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Second batch of index cleanup and code-blocks

This commit is contained in:
Richard Berger 2020-02-26 16:31:05 -05:00
parent 8e1928aa65
commit 9ef5949798
54 changed files with 935 additions and 936 deletions
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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/kk command
pair_style coul/cut/gpu command
===============================
pair\_style coul/cut/omp command
================================
pair\_style coul/debye command
pair_style coul/cut/kk command
==============================
pair\_style coul/debye/gpu command
==================================
pair\_style coul/debye/kk command
=================================
pair\_style coul/debye/omp command
==================================
pair\_style coul/dsf command
============================
pair\_style coul/dsf/gpu command
================================
pair\_style coul/dsf/kk command
pair_style coul/cut/omp command
===============================
pair\_style coul/dsf/omp command
================================
pair\_style coul/long command
pair_style coul/debye command
=============================
pair\_style coul/long/omp command
pair_style coul/debye/gpu command
=================================
pair\_style coul/long/gpu command
pair_style coul/debye/kk command
================================
pair_style coul/debye/omp command
=================================
pair\_style coul/long/kk command
================================
pair_style coul/dsf command
===========================
pair\_style coul/msm command
============================
pair_style coul/dsf/gpu command
===============================
pair\_style coul/msm/omp command
================================
pair\_style coul/streitz command
================================
pair\_style coul/wolf command
=============================
pair\_style coul/wolf/kk command
================================
pair\_style coul/wolf/omp command
=================================
pair\_style tip4p/cut command
=============================
pair\_style tip4p/long command
pair_style coul/dsf/kk command
==============================
pair\_style tip4p/cut/omp command
=================================
pair_style coul/dsf/omp command
===============================
pair\_style tip4p/long/omp command
==================================
pair_style coul/long command
============================
pair_style coul/long/omp command
================================
pair_style coul/long/gpu command
================================
pair_style coul/long/kk command
===============================
pair_style coul/msm command
===========================
pair_style coul/msm/omp command
===============================
pair_style coul/streitz command
===============================
pair_style coul/wolf command
============================
pair_style coul/wolf/kk command
===============================
pair_style coul/wolf/omp command
================================
pair_style tip4p/cut command
============================
pair_style tip4p/long command
=============================
pair_style tip4p/cut/omp command
================================
pair_style tip4p/long/omp command
=================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style coul/cut cutoff
pair_style coul/debye kappa cutoff
@ -102,37 +102,37 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style coul/cut 2.5
pair_coeff \* \*
pair_coeff * *
pair_coeff 2 2 3.5
pair_style coul/debye 1.4 3.0
pair_coeff \* \*
pair_coeff * *
pair_coeff 2 2 3.5
pair_style coul/dsf 0.05 10.0
pair_coeff \* \*
pair_coeff * *
pair_style coul/long 10.0
pair_coeff \* \*
pair_coeff * *
pair_style coul/msm 10.0
pair_coeff \* \*
pair_coeff * *
pair_style coul/wolf 0.2 9.0
pair_coeff \* \*
pair_coeff * *
pair_style coul/streitz 12.0 ewald
pair_style coul/streitz 12.0 wolf 0.30
pair_coeff \* \* AlO.streitz Al O
pair_coeff * * AlO.streitz Al O
pair_style tip4p/cut 1 2 7 8 0.15 12.0
pair_coeff \* \*
pair_coeff * *
pair_style tip4p/long 1 2 7 8 0.15 10.0
pair_coeff \* \*
pair_coeff * *
Description
"""""""""""
@ -142,7 +142,7 @@ potential given by
.. math::
E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
where C is an energy-conversion constant, Qi and Qj are the charges on
@ -159,7 +159,7 @@ Coulombic term, given by
.. math::
E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c
E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c
where :math:`\kappa` is the Debye length. This potential is another way to
@ -174,9 +174,8 @@ shifted force model described in :ref:`Fennell <Fennell1>`, given by:
.. math::
E =
q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
E = q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
where :math:`\alpha` is the damping parameter and erfc() is the
@ -194,10 +193,10 @@ summation method, described in :ref:`Wolf <Wolf1>`, given by:
.. math::
E_i = \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
\frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
E_i = \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
\frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
where :math:`\alpha` is the damping parameter, and erc() and erfc() are
@ -228,11 +227,11 @@ the :doc:`pair_style hybrid/overlay <pair_hybrid>` command. Likewise,
charge equilibration must be performed via the :doc:`fix qeq/slater <fix_qeq>` command. For example:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
pair_coeff \* \* coul/streitz AlO.streitz Al O
pair_coeff \* \* eam/alloy AlO.eam.alloy Al O
pair_coeff * * coul/streitz AlO.streitz Al O
pair_coeff * * eam/alloy AlO.eam.alloy Al O
fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
The keyword *wolf* in the coul/streitz command denotes computing
@ -242,7 +241,7 @@ coul/wolf potential above. Alternatively, Coulombic interactions can
be computed via an Ewald summation. For example:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
kspace_style ewald 1e-6

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

16
doc/src/pair_coul_shield.rst
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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
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style coul/shield cutoff tap_flag
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style coul/shield 16.0 1
pair_coeff 1 2 0.70
@ -41,9 +41,9 @@ the pair style :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
.. math::
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\
{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\
{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

38
doc/src/pair_cs.rst
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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
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -71,33 +71,33 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style born/coul/dsf/cs 0.1 10.0 12.0
pair_coeff \* \* 0.0 1.00 0.00 0.00 0.00
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50
pair_style born/coul/long/cs 10.0 8.0
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
pair_style born/coul/wolf/cs 0.25 10.0 12.0
pair_coeff \* \* 0.0 1.00 0.00 0.00 0.00
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50
pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long/cs 10.0 8.0
pair_coeff \* \* 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_style coul/long/cs 10.0
pair_coeff \* \*
pair_coeff * *
pair_style coul/wolf/cs 0.2 9.0
pair_coeff \* \*
pair_coeff * *
pair_style lj/cut/coul/long/cs 10.0
pair_style lj/cut/coul/long/cs 10.0 8.0
pair_coeff \* \* 100.0 3.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
Description

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

38
doc/src/pair_dpd.rst
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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
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style dpd T cutoff seed
pair_style dpd/tstat Tstart Tstop cutoff seed
@ -39,14 +39,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style dpd 1.0 2.5 34387
pair_coeff \* \* 3.0 1.0
pair_coeff * * 3.0 1.0
pair_coeff 1 1 3.0 1.0 1.0
pair_style dpd/tstat 1.0 1.0 2.5 34387
pair_coeff \* \* 1.0
pair_coeff * * 1.0
pair_coeff 1 1 1.0 1.0
Description

34
doc/src/pair_dpd_fdt.rst
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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
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -35,13 +35,13 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style dpd/fdt 300.0 2.5 34387
pair_coeff \* \* 3.0 1.0 2.5
pair_coeff * * 3.0 1.0 2.5
pair_style dpd/fdt/energy 2.5 34387
pair_coeff \* \* 3.0 1.0 0.1 2.5
pair_coeff * * 3.0 1.0 0.1 2.5
Description
"""""""""""
@ -107,18 +107,18 @@ energies are computed within style *dpd/fdt/energy* as:
.. math::
du_{i}^{cond} = & \kappa_{ij}(\frac{1}{\theta_{i}}-\frac{1}{\theta_{j}})\omega_{ij}^{2} + \alpha_{ij}\omega_{ij}\zeta_{ij}^{q}(\Delta{t})^{-1/2} \\
du_{i}^{mech} = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} -
\frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} -
\frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2}
du_{i}^{mech} = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} -
\frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} -
\frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2}
where
.. math::
\alpha_{ij}^{2} = & 2k_{B}\kappa_{ij} \\
\sigma^{2}_{ij} = & 2\gamma_{ij}k_{B}\Theta_{ij} \\
\Theta_{ij}^{-1} = & \frac{1}{2}(\frac{1}{\theta_{i}}+\frac{1}{\theta_{j}})
\alpha_{ij}^{2} = & 2k_{B}\kappa_{ij} \\
\sigma^{2}_{ij} = & 2\gamma_{ij}k_{B}\Theta_{ij} \\
\Theta_{ij}^{-1} = & \frac{1}{2}(\frac{1}{\theta_{i}}+\frac{1}{\theta_{j}})
:math:`\zeta_ij^q` is a second Gaussian random number with zero mean and unit

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

18
doc/src/pair_dsmc.rst
View File

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

18
doc/src/pair_e3b.rst
View File

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

126
doc/src/pair_eam.rst
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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/intel command
=============================
pair\_style eam/kk command
pair_style eam/gpu command
==========================
pair\_style eam/omp command
===========================
pair_style eam/intel command
============================
pair\_style eam/opt command
===========================
pair_style eam/kk command
=========================
pair\_style eam/alloy command
=============================
pair_style eam/omp command
==========================
pair\_style eam/alloy/gpu command
=================================
pair_style eam/opt command
==========================
pair\_style eam/alloy/intel command
===================================
pair_style eam/alloy command
============================
pair\_style eam/alloy/kk command
pair_style eam/alloy/gpu command
================================
pair\_style eam/alloy/omp command
=================================
pair\_style eam/alloy/opt command
=================================
pair\_style eam/cd command
==========================
pair\_style eam/cd/omp command
==============================
pair\_style eam/cd/old command
==============================
pair\_style eam/cd/old/omp command
pair_style eam/alloy/intel command
==================================
pair\_style eam/fs command
==========================
pair_style eam/alloy/kk command
===============================
pair\_style eam/fs/gpu command
==============================
pair\_style eam/fs/intel command
pair_style eam/alloy/omp command
================================
pair\_style eam/fs/kk command
pair_style eam/alloy/opt command
================================
pair_style eam/cd command
=========================
pair_style eam/cd/omp command
=============================
pair\_style eam/fs/omp command
==============================
pair_style eam/cd/old command
=============================
pair\_style eam/fs/opt command
==============================
pair_style eam/cd/old/omp command
=================================
pair_style eam/fs command
=========================
pair_style eam/fs/gpu command
=============================
pair_style eam/fs/intel command
===============================
pair_style eam/fs/kk command
============================
pair_style eam/fs/omp command
=============================
pair_style eam/fs/opt command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style
@ -80,20 +80,20 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style eam
pair_coeff \* \* cuu3
pair_coeff 1\*3 1\*3 niu3.eam
pair_coeff * * cuu3
pair_coeff 1*3 1\*3 niu3.eam
pair_style eam/alloy
pair_coeff \* \* ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
pair_style eam/cd
pair_coeff \* \* ../potentials/FeCr.cdeam Fe Cr
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
pair_style eam/fs
pair_coeff \* \* NiAlH_jea.eam.fs Ni Al Ni Ni
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
Description
"""""""""""
@ -182,9 +182,9 @@ single argument:
Thus the following command
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \*2 1\*2 cuu3.eam
pair_coeff *2 1*2 cuu3.eam
will read the cuu3 potential file and use the tabulated Cu values for
F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
@ -233,9 +233,9 @@ by LAMMPS to compute the pair potential term in the EAM energy
expression as r\*phi, in units of eV-Angstroms, via the formula
.. parsed-literal::
.. math::
r\*phi = 27.2 \* 0.529 \* Zi \* Zj
r \cdot \phi = 27.2 \cdot 0.529 \cdot Z_i \cdot Z_j
where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
@ -277,9 +277,9 @@ be Ni, and the 4th to be Al, you would use the following pair\_coeff
command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* NiAlH_jea.eam.alloy Ni Ni Ni Al
pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
@ -402,9 +402,9 @@ For style *eam/fs*\ , the form of the pair\_coeff command is exactly the
same as for style *eam/alloy*\ , e.g.
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* NiAlH_jea.eam.fs Ni Ni Ni Al
pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
where there are N additional arguments after the filename, where N is
the number of LAMMPS atom types. See the :doc:`pair_coeff <pair_coeff>`

36
doc/src/pair_edip.rst
View File

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

15
doc/src/pair_eff.rst
View File

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

24
doc/src/pair_eim.rst
View File

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

24
doc/src/pair_exp6_rx.rst
View File

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

14
doc/src/pair_extep.rst
View File

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

130
doc/src/pair_fep_soft.rst
View File

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

30
doc/src/pair_gauss.rst
View File

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

24
doc/src/pair_gayberne.rst
View File

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

38
doc/src/pair_gran.rst
View File

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

20
doc/src/pair_granular.rst
View File

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

38
doc/src/pair_gromacs.rst
View File

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

25
doc/src/pair_gw.rst
View File

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

24
doc/src/pair_hbond_dreiding.rst
View File

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

71
doc/src/pair_hybrid.rst
View File

@ -1,22 +1,22 @@
.. index:: pair\_style hybrid
.. index:: pair_style hybrid
pair\_style hybrid command
==========================
pair_style hybrid command
=========================
pair\_style hybrid/kk command
=============================
pair_style hybrid/kk command
============================
pair\_style hybrid/overlay command
==================================
pair_style hybrid/overlay command
=================================
pair\_style hybrid/overlay/kk command
=====================================
pair_style hybrid/overlay/kk command
====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid style1 args style2 args ...
pair_style hybrid/overlay style1 args style2 args ...
@ -27,16 +27,16 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
pair_coeff 1\*2 1\*2 eam niu3
pair_coeff 1*2 1*2 eam niu3
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1\*2 3 lj/cut 0.5 1.2
pair_coeff 1*2 3 lj/cut 0.5 1.2
pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
pair_coeff \* \* lj/cut 1.0 1.0
pair_coeff \* \* coul/long
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * coul/long
Description
"""""""""""
@ -101,12 +101,12 @@ are Ni atoms, type 3 are LJ atoms with charges. The following
commands would set up a hybrid simulation:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
pair_coeff \* \* eam/alloy nialhjea Ni Ni NULL
pair_coeff * * eam/alloy nialhjea Ni Ni NULL
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1\*2 3 lj/cut 0.8 1.3
pair_coeff 1*2 3 lj/cut 0.8 1.3
As an example of using the same pair style multiple times, consider a
simulation with 2 atom types. Type 1 is Si, type 2 is C. The
@ -114,11 +114,11 @@ following commands would model the Si atoms with Tersoff, the C atoms
with Tersoff, and the cross-interactions with Lennard-Jones:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid lj/cut 2.5 tersoff tersoff
pair_coeff \* \* tersoff 1 Si.tersoff Si NULL
pair_coeff \* \* tersoff 2 C.tersoff NULL C
pair_coeff * * tersoff 1 Si.tersoff Si NULL
pair_coeff * * tersoff 2 C.tersoff NULL C
pair_coeff 1 2 lj/cut 1.0 1.5
If pair coefficients are specified in the data file read via the
@ -159,14 +159,14 @@ normal usage of the pair\_coeff command. E.g. these two sets of
commands are the same:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/cut 2.5
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 2 2 1.5 0.8
pair_style hybrid/overlay lj/cut 2.5
pair_coeff \* \* lj/cut 1.0 1.0
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 2 2 lj/cut 1.5 0.8
Coefficients must be defined for each pair of atoms types via the
@ -190,7 +190,7 @@ LJ potential). Or, for *hybrid* and *hybrid/overlay* simulations, you
can use this form of the pair\_coeff command in your input script:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff 2 3 none
@ -230,7 +230,7 @@ setting sets the 1-4 interactions to non-zero scaling factors and
then overrides them with 0.0 only for CHARMM:
.. parsed-literal::
.. code-block:: LAMMPS
special_bonds amber
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
@ -239,7 +239,7 @@ then overrides them with 0.0 only for CHARMM:
The this input achieves the same effect:
.. parsed-literal::
.. code-block:: LAMMPS
special_bonds 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
@ -254,7 +254,7 @@ interactions have been set to 0. Note the global settings are
effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA:
.. parsed-literal::
.. code-block:: LAMMPS
special_bonds lj/coul 1e-20 1e-20 0.5
pair_hybrid tersoff lj/cut/coul/long 12.0
@ -323,14 +323,14 @@ surface, but not between surfaces. Then either of these two command
sequences would implement that model:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid tersoff
pair_coeff \* \* tersoff SiC.tersoff C C
pair_coeff * * tersoff SiC.tersoff C C
pair_coeff 1 2 none
pair_style tersoff
pair_coeff \* \* SiC.tersoff C C
pair_coeff * * SiC.tersoff C C
neigh_modify exclude type 1 2
Either way, only neighbor lists with 1-1 or 2-2 interactions would be
@ -344,11 +344,11 @@ interactions, and AIREBO for C/C interactions. Si atoms are type 1; C
atoms are type 2. Something like this will work:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay tersoff airebo 3.0
pair_coeff \* \* tersoff SiC.tersoff.custom Si C
pair_coeff \* \* airebo CH.airebo NULL C
pair_coeff * * tersoff SiC.tersoff.custom Si C
pair_coeff * * airebo CH.airebo NULL C
Note that to prevent the Tersoff potential from computing C/C
interactions, you would need to modify the SiC.tersoff file to turn
@ -436,4 +436,5 @@ Related commands
:doc:`pair_coeff <pair_coeff>`
**Default:** none
**Default:**
none

44
doc/src/pair_ilp_graphene_hbn.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style ilp/graphene/hbn
.. index:: pair_style ilp/graphene/hbn
pair\_style ilp/graphene/hbn command
====================================
pair_style ilp/graphene/hbn command
===================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style [hybrid/overlay ...] ilp/graphene/hbn cutoff tap_flag
@ -18,15 +18,15 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
pair_coeff \* \* ilp/graphene/hbn BNCH.ILP B N C
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
pair_coeff \* \* rebo CH.rebo NULL NULL C
pair_coeff \* \* tersoff BNC.tersoff B N NULL
pair_coeff \* \* ilp/graphene/hbn BNCH.ILP B N C
pair_coeff * * rebo CH.rebo NULL NULL C
pair_coeff * * tersoff BNC.tersoff B N NULL
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.695
pair_coeff 2 2 coul/shield 0.69
@ -42,18 +42,18 @@ in :ref:`(Kolmogorov) <Kolmogorov2>`.
.. math::
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
\left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
\frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
\cdot \frac{C_6}{r^6_{ij}} \right \}\\
\rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
\rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
f(\rho) = & C e^{ -( \rho / \delta )^2 } \\
{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
\left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
\frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
\cdot \frac{C_6}{r^6_{ij}} \right \}\\
\rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
\rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
f(\rho) = & C e^{ -( \rho / \delta )^2 } \\
{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides
@ -120,7 +120,7 @@ To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
.. parsed-literal::
.. code-block:: LAMMPS
compute 0 all pair ilp/graphene/hbn
variable Evdw equal c_0[1]

16
doc/src/pair_kim.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style kim
.. index:: pair_style kim
pair\_style kim command
=======================
pair_style kim command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style kim model
@ -17,10 +17,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff \* \* Si
pair_coeff * * Si
Description
"""""""""""
@ -68,9 +68,9 @@ If the LAMMPS simulation has four atom types, where the first three are Si,
and the fourth is C, the following *pair\_coeff* command would be used:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* Si Si Si C
pair_coeff * * Si Si Si C
The first two arguments must be \* \* so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as

20
doc/src/pair_kolmogorov_crespi_full.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style kolmogorov/crespi/full
.. index:: pair_style kolmogorov/crespi/full
pair\_style kolmogorov/crespi/full command
==========================================
pair_style kolmogorov/crespi/full command
=========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag
@ -18,15 +18,15 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
pair_coeff \* \* none
pair_coeff \* \* kolmogorov/crespi/full CH.KC C C
pair_coeff * * none
pair_coeff * * kolmogorov/crespi/full CH.KC C C
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
pair_coeff \* \* rebo CH.rebo C H
pair_coeff \* \* kolmogorov/crespi/full CH_taper.KC C H
pair_coeff * * rebo CH.rebo C H
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H
Description
"""""""""""
@ -100,7 +100,7 @@ To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
.. parsed-literal::
.. code-block:: LAMMPS
compute 0 all pair kolmogorov/crespi/full
variable Evdw equal c_0[1]

22
doc/src/pair_kolmogorov_crespi_z.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style kolmogorov/crespi/z
.. index:: pair_style kolmogorov/crespi/z
pair\_style kolmogorov/crespi/z command
=======================================
pair_style kolmogorov/crespi/z command
======================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style [hybrid/overlay ...] kolmogorov/crespi/z cutoff
@ -15,14 +15,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay kolmogorov/crespi/z 20.0
pair_coeff \* \* none
pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
pair_coeff \* \* rebo CH.rebo C C
pair_coeff * * rebo CH.rebo C C
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C
Description
@ -34,10 +34,10 @@ which is to take all normals along the z-axis.
.. math::
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\
\rho_{ij}^2 = & \rho_{ji}^2 = x_{ij}^2 + y_{ij}^2 \qquad \qquad (\mathbf{n}_i \equiv \mathbf{\hat{z}}) \\
f(\rho) = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right)^{2n}
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\
\rho_{ij}^2 = & \rho_{ji}^2 = x_{ij}^2 + y_{ij}^2 \qquad \qquad (\mathbf{n}_i \equiv \mathbf{\hat{z}}) \\
f(\rho) = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right)^{2n}

16
doc/src/pair_lcbop.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style lcbop
.. index:: pair_style lcbop
pair\_style lcbop command
=========================
pair_style lcbop command
========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lcbop
@ -15,10 +15,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lcbop
pair_coeff \* \* ../potentials/C.lcbop C
pair_coeff * * ../potentials/C.lcbop C
Description
"""""""""""
@ -43,9 +43,9 @@ As an example, if your LAMMPS simulation has 4 atom types and you want
the 1st 3 to be C you would use the following pair\_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* C.lcbop C C C NULL
pair_coeff * * C.lcbop C C C NULL
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The first C argument maps LAMMPS atom type 1 to the C element in the

14
doc/src/pair_lebedeva_z.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style lebedeva/z
.. index:: pair_style lebedeva/z
pair\_style lebedeva/z command
==============================
pair_style lebedeva/z command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style [hybrid/overlay ...] lebedeva/z cutoff
@ -15,14 +15,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay lebedeva/z 20.0
pair_coeff \* \* none
pair_coeff * * none
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C
pair_style hybrid/overlay rebo lebedeva/z 14.0
pair_coeff \* \* rebo CH.rebo C C
pair_coeff * * rebo CH.rebo C C
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C
Description

12
doc/src/pair_line_lj.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style line/lj
.. index:: pair_style line/lj
pair\_style line/lj command
===========================
pair_style line/lj command
==========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style line/lj cutoff
@ -17,10 +17,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style line/lj 3.0
pair_coeff \* \* 1.0 1.0 1.0 0.8 1.12
pair_coeff * * 1.0 1.0 1.0 0.8 1.12
pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5

190
doc/src/pair_lj.rst
View File

@ -1,115 +1,115 @@
.. index:: pair\_style lj/cut
.. index:: pair_style lj/cut
pair\_style lj/cut command
==========================
pair_style lj/cut command
=========================
pair\_style lj/cut/gpu command
==============================
pair\_style lj/cut/intel command
================================
pair\_style lj/cut/kk command
pair_style lj/cut/gpu command
=============================
pair\_style lj/cut/opt command
==============================
pair_style lj/cut/intel command
===============================
pair\_style lj/cut/omp command
==============================
pair_style lj/cut/kk command
============================
pair\_style lj/cut/coul/cut command
===================================
pair_style lj/cut/opt command
=============================
pair\_style lj/cut/coul/cut/gpu command
=======================================
pair_style lj/cut/omp command
=============================
pair\_style lj/cut/coul/cut/kk command
pair_style lj/cut/coul/cut command
==================================
pair_style lj/cut/coul/cut/gpu command
======================================
pair\_style lj/cut/coul/cut/omp command
=======================================
pair\_style lj/cut/coul/debye command
pair_style lj/cut/coul/cut/kk command
=====================================
pair\_style lj/cut/coul/debye/gpu command
=========================================
pair\_style lj/cut/coul/debye/kk command
========================================
pair\_style lj/cut/coul/debye/omp command
=========================================
pair\_style lj/cut/coul/dsf command
===================================
pair\_style lj/cut/coul/dsf/gpu command
=======================================
pair\_style lj/cut/coul/dsf/kk command
pair_style lj/cut/coul/cut/omp command
======================================
pair\_style lj/cut/coul/dsf/omp command
=======================================
pair\_style lj/cut/coul/long command
pair_style lj/cut/coul/debye command
====================================
pair\_style lj/cut/coul/long/gpu command
pair_style lj/cut/coul/debye/gpu command
========================================
pair\_style lj/cut/coul/long/kk command
pair_style lj/cut/coul/debye/kk command
=======================================
pair\_style lj/cut/coul/long/intel command
==========================================
pair\_style lj/cut/coul/long/opt command
pair_style lj/cut/coul/debye/omp command
========================================
pair\_style lj/cut/coul/long/omp command
========================================
pair_style lj/cut/coul/dsf command
==================================
pair\_style lj/cut/coul/msm command
===================================
pair_style lj/cut/coul/dsf/gpu command
======================================
pair\_style lj/cut/coul/msm/gpu command
=======================================
pair\_style lj/cut/coul/msm/omp command
=======================================
pair\_style lj/cut/coul/wolf command
====================================
pair\_style lj/cut/coul/wolf/omp command
========================================
pair\_style lj/cut/tip4p/cut command
====================================
pair\_style lj/cut/tip4p/cut/omp command
========================================
pair\_style lj/cut/tip4p/long command
pair_style lj/cut/coul/dsf/kk command
=====================================
pair\_style lj/cut/tip4p/long/gpu command
pair_style lj/cut/coul/dsf/omp command
======================================
pair_style lj/cut/coul/long command
===================================
pair_style lj/cut/coul/long/gpu command
=======================================
pair_style lj/cut/coul/long/kk command
======================================
pair_style lj/cut/coul/long/intel command
=========================================
pair\_style lj/cut/tip4p/long/omp command
=========================================
pair_style lj/cut/coul/long/opt command
=======================================
pair\_style lj/cut/tip4p/long/opt command
=========================================
pair_style lj/cut/coul/long/omp command
=======================================
pair_style lj/cut/coul/msm command
==================================
pair_style lj/cut/coul/msm/gpu command
======================================
pair_style lj/cut/coul/msm/omp command
======================================
pair_style lj/cut/coul/wolf command
===================================
pair_style lj/cut/coul/wolf/omp command
=======================================
pair_style lj/cut/tip4p/cut command
===================================
pair_style lj/cut/tip4p/cut/omp command
=======================================
pair_style lj/cut/tip4p/long command
====================================
pair_style lj/cut/tip4p/long/gpu command
========================================
pair_style lj/cut/tip4p/long/omp command
========================================
pair_style lj/cut/tip4p/long/opt command
========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -159,50 +159,50 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/cut 2.5
pair_coeff \* \* 1 1
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8
pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut 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 9.0
pair_style lj/cut/coul/debye 1.5 3.0
pair_style lj/cut/coul/debye 1.5 2.5 5.0
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0
pair_style lj/cut/coul/dsf 0.05 2.5 10.0
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long 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_style lj/cut/coul/msm 10.0
pair_style lj/cut/coul/msm 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_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
pair_coeff \* \* 100.0 3.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_style lj/cut/coul/wolf 0.2 5. 10.0
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
pair_coeff \* \* 100.0 3.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
Description
@ -250,9 +250,9 @@ shifted force model described in :ref:`Fennell <Fennell2>`, given by:
.. math::
E =
q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
E =
q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
where :math:`\alpha` is the damping parameter and erfc() is the complementary
@ -281,10 +281,10 @@ summation method, described in :ref:`Wolf <Wolf1>`, given by:
.. math::
E_i = \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
\frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
E_i = \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
\frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
where :math:`\alpha` is the damping parameter, and erfc() is the

22
doc/src/pair_lj96.rst
View File

@ -1,19 +1,19 @@
.. index:: pair\_style lj96/cut
.. index:: pair_style lj96/cut
pair\_style lj96/cut command
============================
pair_style lj96/cut command
===========================
pair\_style lj96/cut/gpu command
================================
pair_style lj96/cut/gpu command
===============================
pair\_style lj96/cut/omp command
================================
pair_style lj96/cut/omp command
===============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj96/cut cutoff
@ -23,10 +23,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj96/cut 2.5
pair_coeff \* \* 1.0 1.0 4.0
pair_coeff * * 1.0 1.0 4.0
pair_coeff 1 1 1.0 1.0
Description
@ -115,7 +115,7 @@ details.
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

20
doc/src/pair_lj_cubic.rst
View File

@ -1,19 +1,19 @@
.. index:: pair\_style lj/cubic
.. index:: pair_style lj/cubic
pair\_style lj/cubic command
============================
pair_style lj/cubic command
===========================
pair\_style lj/cubic/gpu command
================================
pair_style lj/cubic/gpu command
===============================
pair\_style lj/cubic/omp command
================================
pair_style lj/cubic/omp command
===============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/cubic
@ -21,10 +21,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/cubic
pair_coeff \* \* 1.0 0.8908987
pair_coeff * * 1.0 0.8908987
Description
"""""""""""

42
doc/src/pair_lj_expand.rst
View File

@ -1,28 +1,28 @@
.. index:: pair\_style lj/expand
.. index:: pair_style lj/expand
pair\_style lj/expand command
=============================
pair_style lj/expand command
============================
pair\_style lj/expand/gpu command
=================================
pair\_style lj/expand/kk command
pair_style lj/expand/gpu command
================================
pair\_style lj/expand/omp command
=================================
pair_style lj/expand/kk command
===============================
pair\_style lj/expand/coul/long command
=======================================
pair_style lj/expand/omp command
================================
pair\_style lj/expand/coul/long/gpu command
===========================================
pair_style lj/expand/coul/long command
======================================
pair_style lj/expand/coul/long/gpu command
==========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/expand cutoff
@ -32,15 +32,15 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/expand 2.5
pair_coeff \* \* 1.0 1.0 0.5
pair_coeff * * 1.0 1.0 0.5
pair_coeff 1 1 1.0 1.0 -0.2 2.0
pair_style lj/expand/coul/long 2.5
pair_style lj/expand/coul/long 2.5 4.0
pair_coeff \* \* 1.0 1.0 0.5
pair_coeff * * 1.0 1.0 0.5
pair_coeff 1 1 1.0 1.0 -0.2 3.0
Description
@ -53,9 +53,9 @@ formula:
.. math::
E = 4 \epsilon \left[ \left(\frac{\sigma}{r - \Delta}\right)^{12} -
\left(\frac{\sigma}{r - \Delta}\right)^6 \right]
\qquad r < r_c + \Delta
E = 4 \epsilon \left[ \left(\frac{\sigma}{r - \Delta}\right)^{12} -
\left(\frac{\sigma}{r - \Delta}\right)^6 \right]
\qquad r < r_c + \Delta
:math:`r_c` is the cutoff which does not include the :math:`\Delta`
@ -139,7 +139,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

38
doc/src/pair_lj_long.rst
View File

@ -1,28 +1,28 @@
.. index:: pair\_style lj/long/coul/long
.. index:: pair_style lj/long/coul/long
pair\_style lj/long/coul/long command
pair_style lj/long/coul/long command
====================================
pair_style lj/long/coul/long/intel command
==========================================
pair_style lj/long/coul/long/omp command
========================================
pair_style lj/long/coul/long/opt command
========================================
pair_style lj/long/tip4p/long command
=====================================
pair\_style lj/long/coul/long/intel command
===========================================
pair\_style lj/long/coul/long/omp command
pair_style lj/long/tip4p/long/omp command
=========================================
pair\_style lj/long/coul/long/opt command
=========================================
pair\_style lj/long/tip4p/long command
======================================
pair\_style lj/long/tip4p/long/omp command
==========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -59,17 +59,17 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/long/coul/long cut off 2.5
pair_style lj/long/coul/long cut long 2.5 4.0
pair_style lj/long/coul/long long long 2.5 4.0
pair_coeff \* \* 1 1
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4
pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0
pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0
pair_coeff \* \* 100.0 3.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
Description

26
doc/src/pair_lj_smooth.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style lj/smooth
.. index:: pair_style lj/smooth
pair\_style lj/smooth command
=============================
pair_style lj/smooth command
============================
pair\_style lj/smooth/omp command
=================================
pair_style lj/smooth/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/smooth Rin Rc
@ -21,10 +21,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/smooth 8.0 10.0
pair_coeff \* \* 10.0 1.5
pair_coeff * * 10.0 1.5
pair_coeff 1 1 20.0 1.3 7.0 9.0
Description
@ -35,10 +35,10 @@ applied between the inner and outer cutoff.
.. math::
E & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_{in} \\
F & = C_1 + C_2 (r - r_{in}) + C_3 (r - r_{in})^2 + C_4 (r - r_{in})^3
E & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_{in} \\
F & = C_1 + C_2 (r - r_{in}) + C_3 (r - r_{in})^2 + C_4 (r - r_{in})^3
\qquad r_{in} < r < r_c
@ -131,7 +131,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

16
doc/src/pair_lj_smooth_linear.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style lj/smooth/linear
.. index:: pair_style lj/smooth/linear
pair\_style lj/smooth/linear command
====================================
pair_style lj/smooth/linear command
===================================
pair\_style lj/smooth/linear/omp command
========================================
pair_style lj/smooth/linear/omp command
=======================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/smooth/linear cutoff
@ -20,10 +20,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/smooth/linear 2.5
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 0.3 3.0 9.0
Description

10
doc/src/pair_lj_switch3_coulgauss_long.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style lj/switch3/coulgauss/long
.. index:: pair_style lj/switch3/coulgauss/long
pair\_style lj/switch3/coulgauss/long command
=============================================
pair_style lj/switch3/coulgauss/long command
============================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -26,7 +26,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/switch3/coulgauss/long 12.0 3.0
pair_coeff 1 0.2 2.5 1.2

12
doc/src/pair_local_density.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style local/density
.. index:: pair_style local/density
pair\_style local/density command
=================================
pair_style local/density command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style arg
@ -18,12 +18,12 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style local/density benzene_water.localdensity.table
pair_style hybrid/overlay table spline 500 local/density
pair_coeff \* \* local/density benzene_water.localdensity.table
pair_coeff * * local/density benzene_water.localdensity.table
Description
"""""""""""

28
doc/src/pair_lubricate.rst
View File

@ -1,22 +1,22 @@
.. index:: pair\_style lubricate
.. index:: pair_style lubricate
pair\_style lubricate command
=============================
pair_style lubricate command
============================
pair\_style lubricate/omp command
pair_style lubricate/omp command
================================
pair_style lubricate/poly command
=================================
pair\_style lubricate/poly command
==================================
pair\_style lubricate/poly/omp command
======================================
pair_style lubricate/poly/omp command
=====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF
@ -32,16 +32,16 @@ Syntax
**Examples:** (all assume radius = 1)
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lubricate 1.5 1 1 2.01 2.5
pair_coeff 1 1 2.05 2.8
pair_coeff \* \*
pair_coeff * *
pair_style lubricate 1.5 1 1 2.01 2.5
pair_coeff \* \*
pair_coeff * *
variable mu equal ramp(1,2)
fix 1 all adapt 1 pair lubricate mu \* \* v_mu
fix 1 all adapt 1 pair lubricate mu * * v_mu
Description
"""""""""""

16
doc/src/pair_lubricateU.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style lubricateU
.. index:: pair_style lubricateU
pair\_style lubricateU command
==============================
pair_style lubricateU command
=============================
pair\_style lubricateU/poly command
===================================
pair_style lubricateU/poly command
==================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF
@ -26,11 +26,11 @@ Syntax
**Examples:** (all assume radius = 1)
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1
pair_coeff 1 1 2.05 2.8
pair_coeff \* \*
pair_coeff * *
Description
"""""""""""

26
doc/src/pair_mdf.rst
View File

@ -1,19 +1,19 @@
.. index:: pair\_style lj/mdf
.. index:: pair_style lj/mdf
pair\_style lj/mdf command
==========================
pair_style lj/mdf command
=========================
pair\_style buck/mdf command
============================
pair_style buck/mdf command
===========================
pair\_style lennard/mdf command
===============================
pair_style lennard/mdf command
==============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -38,18 +38,18 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/mdf 2.5 3.0
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.1 2.8 3.0 3.2
pair_style buck 2.5 3.0
pair_coeff \* \* 100.0 1.5 200.0
pair_coeff \* \* 100.0 1.5 200.0 3.0 3.5
pair_coeff * * 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0 3.0 3.5
pair_style lennard/mdf 2.5 3.0
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1021760.3664 2120.317338 3.0 3.2
Description

26
doc/src/pair_meam_spline.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style meam/spline
.. index:: pair_style meam/spline
pair\_style meam/spline command
===============================
pair_style meam/spline command
==============================
pair\_style meam/spline/omp command
===================================
pair_style meam/spline/omp command
==================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style meam/spline
@ -18,11 +18,11 @@ Examples
""""""""
.. parsed-literal::
.. code:: LAMMPS
pair_style meam/spline
pair_coeff \* \* Ti.meam.spline Ti
pair_coeff \* \* Ti.meam.spline Ti Ti Ti
pair_coeff * * Ti.meam.spline Ti
pair_coeff * * Ti.meam.spline Ti Ti Ti
Description
"""""""""""
@ -92,9 +92,9 @@ treated with this potentials, you would use the following pair\_coeff
command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* Ti.meam.spline Ti Ti Ti
pair_coeff * * Ti.meam.spline Ti Ti Ti
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element
@ -109,9 +109,9 @@ An example with a two component spline (new style) is TiO.meam.spline, where
the command
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* TiO.meam.spline Ti O
pair_coeff * * TiO.meam.spline Ti O
will map the 1st atom type to Ti and the second atom type to O. Note
in this case that the species names need to match exactly with the

14
doc/src/pair_meam_sw_spline.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style meam/sw/spline
.. index:: pair_style meam/sw/spline
pair\_style meam/sw/spline command
==================================
pair_style meam/sw/spline command
=================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style meam/sw/spline
@ -15,11 +15,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style meam/sw/spline
pair_coeff \* \* Ti.meam.sw.spline Ti
pair_coeff \* \* Ti.meam.sw.spline Ti Ti Ti
pair_coeff * * Ti.meam.sw.spline Ti
pair_coeff * * Ti.meam.sw.spline Ti Ti Ti
Description
"""""""""""

31
doc/src/pair_meamc.rst
View File

@ -1,27 +1,24 @@
.. index:: pair\_style meam/c
.. index:: pair_style meam/c
pair\_style meam/c command
==========================
pair_style meam/c command
=========================
Syntax
""""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style style
style = *meam/c*
pair_style meam/c
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style meam/c
pair_coeff \* \* ../potentials/library.meam Si ../potentials/si.meam Si
pair_coeff \* \* ../potentials/library.meam Ni Al NULL Ni Al Ni Ni
pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni
Description
"""""""""""
@ -48,8 +45,8 @@ given by:
.. math::
E = \sum_i \left\{ F_i(\bar{\rho}_i)
+ \frac{1}{2} \sum_{i \neq j} \phi_{ij} (r_{ij}) \right\}
E = \sum_i \left\{ F_i(\bar{\rho}_i)
+ \frac{1}{2} \sum_{i \neq j} \phi_{ij} (r_{ij}) \right\}
where *F* is the embedding energy which is a function of the atomic
@ -94,9 +91,9 @@ LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
and the 4th to be C, you would use the following pair\_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* library.meam Si C sic.meam Si Si Si C
pair_coeff * * library.meam Si C sic.meam Si Si Si C
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The two filenames are for the library and parameter file respectively.
@ -204,9 +201,9 @@ MEAM library file numbered in the order of how those elements were
selected starting from 1. Thus for the example given below
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* library.meam Si C sic.meam Si Si Si C
pair_coeff * * library.meam Si C sic.meam Si Si Si C
an index of 1 would refer to Si and an index of 2 to C.

34
doc/src/pair_meso.rst
View File

@ -1,22 +1,22 @@
.. index:: pair\_style edpd
.. index:: pair_style edpd
pair\_style edpd command
========================
pair_style edpd command
=======================
pair\_style mdpd command
========================
pair_style mdpd command
=======================
pair\_style mdpd/rhosum command
===============================
pair_style mdpd/rhosum command
==============================
pair\_style tdpd command
========================
pair_style tdpd command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -44,10 +44,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style edpd 1.58 9872598
pair_coeff \* \* 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58
pair_coeff * * 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
@ -56,7 +56,7 @@ Examples
pair_coeff 1 1 mdpd -40.0 25.0 18.0 1.0 0.75
pair_style tdpd 1.0 1.58 935662
pair_coeff \* \* 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0
pair_coeff * * 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
Description
@ -207,10 +207,10 @@ by
.. math::
Q_{ij}^D & = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right) \\
Q_{ij}^R & = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij} \\
w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power\_{cc}} \\
\epsilon_{ij}^2 & = m_s^2\kappa_{ij}\rho
Q_{ij}^D & = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right) \\
Q_{ij}^R & = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij} \\
w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power\_{cc}} \\
\epsilon_{ij}^2 & = m_s^2\kappa_{ij}\rho
where the parameters kappa and epsilon determine the strength of the
Fickian and random fluxes. :math:`m_s` is the mass of a single solute

12
doc/src/pair_mesocnt.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style mesocnt
.. index:: pair_style mesocnt
pair\_style mesocnt command
===========================
pair_style mesocnt command
==========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style mesocnt
@ -15,10 +15,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style mesocnt
pair_coeff \* \* 10_10.cnt
pair_coeff * * 10_10.cnt
Description
"""""""""""

16
doc/src/pair_mgpt.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style mgpt
.. index:: pair_style mgpt
pair\_style mgpt command
========================
pair_style mgpt command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style mgpt
@ -15,14 +15,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style mgpt
pair_coeff \* \* Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
pair_coeff \* \* parmin potin Omega volpress yes nbody 1234 precision double
pair_coeff \* \* parmin potin Omega volpress yes nbody 12
pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
pair_coeff * * parmin potin Omega volpress yes nbody 12
Description
"""""""""""

22
doc/src/pair_mie.rst
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@ -1,16 +1,16 @@
.. index:: pair\_style mie/cut
.. index:: pair_style mie/cut
pair\_style mie/cut command
===========================
pair_style mie/cut command
==========================
pair\_style mie/cut/gpu command
===============================
pair_style mie/cut/gpu command
==============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style mie/cut cutoff
@ -20,7 +20,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style mie/cut 10.0
pair_coeff 1 1 0.72 3.40 23.00 6.66
@ -34,8 +34,8 @@ The *mie/cut* style computes the Mie potential, given by
.. math::
E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right]
\qquad r < r_c
E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right]
\qquad r < r_c
Rc is the cutoff and C is a function that depends on the repulsive and
@ -43,7 +43,7 @@ attractive exponents, given by:
.. math::
C = \left(\frac{\gamma_{rep}}{\gamma_{rep}-\gamma_{att}}\right) \left(\frac{\gamma_{rep}}{\gamma_{att}}\right)^{\left(\frac{\gamma_{att}}{\gamma_{rep}-\gamma_{att}}\right)}
C = \left(\frac{\gamma_{rep}}{\gamma_{rep}-\gamma_{att}}\right) \left(\frac{\gamma_{rep}}{\gamma_{att}}\right)^{\left(\frac{\gamma_{att}}{\gamma_{rep}-\gamma_{att}}\right)}
Note that for 12/6 exponents, C is equal to 4 and the formula is the
@ -99,7 +99,7 @@ details.
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

26
doc/src/pair_mm3_switch3_coulgauss_long.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style mm3/switch3/coulgauss/long
.. index:: pair_style mm3/switch3/coulgauss/long
pair\_style mm3/switch3/coulgauss/long command
pair_style mm3/switch3/coulgauss/long command
==============================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -26,7 +26,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style mm3/switch3/coulgauss/long 12.0 3.0
pair_coeff 1 0.2 2.5 1.2
@ -42,9 +42,9 @@ vdW potential :ref:`(Allinger) <mm3-allinger1989>`
.. math::
E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
r_{v,ij} & = r_{v,i} + r_{v,j} \\
\epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
r_{v,ij} & = r_{v,i} + r_{v,j} \\
\epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
, which goes smoothly to zero at the cutoff r\_c as defined
@ -52,11 +52,11 @@ by the switching function
.. math::
S_3(r) = \left\lbrace \begin{array}{ll}
1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
\end{array} \right.
S_3(r) = \left\lbrace \begin{array}{ll}
1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
\end{array} \right.
where w is the width defined in the arguments. This potential
@ -64,7 +64,7 @@ is combined with Coulomb interaction between Gaussian charge densities:
.. math::
E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
where :math:`q_i` and :math:`q_j` are the charges on the 2 atoms,

22
doc/src/pair_modify.rst
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@ -1,13 +1,13 @@
.. index:: pair\_modify
.. index:: pair_modify
pair\_modify command
====================
pair_modify command
===================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_modify keyword values ...
@ -44,7 +44,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_modify shift yes mix geometric
pair_modify tail yes
@ -63,12 +63,12 @@ specified parameters are by default modified for all the hybrid sub-styles.
.. note::
The behavior for hybrid pair styles can be changed by using the *pair*
keyword, which allows selection of a specific sub-style to apply all
remaining keywords to.
The *special* and *compute/tally* keywords can **only** be
used in conjunction with the *pair* keyword. See further details about
these 3 keywords below.
The behavior for hybrid pair styles can be changed by using the *pair*
keyword, which allows selection of a specific sub-style to apply all
remaining keywords to.
The *special* and *compute/tally* keywords can **only** be
used in conjunction with the *pair* keyword. See further details about
these 3 keywords below.
The *mix* keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not

10
doc/src/pair_momb.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style momb
.. index:: pair_style momb
pair\_style momb command
========================
pair_style momb command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style momb cutoff s6 d
@ -19,7 +19,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style momb 12.0 0.75 20.0
pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5