diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst index 21792be179..db8608ea99 100644 --- a/doc/src/fix_spring.rst +++ b/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 diff --git a/doc/src/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst index b6e1410905..01def4cabc 100644 --- a/doc/src/fix_spring_chunk.rst +++ b/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 diff --git a/doc/src/fix_spring_rg.rst b/doc/src/fix_spring_rg.rst index 8f6edec46e..1d552c4d33 100644 --- a/doc/src/fix_spring_rg.rst +++ b/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 diff --git a/doc/src/fix_spring_self.rst b/doc/src/fix_spring_self.rst index 63a9893549..8f8d2fb97e 100644 --- a/doc/src/fix_spring_self.rst +++ b/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 diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst index 827dc684e2..96ddcb6329 100644 --- a/doc/src/fix_srd.rst +++ b/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 diff --git a/doc/src/fix_store_force.rst b/doc/src/fix_store_force.rst index 32f4540e3d..e99d5db964 100644 --- a/doc/src/fix_store_force.rst +++ b/doc/src/fix_store_force.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS fix 1 all store/force diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index f6d96841d3..2e2049bbdd 100644 --- a/doc/src/fix_store_state.rst +++ b/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 diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst index 400ba2d399..33eee84bce 100644 --- a/doc/src/fix_temp_berendsen.rst +++ b/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 diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 488eccfb69..7a528bcfa2 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/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 ` 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 diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index 23d6d9f7fc..d6a433ae42 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/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 diff --git a/doc/src/fix_temp_rescale_eff.rst b/doc/src/fix_temp_rescale_eff.rst index 339c35d631..679913ab2d 100644 --- a/doc/src/fix_temp_rescale_eff.rst +++ b/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 diff --git a/doc/src/fix_tfmc.rst b/doc/src/fix_tfmc.rst index 853c094288..952850be59 100644 --- a/doc/src/fix_tfmc.rst +++ b/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 diff --git a/doc/src/fix_thermal_conductivity.rst b/doc/src/fix_thermal_conductivity.rst index d6a360ec10..133a091b8a 100644 --- a/doc/src/fix_thermal_conductivity.rst +++ b/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 diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst index 0a5a137e1b..0c764895c5 100644 --- a/doc/src/fix_ti_spring.rst +++ b/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 diff --git a/doc/src/fix_tmd.rst b/doc/src/fix_tmd.rst index 81b7013962..4e9b410490 100644 --- a/doc/src/fix_tmd.rst +++ b/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 diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 8d497534fa..e70243231e 100644 --- a/doc/src/fix_ttm.rst +++ b/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 diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst index b9a25778b9..1f201799cb 100644 --- a/doc/src/fix_tune_kspace.rst +++ b/doc/src/fix_tune_kspace.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS fix 2 all tune/kspace 100 diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index 7d16d6c1d0..4a6d415a22 100644 --- a/doc/src/fix_vector.rst +++ b/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() ` 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 diff --git a/doc/src/fix_viscosity.rst b/doc/src/fix_viscosity.rst index 919aea0e1d..b3c1b92bd3 100644 --- a/doc/src/fix_viscosity.rst +++ b/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 diff --git a/doc/src/fix_viscous.rst b/doc/src/fix_viscous.rst index ec8e05aa91..5a6d966822 100644 --- a/doc/src/fix_viscous.rst +++ b/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 diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index 93bf208919..acd97d83c6 100644 --- a/doc/src/fix_wall.rst +++ b/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 `. 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: diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index 7bffa0d46f..0371710604 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/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 """"""""""" diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index ca6fdf4be5..a36d8a5fca 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/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 """"""""""" diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index e915b9d890..79f96765f8 100644 --- a/doc/src/fix_wall_ees.rst +++ b/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 diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index ea8d32686a..98cc251fcc 100644 --- a/doc/src/fix_wall_gran.rst +++ b/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/\* `, versions of LAMMPS before 9Jan09 used a + As discussed on the doc page for :doc:`pair_style 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 diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index 00ad42b639..9d9950e514 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/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 diff --git a/doc/src/fix_wall_piston.rst b/doc/src/fix_wall_piston.rst index 20f7774c0a..fe12bbc13c 100644 --- a/doc/src/fix_wall_piston.rst +++ b/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 diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 89b7dd21df..76591bebf0 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/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 `. -.. 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: diff --git a/doc/src/fix_wall_reflect_stochastic.rst b/doc/src/fix_wall_reflect_stochastic.rst index 96380d7bf1..ddeebfbe38 100644 --- a/doc/src/fix_wall_reflect_stochastic.rst +++ b/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 diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index c56c604a15..9581966b61 100644 --- a/doc/src/fix_wall_region.rst +++ b/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 diff --git a/doc/src/fix_wall_srd.rst b/doc/src/fix_wall_srd.rst index 09434d96ea..fbcdca3035 100644 --- a/doc/src/fix_wall_srd.rst +++ b/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 `. -.. 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: