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Merge branch 'doc-updates' of github.com:rbberger/lammps into release-preparation

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Axel Kohlmeyer 2020-02-27 11:26:15 -05:00
parent 1bb38ed09b 25ec8d36a8
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44
doc/src/pair_morse.rst
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@ -1,31 +1,31 @@
.. index:: pair\_style morse
.. index:: pair_style morse
pair\_style morse command
=========================
pair_style morse command
========================
pair\_style morse/gpu command
=============================
pair\_style morse/omp command
=============================
pair\_style morse/opt command
=============================
pair\_style morse/smooth/linear command
=======================================
pair\_style morse/smooth/linear/omp command
===========================================
pair\_style morse/kk command
pair_style morse/gpu command
============================
pair_style morse/omp command
============================
pair_style morse/opt command
============================
pair_style morse/smooth/linear command
======================================
pair_style morse/smooth/linear/omp command
==========================================
pair_style morse/kk command
===========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -44,11 +44,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style morse 2.5
pair_style morse/smooth/linear 2.5
pair_coeff \* \* 100.0 2.0 1.5
pair_coeff * * 100.0 2.0 1.5
pair_coeff 1 1 100.0 2.0 1.5 3.0
Description

12
doc/src/pair_multi_lucy.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style multi/lucy
.. index:: pair_style multi/lucy
pair\_style multi/lucy command
==============================
pair_style multi/lucy command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style multi/lucy style N keyword ...
@ -18,10 +18,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style multi/lucy linear 1000
pair_coeff \* \* multibody.table ENTRY1 7.0
pair_coeff * * multibody.table ENTRY1 7.0
Description
"""""""""""

18
doc/src/pair_multi_lucy_rx.rst
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@ -1,16 +1,16 @@
.. index:: pair\_style multi/lucy/rx
.. index:: pair_style multi/lucy/rx
pair\_style multi/lucy/rx command
=================================
pair_style multi/lucy/rx command
================================
pair\_style multi/lucy/rx/kk command
====================================
pair_style multi/lucy/rx/kk command
===================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style multi/lucy/rx style N keyword ...
@ -22,13 +22,13 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style multi/lucy/rx linear 1000
pair_style multi/lucy/rx linear 1000 fractional
pair_style multi/lucy/rx linear 1000 molecular
pair_coeff \* \* multibody.table ENTRY1 h2o h2o 7.0
pair_coeff \* \* multibody.table ENTRY1 h2o 1fluid 7.0
pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0
pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0
Description
"""""""""""

16
doc/src/pair_nb3b_harmonic.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style nb3b/harmonic
.. index:: pair_style nb3b/harmonic
pair\_style nb3b/harmonic command
=================================
pair_style nb3b/harmonic command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style nb3b/harmonic
@ -15,10 +15,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style nb3b/harmonic
pair_coeff \* \* MgOH.nb3bharmonic Mg O H
pair_coeff * * MgOH.nb3bharmonic Mg O H
Description
"""""""""""
@ -54,9 +54,9 @@ 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 \* \* SiC.nb3b.harmonic Si Si Si C
pair_coeff * * SiC.nb3b.harmonic Si Si Si C
The 1st 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

34
doc/src/pair_nm.rst
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@ -1,28 +1,28 @@
.. index:: pair\_style nm/cut
.. index:: pair_style nm/cut
pair\_style nm/cut command
==========================
pair_style nm/cut command
=========================
pair\_style nm/cut/coul/cut command
pair_style nm/cut/coul/cut command
==================================
pair_style nm/cut/coul/long command
===================================
pair\_style nm/cut/coul/long command
====================================
pair_style nm/cut/omp command
=============================
pair\_style nm/cut/omp command
==============================
pair_style nm/cut/coul/cut/omp command
======================================
pair\_style nm/cut/coul/cut/omp command
pair_style nm/cut/coul/long/omp command
=======================================
pair\_style nm/cut/coul/long/omp command
========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -46,18 +46,18 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style nm/cut 12.0
pair_coeff \* \* 0.01 5.4 8.0 7.0
pair_coeff * * 0.01 5.4 8.0 7.0
pair_coeff 1 1 0.01 4.4 7.0 6.0
pair_style nm/cut/coul/cut 12.0 15.0
pair_coeff \* \* 0.01 5.4 8.0 7.0
pair_coeff * * 0.01 5.4 8.0 7.0
pair_coeff 1 1 0.01 4.4 7.0 6.0
pair_style nm/cut/coul/long 12.0 15.0
pair_coeff \* \* 0.01 5.4 8.0 7.0
pair_coeff * * 0.01 5.4 8.0 7.0
pair_coeff 1 1 0.01 4.4 7.0 6.0
Description

13
doc/src/pair_none.rst
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@ -1,13 +1,12 @@
.. index:: pair\_style none
.. index:: pair_style none
pair\_style none command
========================
pair_style none command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style none
@ -15,7 +14,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style none
@ -43,7 +42,7 @@ building of a neighbor lists, but compute no pairwise interactions.
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

36
doc/src/pair_oxdna.rst
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@ -1,29 +1,29 @@
.. index:: pair\_style oxdna/excv
.. index:: pair_style oxdna/excv
pair\_style oxdna/excv command
==============================
pair\_style oxdna/stk command
pair_style oxdna/excv command
=============================
pair\_style oxdna/hbond command
===============================
pair_style oxdna/stk command
============================
pair\_style oxdna/xstk command
pair_style oxdna/hbond command
==============================
pair\_style oxdna/coaxstk command
=================================
pair_style oxdna/xstk command
=============================
pair_style oxdna/coaxstk command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style1
pair_coeff \* \* style2 args
pair_coeff * * style2 args
* style1 = *hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk*
@ -46,16 +46,16 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff \* \* oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff \* \* oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff \* \* oxdna/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff \* \* oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff \* \* oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
Description
"""""""""""

42
doc/src/pair_oxdna2.rst
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@ -1,32 +1,32 @@
.. index:: pair\_style oxdna2/excv
.. index:: pair_style oxdna2/excv
pair\_style oxdna2/excv command
===============================
pair\_style oxdna2/stk command
pair_style oxdna2/excv command
==============================
pair\_style oxdna2/hbond command
================================
pair_style oxdna2/stk command
=============================
pair\_style oxdna2/xstk command
pair_style oxdna2/hbond command
===============================
pair\_style oxdna2/coaxstk command
==================================
pair_style oxdna2/xstk command
==============================
pair\_style oxdna2/dh command
=============================
pair_style oxdna2/coaxstk command
=================================
pair_style oxdna2/dh command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style1
pair_coeff \* \* style2 args
pair_coeff * * style2 args
* style1 = *hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh*
@ -53,17 +53,17 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff \* \* oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff \* \* oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff \* \* oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff \* \* oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff \* \* oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff \* \* oxdna2/dh 0.1 0.5 0.815
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 0.5 0.815
Description
"""""""""""

38
doc/src/pair_peri.rst
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@ -1,28 +1,28 @@
.. index:: pair\_style peri/pmb
.. index:: pair_style peri/pmb
pair\_style peri/pmb command
============================
pair_style peri/pmb command
===========================
pair\_style peri/pmb/omp command
================================
pair_style peri/pmb/omp command
===============================
pair\_style peri/lps command
============================
pair_style peri/lps command
===========================
pair\_style peri/lps/omp command
================================
pair_style peri/lps/omp command
===============================
pair\_style peri/ves command
============================
pair_style peri/ves command
===========================
pair\_style peri/eps command
============================
pair_style peri/eps command
===========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style
@ -32,19 +32,19 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style peri/pmb
pair_coeff \* \* 1.6863e22 0.0015001 0.0005 0.25
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
pair_style peri/lps
pair_coeff \* \* 14.9e9 14.9e9 0.0015001 0.0005 0.25
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
pair_style peri/ves
pair_coeff \* \* 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
pair_style peri/eps
pair_coeff \* \* 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
Description
"""""""""""

18
doc/src/pair_polymorphic.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style polymorphic
.. index:: pair_style polymorphic
pair\_style polymorphic command
===============================
pair_style polymorphic command
==============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style polymorphic
@ -17,13 +17,13 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style polymorphic
pair_coeff \* \* TlBr_msw.polymorphic Tl Br
pair_coeff \* \* AlCu_eam.polymorphic Al Cu
pair_coeff \* \* GaN_tersoff.polymorphic Ga N
pair_coeff \* \* GaN_sw.polymorphic GaN
pair_coeff * * TlBr_msw.polymorphic Tl Br
pair_coeff * * AlCu_eam.polymorphic Al Cu
pair_coeff * * GaN_tersoff.polymorphic Ga N
pair_coeff * * GaN_sw.polymorphic GaN
Description
"""""""""""

36
doc/src/pair_python.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style python
.. index:: pair_style python
pair\_style python command
==========================
pair_style python command
=========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style python cutoff
@ -17,14 +17,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style python 2.5
pair_coeff \* \* py_pot.LJCutMelt lj
pair_coeff * * py_pot.LJCutMelt lj
pair_style hybrid/overlay coul/long 12.0 python 12.0
pair_coeff \* \* coul/long
pair_coeff \* \* python py_pot.LJCutSPCE OW NULL
pair_coeff * * coul/long
pair_coeff * * python py_pot.LJCutSPCE OW NULL
Description
"""""""""""
@ -62,9 +62,9 @@ two are supposed to be using the 'LJ1' parameters and the third the
'LJ2' parameters, then you would use the following pair\_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* py_pot.LJCutMelt LJ1 LJ1 LJ2
pair_coeff * * py_pot.LJCutMelt LJ1 LJ1 LJ2
The first two arguments **must** be \* \* so as to span all LAMMPS atom
types. The first two LJ1 arguments map LAMMPS atom types 1 and 2 to
@ -83,10 +83,10 @@ placeholders for atom types that will be used with other potentials.
The python potential file has to start with the following code:
.. parsed-literal::
.. code-block:: python
from __future_\_ import print_function
#
from __future__ import print_function
class LAMMPSPairPotential(object):
def __init__(self):
self.pmap=dict()
@ -115,7 +115,7 @@ Here is an example for a single type Lennard-Jones potential class
which the parameters epsilon and sigma are both 1.0:
.. parsed-literal::
.. code-block:: python
class LJCutMelt(LAMMPSPairPotential):
def __init__(self):
@ -140,7 +140,7 @@ value of the internal potential parameter data structure. Following
the *LJCutMelt* example, here are the two functions:
.. parsed-literal::
.. code-block:: python
def compute_force(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
@ -181,10 +181,10 @@ the *LJCutMelt* example, here are the two functions:
for an example LAMMPS input of how to build a table file:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style python 2.5
pair_coeff \* \* py_pot.LJCutMelt lj
pair_coeff * * py_pot.LJCutMelt lj
shell rm -f melt.table
pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj
@ -199,7 +199,7 @@ After switching the pair style to *table*\ , the potential tables need
to be assigned to the LAMMPS atom types like this:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style table linear 2000
pair_coeff 1 1 melt.table lj

14
doc/src/pair_quip.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style quip
.. index:: pair_style quip
pair\_style quip command
========================
pair_style quip command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style quip
@ -15,11 +15,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style quip
pair_coeff \* \* gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
pair_coeff \* \* sw_example.xml "IP SW" 14
pair_coeff * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
pair_coeff * * sw_example.xml "IP SW" 14
Description
"""""""""""

26
doc/src/pair_reaxc.rst
View File

@ -1,19 +1,19 @@
.. index:: pair\_style reax/c
.. index:: pair_style reax/c
pair\_style reax/c command
==========================
pair_style reax/c command
=========================
pair\_style reax/c/kk command
pair_style reax/c/kk command
============================
pair_style reax/c/omp command
=============================
pair\_style reax/c/omp command
==============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style reax/c cfile keyword value
@ -35,13 +35,13 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style reax/c NULL
pair_style reax/c controlfile checkqeq no
pair_style reax/c NULL lgvdw yes
pair_style reax/c NULL safezone 1.6 mincap 100
pair_coeff \* \* ffield.reax C H O N
pair_coeff * * ffield.reax C H O N
Description
"""""""""""
@ -189,7 +189,7 @@ 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 reax all pair reax/c
variable eb equal c_reax[1]
@ -227,9 +227,9 @@ the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair\_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* ffield.reax C C N H
pair_coeff * * ffield.reax C C N H
----------

20
doc/src/pair_resquared.rst
View File

@ -1,19 +1,19 @@
.. index:: pair\_style resquared
.. index:: pair_style resquared
pair\_style resquared command
=============================
pair_style resquared command
============================
pair\_style resquared/gpu command
=================================
pair_style resquared/gpu command
================================
pair\_style resquared/omp command
=================================
pair_style resquared/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style resquared cutoff
@ -23,10 +23,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style resquared 10.0
pair_coeff \* \* 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
Description
"""""""""""

60
doc/src/pair_sdk.rst
View File

@ -1,37 +1,37 @@
.. index:: pair\_style lj/sdk
.. index:: pair_style lj/sdk
pair\_style lj/sdk command
==========================
pair_style lj/sdk command
=========================
pair\_style lj/sdk/gpu command
==============================
pair\_style lj/sdk/kk command
pair_style lj/sdk/gpu command
=============================
pair\_style lj/sdk/omp command
==============================
pair_style lj/sdk/kk command
============================
pair\_style lj/sdk/coul/long command
====================================
pair_style lj/sdk/omp command
=============================
pair\_style lj/sdk/coul/long/gpu command
========================================
pair\_style lj/sdk/coul/long/omp command
========================================
pair\_style lj/sdk/coul/msm command
pair_style lj/sdk/coul/long command
===================================
pair\_style lj/sdk/coul/msm/omp command
pair_style lj/sdk/coul/long/gpu command
=======================================
pair_style lj/sdk/coul/long/omp command
=======================================
pair_style lj/sdk/coul/msm command
==================================
pair_style lj/sdk/coul/msm/omp command
======================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -51,7 +51,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/sdk 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8
@ -72,15 +72,15 @@ given by
.. math::
E = & \frac{27}{4} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c \\
E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^4 \right]
\qquad r < r_c \\
E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
E = & \frac{27}{4} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c \\
E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^4 \right]
\qquad r < r_c \\
E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
as required for the SDK Coarse-grained MD parameterization discussed in

