forked from lijiext/lammps
fix up some escaped '*' characters in "code-block" sections that do not need to be escaped
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@ -32,7 +32,7 @@ Examples
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bond_coeff * 2.0 0.25 0.7564
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bond_style oxrna2/fene
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bond_coeff \* 2.0 0.25 0.76107
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bond_coeff * 2.0 0.25 0.76107
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Description
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"""""""""""
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@ -132,9 +132,9 @@ and Te. If your LAMMPS simulation has 4 atoms types and you want the
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1st 3 to be Cd, and the 4th to be Te, you would use the following
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pair_coeff command:
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.. parsed-literal::
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.. code-block:: LAMMPS
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pair_coeff \* \* CdTe Cd Cd Cd Te
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pair_coeff * * CdTe Cd Cd Cd Te
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The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
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The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd
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@ -60,18 +60,18 @@ Examples
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.. code-block:: LAMMPS
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pair_style lj/class2 10.0
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pair_coeff \* \* 100.0 2.5
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pair_coeff 1 2\* 100.0 2.5 9.0
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pair_coeff * * 100.0 2.5
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pair_coeff 1 2* 100.0 2.5 9.0
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pair_style lj/class2/coul/cut 10.0
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pair_style lj/class2/coul/cut 10.0 8.0
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pair_coeff \* \* 100.0 3.0
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pair_coeff * * 100.0 3.0
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pair_coeff 1 1 100.0 3.5 9.0
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pair_coeff 1 1 100.0 3.5 9.0 9.0
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pair_style lj/class2/coul/long 10.0
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pair_style lj/class2/coul/long 10.0 8.0
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pair_coeff \* \* 100.0 3.0
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pair_coeff * * 100.0 3.0
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pair_coeff 1 1 100.0 3.5 9.0
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Description
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@ -19,11 +19,11 @@ Examples
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.. code-block:: LAMMPS
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pair_coeff 1 2 1.0 1.0 2.5
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pair_coeff 2 \* 1.0 1.0
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pair_coeff 3\* 1\*2 1.0 1.0 2.5
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pair_coeff \* \* 1.0 1.0
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pair_coeff \* \* nialhjea 1 1 2
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pair_coeff \* 3 morse.table ENTRY1
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pair_coeff 2 * 1.0 1.0
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pair_coeff 3* 1*2 1.0 1.0 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff * * nialhjea 1 1 2
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pair_coeff * 3 morse.table ENTRY1
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pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid)
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Description
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@ -55,7 +55,7 @@ pairs, then overwrite the coeffs for just the I,J = 2,3 pair:
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.. code-block:: LAMMPS
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pair_coeff \* \* 1.0 1.0 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_coeff 2 3 2.0 1.0 1.12
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A line in a data file that specifies pair coefficients uses the exact
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@ -31,7 +31,7 @@ Examples
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.. code-block:: LAMMPS
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pair_style cosine/squared 3.0
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pair_coeff \* \* 1.0 1.3
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pair_coeff * * 1.0 1.3
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pair_coeff 1 3 1.0 1.3 2.0
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pair_coeff 1 3 1.0 1.3 wca
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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
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treated with this potential, you would use the following pair_coeff
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command:
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pair_coeff \* \* Ti.meam.sw.spline Ti Ti Ti
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.. code-block:: LAMMPS
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pair_coeff * * Ti.meam.sw.spline Ti Ti Ti
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The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types.
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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
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other potentials. An example of a pair_coeff command for use with the
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*hybrid* pair style is:
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pair_coeff \* \* nb3b/harmonic MgOH.nb3b.harmonic Mg O H
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.. code-block:: LAMMPS
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pair_coeff * * nb3b/harmonic MgOH.nb3b.harmonic Mg O H
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Three-body non-bonded harmonic files in the *potentials* directory of
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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
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atoms types and you want the 1st 3 to be Si, and the 4th to be C, you
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would use the following pair_coeff command:
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.. parsed-literal::
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.. code-block:: LAMMPS
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pair_coeff \* \* SiC_tersoff.poly Si Si Si C
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pair_coeff * * SiC_tersoff.poly Si Si Si C
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The 1st 2 arguments must be \* \* so as to span all LAMMPS atom
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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:
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class LJCutMelt(LAMMPSPairPotential):
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def __init__(self):
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super(LJCutMelt,self).__init__()
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# set coeffs: 48\*eps\*sig\*\*12, 24\*eps\*sig\*\*6,
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# 4\*eps\*sig\*\*12, 4\*eps\*sig\*\*6
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# set coeffs: 48*eps*sig**12, 24*eps*sig**6,
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# 4*eps*sig**12, 4*eps*sig**6
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self.units = 'lj'
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self.coeff = {'lj' : {'lj' : (48.0,24.0,4.0,4.0)}}
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@ -137,18 +137,18 @@ the *LJCutMelt* example, here are the two functions:
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def compute_force(self,rsq,itype,jtype):
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coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
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r2inv = 1.0/rsq
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r6inv = r2inv\*r2inv\*r2inv
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r6inv = r2inv*r2inv*r2inv
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lj1 = coeff[0]
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lj2 = coeff[1]
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return (r6inv \* (lj1\*r6inv - lj2))\*r2inv
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return (r6inv * (lj1*r6inv - lj2))*r2inv
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def compute_energy(self,rsq,itype,jtype):
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coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
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r2inv = 1.0/rsq
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r6inv = r2inv\*r2inv\*r2inv
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r6inv = r2inv*r2inv*r2inv
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lj3 = coeff[2]
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lj4 = coeff[3]
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return (r6inv \* (lj3\*r6inv - lj4))
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return (r6inv * (lj3*r6inv - lj4))
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.. note::
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@ -18,7 +18,7 @@ Examples
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.. code-block:: LAMMPS
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pair_style spin/magelec 4.5
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pair_coeff \* \* magelec 4.5 0.00109 1.0 1.0 1.0
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pair_coeff * * magelec 4.5 0.00109 1.0 1.0 1.0
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Description
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"""""""""""
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