fix up some escaped '*' characters in "code-block" sections that do not need to be escaped

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Axel Kohlmeyer 2020-03-24 11:35:21 -04:00
parent 98bfbbd576
commit 0060473cee
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10 changed files with 29 additions and 25 deletions

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@ -32,7 +32,7 @@ Examples
bond_coeff * 2.0 0.25 0.7564 bond_coeff * 2.0 0.25 0.7564
bond_style oxrna2/fene bond_style oxrna2/fene
bond_coeff \* 2.0 0.25 0.76107 bond_coeff * 2.0 0.25 0.76107
Description Description
""""""""""" """""""""""

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@ -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 1st 3 to be Cd, and the 4th to be Te, you would use the following
pair_coeff command: 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 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 The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd

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@ -60,18 +60,18 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
pair_style lj/class2 10.0 pair_style lj/class2 10.0
pair_coeff \* \* 100.0 2.5 pair_coeff * * 100.0 2.5
pair_coeff 1 2\* 100.0 2.5 9.0 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
pair_style lj/class2/coul/cut 10.0 8.0 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
pair_coeff 1 1 100.0 3.5 9.0 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
pair_style lj/class2/coul/long 10.0 8.0 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 pair_coeff 1 1 100.0 3.5 9.0
Description Description

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@ -19,11 +19,11 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
pair_coeff 1 2 1.0 1.0 2.5 pair_coeff 1 2 1.0 1.0 2.5
pair_coeff 2 \* 1.0 1.0 pair_coeff 2 * 1.0 1.0
pair_coeff 3\* 1\*2 1.0 1.0 2.5 pair_coeff 3* 1*2 1.0 1.0 2.5
pair_coeff \* \* 1.0 1.0 pair_coeff * * 1.0 1.0
pair_coeff \* \* nialhjea 1 1 2 pair_coeff * * nialhjea 1 1 2
pair_coeff \* 3 morse.table ENTRY1 pair_coeff * 3 morse.table ENTRY1
pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid) pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
Description Description
@ -55,7 +55,7 @@ pairs, then overwrite the coeffs for just the I,J = 2,3 pair:
.. code-block:: LAMMPS .. 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 pair_coeff 2 3 2.0 1.0 1.12
A line in a data file that specifies pair coefficients uses the exact A line in a data file that specifies pair coefficients uses the exact

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@ -31,7 +31,7 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
pair_style cosine/squared 3.0 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 2.0
pair_coeff 1 3 1.0 1.3 wca pair_coeff 1 3 1.0 1.3 wca
pair_coeff 1 3 1.0 1.3 2.0 wca pair_coeff 1 3 1.0 1.3 2.0 wca

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@ -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 treated with this potential, you would use the following pair_coeff
command: 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 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 The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element

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@ -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 other potentials. An example of a pair_coeff command for use with the
*hybrid* pair style is: *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 Three-body non-bonded harmonic files in the *potentials* directory of
the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that

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@ -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 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: 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 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 types. The first three Si arguments map LAMMPS atom types 1,2,3 to the

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@ -113,8 +113,8 @@ which the parameters epsilon and sigma are both 1.0:
class LJCutMelt(LAMMPSPairPotential): class LJCutMelt(LAMMPSPairPotential):
def __init__(self): def __init__(self):
super(LJCutMelt,self).__init__() super(LJCutMelt,self).__init__()
# set coeffs: 48\*eps\*sig\*\*12, 24\*eps\*sig\*\*6, # set coeffs: 48*eps*sig**12, 24*eps*sig**6,
# 4\*eps\*sig\*\*12, 4\*eps\*sig\*\*6 # 4*eps*sig**12, 4*eps*sig**6
self.units = 'lj' self.units = 'lj'
self.coeff = {'lj' : {'lj' : (48.0,24.0,4.0,4.0)}} 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): 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]]
r2inv = 1.0/rsq r2inv = 1.0/rsq
r6inv = r2inv\*r2inv\*r2inv r6inv = r2inv*r2inv*r2inv
lj1 = coeff[0] lj1 = coeff[0]
lj2 = coeff[1] lj2 = coeff[1]
return (r6inv \* (lj1\*r6inv - lj2))\*r2inv return (r6inv * (lj1*r6inv - lj2))*r2inv
def compute_energy(self,rsq,itype,jtype): def compute_energy(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r2inv = 1.0/rsq r2inv = 1.0/rsq
r6inv = r2inv\*r2inv\*r2inv r6inv = r2inv*r2inv*r2inv
lj3 = coeff[2] lj3 = coeff[2]
lj4 = coeff[3] lj4 = coeff[3]
return (r6inv \* (lj3\*r6inv - lj4)) return (r6inv * (lj3*r6inv - lj4))
.. note:: .. note::

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@ -18,7 +18,7 @@ Examples
.. code-block:: LAMMPS .. 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
Description Description
""""""""""" """""""""""