diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 8e69b298bf..71e5105436 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -32,7 +32,7 @@ Examples bond_coeff * 2.0 0.25 0.7564 bond_style oxrna2/fene - bond_coeff \* 2.0 0.25 0.76107 + bond_coeff * 2.0 0.25 0.76107 Description """"""""""" diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index ce7b69f41f..5cd045931a 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -132,9 +132,9 @@ and Te. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Cd, and the 4th to be Te, you would use the following pair_coeff command: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* CdTe Cd Cd Cd Te + pair_coeff * * CdTe Cd Cd Cd Te The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types. The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index d1c673ab97..8131799181 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -60,18 +60,18 @@ Examples .. code-block:: LAMMPS pair_style lj/class2 10.0 - pair_coeff \* \* 100.0 2.5 - pair_coeff 1 2\* 100.0 2.5 9.0 + pair_coeff * * 100.0 2.5 + pair_coeff 1 2* 100.0 2.5 9.0 pair_style lj/class2/coul/cut 10.0 pair_style lj/class2/coul/cut 10.0 8.0 - pair_coeff \* \* 100.0 3.0 + pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 pair_coeff 1 1 100.0 3.5 9.0 9.0 pair_style lj/class2/coul/long 10.0 pair_style lj/class2/coul/long 10.0 8.0 - pair_coeff \* \* 100.0 3.0 + pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 Description diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index 26910c1746..1886ce1118 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -19,11 +19,11 @@ Examples .. code-block:: LAMMPS pair_coeff 1 2 1.0 1.0 2.5 - pair_coeff 2 \* 1.0 1.0 - pair_coeff 3\* 1\*2 1.0 1.0 2.5 - pair_coeff \* \* 1.0 1.0 - pair_coeff \* \* nialhjea 1 1 2 - pair_coeff \* 3 morse.table ENTRY1 + pair_coeff 2 * 1.0 1.0 + pair_coeff 3* 1*2 1.0 1.0 2.5 + pair_coeff * * 1.0 1.0 + pair_coeff * * nialhjea 1 1 2 + pair_coeff * 3 morse.table ENTRY1 pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid) Description @@ -55,7 +55,7 @@ pairs, then overwrite the coeffs for just the I,J = 2,3 pair: .. code-block:: LAMMPS - pair_coeff \* \* 1.0 1.0 2.5 + pair_coeff * * 1.0 1.0 2.5 pair_coeff 2 3 2.0 1.0 1.12 A line in a data file that specifies pair coefficients uses the exact diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index 4f19ddd1e4..b7fa29bbd5 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -31,7 +31,7 @@ Examples .. code-block:: LAMMPS pair_style cosine/squared 3.0 - pair_coeff \* \* 1.0 1.3 + pair_coeff * * 1.0 1.3 pair_coeff 1 3 1.0 1.3 2.0 pair_coeff 1 3 1.0 1.3 wca pair_coeff 1 3 1.0 1.3 2.0 wca diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index ebb51795c2..0cf4c57975 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -75,7 +75,9 @@ If your LAMMPS simulation has 3 atoms types and they are all to be treated with this potential, you would use the following pair_coeff command: -pair_coeff \* \* Ti.meam.sw.spline Ti Ti Ti +.. code-block:: LAMMPS + + pair_coeff * * Ti.meam.sw.spline Ti Ti Ti The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types. The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element diff --git a/doc/src/pair_nb3b_harmonic.rst b/doc/src/pair_nb3b_harmonic.rst index c4f3f3c3e8..9d63df65d5 100644 --- a/doc/src/pair_nb3b_harmonic.rst +++ b/doc/src/pair_nb3b_harmonic.rst @@ -64,7 +64,9 @@ NULL values are placeholders for atom types that will be used with other potentials. An example of a pair_coeff command for use with the *hybrid* pair style is: -pair_coeff \* \* nb3b/harmonic MgOH.nb3b.harmonic Mg O H +.. code-block:: LAMMPS + + pair_coeff * * nb3b/harmonic MgOH.nb3b.harmonic Mg O H Three-body non-bonded harmonic files in the *potentials* directory of the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index e06e9e7855..c0db3f10a4 100644 --- a/doc/src/pair_polymorphic.rst +++ b/doc/src/pair_polymorphic.rst @@ -180,9 +180,9 @@ functions for Si-C tersoff potential. 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: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* SiC_tersoff.poly Si Si Si C + pair_coeff * * SiC_tersoff.poly 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 diff --git a/doc/src/pair_python.rst b/doc/src/pair_python.rst index fa76d4c16c..e654a6025f 100644 --- a/doc/src/pair_python.rst +++ b/doc/src/pair_python.rst @@ -113,8 +113,8 @@ which the parameters epsilon and sigma are both 1.0: class LJCutMelt(LAMMPSPairPotential): def __init__(self): super(LJCutMelt,self).__init__() - # set coeffs: 48\*eps\*sig\*\*12, 24\*eps\*sig\*\*6, - # 4\*eps\*sig\*\*12, 4\*eps\*sig\*\*6 + # set coeffs: 48*eps*sig**12, 24*eps*sig**6, + # 4*eps*sig**12, 4*eps*sig**6 self.units = 'lj' self.coeff = {'lj' : {'lj' : (48.0,24.0,4.0,4.0)}} @@ -137,18 +137,18 @@ the *LJCutMelt* example, here are the two functions: def compute_force(self,rsq,itype,jtype): coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] r2inv = 1.0/rsq - r6inv = r2inv\*r2inv\*r2inv + r6inv = r2inv*r2inv*r2inv lj1 = coeff[0] lj2 = coeff[1] - return (r6inv \* (lj1\*r6inv - lj2))\*r2inv + return (r6inv * (lj1*r6inv - lj2))*r2inv def compute_energy(self,rsq,itype,jtype): coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] r2inv = 1.0/rsq - r6inv = r2inv\*r2inv\*r2inv + r6inv = r2inv*r2inv*r2inv lj3 = coeff[2] lj4 = coeff[3] - return (r6inv \* (lj3\*r6inv - lj4)) + return (r6inv * (lj3*r6inv - lj4)) .. note:: diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index a220299b07..e4d6b81b8a 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -18,7 +18,7 @@ Examples .. code-block:: LAMMPS 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 Description """""""""""