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replace parsed-literal with code-block where appropriate. typeset keywords in cursive

This commit is contained in:
Axel Kohlmeyer 2020-03-10 16:54:04 -04:00
parent 2d329a8b76
commit 1f4725d652
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GPG Key ID: D9B44E93BF0C375A
31 changed files with 71 additions and 68 deletions
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2
doc/src/fix_spring.rst
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@ -29,7 +29,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix pull ligand spring tether 50.0 0.0 0.0 0.0 0.0
fix pull ligand spring tether 50.0 0.0 0.0 0.0 5.0

2
doc/src/fix_spring_chunk.rst
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@ -19,7 +19,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix restrain all spring/chunk 100 chunkID comID

2
doc/src/fix_spring_rg.rst
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@ -22,7 +22,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 protein spring/rg 5.0 10.0
fix 2 micelle spring/rg 5.0 NULL

2
doc/src/fix_spring_self.rst
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@ -18,7 +18,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix tether boundary-atoms spring/self 10.0
fix zrest move spring/self 10.0 z

2
doc/src/fix_srd.rst
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@ -50,7 +50,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 srd srd 10 big 1.0 0.25 482984
fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5

2
doc/src/fix_store_force.rst
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@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all store/force

2
doc/src/fix_store_state.rst
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@ -64,7 +64,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all store/state 0 x y z
fix 1 all store/state 0 xu yu zu com yes

4
doc/src/fix_temp_berendsen.rst
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@ -23,7 +23,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all temp/berendsen 300.0 300.0 100.0
@ -84,7 +84,7 @@ This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp

6
doc/src/fix_temp_csvr.rst
View File

@ -12,7 +12,6 @@ Syntax
.. parsed-literal::
fix ID group-ID temp/csvr Tstart Tstop Tdamp seed
fix ID group-ID temp/csld Tstart Tstop Tdamp seed
* ID, group-ID are documented in :doc:`fix <fix>` command
@ -29,10 +28,9 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all temp/csvr 300.0 300.0 100.0 54324
fix 1 all temp/csld 100.0 300.0 10.0 123321
Description
@ -94,7 +92,7 @@ These fixes compute a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp

4
doc/src/fix_temp_rescale.rst
View File

@ -25,7 +25,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
@ -91,7 +91,7 @@ This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if one of this command had
been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp

2
doc/src/fix_temp_rescale_eff.rst
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@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0

2
doc/src/fix_tfmc.rst
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@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all tfmc 0.1 1000.0 159345
fix 1 all tfmc 0.05 600.0 658943 com 1 1 0

4
doc/src/fix_thermal_conductivity.rst
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@ -25,7 +25,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all thermal/conductivity 100 z 20
fix 1 all thermal/conductivity 50 z 20 swap 2
@ -63,7 +63,7 @@ this induces a temperature gradient in the system which can be
measured using commands such as the following, which writes the
temperature profile (assuming z = edim) to the file tmp.profile:
.. parsed-literal::
.. code-block:: LAMMPS
compute ke all ke/atom
variable temp atom c_ke/1.5

2
doc/src/fix_ti_spring.rst
View File

@ -25,7 +25,7 @@ Syntax
**Example:**
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all ti/spring 50.0 2000 1000 function 2

2
doc/src/fix_tmd.rst
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@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve
fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file

2
doc/src/fix_ttm.rst
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@ -49,7 +49,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out
fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out

2
doc/src/fix_tune_kspace.rst
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@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 2 all tune/kspace 100

6
doc/src/fix_vector.rst
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@ -28,7 +28,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all vector 100 c_myTemp
fix 1 all vector 5 c_myTemp v_integral
@ -48,11 +48,11 @@ time-integrated using the :doc:`variable trap() <variable>` function.
For example the velocity auto-correlation function (VACF) can be
time-integrated, to yield a diffusion coefficient, as follows:
.. parsed-literal::
.. code-block:: LAMMPS
compute 2 all vacf
fix 5 all vector 1 c_2[4]
variable diff equal dt\*trap(f_5)
variable diff equal dt*trap(f_5)
thermo_style custom step v_diff
The group specified with this command is ignored. However, note that

4
doc/src/fix_viscosity.rst
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@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all viscosity 100 x z 20
fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5
@ -62,7 +62,7 @@ directions. Over time, this induces a shear velocity profile in the
system which can be measured using commands such as the following,
which writes the profile to the file tmp.profile:
.. parsed-literal::
.. code-block:: LAMMPS
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
fix f1 all ave/chunk 100 10 1000 layers vx file tmp.profile

2
doc/src/fix_viscous.rst
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@ -25,7 +25,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 flow viscous 0.1
fix 1 damp viscous 0.5 scale 3 2.5

20
doc/src/fix_wall.rst
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@ -82,7 +82,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
@ -285,7 +285,7 @@ in a time-dependent fashion using equal-style
:doc:`variables <variable>`. The wall interaction parameters (epsilon,
sigma) could be varied with additional variable definitions.
.. parsed-literal::
.. code-block:: LAMMPS
variable ramp equal ramp(0,10)
fix 1 all wall xlo v_ramp 1.0 1.0 2.5
@ -299,20 +299,20 @@ sigma) could be varied with additional variable definitions.
variable wiggle equal cwiggle(0.0,5.0,3.0)
fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
The ramp(lo,hi) function adjusts the wall position linearly from lo to
hi over the course of a run. The vdisplace(c0,velocity) function does
something similar using the equation position = c0 + velocity\*delta,
where delta is the elapsed time.
The *ramp(lo,hi)* function adjusts the wall position linearly from *lo* to
*hi* over the course of a run. The *vdisplace(c0,velocity)* function does
something similar using the equation *position = c0 + velocity\*delta*\ ,
where *delta* is the elapsed time.
The swiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, where omega = 2 PI
/ period:
The *swiggle(c0,A,period)* function causes the wall position to
oscillate sinusoidally according to this equation, where *omega = 2 PI
/ period*\ :
.. parsed-literal::
position = c0 + A sin(omega\*delta)
The cwiggle(c0,A,period) function causes the wall position to
The *cwiggle(c0,A,period)* function causes the wall position to
oscillate sinusoidally according to this equation, which will have an
initial wall velocity of 0.0, and thus may impose a gentler
perturbation on the particles:

4
doc/src/fix_wall_body_polygon.rst
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@ -38,7 +38,9 @@ Syntax
Examples
""""""""
fix 1 all wall/body/polygon 1000.0 20.0 5.0 xplane -10.0 10.0
.. code-block:: LAMMPS
fix 1 all wall/body/polygon 1000.0 20.0 5.0 xplane -10.0 10.0
Description
"""""""""""

4
doc/src/fix_wall_body_polyhedron.rst
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@ -38,7 +38,9 @@ Syntax
Examples
""""""""
fix 1 all wall/body/polyhedron 1000.0 20.0 5.0 xplane -10.0 10.0
.. code-block:: LAMMPS
fix 1 all wall/body/polyhedron 1000.0 20.0 5.0 xplane -10.0 10.0
Description
"""""""""""

2
doc/src/fix_wall_ees.rst
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@ -42,7 +42,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix wallhi all wall/ees xlo -1.0 1.0 1.0 2.5 units box
fix wallhi all wall/ees xhi EDGE 1.0 1.0 2.5

5
doc/src/fix_wall_gran.rst
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@ -60,7 +60,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all wall/gran hooke 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
@ -111,7 +111,8 @@ material.
.. note::
As discussed on the doc page for :doc:`pair_style gran/\* <pair_gran>`, versions of LAMMPS before 9Jan09 used a
As discussed on the doc page for :doc:`pair_style gran/\* <pair_gran>`,
versions of LAMMPS before 9Jan09 used a
different equation for Hertzian interactions. This means Hertizian
wall/particle interactions have also changed. They now include a
sqrt(radius) term which was not present before. Also the previous

2
doc/src/fix_wall_gran_region.rst
View File

@ -40,7 +40,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone
fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox

2
doc/src/fix_wall_piston.rst
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@ -35,7 +35,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix xwalls all wall/piston zlo
fix walls all wall/piston zlo pos 1.0 vel 10.0 units box

20
doc/src/fix_wall_reflect.rst
View File

@ -37,7 +37,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix xwalls all wall/reflect xlo EDGE xhi EDGE
fix walls all wall/reflect xlo 0.0 ylo 10.0 units box
@ -101,7 +101,7 @@ Here are examples of variable definitions that move the wall position
in a time-dependent fashion using equal-style
:doc:`variables <variable>`.
.. parsed-literal::
.. code-block:: LAMMPS
variable ramp equal ramp(0,10)
fix 1 all wall/reflect xlo v_ramp
@ -115,20 +115,20 @@ in a time-dependent fashion using equal-style
variable wiggle equal cwiggle(0.0,5.0,3.0)
fix 1 all wall/reflect xlo v_wiggle
The ramp(lo,hi) function adjusts the wall position linearly from lo to
hi over the course of a run. The vdisplace(c0,velocity) function does
something similar using the equation position = c0 + velocity\*delta,
where delta is the elapsed time.
The *ramp(lo,hi)* function adjusts the wall position linearly from *lo* to
*hi* over the course of a run. The *vdisplace(c0,velocity)* function does
something similar using the equation *position = c0 + velocity\*delta*\ ,
where *delta* is the elapsed time.
The swiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, where omega = 2 PI
/ period:
The *swiggle(c0,A,period)* function causes the wall position to
oscillate sinusoidally according to this equation, where *omega = 2 PI
/ period*\ :
.. parsed-literal::
position = c0 + A sin(omega\*delta)
The cwiggle(c0,A,period) function causes the wall position to
The *cwiggle(c0,A,period)* function causes the wall position to
oscillate sinusoidally according to this equation, which will have an
initial wall velocity of 0.0, and thus may impose a gentler
perturbation on the particles:

2
doc/src/fix_wall_reflect_stochastic.rst
View File

@ -42,7 +42,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix zwalls all wall/reflect/stochastic diffusive 23424 zlo EDGE 300 0.1 0.1 0 zhi EDGE 200 0.1 0.1 0
fix ywalls all wall/reflect/stochastic maxwell 345533 ylo 5.0 300 0.1 0.0 0.0 0.8 yhi 10.0 300 0.1 0.0 0.0 0.8

2
doc/src/fix_wall_region.rst
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@ -34,7 +34,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix wall all wall/region mySphere lj93 1.0 1.0 2.5
fix wall all wall/region mySphere harmonic 1.0 0.0 2.5

20
doc/src/fix_wall_srd.rst
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@ -38,7 +38,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix xwalls all wall/srd xlo EDGE xhi EDGE
fix walls all wall/srd xlo 0.0 ylo 10.0 units box
@ -139,7 +139,7 @@ Here are examples of variable definitions that move the wall position
in a time-dependent fashion using equal-style
:doc:`variables <variable>`.
.. parsed-literal::
.. code-block:: LAMMPS
variable ramp equal ramp(0,10)
fix 1 all wall/srd xlo v_ramp
@ -153,20 +153,20 @@ in a time-dependent fashion using equal-style
variable wiggle equal cwiggle(0.0,5.0,3.0)
fix 1 all wall/srd xlo v_wiggle
The ramp(lo,hi) function adjusts the wall position linearly from lo to
hi over the course of a run. The displace(c0,velocity) function does
something similar using the equation position = c0 + velocity\*delta,
where delta is the elapsed time.
The *ramp(lo,hi)* function adjusts the wall position linearly from *lo*
to *hi* over the course of a run. The *vdisplace(c0,velocity)* function
does something similar using the equation *position = c0 +
velocity\*delta*, where *delta* is the elapsed time.
The swiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, where omega = 2 PI
/ period:
The *swiggle(c0,A,period)* function causes the wall position to
oscillate sinusoidally according to this equation, where *omega = 2 PI
/ period*\ :
.. parsed-literal::
position = c0 + A sin(omega\*delta)
The cwiggle(c0,A,period) function causes the wall position to
The *cwiggle(c0,A,period)* function causes the wall position to
oscillate sinusoidally according to this equation, which will have an
initial wall velocity of 0.0, and thus may impose a gentler
perturbation on the particles: