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small documentation fixes to fix typos and formatting issues

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This commit is contained in:
Axel Kohlmeyer
2017-05-21 11:13:47 -04:00
parent 2225fce94e
commit 97d3c843c4
9 changed files with 38 additions and 34 deletions
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40
doc/src/compute_saed.txt
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@ -111,26 +111,26 @@ Coefficients parameterized by "(Fox)"_#Fox are assigned for each
atom type designating the chemical symbol and charge of each atom
type. Valid chemical symbols for compute saed are:
H: He: Li: Be: B:
C: N: O: F: Ne:
Na: Mg: Al: Si: P:
S: Cl: Ar: K: Ca:
Sc: Ti: V: Cr: Mn:
Fe: Co: Ni: Cu: Zn:
Ga: Ge: As: Se: Br:
Kr: Rb: Sr: Y: Zr:
Nb: Mo: Tc: Ru: Rh:
Pd: Ag: Cd: In: Sn:
Sb: Te: I: Xe: Cs:
Ba: La: Ce: Pr: Nd:
Pm: Sm: Eu: Gd: Tb:
Dy: Ho: Er: Tm: Yb:
Lu: Hf: Ta: W: Re:
Os: Ir: Pt: Au: Hg:
Tl: Pb: Bi: Po: At:
Rn: Fr: Ra: Ac: Th:
Pa: U: Np: Pu: Am:
Cm: Bk: Cf:tb(c=5,s=:)
H: He: Li: Be: B:
C: N: O: F: Ne:
Na: Mg: Al: Si: P:
S: Cl: Ar: K: Ca:
Sc: Ti: V: Cr: Mn:
Fe: Co: Ni: Cu: Zn:
Ga: Ge: As: Se: Br:
Kr: Rb: Sr: Y: Zr:
Nb: Mo: Tc: Ru: Rh:
Pd: Ag: Cd: In: Sn:
Sb: Te: I: Xe: Cs:
Ba: La: Ce: Pr: Nd:
Pm: Sm: Eu: Gd: Tb:
Dy: Ho: Er: Tm: Yb:
Lu: Hf: Ta: W: Re:
Os: Ir: Pt: Au: Hg:
Tl: Pb: Bi: Po: At:
Rn: Fr: Ra: Ac: Th:
Pa: U: Np: Pu: Am:
Cm: Bk: Cf:tb(c=5,s=:)
If the {echo} keyword is specified, compute saed will provide extra

1
doc/src/dihedral_spherical.txt
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@ -18,6 +18,7 @@ dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0
dihedral_coeff 1 3 69.3 1 93.9 1 1 90 0 1 90 0 &
49.1 0 0.00 0 1 74.4 1 0 0.00 0 &
25.2 0 0.00 0 0 0.00 0 1 48.1 1
:pre
[Description:]

2
doc/src/fix_gle.txt
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@ -68,7 +68,7 @@ matrix that gives canonical sampling for a given A is computed automatically.
However, the GLE framework also allow for non-equilibrium sampling, that
can be used for instance to model inexpensively zero-point energy
effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq}
keyword followed by the name of the file that contains the static covariance
keyword followed by the name of the file that contains the static covariance
matrix for the non-equilibrium dynamics. Please note, that the covariance
matrix is expected to be given in [temperature units].

4
doc/src/fix_langevin_drude.txt
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@ -67,11 +67,11 @@ The Langevin forces are computed as
\(F_r'\) is a random force proportional to
\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tcom\}\, m'\}
\{\mathrm dt\, \mathtt\{damp\_com\} \}
\} \). :b
\} \).
\(f_r'\) is a random force proportional to
\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tdrude\}\, m'\}
\{\mathrm dt\, \mathtt\{damp\_drude\} \}
\} \). :b
\} \).
Then the real forces acting on the particles are computed from the inverse
transform:
\begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\}

6
doc/src/package.txt
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@ -574,9 +574,9 @@ is used. If it is not used, you must invoke the package intel
command in your input script or or via the "-pk intel" "command-line
switch"_Section_start.html#start_7.
For the KOKKOS package, the option defaults neigh = full, neigh/qeq
= full, newton = off, binsize = 0.0, and comm = device. These settings
are made automatically by the required "-k on" "command-line
For the KOKKOS package, the option defaults neigh = full,
neigh/qeq = full, newton = off, binsize = 0.0, and comm = device.
These settings are made automatically by the required "-k on" "command-line
switch"_Section_start.html#start_7. You can change them bu using the
package kokkos command in your input script or via the "-pk kokkos"
"command-line switch"_Section_start.html#start_7.

9
doc/src/pair_python.txt
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@ -74,7 +74,7 @@ placeholders for atom types that will be used with other potentials.
The python potential file has to start with the following code:
from __future__ import print_function
#
class LAMMPSPairPotential(object):
def __init__(self):
self.pmap=dict()
@ -163,9 +163,10 @@ pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj :pre
Note that it is strongly recommended to try to [delete] the potential
table file before generating it. Since the {pair_write} command will
always append to a table file, which pair style table will use the
first match. Thus when changing the potential function in the python
class, the table pair style will still read the old variant.
always [append] to a table file, while pair style table will use the
[first match]. Thus when changing the potential function in the python
class, the table pair style will still read the old variant unless the
table file is first deleted.
After switching the pair style to {table}, the potential tables need
to be assigned to the LAMMPS atom types like this:

7
doc/src/pair_snap.txt
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@ -10,7 +10,8 @@ pair_style snap command :h3
[Syntax:]
pair_style snap :pre
pair_style snap
:pre
[Examples:]
@ -19,11 +20,11 @@ pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
[Description:]
Style {snap} computes interactions
Pair style {snap} computes interactions
using the spectral neighbor analysis potential (SNAP)
"(Thompson)"_#Thompson20142. Like the GAP framework of Bartok et al.
"(Bartok2010)"_#Bartok20102, "(Bartok2013)"_#Bartok2013
it uses bispectrum components
which uses bispectrum components
to characterize the local neighborhood of each atom
in a very general way. The mathematical definition of the
bispectrum calculation used by SNAP is identical

2
doc/src/pair_zero.txt
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@ -14,7 +14,7 @@ pair_style zero cutoff {nocoeff} :pre
zero = style name of this pair style
cutoff = global cutoff (distance units)
nocoeff = ignore all pair_coeff parameters (optional) :l
nocoeff = ignore all pair_coeff parameters (optional) :ul
[Examples:]

1
doc/src/tutorial_pylammps.txt
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@ -10,6 +10,7 @@ PyLammps Tutorial :h1
<!-- RST
.. contents::
END_RST -->
Overview :h2