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

doc/src/fix_spring.rst

@@ -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

doc/src/fix_spring_chunk.rst

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

doc/src/fix_spring_rg.rst

@@ -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

doc/src/fix_spring_self.rst

@@ -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

doc/src/fix_srd.rst

@@ -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

doc/src/fix_store_force.rst

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

doc/src/fix_store_state.rst

@@ -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

doc/src/fix_temp_berendsen.rst

@@ -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
 

doc/src/fix_temp_csvr.rst

@@ -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
 

doc/src/fix_temp_rescale.rst

@@ -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
 

doc/src/fix_temp_rescale_eff.rst

@@ -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
 

doc/src/fix_tfmc.rst

@@ -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

doc/src/fix_thermal_conductivity.rst

@@ -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

doc/src/fix_ti_spring.rst

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

doc/src/fix_tmd.rst

@@ -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

doc/src/fix_ttm.rst

@@ -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

doc/src/fix_tune_kspace.rst

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

doc/src/fix_vector.rst

@@ -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

doc/src/fix_viscosity.rst

@@ -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

doc/src/fix_viscous.rst

@@ -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

doc/src/fix_wall.rst

@@ -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
+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
+*hi* over the course of a run.  The *vdisplace(c0,velocity)* function does
-something similar using the equation position = c0 + velocity\*delta,
+something similar using the equation *position = c0 + velocity\*delta*\ ,
-where delta is the elapsed time.
+where *delta* is the elapsed time.
 
-The swiggle(c0,A,period) function causes the wall position to
+The *swiggle(c0,A,period)* function causes the wall position to
-oscillate sinusoidally according to this equation, where omega = 2 PI
+oscillate sinusoidally according to this equation, where *omega = 2 PI
-/ period:
+/ 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:

doc/src/fix_wall_body_polygon.rst

@@ -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
 """""""""""

doc/src/fix_wall_body_polyhedron.rst

@@ -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
 """""""""""

doc/src/fix_wall_ees.rst

@@ -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

doc/src/fix_wall_gran.rst

@@ -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

doc/src/fix_wall_gran_region.rst

@@ -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

doc/src/fix_wall_piston.rst

@@ -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

doc/src/fix_wall_reflect.rst

@@ -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
+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
+*hi* over the course of a run.  The *vdisplace(c0,velocity)* function does
-something similar using the equation position = c0 + velocity\*delta,
+something similar using the equation *position = c0 + velocity\*delta*\ ,
-where delta is the elapsed time.
+where *delta* is the elapsed time.
 
-The swiggle(c0,A,period) function causes the wall position to
+The *swiggle(c0,A,period)* function causes the wall position to
-oscillate sinusoidally according to this equation, where omega = 2 PI
+oscillate sinusoidally according to this equation, where *omega = 2 PI
-/ period:
+/ 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:

doc/src/fix_wall_reflect_stochastic.rst

@@ -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

doc/src/fix_wall_region.rst

@@ -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

doc/src/fix_wall_srd.rst

@@ -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
+The *ramp(lo,hi)* function adjusts the wall position linearly from *lo*
-hi over the course of a run.  The displace(c0,velocity) function does
+to *hi* over the course of a run.  The *vdisplace(c0,velocity)* function
-something similar using the equation position = c0 + velocity\*delta,
+does something similar using the equation *position = c0 +
-where delta is the elapsed time.
+velocity\*delta*, where *delta* is the elapsed time.
 
-The swiggle(c0,A,period) function causes the wall position to
+The *swiggle(c0,A,period)* function causes the wall position to
-oscillate sinusoidally according to this equation, where omega = 2 PI
+oscillate sinusoidally according to this equation, where *omega = 2 PI
-/ period:
+/ 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: