diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 0cd27650b5..3dd079500f 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -18,7 +18,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all temp compute newtemp flow temp/partial 1 1 0 @@ -129,7 +129,7 @@ Three computes are always created, named "thermo\_temp", "thermo\_press", and "thermo\_pe", as if these commands had been invoked in the input script: -.. parsed-literal:: +.. code-block:: LAMMPS compute thermo_temp all temp compute thermo_press all pressure thermo_temp diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index d3db52e437..ab0c1fe59b 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all erotate/asphere diff --git a/doc/src/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst index 42d2715e7e..f07751eff5 100644 --- a/doc/src/compute_erotate_rigid.rst +++ b/doc/src/compute_erotate_rigid.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all erotate/rigid myRigid diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index fadaf61fcc..17656ef0be 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all erotate/sphere diff --git a/doc/src/compute_erotate_sphere_atom.rst b/doc/src/compute_erotate_sphere_atom.rst index 8523ed7df6..f7450be9c2 100644 --- a/doc/src/compute_erotate_sphere_atom.rst +++ b/doc/src/compute_erotate_sphere_atom.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all erotate/sphere/atom diff --git a/doc/src/compute_event_displace.rst b/doc/src/compute_event_displace.rst index 4ef3a63ac5..679e455465 100644 --- a/doc/src/compute_event_displace.rst +++ b/doc/src/compute_event_displace.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all event/displace 0.5 diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index b95fff8e80..a7d64caa98 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -43,9 +43,9 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS - compute 1 all fep 298 pair lj/cut epsilon 1 \* v_delta pair lj/cut sigma 1 \* v_delta volume yes + compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes compute 1 all fep 300 atom charge 2 v_delta Description diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst index a6bb0373e9..ae6ca73a36 100644 --- a/doc/src/compute_global_atom.rst +++ b/doc/src/compute_global_atom.rst @@ -36,10 +36,10 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS - compute 1 all global/atom c_chunk c_com[1\] c_com[2\] c_com[3\] - compute 1 all global/atom c_chunk c_com[\*\] + compute 1 all global/atom c_chunk c_com[1] c_com[2] c_com[3] + compute 1 all global/atom c_chunk c_com[*] Description """"""""""" @@ -80,16 +80,16 @@ of each atom from the center-of-mass of the molecule it is in, and dump those values to a dump file. In this case, each molecule is a chunk. -.. parsed-literal:: +.. code-block:: LAMMPS compute cc1 all chunk/atom molecule compute myChunk all com/chunk cc1 compute prop all property/atom xu yu zu - compute glob all global/atom c_cc1 c_myChunk[\*] + compute glob all global/atom c_cc1 c_myChunk[*] variable dx atom c_prop[1]-c_glob[1] variable dy atom c_prop[2]-c_glob[2] variable dz atom c_prop[3]-c_glob[3] - variable dist atom sqrt(v_dx\*v_dx+v_dy\*v_dy+v_dz\*v_dz) + variable dist atom sqrt(v_dx*v_dx+v_dy*v_dy+v_dz*v_dz) dump 1 all custom 100 tmp.dump id xu yu zu c_glob[1] c_glob[2] c_glob[3] & v_dx v_dy v_dz v_dist dump_modify 1 sort id @@ -114,12 +114,12 @@ had been listed one by one. E.g. these 2 compute global/atom commands are equivalent, since the :doc:`compute com/chunk ` command creates a global array with 3 columns: -.. parsed-literal:: +.. code-block:: LAMMPS compute cc1 all chunk/atom molecule compute com all com/chunk cc1 compute 1 all global/atom c_cc1 c_com[1] c_com[2] c_com[3] - compute 1 all global/atom c_cc1 c_com[\*] + compute 1 all global/atom c_cc1 c_com[*] ---------- diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index 5df21103b6..f0b65c797a 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -26,7 +26,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 lower group/group upper compute 1 lower group/group upper kspace yes diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index 55e55adc40..42ca1e53e5 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 molecule gyration diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst index 5de32198e9..2ba632ded1 100644 --- a/doc/src/compute_gyration_chunk.rst +++ b/doc/src/compute_gyration_chunk.rst @@ -23,7 +23,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 molecule gyration/chunk molchunk compute 2 molecule gyration/chunk molchunk tensor @@ -86,7 +86,7 @@ The simplest way to output the results of the compute gyration/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: -.. parsed-literal:: +.. code-block:: LAMMPS compute cc1 all chunk/atom molecule compute myChunk all gyration/chunk cc1 diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index 5aeb599a0f..81fc628a21 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 molecule gyration/shape pe diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index 69fc0d5c31..50dd4822ce 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 molecule gyration/shape/chunk pe diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index aef61a7707..1b28c08ae5 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -19,7 +19,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute myFlux all heat/flux myKE myPE myStress @@ -161,7 +161,7 @@ Related commands ---------- -.. parsed-literal:: +.. code-block:: LAMMPS # Sample LAMMPS input script for thermal conductivity of solid Ar @@ -171,7 +171,7 @@ Related commands variable dt equal 4.0 variable p equal 200 # correlation length variable s equal 10 # sample interval - variable d equal $p\*$s # dump interval + variable d equal $p*$s # dump interval # convert from LAMMPS real units to SI @@ -179,7 +179,7 @@ Related commands variable kCal2J equal 4186.0/6.02214e23 variable A2m equal 1.0e-10 variable fs2s equal 1.0e-15 - variable convert equal ${kCal2J}\*${kCal2J}/${fs2s}/${A2m} + variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m} # setup problem @@ -191,7 +191,7 @@ Related commands create_atoms 1 box mass 1 39.948 pair_style lj/cut 13.0 - pair_coeff \* \* 0.2381 3.405 + pair_coeff * * 0.2381 3.405 timestep ${dt} thermo $d @@ -216,10 +216,10 @@ Related commands variable Jz equal c_flux[3]/vol fix JJ all ave/correlate $s $p $d & c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running - variable scale equal ${convert}/${kB}/$T/$T/$V\*$s\*${dt} - variable k11 equal trap(f_JJ[3])\*${scale} - variable k22 equal trap(f_JJ[4])\*${scale} - variable k33 equal trap(f_JJ[5])\*${scale} + variable scale equal ${convert}/${kB}/$T/$T/$V*$s*${dt} + variable k11 equal trap(f_JJ[3])*${scale} + variable k22 equal trap(f_JJ[4])*${scale} + variable k33 equal trap(f_JJ[5])*${scale} thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 run 100000 variable k equal (v_k11+v_k22+v_k33)/3.0 diff --git a/doc/src/compute_hexorder_atom.rst b/doc/src/compute_hexorder_atom.rst index a7edca0153..31f7dbe662 100644 --- a/doc/src/compute_hexorder_atom.rst +++ b/doc/src/compute_hexorder_atom.rst @@ -24,7 +24,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all hexorder/atom compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2 diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index 3971f328a3..20807ec0db 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -25,7 +25,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 2 all hma 1 u compute 2 all hma 1 anharmonic u p 0.9 @@ -113,7 +113,7 @@ round-off error when computing :math:`C_V`. To address this, the *anharmonic* keyword can be passed and/or the output format can be specified with more digits. -.. parsed-literal:: +.. code-block:: LAMMPS thermo_modify format float '%22.15e' @@ -136,7 +136,7 @@ should be avoided as its extra forces interfere with the HMA implementation. The following example illustrates the placement of this command in the input script: -.. parsed-literal:: +.. code-block:: LAMMPS min_style cg minimize 1e-35 1e-15 50000 500000 diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst index 62671a1cf8..bb4b150c6a 100644 --- a/doc/src/compute_improper.rst +++ b/doc/src/compute_improper.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all improper diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst index fbf4c50bd6..7a14daf161 100644 --- a/doc/src/compute_improper_local.rst +++ b/doc/src/compute_improper_local.rst @@ -22,7 +22,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all improper/local chi @@ -54,7 +54,7 @@ command in a consistent way. Here is an example of how to do this: -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all property/local itype iatom1 iatom2 iatom3 iatom4 compute 2 all improper/local chi diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index 2e0ecb7f7a..f667929807 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 fluid inertia/chunk molchunk @@ -61,11 +61,11 @@ The simplest way to output the results of the compute inertia/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: -.. parsed-literal:: +.. code-block:: LAMMPS compute cc1 all chunk/atom molecule compute myChunk all inertia/chunk cc1 - fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector + fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector **Output info:** diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst index 0e50c968b3..d98d39247c 100644 --- a/doc/src/compute_ke.rst +++ b/doc/src/compute_ke.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all ke diff --git a/doc/src/compute_ke_atom.rst b/doc/src/compute_ke_atom.rst index 81d17e6208..42294dbca1 100644 --- a/doc/src/compute_ke_atom.rst +++ b/doc/src/compute_ke_atom.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all ke/atom diff --git a/doc/src/compute_ke_eff.rst b/doc/src/compute_ke_eff.rst index 5721472622..dddb5273f8 100644 --- a/doc/src/compute_ke_eff.rst +++ b/doc/src/compute_ke_eff.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all ke/eff @@ -56,7 +56,7 @@ freedom. :doc:`thermo_modify ` command, as shown in the following example: -.. parsed-literal:: +.. code-block:: LAMMPS compute effTemp all temp/eff thermo_style custom step etotal pe ke temp press diff --git a/doc/src/compute_ke_rigid.rst b/doc/src/compute_ke_rigid.rst index 2a11b6bb44..fd4706de19 100644 --- a/doc/src/compute_ke_rigid.rst +++ b/doc/src/compute_ke_rigid.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all ke/rigid myRigid diff --git a/doc/src/compute_meso_e_atom.rst b/doc/src/compute_meso_e_atom.rst index e61af26d2b..ad8e46cafb 100644 --- a/doc/src/compute_meso_e_atom.rst +++ b/doc/src/compute_meso_e_atom.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all meso/e/atom diff --git a/doc/src/compute_meso_rho_atom.rst b/doc/src/compute_meso_rho_atom.rst index 0461a5d403..d4611c5cb7 100644 --- a/doc/src/compute_meso_rho_atom.rst +++ b/doc/src/compute_meso_rho_atom.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all meso/rho/atom diff --git a/doc/src/compute_meso_t_atom.rst b/doc/src/compute_meso_t_atom.rst index 60d9f44b82..9f5385dd48 100644 --- a/doc/src/compute_meso_t_atom.rst +++ b/doc/src/compute_meso_t_atom.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all meso/t/atom diff --git a/doc/src/compute_momentum.rst b/doc/src/compute_momentum.rst index 13449d56f8..af968efb59 100644 --- a/doc/src/compute_momentum.rst +++ b/doc/src/compute_momentum.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all momentum diff --git a/doc/src/compute_msd.rst b/doc/src/compute_msd.rst index 982962ed05..05a414a0d5 100644 --- a/doc/src/compute_msd.rst +++ b/doc/src/compute_msd.rst @@ -23,7 +23,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all msd compute 1 upper msd com yes average yes diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index 248e602616..9a9a926030 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all msd/chunk molchunk @@ -99,11 +99,11 @@ The simplest way to output the results of the compute msd/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: -.. parsed-literal:: +.. code-block:: LAMMPS compute cc1 all chunk/atom molecule compute myChunk all msd/chunk cc1 - fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector + fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector **Output info:** diff --git a/doc/src/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst index 2a2cce5abf..2dfc00fb68 100644 --- a/doc/src/compute_msd_nongauss.rst +++ b/doc/src/compute_msd_nongauss.rst @@ -22,7 +22,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all msd/nongauss compute 1 upper msd/nongauss com yes diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index e07e64cb05..73895b585c 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 fluid omega/chunk molchunk @@ -62,11 +62,11 @@ The simplest way to output the results of the compute omega/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: -.. parsed-literal:: +.. code-block:: LAMMPS compute cc1 all chunk/atom molecule compute myChunk all omega/chunk cc1 - fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector + fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector **Output info:** diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index 278d281d32..c651804f0a 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -27,7 +27,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all orientorder/atom compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 diff --git a/doc/src/compute_pair.rst b/doc/src/compute_pair.rst index 5b0e3d613d..40c758ebf0 100644 --- a/doc/src/compute_pair.rst +++ b/doc/src/compute_pair.rst @@ -19,7 +19,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all pair gauss compute 1 all pair lj/cut/coul/cut ecoul diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index 403b03bf5a..31030cd97e 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -33,7 +33,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all pair/local eng compute 1 all pair/local dist eng force @@ -115,7 +115,7 @@ command in a consistent way. Here is an example of how to do this: -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all property/local patom1 patom2 compute 2 all pair/local dist eng force diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst index afadb7a8c0..2efaf78b01 100644 --- a/doc/src/compute_pe.rst +++ b/doc/src/compute_pe.rst @@ -18,7 +18,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all pe compute molPE all pe bond angle dihedral improper @@ -57,7 +57,7 @@ potential energy. A compute of this style with the ID of "thermo\_pe" is created when LAMMPS starts up, as if this command were in the input script: -.. parsed-literal:: +.. code-block:: LAMMPS compute thermo_pe all pe diff --git a/doc/src/compute_pe_atom.rst b/doc/src/compute_pe_atom.rst index 979960b50a..b616cecd89 100644 --- a/doc/src/compute_pe_atom.rst +++ b/doc/src/compute_pe_atom.rst @@ -18,7 +18,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all pe/atom compute 1 all pe/atom pair @@ -72,7 +72,7 @@ As an example of per-atom potential energy compared to total potential energy, these lines in an input script should yield the same result in the last 2 columns of thermo output: -.. parsed-literal:: +.. code-block:: LAMMPS compute peratom all pe/atom compute pe all reduce sum c_peratom diff --git a/doc/src/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst index f561d39045..9d8dea535d 100644 --- a/doc/src/compute_plasticity_atom.rst +++ b/doc/src/compute_plasticity_atom.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all plasticity/atom diff --git a/doc/src/compute_pressure_cylinder.rst b/doc/src/compute_pressure_cylinder.rst index 7407053f01..b3e7accb37 100644 --- a/doc/src/compute_pressure_cylinder.rst +++ b/doc/src/compute_pressure_cylinder.rst @@ -20,7 +20,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25 diff --git a/doc/src/compute_pressure_uef.rst b/doc/src/compute_pressure_uef.rst index 02545dfa17..07302ba46d 100644 --- a/doc/src/compute_pressure_uef.rst +++ b/doc/src/compute_pressure_uef.rst @@ -19,7 +19,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all pressure/uef my_temp_uef compute 2 all pressure/uef my_temp_uef virial diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index e3cffa2c35..23dd8806d9 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -96,7 +96,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all property/atom xs vx fx mux compute 2 all property/atom type diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index 995a2b5dbf..ed49833a48 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -24,7 +24,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all property/chunk count compute 1 all property/chunk ID coord1 @@ -81,12 +81,12 @@ The simplest way to output the results of the compute property/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: -.. parsed-literal:: +.. code-block:: LAMMPS compute cc1 all chunk/atom molecule compute myChunk1 all property/chunk cc1 count compute myChunk2 all com/chunk cc1 - fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[\*] file tmp.out mode vector + fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector **Output info:** diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index 210bc943f9..4e29bb7fc0 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -48,7 +48,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all property/local btype batom1 batom2 compute 1 all property/local atype aatom2 diff --git a/doc/src/compute_ptm_atom.rst b/doc/src/compute_ptm_atom.rst index a1bf48e40a..3fac1d8810 100644 --- a/doc/src/compute_ptm_atom.rst +++ b/doc/src/compute_ptm_atom.rst @@ -19,7 +19,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all ptm/atom default 0.1 all compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15 all diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index b5c30adbb2..c977e2ac12 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -26,13 +26,13 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all rdf 100 compute 1 all rdf 100 1 1 - compute 1 all rdf 100 \* 3 cutoff 5.0 + compute 1 all rdf 100 * 3 cutoff 5.0 compute 1 fluid rdf 500 1 1 1 2 2 1 2 2 - compute 1 fluid rdf 500 1\*3 2 5 \*10 cutoff 3.5 + compute 1 fluid rdf 500 1*3 2 5 *10 cutoff 3.5 Description """"""""""" @@ -147,10 +147,10 @@ The simplest way to output the results of the compute rdf calculation to a file is to use the :doc:`fix ave/time ` command, for example: -.. parsed-literal:: +.. code-block:: LAMMPS compute myRDF all rdf 50 - fix 1 all ave/time 100 1 100 c_myRDF[\*] file tmp.rdf mode vector + fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp.rdf mode vector **Output info:** diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index a91e276199..3772a788e0 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -47,7 +47,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all reduce sum c_force compute 1 all reduce/region subbox sum c_force @@ -108,10 +108,10 @@ had been listed one by one. E.g. these 2 compute reduce commands are equivalent, since the :doc:`compute stress/atom ` command creates a per-atom array with 6 columns: -.. parsed-literal:: +.. code-block:: LAMMPS compute myPress all stress/atom NULL - compute 2 all reduce min c_myPress[\*] + compute 2 all reduce min c_myPress[*] compute 2 all reduce min c_myPress[1] c_myPress[2] c_myPress[3] & c_myPress[4] c_myPress[5] c_myPress[6] @@ -166,7 +166,7 @@ stored index is used to select the Nth element of the *vec1* vector. Thus, for example, if you wish to use this compute to find the bond with maximum stretch, you can do it as follows: -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all property/local batom1 batom2 compute 2 all bond/local dist diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index 8b792fa2f0..3404613875 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -28,7 +28,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all reduce/chunk/atom mychunk min c_cluster @@ -87,10 +87,10 @@ had been listed one by one. E.g. these 2 compute reduce/chunk commands are equivalent, since the :doc:`compute property/chunk ` command creates a per-atom array with 3 columns: -.. parsed-literal:: +.. code-block:: LAMMPS compute prop all property/atom vx vy vz - compute 10 all reduce/chunk mychunk max c_prop[\*] + compute 10 all reduce/chunk mychunk max c_prop[*] compute 10 all reduce/chunk mychunk max c_prop[1] c_prop[2] c_prop[3] ---------- @@ -111,7 +111,7 @@ attraction induced by the hydrophobicity. The output of the chunk/reduce command will be a cluster ID per chunk (molecule). Molecules with the same cluster ID are in the same micelle. -.. parsed-literal:: +.. code-block:: LAMMPS group phobic type 4 # specific to in.micelle model compute cluster phobic cluster/atom 2.0 @@ -120,7 +120,7 @@ Molecules with the same cluster ID are in the same micelle. This per-chunk info could be output in at least two ways: -.. parsed-literal:: +.. code-block:: LAMMPS fix 10 all ave/time 1000 1 1000 c_reduce file tmp.phobic mode vector @@ -138,7 +138,7 @@ The result from compute chunk/spread/atom can be used to define a new set of chunks, where all the atoms in all the molecules in the same micelle are assigned to the same chunk, i.e. one chunk per micelle. -.. parsed-literal:: +.. code-block:: LAMMPS compute micelle all chunk/atom c_spread compress yes @@ -148,7 +148,7 @@ doc page. E.g. count the number of atoms in each micelle, calculate its center or mass, shape (moments of inertia), radius of gyration, etc. -.. parsed-literal:: +.. code-block:: LAMMPS compute prop all property/chunk micelle count fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector diff --git a/doc/src/compute_rigid_local.rst b/doc/src/compute_rigid_local.rst index 8702a006f3..4fc0f3c2dd 100644 --- a/doc/src/compute_rigid_local.rst +++ b/doc/src/compute_rigid_local.rst @@ -42,7 +42,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all rigid/local myRigid mol x y z @@ -87,7 +87,7 @@ vector or array from one timestep to the next. Here is an example of how to use this compute to dump rigid body info to a file: -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all rigid/local myRigid mol x y z fx fy fz dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7] diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index 9d2f6cf4aa..ac596962c0 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -36,7 +36,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst index c7ccb35be8..6667dfd880 100644 --- a/doc/src/compute_slice.rst +++ b/doc/src/compute_slice.rst @@ -28,7 +28,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all slice 1 100 10 c_msdmol[4] compute 1 all slice 301 400 1 c_msdmol[4] v_myVec diff --git a/doc/src/compute_smd_contact_radius.rst b/doc/src/compute_smd_contact_radius.rst index 698c4ec4ac..4f9e36db7d 100644 --- a/doc/src/compute_smd_contact_radius.rst +++ b/doc/src/compute_smd_contact_radius.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/contact/radius diff --git a/doc/src/compute_smd_damage.rst b/doc/src/compute_smd_damage.rst index 4d33cec4e7..eb39c4e452 100644 --- a/doc/src/compute_smd_damage.rst +++ b/doc/src/compute_smd_damage.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/damage diff --git a/doc/src/compute_smd_hourglass_error.rst b/doc/src/compute_smd_hourglass_error.rst index 98ca7b2596..612d4d0aba 100644 --- a/doc/src/compute_smd_hourglass_error.rst +++ b/doc/src/compute_smd_hourglass_error.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/hourglass/error diff --git a/doc/src/compute_smd_internal_energy.rst b/doc/src/compute_smd_internal_energy.rst index ec36346079..7613d5bb3e 100644 --- a/doc/src/compute_smd_internal_energy.rst +++ b/doc/src/compute_smd_internal_energy.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/internal/energy diff --git a/doc/src/compute_smd_plastic_strain.rst b/doc/src/compute_smd_plastic_strain.rst index c443162459..772169310f 100644 --- a/doc/src/compute_smd_plastic_strain.rst +++ b/doc/src/compute_smd_plastic_strain.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/plastic/strain diff --git a/doc/src/compute_smd_plastic_strain_rate.rst b/doc/src/compute_smd_plastic_strain_rate.rst index a572f91b9e..7b0480a211 100644 --- a/doc/src/compute_smd_plastic_strain_rate.rst +++ b/doc/src/compute_smd_plastic_strain_rate.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/plastic/strain/rate diff --git a/doc/src/compute_smd_rho.rst b/doc/src/compute_smd_rho.rst index 7ef76160c5..50c74b8c26 100644 --- a/doc/src/compute_smd_rho.rst +++ b/doc/src/compute_smd_rho.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/rho diff --git a/doc/src/compute_smd_tlsph_defgrad.rst b/doc/src/compute_smd_tlsph_defgrad.rst index 68c819e190..c599b82709 100644 --- a/doc/src/compute_smd_tlsph_defgrad.rst +++ b/doc/src/compute_smd_tlsph_defgrad.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/tlsph/defgrad diff --git a/doc/src/compute_smd_tlsph_dt.rst b/doc/src/compute_smd_tlsph_dt.rst index 7a95da63fa..7835f0642d 100644 --- a/doc/src/compute_smd_tlsph_dt.rst +++ b/doc/src/compute_smd_tlsph_dt.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/tlsph/dt diff --git a/doc/src/compute_smd_tlsph_num_neighs.rst b/doc/src/compute_smd_tlsph_num_neighs.rst index 5ebe3d3812..202f1640d6 100644 --- a/doc/src/compute_smd_tlsph_num_neighs.rst +++ b/doc/src/compute_smd_tlsph_num_neighs.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/tlsph/num/neighs diff --git a/doc/src/compute_smd_tlsph_shape.rst b/doc/src/compute_smd_tlsph_shape.rst index d968b5e636..f4ed10a232 100644 --- a/doc/src/compute_smd_tlsph_shape.rst +++ b/doc/src/compute_smd_tlsph_shape.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/tlsph/shape diff --git a/doc/src/compute_smd_tlsph_strain.rst b/doc/src/compute_smd_tlsph_strain.rst index 9d615e451a..24c5937462 100644 --- a/doc/src/compute_smd_tlsph_strain.rst +++ b/doc/src/compute_smd_tlsph_strain.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/tlsph/strain diff --git a/doc/src/compute_smd_tlsph_strain_rate.rst b/doc/src/compute_smd_tlsph_strain_rate.rst index c6f8d4f4fa..0eb68432c1 100644 --- a/doc/src/compute_smd_tlsph_strain_rate.rst +++ b/doc/src/compute_smd_tlsph_strain_rate.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/tlsph/strain/rate diff --git a/doc/src/compute_smd_tlsph_stress.rst b/doc/src/compute_smd_tlsph_stress.rst index 589ef5785e..10d01ea9c0 100644 --- a/doc/src/compute_smd_tlsph_stress.rst +++ b/doc/src/compute_smd_tlsph_stress.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/tlsph/stress diff --git a/doc/src/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst index 3c9abfaa86..f510ca4bb0 100644 --- a/doc/src/compute_smd_triangle_vertices.rst +++ b/doc/src/compute_smd_triangle_vertices.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/triangle/mesh/vertices diff --git a/doc/src/compute_smd_vol.rst b/doc/src/compute_smd_vol.rst index ba40ea48ef..abcc6fca22 100644 --- a/doc/src/compute_smd_vol.rst +++ b/doc/src/compute_smd_vol.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/vol diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 8fc2aa9a7a..c6ed12d5a8 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -48,7 +48,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0 compute db all sna/atom 1.4 0.95 6 2.0 1.0 @@ -181,7 +181,7 @@ The stress calculation uses a compute called *snap\_press* that is automatically created behind the scenes, according to the following command: -.. parsed-literal:: +.. code-block:: LAMMPS compute snap_press all pressure NULL virial diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index 7301337111..48e8b9c69c 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -21,7 +21,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 mobile stress/atom NULL compute 1 mobile stress/atom myRamp @@ -195,11 +195,11 @@ is the total pressure of the system. These lines in an input script for a 3d system should yield that result. I.e. the last 2 columns of thermo output will be the same: -.. parsed-literal:: +.. code-block:: LAMMPS compute peratom all stress/atom NULL compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] - variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3\*vol) + variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) thermo_style custom step temp etotal press v_press .. note:: diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index b311590298..5988e7791c 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -29,7 +29,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 lower force/tally upper compute 1 left pe/tally right diff --git a/doc/src/compute_tdpd_cc_atom.rst b/doc/src/compute_tdpd_cc_atom.rst index 98840c41b8..00eee60f62 100644 --- a/doc/src/compute_tdpd_cc_atom.rst +++ b/doc/src/compute_tdpd_cc_atom.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all tdpd/cc/atom 2 diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index 871ffba2f9..5616917572 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -19,7 +19,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all temp compute myTemp mobile temp @@ -57,7 +57,7 @@ needed, the subtracted degrees-of-freedom can be altered using the A compute of this style with the ID of "thermo\_temp" is created when LAMMPS starts up, as if this command were in the input script: -.. parsed-literal:: +.. code-block:: LAMMPS compute thermo_temp all temp diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index 215d310e9b..46fadc2ff5 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -26,7 +26,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all temp/asphere compute myTemp mobile temp/asphere bias tempCOM diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index 4f8198fb1c..75477eff36 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -26,7 +26,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all temp/body compute myTemp mobile temp/body bias tempCOM diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index 1c6e260377..89bef3a327 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -40,7 +40,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 fluid temp/chunk molchunk compute 1 fluid temp/chunk molchunk temp internal @@ -149,7 +149,7 @@ calculating the temperature; fix ave/chunk does not. The simplest way to output the per-chunk results of the compute temp/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: -.. parsed-literal:: +.. code-block:: LAMMPS compute cc1 all chunk/atom molecule compute myChunk all temp/chunk cc1 temp diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index 017de2b6fc..b21db2ac27 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all temp/com compute myTemp mobile temp/com diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 253baa26e7..f3c82c2b1a 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -18,7 +18,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute oxygen_c-s all temp/cs O_core O_shell compute core_shells all temp/cs cores shells diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index cd5f5e56a0..d73670485b 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute myTemp all temp/deform diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index a220893919..b5d6659573 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute myTemp all temp/deform/eff diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index aa5086caa1..bd49cb377f 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute TDRUDE all temp/drude diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index b1e5a368bd..84a2028920 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all temp/eff compute myTemp mobile temp/eff @@ -51,7 +51,7 @@ densities two to five times the density of liquid H2 ranges from :doc:`thermo_modify ` command, as shown in the following example: -.. parsed-literal:: +.. code-block:: LAMMPS compute effTemp all temp/eff thermo_style custom step etotal pe ke temp press diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index c74ed4a02f..e2fd36f35a 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute newT flow temp/partial 1 1 0 diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index b75d944c74..53870fa300 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -36,7 +36,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute myTemp flow temp/profile 1 1 1 x 10 compute myTemp flow temp/profile 1 1 1 x 10 out bin diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 0f321520e6..4ac22bdfef 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -26,7 +26,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index 6c6ca29c82..e207d75d9f 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute mine flow temp/region boundary diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index 8bffb2577d..a05cc5597c 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute mine flow temp/region/eff boundary diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index d30211228e..7d3ed4d63d 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute Tbead bead temp/rotate diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index 323a01e7da..f0cd4c3ba0 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -26,7 +26,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all temp/sphere compute myTemp mobile temp/sphere bias tempCOM diff --git a/doc/src/compute_temp_uef.rst b/doc/src/compute_temp_uef.rst index 368774ae4a..2ce288a66f 100644 --- a/doc/src/compute_temp_uef.rst +++ b/doc/src/compute_temp_uef.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all temp/uef compute 2 sel temp/uef diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index 9cd78503ef..8fe294a2db 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -33,10 +33,10 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks - compute 1 all ti lj/cut 1\*3 v_lj v_dlj coul/long \* v_c v_dc kspace \* v_ks v_dks + compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks Description """"""""""" diff --git a/doc/src/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst index 5ed4b2cb7d..258ce03aa0 100644 --- a/doc/src/compute_torque_chunk.rst +++ b/doc/src/compute_torque_chunk.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 fluid torque/chunk molchunk @@ -61,11 +61,11 @@ The simplest way to output the results of the compute torque/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: -.. parsed-literal:: +.. code-block:: LAMMPS compute cc1 all chunk/atom molecule compute myChunk all torque/chunk cc1 - fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector + fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector **Output info:** diff --git a/doc/src/compute_vacf.rst b/doc/src/compute_vacf.rst index 57dd7996ac..ce2757c115 100644 --- a/doc/src/compute_vacf.rst +++ b/doc/src/compute_vacf.rst @@ -16,7 +16,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all vacf compute 1 upper vacf @@ -41,11 +41,11 @@ The integral of the VACF versus time is proportional to the diffusion coefficient of the diffusing atoms. This can be computed in the following manner, using the :doc:`variable trap() ` function: -.. 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 .. note:: diff --git a/doc/src/compute_vcm_chunk.rst b/doc/src/compute_vcm_chunk.rst index 5ce42e2a2e..415038d7c2 100644 --- a/doc/src/compute_vcm_chunk.rst +++ b/doc/src/compute_vcm_chunk.rst @@ -17,7 +17,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 fluid vcm/chunk molchunk @@ -51,11 +51,11 @@ The simplest way to output the results of the compute vcm/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: -.. parsed-literal:: +.. code-block:: LAMMPS compute cc1 all chunk/atom molecule compute myChunk all vcm/chunk cc1 - fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector + fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector **Output info:** diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 1d72e739ff..88b65ee8b2 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -37,7 +37,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all voronoi/atom compute 2 precipitate voronoi/atom surface matrix @@ -86,9 +86,9 @@ If the *radius* keyword is specified with an atom style variable as the argument, a poly-disperse Voronoi tessellation is performed. Examples for radius variables are -.. parsed-literal:: +.. code-block:: LAMMPS - variable r1 atom (type==1)\*0.1+(type==2)\*0.4 + variable r1 atom (type==1)*0.1+(type==2)*0.4 compute radius all property/atom radius variable r2 atom c_radius @@ -139,7 +139,7 @@ overview of LAMMPS output options. More specifically, the array can be accessed by a :doc:`dump local ` command to write a file containing all the Voronoi neighbors in a system: -.. parsed-literal:: +.. code-block:: LAMMPS compute 6 all voronoi/atom neighbors yes dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3] diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index 80f5e9cb2c..27da6fd0d7 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -34,7 +34,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual diff --git a/doc/src/dielectric.rst b/doc/src/dielectric.rst index 1b057302e2..bd4f4dff56 100644 --- a/doc/src/dielectric.rst +++ b/doc/src/dielectric.rst @@ -15,7 +15,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dielectric 2.0 @@ -42,6 +42,6 @@ Related commands Default """"""" -.. parsed-literal:: +.. code-block:: LAMMPS dielectric 1.0 diff --git a/doc/src/dimension.rst b/doc/src/dimension.rst index cb7ca1c437..be711815a6 100644 --- a/doc/src/dimension.rst +++ b/doc/src/dimension.rst @@ -15,7 +15,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dimension 2 @@ -52,6 +52,6 @@ Related commands Default """"""" -.. parsed-literal:: +.. code-block:: LAMMPS dimension 3 diff --git a/doc/src/dump_adios.rst b/doc/src/dump_adios.rst index 89e1c9836d..ba09b9e6ed 100644 --- a/doc/src/dump_adios.rst +++ b/doc/src/dump_adios.rst @@ -26,7 +26,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dump adios1 all atom/adios 100 atoms.bp dump 4a all custom/adios 100 dump_adios.bp id v_p x y z @@ -49,7 +49,7 @@ It is possible to use these dump styles with the must not be set at all. The write\_dump command can be used to create a new file at each individual dump. -.. parsed-literal:: +.. code-block:: LAMMPS dump 4 all atom/adios 100 dump.bp write_dump all atom/adios singledump.bp diff --git a/doc/src/dump_cfg_uef.rst b/doc/src/dump_cfg_uef.rst index acef1b0bbd..fdefad62ff 100644 --- a/doc/src/dump_cfg_uef.rst +++ b/doc/src/dump_cfg_uef.rst @@ -22,7 +22,7 @@ Syntax Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dump 1 all cfg/uef 10 dump.\*.cfg mass type xs ys zs dump 2 all cfg/uef 100 dump.\*.cfg mass type xs ys zs id c_stress diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst index 53a9b5cf78..6b6b4cf88e 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -44,7 +44,7 @@ specified by this option directly following the element declaration: Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dump h5md1 all h5md 100 dump_h5md.h5 position image dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10 @@ -91,7 +91,7 @@ Typically, the *species* data is fixed. The following two commands store the position data every 100 timesteps, with the image data, and store once the species data in the same file. -.. parsed-literal:: +.. code-block:: LAMMPS dump h5md1 all h5md 100 dump.h5 position image write_dump all h5md dump.h5 file_from h5md1 species