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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
""""""""
.. 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

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

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

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

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

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

4
doc/src/compute_fep.rst
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@ -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

16
doc/src/compute_global_atom.rst
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@ -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 <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[*]
----------

2
doc/src/compute_group_group.rst
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@ -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

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

4
doc/src/compute_gyration_chunk.rst
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@ -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 <fix_ave_time>`
command, for example:
.. parsed-literal::
.. code-block:: LAMMPS
compute cc1 all chunk/atom molecule
compute myChunk all gyration/chunk cc1

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

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

18
doc/src/compute_heat_flux.rst
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@ -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

2
doc/src/compute_hexorder_atom.rst
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@ -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

6
doc/src/compute_hma.rst
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@ -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

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

4
doc/src/compute_improper_local.rst
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@ -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

6
doc/src/compute_inertia_chunk.rst
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@ -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 <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:**

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

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

4
doc/src/compute_ke_eff.rst
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@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all ke/eff
@ -56,7 +56,7 @@ freedom.
:doc:`thermo_modify <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

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

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

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

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

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

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

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

6
doc/src/compute_omega_chunk.rst
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@ -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 <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:**

2
doc/src/compute_orientorder_atom.rst
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@ -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

2
doc/src/compute_pair.rst
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@ -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

4
doc/src/compute_pair_local.rst
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@ -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

4
doc/src/compute_pe.rst
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@ -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

4
doc/src/compute_pe_atom.rst
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@ -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

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

2
doc/src/compute_pressure_cylinder.rst
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@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
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
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all pressure/uef my_temp_uef
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
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all property/atom xs vx fx mux
compute 2 all property/atom type

6
doc/src/compute_property_chunk.rst
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@ -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 <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:**

2
doc/src/compute_property_local.rst
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@ -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

2
doc/src/compute_ptm_atom.rst
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@ -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

10
doc/src/compute_rdf.rst
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@ -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 <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:**

8
doc/src/compute_reduce.rst
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@ -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 <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

14
doc/src/compute_reduce_chunk.rst
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@ -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 <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

4
doc/src/compute_rigid_local.rst
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@ -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]

2
doc/src/compute_saed.rst
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@ -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

2
doc/src/compute_slice.rst
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@ -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

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

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

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

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

2
doc/src/compute_smd_plastic_strain.rst
View File

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

2
doc/src/compute_smd_plastic_strain_rate.rst
View File

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

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

2
doc/src/compute_smd_tlsph_defgrad.rst
View File

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

2
doc/src/compute_smd_tlsph_dt.rst
View File

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

2
doc/src/compute_smd_tlsph_num_neighs.rst
View File

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

2
doc/src/compute_smd_tlsph_shape.rst
View File

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

2
doc/src/compute_smd_tlsph_strain.rst
View File

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

2
doc/src/compute_smd_tlsph_strain_rate.rst
View File

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

2
doc/src/compute_smd_tlsph_stress.rst
View File

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

2
doc/src/compute_smd_triangle_vertices.rst
View File

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

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

4
doc/src/compute_sna_atom.rst
View File

@ -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

6
doc/src/compute_stress_atom.rst
View File

@ -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::

2
doc/src/compute_tally.rst
View File

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

2
doc/src/compute_tdpd_cc_atom.rst
View File

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

4
doc/src/compute_temp.rst
View File

@ -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

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

2
doc/src/compute_temp_body.rst
View File

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

4
doc/src/compute_temp_chunk.rst
View File

@ -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 <fix_ave_time>` command, for example:
.. parsed-literal::
.. code-block:: LAMMPS
compute cc1 all chunk/atom molecule
compute myChunk all temp/chunk cc1 temp

2
doc/src/compute_temp_com.rst
View File

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

2
doc/src/compute_temp_cs.rst
View File

@ -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

2
doc/src/compute_temp_deform.rst
View File

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

2
doc/src/compute_temp_deform_eff.rst
View File

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

2
doc/src/compute_temp_drude.rst
View File

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

4
doc/src/compute_temp_eff.rst
View File

@ -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 <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

2
doc/src/compute_temp_partial.rst
View File

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

2
doc/src/compute_temp_profile.rst
View File

@ -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

2
doc/src/compute_temp_ramp.rst
View File

@ -26,7 +26,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
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
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute mine flow temp/region boundary

2
doc/src/compute_temp_region_eff.rst
View File

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

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

2
doc/src/compute_temp_sphere.rst
View File

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

2
doc/src/compute_temp_uef.rst
View File

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

4
doc/src/compute_ti.rst
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@ -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
"""""""""""

6
doc/src/compute_torque_chunk.rst
View File

@ -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 <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:**

6
doc/src/compute_vacf.rst
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@ -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() <variable>` 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::

6
doc/src/compute_vcm_chunk.rst
View File

@ -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 <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:**

8
doc/src/compute_voronoi_atom.rst
View File

@ -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 <dump>` 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]

2
doc/src/compute_xrd.rst
View File

@ -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

4
doc/src/dielectric.rst
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@ -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

4
doc/src/dimension.rst
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@ -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

4
doc/src/dump_adios.rst
View File

@ -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

2
doc/src/dump_cfg_uef.rst
View File

@ -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

4
doc/src/dump_h5md.rst
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@ -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