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

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This commit is contained in:
Axel Kohlmeyer
2020-02-27 01:15:17 -05:00
parent 3563d2f10d 9ef5949798
commit 1bb38ed09b
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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
change_box group-ID parameter args ... keyword args ... 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 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 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: 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 change_box all x final -10 20
create_atoms 1 single -5 5 5 # this will fail to insert an atom 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: 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 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: 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 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: 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 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 of 10% larger in x and y, and a factor of 21% smaller in z, so as to
keep the volume constant: keep the volume constant:
.. parsed-literal:: .. code-block:: LAMMPS
change_box all x scale 1.1 z volume y scale 1.1 z volume 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
comm_modify keyword value ... comm_modify keyword value ...
@ -30,14 +30,14 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
comm_modify mode multi comm_modify mode multi
comm_modify mode multi group solvent 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 vel yes
comm_modify mode single cutoff 5.0 vel yes comm_modify mode single cutoff 5.0 vel yes
comm_modify cutoff/multi \* 0.0 comm_modify cutoff/multi * 0.0
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
comm_style style comm_style style
@ -17,7 +17,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
comm_style brick comm_style brick
comm_style tiled 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
compute_modify compute-ID keyword value ... compute_modify compute-ID keyword value ...
@ -30,7 +30,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute_modify myTemp extra/dof 0 compute_modify myTemp extra/dof 0
compute_modify newtemp dynamic/dof yes extra/dof 600 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 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 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 compute ID group-ID smd/ulsph/strain
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/ulsph/strain 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 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 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 compute ID group-ID smd/ulsph/stress
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/ulsph/stress 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
create_atoms type style args keyword values ... create_atoms type style args keyword values ...
@ -29,7 +29,7 @@ Syntax
* zero or more keyword/value pairs may be appended * 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* * 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 *mol* value = template-ID seed
template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command 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 1 box
create_atoms 3 region regsphere basis 2 3 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. larger version.
.. parsed-literal:: .. code-block:: LAMMPS
dimension 2 dimension 2
variable x equal 100 variable x equal 100
@ -280,7 +280,7 @@ larger version.
variable xx internal 0.0 variable xx internal 0.0
variable yy 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 create_atoms 1 box var v set x xx set y yy
write_dump all atom sinusoid.lammpstrj 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
create_bonds style args ... keyword value ... 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 all all 1 1.0 1.2
create_bonds many surf solvent 3 2.0 2.4 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: 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 52 98 special no
create_bonds single/bond 5 73 74 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
create_box N region-ID keyword value ... 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
create_box 2 mybox bond/types 2 extra/bond/per/atom 1 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
delete_atoms style args keyword value ... delete_atoms style args keyword value ...
@ -41,7 +41,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
delete_atoms group edge delete_atoms group edge
delete_atoms region sphere compress no 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
delete_bonds group-ID style arg keyword ... delete_bonds group-ID style arg keyword ...
* group-ID = group ID * group-ID = group ID
* style = *multi* or *atom* or *bond* or *angle* or *dihedral* or * style = *multi* or *atom* or *bond* or *angle* or *dihedral* or *improper* or *stats*
*improper* or *stats*
.. parsed-literal:: .. parsed-literal::
@ -33,11 +32,11 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
delete_bonds frozen multi remove delete_bonds frozen multi remove
delete_bonds all atom 4 special delete_bonds all atom 4 special
delete_bonds all bond 0\*3 special delete_bonds all bond 0*3 special
delete_bonds all stats delete_bonds all stats
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style style dihedral_style style
@ -29,7 +29,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style charmm dihedral_style charmm
dihedral_style charmmfsw dihedral_style charmmfsw
@ -44,7 +44,7 @@ The *charmm* and *charmmfsw* dihedral styles use the potential
.. math:: .. 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 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/omp command
==================================
dihedral\_style class2/kk command
================================= =================================
dihedral_style class2/kk command
================================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style class2 dihedral_style class2
@ -21,15 +21,15 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style class2 dihedral_style class2
dihedral_coeff 1 100 75 100 70 80 60 dihedral_coeff 1 100 75 100 70 80 60
dihedral_coeff \* mbt 3.5945 0.1704 -0.5490 1.5228 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 * 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 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 * aat -13.5271 110.2453 105.1270
dihedral_coeff \* bb13 0.0 1.0119 1.1010 dihedral_coeff * bb13 0.0 1.0119 1.1010
Description Description
""""""""""" """""""""""
@ -38,15 +38,15 @@ The *class2* dihedral style uses the potential
.. math:: .. math::
E = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\ 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_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_{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) ] + \\ 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) ] \\ & (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) ] + \\ 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) ] \\ & (\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_{aat} = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\
E_{bb13} = & N (r_{ij} - r_1) (r_{kl} - r_3) 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, 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_coeff N args dihedral_coeff N args
@ -18,11 +18,11 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_coeff 1 80.0 1 3 dihedral_coeff 1 80.0 1 3
dihedral_coeff \* 80.0 1 3 0.5 dihedral_coeff * 80.0 1 3 0.5
dihedral_coeff 2\* 80.0 1 3 0.5 dihedral_coeff 2* 80.0 1 3 0.5
Description 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: 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 dihedral_coeff 2 200.0 1 3
A line in a data file that specifies dihedral coefficients uses the exact 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style cosine/shift/exp dihedral_style cosine/shift/exp
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style cosine/shift/exp dihedral_style cosine/shift/exp
dihedral_coeff 1 10.0 45.0 2.0 dihedral_coeff 1 10.0 45.0 2.0
@ -30,7 +30,7 @@ The *cosine/shift/exp* dihedral style uses the potential
.. math:: .. 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style fourier dihedral_style fourier
@ -21,7 +21,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style fourier dihedral_style fourier
dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 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:: .. 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style harmonic dihedral_style harmonic
@ -24,7 +24,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style harmonic dihedral_style harmonic
dihedral_coeff 1 80.0 1 2 dihedral_coeff 1 80.0 1 2
@ -36,7 +36,7 @@ The *harmonic* dihedral style uses the potential
.. math:: .. 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style helix dihedral_style helix
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style helix dihedral_style helix
dihedral_coeff 1 80.0 100.0 40.0 dihedral_coeff 1 80.0 100.0 40.0
@ -30,8 +30,8 @@ The *helix* dihedral style uses the potential
.. math:: .. math::
E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] +
C [1 + \cos(\theta + \frac{\pi}{4})] C [1 + \cos(\theta + \frac{\pi}{4})]
This coarse-grain dihedral potential is described in :ref:`(Guo) <Guo>`. 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style hybrid style1 style2 ... dihedral_style hybrid style1 style2 ...
@ -17,11 +17,11 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style hybrid harmonic helix dihedral_style hybrid harmonic helix
dihedral_coeff 1 harmonic 6.0 1 3 dihedral_coeff 1 harmonic 6.0 1 3
dihedral_coeff 2\* helix 10 10 10 dihedral_coeff 2* helix 10 10 10
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style multi/harmonic dihedral_style multi/harmonic
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style multi/harmonic dihedral_style multi/harmonic
dihedral_coeff 1 20 20 20 20 20 dihedral_coeff 1 20 20 20 20 20
@ -30,7 +30,7 @@ The *multi/harmonic* dihedral style uses the potential
.. math:: .. 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style nharmonic dihedral_style nharmonic
@ -18,10 +18,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style nharmonic dihedral_style nharmonic
dihedral_coeff \* 3 10.0 20.0 30.0 dihedral_coeff * 3 10.0 20.0 30.0
Description Description
""""""""""" """""""""""
@ -30,7 +30,7 @@ The *nharmonic* dihedral style uses the potential:
.. math:: .. 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style none dihedral_style none
@ -15,7 +15,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style none 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style opls dihedral_style opls
@ -24,7 +24,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style opls dihedral_style opls
dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT 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:: .. math::
E = & \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \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)] & \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. 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style quadratic dihedral_style quadratic
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style quadratic dihedral_style quadratic
dihedral_coeff 100.0 80.0 dihedral_coeff 100.0 80.0
@ -30,7 +30,7 @@ The *quadratic* dihedral style uses the potential:
.. math:: .. 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style spherical 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 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 & 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:: .. 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) \\ 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) \\ \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_{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) \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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style style dihedral_style style
@ -17,7 +17,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style harmonic dihedral_style harmonic
dihedral_style multi/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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style table style Ntable dihedral_style table style Ntable
@ -21,7 +21,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style table spline 400 dihedral_style table spline 400
dihedral_style table linear 1000 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style table/cut style Ntable dihedral_style table/cut style Ntable
@ -17,8 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
dihedral_style table/cut spline 400 dihedral_style table/cut spline 400
dihedral_style table/cut linear 1000 dihedral_style table/cut linear 1000
@ -68,8 +67,8 @@ cutoff function:
.. math:: .. math::
f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\ 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 \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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dihedral_style zero *nocoeff* dihedral_style zero [nocoeff]
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
dihedral_style zero dihedral_style zero
dihedral_style zero nocoeff dihedral_style zero nocoeff
dihedral_coeff \* dihedral_coeff *
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
displace_atoms group-ID style args keyword value ... 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 top move 0 -5 0 units box
displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dump_modify dump-ID keyword values ... 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 line "%d %d %20.15g %g %g" scale yes
dump_modify 1 format float %20.15g 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: 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) variable s equal logfreq(10,3,10)
dump 1 all atom 100 tmp.dump 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: in file tmp.times:
.. parsed-literal:: .. code-block:: LAMMPS
variable f file tmp.times variable f file tmp.times
variable s equal next(f) variable s equal next(f)
@ -372,7 +372,7 @@ settings, reverting all values to their default format.
example, these commands: example, these commands:
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all property/local batom1 batom2 compute 1 all property/local batom1 batom2
dump 1 all local 100 tmp.bonds index c_1[1] c_1[2] 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: commands:
.. parsed-literal:: .. code-block:: LAMMPS
variable Dhop equal 0.6 variable Dhop equal 0.6
variable check atom "c_dsp[4] > v_Dhop" 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. Three examples follow.
.. parsed-literal:: .. code-block:: LAMMPS
dump_modify ... thresh ix != LAST dump_modify ... thresh ix != LAST
@ -688,20 +688,20 @@ once and then crossed back between the two dump timesteps would not be
included.) included.)
.. parsed-literal:: .. code-block:: LAMMPS
region foo sphere 10 20 10 15 region foo sphere 10 20 10 15
variable inregion atom rmask(foo) 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 This will dump atoms which crossed the boundary of the spherical
region since the last dump. region since the last dump.
.. parsed-literal:: .. code-block:: LAMMPS
variable charge atom "(q > 0.5) \|\| (q < -0.5)" variable charge atom "(q > 0.5) || (q < -0.5)"
dump_modify ... thresh v_charge \|\^ LAST dump_modify ... thresh v_charge |^ LAST
This will dump atoms whose charge has changed from an absolute value 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. 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. this is used.
.. parsed-literal:: .. code-block:: LAMMPS
variable colors string & variable colors string &
"red green blue yellow white & "red green blue yellow white &
purple pink orange lime gray" purple pink orange lime gray"
variable mol atom mol%10 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 zoom 1.6 adiam 1.5
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors} 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
dynamical_matrix group-ID style gamma args keyword value ... 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 regular 0.000001
dynamical_matrix 1 eskm 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix_modify fix-ID keyword value ... 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 3 temp myTemp press myPress
fix_modify 1 energy yes fix_modify 1 energy yes
@ -154,7 +154,7 @@ will give a warning if that is the case.
Restrictions Restrictions
"""""""""""" """"""""""""
none none
Related commands 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID smd/adjust_dt arg 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID smd/integrate_tlsph keyword values 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
fix 1 all smd/integrate_tlsph limit_velocity 1000 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID smd/integrate_ulsph keyword fix ID group-ID smd/integrate_ulsph keyword
@ -26,8 +26,7 @@ limit\_velocity values = max\_velocity
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
fix 1 all smd/integrate_ulsph limit_velocity 1000 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID smd/move_tri_surf keyword 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 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 *WIGGLE 20 20 10
fix 2 tool smd/move_tri_surf \*ROTATE 0 0 0 5 2 1 fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
fix ID group-ID smd/wall_surface arg type mol-ID 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 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/omp command
==================================
improper\_style class2/kk command
================================= =================================
improper_style class2/kk command
================================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style class2 improper_style class2
@ -21,11 +21,11 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style class2 improper_style class2
improper_coeff 1 100.0 0 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 Description
""""""""""" """""""""""
@ -34,11 +34,11 @@ The *class2* improper style uses the potential
.. math:: .. math::
E = & E_i + E_{aa} \\ E = & E_i + E_{aa} \\
E_i = & K [ \frac{\chi_{ijkl} + \chi_{kjli} + \chi_{ljik}}{3} - \chi_0 ]^2 \\ 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) + \\ E_{aa} = & M_1 (\theta_{ijk} - \theta_1) (\theta_{kjl} - \theta_3) + \\
& M_2 (\theta_{ijk} - \theta_1) (\theta_{ijl} - \theta_2) + \\ & M_2 (\theta_{ijk} - \theta_1) (\theta_{ijl} - \theta_2) + \\
& M_3 (\theta_{ijl} - \theta_2) (\theta_{kjl} - \theta_3) & M_3 (\theta_{ijl} - \theta_2) (\theta_{kjl} - \theta_3)
where :math:`E_i` is the improper term and :math:`E_{aa}` is an 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_coeff N args improper_coeff N args
@ -18,11 +18,11 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_coeff 1 300.0 0.0 improper_coeff 1 300.0 0.0
improper_coeff \* 80.2 -1 2 improper_coeff * 80.2 -1 2
improper_coeff \*4 80.2 -1 2 improper_coeff *4 80.2 -1 2
Description Description
""""""""""" """""""""""
@ -48,9 +48,9 @@ the coeffs for all improper types, then overwrite the coeffs for just
improper type 2: 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 improper_coeff 2 50.0 0.0
A line in a data file that specifies improper coefficients uses the 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style cossq improper_style cossq
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style cossq improper_style cossq
improper_coeff 1 4.0 0.0 improper_coeff 1 4.0 0.0
@ -30,7 +30,7 @@ The *cossq* improper style uses the potential
.. math:: .. 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style cvff improper_style cvff
@ -21,7 +21,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style cvff improper_style cvff
improper_coeff 1 80.0 -1 4 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 Syntax
"""""" """"""
improper\_style distance .. code-block:: LAMMPS
improper_style distance
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style distance improper_style distance
improper_coeff 1 80.0 100.0 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 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 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>` (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 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 Syntax
"""""" """"""
improper\_style distharm .. code-block:: LAMMPS
improper_style distharm
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style distharm improper_style distharm
improper_coeff 1 25.0 0.5 improper_coeff 1 25.0 0.5
@ -24,10 +26,10 @@ The *distharm* improper style uses the potential
.. math:: .. 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 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>` (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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style fourier improper_style fourier
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style fourier improper_style fourier
improper_coeff 1 100.0 0.0 1.0 0.5 1 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style harmonic improper_style harmonic
@ -24,7 +24,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style harmonic improper_style harmonic
improper_coeff 1 100.0 0 improper_coeff 1 100.0 0
@ -36,7 +36,7 @@ The *harmonic* improper style uses the potential
.. math:: .. 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style hybrid style1 style2 ... improper_style hybrid style1 style2 ...
@ -17,7 +17,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style hybrid harmonic helix improper_style hybrid harmonic helix
improper_coeff 1 harmonic 120.0 30 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style inversion/harmonic improper_style inversion/harmonic
@ -15,7 +15,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style inversion/harmonic improper_style inversion/harmonic
improper_coeff 1 18.776340 0.000000 improper_coeff 1 18.776340 0.000000
@ -28,7 +28,7 @@ out-of-plane angle definition and uses an harmonic potential:
.. math:: .. 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style none improper_style none
@ -15,7 +15,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style none 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style ring improper_style ring
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style ring improper_style ring
improper_coeff 1 8000 70.5 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 Syntax
"""""" """"""
improper\_style sqdistharm .. code-block:: LAMMPS
improper_style sqdistharm
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
improper_style sqdistharm improper_style sqdistharm
improper_coeff 1 50.0 0.1 improper_coeff 1 50.0 0.1
@ -24,8 +25,7 @@ The *sqdistharm* improper style uses the potential
.. math:: .. 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 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style style improper_style style
@ -17,7 +17,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style harmonic improper_style harmonic
improper_style cvff improper_style cvff
@ -118,6 +118,6 @@ Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style none improper_style none

18
doc/src/improper_umbrella.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style umbrella improper_style umbrella
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style umbrella improper_style umbrella
improper_coeff 1 100.0 180.0 improper_coeff 1 100.0 180.0
@ -32,8 +32,8 @@ commonly referred to as a classic inversion and used in the
.. math:: .. 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 = & \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 = & 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style zero *nocoeff* improper_style zero [nocoeff]
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
improper_style zero improper_style zero
improper_style zero nocoeff improper_style zero nocoeff
improper_coeff \* improper_coeff *
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
kim_init model user_units unitarg kim_init model user_units unitarg
kim_interactions typeargs kim_interactions typeargs
@ -56,7 +56,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
kim_interactions Si kim_interactions Si
@ -238,7 +238,7 @@ of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994)
potential for Al: potential for Al:
.. parsed-literal:: .. code-block:: LAMMPS
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
boundary p p p 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. 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 kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode
boundary p p p 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 region simbox block 0 1 0 1 0 1 units lattice
create_box 1 simbox create_box 1 simbox
create_atoms 1 box create_atoms 1 box
mass 1 4.480134e-26\*${_u_mass} mass 1 4.480134e-26*${_u_mass}
kim_interactions Al kim_interactions Al
run 0 run 0
variable Ec_in_J equal (pe/count(all))/${_u_energy} variable Ec_in_J equal (pe/count(all))/${_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: be done to convert the box and all atomic positions to the correct units:
.. parsed-literal:: .. code-block:: LAMMPS
variable xyfinal equal xy\*${_u_distance} variable xyfinal equal xy*${_u_distance}
variable xzfinal equal xz\*${_u_distance} variable xzfinal equal xz*${_u_distance}
variable yzfinal equal yz\*${_u_distance} variable yzfinal equal yz*${_u_distance}
change_box all x scale ${_u_distance} & change_box all x scale ${_u_distance} &
y scale ${_u_distance} & y scale ${_u_distance} &
z 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: and the fourth is C, the following *kim\_interactions* command would be used:
.. parsed-literal:: .. code-block:: LAMMPS
kim_interactions Si Si Si C kim_interactions Si Si Si C
Alternatively, for a model with a fixed mapping the command would be: Alternatively, for a model with a fixed mapping the command would be:
.. parsed-literal:: .. code-block:: LAMMPS
kim_interactions fixed_types 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: 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 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: 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_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 For a KIM SM, the generated input commands may be more complex
and require that LAMMPS is built with the required packages included 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: set by the following commands:
.. parsed-literal:: .. code-block:: LAMMPS
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real 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: 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_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 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* 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: The syntax for the *kim\_query* command is as follows:
.. parsed-literal:: .. code-block:: LAMMPS
kim_query variable formatarg query_function queryargs 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** **Define an equilibrium fcc crystal**
.. parsed-literal:: .. code-block:: LAMMPS
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
boundary p p p boundary p p p
@ -533,7 +533,7 @@ changed to: "lattice fcc ${a0}\*${\_u_distance}".
**Define an equilibrium hcp crystal** **Define an equilibrium hcp crystal**
.. parsed-literal:: .. code-block:: LAMMPS
kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal
boundary p p p boundary p p p
@ -556,14 +556,14 @@ input script more readable.
**Define a crystal at finite temperature accounting for thermal expansion** **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 kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
boundary p p p boundary p p p
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Al"] units=["angstrom"] 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"] 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 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 As in the previous example, the equilibrium lattice constant is obtained
@ -587,7 +587,7 @@ potential.
**Compute defect formation energy** **Compute defect formation energy**
.. parsed-literal:: .. code-block:: LAMMPS
kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
... ...
@ -595,7 +595,7 @@ potential.
... which is stored in the variable *Etot* ... which is stored in the variable *Etot*
... ...
kim_query Ec get_cohesive_energy_cubic crystal=["fcc"] species=["Al"] units=["eV"] 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 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: 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 get param_name index_range variable formatarg
kim_param set param_name index_range values kim_param set param_name index_range values
@ -715,7 +715,7 @@ clarifications are provided below.
**Getting a scalar parameter** **Getting a scalar parameter**
.. parsed-literal:: .. code-block:: LAMMPS
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
... ...
@ -729,7 +729,7 @@ LAMMPS variable.
**Getting multiple scalar parameters with a single call** **Getting multiple scalar parameters with a single call**
.. parsed-literal:: .. code-block:: LAMMPS
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal 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. determined by the *formatarg* argument.
.. parsed-literal:: .. code-block:: LAMMPS
kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal 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. is provided at the top of the model page.
.. parsed-literal:: .. code-block:: LAMMPS
kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal 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. contains the current value of lambda.
.. parsed-literal:: .. code-block:: LAMMPS
kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal 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** **Setting a scalar parameter**
.. parsed-literal:: .. code-block:: LAMMPS
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal 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: operation will return the new value that was set. For example:
.. parsed-literal:: .. code-block:: LAMMPS
... ...
kim_interactions Si kim_interactions Si
@ -849,7 +849,7 @@ be used when setting parameters.
**Setting a range of values of a parameter** **Setting a range of values of a parameter**
.. parsed-literal:: .. code-block:: LAMMPS
kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
kspace_modify keyword value ... kspace_modify keyword value ...
@ -62,7 +62,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
kspace_modify mesh 24 24 30 order 6 kspace_modify mesh 24 24 30 order 6
kspace_modify slab 3.0 kspace_modify slab 3.0
@ -483,7 +483,8 @@ parameters, see the :doc:`Howto dispersion <Howto_dispersion>` doc page.
Restrictions Restrictions
"""""""""""" """"""""""""
none
none
Related commands 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
kspace_style style value kspace_style style value
@ -82,7 +82,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
kspace_style pppm 1.0e-4 kspace_style pppm 1.0e-4
kspace_style pppm/cg 1.0e-5 1.0e-6 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 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, Most of the long-range solvers perform their computation in K-space,
hence the name of this command. hence the name of this command.
When such a solver is used in conjunction with an appropriate pair 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 infinite. If the Coulombic case, this means each charge in the system
interacts with charges in an infinite array of periodic images of the interacts with charges in an infinite array of periodic images of the
simulation domain. simulation domain.
@ -128,9 +128,9 @@ The *ewald* style performs a standard Ewald summation as described in
any solid-state physics text. any solid-state physics text.
The *ewald/disp* style adds a long-range dispersion sum option for 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, :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 capability means that Lennard-Jones or Buckingham potentials can be
used without a cutoff, i.e. they become full long-range potentials. used without a cutoff, i.e. they become full long-range potentials.
The *ewald/disp* style can also be used with point-dipoles, see 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 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 the particle-mesh Ewald technique (PME) :ref:`(Darden) <Darden>` used in
AMBER and CHARMM. The cost of traditional Ewald summation scales as 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 :math:`N^{\frac{3}{2}}` where :math:`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 scales as :math:`N \log{N}` due to the FFTs, so it is almost always a faster
choice :ref:`(Pollock) <Pollock>`. choice :ref:`(Pollock) <Pollock>`.
The *pppm/cg* style is identical to the *pppm* style except that it 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 :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 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 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 K-space solvers for relatively large problems when running on large
core counts. MSM can also be used for non-periodic boundary conditions core counts. MSM can also be used for non-periodic boundary conditions
and for mixed periodic and non-periodic boundaries. and for mixed periodic and non-periodic boundaries.
@ -466,7 +466,7 @@ Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
kspace_style none 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
min_modify keyword values ... min_modify keyword values ...
@ -39,7 +39,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
min_modify dmax 0.2 min_modify dmax 0.2
min_modify integrator verlet tmax 4 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: the 2-norm (Euclidean length) of the global force vector:
.. math:: .. 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 The *max* norm computes the length of the 3-vector force
for each atom (2-norm), and takes the maximum value of those across for each atom (2-norm), and takes the maximum value of those across
all atoms all atoms
.. math:: .. 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 The *inf* norm takes the maximum component across the forces of
all atoms in the system: all atoms in the system:
.. math:: .. 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 For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force
norm is replaced by the spin-torque norm. 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 :doc:`min_style <min_style>` *fire/old*. It can however behave similarly
to the *fire/old* style by using the following set of parameters: to the *fire/old* style by using the following set of parameters:
.. parsed-literal:: .. code-block:: LAMMPS
min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 &
min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 &
dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 & dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 &
vdfmax 100000 halfstepback no initialdelay no 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
min_style spin min_style spin
min_style spin/cg min_style spin/cg
@ -23,7 +23,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
min_style spin/lbfgs min_style spin/lbfgs
min_modify line spin_cubic discrete_factor 10.0 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: timestep, according to:
.. math:: .. 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 with :math:`\lambda` a damping coefficient (similar to a Gilbert
damping). :math:`\lambda` can be defined by setting the 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: system:
.. math:: .. 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 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
min_style style min_style style
@ -17,7 +17,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
min_style cg min_style cg
min_style spin min_style spin
@ -148,7 +148,8 @@ instructions on how to use the accelerated styles effectively.
Restrictions Restrictions
"""""""""""" """"""""""""
none
none
Related commands Related commands
"""""""""""""""" """"""""""""""""
@ -159,7 +160,7 @@ Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
min_style cg 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
neigh_modify keyword values ... 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 every 2 delay 10 check yes page 100000
neigh_modify exclude type 2 3 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style awpmd/cut Rc keyword value ... 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 -1
pair_style awpmd/cut 40.0 uhf free pair_style awpmd/cut 40.0 uhf free
pair_coeff \* \* pair_coeff * *
pair_coeff 2 2 20.0 pair_coeff 2 2 20.0
Description Description

14
doc/src/pair_bop.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style bop .. index:: pair_style bop
pair\_style bop command pair_style bop command
======================= ======================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style bop keyword ... pair_style bop keyword ...
@ -24,12 +24,12 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style bop pair_style bop
pair_coeff \* \* ../potentials/CdTe_bop Cd Te pair_coeff * * ../potentials/CdTe_bop Cd Te
pair_style bop save 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 comm_modify cutoff 14.70
Description 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 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/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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -71,29 +71,29 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style born 10.0 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_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
pair_style born/coul/long 10.0 8. 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_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
pair_style born/coul/msm 10.0 8.0 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_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
pair_style born/coul/wolf 0.25 10.0 9.0 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_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_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 pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF 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_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 1 1 2.05 2.8
pair_coeff \* \* pair_coeff * *
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -81,26 +81,26 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style buck 2.5 pair_style buck 2.5
pair_coeff \* \* 100.0 1.5 200.0 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 3.0
pair_style buck/coul/cut 10.0 pair_style buck/coul/cut 10.0
pair_style buck/coul/cut 10.0 8.0 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
pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 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
pair_style buck/coul/long 10.0 8.0 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_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
pair_style buck/coul/msm 10.0 8.0 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 pair_coeff 1 1 100.0 1.5 200.0 9.0
Description Description

18
doc/src/pair_buck6d_coul_gauss.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args 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_style buck6d/coul/gauss/dsf 0.9000 12.0000
pair_coeff 1 1 1030. 3.061 457.179 4.521 0.608 pair_coeff 1 1 1030. 3.061 457.179 4.521 0.608
@ -52,7 +52,7 @@ computes a dispersion damped Buckingham potential:
.. math:: .. 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 where A and C are a force constant, :math:`\kappa` is an ionic-pair dependent
@ -82,7 +82,7 @@ is thus evaluated as:
.. math:: .. 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` where C is an energy-conversion constant, :math:`q_i` and :math:`q_j`

12
doc/src/pair_buck_long.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2) 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 off 2.5
pair_style buck/long/coul/long cut long 2.5 4.0 pair_style buck/long/coul/long cut long 2.5 4.0
pair_style buck/long/coul/long long long 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 pair_coeff 1 1 1 3 4
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args 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
pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0 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
pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 9.0 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_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
pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0 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_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
pair_style lj/charmm/coul/long 8.0 10.0 9.0 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
pair_style lj/charmmfsw/coul/long 8.0 10.0 9.0 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_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
pair_style lj/charmm/coul/msm 8.0 10.0 9.0 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 pair_coeff 1 1 100.0 2.0 150.0 3.5
Description Description
@ -162,18 +162,18 @@ artifacts.
.. math:: .. math::
E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\ E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\
= & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ = & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
= & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\ E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\
= & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
= & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \\ \left(\frac{\sigma}{r}\right)^6 \right] \\
C(r) = & \frac{C q_i q_j}{ \epsilon r} \\ C(r) = & \frac{C q_i q_j}{ \epsilon r} \\
S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 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 + 2r^2 - 3{r_{\rm in}^2}\right]}
{ \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
where S(r) is the energy switching function mentioned above for the 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/gpu command
=================================
pair\_style lj/class2/kk 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/omp command
===========================================
pair\_style lj/class2/coul/long/kk command
========================================== ==========================================
pair\_style lj/class2/coul/long/omp command
===========================================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -60,7 +60,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style lj/class2 10.0 pair_style lj/class2 10.0
pair_coeff \* \* 100.0 2.5 pair_coeff \* \* 100.0 2.5
@ -84,9 +84,9 @@ The *lj/class2* styles compute a 6/9 Lennard-Jones potential given by
.. math:: .. math::
E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 - E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 -
3 \left(\frac{\sigma}{r}\right)^6 \right] 3 \left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c \qquad r < r_c
:math:`r_c` is the cutoff. :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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_coeff I J args 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 1 2 1.0 1.0 2.5
pair_coeff 2 \* 1.0 1.0 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: 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 \* \* 1.0 1.0 2.5
pair_coeff 2 3 2.0 1.0 1.12 pair_coeff 2 3 2.0 1.0 1.12

20
doc/src/pair_colloid.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style colloid cutoff pair_style colloid cutoff
@ -23,10 +23,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style colloid 10.0 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 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 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 pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0

33
doc/src/pair_comb.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style comb pair_style comb
pair_style comb3 keyword pair_style comb3 keyword
.. parsed-literal::
keyword = *polar* keyword = *polar*
*polar* value = *polar_on* or *polar_off* = whether or not to include atomic polarization *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_style comb
pair_coeff \* \* ../potentials/ffield.comb Si pair_coeff * * ../potentials/ffield.comb Si
pair_coeff \* \* ../potentials/ffield.comb Hf Si O pair_coeff * * ../potentials/ffield.comb Hf Si O
pair_style comb3 polar_off 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 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: 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 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 types. The first and last Si arguments map LAMMPS atom types 1 and 4

12
doc/src/pair_cosine_squared.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style cosine/squared cutoff pair_style cosine/squared cutoff
* cutoff = global cutoff for cosine-squared interactions (distance units) * 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
pair_coeff i j eps sigma cutoff pair_coeff i j eps sigma cutoff
@ -31,7 +31,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style cosine/squared 3.0 pair_style cosine/squared 3.0
pair_coeff \* \* 1.0 1.3 pair_coeff \* \* 1.0 1.3

167
doc/src/pair_coul.rst
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@ -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/gpu command
================================
pair\_style coul/cut/kk command
=============================== ===============================
pair\_style coul/cut/omp command pair_style coul/cut/kk command
================================
pair\_style coul/debye command
============================== ==============================
pair\_style coul/debye/gpu command pair_style coul/cut/omp 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/dsf/omp command pair_style coul/debye command
================================
pair\_style coul/long 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/dsf/kk 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style coul/cut cutoff pair_style coul/cut cutoff
pair_style coul/debye kappa cutoff pair_style coul/debye kappa cutoff
@ -102,37 +102,37 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style coul/cut 2.5 pair_style coul/cut 2.5
pair_coeff \* \* pair_coeff * *
pair_coeff 2 2 3.5 pair_coeff 2 2 3.5
pair_style coul/debye 1.4 3.0 pair_style coul/debye 1.4 3.0
pair_coeff \* \* pair_coeff * *
pair_coeff 2 2 3.5 pair_coeff 2 2 3.5
pair_style coul/dsf 0.05 10.0 pair_style coul/dsf 0.05 10.0
pair_coeff \* \* pair_coeff * *
pair_style coul/long 10.0 pair_style coul/long 10.0
pair_coeff \* \* pair_coeff * *
pair_style coul/msm 10.0 pair_style coul/msm 10.0
pair_coeff \* \* pair_coeff * *
pair_style coul/wolf 0.2 9.0 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 ewald
pair_style coul/streitz 12.0 wolf 0.30 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_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_style tip4p/long 1 2 7 8 0.15 10.0
pair_coeff \* \* pair_coeff * *
Description Description
""""""""""" """""""""""
@ -142,7 +142,7 @@ potential given by
.. math:: .. 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 where C is an energy-conversion constant, Qi and Qj are the charges on
@ -159,7 +159,7 @@ Coulombic term, given by
.. math:: .. 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 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:: .. math::
E = E = q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
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
\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 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:: .. math::
E_i = \frac{1}{2} \sum_{j \neq i} E_i = \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
\frac{1}{2} \sum_{j \neq i} \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c \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 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: 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_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
pair_coeff \* \* coul/streitz AlO.streitz Al O pair_coeff * * coul/streitz AlO.streitz Al O
pair_coeff \* \* eam/alloy AlO.eam.alloy 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 fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
The keyword *wolf* in the coul/streitz command denotes computing 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: be computed via an Ewald summation. For example:
.. parsed-literal:: .. code-block:: LAMMPS
pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
kspace_style ewald 1e-6 kspace_style ewald 1e-6

14
doc/src/pair_coul_diel.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style coul/diel cutoff pair_style coul/diel cutoff
@ -20,7 +20,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style coul/diel 3.5 pair_style coul/diel 3.5
pair_coeff 1 4 78. 1.375 0.112 pair_coeff 1 4 78. 1.375 0.112

16
doc/src/pair_coul_shield.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style coul/shield cutoff tap_flag 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_style coul/shield 16.0 1
pair_coeff 1 2 0.70 pair_coeff 1 2 0.70
@ -41,9 +41,9 @@ the pair style :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
.. math:: .. math::
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ 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}}\\ 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 - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

38
doc/src/pair_cs.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args 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_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_coeff 1 1 480.0 0.25 0.00 1.05 0.50
pair_style born/coul/long/cs 10.0 8.0 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_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_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_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
pair_style buck/coul/long/cs 10.0 8.0 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_coeff 1 1 100.0 1.5 200.0 9.0
pair_style coul/long/cs 10.0 pair_style coul/long/cs 10.0
pair_coeff \* \* pair_coeff * *
pair_style coul/wolf/cs 0.2 9.0 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
pair_style lj/cut/coul/long/cs 10.0 8.0 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 pair_coeff 1 1 100.0 3.5 9.0
Description 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/gpu command
=======================================
pair\_style lj/sf/dipole/sf/omp command
=======================================
pair\_style lj/cut/dipole/long 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style lj/cut/dipole/cut cutoff (cutoff2) pair_style lj/cut/dipole/cut cutoff (cutoff2)
pair_style lj/sf/dipole/sf 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_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_coeff 2 3 1.0 1.0 2.5 4.0
pair_style lj/sf/dipole/sf 9.0 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 scale 0.5
pair_coeff 2 3 1.0 1.0 2.5 4.0 pair_coeff 2 3 1.0 1.0 2.5 4.0
pair_style lj/cut/dipole/long 10.0 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_coeff 2 3 1.0 1.0 2.5 4.0
pair_style lj/long/dipole/long long long 3.5 10.0 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 pair_coeff 2 3 1.0 1.0 2.5 4.0
Description Description

38
doc/src/pair_dpd.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style dpd T cutoff seed pair_style dpd T cutoff seed
pair_style dpd/tstat Tstart Tstop 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_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_coeff 1 1 3.0 1.0 1.0
pair_style dpd/tstat 1.0 1.0 2.5 34387 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 pair_coeff 1 1 1.0 1.0
Description Description

34
doc/src/pair_dpd_fdt.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -35,13 +35,13 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style dpd/fdt 300.0 2.5 34387 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_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 Description
""""""""""" """""""""""
@ -107,18 +107,18 @@ energies are computed within style *dpd/fdt/energy* as:
.. math:: .. 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}^{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} - 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{\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} \frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2}
where where
.. math:: .. math::
\alpha_{ij}^{2} = & 2k_{B}\kappa_{ij} \\ \alpha_{ij}^{2} = & 2k_{B}\kappa_{ij} \\
\sigma^{2}_{ij} = & 2\gamma_{ij}k_{B}\Theta_{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}}) \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 :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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style hybrid/overlay drip [styles ...] pair_style hybrid/overlay drip [styles ...]
@ -17,19 +17,19 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style hybrid/overlay drip pair_style hybrid/overlay drip
pair_coeff \* \* none pair_coeff * * none
pair_coeff \* \* drip C.drip C pair_coeff * * drip C.drip C
pair_style hybrid/overlay drip rebo pair_style hybrid/overlay drip rebo
pair_coeff \* \* drip C.drip C pair_coeff * * drip C.drip C
pair_coeff \* \* rebo CH.airebo C pair_coeff * * rebo CH.airebo C
pair_style hybrid/overlay drip rebo pair_style hybrid/overlay drip rebo
pair_coeff \* \* drip C.drip C NULL pair_coeff * * drip C.drip C NULL
pair_coeff \* \* rebo CH.airebo C H pair_coeff * * rebo CH.airebo C H
Description 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] \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 the exponential term is designed to capture the registry effect due to
overlapping *pi* bonds, and *fc* is a cutoff function. 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: 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 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 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: model H atoms:
.. parsed-literal:: .. code-block:: LAMMPS
pair_style hybrid/overlay drip rebo pair_style hybrid/overlay drip rebo
pair_coeff \* \* drip C.drip C NULL pair_coeff * * drip C.drip C NULL
pair_coeff \* \* rebo CH.airebo C H pair_coeff * * rebo CH.airebo C H
.. note:: .. note::

18
doc/src/pair_dsmc.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style dsmc .. index:: pair_style dsmc
pair\_style dsmc command pair_style dsmc command
======================== =======================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample 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_style dsmc 2.5 34387 10 1.0 100 20
pair_coeff \* \* 1.0 pair_coeff * * 1.0
pair_coeff 1 1 1.0 pair_coeff 1 1 1.0
Description Description
@ -74,7 +74,7 @@ the "fix nve/noforce" time integration fix for the DSMC particles,
e.g. e.g.
.. parsed-literal:: .. code-block:: LAMMPS
fix 1 all nve/noforce fix 1 all nve/noforce
@ -85,7 +85,7 @@ on the same processor. To ensure this occurs, you should use
these commands: these commands:
.. parsed-literal:: .. code-block:: LAMMPS
neighbor 0.0 bin neighbor 0.0 bin
neigh_modify every 1 delay 0 check no 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: as in the following:
.. parsed-literal:: .. code-block:: LAMMPS
velocity all create 594.6 87287 loop geom dist gaussian velocity all create 594.6 87287 loop geom dist gaussian

18
doc/src/pair_e3b.rst
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@ -1,21 +1,21 @@
.. index:: pair\_style e3b .. index:: pair_style e3b
pair\_style e3b command pair_style e3b command
======================= ======================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style e3b Otype pair_style e3b Otype
* Otype = atom type for oxygen * 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. * 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* * 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_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_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 Description
""""""""""" """""""""""

126
doc/src/pair_eam.rst
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@ -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/gpu command
===========================
pair\_style eam/intel command
=============================
pair\_style eam/kk 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/intel 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/fs command pair_style eam/alloy/kk command
========================== ===============================
pair\_style eam/fs/gpu command pair_style eam/alloy/omp command
==============================
pair\_style eam/fs/intel 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style pair_style style
@ -80,20 +80,20 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style eam pair_style eam
pair_coeff \* \* cuu3 pair_coeff * * cuu3
pair_coeff 1\*3 1\*3 niu3.eam pair_coeff 1*3 1\*3 niu3.eam
pair_style eam/alloy 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_style eam/cd
pair_coeff \* \* ../potentials/FeCr.cdeam Fe Cr pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
pair_style eam/fs 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 Description
""""""""""" """""""""""
@ -182,9 +182,9 @@ single argument:
Thus the following command 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 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 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 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. 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: 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 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 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. 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 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>` the number of LAMMPS atom types. See the :doc:`pair_coeff <pair_coeff>`

36
doc/src/pair_edip.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style pair_style style
@ -22,8 +22,10 @@ Syntax
Examples Examples
"""""""" """"""""
pair\_style edip .. code-block:: LAMMPS
pair\_coeff \* \* Si.edip Si
pair_style edip
pair_coeff * * Si.edip Si
Description 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_{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) \\ \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 Z_i = & \sum_{m \ne i} f(R_{im}) \qquad
f(r) = \begin{cases} f(r) = \begin{cases}
1 & \quad r<c \\ 1 & \quad r<c \\
\exp\left(\frac{\alpha}{1-x^{-3}}\right) & \quad c<r<a \\ \exp\left(\frac{\alpha}{1-x^{-3}}\right) & \quad c<r<a \\
0 & \quad r>a 0 & \quad r>a
\end{cases} \\ \end{cases} \\
h(l,Z) = & \lambda [(1-e^{-Q(Z)(l+\tau(Z))^2}) + \eta Q(Z)(l+\tau(Z))^2 ] \\ 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}) 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 where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a

15
doc/src/pair_eff.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style eff/cut cutoff keyword args ... 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 39.7
pair_style eff/cut 40.0 limit/eradius pair_style eff/cut 40.0 limit/eradius
pair_style eff/cut 40.0 limit/eradius pressure/evirials pair_style eff/cut 40.0 limit/eradius pressure/evirials
pair_style eff/cut 40.0 ecp 1 Si 3 C pair_style eff/cut 40.0 ecp 1 Si 3 C
pair_coeff \* \* pair_coeff * *
pair_coeff 2 2 20.0 pair_coeff 2 2 20.0
pair_coeff 1 s 0.320852 2.283269 0.814857 pair_coeff 1 s 0.320852 2.283269 0.814857
pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621 pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621
@ -100,7 +100,7 @@ given as,
.. math:: .. 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: 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: electrons (i.e. Pauli repulsion) with one of the functional forms:
.. math:: .. math::
E_{Pauli(ECP_s)} = & p_1\exp\left(-\frac{p_2r^2}{p_3+s^2} \right) \\ 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] 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
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style pair_style style
@ -20,12 +20,12 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style eim pair_style eim
pair_coeff \* \* Na Cl ../potentials/ffield.eim Na Cl pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
pair_coeff \* \* Na Cl ffield.eim Na Na 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 Cl NULL Na
Description 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: 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 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 The filename is the EIM potential file. The Na and Cl arguments

24
doc/src/pair_exp6_rx.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style exp6/rx cutoff ... 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
pair_style exp6/rx 10.0 fractional pair_style exp6/rx 10.0 fractional
pair_style exp6/rx 10.0 molecular 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 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 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 exponent 1.0 1.0 10.0
pair_coeff \* \* exp6.params 1fluid 1fluid none 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 1fluid 1fluid polynomial filename 10.0
Description Description
""""""""""" """""""""""

14
doc/src/pair_extep.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style extep .. index:: pair_style extep
pair\_style extep command pair_style extep command
========================= ========================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style extep pair_style extep
@ -15,10 +15,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style extep pair_style extep
pair_coeff \* \* BN.extep B N pair_coeff * * BN.extep B N
Description Description
""""""""""" """""""""""
@ -32,7 +32,7 @@ interactions as described in :ref:`(Los2017) <Los2017>`.
Restrictions Restrictions
"""""""""""" """"""""""""
none none
Related commands 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/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/class2/coul/cut/soft command pair_style lj/cut/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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args 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_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_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
pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 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
pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5 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
pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 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
pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 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
pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5 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_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
pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0 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_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
pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 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
pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 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_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_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_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_coeff 1 1 1.0 9.5
pair_style morse/soft 4 0.9 10.0 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 pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
Description Description

30
doc/src/pair_gauss.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style gauss cutoff pair_style gauss cutoff
pair_style gauss/cut cutoff pair_style gauss/cut cutoff
@ -30,10 +30,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style gauss 12.0 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_coeff 1 4 1.0 0.9 10.0
pair_style gauss/cut 3.5 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: heading) the following commands could be included in an input script:
.. parsed-literal:: .. code-block:: LAMMPS
compute gauss all pair gauss compute gauss all pair gauss
variable occ equal c_gauss[1] variable occ equal c_gauss[1]

24
doc/src/pair_gayberne.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style gayberne gamma upsilon mu cutoff 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_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 Description
""""""""""" """""""""""

38
doc/src/pair_gran.rst
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@ -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/omp command
==========================================
pair\_style gran/hooke/history/kk 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style Kn Kt gamma_n gamma_t xmu dampflag 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/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 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 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 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 potential (i.e. one of the pair styles above is used). If a granular

20
doc/src/pair_granular.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style granular .. index:: pair_style granular
pair\_style granular command pair_style granular command
============================ ===========================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style granular cutoff pair_style granular cutoff
@ -17,22 +17,22 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style granular 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_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_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_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_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_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 pair_style granular

38
doc/src/pair_gromacs.rst
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@ -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/gpu command
==================================
pair\_style lj/gromacs/kk 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -45,15 +45,15 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style lj/gromacs 9.0 12.0 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_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 9.0 12.0
pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0 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 Description
""""""""""" """""""""""

25
doc/src/pair_gw.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style pair_style style
@ -19,14 +19,13 @@ Syntax
Examples Examples
"""""""" """"""""
pair\_style gw .. code-block:: LAMMPS
pair\_coeff \* \* SiC.gw Si C C
pair_style gw
.. parsed-literal:: pair_coeff * * SiC.gw Si C C
pair_style gw/zbl pair_style gw/zbl
pair_coeff \* \* SiC.gw.zbl C Si pair_coeff * * SiC.gw.zbl C Si
Description 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: 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 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 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si

24
doc/src/pair_hbond_dreiding.rst
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@ -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/lj/omp command
=========================================
pair\_style hbond/dreiding/morse command
======================================== ========================================
pair\_style hbond/dreiding/morse/omp command pair_style hbond/dreiding/morse command
============================================ =======================================
pair_style hbond/dreiding/morse/omp command
===========================================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof 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_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 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: heading) the following commands could be included in an input script:
.. parsed-literal:: .. code-block:: LAMMPS
compute hb all pair hbond/dreiding/lj compute hb all pair hbond/dreiding/lj
variable n_hbond equal c_hb[1] #number hbonds variable n_hbond equal c_hb[1] #number hbonds

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