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Final batch of index cleanup and code-blocks

This commit is contained in:
Richard Berger 2020-02-27 11:08:04 -05:00
parent 9ef5949798
commit 25ec8d36a8
63 changed files with 690 additions and 702 deletions
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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/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/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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -44,11 +44,11 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style morse 2.5 pair_style morse 2.5
pair_style morse/smooth/linear 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 pair_coeff 1 1 100.0 2.0 1.5 3.0
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style multi/lucy style N keyword ... pair_style multi/lucy style N keyword ...
@ -18,10 +18,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style multi/lucy linear 1000 pair_style multi/lucy linear 1000
pair_coeff \* \* multibody.table ENTRY1 7.0 pair_coeff * * multibody.table ENTRY1 7.0
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style multi/lucy/rx style N keyword ... 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
pair_style multi/lucy/rx linear 1000 fractional pair_style multi/lucy/rx linear 1000 fractional
pair_style multi/lucy/rx linear 1000 molecular pair_style multi/lucy/rx linear 1000 molecular
pair_coeff \* \* multibody.table ENTRY1 h2o h2o 7.0 pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0
pair_coeff \* \* multibody.table ENTRY1 h2o 1fluid 7.0 pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style nb3b/harmonic pair_style nb3b/harmonic
@ -15,10 +15,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style nb3b/harmonic pair_style nb3b/harmonic
pair_coeff \* \* MgOH.nb3bharmonic Mg O H pair_coeff * * MgOH.nb3bharmonic Mg O H
Description 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: 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 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -46,18 +46,18 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style nm/cut 12.0 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_coeff 1 1 0.01 4.4 7.0 6.0
pair_style nm/cut/coul/cut 12.0 15.0 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_coeff 1 1 0.01 4.4 7.0 6.0
pair_style nm/cut/coul/long 12.0 15.0 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 pair_coeff 1 1 0.01 4.4 7.0 6.0
Description 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 Syntax
"""""" """"""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style none pair_style none
@ -15,7 +14,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style none pair_style none
@ -43,7 +42,7 @@ building of a neighbor lists, but compute no pairwise interactions.
Restrictions Restrictions
"""""""""""" """"""""""""
none none
Related commands 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/excv command
==============================
pair\_style oxdna/stk 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style1 pair_style style1
pair_coeff \* \* style2 args pair_coeff * * style2 args
* style1 = *hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk* * 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_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/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/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/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 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 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/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/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 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/excv command
===============================
pair\_style oxdna2/stk 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style1 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* * 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_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/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/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/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 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 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/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/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/dh 0.1 0.5 0.815
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style pair_style style
@ -32,19 +32,19 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style peri/pmb 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_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_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_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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style polymorphic pair_style polymorphic
@ -17,13 +17,13 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style polymorphic pair_style polymorphic
pair_coeff \* \* TlBr_msw.polymorphic Tl Br pair_coeff * * TlBr_msw.polymorphic Tl Br
pair_coeff \* \* AlCu_eam.polymorphic Al Cu pair_coeff * * AlCu_eam.polymorphic Al Cu
pair_coeff \* \* GaN_tersoff.polymorphic Ga N pair_coeff * * GaN_tersoff.polymorphic Ga N
pair_coeff \* \* GaN_sw.polymorphic GaN pair_coeff * * GaN_sw.polymorphic GaN
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style python cutoff pair_style python cutoff
@ -17,14 +17,14 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style python 2.5 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_style hybrid/overlay coul/long 12.0 python 12.0
pair_coeff \* \* coul/long pair_coeff * * coul/long
pair_coeff \* \* python py_pot.LJCutSPCE OW NULL pair_coeff * * python py_pot.LJCutSPCE OW NULL
Description 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: '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 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 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: 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): class LAMMPSPairPotential(object):
def __init__(self): def __init__(self):
self.pmap=dict() 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: which the parameters epsilon and sigma are both 1.0:
.. parsed-literal:: .. code-block:: python
class LJCutMelt(LAMMPSPairPotential): class LJCutMelt(LAMMPSPairPotential):
def __init__(self): def __init__(self):
@ -140,7 +140,7 @@ value of the internal potential parameter data structure. Following
the *LJCutMelt* example, here are the two functions: the *LJCutMelt* example, here are the two functions:
.. parsed-literal:: .. code-block:: python
def compute_force(self,rsq,itype,jtype): def compute_force(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[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: for an example LAMMPS input of how to build a table file:
.. parsed-literal:: .. code-block:: LAMMPS
pair_style python 2.5 pair_style python 2.5
pair_coeff \* \* py_pot.LJCutMelt lj pair_coeff * * py_pot.LJCutMelt lj
shell rm -f melt.table shell rm -f melt.table
pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj 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: to be assigned to the LAMMPS atom types like this:
.. parsed-literal:: .. code-block:: LAMMPS
pair_style table linear 2000 pair_style table linear 2000
pair_coeff 1 1 melt.table lj 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style quip pair_style quip
@ -15,11 +15,11 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style quip pair_style quip
pair_coeff \* \* gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 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 pair_coeff * * sw_example.xml "IP SW" 14
Description Description
""""""""""" """""""""""

26
doc/src/pair_reaxc.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style reax/c cfile keyword value 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 NULL
pair_style reax/c controlfile checkqeq no pair_style reax/c controlfile checkqeq no
pair_style reax/c NULL lgvdw yes pair_style reax/c NULL lgvdw yes
pair_style reax/c NULL safezone 1.6 mincap 100 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 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: headings) the following commands could be included in an input script:
.. parsed-literal:: .. code-block:: LAMMPS
compute reax all pair reax/c compute reax all pair reax/c
variable eb equal c_reax[1] 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: 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
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style resquared cutoff pair_style resquared cutoff
@ -23,10 +23,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style resquared 10.0 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 Description
""""""""""" """""""""""

60
doc/src/pair_sdk.rst
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@ -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/gpu command
==============================
pair\_style lj/sdk/kk 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 command
========================================
pair\_style lj/sdk/coul/long/omp command
========================================
pair\_style lj/sdk/coul/msm 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -51,7 +51,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style lj/sdk 2.5 pair_style lj/sdk 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8 pair_coeff 1 1 lj12_6 1 1.1 2.8
@ -72,15 +72,15 @@ given by
.. math:: .. math::
E = & \frac{27}{4} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} - E = & \frac{27}{4} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} -
\left(\frac{\sigma}{r}\right)^6 \right] \left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c \\ \qquad r < r_c \\
E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^4 \right] \left(\frac{\sigma}{r}\right)^4 \right]
\qquad r < r_c \\ \qquad r < r_c \\
E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c \qquad r < r_c
as required for the SDK Coarse-grained MD parameterization discussed in as required for the SDK Coarse-grained MD parameterization discussed in

14
doc/src/pair_sdpd_taitwater_isothermal.rst
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@ -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 Syntax
"""""" """"""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style sdpd/taitwater/isothermal temperature viscosity seed pair_style sdpd/taitwater/isothermal temperature viscosity seed
@ -18,11 +17,10 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style sdpd/taitwater/isothermal 300. 1. 28681 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 Description
""""""""""" """""""""""

14
doc/src/pair_smd_hertz.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style smd/hertz scale_factor pair_style smd/hertz scale_factor
Examples Examples
"""""""" """"""""
pair\_style smd/hertz 1.0 .. code-block:: LAMMPS
pair\_coeff 1 1 <contact\_stiffness>
pair_style smd/hertz 1.0
pair_coeff 1 1 <contact_stiffness>
Description Description
""""""""""" """""""""""

19
doc/src/pair_smd_tlsph.rst
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@ -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 Syntax
"""""" """"""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style smd/tlsph args pair_style smd/tlsph args
Examples Examples
"""""""" """"""""
pair\_style smd/tlsph .. code-block:: LAMMPS
pair_style smd/tlsph
Description Description
""""""""""" """""""""""
@ -26,11 +27,11 @@ Smooth-Particle Hydrodynamics algorithm.
This pair style is invoked with the following command: This pair style is invoked with the following command:
.. parsed-literal:: .. code-block:: LAMMPS
pair_style smd/tlsph pair_style smd/tlsph
pair_coeff i j \*COMMON rho0 E nu Q1 Q2 hg Cp & pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
\*END *END
Here, *i* and *j* denote the *LAMMPS* particle types for which this 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 pair style is defined. Note that *i* and *j* must be equal, i.e., no

15
doc/src/pair_smd_triangulated_surface.rst
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@ -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 Syntax
"""""" """"""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style smd/tri_surface scale_factor pair_style smd/tri_surface scale_factor
Examples Examples
"""""""" """"""""
pair\_style smd/tri\_surface 1.0 .. code-block:: LAMMPS
pair\_coeff 1 1 <contact\_stiffness>
pair_style smd/tri_surface 1.0
pair_coeff 1 1 <contact_stiffness>
Description Description
""""""""""" """""""""""

16
doc/src/pair_smtbq.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style smtbq .. index:: pair_style smtbq
pair\_style smtbq command pair_style smtbq command
========================= ========================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style smtbq pair_style smtbq
@ -15,10 +15,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style smtbq pair_style smtbq
pair_coeff \* \* ffield.smtbq.Al2O3 O Al pair_coeff * * ffield.smtbq.Al2O3 O Al
Description 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: 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 The electrostatic part of the energy consists of two components

38
doc/src/pair_snap.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style snap pair_style snap
@ -18,10 +18,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style snap pair_style snap
pair_coeff \* \* InP.snapcoeff InP.snapparam In In P P pair_coeff * * InP.snapcoeff InP.snapparam In In P P
Description 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: 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 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
The two filenames are for the coefficient and parameter files, respectively. 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: by the following commands:
.. parsed-literal:: .. code-block:: LAMMPS
variable zblcutinner equal 4 variable zblcutinner equal 4
variable zblcutouter equal 4.8 variable zblcutouter equal 4.8
variable zblz equal 73 variable zblz equal 73
pair_style hybrid/overlay & pair_style hybrid/overlay &
zbl ${zblcutinner} ${zblcutouter} snap zbl ${zblcutinner} ${zblcutouter} snap
pair_coeff \* \* zbl 0.0 pair_coeff \* \* zbl 0.0
pair_coeff 1 1 zbl ${zblz} pair_coeff 1 1 zbl ${zblz}
pair_coeff \* \* snap Ta06A.snapcoeff Ta06A.snapparam Ta pair_coeff \* \* snap Ta06A.snapcoeff Ta06A.snapparam Ta
It is convenient to keep these commands in a separate file that can 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>` be inserted in any LAMMPS input script using the :doc:`include <include>`

28
doc/src/pair_soft.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style soft cutoff pair_style soft cutoff
@ -23,16 +23,16 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style soft 1.0 pair_style soft 1.0
pair_coeff \* \* 10.0 pair_coeff * * 10.0
pair_coeff 1 1 10.0 3.0 pair_coeff 1 1 10.0 3.0
pair_style soft 1.0 pair_style soft 1.0
pair_coeff \* \* 0.0 pair_coeff * * 0.0
variable prefactor equal ramp(0,30) 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 Description
""""""""""" """""""""""
@ -83,10 +83,10 @@ all pairwise interactions from 0.0 at the beginning to 30.0 at the end
of a run: of a run:
.. parsed-literal:: .. code-block:: LAMMPS
variable prefactor equal ramp(0,30) 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>` Note that a formula defined by an :doc:`equal-style variable <variable>`
can use the current timestep, elapsed time in the current run, elapsed can use the current timestep, elapsed time in the current run, elapsed

12
doc/src/pair_sph_heatconduction.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/heatconduction pair_style sph/heatconduction
@ -15,10 +15,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/heatconduction pair_style sph/heatconduction
pair_coeff \* \* 1.0 2.4 pair_coeff * * 1.0 2.4
Description Description
""""""""""" """""""""""

14
doc/src/pair_sph_idealgas.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/idealgas pair_style sph/idealgas
@ -15,10 +15,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/idealgas pair_style sph/idealgas
pair_coeff \* \* 1.0 2.4 pair_coeff * * 1.0 2.4
Description Description
""""""""""" """""""""""
@ -28,7 +28,7 @@ according to the ideal gas equation of state:
.. math:: .. math::
p = (\gamma - 1) \rho e p = (\gamma - 1) \rho e
where :math:`\gamma = 1.4` is the heat capacity ratio, :math:`\rho` is where :math:`\gamma = 1.4` is the heat capacity ratio, :math:`\rho` is