14
doc/src/pair_sdpd_taitwater_isothermal.rst
View File

@ -1,13 +1,12 @@
.. index:: pair\_style sdpd/taitwater/isothermal
.. index:: pair_style sdpd/taitwater/isothermal
pair\_style sdpd/taitwater/isothermal command
=============================================
pair_style sdpd/taitwater/isothermal command
============================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sdpd/taitwater/isothermal temperature viscosity seed
@ -18,11 +17,10 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sdpd/taitwater/isothermal 300. 1. 28681
pair_coeff \* \* 1000.0 1430.0 2.4
pair_coeff * * 1000.0 1430.0 2.4
Description
"""""""""""

14
doc/src/pair_smd_hertz.rst
View File

@ -1,21 +1,23 @@
.. index:: pair\_style smd/hertz
.. index:: pair_style smd/hertz
pair\_style smd/hertz command
=============================
pair_style smd/hertz command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style smd/hertz scale_factor
Examples
""""""""
pair\_style smd/hertz 1.0
pair\_coeff 1 1 <contact\_stiffness>
.. code-block:: LAMMPS
pair_style smd/hertz 1.0
pair_coeff 1 1 <contact_stiffness>
Description
"""""""""""

19
doc/src/pair_smd_tlsph.rst
View File

@ -1,20 +1,21 @@
.. index:: pair\_style smd/tlsph
.. index:: pair_style smd/tlsph
pair\_style smd/tlsph command
=============================
pair_style smd/tlsph command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style smd/tlsph args
Examples
""""""""
pair\_style smd/tlsph
.. code-block:: LAMMPS
pair_style smd/tlsph
Description
"""""""""""
@ -26,11 +27,11 @@ Smooth-Particle Hydrodynamics algorithm.
This pair style is invoked with the following command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_style smd/tlsph
pair_coeff i j \*COMMON rho0 E nu Q1 Q2 hg Cp &
\*END
pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
*END
Here, *i* and *j* denote the *LAMMPS* particle types for which this
pair style is defined. Note that *i* and *j* must be equal, i.e., no

15
doc/src/pair_smd_triangulated_surface.rst
View File

@ -1,21 +1,22 @@
.. index:: pair\_style smd/tri\_surface
.. index:: pair_style smd/tri_surface
pair\_style smd/tri\_surface command
====================================
pair_style smd/tri\_surface command
===================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style smd/tri_surface scale_factor
Examples
""""""""
pair\_style smd/tri\_surface 1.0
pair\_coeff 1 1 <contact\_stiffness>
.. code-block:: LAMMPS
pair_style smd/tri_surface 1.0
pair_coeff 1 1 <contact_stiffness>
Description
"""""""""""

16
doc/src/pair_smtbq.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style smtbq
.. index:: pair_style smtbq
pair\_style smtbq command
=========================
pair_style smtbq command
========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style smtbq
@ -15,10 +15,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style smtbq
pair_coeff \* \* ffield.smtbq.Al2O3 O Al
pair_coeff * * ffield.smtbq.Al2O3 O Al
Description
"""""""""""
@ -58,9 +58,9 @@ atom type 1 has to be oxygen and atom type 2 Ti. The following
pair\_coeff command should then be used:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
The electrostatic part of the energy consists of two components

38
doc/src/pair_snap.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style snap
.. index:: pair_style snap
pair\_style snap command
========================
pair_style snap command
=======================
pair\_style snap/kk command
===========================
pair_style snap/kk command
==========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style snap
@ -18,10 +18,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style snap
pair_coeff \* \* InP.snapcoeff InP.snapparam In In P P
pair_coeff * * InP.snapcoeff InP.snapparam In In P P
Description
"""""""""""
@ -71,9 +71,9 @@ types, with the first two being indium and the 3rd and 4th being
phophorous, the pair\_coeff command would look like this:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* snap InP.snapcoeff InP.snapparam In In P P
pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The two filenames are for the coefficient and parameter files, respectively.
@ -106,16 +106,16 @@ combines the *snap* and *zbl* pair styles. It is invoked
by the following commands:
.. parsed-literal::
.. code-block:: LAMMPS
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
pair_style hybrid/overlay &
zbl ${zblcutinner} ${zblcutouter} snap
pair_coeff \* \* zbl 0.0
pair_coeff 1 1 zbl ${zblz}
pair_coeff \* \* snap Ta06A.snapcoeff Ta06A.snapparam Ta
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
pair_style hybrid/overlay &
zbl ${zblcutinner} ${zblcutouter} snap
pair_coeff \* \* zbl 0.0
pair_coeff 1 1 zbl ${zblz}
pair_coeff \* \* snap Ta06A.snapcoeff Ta06A.snapparam Ta
It is convenient to keep these commands in a separate file that can
be inserted in any LAMMPS input script using the :doc:`include <include>`

28
doc/src/pair_soft.rst
View File

@ -1,19 +1,19 @@
.. index:: pair\_style soft
.. index:: pair_style soft
pair\_style soft command
========================
pair_style soft command
=======================
pair\_style soft/gpu command
============================
pair_style soft/gpu command
===========================
pair\_style soft/omp command
============================
pair_style soft/omp command
===========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style soft cutoff
@ -23,16 +23,16 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style soft 1.0
pair_coeff \* \* 10.0
pair_coeff * * 10.0
pair_coeff 1 1 10.0 3.0
pair_style soft 1.0
pair_coeff \* \* 0.0
pair_coeff * * 0.0
variable prefactor equal ramp(0,30)
fix 1 all adapt 1 pair soft a \* \* v_prefactor
fix 1 all adapt 1 pair soft a * * v_prefactor
Description
"""""""""""
@ -83,10 +83,10 @@ all pairwise interactions from 0.0 at the beginning to 30.0 at the end
of a run:
.. parsed-literal::
.. code-block:: LAMMPS
variable prefactor equal ramp(0,30)
fix 1 all adapt 1 pair soft a \* \* v_prefactor
fix 1 all adapt 1 pair soft a * * v_prefactor
Note that a formula defined by an :doc:`equal-style variable <variable>`
can use the current timestep, elapsed time in the current run, elapsed

12
doc/src/pair_sph_heatconduction.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style sph/heatconduction
.. index:: pair_style sph/heatconduction
pair\_style sph/heatconduction command
======================================
pair_style sph/heatconduction command
=====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/heatconduction
@ -15,10 +15,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/heatconduction
pair_coeff \* \* 1.0 2.4
pair_coeff * * 1.0 2.4
Description
"""""""""""

14
doc/src/pair_sph_idealgas.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style sph/idealgas
.. index:: pair_style sph/idealgas
pair\_style sph/idealgas command
================================
pair_style sph/idealgas command
===============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/idealgas
@ -15,10 +15,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/idealgas
pair_coeff \* \* 1.0 2.4
pair_coeff * * 1.0 2.4
Description
"""""""""""
@ -28,7 +28,7 @@ according to the ideal gas equation of state:
.. math::
p = (\gamma - 1) \rho e
p = (\gamma - 1) \rho e
where :math:`\gamma = 1.4` is the heat capacity ratio, :math:`\rho` is

12
doc/src/pair_sph_lj.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style sph/lj
.. index:: pair_style sph/lj
pair\_style sph/lj command
==========================
pair_style sph/lj command
=========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/lj
@ -15,10 +15,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/lj
pair_coeff \* \* 1.0 2.4
pair_coeff * * 1.0 2.4
Description
"""""""""""

12
doc/src/pair_sph_rhosum.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style sph/rhosum
.. index:: pair_style sph/rhosum
pair\_style sph/rhosum command
==============================
pair_style sph/rhosum command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/rhosum Nstep
@ -17,10 +17,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/rhosum 10
pair_coeff \* \* 2.4
pair_coeff * * 2.4
Description
"""""""""""

14
doc/src/pair_sph_taitwater.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style sph/taitwater
.. index:: pair_style sph/taitwater
pair\_style sph/taitwater command
=================================
pair_style sph/taitwater command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/taitwater
@ -15,10 +15,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/taitwater
pair_coeff \* \* 1000.0 1430.0 1.0 2.4
pair_coeff * * 1000.0 1430.0 1.0 2.4
Description
"""""""""""
@ -28,7 +28,7 @@ according to Tait's equation of state:
.. math::
p = B \biggl[\left(\frac{\rho}{\rho_0}\right)^{\gamma} - 1\biggr]
p = B \biggl[\left(\frac{\rho}{\rho_0}\right)^{\gamma} - 1\biggr]
where :math:`\gamma = 7` and :math:`B = c_0^2 \rho_0 / \gamma`, with

14
doc/src/pair_sph_taitwater_morris.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style sph/taitwater/morris
.. index:: pair_style sph/taitwater/morris
pair\_style sph/taitwater/morris command
========================================
pair_style sph/taitwater/morris command
=======================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/taitwater/morris
@ -15,10 +15,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sph/taitwater/morris
pair_coeff \* \* 1000.0 1430.0 1.0 2.4
pair_coeff * * 1000.0 1430.0 1.0 2.4
Description
"""""""""""
@ -28,7 +28,7 @@ particles according to Tait's equation of state:
.. math::
p = B \biggl[\left(\frac{\rho}{\rho_0}\right)^{\gamma} - 1\biggr]
p = B \biggl[\left(\frac{\rho}{\rho_0}\right)^{\gamma} - 1\biggr]
where :math:`\gamma = 7` and :math:`B = c_0^2 \rho_0 / \gamma`, with

19
doc/src/pair_spin_dipole.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style spin/dipole/cut
.. index:: pair_style spin/dipole/cut
pair\_style spin/dipole/cut command
pair_style spin/dipole/cut command
==================================
pair_style spin/dipole/long command
===================================
pair\_style spin/dipole/long command
====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style spin/dipole/cut cutoff
pair_style spin/dipole/long cutoff
@ -22,15 +22,14 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style spin/dipole/cut 10.0
pair_coeff \* \* 10.0
pair_coeff * * 10.0
pair_coeff 2 3 8.0
pair_style spin/dipole/long 9.0
pair_coeff \* \* 10.0
pair_coeff * * 10.0
pair_coeff 2 3 6.0
Description

14
doc/src/pair_spin_dmi.rst
View File

@ -1,13 +1,12 @@
.. index:: pair\_style spin/dmi
.. index:: pair_style spin/dmi
pair\_style spin/dmi command
============================
pair_style spin/dmi command
===========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style spin/dmi cutoff
@ -17,11 +16,10 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style spin/dmi 4.0
pair_coeff \* \* dmi 2.6 0.001 1.0 0.0 0.0
pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0
pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0
Description

6
doc/src/pair_spin_exchange.rst
View File

@ -1,7 +1,7 @@
.. index:: pair\_style spin/exchange
.. index:: pair_style spin/exchange
pair\_style spin/exchange command
=================================
pair_style spin/exchange command
================================
Syntax
""""""

8
doc/src/pair_spin_magelec.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style spin/magelec
.. index:: pair_style spin/magelec
pair\_style spin/magelec command
pair_style spin/magelec command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style spin/magelec cutoff
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style spin/magelec 4.5
pair_coeff \* \* magelec 4.5 0.00109 1.0 1.0 1.0

12
doc/src/pair_srp.rst
View File

@ -1,12 +1,14 @@
.. index:: pair\_style srp
.. index:: pair_style srp
pair\_style srp command
=======================
pair_style srp command
======================
Syntax
""""""
pair\_style srp cutoff btype dist keyword value ...
.. code-block:: LAMMPS
pair_style srp cutoff btype dist keyword value ...
* cutoff = global cutoff for SRP interactions (distance units)
* btype = bond type to apply SRP interactions to (can be wildcard, see below)
@ -25,7 +27,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
pair_coeff 1 1 dpd 60.0 4.5 1.0

12
doc/src/pair_style.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style
.. index:: pair_style
pair\_style command
===================
pair_style command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/cut 2.5
pair_style eam/alloy
@ -354,6 +354,6 @@ Default
"""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style none

38
doc/src/pair_sw.rst
View File

@ -1,37 +1,36 @@
.. index:: pair\_style sw
.. index:: pair_style sw
pair\_style sw command
======================
pair_style sw command
=====================
pair\_style sw/gpu command
==========================
pair\_style sw/intel command
============================
pair\_style sw/kk command
pair_style sw/gpu command
=========================
pair\_style sw/omp command
==========================
pair_style sw/intel command
===========================
pair_style sw/kk command
========================
pair_style sw/omp command
=========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sw
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style sw
pair_coeff \* \* si.sw Si
pair_coeff \* \* GaN.sw Ga N Ga
pair_coeff * * si.sw Si
pair_coeff * * GaN.sw Ga N Ga
Description
"""""""""""
@ -74,10 +73,9 @@ Si and C. If your 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:
.. code-block:: LAMMPS
.. parsed-literal::
pair_coeff \* \* SiC.sw Si Si Si C
pair_coeff * * SiC.sw Si Si Si C
The 1st 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

29
doc/src/pair_table.rst
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@ -1,22 +1,22 @@
.. index:: pair\_style table
.. index:: pair_style table
pair\_style table command
=========================
pair_style table command
========================
pair\_style table/gpu command
=============================
pair\_style table/kk command
pair_style table/gpu command
============================
pair\_style table/omp command
=============================
pair_style table/kk command
===========================
pair_style table/omp command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style table style N keyword ...
@ -29,14 +29,13 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style table linear 1000
pair_style table linear 1000 pppm
pair_style table bitmap 12
pair_coeff \* 3 morse.table ENTRY1
pair_coeff \* 3 morse.table ENTRY1 7.0
pair_coeff * 3 morse.table ENTRY1
pair_coeff * 3 morse.table ENTRY1 7.0
Description
"""""""""""
@ -276,7 +275,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

21
doc/src/pair_table_rx.rst
View File

@ -1,16 +1,16 @@
.. index:: pair\_style table/rx
.. index:: pair_style table/rx
pair\_style table/rx command
============================
pair_style table/rx command
===========================
pair\_style table/rx/kk command
===============================
pair_style table/rx/kk command
==============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style table style N ...
@ -21,15 +21,14 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style table/rx linear 1000
pair_style table/rx linear 1000 fractional
pair_style table/rx linear 1000 molecular
pair_coeff \* \* rxn.table ENTRY1 h2o h2o 10.0
pair_coeff \* \* rxn.table ENTRY1 1fluid 1fluid 10.0
pair_coeff \* 3 rxn.table ENTRY1 h2o no2 10.0
pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0
pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0
pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0
Description
"""""""""""

47
doc/src/pair_tersoff.rst
View File

@ -1,31 +1,30 @@
.. index:: pair\_style tersoff
.. index:: pair_style tersoff
pair\_style tersoff command
===========================
pair_style tersoff command
==========================
pair\_style tersoff/table command
=================================
pair_style tersoff/table command
================================
pair\_style tersoff/gpu command
===============================
pair\_style tersoff/intel command
=================================
pair\_style tersoff/kk command
pair_style tersoff/gpu command
==============================
pair\_style tersoff/omp command
===============================
pair_style tersoff/intel command
================================
pair\_style tersoff/table/omp command
=====================================
pair_style tersoff/kk command
=============================
pair_style tersoff/omp command
==============================
pair_style tersoff/table/omp command
====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style
@ -35,14 +34,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style tersoff
pair_coeff \* \* Si.tersoff Si
pair_coeff \* \* SiC.tersoff Si C Si
pair_coeff * * Si.tersoff Si
pair_coeff * * SiC.tersoff Si C Si
pair_style tersoff/table
pair_coeff \* \* SiCGe.tersoff Si(D)
pair_coeff * * SiCGe.tersoff Si(D)
Description
"""""""""""
@ -97,9 +96,9 @@ and C. If your LAMMPS simulation has 4 atoms types and you want the
pair\_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* SiC.tersoff Si Si Si C
pair_coeff * * SiC.tersoff Si Si Si C
The 1st 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

73
doc/src/pair_tersoff_mod.rst
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@ -1,28 +1,28 @@
.. index:: pair\_style tersoff/mod
.. index:: pair_style tersoff/mod
pair\_style tersoff/mod command
===============================
pair_style tersoff/mod command
==============================
pair\_style tersoff/mod/c command
=================================
pair_style tersoff/mod/c command
================================
pair\_style tersoff/mod/gpu command
===================================
pair\_style tersoff/mod/kk command
pair_style tersoff/mod/gpu command
==================================
pair\_style tersoff/mod/omp command
===================================
pair_style tersoff/mod/kk command
=================================
pair\_style tersoff/mod/c/omp command
=====================================
pair_style tersoff/mod/omp command
==================================
pair_style tersoff/mod/c/omp command
====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style tersoff/mod
@ -31,14 +31,13 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style tersoff/mod
pair_coeff \* \* Si.tersoff.mod Si Si
pair_coeff * * Si.tersoff.mod Si Si
pair_style tersoff/mod/c
pair_coeff \* \* Si.tersoff.modc Si Si
pair_coeff * * Si.tersoff.modc Si Si
Description
"""""""""""
@ -51,22 +50,22 @@ E of a system of atoms as
.. math::
E & = \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
f_C(r) & = \left\{ \begin{array} {r@{\quad:\quad}l}
1 & r < R - D \\
\frac{1}{2} - \frac{9}{16} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) - \frac{1}{16} \sin \left( \frac{3\pi}{2} \frac{r-R}{D} \right) &
R-D < r < R + D \\
0 & r > R + D
\end{array} \right. \\
f_R(r) & = A \exp (-\lambda_1 r) \\
f_A(r) & = -B \exp (-\lambda_2 r) \\
b_{ij} & = \left( 1 + {\zeta_{ij}}^\eta \right)^{-\frac{1}{2n}} \\
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
\exp \left[ \alpha (r_{ij} - r_{ik})^\beta \right] \\
g(\theta) & = c_1 + g_o(\theta) g_a(\theta) \\
g_o(\theta) & = \frac{c_2 (h - \cos \theta)^2}{c_3 + (h - \cos \theta)^2} \\
g_a(\theta) & = 1 + c_4 \exp \left[ -c_5 (h - \cos \theta)^2 \right] \\
E & = \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
f_C(r) & = \left\{ \begin{array} {r@{\quad:\quad}l}
1 & r < R - D \\
\frac{1}{2} - \frac{9}{16} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) - \frac{1}{16} \sin \left( \frac{3\pi}{2} \frac{r-R}{D} \right) &
R-D < r < R + D \\
0 & r > R + D
\end{array} \right. \\
f_R(r) & = A \exp (-\lambda_1 r) \\
f_A(r) & = -B \exp (-\lambda_2 r) \\
b_{ij} & = \left( 1 + {\zeta_{ij}}^\eta \right)^{-\frac{1}{2n}} \\
\zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
\exp \left[ \alpha (r_{ij} - r_{ik})^\beta \right] \\
g(\theta) & = c_1 + g_o(\theta) g_a(\theta) \\
g_o(\theta) & = \frac{c_2 (h - \cos \theta)^2}{c_3 + (h - \cos \theta)^2} \\
g_a(\theta) & = 1 + c_4 \exp \left[ -c_5 (h - \cos \theta)^2 \right] \\
where :math:`f_R` is a two-body term and :math:`f_A` includes three-body interactions.
@ -77,7 +76,7 @@ formulation of the V\_ij term, where it contains an additional c0 term.
.. math::
V_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
V_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
The modified cutoff function :math:`f_C` proposed by :ref:`(Murty) <Murty>` and
@ -105,9 +104,9 @@ If your LAMMPS simulation has 3 Si atoms types, you would use the following
pair\_coeff command:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff \* \* Si.tersoff_mod Si Si Si
pair_coeff * * Si.tersoff_mod Si Si Si
The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The three Si arguments map LAMMPS atom types 1,2,3 to the Si element

28
doc/src/pair_tersoff_zbl.rst
View File

@ -1,22 +1,22 @@
.. index:: pair\_style tersoff/zbl
.. index:: pair_style tersoff/zbl
pair\_style tersoff/zbl command
===============================
pair_style tersoff/zbl command
==============================
pair\_style tersoff/zbl/gpu command
===================================
pair\_style tersoff/zbl/kk command
pair_style tersoff/zbl/gpu command
==================================
pair\_style tersoff/zbl/omp command
===================================
pair_style tersoff/zbl/kk command
=================================
pair_style tersoff/zbl/omp command
==================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style tersoff/zbl
@ -24,10 +24,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style tersoff/zbl
pair_coeff \* \* SiC.tersoff.zbl Si C Si
pair_coeff * * SiC.tersoff.zbl Si C Si
Description
"""""""""""
@ -106,9 +106,9 @@ 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 \* \* SiC.tersoff Si Si Si C
pair_coeff * * SiC.tersoff Si Si Si C
The 1st 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

20
doc/src/pair_thole.rst
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@ -1,19 +1,19 @@
.. index:: pair\_style thole
.. index:: pair_style thole
pair\_style thole command
=========================
pair_style thole command
========================
pair\_style lj/cut/thole/long command
=====================================
pair_style lj/cut/thole/long command
====================================
pair\_style lj/cut/thole/long/omp command
=========================================
pair_style lj/cut/thole/long/omp command
========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -35,12 +35,12 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style hybrid/overlay ... thole 2.6 12.0
pair_coeff 1 1 thole 1.0
pair_coeff 1 2 thole 1.0 2.6 10.0
pair_coeff \* 2 thole 1.0 2.6
pair_coeff * 2 thole 1.0 2.6
pair_style lj/cut/thole/long 2.6 12.0

14
doc/src/pair_tri_lj.rst
View File

@ -1,13 +1,12 @@
.. index:: pair\_style tri/lj
.. index:: pair_style tri/lj
pair\_style tri/lj command
==========================
pair_style tri/lj command
=========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style tri/lj cutoff
@ -16,11 +15,10 @@ cutoff = global cutoff for interactions (distance units)
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style tri/lj 3.0
pair_coeff \* \* 1.0 1.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.5 2.5
Description

37
doc/src/pair_ufm.rst
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@ -1,22 +1,22 @@
.. index:: pair\_style ufm
.. index:: pair_style ufm
pair\_style ufm command
=======================
pair_style ufm command
======================
pair\_style ufm/gpu command
===========================
pair_style ufm/gpu command
==========================
pair\_style ufm/omp command
===========================
pair_style ufm/omp command
==========================
pair\_style ufm/opt command
===========================
pair_style ufm/opt command
==========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style ufm cutoff
@ -25,17 +25,16 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style ufm 4.0
pair_coeff 1 1 100.0 1.0 2.5
pair_coeff \* \* 100.0 1.0
pair_coeff * * 100.0 1.0
pair_style ufm 4.0
pair_coeff \* \* 10.0 1.0
pair_coeff * * 10.0 1.0
variable prefactor equal ramp(10,100)
fix 1 all adapt 1 pair ufm epsilon \* \* v_prefactor
fix 1 all adapt 1 pair ufm epsilon * * v_prefactor
Description
"""""""""""
@ -45,7 +44,7 @@ Style *ufm* computes pairwise interactions using the Uhlenbeck-Ford model (UFM)
.. math::
E & = -\varepsilon\, \ln{\left[1-\exp{\left(-r^{2}/\sigma^{2}\right)}\right]} \qquad r < r_c \\
\varepsilon & = p\,k_B\,T
\varepsilon & = p\,k_B\,T
where :math:`r_c` is the cutoff, :math:`\sigma` is a distance-scale and
@ -75,10 +74,10 @@ all pairwise interactions from 10.0 at the beginning to 100.0 at the end
of a run:
.. parsed-literal::
.. code-block:: LAMMPS
variable prefactor equal ramp(10,100)
fix 1 all adapt 1 pair ufm epsilon \* \* v_prefactor
fix 1 all adapt 1 pair ufm epsilon * * v_prefactor
.. note::
@ -144,7 +143,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

48
doc/src/pair_vashishta.rst
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@ -1,28 +1,28 @@
.. index:: pair\_style vashishta
.. index:: pair_style vashishta
pair\_style vashishta command
=============================
pair_style vashishta command
============================
pair\_style vashishta/gpu command
=================================
pair\_style vashishta/omp command
=================================
pair\_style vashishta/kk command
pair_style vashishta/gpu command
================================
pair\_style vashishta/table command
===================================
pair_style vashishta/omp command
================================
pair\_style vashishta/table/omp command
=======================================
pair_style vashishta/kk command
===============================
pair_style vashishta/table command
==================================
pair_style vashishta/table/omp command
======================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style style args
@ -41,13 +41,13 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style vashishta
pair_coeff \* \* SiC.vashishta Si C
pair_coeff * * SiC.vashishta Si C
pair_style vashishta/table 100000 0.2
pair_coeff \* \* SiC.vashishta Si C
pair_coeff * * SiC.vashishta Si C
Description
"""""""""""
@ -65,10 +65,10 @@ The potential for the energy U of a system of atoms is
.. math::
U & = \sum_i^N \sum_{j > i}^N U_{ij}^{(2)} (r_{ij}) + \sum_i^N \sum_{j \neq i}^N \sum_{k > j, k \neq i}^N U_{ijk}^{(3)} (r_{ij}, r_{ik}, \theta_{ijk}) \\
U_{ij}^{(2)} (r) & = \frac{H_{ij}}{r^{\eta_{ij}}} + \frac{Z_i Z_j}{r}\exp(-r/\lambda_{1,ij}) - \frac{D_{ij}}{r^4}\exp(-r/\lambda_{4,ij}) - \frac{W_{ij}}{r^6}, r < r_{c,{ij}} \\
U_{ijk}^{(3)}(r_{ij},r_{ik},\theta_{ijk}) & = B_{ijk} \frac{\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} {1+C_{ijk}\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} \times \\
& \exp \left( \frac{\gamma_{ij}}{r_{ij} - r_{0,ij}} \right) \exp \left( \frac{\gamma_{ik}}{r_{ik} - r_{0,ik}} \right), r_{ij} < r_{0,ij}, r_{ik} < r_{0,ik}
U & = \sum_i^N \sum_{j > i}^N U_{ij}^{(2)} (r_{ij}) + \sum_i^N \sum_{j \neq i}^N \sum_{k > j, k \neq i}^N U_{ijk}^{(3)} (r_{ij}, r_{ik}, \theta_{ijk}) \\
U_{ij}^{(2)} (r) & = \frac{H_{ij}}{r^{\eta_{ij}}} + \frac{Z_i Z_j}{r}\exp(-r/\lambda_{1,ij}) - \frac{D_{ij}}{r^4}\exp(-r/\lambda_{4,ij}) - \frac{W_{ij}}{r^6}, r < r_{c,{ij}} \\
U_{ijk}^{(3)}(r_{ij},r_{ik},\theta_{ijk}) & = B_{ijk} \frac{\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} {1+C_{ijk}\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} \times \\
& \exp \left( \frac{\gamma_{ij}}{r_{ij} - r_{0,ij}} \right) \exp \left( \frac{\gamma_{ik}}{r_{ik} - r_{0,ik}} \right), r_{ij} < r_{0,ij}, r_{ik} < r_{0,ik}
where we follow the notation used in :ref:`Branicio2009 <Branicio2009>`.
@ -109,9 +109,9 @@ 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 \* \* SiC.vashishta Si Si Si C
pair_coeff * * SiC.vashishta Si Si Si C
The 1st 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

10
doc/src/pair_write.rst
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@ -1,13 +1,13 @@
.. index:: pair\_write
.. index:: pair_write
pair\_write command
===================
pair_write command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_write itype jtype N style inner outer file keyword Qi Qj
@ -23,7 +23,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_write 1 3 500 r 1.0 10.0 table.txt LJ
pair_write 1 1 1000 rsq 2.0 8.0 table.txt Yukawa_1_1 -0.5 0.5

26
doc/src/pair_yukawa.rst
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@ -1,22 +1,22 @@
.. index:: pair\_style yukawa
.. index:: pair_style yukawa
pair\_style yukawa command
==========================
pair_style yukawa command
=========================
pair\_style yukawa/gpu command
==============================
pair\_style yukawa/omp command
==============================
pair\_style yukawa/kk command
pair_style yukawa/gpu command
=============================
pair_style yukawa/omp command
=============================
pair_style yukawa/kk command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style yukawa kappa cutoff
@ -27,11 +27,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style yukawa 2.0 2.5
pair_coeff 1 1 100.0 2.3
pair_coeff \* \* 100.0
pair_coeff * * 100.0
Description
"""""""""""

20
doc/src/pair_yukawa_colloid.rst
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@ -1,19 +1,19 @@
.. index:: pair\_style yukawa/colloid
.. index:: pair_style yukawa/colloid
pair\_style yukawa/colloid command
==================================
pair_style yukawa/colloid command
=================================
pair\_style yukawa/colloid/gpu command
======================================
pair_style yukawa/colloid/gpu command
=====================================
pair\_style yukawa/colloid/omp command
======================================
pair_style yukawa/colloid/omp command
=====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style yukawa/colloid kappa cutoff
@ -24,11 +24,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style yukawa/colloid 2.0 2.5
pair_coeff 1 1 100.0 2.3
pair_coeff \* \* 100.0
pair_coeff * * 100.0
Description
"""""""""""

30
doc/src/pair_zbl.rst
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@ -1,22 +1,22 @@
.. index:: pair\_style zbl
.. index:: pair_style zbl
pair\_style zbl command
=======================
pair_style zbl command
======================
pair\_style zbl/gpu command
===========================
pair\_style zbl/kk command
pair_style zbl/gpu command
==========================
pair\_style zbl/omp command
===========================
pair_style zbl/kk command
=========================
pair_style zbl/omp command
==========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style zbl inner outer
@ -27,10 +27,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style zbl 3.0 4.0
pair_coeff \* \* 73.0 73.0
pair_coeff * * 73.0 73.0
pair_coeff 1 1 14.0 14.0
Description
@ -45,9 +45,9 @@ energy due to a pair of atoms at a distance r\_ij is given by:
.. math::
E^{ZBL}_{ij} & = \frac{1}{4\pi\epsilon_0} \frac{Z_i Z_j \,e^2}{r_{ij}} \phi(r_{ij}/a)+ S(r_{ij})\\
a & = \frac{0.46850}{Z_{i}^{0.23} + Z_{j}^{0.23}}\\
\phi(x) & = 0.18175e^{-3.19980x} + 0.50986e^{-0.94229x} + 0.28022e^{-0.40290x} + 0.02817e^{-0.20162x}\\
E^{ZBL}_{ij} & = \frac{1}{4\pi\epsilon_0} \frac{Z_i Z_j \,e^2}{r_{ij}} \phi(r_{ij}/a)+ S(r_{ij})\\
a & = \frac{0.46850}{Z_{i}^{0.23} + Z_{j}^{0.23}}\\
\phi(x) & = 0.18175e^{-3.19980x} + 0.50986e^{-0.94229x} + 0.28022e^{-0.40290x} + 0.02817e^{-0.20162x}\\
where *e* is the electron charge, :math:`\epsilon_0` is the electrical
permittivity of vacuum, and :math:`Z_i` and :math:`Z_j` are the nuclear

18
doc/src/pair_zero.rst
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@ -1,15 +1,15 @@
.. index:: pair\_style zero
.. index:: pair_style zero
pair\_style zero command
========================
pair_style zero command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style zero cutoff *nocoeff*
pair_style zero cutoff [nocoeff]
* zero = style name of this pair style
* cutoff = global cutoff (distance units)
@ -19,12 +19,12 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style zero 10.0
pair_style zero 5.0 nocoeff
pair_coeff \* \*
pair_coeff 1 2\*4 3.0
pair_coeff * *
pair_coeff 1 2*4 3.0
Description
"""""""""""
@ -84,7 +84,7 @@ and *outer* keywords of the :doc:`run_style respa <run_style>` command.
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

14
doc/src/read_data.rst
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@ -1,13 +1,13 @@
.. index:: read\_data
.. index:: read_data
read\_data command
==================
read_data command
=================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
read_data file keyword args ...
@ -54,7 +54,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
read_data data.lj
read_data ../run7/data.polymer.gz
@ -1401,7 +1401,7 @@ appear. These are listed in the same order they appear as listed
above. Thus if
.. parsed-literal::
.. code-block:: LAMMPS
atom_style hybrid electron sphere

10
doc/src/read_dump.rst
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@ -1,13 +1,13 @@
.. index:: read\_dump
.. index:: read_dump
read\_dump command
==================
read_dump command
=================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
read_dump file Nstep field1 field2 ... keyword values ...
@ -56,7 +56,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
read_dump dump.file 5000 x y z
read_dump dump.xyz 5 x y z box no format xyz

18
doc/src/read_restart.rst
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@ -1,13 +1,13 @@
.. index:: read\_restart
.. index:: read_restart
read\_restart command
=====================
read_restart command
====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
read_restart file flag
@ -18,13 +18,13 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
read_restart save.10000
read_restart save.10000 remap
read_restart restart.\*
read_restart restart.\*.mpiio
read_restart poly.\*.% remap
read_restart restart.*
read_restart restart.*.mpiio
read_restart poly.*.% remap
Description
"""""""""""
@ -125,7 +125,7 @@ MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
installed, e.g.
.. parsed-literal::
.. code-block:: bash
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform

12
doc/src/reset_ids.rst
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@ -1,13 +1,13 @@
.. index:: reset\_ids
.. index:: reset_ids
reset\_ids command
==================
reset_ids command
=================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
reset_ids
@ -15,7 +15,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
reset_ids
@ -54,7 +54,7 @@ as the :doc:`create_atoms <create_atoms>` command explains.
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

12
doc/src/reset_timestep.rst
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@ -1,13 +1,13 @@
.. index:: reset\_timestep
.. index:: reset_timestep
reset\_timestep command
=======================
reset_timestep command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
reset_timestep N
@ -17,7 +17,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
reset_timestep 0
reset_timestep 4000000
@ -37,7 +37,7 @@ was written.
Restrictions
""""""""""""
none
none
This command cannot be used when any fixes are defined that keep track
of elapsed time to perform certain kinds of time-dependent operations.

27
doc/src/run_style.rst
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@ -1,13 +1,13 @@
.. index:: run\_style
.. index:: run_style
run\_style command
==================
run_style command
=================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
run_style style args
@ -57,8 +57,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
run_style verlet
run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
@ -112,16 +111,16 @@ match the integer multiple constraint. See the
to control this, e.g.
.. parsed-literal::
.. code-block:: LAMMPS
procssors \* \* \* part 1 2 multiple
processors * * * part 1 2 multiple
You can also use the :doc:`partition <partition>` command to explicitly
specify the processor layout on each partition. E.g. for 2 partitions
of 60 and 15 processors each:
.. parsed-literal::
.. code-block:: LAMMPS
partition yes 1 processors 3 4 5
partition yes 2 processors 3 1 5
@ -235,7 +234,7 @@ settings for use of the *respa* style without SHAKE in biomolecular
simulations:
.. parsed-literal::
.. code-block:: LAMMPS
timestep 4.0
run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
@ -257,7 +256,7 @@ settings can be used for biomolecular simulations with SHAKE and
rRESPA:
.. parsed-literal::
.. code-block:: LAMMPS
fix 2 all shake 0.000001 500 0 m 1.0 a 1
timestep 4.0
@ -273,7 +272,7 @@ slow modes in the simulation. For example, a system of slowly-moving
charged polymer chains could be setup as follows:
.. parsed-literal::
.. code-block:: LAMMPS
timestep 4.0
run_style respa 2 8
@ -292,7 +291,7 @@ In real units, for a pure LJ fluid at liquid density, with a sigma of
seem to work well:
.. parsed-literal::
.. code-block:: LAMMPS
timestep 36.0
run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
@ -342,7 +341,7 @@ Default
"""""""
.. parsed-literal::
.. code-block:: LAMMPS
run_style verlet

16
doc/src/special_bonds.rst
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@ -1,13 +1,13 @@
.. index:: special\_bonds
.. index:: special_bonds
special\_bonds command
======================
special_bonds command
=====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
special_bonds keyword values ...
@ -34,7 +34,7 @@ Syntax
Examples:
.. parsed-literal::
.. code-block:: LAMMPS
special_bonds amber
special_bonds charmm
@ -216,7 +216,7 @@ default, then the 2,5 interaction will also be weighted by 0.5.
time incrementally. E.g. these two commands:
.. parsed-literal::
.. code-block:: LAMMPS
special_bonds lj 0.0 1.0 1.0
special_bonds coul 0.0 0.0 1.0
@ -224,7 +224,7 @@ default, then the 2,5 interaction will also be weighted by 0.5.
are not the same as
.. parsed-literal::
.. code-block:: LAMMPS
special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0
@ -250,7 +250,7 @@ their default values before modifying them, each time the
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

14
doc/src/thermo_modify.rst
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@ -1,13 +1,13 @@
.. index:: thermo\_modify
.. index:: thermo_modify
thermo\_modify command
======================
thermo_modify command
=====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
thermo_modify keyword value ...
@ -33,7 +33,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
thermo_modify lost ignore flush yes
thermo_modify temp myTemp format 3 %15.8g
@ -175,7 +175,7 @@ user to override the default.
Restrictions
""""""""""""
none
none
Related commands
""""""""""""""""

28
doc/src/thermo_style.rst
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@ -1,13 +1,12 @@
.. index:: thermo\_style
.. index:: thermo_style
thermo\_style command
=====================
thermo_style command
====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
thermo_style style args
@ -89,13 +88,12 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
thermo_style multi
thermo_style custom step temp pe etotal press vol
thermo_style custom step temp etotal c_myTemp v_abc
thermo_style custom step temp etotal c_myTemp[\*] v_abc
thermo_style custom step temp etotal c_myTemp[*] v_abc
Description
"""""""""""
@ -155,7 +153,7 @@ default this is done by using a *temperature* compute which is created
when LAMMPS starts up, as if this command had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute thermo_temp all temp
@ -174,7 +172,7 @@ using a *pressure* compute which is created when LAMMPS starts up, as
if this command had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute thermo_press all pressure thermo_temp
@ -193,7 +191,7 @@ be computed: "pe", "etotal", "ebond", etc. This is done by using a
command had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute thermo_pe all pe
@ -286,7 +284,7 @@ if the timer is expired, it is negative. This allows for example to exit
loops cleanly, if the timeout is expired with:
.. parsed-literal::
.. code-block:: LAMMPS
if "$(timeremain) < 0.0" then "quit 0"
@ -337,10 +335,10 @@ are equivalent, since the :doc:`compute temp <compute_temp>` command
creates a global vector with 6 values.
.. parsed-literal::
.. code-block:: LAMMPS
compute myTemp all temp
thermo_style custom step temp etotal c_myTemp[\*]
thermo_style custom step temp etotal c_myTemp[*]
thermo_style custom step temp etotal &
c_myTemp[1] c_myTemp[2] c_myTemp[3] &
c_myTemp[4] c_myTemp[5] c_myTemp[6]
@ -441,6 +439,6 @@ Default
"""""""
.. parsed-literal::
.. code-block:: LAMMPS
thermo_style one

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

12
doc/src/write_coeff.rst
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@ -1,23 +1,23 @@
.. index:: write\_coeff
.. index:: write_coeff
write\_coeff command
====================
write_coeff command
===================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
write_coeff file
file = name of data file to write out
* file = name of data file to write out
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
write_coeff polymer.coeff

10
doc/src/write_data.rst
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@ -1,13 +1,13 @@
.. index:: write\_data
.. index:: write_data
write\_data command
write_data command
===================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
write_data file keyword value ...
@ -29,10 +29,10 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
write_data data.polymer
write_data data.\*
write_data data.*
Description
"""""""""""

16
doc/src/write_dump.rst
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@ -1,13 +1,13 @@
.. index:: write\_dump
.. index:: write_dump
write\_dump command
===================
write_dump command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
write_dump group-ID style file dump-args modify dump_modify-args
@ -23,15 +23,15 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
write_dump all atom dump.atom
write_dump subgroup atom dump.run.bin
write_dump all custom dump.myforce.\* id type x y vx fx
write_dump all custom dump.myforce.* id type x y vx fx
write_dump flow custom dump.%.myforce id type c_myF[3] v_ke modify sort id
write_dump all xyz system.xyz modify sort id element O H
write_dump all image snap\*.jpg type type size 960 960 modify backcolor white
write_dump all image snap\*.jpg element element &
write_dump all image snap*.jpg type type size 960 960 modify backcolor white
write_dump all image snap*.jpg element element &
bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600 &
modify backcolor white element C C O H N C C C O H H S O H

14
doc/src/write_restart.rst
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@ -1,13 +1,13 @@
.. index:: write\_restart
.. index:: write_restart
write\_restart command
======================
write_restart command
=====================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
write_restart file keyword value ...
@ -28,11 +28,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
write_restart restart.equil
write_restart restart.equil.mpiio
write_restart poly.%.\* nfile 10
write_restart poly.%.* nfile 10
Description
"""""""""""
@ -63,7 +63,7 @@ versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g.
.. parsed-literal::
.. code-block:: bash
make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform