diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 3883fb3855..eb0666d3cb 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -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 diff --git a/doc/src/pair_multi_lucy.rst b/doc/src/pair_multi_lucy.rst index e116951550..39b641361e 100644 --- a/doc/src/pair_multi_lucy.rst +++ b/doc/src/pair_multi_lucy.rst @@ -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 """"""""""" diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index 9d8d449b76..e057b184f7 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -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 """"""""""" diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst index 7f6e1beef0..48a7038fb2 100644 --- a/doc/src/pair_nb3b_harmonic.rst +++ b/doc/src/pair_nb3b_harmonic.rst @@ -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 diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index 6d319c6d06..27bb11fe65 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -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 diff --git a/doc/src/pair_none.rst b/doc/src/pair_none.rst index 43f56d20bc..11a4a79163 100644 --- a/doc/src/pair_none.rst +++ b/doc/src/pair_none.rst @@ -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 """""""""""""""" diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index 8faef5decd..f24520f473 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -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 """"""""""" diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 8c903f023f..368a203b8a 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -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 """"""""""" diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index f9f183ea27..5f74f98554 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -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 """"""""""" diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index d3a83f5567..b19f3b9f3b 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -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 """"""""""" diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst index 3545a83003..23c83ed52e 100644 --- a/doc/src/pair_python.rst +++ b/doc/src/pair_python.rst @@ -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 diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index 304edced31..4c91677f08 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -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 """"""""""" diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index 9f433fe237..ee5eb878c8 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -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 ---------- diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index 5739efa4af..a28549c344 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -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 """"""""""" diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 8585efaccf..ba28262813 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -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 diff --git a/doc/src/pair_sdpd_taitwater_isothermal.rst b/doc/src/pair_sdpd_taitwater_isothermal.rst index 3a9c7e80be..7a60fdef65 100644 --- a/doc/src/pair_sdpd_taitwater_isothermal.rst +++ b/doc/src/pair_sdpd_taitwater_isothermal.rst @@ -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 """"""""""" diff --git a/doc/src/pair_smd_hertz.rst b/doc/src/pair_smd_hertz.rst index d3070c08c5..6395c76a1b 100644 --- a/doc/src/pair_smd_hertz.rst +++ b/doc/src/pair_smd_hertz.rst @@ -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 +.. code-block:: LAMMPS + + pair_style smd/hertz 1.0 + pair_coeff 1 1 Description """"""""""" diff --git a/doc/src/pair_smd_tlsph.rst b/doc/src/pair_smd_tlsph.rst index 56570ddd5f..4b5d7cf1cc 100644 --- a/doc/src/pair_smd_tlsph.rst +++ b/doc/src/pair_smd_tlsph.rst @@ -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 diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 78edd2683b..14495d6b06 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -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 +.. code-block:: LAMMPS + + pair_style smd/tri_surface 1.0 + pair_coeff 1 1 Description """"""""""" diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst index f69960e5a9..843e8ce2ca 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -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 diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 975a7fcd79..00e07dc82c 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -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 ` diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index d32e9f9106..f1fa0af802 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -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 ` can use the current timestep, elapsed time in the current run, elapsed diff --git a/doc/src/pair_sph_heatconduction.rst b/doc/src/pair_sph_heatconduction.rst index 3322a1aa10..efd4b426da 100644 --- a/doc/src/pair_sph_heatconduction.rst +++ b/doc/src/pair_sph_heatconduction.rst @@ -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 """"""""""" diff --git a/doc/src/pair_sph_idealgas.rst b/doc/src/pair_sph_idealgas.rst index 750bd08571..2e1a2b9d53 100644 --- a/doc/src/pair_sph_idealgas.rst +++ b/doc/src/pair_sph_idealgas.rst @@ -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 diff --git a/doc/src/pair_sph_lj.rst b/doc/src/pair_sph_lj.rst index e8873416b3..45b611e441 100644 --- a/doc/src/pair_sph_lj.rst +++ b/doc/src/pair_sph_lj.rst @@ -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 """"""""""" diff --git a/doc/src/pair_sph_rhosum.rst b/doc/src/pair_sph_rhosum.rst index dad7b1852a..68f55021e3 100644 --- a/doc/src/pair_sph_rhosum.rst +++ b/doc/src/pair_sph_rhosum.rst @@ -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 """"""""""" diff --git a/doc/src/pair_sph_taitwater.rst b/doc/src/pair_sph_taitwater.rst index 71bb72ae02..ae200ee024 100644 --- a/doc/src/pair_sph_taitwater.rst +++ b/doc/src/pair_sph_taitwater.rst @@ -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 diff --git a/doc/src/pair_sph_taitwater_morris.rst b/doc/src/pair_sph_taitwater_morris.rst index 5982821a76..c4dcb87758 100644 --- a/doc/src/pair_sph_taitwater_morris.rst +++ b/doc/src/pair_sph_taitwater_morris.rst @@ -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 diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index c4c5ffd3b7..d1d35f9b8d 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -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 diff --git a/doc/src/pair_spin_dmi.rst b/doc/src/pair_spin_dmi.rst index 84feccea56..6ef65dfa93 100644 --- a/doc/src/pair_spin_dmi.rst +++ b/doc/src/pair_spin_dmi.rst @@ -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 diff --git a/doc/src/pair_spin_exchange.rst b/doc/src/pair_spin_exchange.rst index 1393e47cdd..b2ad9a8f69 100644 --- a/doc/src/pair_spin_exchange.rst +++ b/doc/src/pair_spin_exchange.rst @@ -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 """""" diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 142b24fbdc..526806959f 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -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 diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index 822bd0dddb..8762f3e4a9 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -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 diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 5fedfcbf30..96d8eb1d04 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -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 diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index 2df9958ba1..39ece6ea97 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -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 diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 042e989209..9bfd22f8dc 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -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 """""""""""""""" diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index 38e431ff5c..c98e3372e0 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -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 """"""""""" diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index f2e44d0362..655a4bb47a 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -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 diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index 94cc9300ed..bcbeb6f138 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -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) ` 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 diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index e60de64f28..19cbafa192 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -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 diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index dbf282ecab..68dc270500 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -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 diff --git a/doc/src/pair_tri_lj.rst b/doc/src/pair_tri_lj.rst index c5fbd90e1d..9d021f79a4 100644 --- a/doc/src/pair_tri_lj.rst +++ b/doc/src/pair_tri_lj.rst @@ -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 diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst index c8a7e42743..bf567bb821 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -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 """""""""""""""" diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index 2dde0482be..f3e9ce1db0 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -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 `. @@ -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 diff --git a/doc/src/pair_write.rst b/doc/src/pair_write.rst index 7a67bcc5bd..69639e3f99 100644 --- a/doc/src/pair_write.rst +++ b/doc/src/pair_write.rst @@ -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 diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index b7cb6818d2..15b9f0fc0b 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -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 """"""""""" diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index 2c337bdb94..c8659cb157 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -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 """"""""""" diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index bffcf9fbda..f2f310dae9 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -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 diff --git a/doc/src/pair_zero.rst b/doc/src/pair_zero.rst index d03cd03f76..0a9db6472a 100644 --- a/doc/src/pair_zero.rst +++ b/doc/src/pair_zero.rst @@ -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 ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index ce466108cf..ea36675bc6 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -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 diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index acf08866a9..5de1e8f25d 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -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 diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst index 06f4ddb2e3..e4c7a7b7cf 100644 --- a/doc/src/read_restart.rst +++ b/doc/src/read_restart.rst @@ -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 diff --git a/doc/src/reset_ids.rst b/doc/src/reset_ids.rst index 3bcc0a5b61..29b8c1ca70 100644 --- a/doc/src/reset_ids.rst +++ b/doc/src/reset_ids.rst @@ -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 ` command explains. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/reset_timestep.rst b/doc/src/reset_timestep.rst index e287605fbb..5dcaf9daf4 100644 --- a/doc/src/reset_timestep.rst +++ b/doc/src/reset_timestep.rst @@ -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. diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index 663e61b308..7008f6f6bf 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -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 ` 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 diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index 1306535f0b..8c9a082c28 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -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 """""""""""""""" diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index a1ae2516d8..1fa84a40f4 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -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 """""""""""""""" diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 4b2b875e56..bb549cadf1 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -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 ` 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 diff --git a/doc/src/third_order.rst b/doc/src/third_order.rst index 464ce82cf2..3356bd007f 100644 --- a/doc/src/third_order.rst +++ b/doc/src/third_order.rst @@ -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 diff --git a/doc/src/write_coeff.rst b/doc/src/write_coeff.rst index d7c82cbeb6..67e0c1e48b 100644 --- a/doc/src/write_coeff.rst +++ b/doc/src/write_coeff.rst @@ -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 diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index 3d7b7cf607..31f4bb64ac 100644 --- a/doc/src/write_data.rst +++ b/doc/src/write_data.rst @@ -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 """"""""""" diff --git a/doc/src/write_dump.rst b/doc/src/write_dump.rst index ae0975cf11..54a55db6c6 100644 --- a/doc/src/write_dump.rst +++ b/doc/src/write_dump.rst @@ -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 diff --git a/doc/src/write_restart.rst b/doc/src/write_restart.rst index 503b585cc3..cade19c0dc 100644 --- a/doc/src/write_restart.rst +++ b/doc/src/write_restart.rst @@ -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