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convert all remaining compute styles to use code-block instead of parsed literal

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This commit is contained in:
Axel Kohlmeyer
2020-03-12 01:56:13 -04:00
parent c6f846b925
commit 23a402ddd3
98 changed files with 165 additions and 165 deletions
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4
doc/src/compute.rst
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@ -18,7 +18,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all temp compute 1 all temp
compute newtemp flow temp/partial 1 1 0 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 "thermo\_press", and "thermo\_pe", as if these commands had been invoked
in the input script: in the input script:
.. parsed-literal:: .. code-block:: LAMMPS
compute thermo_temp all temp compute thermo_temp all temp
compute thermo_press all pressure thermo_temp compute thermo_press all pressure thermo_temp

2
doc/src/compute_erotate_asphere.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all erotate/asphere compute 1 all erotate/asphere

2
doc/src/compute_erotate_rigid.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all erotate/rigid myRigid compute 1 all erotate/rigid myRigid

2
doc/src/compute_erotate_sphere.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all erotate/sphere compute 1 all erotate/sphere

2
doc/src/compute_erotate_sphere_atom.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all erotate/sphere/atom compute 1 all erotate/sphere/atom

2
doc/src/compute_event_displace.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all event/displace 0.5 compute 1 all event/displace 0.5

4
doc/src/compute_fep.rst
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@ -43,9 +43,9 @@ Syntax
Examples 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 compute 1 all fep 300 atom charge 2 v_delta
Description Description

16
doc/src/compute_global_atom.rst
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@ -36,10 +36,10 @@ Syntax
Examples 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[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[*]
Description 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 dump those values to a dump file. In this case, each molecule is a
chunk. chunk.
.. parsed-literal:: .. code-block:: LAMMPS
compute cc1 all chunk/atom molecule compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1 compute myChunk all com/chunk cc1
compute prop all property/atom xu yu zu 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 dx atom c_prop[1]-c_glob[1]
variable dy atom c_prop[2]-c_glob[2] variable dy atom c_prop[2]-c_glob[2]
variable dz atom c_prop[3]-c_glob[3] 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] & 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 v_dx v_dy v_dz v_dist
dump_modify 1 sort id 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 <compute_com_chunk>` are equivalent, since the :doc:`compute com/chunk <compute_com_chunk>`
command creates a global array with 3 columns: command creates a global array with 3 columns:
.. parsed-literal:: .. code-block:: LAMMPS
compute cc1 all chunk/atom molecule compute cc1 all chunk/atom molecule
compute com all com/chunk cc1 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[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[*]
---------- ----------

2
doc/src/compute_group_group.rst
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@ -26,7 +26,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 lower group/group upper compute 1 lower group/group upper
compute 1 lower group/group upper kspace yes compute 1 lower group/group upper kspace yes

2
doc/src/compute_gyration.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 molecule gyration compute 1 molecule gyration

4
doc/src/compute_gyration_chunk.rst
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@ -23,7 +23,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 molecule gyration/chunk molchunk compute 1 molecule gyration/chunk molchunk
compute 2 molecule gyration/chunk molchunk tensor 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 <fix_ave_time>` calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
command, for example: command, for example:
.. parsed-literal:: .. code-block:: LAMMPS
compute cc1 all chunk/atom molecule compute cc1 all chunk/atom molecule
compute myChunk all gyration/chunk cc1 compute myChunk all gyration/chunk cc1

2
doc/src/compute_gyration_shape.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 molecule gyration/shape pe compute 1 molecule gyration/shape pe

2
doc/src/compute_gyration_shape_chunk.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 molecule gyration/shape/chunk pe compute 1 molecule gyration/shape/chunk pe

18
doc/src/compute_heat_flux.rst
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@ -19,7 +19,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute myFlux all heat/flux myKE myPE myStress 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 # Sample LAMMPS input script for thermal conductivity of solid Ar
@ -171,7 +171,7 @@ Related commands
variable dt equal 4.0 variable dt equal 4.0
variable p equal 200 # correlation length variable p equal 200 # correlation length
variable s equal 10 # sample interval 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 # convert from LAMMPS real units to SI
@ -179,7 +179,7 @@ Related commands
variable kCal2J equal 4186.0/6.02214e23 variable kCal2J equal 4186.0/6.02214e23
variable A2m equal 1.0e-10 variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15 variable fs2s equal 1.0e-15
variable convert equal ${kCal2J}\*${kCal2J}/${fs2s}/${A2m} variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
# setup problem # setup problem
@ -191,7 +191,7 @@ Related commands
create_atoms 1 box create_atoms 1 box
mass 1 39.948 mass 1 39.948
pair_style lj/cut 13.0 pair_style lj/cut 13.0
pair_coeff \* \* 0.2381 3.405 pair_coeff * * 0.2381 3.405
timestep ${dt} timestep ${dt}
thermo $d thermo $d
@ -216,10 +216,10 @@ Related commands
variable Jz equal c_flux[3]/vol variable Jz equal c_flux[3]/vol
fix JJ all ave/correlate $s $p $d & fix JJ all ave/correlate $s $p $d &
c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running 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 scale equal ${convert}/${kB}/$T/$T/$V*$s*${dt}
variable k11 equal trap(f_JJ[3])\*${scale} variable k11 equal trap(f_JJ[3])*${scale}
variable k22 equal trap(f_JJ[4])\*${scale} variable k22 equal trap(f_JJ[4])*${scale}
variable k33 equal trap(f_JJ[5])\*${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 thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run 100000 run 100000
variable k equal (v_k11+v_k22+v_k33)/3.0 variable k equal (v_k11+v_k22+v_k33)/3.0

2
doc/src/compute_hexorder_atom.rst
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@ -24,7 +24,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all hexorder/atom compute 1 all hexorder/atom
compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2 compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2

6
doc/src/compute_hma.rst
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@ -25,7 +25,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 2 all hma 1 u compute 2 all hma 1 u
compute 2 all hma 1 anharmonic u p 0.9 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 keyword can be passed and/or the output format can be specified with more
digits. digits.
.. parsed-literal:: .. code-block:: LAMMPS
thermo_modify format float '%22.15e' 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: The following example illustrates the placement of this command in the input script:
.. parsed-literal:: .. code-block:: LAMMPS
min_style cg min_style cg
minimize 1e-35 1e-15 50000 500000 minimize 1e-35 1e-15 50000 500000

2
doc/src/compute_improper.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all improper compute 1 all improper

4
doc/src/compute_improper_local.rst
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@ -22,7 +22,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all improper/local chi compute 1 all improper/local chi
@ -54,7 +54,7 @@ command in a consistent way.
Here is an example of how to do this: 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 1 all property/local itype iatom1 iatom2 iatom3 iatom4
compute 2 all improper/local chi compute 2 all improper/local chi

6
doc/src/compute_inertia_chunk.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 fluid inertia/chunk molchunk 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 <fix_ave_time>` calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
command, for example: command, for example:
.. parsed-literal:: .. code-block:: LAMMPS
compute cc1 all chunk/atom molecule compute cc1 all chunk/atom molecule
compute myChunk all inertia/chunk cc1 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:** **Output info:**

2
doc/src/compute_ke.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all ke compute 1 all ke

2
doc/src/compute_ke_atom.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all ke/atom compute 1 all ke/atom

4
doc/src/compute_ke_eff.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all ke/eff compute 1 all ke/eff
@ -56,7 +56,7 @@ freedom.
:doc:`thermo_modify <thermo_modify>` command, as shown in the following :doc:`thermo_modify <thermo_modify>` command, as shown in the following
example: example:
.. parsed-literal:: .. code-block:: LAMMPS
compute effTemp all temp/eff compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press thermo_style custom step etotal pe ke temp press

2
doc/src/compute_ke_rigid.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all ke/rigid myRigid compute 1 all ke/rigid myRigid

2
doc/src/compute_meso_e_atom.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all meso/e/atom compute 1 all meso/e/atom

2
doc/src/compute_meso_rho_atom.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all meso/rho/atom compute 1 all meso/rho/atom

2
doc/src/compute_meso_t_atom.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all meso/t/atom compute 1 all meso/t/atom

2
doc/src/compute_momentum.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all momentum compute 1 all momentum

2
doc/src/compute_msd.rst
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@ -23,7 +23,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all msd compute 1 all msd
compute 1 upper msd com yes average yes compute 1 upper msd com yes average yes

6
doc/src/compute_msd_chunk.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all msd/chunk molchunk 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 <fix_ave_time>` calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
command, for example: command, for example:
.. parsed-literal:: .. code-block:: LAMMPS
compute cc1 all chunk/atom molecule compute cc1 all chunk/atom molecule
compute myChunk all msd/chunk cc1 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:** **Output info:**

2
doc/src/compute_msd_nongauss.rst
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@ -22,7 +22,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all msd/nongauss compute 1 all msd/nongauss
compute 1 upper msd/nongauss com yes compute 1 upper msd/nongauss com yes

6
doc/src/compute_omega_chunk.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 fluid omega/chunk molchunk 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 <fix_ave_time>` calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
command, for example: command, for example:
.. parsed-literal:: .. code-block:: LAMMPS
compute cc1 all chunk/atom molecule compute cc1 all chunk/atom molecule
compute myChunk all omega/chunk cc1 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:** **Output info:**

2
doc/src/compute_orientorder_atom.rst
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@ -27,7 +27,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all orientorder/atom compute 1 all orientorder/atom
compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5

2
doc/src/compute_pair.rst
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@ -19,7 +19,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all pair gauss compute 1 all pair gauss
compute 1 all pair lj/cut/coul/cut ecoul compute 1 all pair lj/cut/coul/cut ecoul

4
doc/src/compute_pair_local.rst
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@ -33,7 +33,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all pair/local eng compute 1 all pair/local eng
compute 1 all pair/local dist eng force 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: Here is an example of how to do this:
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all property/local patom1 patom2 compute 1 all property/local patom1 patom2
compute 2 all pair/local dist eng force compute 2 all pair/local dist eng force

4
doc/src/compute_pe.rst
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@ -18,7 +18,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all pe compute 1 all pe
compute molPE all pe bond angle dihedral improper 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 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: LAMMPS starts up, as if this command were in the input script:
.. parsed-literal:: .. code-block:: LAMMPS
compute thermo_pe all pe compute thermo_pe all pe

4
doc/src/compute_pe_atom.rst
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@ -18,7 +18,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all pe/atom compute 1 all pe/atom
compute 1 all pe/atom pair 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 energy, these lines in an input script should yield the same result
in the last 2 columns of thermo output: in the last 2 columns of thermo output:
.. parsed-literal:: .. code-block:: LAMMPS
compute peratom all pe/atom compute peratom all pe/atom
compute pe all reduce sum c_peratom compute pe all reduce sum c_peratom

2
doc/src/compute_plasticity_atom.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all plasticity/atom compute 1 all plasticity/atom

2
doc/src/compute_pressure_cylinder.rst
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@ -20,7 +20,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25 compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25

2
doc/src/compute_pressure_uef.rst
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@ -19,7 +19,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all pressure/uef my_temp_uef compute 1 all pressure/uef my_temp_uef
compute 2 all pressure/uef my_temp_uef virial compute 2 all pressure/uef my_temp_uef virial

2
doc/src/compute_property_atom.rst
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@ -96,7 +96,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all property/atom xs vx fx mux compute 1 all property/atom xs vx fx mux
compute 2 all property/atom type compute 2 all property/atom type

6
doc/src/compute_property_chunk.rst
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@ -24,7 +24,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all property/chunk count compute 1 all property/chunk count
compute 1 all property/chunk ID coord1 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 <fix_ave_time>` calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
command, for example: command, for example:
.. parsed-literal:: .. code-block:: LAMMPS
compute cc1 all chunk/atom molecule compute cc1 all chunk/atom molecule
compute myChunk1 all property/chunk cc1 count compute myChunk1 all property/chunk cc1 count
compute myChunk2 all com/chunk cc1 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:** **Output info:**

2
doc/src/compute_property_local.rst
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@ -48,7 +48,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all property/local btype batom1 batom2 compute 1 all property/local btype batom1 batom2
compute 1 all property/local atype aatom2 compute 1 all property/local atype aatom2

2
doc/src/compute_ptm_atom.rst
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@ -19,7 +19,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all ptm/atom default 0.1 all compute 1 all ptm/atom default 0.1 all
compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15 all compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15 all

10
doc/src/compute_rdf.rst
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@ -26,13 +26,13 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all rdf 100 compute 1 all rdf 100
compute 1 all rdf 100 1 1 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 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 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 <fix_ave_time>` command, for to a file is to use the :doc:`fix ave/time <fix_ave_time>` command, for
example: example:
.. parsed-literal:: .. code-block:: LAMMPS
compute myRDF all rdf 50 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:** **Output info:**

8
doc/src/compute_reduce.rst
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@ -47,7 +47,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all reduce sum c_force compute 1 all reduce sum c_force
compute 1 all reduce/region subbox 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 <compute_stress_atom>` equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
command creates a per-atom array with 6 columns: command creates a per-atom array with 6 columns:
.. parsed-literal:: .. code-block:: LAMMPS
compute myPress all stress/atom NULL 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] & compute 2 all reduce min c_myPress[1] c_myPress[2] c_myPress[3] &
c_myPress[4] c_myPress[5] c_myPress[6] 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 Thus, for example, if you wish to use this compute to find the bond
with maximum stretch, you can do it as follows: with maximum stretch, you can do it as follows:
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all property/local batom1 batom2 compute 1 all property/local batom1 batom2
compute 2 all bond/local dist compute 2 all bond/local dist

14
doc/src/compute_reduce_chunk.rst
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@ -28,7 +28,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all reduce/chunk/atom mychunk min c_cluster 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 <compute_property_chunk>` command creates a per-atom commands are equivalent, since the :doc:`compute property/chunk <compute_property_chunk>` command creates a per-atom
array with 3 columns: array with 3 columns:
.. parsed-literal:: .. code-block:: LAMMPS
compute prop all property/atom vx vy vz 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] 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). chunk/reduce command will be a cluster ID per chunk (molecule).
Molecules with the same cluster ID are in the same micelle. 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 group phobic type 4 # specific to in.micelle model
compute cluster phobic cluster/atom 2.0 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: 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 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 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. 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 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, its center or mass, shape (moments of inertia), radius of gyration,
etc. etc.
.. parsed-literal:: .. code-block:: LAMMPS
compute prop all property/chunk micelle count compute prop all property/chunk micelle count
fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector

4
doc/src/compute_rigid_local.rst
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@ -42,7 +42,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all rigid/local myRigid mol x y z 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 Here is an example of how to use this compute to dump rigid body info
to a file: to a file:
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all rigid/local myRigid mol x y z fx fy fz 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] 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]

2
doc/src/compute_saed.rst
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@ -36,7 +36,7 @@ Syntax
Examples 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 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 compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo

2
doc/src/compute_slice.rst
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@ -28,7 +28,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all slice 1 100 10 c_msdmol[4] compute 1 all slice 1 100 10 c_msdmol[4]
compute 1 all slice 301 400 1 c_msdmol[4] v_myVec compute 1 all slice 301 400 1 c_msdmol[4] v_myVec

2
doc/src/compute_smd_contact_radius.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/contact/radius compute 1 all smd/contact/radius

2
doc/src/compute_smd_damage.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/damage compute 1 all smd/damage

2
doc/src/compute_smd_hourglass_error.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/hourglass/error compute 1 all smd/hourglass/error

2
doc/src/compute_smd_internal_energy.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/internal/energy compute 1 all smd/internal/energy

2
doc/src/compute_smd_plastic_strain.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/plastic/strain compute 1 all smd/plastic/strain

2
doc/src/compute_smd_plastic_strain_rate.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/plastic/strain/rate compute 1 all smd/plastic/strain/rate

2
doc/src/compute_smd_rho.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/rho compute 1 all smd/rho

2
doc/src/compute_smd_tlsph_defgrad.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/tlsph/defgrad compute 1 all smd/tlsph/defgrad

2
doc/src/compute_smd_tlsph_dt.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/tlsph/dt compute 1 all smd/tlsph/dt

2
doc/src/compute_smd_tlsph_num_neighs.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/tlsph/num/neighs compute 1 all smd/tlsph/num/neighs

2
doc/src/compute_smd_tlsph_shape.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/tlsph/shape compute 1 all smd/tlsph/shape

2
doc/src/compute_smd_tlsph_strain.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/tlsph/strain compute 1 all smd/tlsph/strain

2
doc/src/compute_smd_tlsph_strain_rate.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/tlsph/strain/rate compute 1 all smd/tlsph/strain/rate

2
doc/src/compute_smd_tlsph_stress.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/tlsph/stress compute 1 all smd/tlsph/stress

2
doc/src/compute_smd_triangle_vertices.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/triangle/mesh/vertices compute 1 all smd/triangle/mesh/vertices

2
doc/src/compute_smd_vol.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all smd/vol compute 1 all smd/vol

4
doc/src/compute_sna_atom.rst
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@ -48,7 +48,7 @@ Syntax
Examples 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 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 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 automatically created behind the scenes, according to the following
command: command:
.. parsed-literal:: .. code-block:: LAMMPS
compute snap_press all pressure NULL virial compute snap_press all pressure NULL virial

6
doc/src/compute_stress_atom.rst
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@ -21,7 +21,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 mobile stress/atom NULL compute 1 mobile stress/atom NULL
compute 1 mobile stress/atom myRamp 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 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: 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 peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] 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 thermo_style custom step temp etotal press v_press
.. note:: .. note::

2
doc/src/compute_tally.rst
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@ -29,7 +29,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 lower force/tally upper compute 1 lower force/tally upper
compute 1 left pe/tally right compute 1 left pe/tally right

2
doc/src/compute_tdpd_cc_atom.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all tdpd/cc/atom 2 compute 1 all tdpd/cc/atom 2

4
doc/src/compute_temp.rst
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@ -19,7 +19,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all temp compute 1 all temp
compute myTemp mobile 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 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: LAMMPS starts up, as if this command were in the input script:
.. parsed-literal:: .. code-block:: LAMMPS
compute thermo_temp all temp compute thermo_temp all temp

2
doc/src/compute_temp_asphere.rst
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@ -26,7 +26,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all temp/asphere compute 1 all temp/asphere
compute myTemp mobile temp/asphere bias tempCOM compute myTemp mobile temp/asphere bias tempCOM

2
doc/src/compute_temp_body.rst
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@ -26,7 +26,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all temp/body compute 1 all temp/body
compute myTemp mobile temp/body bias tempCOM compute myTemp mobile temp/body bias tempCOM

4
doc/src/compute_temp_chunk.rst
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@ -40,7 +40,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 fluid temp/chunk molchunk compute 1 fluid temp/chunk molchunk
compute 1 fluid temp/chunk molchunk temp internal 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 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 <fix_ave_time>` command, for example: temp/chunk calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>` command, for example:
.. parsed-literal:: .. code-block:: LAMMPS
compute cc1 all chunk/atom molecule compute cc1 all chunk/atom molecule
compute myChunk all temp/chunk cc1 temp compute myChunk all temp/chunk cc1 temp

2
doc/src/compute_temp_com.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all temp/com compute 1 all temp/com
compute myTemp mobile temp/com compute myTemp mobile temp/com

2
doc/src/compute_temp_cs.rst
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@ -18,7 +18,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute oxygen_c-s all temp/cs O_core O_shell compute oxygen_c-s all temp/cs O_core O_shell
compute core_shells all temp/cs cores shells compute core_shells all temp/cs cores shells

2
doc/src/compute_temp_deform.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute myTemp all temp/deform compute myTemp all temp/deform

2
doc/src/compute_temp_deform_eff.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute myTemp all temp/deform/eff compute myTemp all temp/deform/eff

2
doc/src/compute_temp_drude.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute TDRUDE all temp/drude compute TDRUDE all temp/drude

4
doc/src/compute_temp_eff.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all temp/eff compute 1 all temp/eff
compute myTemp mobile 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 <thermo_modify>` command, as shown in the following :doc:`thermo_modify <thermo_modify>` command, as shown in the following
example: example:
.. parsed-literal:: .. code-block:: LAMMPS
compute effTemp all temp/eff compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press thermo_style custom step etotal pe ke temp press

2
doc/src/compute_temp_partial.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute newT flow temp/partial 1 1 0 compute newT flow temp/partial 1 1 0

2
doc/src/compute_temp_profile.rst
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@ -36,7 +36,7 @@ Syntax
Examples 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
compute myTemp flow temp/profile 1 1 1 x 10 out bin compute myTemp flow temp/profile 1 1 1 x 10 out bin

2
doc/src/compute_temp_ramp.rst
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@ -26,7 +26,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice

2
doc/src/compute_temp_region.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute mine flow temp/region boundary compute mine flow temp/region boundary

2
doc/src/compute_temp_region_eff.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute mine flow temp/region/eff boundary compute mine flow temp/region/eff boundary

2
doc/src/compute_temp_rotate.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute Tbead bead temp/rotate compute Tbead bead temp/rotate

2
doc/src/compute_temp_sphere.rst
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@ -26,7 +26,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all temp/sphere compute 1 all temp/sphere
compute myTemp mobile temp/sphere bias tempCOM compute myTemp mobile temp/sphere bias tempCOM

2
doc/src/compute_temp_uef.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all temp/uef compute 1 all temp/uef
compute 2 sel temp/uef compute 2 sel temp/uef

4
doc/src/compute_ti.rst
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@ -33,10 +33,10 @@ Syntax
Examples 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 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 Description
""""""""""" """""""""""

6
doc/src/compute_torque_chunk.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 fluid torque/chunk molchunk 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 <fix_ave_time>` calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
command, for example: command, for example:
.. parsed-literal:: .. code-block:: LAMMPS
compute cc1 all chunk/atom molecule compute cc1 all chunk/atom molecule
compute myChunk all torque/chunk cc1 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:** **Output info:**

6
doc/src/compute_vacf.rst
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@ -16,7 +16,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all vacf compute 1 all vacf
compute 1 upper 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 coefficient of the diffusing atoms. This can be computed in the
following manner, using the :doc:`variable trap() <variable>` function: following manner, using the :doc:`variable trap() <variable>` function:
.. parsed-literal:: .. code-block:: LAMMPS
compute 2 all vacf compute 2 all vacf
fix 5 all vector 1 c_2[4] 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 thermo_style custom step v_diff
.. note:: .. note::

6
doc/src/compute_vcm_chunk.rst
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@ -17,7 +17,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 fluid vcm/chunk molchunk 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 <fix_ave_time>` calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
command, for example: command, for example:
.. parsed-literal:: .. code-block:: LAMMPS
compute cc1 all chunk/atom molecule compute cc1 all chunk/atom molecule
compute myChunk all vcm/chunk cc1 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:** **Output info:**

8
doc/src/compute_voronoi_atom.rst
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@ -37,7 +37,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
compute 1 all voronoi/atom compute 1 all voronoi/atom
compute 2 precipitate voronoi/atom surface matrix 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 the argument, a poly-disperse Voronoi tessellation is
performed. Examples for radius variables are 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 compute radius all property/atom radius
variable r2 atom c_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 <dump>` command to write a file accessed by a :doc:`dump local <dump>` command to write a file
containing all the Voronoi neighbors in a system: containing all the Voronoi neighbors in a system:
.. parsed-literal:: .. code-block:: LAMMPS
compute 6 all voronoi/atom neighbors yes compute 6 all voronoi/atom neighbors yes
dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3] dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]

2
doc/src/compute_xrd.rst
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@ -34,7 +34,7 @@ Syntax
Examples 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 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 compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual

4
doc/src/dielectric.rst
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@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dielectric 2.0 dielectric 2.0
@ -42,6 +42,6 @@ Related commands
Default Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
dielectric 1.0 dielectric 1.0

4
doc/src/dimension.rst
View File

@ -15,7 +15,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dimension 2 dimension 2
@ -52,6 +52,6 @@ Related commands
Default Default
""""""" """""""
.. parsed-literal:: .. code-block:: LAMMPS
dimension 3 dimension 3

4
doc/src/dump_adios.rst
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@ -26,7 +26,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dump adios1 all atom/adios 100 atoms.bp dump adios1 all atom/adios 100 atoms.bp
dump 4a all custom/adios 100 dump_adios.bp id v_p x y z 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 must not be set at all. The write\_dump command can be used to
create a new file at each individual dump. create a new file at each individual dump.
.. parsed-literal:: .. code-block:: LAMMPS
dump 4 all atom/adios 100 dump.bp dump 4 all atom/adios 100 dump.bp
write_dump all atom/adios singledump.bp write_dump all atom/adios singledump.bp

2
doc/src/dump_cfg_uef.rst
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@ -22,7 +22,7 @@ Syntax
Examples Examples
"""""""" """"""""
.. parsed-literal:: .. code-block:: LAMMPS
dump 1 all cfg/uef 10 dump.\*.cfg mass type xs ys zs 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 dump 2 all cfg/uef 100 dump.\*.cfg mass type xs ys zs id c_stress

4
doc/src/dump_h5md.rst
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@ -44,7 +44,7 @@ specified by this option directly following the element declaration:
Examples 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 image
dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10 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 the position data every 100 timesteps, with the image data, and
store once the species data in the same file. store once the species data in the same file.
.. parsed-literal:: .. code-block:: LAMMPS
dump h5md1 all h5md 100 dump.h5 position image dump h5md1 all h5md 100 dump.h5 position image
write_dump all h5md dump.h5 file_from h5md1 species write_dump all h5md dump.h5 file_from h5md1 species