 @@
.. index:: dihedral\_style multi/harmonic
.. index:: dihedral_style multi/harmonic
dihedral\_style multi/harmonic command
======================================
dihedral_style multi/harmonic command
=====================================
dihedral\_style multi/harmonic/omp command
==========================================
dihedral_style multi/harmonic/omp command
=========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style multi/harmonic
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style multi/harmonic
dihedral_coeff 1 20 20 20 20 20
@ -30,7 +30,7 @@ The *multi/harmonic* dihedral style uses the potential
.. math::
E = \sum_{n=1,5} A_n \cos^{n-1}(\phi)
E = \sum_{n=1,5} A_n \cos^{n-1}(\phi)
The following coefficients must be defined for each dihedral type via the

14
doc/src/dihedral_nharmonic.rst
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@ -1,16 +1,16 @@
.. index:: dihedral\_style nharmonic
.. index:: dihedral_style nharmonic
dihedral\_style nharmonic command
dihedral_style nharmonic command
=================================
dihedral\_style nharmonic/omp command
dihedral_style nharmonic/omp command
=====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style nharmonic
@ -18,10 +18,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style nharmonic
dihedral_coeff \* 3 10.0 20.0 30.0
dihedral_coeff * 3 10.0 20.0 30.0
Description
"""""""""""
@ -30,7 +30,7 @@ The *nharmonic* dihedral style uses the potential:
.. math::
E = \sum_{n=1,n} A_n \cos^{n-1}(\phi)
E = \sum_{n=1,n} A_n \cos^{n-1}(\phi)
The following coefficients must be defined for each dihedral type via the

10
doc/src/dihedral_none.rst
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@ -1,13 +1,13 @@
.. index:: dihedral\_style none
.. index:: dihedral_style none
dihedral\_style none command
============================
dihedral_style none command
===========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style none
@ -15,7 +15,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style none

26
doc/src/dihedral_opls.rst
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@ -1,22 +1,22 @@
.. index:: dihedral\_style opls
.. index:: dihedral_style opls
dihedral\_style opls command
============================
dihedral_style opls command
===========================
dihedral\_style opls/intel command
==================================
dihedral_style opls/intel command
=================================
dihedral\_style opls/kk command
dihedral_style opls/kk command
==============================
dihedral_style opls/omp command
===============================
dihedral\_style opls/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style opls
@ -24,7 +24,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style opls
dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT
@ -38,8 +38,8 @@ The *opls* dihedral style uses the potential
.. math::
E = & \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] + \\
& \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)]
E = & \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] + \\
& \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)]
Note that the usual 1/2 factor is not included in the K values.

16
doc/src/dihedral_quadratic.rst
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@ -1,16 +1,16 @@
.. index:: dihedral\_style quadratic
.. index:: dihedral_style quadratic
dihedral\_style quadratic command
=================================
dihedral_style quadratic command
================================
dihedral\_style quadratic/omp command
=====================================
dihedral_style quadratic/omp command
====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style quadratic
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style quadratic
dihedral_coeff 100.0 80.0
@ -30,7 +30,7 @@ The *quadratic* dihedral style uses the potential:
.. math::
E = K (\phi - \phi_0)^2
E = K (\phi - \phi_0)^2
This dihedral potential can be used to keep a dihedral in a predefined

18
doc/src/dihedral_spherical.rst
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@ -1,13 +1,13 @@
.. index:: dihedral\_style spherical
.. index:: dihedral_style spherical
dihedral\_style spherical command
=================================
dihedral_style spherical command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style spherical
@ -15,7 +15,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0
dihedral_coeff 1 3 69.3 1 93.9 1 1 90 0 1 90 0 &
@ -32,10 +32,10 @@ The *spherical* dihedral style uses the potential:
.. math::
E(\phi,\theta_1,\theta_2) & = \sum_{i=1}^N\nolimits\ C_i\ \Phi_i(\phi)\ \Theta_{1i}(\theta_1)\ \Theta_{2i}(\theta_2) \\
\Phi_{i}(\phi) & = u_i - \mathrm{cos}((\phi - a_i)K_i) \\
\Theta_{1i}(\theta_1) & = v_i - \mathrm{cos}((\theta_1-b_i)L_i) \\
\Theta_{2i}(\theta_2) & = w_i - \mathrm{cos}((\theta_2-c_i)M_i)
E(\phi,\theta_1,\theta_2) & = \sum_{i=1}^N\nolimits\ C_i\ \Phi_i(\phi)\ \Theta_{1i}(\theta_1)\ \Theta_{2i}(\theta_2) \\
\Phi_{i}(\phi) & = u_i - \mathrm{cos}((\phi - a_i)K_i) \\
\Theta_{1i}(\theta_1) & = v_i - \mathrm{cos}((\theta_1-b_i)L_i) \\
\Theta_{2i}(\theta_2) & = w_i - \mathrm{cos}((\theta_2-c_i)M_i)
For this dihedral style, the energy can be any function that combines the

10
doc/src/dihedral_style.rst
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@ -1,13 +1,13 @@
.. index:: dihedral\_style
.. index:: dihedral_style
dihedral\_style command
=======================
dihedral_style command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style style
@ -17,7 +17,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style harmonic
dihedral_style multi/harmonic

14
doc/src/dihedral_table.rst
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@ -1,16 +1,16 @@
.. index:: dihedral\_style table
.. index:: dihedral_style table
dihedral\_style table command
=============================
dihedral_style table command
============================
dihedral\_style table/omp command
=================================
dihedral_style table/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style table style Ntable
@ -21,7 +21,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style table spline 400
dihedral_style table linear 1000

15
doc/src/dihedral_table_cut.rst
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@ -1,13 +1,13 @@
.. index:: dihedral\_style table/cut
.. index:: dihedral_style table/cut
dihedral\_style table/cut command
=================================
dihedral_style table/cut command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style table/cut style Ntable
@ -17,8 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style table/cut spline 400
dihedral_style table/cut linear 1000
@ -68,8 +67,8 @@ cutoff function:
.. math::
f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
The cutoff specifies an prefactor to the cutoff function. While this value

13
doc/src/dihedral_zero.rst
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@ -1,25 +1,24 @@
.. index:: dihedral\_style zero
.. index:: dihedral_style zero
dihedral\_style zero command
dihedral_style zero command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style zero *nocoeff*
dihedral_style zero [nocoeff]
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dihedral_style zero
dihedral_style zero nocoeff
dihedral_coeff \*
dihedral_coeff *
Description
"""""""""""

10
doc/src/displace_atoms.rst
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@ -1,13 +1,13 @@
.. index:: displace\_atoms
.. index:: displace_atoms
displace\_atoms command
=======================
displace_atoms command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
displace_atoms group-ID style args keyword value ...
@ -45,7 +45,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
displace_atoms top move 0 -5 0 units box
displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5

34
doc/src/dump_modify.rst
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@ -1,13 +1,13 @@
.. index:: dump\_modify
.. index:: dump_modify
dump\_modify command
====================
dump_modify command
===================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dump_modify dump-ID keyword values ...
@ -121,7 +121,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
dump_modify 1 format float %20.15g scale yes
@ -265,7 +265,7 @@ For example, the following commands will
write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
.. parsed-literal::
.. code-block:: LAMMPS
variable s equal logfreq(10,3,10)
dump 1 all atom 100 tmp.dump
@ -275,7 +275,7 @@ The following commands would write snapshots at the timesteps listed
in file tmp.times:
.. parsed-literal::
.. code-block:: LAMMPS
variable f file tmp.times
variable s equal next(f)
@ -372,7 +372,7 @@ settings, reverting all values to their default format.
example, these commands:
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all property/local batom1 batom2
dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
@ -535,7 +535,7 @@ last snapshot. This can be accomplished with something the following
commands:
.. parsed-literal::
.. code-block:: LAMMPS
variable Dhop equal 0.6
variable check atom "c_dsp[4] > v_Dhop"
@ -678,7 +678,7 @@ only dump atoms whose attribute has changed (or not changed).
Three examples follow.
.. parsed-literal::
.. code-block:: LAMMPS
dump_modify ... thresh ix != LAST
@ -688,20 +688,20 @@ once and then crossed back between the two dump timesteps would not be
included.)
.. parsed-literal::
.. code-block:: LAMMPS
region foo sphere 10 20 10 15
variable inregion atom rmask(foo)
dump_modify ... thresh v_inregion \|\^ LAST
dump_modify ... thresh v_inregion |^ LAST
This will dump atoms which crossed the boundary of the spherical
region since the last dump.
.. parsed-literal::
.. code-block:: LAMMPS
variable charge atom "(q > 0.5) \|\| (q < -0.5)"
dump_modify ... thresh v_charge \|\^ LAST
variable charge atom "(q > 0.5) || (q < -0.5)"
dump_modify ... thresh v_charge |^ LAST
This will dump atoms whose charge has changed from an absolute value
less than 1/2 to greater than 1/2 (or vice versa) since the last dump.
@ -935,13 +935,13 @@ examples/pour/in.pour.2d.molecule input script for an example of how
this is used.
.. parsed-literal::
.. code-block:: LAMMPS
variable colors string &
"red green blue yellow white &
purple pink orange lime gray"
variable mol atom mol%10
dump 1 all image 250 image.\*.jpg v_mol type &
dump 1 all image 250 image.*.jpg v_mol type &
zoom 1.6 adiam 1.5
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}

10
doc/src/dynamical_matrix.rst
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@ -1,13 +1,13 @@
.. index:: dynamical\_matrix
.. index:: dynamical_matrix
dynamical\_matrix command
=========================
dynamical_matrix command
========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
dynamical_matrix group-ID style gamma args keyword value ...
@ -28,7 +28,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
dynamical_matrix 1 regular 0.000001
dynamical_matrix 1 eskm 0.000001

12
doc/src/fix_modify.rst
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@ -1,13 +1,13 @@
.. index:: fix\_modify
.. index:: fix_modify
fix\_modify command
===================
fix_modify command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify fix-ID keyword value ...
@ -33,7 +33,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix_modify 3 temp myTemp press myPress
fix_modify 1 energy yes
@ -154,7 +154,7 @@ will give a warning if that is the case.
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

10
doc/src/fix_smd_adjust_dt.rst
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@ -1,13 +1,13 @@
.. index:: fix smd/adjust\_dt
.. index:: fix smd/adjust_dt
fix smd/adjust\_dt command
==========================
fix smd/adjust_dt command
=========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID smd/adjust_dt arg
@ -25,7 +25,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all smd/adjust_dt 0.1

10
doc/src/fix_smd_integrate_tlsph.rst
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@ -1,13 +1,13 @@
.. index:: fix smd/integrate\_tlsph
.. index:: fix smd/integrate_tlsph
fix smd/integrate\_tlsph command
================================
fix smd/integrate_tlsph command
===============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID smd/integrate_tlsph keyword values
@ -26,7 +26,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all smd/integrate_tlsph
fix 1 all smd/integrate_tlsph limit_velocity 1000

9
doc/src/fix_smd_integrate_ulsph.rst
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@ -1,13 +1,13 @@
.. index:: fix smd/integrate\_ulsph
.. index:: fix smd/integrate_ulsph
fix smd/integrate\_ulsph command
fix smd/integrate_ulsph command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID smd/integrate_ulsph keyword
@ -26,8 +26,7 @@ limit\_velocity values = max\_velocity
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
fix 1 all smd/integrate_ulsph limit_velocity 1000

16
doc/src/fix_smd_move_triangulated_surface.rst
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@ -1,13 +1,13 @@
.. index:: fix smd/move\_tri\_surf
.. index:: fix smd/move_tri_surf
fix smd/move\_tri\_surf command
===============================
fix smd/move_tri_surf command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID smd/move_tri_surf keyword
@ -33,11 +33,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 tool smd/move_tri_surf \*LINEAR 20 20 10
fix 2 tool smd/move_tri_surf \*WIGGLE 20 20 10
fix 2 tool smd/move_tri_surf \*ROTATE 0 0 0 5 2 1
fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
Description
"""""""""""

10
doc/src/fix_smd_wall_surface.rst
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@ -1,13 +1,13 @@
.. index:: fix smd/wall\_surface
.. index:: fix smd/wall_surface
fix smd/wall\_surface command
=============================
fix smd/wall_surface command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID smd/wall_surface arg type mol-ID
@ -26,7 +26,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix stl_surf all smd/wall_surface tool.stl 2 65535

30
doc/src/improper_class2.rst
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@ -1,19 +1,19 @@
.. index:: improper\_style class2
.. index:: improper_style class2
improper\_style class2 command
==============================
improper_style class2 command
=============================
improper\_style class2/omp command
==================================
improper\_style class2/kk command
improper_style class2/omp command
=================================
improper_style class2/kk command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style class2
@ -21,11 +21,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style class2
improper_coeff 1 100.0 0
improper_coeff \* aa 0.0 0.0 0.0 115.06 130.01 115.06
improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06
Description
"""""""""""
@ -34,11 +34,11 @@ The *class2* improper style uses the potential
.. math::
E = & E_i + E_{aa} \\
E_i = & K [ \frac{\chi_{ijkl} + \chi_{kjli} + \chi_{ljik}}{3} - \chi_0 ]^2 \\
E_{aa} = & M_1 (\theta_{ijk} - \theta_1) (\theta_{kjl} - \theta_3) + \\
& M_2 (\theta_{ijk} - \theta_1) (\theta_{ijl} - \theta_2) + \\
& M_3 (\theta_{ijl} - \theta_2) (\theta_{kjl} - \theta_3)
E = & E_i + E_{aa} \\
E_i = & K [ \frac{\chi_{ijkl} + \chi_{kjli} + \chi_{ljik}}{3} - \chi_0 ]^2 \\
E_{aa} = & M_1 (\theta_{ijk} - \theta_1) (\theta_{kjl} - \theta_3) + \\
& M_2 (\theta_{ijk} - \theta_1) (\theta_{ijl} - \theta_2) + \\
& M_3 (\theta_{ijl} - \theta_2) (\theta_{kjl} - \theta_3)
where :math:`E_i` is the improper term and :math:`E_{aa}` is an

18
doc/src/improper_coeff.rst
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@ -1,13 +1,13 @@
.. index:: improper\_coeff
.. index:: improper_coeff
improper\_coeff command
=======================
improper_coeff command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_coeff N args
@ -18,11 +18,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_coeff 1 300.0 0.0
improper_coeff \* 80.2 -1 2
improper_coeff \*4 80.2 -1 2
improper_coeff * 80.2 -1 2
improper_coeff *4 80.2 -1 2
Description
"""""""""""
@ -48,9 +48,9 @@ the coeffs for all improper types, then overwrite the coeffs for just
improper type 2:
.. parsed-literal::
.. code-block:: LAMMPS
improper_coeff \* 300.0 0.0
improper_coeff * 300.0 0.0
improper_coeff 2 50.0 0.0
A line in a data file that specifies improper coefficients uses the

16
doc/src/improper_cossq.rst
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@ -1,16 +1,16 @@
.. index:: improper\_style cossq
.. index:: improper_style cossq
improper\_style cossq command
=============================
improper_style cossq command
============================
improper\_style cossq/omp command
=================================
improper_style cossq/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style cossq
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style cossq
improper_coeff 1 4.0 0.0
@ -30,7 +30,7 @@ The *cossq* improper style uses the potential
.. math::
E = \frac{1}{2} K \cos^2{\left(\chi - \chi_0\right)}
E = \frac{1}{2} K \cos^2{\left(\chi - \chi_0\right)}
where :math:`\chi` is the improper angle, :math:`\chi_0` is its

18
doc/src/improper_cvff.rst
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@ -1,19 +1,19 @@
.. index:: improper\_style cvff
.. index:: improper_style cvff
improper\_style cvff command
============================
improper_style cvff command
===========================
improper\_style cvff/intel command
==================================
improper_style cvff/intel command
=================================
improper\_style cvff/omp command
================================
improper_style cvff/omp command
===============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style cvff
@ -21,7 +21,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style cvff
improper_coeff 1 80.0 -1 4

14
doc/src/improper_distance.rst
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@ -1,18 +1,20 @@
.. index:: improper\_style distance
.. index:: improper_style distance
improper\_style distance command
================================
improper_style distance command
===============================
Syntax
""""""
improper\_style distance
.. code-block:: LAMMPS
improper_style distance
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style distance
improper_coeff 1 80.0 100.0
@ -27,7 +29,7 @@ The *distance* improper style uses the potential
E = K_2 d^2 + K_4 d^4
where d is the distance between the central atom and the plane formed
where :math:`d` is the distance between the central atom and the plane formed
by the other three atoms. If the 4 atoms in an improper quadruplet
(listed in the data file read by the :doc:`read_data <read_data>`
command) are ordered I,J,K,L then the I-atom is assumed to be the

16
doc/src/improper_distharm.rst
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@ -1,18 +1,20 @@
.. index:: improper\_style distharm
.. index:: improper_style distharm
improper\_style distharm command
================================
improper_style distharm command
===============================
Syntax
""""""
improper\_style distharm
.. code-block:: LAMMPS
improper_style distharm
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style distharm
improper_coeff 1 25.0 0.5
@ -24,10 +26,10 @@ The *distharm* improper style uses the potential
.. math::
E = K (d - d_0)^2
E = K (d - d_0)^2
where d is the oriented distance between the central atom and the plane formed
where :math:`d` is the oriented distance between the central atom and the plane formed
by the other three atoms. If the 4 atoms in an improper quadruplet
(listed in the data file read by the :doc:`read_data <read_data>`
command) are ordered I,J,K,L then the L-atom is assumed to be the

14
doc/src/improper_fourier.rst
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@ -1,16 +1,16 @@
.. index:: improper\_style fourier
.. index:: improper_style fourier
improper\_style fourier command
===============================
improper_style fourier command
==============================
improper\_style fourier/omp command
===================================
improper_style fourier/omp command
==================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style fourier
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style fourier
improper_coeff 1 100.0 0.0 1.0 0.5 1

24
doc/src/improper_harmonic.rst
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@ -1,22 +1,22 @@
.. index:: improper\_style harmonic
.. index:: improper_style harmonic
improper\_style harmonic command
================================
improper_style harmonic command
===============================
improper\_style harmonic/intel command
======================================
improper_style harmonic/intel command
=====================================
improper\_style harmonic/kk command
improper_style harmonic/kk command
==================================
improper_style harmonic/omp command
===================================
improper\_style harmonic/omp command
====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style harmonic
@ -24,7 +24,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style harmonic
improper_coeff 1 100.0 0
@ -36,7 +36,7 @@ The *harmonic* improper style uses the potential
.. math::
E = K (\chi - \chi_0)^2
E = K (\chi - \chi_0)^2
where :math:`\chi` is the improper angle, :math:`\chi_0` is its equilibrium

10
doc/src/improper_hybrid.rst
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@ -1,13 +1,13 @@
.. index:: improper\_style hybrid
.. index:: improper_style hybrid
improper\_style hybrid command
==============================
improper_style hybrid command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style hybrid style1 style2 ...
@ -17,7 +17,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style hybrid harmonic helix
improper_coeff 1 harmonic 120.0 30

12
doc/src/improper_inversion_harmonic.rst
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@ -1,13 +1,13 @@
.. index:: improper\_style inversion/harmonic
.. index:: improper_style inversion/harmonic
improper\_style inversion/harmonic command
==========================================
improper_style inversion/harmonic command
=========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style inversion/harmonic
@ -15,7 +15,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style inversion/harmonic
improper_coeff 1 18.776340 0.000000
@ -28,7 +28,7 @@ out-of-plane angle definition and uses an harmonic potential:
.. math::
E = K \left(\omega - \omega_0\right)^2
E = K \left(\omega - \omega_0\right)^2
where :math:`K` is the force constant and :math:`\omega` is the angle

10
doc/src/improper_none.rst
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@ -1,13 +1,13 @@
.. index:: improper\_style none
.. index:: improper_style none
improper\_style none command
============================
improper_style none command
===========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style none
@ -15,7 +15,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style none

14
doc/src/improper_ring.rst
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@ -1,16 +1,16 @@
.. index:: improper\_style ring
.. index:: improper_style ring
improper\_style ring command
============================
improper_style ring command
===========================
improper\_style ring/omp command
================================
improper_style ring/omp command
===============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style ring
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style ring
improper_coeff 1 8000 70.5

16
doc/src/improper_sqdistharm.rst
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@ -1,18 +1,19 @@
.. index:: improper\_style sqdistharm
.. index:: improper_style sqdistharm
improper\_style sqdistharm command
==================================
improper_style sqdistharm command
=================================
Syntax
""""""
improper\_style sqdistharm
.. code-block:: LAMMPS
improper_style sqdistharm
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style sqdistharm
improper_coeff 1 50.0 0.1
@ -24,8 +25,7 @@ The *sqdistharm* improper style uses the potential
.. math::
E = K (d^2 - {d_0}^2)^2
E = K (d^2 - {d_0}^2)^2
where :math:`d` is the distance between the central atom and the plane formed
by the other three atoms. If the 4 atoms in an improper quadruplet

12
doc/src/improper_style.rst
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@ -1,13 +1,13 @@
.. index:: improper\_style
.. index:: improper_style
improper\_style command
=======================
improper_style command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style style
@ -17,7 +17,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style harmonic
improper_style cvff
@ -118,6 +118,6 @@ Default
"""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style none

18
doc/src/improper_umbrella.rst
View File

@ -1,16 +1,16 @@
.. index:: improper\_style umbrella
.. index:: improper_style umbrella
improper\_style umbrella command
================================
improper_style umbrella command
===============================
improper\_style umbrella/omp command
====================================
improper_style umbrella/omp command
===================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style umbrella
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style umbrella
improper_coeff 1 100.0 180.0
@ -32,8 +32,8 @@ commonly referred to as a classic inversion and used in the
.. math::
E = & \frac{1}{2}K\left( \frac{1}{\sin\omega_0}\right) ^2 \left( \cos\omega - \cos\omega_0\right) ^2 \qquad \omega_0 \neq 0^o \\
E = & K\left( 1-cos\omega\right) \qquad \omega_0 = 0^o
E = & \frac{1}{2}K\left( \frac{1}{\sin\omega_0}\right) ^2 \left( \cos\omega - \cos\omega_0\right) ^2 \qquad \omega_0 \neq 0^o \\
E = & K\left( 1-cos\omega\right) \qquad \omega_0 = 0^o
where :math:`K` is the force constant and :math:`\omega` is the angle between the IL

14
doc/src/improper_zero.rst
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@ -1,25 +1,25 @@
.. index:: improper\_style zero
.. index:: improper_style zero
improper\_style zero command
============================
improper_style zero command
===========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style zero *nocoeff*
improper_style zero [nocoeff]
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
improper_style zero
improper_style zero nocoeff
improper_coeff \*
improper_coeff *
Description
"""""""""""

78
doc/src/kim_commands.rst
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@ -1,22 +1,22 @@
.. index:: kim\_init
.. index:: kim_init, kim_interactions, kim_query, kim_param
kim\_init command
kim_init command
=================
kim\_interactions command
kim_interactions command
=========================
kim\_query command
kim_query command
==================
kim\_param command
kim_param command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
kim_init model user_units unitarg
kim_interactions typeargs
@ -56,7 +56,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
kim_interactions Si
@ -238,7 +238,7 @@ of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994)
potential for Al:
.. parsed-literal::
.. code-block:: LAMMPS
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
boundary p p p
@ -293,15 +293,15 @@ meters, computes the total energy, and prints the cohesive energy in
Joules regardless of the units of the IM.
.. parsed-literal::
.. code-block:: LAMMPS
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode
boundary p p p
lattice fcc 4.032e-10\*${_u_distance}
lattice fcc 4.032e-10*${_u_distance}
region simbox block 0 1 0 1 0 1 units lattice
create_box 1 simbox
create_atoms 1 box
mass 1 4.480134e-26\*${_u_mass}
mass 1 4.480134e-26*${_u_mass}
kim_interactions Al
run 0
variable Ec_in_J equal (pe/count(all))/${_u_energy}
@ -320,11 +320,11 @@ dump file using the :doc:`read_dump <read_dump>` command, the following can
be done to convert the box and all atomic positions to the correct units:
.. parsed-literal::
.. code-block:: LAMMPS
variable xyfinal equal xy\*${_u_distance}
variable xzfinal equal xz\*${_u_distance}
variable yzfinal equal yz\*${_u_distance}
variable xyfinal equal xy*${_u_distance}
variable xzfinal equal xz*${_u_distance}
variable yzfinal equal yz*${_u_distance}
change_box all x scale ${_u_distance} &
y scale ${_u_distance} &
z scale ${_u_distance} &
@ -360,14 +360,14 @@ If the LAMMPS simulation has four atom types, where the first three are Si,
and the fourth is C, the following *kim\_interactions* command would be used:
.. parsed-literal::
.. code-block:: LAMMPS
kim_interactions Si Si Si C
Alternatively, for a model with a fixed mapping the command would be:
.. parsed-literal::
.. code-block:: LAMMPS
kim_interactions fixed_types
@ -379,7 +379,7 @@ the appropriate *pair\_coeff* command. For example, for the
Ercolessi and Adams (1994) KIM PM for Al set by the following commands:
.. parsed-literal::
.. code-block:: LAMMPS
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
...
@ -390,10 +390,10 @@ Ercolessi and Adams (1994) KIM PM for Al set by the following commands:
the *kim\_interactions* command executes the following LAMMPS input commands:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005
pair_coeff \* \* Al
pair_coeff * * Al
For a KIM SM, the generated input commands may be more complex
and require that LAMMPS is built with the required packages included
@ -403,7 +403,7 @@ For example, for the Strachan et al. (2003) ReaxFF SM
set by the following commands:
.. parsed-literal::
.. code-block:: LAMMPS
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
...
@ -414,10 +414,10 @@ set by the following commands:
the *kim\_interactions* command executes the following LAMMPS input commands:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style reax/c lmp_control safezone 2.0 mincap 100
pair_coeff \* \* ffield.reax.rdx C H N O
pair_coeff * * ffield.reax.rdx C H N O
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
Note that the files *lmp\_control*, *ffield.reax.rdx* and *param.qeq*
@ -449,7 +449,7 @@ of an IM set by *kim\_init* for material properties archived in
The syntax for the *kim\_query* command is as follows:
.. parsed-literal::
.. code-block:: LAMMPS
kim_query variable formatarg query_function queryargs
@ -509,7 +509,7 @@ or analysis phases of LAMMPS simulations. Some examples are given below.
**Define an equilibrium fcc crystal**
.. parsed-literal::
.. code-block:: LAMMPS
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
boundary p p p
@ -533,7 +533,7 @@ changed to: "lattice fcc ${a0}\*${\_u_distance}".
**Define an equilibrium hcp crystal**
.. parsed-literal::
.. code-block:: LAMMPS
kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal
boundary p p p
@ -556,14 +556,14 @@ input script more readable.
**Define a crystal at finite temperature accounting for thermal expansion**
.. parsed-literal::
.. code-block:: LAMMPS
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
boundary p p p
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Al"] units=["angstrom"]
kim_query alpha get_linear_thermal_expansion_coefficient_cubic crystal=["fcc"] species=["Al"] units=["1/K"] temperature=[293.15] temperature_units=["K"]
variable DeltaT equal 300
lattice fcc ${a0}\*${alpha}\*${DeltaT}
lattice fcc ${a0}*${alpha}*${DeltaT}
...
As in the previous example, the equilibrium lattice constant is obtained
@ -587,7 +587,7 @@ potential.
**Compute defect formation energy**
.. parsed-literal::
.. code-block:: LAMMPS
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
...
@ -595,7 +595,7 @@ potential.
... which is stored in the variable *Etot*
...
kim_query Ec get_cohesive_energy_cubic crystal=["fcc"] species=["Al"] units=["eV"]
variable Eform equal ${Etot} - count(all)\*${Ec}
variable Eform equal ${Etot} - count(all)*${Ec}
...
The defect formation energy *Eform* is computed by subtracting from *Etot* the
@ -654,7 +654,7 @@ for details).
The syntax for the *kim\_param* command is as follows:
.. parsed-literal::
.. code-block:: LAMMPS
kim_param get param_name index_range variable formatarg
kim_param set param_name index_range values
@ -715,7 +715,7 @@ clarifications are provided below.
**Getting a scalar parameter**
.. parsed-literal::
.. code-block:: LAMMPS
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
...
@ -729,7 +729,7 @@ LAMMPS variable.
**Getting multiple scalar parameters with a single call**
.. parsed-literal::
.. code-block:: LAMMPS
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
...
@ -744,7 +744,7 @@ There are several options when getting a range of values from a parameter
determined by the *formatarg* argument.
.. parsed-literal::
.. code-block:: LAMMPS
kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
...
@ -767,7 +767,7 @@ lambda retrieved by the *get* operation are placed in the LAMMPS variables
is provided at the top of the model page.
.. parsed-literal::
.. code-block:: LAMMPS
kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
...
@ -789,7 +789,7 @@ as shown in the example. At each iteration of the loop *LAM\_VALUE*
contains the current value of lambda.
.. parsed-literal::
.. code-block:: LAMMPS
kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
...
@ -804,7 +804,7 @@ the lambda array is appended to create the variable names.
**Setting a scalar parameter**
.. parsed-literal::
.. code-block:: LAMMPS
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
...
@ -816,7 +816,7 @@ and *set* commands work together, so that a *get* following a *set*
operation will return the new value that was set. For example:
.. parsed-literal::
.. code-block:: LAMMPS
...
kim_interactions Si
@ -849,7 +849,7 @@ be used when setting parameters.
**Setting a range of values of a parameter**
.. parsed-literal::
.. code-block:: LAMMPS
kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal
...

13
doc/src/kspace_modify.rst
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@ -1,13 +1,13 @@
.. index:: kspace\_modify
.. index:: kspace_modify
kspace\_modify command
======================
kspace_modify command
=====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
kspace_modify keyword value ...
@ -62,7 +62,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
kspace_modify mesh 24 24 30 order 6
kspace_modify slab 3.0
@ -483,7 +483,8 @@ parameters, see the :doc:`Howto dispersion <Howto_dispersion>` doc page.
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

26
doc/src/kspace_style.rst
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@ -1,13 +1,13 @@
.. index:: kspace\_style
.. index:: kspace_style
kspace\_style command
=====================
kspace_style command
====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
kspace_style style value
@ -82,7 +82,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
kspace_style pppm 1.0e-4
kspace_style pppm/cg 1.0e-5 1.0e-6
@ -94,12 +94,12 @@ Description
"""""""""""
Define a long-range solver for LAMMPS to use each timestep to compute
long-range Coulombic interactions or long-range 1/r\^6 interactions.
long-range Coulombic interactions or long-range :math:`1/r^6` interactions.
Most of the long-range solvers perform their computation in K-space,
hence the name of this command.
When such a solver is used in conjunction with an appropriate pair
style, the cutoff for Coulombic or 1/r\^N interactions is effectively
style, the cutoff for Coulombic or :math:`1/r^N` interactions is effectively
infinite. If the Coulombic case, this means each charge in the system
interacts with charges in an infinite array of periodic images of the
simulation domain.
@ -128,9 +128,9 @@ The *ewald* style performs a standard Ewald summation as described in
any solid-state physics text.
The *ewald/disp* style adds a long-range dispersion sum option for
1/r\^6 potentials and is useful for simulation of interfaces
:math:`1/r^6` potentials and is useful for simulation of interfaces
:ref:`(Veld) <Veld>`. It also performs standard Coulombic Ewald summations,
but in a more efficient manner than the *ewald* style. The 1/r\^6
but in a more efficient manner than the *ewald* style. The :math:`1/r^6`
capability means that Lennard-Jones or Buckingham potentials can be
used without a cutoff, i.e. they become full long-range potentials.
The *ewald/disp* style can also be used with point-dipoles, see
@ -153,8 +153,8 @@ to solve Poisson's equation on the mesh, then interpolates electric
fields on the mesh points back to the atoms. It is closely related to
the particle-mesh Ewald technique (PME) :ref:`(Darden) <Darden>` used in
AMBER and CHARMM. The cost of traditional Ewald summation scales as
N\^(3/2) where N is the number of atoms in the system. The PPPM solver
scales as Nlog(N) due to the FFTs, so it is almost always a faster
:math:`N^{\frac{3}{2}}` where :math:`N` is the number of atoms in the system. The PPPM solver
scales as :math:`N \log{N}` due to the FFTs, so it is almost always a faster
choice :ref:`(Pollock) <Pollock>`.
The *pppm/cg* style is identical to the *pppm* style except that it
@ -244,7 +244,7 @@ The *msm* style invokes a multi-level summation method MSM solver,
:ref:`(Hardy) <Hardy2006>` or :ref:`(Hardy2) <Hardy2009>`, which maps atom charge
to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser
meshes on which direct Coulomb solvers are done. This method does not
use FFTs and scales as N. It may therefore be faster than the other
use FFTs and scales as :math:`N`. It may therefore be faster than the other
K-space solvers for relatively large problems when running on large
core counts. MSM can also be used for non-periodic boundary conditions
and for mixed periodic and non-periodic boundaries.
@ -466,7 +466,7 @@ Default
"""""""
.. parsed-literal::
.. code-block:: LAMMPS
kspace_style none

24
doc/src/min_modify.rst
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@ -1,13 +1,13 @@
.. index:: min\_modify
.. index:: min_modify
min\_modify command
===================
min_modify command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
min_modify keyword values ...
@ -39,7 +39,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
min_modify dmax 0.2
min_modify integrator verlet tmax 4
@ -91,20 +91,23 @@ The choice of a norm can be modified for the min styles *cg*\ , *sd*\
the 2-norm (Euclidean length) of the global force vector:
.. math::
|| \vec{F} ||_{2} = \sqrt{\vec{F}_1+ \cdots + \vec{F}_N}
|| \vec{F} ||_{2} = \sqrt{\vec{F}_1+ \cdots + \vec{F}_N}
The *max* norm computes the length of the 3-vector force
for each atom (2-norm), and takes the maximum value of those across
all atoms
.. math::
|| \vec{F} ||_{max} = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
|| \vec{F} ||_{max} = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
The *inf* norm takes the maximum component across the forces of
all atoms in the system:
.. math::
|| \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right)
|| \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right)
For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force
norm is replaced by the spin-torque norm.
@ -155,8 +158,9 @@ The :doc:`min_style <min_style>` *fire* is an optimized implementation of
:doc:`min_style <min_style>` *fire/old*. It can however behave similarly
to the *fire/old* style by using the following set of parameters:
.. parsed-literal::
min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 &
.. code-block:: LAMMPS
min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 &
dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 &
vdfmax 100000 halfstepback no initialdelay no

24
doc/src/min_spin.rst
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@ -1,19 +1,19 @@
.. index:: min\_style spin
.. index:: min_style spin
min\_style spin command
=======================
min_style spin command
======================
min\_style spin/cg command
==========================
min_style spin/cg command
=========================
min\_style spin/lbfgs command
=============================
min_style spin/lbfgs command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
min_style spin
min_style spin/cg
@ -23,7 +23,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
min_style spin/lbfgs
min_modify line spin_cubic discrete_factor 10.0
@ -38,7 +38,8 @@ Style *spin* defines a damped spin dynamics with an adaptive
timestep, according to:
.. math::
\frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right)
\frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right)
with :math:`\lambda` a damping coefficient (similar to a Gilbert
damping). :math:`\lambda` can be defined by setting the
@ -50,7 +51,8 @@ by the largest precession frequency that has to be solved in the
system:
.. math::
{\Delta t}_{\rm max} = \frac{2\pi}{\kappa \left|\vec{\omega}_{\rm max} \right|}
{\Delta t}_{\rm max} = \frac{2\pi}{\kappa \left|\vec{\omega}_{\rm max} \right|}
with :math:`\left|\vec{\omega}_{\rm max}\right|` the norm of the largest precession
frequency in the system (across all processes, and across all replicas if a

15
doc/src/min_style.rst
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@ -1,13 +1,13 @@
.. index:: min\_style
.. index:: min_style
min\_style command
==================
min_style command
=================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
min_style style
@ -17,7 +17,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
min_style cg
min_style spin
@ -148,7 +148,8 @@ instructions on how to use the accelerated styles effectively.
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""
@ -159,7 +160,7 @@ Default
"""""""
.. parsed-literal::
.. code-block:: LAMMPS
min_style cg

10
doc/src/neigh_modify.rst
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@ -1,13 +1,13 @@
.. index:: neigh\_modify
.. index:: neigh_modify
neigh\_modify command
=====================
neigh_modify command
====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
neigh_modify keyword values ...
@ -55,7 +55,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
neigh_modify every 2 delay 10 check yes page 100000
neigh_modify exclude type 2 3

12
doc/src/pair_awpmd.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style awpmd/cut
.. index:: pair_style awpmd/cut
pair\_style awpmd/cut command
=============================
pair_style awpmd/cut command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style awpmd/cut Rc keyword value ...
@ -37,11 +37,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style awpmd/cut -1
pair_style awpmd/cut 40.0 uhf free
pair_coeff \* \*
pair_coeff * *
pair_coeff 2 2 20.0
Description

14
doc/src/pair_bop.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style bop
.. index:: pair_style bop
pair\_style bop command
=======================
pair_style bop command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style bop keyword ...
@ -24,12 +24,12 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style bop
pair_coeff \* \* ../potentials/CdTe_bop Cd Te
pair_coeff * * ../potentials/CdTe_bop Cd Te
pair_style bop save
pair_coeff \* \* ../potentials/CdTe.bop.table Cd Te Te
pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te
comm_modify cutoff 14.70
Description

64
doc/src/pair_born.rst
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@ -1,46 +1,46 @@
.. index:: pair\_style born
.. index:: pair_style born
pair\_style born command
========================
pair_style born command
=======================
pair\_style born/omp command
============================
pair_style born/omp command
===========================
pair\_style born/gpu command
============================
pair_style born/gpu command
===========================
pair\_style born/coul/long command
==================================
pair\_style born/coul/long/gpu command
======================================
pair\_style born/coul/long/omp command
======================================
pair\_style born/coul/msm command
pair_style born/coul/long command
=================================
pair\_style born/coul/msm/omp command
pair_style born/coul/long/gpu command
=====================================
pair\_style born/coul/wolf command
==================================
pair_style born/coul/long/omp command
=====================================
pair\_style born/coul/wolf/gpu command
======================================
pair_style born/coul/msm command
================================
pair\_style born/coul/wolf/omp command
======================================
pair_style born/coul/msm/omp command
====================================
pair\_style born/coul/dsf command
pair_style born/coul/wolf command
=================================
pair_style born/coul/wolf/gpu command
=====================================
pair_style born/coul/wolf/omp command
=====================================
pair_style born/coul/dsf command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -71,29 +71,29 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style born 10.0
pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
pair_style born/coul/long 10.0
pair_style born/coul/long 10.0 8.
pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
pair_style born/coul/msm 10.0
pair_style born/coul/msm 10.0 8.0
pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
pair_style born/coul/wolf 0.25 10.0
pair_style born/coul/wolf 0.25 10.0 9.0
pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
pair_style born/coul/dsf 0.1 10.0 12.0
pair_coeff \* \* 0.0 1.00 0.00 0.00 0.00
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50
Description

22
doc/src/pair_brownian.rst
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@ -1,22 +1,22 @@
.. index:: pair\_style brownian
.. index:: pair_style brownian
pair\_style brownian command
============================
pair_style brownian command
===========================
pair\_style brownian/omp command
pair_style brownian/omp command
================================
pair\_style brownian/poly command
=================================
pair_style brownian/poly command
================================
pair\_style brownian/poly/omp command
=====================================
pair_style brownian/poly/omp command
====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
@ -35,11 +35,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
pair_coeff 1 1 2.05 2.8
pair_coeff \* \*
pair_coeff * *
Description
"""""""""""

50
doc/src/pair_buck.rst
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@ -1,61 +1,61 @@
.. index:: pair\_style buck
.. index:: pair_style buck
pair\_style buck command
pair_style buck command
========================
pair\_style buck/gpu command
pair_style buck/gpu command
============================
pair\_style buck/intel command
pair_style buck/intel command
==============================
pair\_style buck/kk command
pair_style buck/kk command
===========================
pair\_style buck/omp command
pair_style buck/omp command
============================
pair\_style buck/coul/cut command
pair_style buck/coul/cut command
=================================
pair\_style buck/coul/cut/gpu command
pair_style buck/coul/cut/gpu command
=====================================
pair\_style buck/coul/cut/intel command
pair_style buck/coul/cut/intel command
=======================================
pair\_style buck/coul/cut/kk command
pair_style buck/coul/cut/kk command
====================================
pair\_style buck/coul/cut/omp command
pair_style buck/coul/cut/omp command
=====================================
pair\_style buck/coul/long command
pair_style buck/coul/long command
==================================
pair\_style buck/coul/long/gpu command
pair_style buck/coul/long/gpu command
======================================
pair\_style buck/coul/long/intel command
pair_style buck/coul/long/intel command
========================================
pair\_style buck/coul/long/kk command
pair_style buck/coul/long/kk command
=====================================
pair\_style buck/coul/long/omp command
pair_style buck/coul/long/omp command
======================================
pair\_style buck/coul/msm command
pair_style buck/coul/msm command
=================================
pair\_style buck/coul/msm/omp command
pair_style buck/coul/msm/omp command
=====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -81,26 +81,26 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style buck 2.5
pair_coeff \* \* 100.0 1.5 200.0
pair_coeff \* \* 100.0 1.5 200.0 3.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0 3.0
pair_style buck/coul/cut 10.0
pair_style buck/coul/cut 10.0 8.0
pair_coeff \* \* 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0
pair_style buck/coul/long 10.0
pair_style buck/coul/long 10.0 8.0
pair_coeff \* \* 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_style buck/coul/msm 10.0
pair_style buck/coul/msm 10.0 8.0
pair_coeff \* \* 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
Description

18
doc/src/pair_buck6d_coul_gauss.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style buck6d/coul/gauss/dsf
.. index:: pair_style buck6d/coul/gauss/dsf
pair\_style buck6d/coul/gauss/dsf command
pair_style buck6d/coul/gauss/dsf command
========================================
pair_style buck6d/coul/gauss/long command
=========================================
pair\_style buck6d/coul/gauss/long command
==========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -34,7 +34,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style buck6d/coul/gauss/dsf 0.9000 12.0000
pair_coeff 1 1 1030. 3.061 457.179 4.521 0.608
@ -52,7 +52,7 @@ computes a dispersion damped Buckingham potential:
.. math::
E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\
E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\
where A and C are a force constant, :math:`\kappa` is an ionic-pair dependent
@ -82,7 +82,7 @@ is thus evaluated as:
.. math::
E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c
E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c
where C is an energy-conversion constant, :math:`q_i` and :math:`q_j`

12
doc/src/pair_buck_long.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style buck/long/coul/long
.. index:: pair_style buck/long/coul/long
pair\_style buck/long/coul/long command
pair_style buck/long/coul/long command
=======================================
pair\_style buck/long/coul/long/omp command
pair_style buck/long/coul/long/omp command
===========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2)
@ -36,12 +36,12 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style buck/long/coul/long cut off 2.5
pair_style buck/long/coul/long cut long 2.5 4.0
pair_style buck/long/coul/long long long 4.0
pair_coeff \* \* 1 1
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4
Description

72
doc/src/pair_charmm.rst
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@ -1,61 +1,61 @@
.. index:: pair\_style lj/charmm/coul/charmm
.. index:: pair_style lj/charmm/coul/charmm
pair\_style lj/charmm/coul/charmm command
pair_style lj/charmm/coul/charmm command
=========================================
pair\_style lj/charmm/coul/charmm/intel command
pair_style lj/charmm/coul/charmm/intel command
===============================================
pair\_style lj/charmm/coul/charmm/kk command
pair_style lj/charmm/coul/charmm/kk command
============================================
pair\_style lj/charmm/coul/charmm/omp command
pair_style lj/charmm/coul/charmm/omp command
=============================================
pair\_style lj/charmm/coul/charmm/implicit command
pair_style lj/charmm/coul/charmm/implicit command
==================================================
pair\_style lj/charmm/coul/charmm/implicit/kk command
pair_style lj/charmm/coul/charmm/implicit/kk command
=====================================================
pair\_style lj/charmm/coul/charmm/implicit/omp command
pair_style lj/charmm/coul/charmm/implicit/omp command
======================================================
pair\_style lj/charmm/coul/long command
pair_style lj/charmm/coul/long command
=======================================
pair\_style lj/charmm/coul/long/gpu command
pair_style lj/charmm/coul/long/gpu command
===========================================
pair\_style lj/charmm/coul/long/intel command
pair_style lj/charmm/coul/long/intel command
=============================================
pair\_style lj/charmm/coul/long/kk command
pair_style lj/charmm/coul/long/kk command
==========================================
pair\_style lj/charmm/coul/long/opt command
pair_style lj/charmm/coul/long/opt command
===========================================
pair\_style lj/charmm/coul/long/omp command
pair_style lj/charmm/coul/long/omp command
===========================================
pair\_style lj/charmm/coul/msm command
pair_style lj/charmm/coul/msm command
======================================
pair\_style lj/charmm/coul/msm/omp command
pair_style lj/charmm/coul/msm/omp command
==========================================
pair\_style lj/charmmfsw/coul/charmmfsh command
pair_style lj/charmmfsw/coul/charmmfsh command
===============================================
pair\_style lj/charmmfsw/coul/long command
pair_style lj/charmmfsw/coul/long command
==========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -88,30 +88,30 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/charmm/coul/charmm 8.0 10.0
pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0
pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 9.0
pair_coeff \* \* 100.0 2.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
pair_coeff \* \* 100.0 2.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
pair_style lj/charmm/coul/long 8.0 10.0
pair_style lj/charmm/coul/long 8.0 10.0 9.0
pair_style lj/charmmfsw/coul/long 8.0 10.0
pair_style lj/charmmfsw/coul/long 8.0 10.0 9.0
pair_coeff \* \* 100.0 2.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
pair_style lj/charmm/coul/msm 8.0 10.0
pair_style lj/charmm/coul/msm 8.0 10.0 9.0
pair_coeff \* \* 100.0 2.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
Description
@ -162,18 +162,18 @@ artifacts.
.. math::
E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\
= & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
= & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\
= & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
= & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \\
C(r) = & \frac{C q_i q_j}{ \epsilon r} \\
S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
\left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
{ \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\
= & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
= & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\
= & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
= & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \\
C(r) = & \frac{C q_i q_j}{ \epsilon r} \\
S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
\left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
{ \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
where S(r) is the energy switching function mentioned above for the

54
doc/src/pair_class2.rst
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@ -1,43 +1,43 @@
.. index:: pair\_style lj/class2
.. index:: pair_style lj/class2
pair\_style lj/class2 command
=============================
pair_style lj/class2 command
============================
pair\_style lj/class2/gpu command
=================================
pair\_style lj/class2/kk command
pair_style lj/class2/gpu command
================================
pair\_style lj/class2/omp command
=================================
pair_style lj/class2/kk command
===============================
pair\_style lj/class2/coul/cut command
======================================
pair_style lj/class2/omp command
================================
pair\_style lj/class2/coul/cut/kk command
pair_style lj/class2/coul/cut command
=====================================
pair_style lj/class2/coul/cut/kk command
========================================
pair_style lj/class2/coul/cut/omp command
=========================================
pair\_style lj/class2/coul/cut/omp command
pair_style lj/class2/coul/long command
======================================
pair_style lj/class2/coul/long/gpu command
==========================================
pair\_style lj/class2/coul/long command
=======================================
pair_style lj/class2/coul/long/kk command
=========================================
pair\_style lj/class2/coul/long/gpu command
===========================================
pair\_style lj/class2/coul/long/kk command
pair_style lj/class2/coul/long/omp command
==========================================
pair\_style lj/class2/coul/long/omp command
===========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -60,7 +60,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/class2 10.0
pair_coeff \* \* 100.0 2.5
@ -84,9 +84,9 @@ The *lj/class2* styles compute a 6/9 Lennard-Jones potential given by
.. math::
E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 -
3 \left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 -
3 \left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
:math:`r_c` is the cutoff.

12
doc/src/pair_coeff.rst
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@ -1,13 +1,13 @@
.. index:: pair\_coeff
.. index:: pair_coeff
pair\_coeff command
===================
pair_coeff command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff I J args
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff 1 2 1.0 1.0 2.5
pair_coeff 2 \* 1.0 1.0
@ -56,7 +56,7 @@ same I,J pair. For example, these commands set the coeffs for all I,J
pairs, then overwrite the coeffs for just the I,J = 2,3 pair:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* 1.0 1.0 2.5
pair_coeff 2 3 2.0 1.0 1.12

20
doc/src/pair_colloid.rst
View File

@ -1,19 +1,19 @@
.. index:: pair\_style colloid
.. index:: pair_style colloid
pair\_style colloid command
===========================
pair_style colloid command
==========================
pair\_style colloid/gpu command
===============================
pair_style colloid/gpu command
==============================
pair\_style colloid/omp command
===============================
pair_style colloid/omp command
==============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style colloid cutoff
@ -23,10 +23,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style colloid 10.0
pair_coeff \* \* 25 1.0 10.0 10.0
pair_coeff * * 25 1.0 10.0 10.0
pair_coeff 1 1 144 1.0 0.0 0.0 3.0
pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0
pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0

33
doc/src/pair_comb.rst
View File

@ -1,23 +1,26 @@
.. index:: pair\_style comb
.. index:: pair_style comb
pair\_style comb command
pair_style comb command
=======================
pair_style comb/omp command
===========================
pair_style comb3 command
========================
pair\_style comb/omp command
============================
pair\_style comb3 command
=========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style comb
pair_style comb3 keyword
.. parsed-literal::
keyword = *polar*
*polar* value = *polar_on* or *polar_off* = whether or not to include atomic polarization
@ -27,14 +30,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style comb
pair_coeff \* \* ../potentials/ffield.comb Si
pair_coeff \* \* ../potentials/ffield.comb Hf Si O
pair_coeff * * ../potentials/ffield.comb Si
pair_coeff * * ../potentials/ffield.comb Hf Si O
pair_style comb3 polar_off
pair_coeff \* \* ../potentials/ffield.comb3 O Cu N C O
pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
Description
"""""""""""
@ -82,9 +85,9 @@ last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
use the following pair\_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* ../potentials/ffield.comb Si Hf O Si
pair_coeff * * ../potentials/ffield.comb Si Hf O Si
The first two arguments must be \* \* so as to span all LAMMPS atom
types. The first and last Si arguments map LAMMPS atom types 1 and 4

12
doc/src/pair_cosine_squared.rst
View File

@ -1,20 +1,20 @@
.. index:: pair\_style cosine/squared
.. index:: pair_style cosine/squared
pair\_style cosine/squared command
==================================
pair_style cosine/squared command
=================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style cosine/squared cutoff
* cutoff = global cutoff for cosine-squared interactions (distance units)
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff i j eps sigma
pair_coeff i j eps sigma cutoff
@ -31,7 +31,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style cosine/squared 3.0
pair_coeff \* \* 1.0 1.3

167
doc/src/pair_coul.rst
View File

@ -1,88 +1,88 @@
.. index:: pair\_style coul/cut
.. index:: pair_style coul/cut
pair\_style coul/cut command
============================
pair_style coul/cut command
===========================
pair\_style coul/cut/gpu command
================================
pair\_style coul/cut/kk command
pair_style coul/cut/gpu command
===============================
pair\_style coul/cut/omp command
================================
pair\_style coul/debye command
pair_style coul/cut/kk command
==============================
pair\_style coul/debye/gpu command
==================================
pair\_style coul/debye/kk command
=================================
pair\_style coul/debye/omp command
==================================
pair\_style coul/dsf command
============================
pair\_style coul/dsf/gpu command
================================
pair\_style coul/dsf/kk command
pair_style coul/cut/omp command
===============================
pair\_style coul/dsf/omp command
================================
pair\_style coul/long command
pair_style coul/debye command
=============================
pair\_style coul/long/omp command
pair_style coul/debye/gpu command
=================================
pair\_style coul/long/gpu command
pair_style coul/debye/kk command
================================
pair_style coul/debye/omp command
=================================
pair\_style coul/long/kk command
================================
pair_style coul/dsf command
===========================
pair\_style coul/msm command
============================
pair_style coul/dsf/gpu command
===============================
pair\_style coul/msm/omp command
================================
pair\_style coul/streitz command
================================
pair\_style coul/wolf command
=============================
pair\_style coul/wolf/kk command
================================
pair\_style coul/wolf/omp command
=================================
pair\_style tip4p/cut command
=============================
pair\_style tip4p/long command
pair_style coul/dsf/kk command
==============================
pair\_style tip4p/cut/omp command
=================================
pair_style coul/dsf/omp command
===============================
pair\_style tip4p/long/omp command
==================================
pair_style coul/long command
============================
pair_style coul/long/omp command
================================
pair_style coul/long/gpu command
================================
pair_style coul/long/kk command
===============================
pair_style coul/msm command
===========================
pair_style coul/msm/omp command
===============================
pair_style coul/streitz command
===============================
pair_style coul/wolf command
============================
pair_style coul/wolf/kk command
===============================
pair_style coul/wolf/omp command
================================
pair_style tip4p/cut command
============================
pair_style tip4p/long command
=============================
pair_style tip4p/cut/omp command
================================
pair_style tip4p/long/omp command
=================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style coul/cut cutoff
pair_style coul/debye kappa cutoff
@ -102,37 +102,37 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style coul/cut 2.5
pair_coeff \* \*
pair_coeff * *
pair_coeff 2 2 3.5
pair_style coul/debye 1.4 3.0
pair_coeff \* \*
pair_coeff * *
pair_coeff 2 2 3.5
pair_style coul/dsf 0.05 10.0
pair_coeff \* \*
pair_coeff * *
pair_style coul/long 10.0
pair_coeff \* \*
pair_coeff * *
pair_style coul/msm 10.0
pair_coeff \* \*
pair_coeff * *
pair_style coul/wolf 0.2 9.0
pair_coeff \* \*
pair_coeff * *
pair_style coul/streitz 12.0 ewald
pair_style coul/streitz 12.0 wolf 0.30
pair_coeff \* \* AlO.streitz Al O
pair_coeff * * AlO.streitz Al O
pair_style tip4p/cut 1 2 7 8 0.15 12.0
pair_coeff \* \*
pair_coeff * *
pair_style tip4p/long 1 2 7 8 0.15 10.0
pair_coeff \* \*
pair_coeff * *
Description
"""""""""""
@ -142,7 +142,7 @@ potential given by
.. math::
E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
where C is an energy-conversion constant, Qi and Qj are the charges on
@ -159,7 +159,7 @@ Coulombic term, given by
.. math::
E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c
E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c
where :math:`\kappa` is the Debye length. This potential is another way to
@ -174,9 +174,8 @@ shifted force model described in :ref:`Fennell <Fennell1>`, given by:
.. math::
E =
q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
E = q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
where :math:`\alpha` is the damping parameter and erfc() is the
@ -194,10 +193,10 @@ summation method, described in :ref:`Wolf <Wolf1>`, given by:
.. math::
E_i = \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
\frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
E_i = \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
\frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
where :math:`\alpha` is the damping parameter, and erc() and erfc() are
@ -228,11 +227,11 @@ the :doc:`pair_style hybrid/overlay <pair_hybrid>` command. Likewise,
charge equilibration must be performed via the :doc:`fix qeq/slater <fix_qeq>` command. For example:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
pair_coeff \* \* coul/streitz AlO.streitz Al O
pair_coeff \* \* eam/alloy AlO.eam.alloy Al O
pair_coeff * * coul/streitz AlO.streitz Al O
pair_coeff * * eam/alloy AlO.eam.alloy Al O
fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
The keyword *wolf* in the coul/streitz command denotes computing
@ -242,7 +241,7 @@ coul/wolf potential above. Alternatively, Coulombic interactions can
be computed via an Ewald summation. For example:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
kspace_style ewald 1e-6

14
doc/src/pair_coul_diel.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style coul/diel
.. index:: pair_style coul/diel
pair\_style coul/diel command
=============================
pair_style coul/diel command
============================
pair\_style coul/diel/omp command
=================================
pair_style coul/diel/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style coul/diel cutoff
@ -20,7 +20,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style coul/diel 3.5
pair_coeff 1 4 78. 1.375 0.112

16
doc/src/pair_coul_shield.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style coul/shield
.. index:: pair_style coul/shield
pair\_style coul/shield command
===============================
pair_style coul/shield command
==============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style coul/shield cutoff tap_flag
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style coul/shield 16.0 1
pair_coeff 1 2 0.70
@ -41,9 +41,9 @@ the pair style :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
.. math::
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\
{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\
{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

38
doc/src/pair_cs.rst
View File

@ -1,40 +1,40 @@
.. index:: pair\_style born/coul/dsf/cs
.. index:: pair_style born/coul/dsf/cs
pair\_style born/coul/dsf/cs command
pair_style born/coul/dsf/cs command
====================================
pair\_style born/coul/long/cs command
pair_style born/coul/long/cs command
=====================================
pair\_style born/coul/long/cs/gpu command
pair_style born/coul/long/cs/gpu command
=========================================
pair\_style born/coul/wolf/cs command
pair_style born/coul/wolf/cs command
=====================================
pair\_style born/coul/wolf/cs/gpu command
pair_style born/coul/wolf/cs/gpu command
=========================================
pair\_style buck/coul/long/cs command
pair_style buck/coul/long/cs command
=====================================
pair\_style coul/long/cs command
pair_style coul/long/cs command
================================
pair\_style coul/long/cs/gpu command
pair_style coul/long/cs/gpu command
====================================
pair\_style coul/wolf/cs command
pair_style coul/wolf/cs command
================================
pair\_style lj/cut/coul/long/cs command
pair_style lj/cut/coul/long/cs command
=======================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -71,33 +71,33 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style born/coul/dsf/cs 0.1 10.0 12.0
pair_coeff \* \* 0.0 1.00 0.00 0.00 0.00
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50
pair_style born/coul/long/cs 10.0 8.0
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
pair_style born/coul/wolf/cs 0.25 10.0 12.0
pair_coeff \* \* 0.0 1.00 0.00 0.00 0.00
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50
pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long/cs 10.0 8.0
pair_coeff \* \* 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_style coul/long/cs 10.0
pair_coeff \* \*
pair_coeff * *
pair_style coul/wolf/cs 0.2 9.0
pair_coeff \* \*
pair_coeff * *
pair_style lj/cut/coul/long/cs 10.0
pair_style lj/cut/coul/long/cs 10.0 8.0
pair_coeff \* \* 100.0 3.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
Description

52
doc/src/pair_dipole.rst
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@ -1,37 +1,37 @@
.. index:: pair\_style lj/cut/dipole/cut
.. index:: pair_style lj/cut/dipole/cut
pair\_style lj/cut/dipole/cut command
=====================================
pair_style lj/cut/dipole/cut command
====================================
pair\_style lj/cut/dipole/cut/gpu command
=========================================
pair_style lj/cut/dipole/cut/gpu command
========================================
pair\_style lj/cut/dipole/cut/omp command
=========================================
pair_style lj/cut/dipole/cut/omp command
========================================
pair\_style lj/sf/dipole/sf command
===================================
pair_style lj/sf/dipole/sf command
==================================
pair\_style lj/sf/dipole/sf/gpu command
=======================================
pair\_style lj/sf/dipole/sf/omp command
=======================================
pair\_style lj/cut/dipole/long command
pair_style lj/sf/dipole/sf/gpu command
======================================
pair\_style lj/cut/dipole/long/gpu command
==========================================
pair_style lj/sf/dipole/sf/omp command
======================================
pair\_style lj/long/dipole/long command
=======================================
pair_style lj/cut/dipole/long command
=====================================
pair_style lj/cut/dipole/long/gpu command
=========================================
pair_style lj/long/dipole/long command
======================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/cut/dipole/cut cutoff (cutoff2)
pair_style lj/sf/dipole/sf cutoff (cutoff2)
@ -61,23 +61,23 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/cut/dipole/cut 10.0
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
pair_style lj/sf/dipole/sf 9.0
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
pair_coeff 2 3 1.0 1.0 2.5 4.0
pair_style lj/cut/dipole/long 10.0
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
pair_style lj/long/dipole/long long long 3.5 10.0
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
Description

38
doc/src/pair_dpd.rst
View File

@ -1,31 +1,31 @@
.. index:: pair\_style dpd
.. index:: pair_style dpd
pair\_style dpd command
=======================
pair_style dpd command
======================
pair\_style dpd/gpu command
===========================
pair_style dpd/gpu command
==========================
pair\_style dpd/intel command
=============================
pair_style dpd/intel command
============================
pair\_style dpd/omp command
===========================
pair_style dpd/omp command
==========================
pair\_style dpd/tstat command
=============================
pair_style dpd/tstat command
============================
pair\_style dpd/tstat/gpu command
=================================
pair_style dpd/tstat/gpu command
================================
pair\_style dpd/tstat/omp command
=================================
pair_style dpd/tstat/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style dpd T cutoff seed
pair_style dpd/tstat Tstart Tstop cutoff seed
@ -39,14 +39,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style dpd 1.0 2.5 34387
pair_coeff \* \* 3.0 1.0
pair_coeff * * 3.0 1.0
pair_coeff 1 1 3.0 1.0 1.0
pair_style dpd/tstat 1.0 1.0 2.5 34387
pair_coeff \* \* 1.0
pair_coeff * * 1.0
pair_coeff 1 1 1.0 1.0
Description

34
doc/src/pair_dpd_fdt.rst
View File

@ -1,19 +1,19 @@
.. index:: pair\_style dpd/fdt
.. index:: pair_style dpd/fdt
pair\_style dpd/fdt command
===========================
pair_style dpd/fdt command
==========================
pair\_style dpd/fdt/energy command
==================================
pair_style dpd/fdt/energy command
=================================
pair\_style dpd/fdt/energy/kk command
=====================================
pair_style dpd/fdt/energy/kk command
====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -35,13 +35,13 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style dpd/fdt 300.0 2.5 34387
pair_coeff \* \* 3.0 1.0 2.5
pair_coeff * * 3.0 1.0 2.5
pair_style dpd/fdt/energy 2.5 34387
pair_coeff \* \* 3.0 1.0 0.1 2.5
pair_coeff * * 3.0 1.0 0.1 2.5
Description
"""""""""""
@ -107,18 +107,18 @@ energies are computed within style *dpd/fdt/energy* as:
.. math::
du_{i}^{cond} = & \kappa_{ij}(\frac{1}{\theta_{i}}-\frac{1}{\theta_{j}})\omega_{ij}^{2} + \alpha_{ij}\omega_{ij}\zeta_{ij}^{q}(\Delta{t})^{-1/2} \\
du_{i}^{mech} = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} -
\frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} -
\frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2}
du_{i}^{mech} = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} -
\frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} -
\frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2}
where
.. math::
\alpha_{ij}^{2} = & 2k_{B}\kappa_{ij} \\
\sigma^{2}_{ij} = & 2\gamma_{ij}k_{B}\Theta_{ij} \\
\Theta_{ij}^{-1} = & \frac{1}{2}(\frac{1}{\theta_{i}}+\frac{1}{\theta_{j}})
\alpha_{ij}^{2} = & 2k_{B}\kappa_{ij} \\
\sigma^{2}_{ij} = & 2\gamma_{ij}k_{B}\Theta_{ij} \\
\Theta_{ij}^{-1} = & \frac{1}{2}(\frac{1}{\theta_{i}}+\frac{1}{\theta_{j}})
:math:`\zeta_ij^q` is a second Gaussian random number with zero mean and unit

34
doc/src/pair_drip.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style drip
.. index:: pair_style drip
pair\_style drip command
========================
pair_style drip command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay drip [styles ...]
@ -17,19 +17,19 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay drip
pair_coeff \* \* none
pair_coeff \* \* drip C.drip C
pair_coeff * * none
pair_coeff * * drip C.drip C
pair_style hybrid/overlay drip rebo
pair_coeff \* \* drip C.drip C
pair_coeff \* \* rebo CH.airebo C
pair_coeff * * drip C.drip C
pair_coeff * * rebo CH.airebo C
pair_style hybrid/overlay drip rebo
pair_coeff \* \* drip C.drip C NULL
pair_coeff \* \* rebo CH.airebo C H
pair_coeff * * drip C.drip C NULL
pair_coeff * * rebo CH.airebo C H
Description
"""""""""""
@ -46,7 +46,7 @@ The total potential energy of a system is
\phi_{ij} = &f_\text{c}(x_r) \left[ e^{-\lambda(r_{ij} - z_0 )} \left[C+f(\rho_{ij})+ g(\rho_{ij}, \{\alpha_{ij}^{(m)}\}) \right]- A\left (\frac{z_0}{r_{ij}} \right)^6 \right]
where the *r\^-6* term models the attractive London dispersion,
where the :math:`r^{-6}` term models the attractive London dispersion,
the exponential term is designed to capture the registry effect due to
overlapping *pi* bonds, and *fc* is a cutoff function.
@ -85,9 +85,9 @@ types and you want all of them to be C, you would use the following pair\_coeff
command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* drip C.drip C C C
pair_coeff * * drip C.drip C C C
If a mapping value is specified as NULL, the mapping is not performed. This
could be useful when DRIP is used to model part of the system where other
@ -96,11 +96,11 @@ and H of atom type 2, you can use the following command to inform DRIP not to
model H atoms:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay drip rebo
pair_coeff \* \* drip C.drip C NULL
pair_coeff \* \* rebo CH.airebo C H
pair_coeff * * drip C.drip C NULL
pair_coeff * * rebo CH.airebo C H
.. note::

18
doc/src/pair_dsmc.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style dsmc
.. index:: pair_style dsmc
pair\_style dsmc command
========================
pair_style dsmc command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
@ -22,10 +22,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style dsmc 2.5 34387 10 1.0 100 20
pair_coeff \* \* 1.0
pair_coeff * * 1.0
pair_coeff 1 1 1.0
Description
@ -74,7 +74,7 @@ the "fix nve/noforce" time integration fix for the DSMC particles,
e.g.
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/noforce
@ -85,7 +85,7 @@ on the same processor. To ensure this occurs, you should use
these commands:
.. parsed-literal::
.. code-block:: LAMMPS
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
@ -105,7 +105,7 @@ uniform, which will not give good DSMC collision rates. Specify
as in the following:
.. parsed-literal::
.. code-block:: LAMMPS
velocity all create 594.6 87287 loop geom dist gaussian

18
doc/src/pair_e3b.rst
View File

@ -1,21 +1,21 @@
.. index:: pair\_style e3b
.. index:: pair_style e3b
pair\_style e3b command
=======================
pair_style e3b command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style e3b Otype
* Otype = atom type for oxygen
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* keyword
pair_coeff * * keyword
* one or more keyword/value pairs must be appended.
* keyword = *preset* or *Ea* or *Eb* or *Ec* or *E2* or *K3* or *K2* or *Rs* or *Rc3* or *Rc2* or *bondL* or *neigh*
@ -44,13 +44,13 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style e3b 1
pair_coeff \* \* Ea 35.85 Eb -240.2 Ec 449.3 E2 108269.9 K3 1.907 K2 4.872 Rc3 5.2 Rc2 5.2 Rs 5.0 bondL 0.9572
pair_coeff * * Ea 35.85 Eb -240.2 Ec 449.3 E2 108269.9 K3 1.907 K2 4.872 Rc3 5.2 Rc2 5.2 Rs 5.0 bondL 0.9572
pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5
pair_coeff \* \* e3b preset 2011
pair_coeff * * e3b preset 2011
Description
"""""""""""

126
doc/src/pair_eam.rst
View File

@ -1,76 +1,76 @@
.. index:: pair\_style eam
.. index:: pair_style eam
pair\_style eam command
=======================
pair_style eam command
======================
pair\_style eam/gpu command
===========================
pair\_style eam/intel command
=============================
pair\_style eam/kk command
pair_style eam/gpu command
==========================
pair\_style eam/omp command
===========================
pair_style eam/intel command
============================
pair\_style eam/opt command
===========================
pair_style eam/kk command
=========================
pair\_style eam/alloy command
=============================
pair_style eam/omp command
==========================
pair\_style eam/alloy/gpu command
=================================
pair_style eam/opt command
==========================
pair\_style eam/alloy/intel command
===================================
pair_style eam/alloy command
============================
pair\_style eam/alloy/kk command
pair_style eam/alloy/gpu command
================================
pair\_style eam/alloy/omp command
=================================
pair\_style eam/alloy/opt command
=================================
pair\_style eam/cd command
==========================
pair\_style eam/cd/omp command
==============================
pair\_style eam/cd/old command
==============================
pair\_style eam/cd/old/omp command
pair_style eam/alloy/intel command
==================================
pair\_style eam/fs command
==========================
pair_style eam/alloy/kk command
===============================
pair\_style eam/fs/gpu command
==============================
pair\_style eam/fs/intel command
pair_style eam/alloy/omp command
================================
pair\_style eam/fs/kk command
pair_style eam/alloy/opt command
================================
pair_style eam/cd command
=========================
pair_style eam/cd/omp command
=============================
pair\_style eam/fs/omp command
==============================
pair_style eam/cd/old command
=============================
pair\_style eam/fs/opt command
==============================
pair_style eam/cd/old/omp command
=================================
pair_style eam/fs command
=========================
pair_style eam/fs/gpu command
=============================
pair_style eam/fs/intel command
===============================
pair_style eam/fs/kk command
============================
pair_style eam/fs/omp command
=============================
pair_style eam/fs/opt command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style
@ -80,20 +80,20 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style eam
pair_coeff \* \* cuu3
pair_coeff 1\*3 1\*3 niu3.eam
pair_coeff * * cuu3
pair_coeff 1*3 1\*3 niu3.eam
pair_style eam/alloy
pair_coeff \* \* ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
pair_style eam/cd
pair_coeff \* \* ../potentials/FeCr.cdeam Fe Cr
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
pair_style eam/fs
pair_coeff \* \* NiAlH_jea.eam.fs Ni Al Ni Ni
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
Description
"""""""""""
@ -182,9 +182,9 @@ single argument:
Thus the following command
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \*2 1\*2 cuu3.eam
pair_coeff *2 1*2 cuu3.eam
will read the cuu3 potential file and use the tabulated Cu values for
F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
@ -233,9 +233,9 @@ by LAMMPS to compute the pair potential term in the EAM energy
expression as r\*phi, in units of eV-Angstroms, via the formula
.. parsed-literal::
.. math::
r\*phi = 27.2 \* 0.529 \* Zi \* Zj
r \cdot \phi = 27.2 \cdot 0.529 \cdot Z_i \cdot Z_j
where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
@ -277,9 +277,9 @@ be Ni, and the 4th to be Al, you would use the following pair\_coeff
command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* NiAlH_jea.eam.alloy Ni Ni Ni Al
pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
@ -402,9 +402,9 @@ For style *eam/fs*\ , the form of the pair\_coeff command is exactly the
same as for style *eam/alloy*\ , e.g.
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* NiAlH_jea.eam.fs Ni Ni Ni Al
pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
where there are N additional arguments after the filename, where N is
the number of LAMMPS atom types. See the :doc:`pair_coeff <pair_coeff>`

36
doc/src/pair_edip.rst
View File

@ -1,19 +1,19 @@
.. index:: pair\_style edip
.. index:: pair_style edip
pair\_style edip command
========================
pair_style edip command
=======================
pair\_style edip/omp command
============================
pair_style edip/omp command
===========================
pair\_style edip/multi command
==============================
pair_style edip/multi command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style
@ -22,8 +22,10 @@ Syntax
Examples
""""""""
pair\_style edip
pair\_coeff \* \* Si.edip Si
.. code-block:: LAMMPS
pair_style edip
pair_coeff * * Si.edip Si
Description
"""""""""""
@ -43,13 +45,13 @@ In EDIP, the energy E of a system of atoms is
\phi_{2}(r, Z) = & A\left[\left(\frac{B}{r}\right)^{\rho} - e^{-\beta Z^2}\right]exp{\left(\frac{\sigma}{r-a}\right)} \\
\phi_{3}(R_{ij}, R_{ik}, Z_i) = & exp{\left(\frac{\gamma}{R_{ij}-a}\right)}exp{\left(\frac{\gamma}{R_{ik}-a}\right)}h(cos\theta_{ijk},Z_i) \\
Z_i = & \sum_{m \ne i} f(R_{im}) \qquad
f(r) = \begin{cases}
1 & \quad r<c \\
\exp\left(\frac{\alpha}{1-x^{-3}}\right) & \quad c<r<a \\
0 & \quad r>a
\end{cases} \\
h(l,Z) = & \lambda [(1-e^{-Q(Z)(l+\tau(Z))^2}) + \eta Q(Z)(l+\tau(Z))^2 ] \\
Q(Z) = & Q_0 e^{-\mu Z} \qquad \tau(Z) = u_1 + u_2 (u_3 e^{-u_4 Z} - e^{-2u_4 Z})
f(r) = \begin{cases}
1 & \quad r<c \\
\exp\left(\frac{\alpha}{1-x^{-3}}\right) & \quad c<r<a \\
0 & \quad r>a
\end{cases} \\
h(l,Z) = & \lambda [(1-e^{-Q(Z)(l+\tau(Z))^2}) + \eta Q(Z)(l+\tau(Z))^2 ] \\
Q(Z) = & Q_0 e^{-\mu Z} \qquad \tau(Z) = u_1 + u_2 (u_3 e^{-u_4 Z} - e^{-2u_4 Z})
where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a

15
doc/src/pair_eff.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style eff/cut
.. index:: pair_style eff/cut
pair\_style eff/cut command
===========================
pair_style eff/cut command
==========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style eff/cut cutoff keyword args ...
@ -29,13 +29,13 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style eff/cut 39.7
pair_style eff/cut 40.0 limit/eradius
pair_style eff/cut 40.0 limit/eradius pressure/evirials
pair_style eff/cut 40.0 ecp 1 Si 3 C
pair_coeff \* \*
pair_coeff * *
pair_coeff 2 2 20.0
pair_coeff 1 s 0.320852 2.283269 0.814857
pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621
@ -100,7 +100,7 @@ given as,
.. math::
U\left(R,r,s\right) = E_{NN} \left( R \right) + E_{Ne} \left( {R,r,s} \right) + E_{ee} \left( {r,s} \right) + E_{KE} \left( {r,s} \right) + E_{PR} \left( { \uparrow \downarrow ,S} \right)
U\left(R,r,s\right) = E_{NN} \left( R \right) + E_{Ne} \left( {R,r,s} \right) + E_{ee} \left( {r,s} \right) + E_{KE} \left( {r,s} \right) + E_{PR} \left( { \uparrow \downarrow ,S} \right)
The individual terms are defined as follows:
@ -224,6 +224,7 @@ representations, after the "ecp" keyword.
electrons (i.e. Pauli repulsion) with one of the functional forms:
.. math::
E_{Pauli(ECP_s)} = & p_1\exp\left(-\frac{p_2r^2}{p_3+s^2} \right) \\
E_{Pauli(ECP_p)} = & p_1\left( \frac{2}{p_2/s+s/p_2} \right)\left( r-p_3s\right)^2\exp \left[ -\frac{p_4\left( r-p_3s \right)^2}{p_5+s^2} \right]

24
doc/src/pair_eim.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style eim
.. index:: pair_style eim
pair\_style eim command
=======================
pair_style eim command
======================
pair\_style eim/omp command
===========================
pair_style eim/omp command
==========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style
@ -20,12 +20,12 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style eim
pair_coeff \* \* Na Cl ../potentials/ffield.eim Na Cl
pair_coeff \* \* Na Cl ffield.eim Na Na Na Cl
pair_coeff \* \* Na Cl ../potentials/ffield.eim Cl NULL Na
pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
pair_coeff * * Na Cl ffield.eim Na Na Na Cl
pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na
Description
"""""""""""
@ -118,9 +118,9 @@ types and you want the 1st 3 to be Na, and the 4th to be Cl, you would
use the following pair\_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* Na Cl ffield.eim Na Na Na Cl
pair_coeff * * Na Cl ffield.eim Na Na Na Cl
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The filename is the EIM potential file. The Na and Cl arguments

24
doc/src/pair_exp6_rx.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style exp6/rx
.. index:: pair_style exp6/rx
pair\_style exp6/rx command
===========================
pair_style exp6/rx command
==========================
pair\_style exp6/rx/kk command
==============================
pair_style exp6/rx/kk command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style exp6/rx cutoff ...
@ -21,16 +21,16 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style exp6/rx 10.0
pair_style exp6/rx 10.0 fractional
pair_style exp6/rx 10.0 molecular
pair_coeff \* \* exp6.params h2o h2o exponent 1.0 1.0 10.0
pair_coeff \* \* exp6.params h2o 1fluid exponent 1.0 1.0 10.0
pair_coeff \* \* exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0
pair_coeff \* \* exp6.params 1fluid 1fluid none 10.0
pair_coeff \* \* exp6.params 1fluid 1fluid polynomial filename 10.0
pair_coeff * * exp6.params h2o h2o exponent 1.0 1.0 10.0
pair_coeff * * exp6.params h2o 1fluid exponent 1.0 1.0 10.0
pair_coeff * * exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0
pair_coeff * * exp6.params 1fluid 1fluid none 10.0
pair_coeff * * exp6.params 1fluid 1fluid polynomial filename 10.0
Description
"""""""""""

14
doc/src/pair_extep.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style extep
.. index:: pair_style extep
pair\_style extep command
=========================
pair_style extep command
========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style extep
@ -15,10 +15,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style extep
pair_coeff \* \* BN.extep B N
pair_coeff * * BN.extep B N
Description
"""""""""""
@ -32,7 +32,7 @@ interactions as described in :ref:`(Los2017) <Los2017>`.
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

130
doc/src/pair_fep_soft.rst
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@ -1,70 +1,70 @@
.. index:: pair\_style lj/cut/soft
.. index:: pair_style lj/cut/soft
pair\_style lj/cut/soft command
===============================
pair_style lj/cut/soft command
==============================
pair\_style lj/cut/soft/omp command
===================================
pair\_style lj/cut/coul/cut/soft command
========================================
pair\_style lj/cut/coul/cut/soft/omp command
============================================
pair\_style lj/cut/coul/long/soft command
=========================================
pair\_style lj/cut/coul/long/soft/omp command
=============================================
pair\_style lj/cut/tip4p/long/soft command
==========================================
pair\_style lj/cut/tip4p/long/soft/omp command
==============================================
pair\_style lj/charmm/coul/long/soft command
============================================
pair\_style lj/charmm/coul/long/soft/omp command
================================================
pair\_style lj/class2/soft command
pair_style lj/cut/soft/omp command
==================================
pair\_style lj/class2/coul/cut/soft command
===========================================
pair\_style lj/class2/coul/long/soft command
============================================
pair\_style coul/cut/soft command
=================================
pair\_style coul/cut/soft/omp command
=====================================
pair\_style coul/long/soft command
==================================
pair\_style coul/long/soft/omp command
======================================
pair\_style tip4p/long/soft command
===================================
pair\_style tip4p/long/soft/omp command
pair_style lj/cut/coul/cut/soft command
=======================================
pair\_style morse/soft command
pair_style lj/cut/coul/cut/soft/omp command
===========================================
pair_style lj/cut/coul/long/soft command
========================================
pair_style lj/cut/coul/long/soft/omp command
============================================
pair_style lj/cut/tip4p/long/soft command
==========================================
pair_style lj/cut/tip4p/long/soft/omp command
==============================================
pair_style lj/charmm/coul/long/soft command
============================================
pair_style lj/charmm/coul/long/soft/omp command
================================================
pair_style lj/class2/soft command
==================================
pair_style lj/class2/coul/cut/soft command
===========================================
pair_style lj/class2/coul/long/soft command
============================================
pair_style coul/cut/soft command
=================================
pair_style coul/cut/soft/omp command
=====================================
pair_style coul/long/soft command
==================================
pair_style coul/long/soft/omp command
======================================
pair_style tip4p/long/soft command
===================================
pair_style tip4p/long/soft/omp command
=======================================
pair_style morse/soft command
==============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -128,50 +128,50 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/cut/soft 2.0 0.5 9.5
pair_coeff \* \* 0.28 3.1 1.0
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 1.0 9.5
pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5
pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
pair_coeff \* \* 0.28 3.1 1.0
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 0.5 10.0
pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5
pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5
pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
pair_coeff \* \* 0.28 3.1 1.0
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 0.0 10.0
pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
pair_coeff \* \* 0.155 3.1536 1.0
pair_coeff * * 0.155 3.1536 1.0
pair_coeff 1 1 0.155 3.1536 1.0 9.5
pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
pair_coeff \* \* 0.28 3.1 1.0
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1
pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5
pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 9.5
pair_coeff \* \* 0.28 3.1 1.0
pair_coeff * * 0.28 3.1 1.0
pair_coeff 1 1 0.28 3.1 0.0 10.0
pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
pair_style coul/long/soft 1.0 10.0 9.5
pair_coeff \* \* 1.0
pair_coeff * * 1.0
pair_coeff 1 1 1.0 9.5
pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
pair_coeff \* \* 1.0
pair_coeff * * 1.0
pair_coeff 1 1 1.0 9.5
pair_style morse/soft 4 0.9 10.0
pair_coeff \* \* 100.0 2.0 1.5 1.0
pair_coeff * * 100.0 2.0 1.5 1.0
pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
Description

30
doc/src/pair_gauss.rst
View File

@ -1,25 +1,25 @@
.. index:: pair\_style gauss
.. index:: pair_style gauss
pair\_style gauss command
=========================
pair_style gauss command
========================
pair\_style gauss/gpu command
=============================
pair_style gauss/gpu command
============================
pair\_style gauss/omp command
=============================
pair_style gauss/omp command
============================
pair\_style gauss/cut command
=============================
pair_style gauss/cut command
============================
pair\_style gauss/cut/omp command
=================================
pair_style gauss/cut/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style gauss cutoff
pair_style gauss/cut cutoff
@ -30,10 +30,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style gauss 12.0
pair_coeff \* \* 1.0 0.9
pair_coeff * * 1.0 0.9
pair_coeff 1 4 1.0 0.9 10.0
pair_style gauss/cut 3.5
@ -175,7 +175,7 @@ To print this quantity to the log file (with a descriptive column
heading) the following commands could be included in an input script:
.. parsed-literal::
.. code-block:: LAMMPS
compute gauss all pair gauss
variable occ equal c_gauss[1]

24
doc/src/pair_gayberne.rst
View File

@ -1,22 +1,22 @@
.. index:: pair\_style gayberne
.. index:: pair_style gayberne
pair\_style gayberne command
============================
pair_style gayberne command
===========================
pair\_style gayberne/gpu command
================================
pair_style gayberne/gpu command
===============================
pair\_style gayberne/intel command
==================================
pair_style gayberne/intel command
=================================
pair\_style gayberne/omp command
================================
pair_style gayberne/omp command
===============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style gayberne gamma upsilon mu cutoff
@ -29,10 +29,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style gayberne 1.0 1.0 1.0 10.0
pair_coeff \* \* 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
Description
"""""""""""

38
doc/src/pair_gran.rst
View File

@ -1,31 +1,31 @@
.. index:: pair\_style gran/hooke
.. index:: pair_style gran/hooke
pair\_style gran/hooke command
==============================
pair_style gran/hooke command
=============================
pair\_style gran/hooke/omp command
==================================
pair_style gran/hooke/omp command
=================================
pair\_style gran/hooke/history command
======================================
pair_style gran/hooke/history command
=====================================
pair\_style gran/hooke/history/omp command
==========================================
pair\_style gran/hooke/history/kk command
pair_style gran/hooke/history/omp command
=========================================
pair\_style gran/hertz/history command
======================================
pair_style gran/hooke/history/kk command
========================================
pair\_style gran/hertz/history/omp command
==========================================
pair_style gran/hertz/history command
=====================================
pair_style gran/hertz/history/omp command
=========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style Kn Kt gamma_n gamma_t xmu dampflag
@ -53,7 +53,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
@ -204,9 +204,9 @@ However you must still use the :doc:`pair_coeff <pair_coeff>` for all
pairs of granular atom types. For example the command
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \*
pair_coeff * *
should be used if all atoms in the simulation interact via a granular
potential (i.e. one of the pair styles above is used). If a granular

20
doc/src/pair_granular.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style granular
.. index:: pair_style granular
pair\_style granular command
============================
pair_style granular command
===========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style granular cutoff
@ -17,22 +17,22 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style granular
pair_coeff \* \* hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping mass_velocity
pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping mass_velocity
pair_style granular
pair_coeff \* \* hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity
pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity
pair_style granular
pair_coeff \* \* hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4
pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4
pair_style granular
pair_coeff \* \* hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji
pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji
pair_style granular
pair_coeff 1 \* jkr 1000.0 500.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 1 * jkr 1000.0 500.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 100.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
pair_style granular

38
doc/src/pair_gromacs.rst
View File

@ -1,31 +1,31 @@
.. index:: pair\_style lj/gromacs
.. index:: pair_style lj/gromacs
pair\_style lj/gromacs command
==============================
pair_style lj/gromacs command
=============================
pair\_style lj/gromacs/gpu command
==================================
pair\_style lj/gromacs/kk command
pair_style lj/gromacs/gpu command
=================================
pair\_style lj/gromacs/omp command
==================================
pair_style lj/gromacs/kk command
================================
pair\_style lj/gromacs/coul/gromacs command
===========================================
pair_style lj/gromacs/omp command
=================================
pair\_style lj/gromacs/coul/gromacs/kk command
pair_style lj/gromacs/coul/gromacs command
==========================================
pair_style lj/gromacs/coul/gromacs/kk command
=============================================
pair_style lj/gromacs/coul/gromacs/omp command
==============================================
pair\_style lj/gromacs/coul/gromacs/omp command
===============================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -45,15 +45,15 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/gromacs 9.0 12.0
pair_coeff \* \* 100.0 2.0
pair_coeff * * 100.0 2.0
pair_coeff 2 2 100.0 2.0 8.0 10.0
pair_style lj/gromacs/coul/gromacs 9.0 12.0
pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
pair_coeff \* \* 100.0 2.0
pair_coeff * * 100.0 2.0
Description
"""""""""""

25
doc/src/pair_gw.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style gw
.. index:: pair_style gw
pair\_style gw command
======================
pair_style gw command
=====================
pair\_style gw/zbl command
==========================
pair_style gw/zbl command
=========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style
@ -19,14 +19,13 @@ Syntax
Examples
""""""""
pair\_style gw
pair\_coeff \* \* SiC.gw Si C C
.. code-block:: LAMMPS
.. parsed-literal::
pair_style gw
pair_coeff * * SiC.gw Si C C
pair_style gw/zbl
pair_coeff \* \* SiC.gw.zbl C Si
pair_coeff * * SiC.gw.zbl C Si
Description
"""""""""""
@ -60,9 +59,9 @@ If your LAMMPS simulation has 4 atoms types and you want the first 3 to
be Si, and the 4th to be C, you would use the following pair\_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* SiC.gw Si Si Si C
pair_coeff * * SiC.gw Si Si Si C
The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si

24
doc/src/pair_hbond_dreiding.rst
View File

@ -1,22 +1,22 @@
.. index:: pair\_style hbond/dreiding/lj
.. index:: pair_style hbond/dreiding/lj
pair\_style hbond/dreiding/lj command
=====================================
pair_style hbond/dreiding/lj command
====================================
pair\_style hbond/dreiding/lj/omp command
=========================================
pair\_style hbond/dreiding/morse command
pair_style hbond/dreiding/lj/omp command
========================================
pair\_style hbond/dreiding/morse/omp command
============================================
pair_style hbond/dreiding/morse command
=======================================
pair_style hbond/dreiding/morse/omp command
===========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
@ -31,7 +31,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
@ -253,7 +253,7 @@ To print these quantities to the log file (with a descriptive column
heading) the following commands could be included in an input script:
.. parsed-literal::
.. code-block:: LAMMPS
compute hb all pair hbond/dreiding/lj
variable n_hbond equal c_hb[1] #number hbonds

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