12
doc/src/pair_sph_lj.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/lj pair_style sph/lj
@ -15,10 +15,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/lj pair_style sph/lj
pair_coeff \* \* 1.0 2.4 pair_coeff * * 1.0 2.4
Description Description
""""""""""" """""""""""

12
doc/src/pair_sph_rhosum.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/rhosum Nstep pair_style sph/rhosum Nstep
@ -17,10 +17,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/rhosum 10 pair_style sph/rhosum 10
pair_coeff \* \* 2.4 pair_coeff * * 2.4
Description Description
""""""""""" """""""""""

14
doc/src/pair_sph_taitwater.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/taitwater pair_style sph/taitwater
@ -15,10 +15,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/taitwater 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 Description
""""""""""" """""""""""
@ -28,7 +28,7 @@ according to Tait's equation of state:
.. math:: .. 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 where :math:`\gamma = 7` and :math:`B = c_0^2 \rho_0 / \gamma`, with

14
doc/src/pair_sph_taitwater_morris.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/taitwater/morris pair_style sph/taitwater/morris
@ -15,10 +15,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sph/taitwater/morris 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 Description
""""""""""" """""""""""
@ -28,7 +28,7 @@ particles according to Tait's equation of state:
.. math:: .. 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 where :math:`\gamma = 7` and :math:`B = c_0^2 \rho_0 / \gamma`, with

19
doc/src/pair_spin_dipole.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style spin/dipole/cut cutoff pair_style spin/dipole/cut cutoff
pair_style spin/dipole/long cutoff pair_style spin/dipole/long cutoff
@ -22,15 +22,14 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style spin/dipole/cut 10.0 pair_style spin/dipole/cut 10.0
pair_coeff \* \* 10.0 pair_coeff * * 10.0
pair_coeff 2 3 8.0 pair_coeff 2 3 8.0
pair_style spin/dipole/long 9.0 pair_style spin/dipole/long 9.0
pair_coeff \* \* 10.0 pair_coeff * * 10.0
pair_coeff 2 3 6.0 pair_coeff 2 3 6.0
Description Description

14
doc/src/pair_spin_dmi.rst
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@ -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 Syntax
"""""" """"""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style spin/dmi cutoff pair_style spin/dmi cutoff
@ -17,11 +16,10 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style spin/dmi 4.0 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 pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0
Description Description

6
doc/src/pair_spin_exchange.rst
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@ -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 Syntax
"""""" """"""

8
doc/src/pair_spin_magelec.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style spin/magelec cutoff pair_style spin/magelec cutoff
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style spin/magelec 4.5 pair_style spin/magelec 4.5
pair_coeff \* \* magelec 4.5 0.00109 1.0 1.0 1.0 pair_coeff \* \* magelec 4.5 0.00109 1.0 1.0 1.0

12
doc/src/pair_srp.rst
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@ -1,12 +1,14 @@
.. index:: pair\_style srp .. index:: pair_style srp
pair\_style srp command pair_style srp command
======================= ======================
Syntax 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) * cutoff = global cutoff for SRP interactions (distance units)
* btype = bond type to apply SRP interactions to (can be wildcard, see below) * 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_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 pair_coeff 1 1 dpd 60.0 4.5 1.0

12
doc/src/pair_style.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style .. index:: pair_style
pair\_style command pair_style command
=================== ==================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -18,7 +18,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_style eam/alloy pair_style eam/alloy
@ -354,6 +354,6 @@ Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style none pair_style none

38
doc/src/pair_sw.rst
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@ -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/gpu command
==========================
pair\_style sw/intel command
============================
pair\_style sw/kk command
========================= =========================
pair\_style sw/omp command pair_style sw/intel command
========================== ===========================
pair_style sw/kk command
========================
pair_style sw/omp command
=========================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style sw pair_style sw
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style sw pair_style sw
pair_coeff \* \* si.sw Si pair_coeff * * si.sw Si
pair_coeff \* \* GaN.sw Ga N Ga pair_coeff * * GaN.sw Ga N Ga
Description 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 the 1st 3 to be Si, and the 4th to be C, you would use the following
pair\_coeff command: 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 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 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/gpu command
=============================
pair\_style table/kk command
============================ ============================
pair\_style table/omp command pair_style table/kk command
============================= ===========================
pair_style table/omp command
============================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style table style N keyword ... pair_style table style N keyword ...
@ -29,14 +29,13 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style table linear 1000 pair_style table linear 1000
pair_style table linear 1000 pppm pair_style table linear 1000 pppm
pair_style table bitmap 12 pair_style table bitmap 12
pair_coeff \* 3 morse.table ENTRY1 pair_coeff * 3 morse.table ENTRY1
pair_coeff \* 3 morse.table ENTRY1 7.0 pair_coeff * 3 morse.table ENTRY1 7.0
Description Description
""""""""""" """""""""""
@ -276,7 +275,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions Restrictions
"""""""""""" """"""""""""
none none
Related commands Related commands
"""""""""""""""" """"""""""""""""

21
doc/src/pair_table_rx.rst
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@ -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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style table style N ... pair_style table style N ...
@ -21,15 +21,14 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style table/rx linear 1000 pair_style table/rx linear 1000
pair_style table/rx linear 1000 fractional pair_style table/rx linear 1000 fractional
pair_style table/rx linear 1000 molecular pair_style table/rx linear 1000 molecular
pair_coeff \* \* rxn.table ENTRY1 h2o h2o 10.0 pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0
pair_coeff \* \* rxn.table ENTRY1 1fluid 1fluid 10.0 pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0
pair_coeff \* 3 rxn.table ENTRY1 h2o no2 10.0 pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0
Description Description
""""""""""" """""""""""

47
doc/src/pair_tersoff.rst
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@ -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/gpu command
===============================
pair\_style tersoff/intel command
=================================
pair\_style tersoff/kk 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 Syntax
"""""" """"""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style style pair_style style
@ -35,14 +34,14 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style tersoff pair_style tersoff
pair_coeff \* \* Si.tersoff Si pair_coeff * * Si.tersoff Si
pair_coeff \* \* SiC.tersoff Si C Si pair_coeff * * SiC.tersoff Si C Si
pair_style tersoff/table pair_style tersoff/table
pair_coeff \* \* SiCGe.tersoff Si(D) pair_coeff * * SiCGe.tersoff Si(D)
Description Description
""""""""""" """""""""""
@ -97,9 +96,9 @@ and C. If your LAMMPS simulation has 4 atoms types and you want the
pair\_coeff command: 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 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 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/gpu command
===================================
pair\_style tersoff/mod/kk 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style tersoff/mod pair_style tersoff/mod
@ -31,14 +31,13 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style tersoff/mod pair_style tersoff/mod
pair_coeff \* \* Si.tersoff.mod Si Si pair_coeff * * Si.tersoff.mod Si Si
pair_style tersoff/mod/c pair_style tersoff/mod/c
pair_coeff \* \* Si.tersoff.modc Si Si pair_coeff * * Si.tersoff.modc Si Si
Description Description
""""""""""" """""""""""
@ -51,22 +50,22 @@ E of a system of atoms as
.. math:: .. math::
E & = \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ E & = \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\ 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} f_C(r) & = \left\{ \begin{array} {r@{\quad:\quad}l}
1 & r < R - D \\ 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) & \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 \\ R-D < r < R + D \\
0 & r > R + D 0 & r > R + D
\end{array} \right. \\ \end{array} \right. \\
f_R(r) & = A \exp (-\lambda_1 r) \\ f_R(r) & = A \exp (-\lambda_1 r) \\
f_A(r) & = -B \exp (-\lambda_2 r) \\ f_A(r) & = -B \exp (-\lambda_2 r) \\
b_{ij} & = \left( 1 + {\zeta_{ij}}^\eta \right)^{-\frac{1}{2n}} \\ 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}) \zeta_{ij} & = \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
\exp \left[ \alpha (r_{ij} - r_{ik})^\beta \right] \\ \exp \left[ \alpha (r_{ij} - r_{ik})^\beta \right] \\
g(\theta) & = c_1 + g_o(\theta) g_a(\theta) \\ 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_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] \\ 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. 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:: .. 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 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: 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 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 The three Si arguments map LAMMPS atom types 1,2,3 to the Si element

28
doc/src/pair_tersoff_zbl.rst
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@ -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/gpu command
===================================
pair\_style tersoff/zbl/kk command
================================== ==================================
pair\_style tersoff/zbl/omp command pair_style tersoff/zbl/kk command
=================================== =================================
pair_style tersoff/zbl/omp command
==================================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style tersoff/zbl pair_style tersoff/zbl
@ -24,10 +24,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style tersoff/zbl pair_style tersoff/zbl
pair_coeff \* \* SiC.tersoff.zbl Si C Si pair_coeff * * SiC.tersoff.zbl Si C Si
Description 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: 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 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -35,12 +35,12 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style hybrid/overlay ... thole 2.6 12.0 pair_style hybrid/overlay ... thole 2.6 12.0
pair_coeff 1 1 thole 1.0 pair_coeff 1 1 thole 1.0
pair_coeff 1 2 thole 1.0 2.6 10.0 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 pair_style lj/cut/thole/long 2.6 12.0

14
doc/src/pair_tri_lj.rst
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@ -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 Syntax
"""""" """"""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style tri/lj cutoff pair_style tri/lj cutoff
@ -16,11 +15,10 @@ cutoff = global cutoff for interactions (distance units)
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style tri/lj 3.0 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 pair_coeff 1 1 1.0 1.5 2.5
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style ufm cutoff pair_style ufm cutoff
@ -25,17 +25,16 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
pair_style ufm 4.0 pair_style ufm 4.0
pair_coeff 1 1 100.0 1.0 2.5 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_style ufm 4.0
pair_coeff \* \* 10.0 1.0 pair_coeff * * 10.0 1.0
variable prefactor equal ramp(10,100) 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 Description
""""""""""" """""""""""
@ -45,7 +44,7 @@ Style *ufm* computes pairwise interactions using the Uhlenbeck-Ford model (UFM)
.. math:: .. math::
E & = -\varepsilon\, \ln{\left[1-\exp{\left(-r^{2}/\sigma^{2}\right)}\right]} \qquad r < r_c \\ 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 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: of a run:
.. parsed-literal:: .. code-block:: LAMMPS
variable prefactor equal ramp(10,100) 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:: .. note::
@ -144,7 +143,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions Restrictions
"""""""""""" """"""""""""
none none
Related commands 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/gpu command
=================================
pair\_style vashishta/omp command
=================================
pair\_style vashishta/kk 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style style args pair_style style args
@ -41,13 +41,13 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style vashishta pair_style vashishta
pair_coeff \* \* SiC.vashishta Si C pair_coeff * * SiC.vashishta Si C
pair_style vashishta/table 100000 0.2 pair_style vashishta/table 100000 0.2
pair_coeff \* \* SiC.vashishta Si C pair_coeff * * SiC.vashishta Si C
Description Description
""""""""""" """""""""""
@ -65,10 +65,10 @@ The potential for the energy U of a system of atoms is
.. math:: .. 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 & = \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_{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 \\ 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} & \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>`. 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: 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 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_write itype jtype N style inner outer file keyword Qi Qj 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 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 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/gpu command
==============================
pair\_style yukawa/omp command
==============================
pair\_style yukawa/kk command
============================= =============================
pair_style yukawa/omp command
=============================
pair_style yukawa/kk command
============================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style yukawa kappa cutoff pair_style yukawa kappa cutoff
@ -27,11 +27,11 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style yukawa 2.0 2.5 pair_style yukawa 2.0 2.5
pair_coeff 1 1 100.0 2.3 pair_coeff 1 1 100.0 2.3
pair_coeff \* \* 100.0 pair_coeff * * 100.0
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style yukawa/colloid kappa cutoff 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_style yukawa/colloid 2.0 2.5
pair_coeff 1 1 100.0 2.3 pair_coeff 1 1 100.0 2.3
pair_coeff \* \* 100.0 pair_coeff * * 100.0
Description 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/gpu command
===========================
pair\_style zbl/kk command
========================== ==========================
pair\_style zbl/omp command pair_style zbl/kk command
=========================== =========================
pair_style zbl/omp command
==========================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style zbl inner outer pair_style zbl inner outer
@ -27,10 +27,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style zbl 3.0 4.0 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 pair_coeff 1 1 14.0 14.0
Description Description
@ -45,9 +45,9 @@ energy due to a pair of atoms at a distance r\_ij is given by:
.. math:: .. 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})\\ 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}}\\ 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}\\ \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 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style zero cutoff *nocoeff* pair_style zero cutoff [nocoeff]
* zero = style name of this pair style * zero = style name of this pair style
* cutoff = global cutoff (distance units) * cutoff = global cutoff (distance units)
@ -19,12 +19,12 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
pair_style zero 10.0 pair_style zero 10.0
pair_style zero 5.0 nocoeff pair_style zero 5.0 nocoeff
pair_coeff \* \* pair_coeff * *
pair_coeff 1 2\*4 3.0 pair_coeff 1 2*4 3.0
Description Description
""""""""""" """""""""""
@ -84,7 +84,7 @@ and *outer* keywords of the :doc:`run_style respa <run_style>` command.
Restrictions Restrictions
"""""""""""" """"""""""""
none none
Related commands 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
read_data file keyword args ... read_data file keyword args ...
@ -54,7 +54,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
read_data data.lj read_data data.lj
read_data ../run7/data.polymer.gz 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 above. Thus if
.. parsed-literal:: .. code-block:: LAMMPS
atom_style hybrid electron sphere 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
read_dump file Nstep field1 field2 ... keyword values ... 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.file 5000 x y z
read_dump dump.xyz 5 x y z box no format xyz 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
read_restart file flag read_restart file flag
@ -18,13 +18,13 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
read_restart save.10000 read_restart save.10000
read_restart save.10000 remap read_restart save.10000 remap
read_restart restart.\* read_restart restart.*
read_restart restart.\*.mpiio read_restart restart.*.mpiio
read_restart poly.\*.% remap read_restart poly.*.% remap
Description Description
""""""""""" """""""""""
@ -125,7 +125,7 @@ MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
installed, e.g. installed, e.g.
.. parsed-literal:: .. code-block:: bash
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
reset_ids reset_ids
@ -15,7 +15,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
reset_ids reset_ids
@ -54,7 +54,7 @@ as the :doc:`create_atoms <create_atoms>` command explains.
Restrictions Restrictions
"""""""""""" """"""""""""
none none
Related commands 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
reset_timestep N reset_timestep N
@ -17,7 +17,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
reset_timestep 0 reset_timestep 0
reset_timestep 4000000 reset_timestep 4000000
@ -37,7 +37,7 @@ was written.
Restrictions Restrictions
"""""""""""" """"""""""""
none none
This command cannot be used when any fixes are defined that keep track This command cannot be used when any fixes are defined that keep track
of elapsed time to perform certain kinds of time-dependent operations. 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
run_style style args run_style style args
@ -57,8 +57,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
run_style verlet run_style verlet
run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4 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. 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 You can also use the :doc:`partition <partition>` command to explicitly
specify the processor layout on each partition. E.g. for 2 partitions specify the processor layout on each partition. E.g. for 2 partitions
of 60 and 15 processors each: of 60 and 15 processors each:
.. parsed-literal:: .. code-block:: LAMMPS
partition yes 1 processors 3 4 5 partition yes 1 processors 3 4 5
partition yes 2 processors 3 1 5 partition yes 2 processors 3 1 5
@ -235,7 +234,7 @@ settings for use of the *respa* style without SHAKE in biomolecular
simulations: simulations:
.. parsed-literal:: .. code-block:: LAMMPS
timestep 4.0 timestep 4.0
run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4 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: rRESPA:
.. parsed-literal:: .. code-block:: LAMMPS
fix 2 all shake 0.000001 500 0 m 1.0 a 1 fix 2 all shake 0.000001 500 0 m 1.0 a 1
timestep 4.0 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: charged polymer chains could be setup as follows:
.. parsed-literal:: .. code-block:: LAMMPS
timestep 4.0 timestep 4.0
run_style respa 2 8 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: seem to work well:
.. parsed-literal:: .. code-block:: LAMMPS
timestep 36.0 timestep 36.0
run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 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 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
special_bonds keyword values ... special_bonds keyword values ...
@ -34,7 +34,7 @@ Syntax
Examples: Examples:
.. parsed-literal:: .. code-block:: LAMMPS
special_bonds amber special_bonds amber
special_bonds charmm 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: time incrementally. E.g. these two commands:
.. parsed-literal:: .. code-block:: LAMMPS
special_bonds lj 0.0 1.0 1.0 special_bonds lj 0.0 1.0 1.0
special_bonds coul 0.0 0.0 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 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 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 Restrictions
"""""""""""" """"""""""""
none none
Related commands 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
thermo_modify keyword value ... thermo_modify keyword value ...
@ -33,7 +33,7 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
thermo_modify lost ignore flush yes thermo_modify lost ignore flush yes
thermo_modify temp myTemp format 3 %15.8g thermo_modify temp myTemp format 3 %15.8g
@ -175,7 +175,7 @@ user to override the default.
Restrictions Restrictions
"""""""""""" """"""""""""
none none
Related commands 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 Syntax
"""""" """"""
.. code-block:: LAMMPS
.. parsed-literal::
thermo_style style args thermo_style style args
@ -89,13 +88,12 @@ Syntax
Examples Examples
"""""""" """"""""
.. code-block:: LAMMPS
.. parsed-literal::
thermo_style multi thermo_style multi
thermo_style custom step temp pe etotal press vol 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 thermo_style custom step temp etotal c_myTemp[*] v_abc
Description 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: when LAMMPS starts up, as if this command had been issued:
.. parsed-literal:: .. code-block:: LAMMPS
compute thermo_temp all temp 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: if this command had been issued:
.. parsed-literal:: .. code-block:: LAMMPS
compute thermo_press all pressure thermo_temp 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: command had been issued:
.. parsed-literal:: .. code-block:: LAMMPS
compute thermo_pe all pe 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: loops cleanly, if the timeout is expired with:
.. parsed-literal:: .. code-block:: LAMMPS
if "$(timeremain) < 0.0" then "quit 0" if "$(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. creates a global vector with 6 values.
.. parsed-literal:: .. code-block:: LAMMPS
compute myTemp all temp 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 & thermo_style custom step temp etotal &
c_myTemp[1] c_myTemp[2] c_myTemp[3] & c_myTemp[1] c_myTemp[2] c_myTemp[3] &
c_myTemp[4] c_myTemp[5] c_myTemp[6] c_myTemp[4] c_myTemp[5] c_myTemp[6]
@ -441,6 +439,6 @@ Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
thermo_style one 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
third_order group-ID style delta args keyword value ... 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 regular 0.000001
third_order 1 eskm 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
write_coeff file write_coeff file
file = name of data file to write out * file = name of data file to write out
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
write_coeff polymer.coeff 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
write_data file keyword value ... write_data file keyword value ...
@ -29,10 +29,10 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
write_data data.polymer write_data data.polymer
write_data data.\* write_data data.*
Description 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 Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
write_dump group-ID style file dump-args modify dump_modify-args 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 all atom dump.atom
write_dump subgroup atom dump.run.bin 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 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 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 type type size 960 960 modify backcolor white
write_dump all image snap\*.jpg element element & write_dump all image snap*.jpg element element &
bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600 & 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 modify backcolor white element C C O H N C C C O H H S O H

14
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@ -1,13 +1,13 @@
.. index:: write\_restart .. index:: write_restart
write\_restart command write_restart command
====================== =====================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. code-block:: LAMMPS
write_restart file keyword value ... write_restart file keyword value ...
@ -28,11 +28,11 @@ Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
write_restart restart.equil write_restart restart.equil
write_restart restart.equil.mpiio write_restart restart.equil.mpiio
write_restart poly.%.\* nfile 10 write_restart poly.%.* nfile 10
Description 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. build LAMMPS with its MPIIO package installed, e.g.
.. parsed-literal:: .. code-block:: bash
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make mpi # build LAMMPS for your platform make mpi # build LAMMPS for your platform