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convert more LAMMPS script examples to use code-block instead of parsed-literal

This commit is contained in:
Axel Kohlmeyer 2020-03-12 01:11:38 -04:00
parent 2775ebeb9d
commit 7e656b6cea
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33 changed files with 89 additions and 89 deletions
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2
doc/src/balance.rst
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@ -59,7 +59,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
balance 0.9 x uniform y 0.4 0.5 0.6
balance 1.2 shift xz 5 1.1

4
doc/src/boundary.rst
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@ -22,7 +22,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
boundary p p f
boundary p fs p
@ -110,6 +110,6 @@ of lost atoms.
Default
"""""""
.. parsed-literal::
.. code-block:: LAMMPS
boundary p p p

2
doc/src/box.rst
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@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
box tilt large
box tilt small

2
doc/src/compute_ackland_atom.rst
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@ -22,7 +22,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all ackland/atom
compute 1 all ackland/atom legacy yes

8
doc/src/compute_adf.rst
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@ -31,7 +31,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 &
1 1 2 0.0 1.2 0.0 1.5 &
@ -39,7 +39,7 @@ Examples
2 1 1 0.0 1.2 0.0 1.2 &
2 1 2 0.0 1.5 2.0 3.5 &
2 2 2 2.0 3.5 2.0 3.5
compute 1 fluid adf 32 1\*2 1\*2 1\*2 0.5 3.5
compute 1 fluid adf 32 1*2 1*2 1*2 0.5 3.5
compute 1 fluid adf 32
Description
@ -168,10 +168,10 @@ The simplest way to output the results of the compute adf calculation
to a file is to use the :doc:`fix ave/time <fix_ave_time>` command, for
example:
.. parsed-literal::
.. code-block:: LAMMPS
compute myADF all adf 32 2 2 2 0.5 3.5 0.5 3.5
fix 1 all ave/time 100 1 100 c_myADF[\*] file tmp.adf mode vector
fix 1 all ave/time 100 1 100 c_myADF[*] file tmp.adf mode vector
**Output info:**

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

8
doc/src/compute_angle_local.rst
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@ -33,7 +33,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all angle/local theta
compute 1 all angle/local eng theta
@ -68,11 +68,11 @@ As an example, these commands can be added to the bench/in.rhodo
script to compute the cosine and cosine\^2 of every angle in the system
and output the statistics in various ways:
.. parsed-literal::
.. code-block:: LAMMPS
variable t internal 0.0
variable cos equal cos(v_t)
variable cossq equal cos(v_t)\*cos(v_t)
variable cossq equal cos(v_t)*cos(v_t)
compute 1 all property/local aatom1 aatom2 aatom3 atype
compute 2 all angle/local eng theta v_cos v_cossq set theta t
@ -113,7 +113,7 @@ command in a consistent way.
Here is an example of how to do this:
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all property/local atype aatom1 aatom2 aatom3
compute 2 all angle/local theta eng

6
doc/src/compute_angmom_chunk.rst
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@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 fluid angmom/chunk molchunk
@ -62,11 +62,11 @@ The simplest way to output the results of the compute angmom/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 angmom/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_basal_atom.rst
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@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all basal/atom

4
doc/src/compute_body_local.rst
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@ -24,7 +24,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all body/local type 1 2 3
compute 1 all body/local 3 6
@ -69,7 +69,7 @@ body sub-particles are x,y,z coordinates, then the dump file will be
formatted similar to the output of a :doc:`dump atom or custom <dump>`
command.
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all body/local type 1 2 3
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4]

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

10
doc/src/compute_bond_local.rst
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@ -41,7 +41,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all bond/local engpot
compute 1 all bond/local dist engpot force
@ -120,10 +120,10 @@ As an example, these commands can be added to the bench/in.rhodo
script to compute the distance\^2 of every bond in the system and
output the statistics in various ways:
.. parsed-literal::
.. code-block:: LAMMPS
variable d internal 0.0
variable dsq equal v_d\*v_d
variable dsq equal v_d*v_d
compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local engpot dist v_dsq set dist d
@ -163,11 +163,11 @@ command in a consistent way.
Here is an example of how to do this:
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all property/local btype batom1 batom2
compute 2 all bond/local dist engpot
dump 1 all local 1000 tmp.dump index c_1[\*] c_2[\*]
dump 1 all local 1000 tmp.dump index c_1[*] c_2[*]
**Output info:**

2
doc/src/compute_centro_atom.rst
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@ -25,7 +25,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all centro/atom fcc

2
doc/src/compute_chunk_atom.rst
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@ -84,7 +84,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all chunk/atom type
compute 1 all chunk/atom bin/1d z lower 0.02 units reduced

18
doc/src/compute_chunk_spread_atom.rst
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@ -26,7 +26,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration
@ -99,7 +99,7 @@ had been listed one by one. E.g. these 2 compute chunk/spread/atom
commands are equivalent, since the :doc:`compute com/chunk <compute_com_chunk>` command creates a per-atom array
with 3 columns:
.. parsed-literal::
.. code-block:: LAMMPS
compute com all com/chunk mychunk
compute 10 all chunk/spread/atom mychunk c_com[*]
@ -111,7 +111,7 @@ Here is an example of writing a dump file the with the center-of-mass
(COM) for the chunk each atom is in. The commands below can be added
to the bench/in.chain script.
.. parsed-literal::
.. code-block:: LAMMPS
compute cmol all chunk/atom molecule
compute com all com/chunk cmol
@ -124,13 +124,13 @@ forces for the :doc:`fix addforce <fix_addforce>` command. In this
example the forces act to pull atoms of an extended polymer chain
towards its COM in an attractive manner.
.. parsed-literal::
.. code-block:: LAMMPS
compute prop all property/atom xu yu zu
variable k equal 0.1
variable fx atom v_k\*(c_comchunk[1]-c_prop[1])
variable fy atom v_k\*(c_comchunk[2]-c_prop[2])
variable fz atom v_k\*(c_comchunk[3]-c_prop[3])
variable fx atom v_k*(c_comchunk[1]-c_prop[1])
variable fy atom v_k*(c_comchunk[2]-c_prop[2])
variable fz atom v_k*(c_comchunk[3]-c_prop[3])
fix 3 all addforce v_fx v_fy v_fz
Note that :doc:`compute property/atom <compute_property_atom>` is used
@ -171,13 +171,13 @@ Then defining a second set of chunks based on spatial bins. And
finally, using the :doc:`fix ave/chunk <fix_ave_chunk>` command to
calculate an average dipole moment vector per spatial bin.
.. parsed-literal::
.. code-block:: LAMMPS
compute cmol all chunk/atom molecule
compute dipole all dipole/chunk cmol
compute spread all chunk/spread/atom cmol c_dipole[1] c_dipole[2] c_dipole[3]
compute cspatial all chunk/atom bin/1d z lower 0.1 units reduced
fix ave all ave/chunk 100 10 1000 cspatial c_spread[\*]
fix ave all ave/chunk 100 10 1000 cspatial c_spread[*]
Note that the :doc:`fix ave/chunk <fix_ave_chunk>` command requires
per-atom values as input. That is why the compute chunk/spread/atom

2
doc/src/compute_cluster_atom.rst
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@ -25,7 +25,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all cluster/atom 3.5
compute 1 all fragment/atom

2
doc/src/compute_cna_atom.rst
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@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all cna/atom 3.08

2
doc/src/compute_cnp_atom.rst
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@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all cnp/atom 3.08

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

6
doc/src/compute_com_chunk.rst
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@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 fluid com/chunk molchunk
@ -60,11 +60,11 @@ The simplest way to output the results of the compute com/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 com/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_contact_atom.rst
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@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all contact/atom

4
doc/src/compute_coord_atom.rst
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@ -27,11 +27,11 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all coord/atom cutoff 2.0
compute 1 all coord/atom cutoff 6.0 1 2
compute 1 all coord/atom cutoff 6.0 2\*4 5\*8 \*
compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
compute 1 solute coord/atom cutoff 2.0 group solvent
compute 1 all coord/atom orientorder 2 0.5

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

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

8
doc/src/compute_dihedral_local.rst
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@ -32,7 +32,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all dihedral/local phi
@ -66,11 +66,11 @@ As an example, these commands can be added to the bench/in.rhodo
script to compute the cosine and cosine\^2 of every dihedral angle in
the system and output the statistics in various ways:
.. parsed-literal::
.. code-block:: LAMMPS
variable p internal 0.0
variable cos equal cos(v_p)
variable cossq equal cos(v_p)\*cos(v_p)
variable cossq equal cos(v_p)*cos(v_p)
compute 1 all property/local datom1 datom2 datom3 datom4 dtype
compute 2 all dihedral/local phi v_cos v_cossq set phi p
@ -107,7 +107,7 @@ command in a consistent way.
Here is an example of how to do this:
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all property/local dtype datom1 datom2 datom3 datom4
compute 2 all dihedral/local phi

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

6
doc/src/compute_dipole_chunk.rst
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@ -18,7 +18,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 fluid dipole/chunk molchunk
compute dw water dipole/chunk 1 geometry
@ -65,11 +65,11 @@ The simplest way to output the results of the compute com/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 dipole/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:**

4
doc/src/compute_displace_atom.rst
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@ -22,7 +22,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all displace/atom
compute 1 all displace/atom refresh myVar
@ -82,7 +82,7 @@ a distance *Dhop*\ . For any snapshot we only want to output atoms that
have hopped since the last snapshot. This can be accomplished with
something like the following commands:
.. parsed-literal::
.. code-block:: LAMMPS
write_dump all custom tmp.dump id type x y z # see comment below

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

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

4
doc/src/compute_entropy_atom.rst
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@ -28,7 +28,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all entropy/atom 0.25 5.
compute 1 all entropy/atom 0.25 5. avg yes 5.
@ -86,7 +86,7 @@ to increase the skin of the neighbor list with:
.. parsed-literal::
neighbor skin bin
neighbor <skin distance> bin
See :doc:`neighbor <neighbor>` for details.

46
doc/src/variable.rst
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@ -76,16 +76,16 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
variable x index run1 run2 run3 run4 run5 run6 run7 run8
variable LoopVar loop $n
variable beta equal temp/3.0
variable b1 equal x[234]+0.5\*vol
variable b1 equal "x[234] + 0.5\*vol"
variable b1 equal x[234]+0.5*vol
variable b1 equal "x[234] + 0.5*vol"
variable b equal xcm(mol1,x)/2.0
variable b equal c_myTemp
variable b atom x\*y/vol
variable b atom x*y/vol
variable foo string myfile
variable foo internal 3.5
variable myPy python increase
@ -225,7 +225,7 @@ script or when the input script is looped over. This can be useful
when breaking out of a loop via the :doc:`if <if>` and :doc:`jump <jump>`
commands before the variable would become exhausted. For example,
.. parsed-literal::
.. code-block:: LAMMPS
label loop
variable a loop 5
@ -388,7 +388,7 @@ to match a function name specified in a :doc:`python <python>` command
which returns a value to this variable as defined by its *return*
keyword. For example these two commands would be self-consistent:
.. parsed-literal::
.. code-block:: LAMMPS
variable foo python myMultiply
python myMultiply return v_foo format f file funcs.py
@ -455,9 +455,9 @@ simple, but multiple quantities can be nested and combined in various
ways to build up formulas of arbitrary complexity. For example, this
is a valid (though strange) variable formula:
.. parsed-literal::
.. code-block:: LAMMPS
variable x equal "pe + c_MyTemp / vol\^(1/3)"
variable x equal "pe + c_MyTemp / vol^(1/3)"
Specifically, a formula can contain numbers, constants, thermo
keywords, math operators, math functions, group functions, region
@ -535,7 +535,7 @@ adapt automatically to LAMMPS versions, when non-backwards compatible
syntax changes are introduced. Here is an illustrative example (which
will not work, since the *version* has been introduced more recently):
.. parsed-literal::
.. code-block:: LAMMPS
if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes"
@ -939,7 +939,7 @@ the checking is also done using suffix flags, if available and enabled.
Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP).
.. parsed-literal::
.. code-block:: LAMMPS
pair_style lj/cut/coul/long 14.0
if $(is_active(package,gpu)) then "suffix off"
@ -947,9 +947,9 @@ Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on
Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step
.. parsed-literal::
.. code-block:: LAMMPS
timestep $(2.0\*(1.0+2.0\*is_active(pair,respa))
timestep $(2.0*(1.0+2.0*is_active(pair,respa))
if $(is_active(pair,respa)) then "run_style respa 4 3 2 2 improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2 improper 1 pair 2 kspace 3"
The *is\_defined()* function allows to query categories like *compute*\ ,
@ -971,7 +971,7 @@ and C++ exceptions for error handling. Corresponding values for name are
This enables writing input scripts which only dump using a given format if
the compiled binary supports it.
.. parsed-literal::
.. code-block:: LAMMPS
if "$(is_available(feature,png))" then "print 'PNG supported'" else "print 'PNG not supported'"
@ -1056,9 +1056,9 @@ global vector. Consider a compute with ID "foo" that does this,
referenced as follows by variable "a", where "myVec" is another
vector-style variable:
.. parsed-literal::
.. code-block:: LAMMPS
variable a vector c_foo\*v_myVec
variable a vector c_foo*v_myVec
The reference "c\_foo" could refer to either the global scalar or
global vector produced by compute "foo". In this case, "c\_foo" will
@ -1219,7 +1219,7 @@ evaluated.
As an example, suppose you use this command in your input script to
define the variable "v" as
.. parsed-literal::
.. code-block:: LAMMPS
variable v equal vol
@ -1233,7 +1233,7 @@ evaluated continuously during the run.
If you want to store the initial volume of the system, you can do it
this way:
.. parsed-literal::
.. code-block:: LAMMPS
variable v equal vol
variable v0 equal $v
@ -1242,7 +1242,7 @@ The second command will force "v" to be evaluated (yielding the
initial volume) and assign that value to the variable "v0". Thus the
command
.. parsed-literal::
.. code-block:: LAMMPS
thermo_style custom step v_v v_v0
@ -1252,7 +1252,7 @@ during the run.
Note that it is a mistake to enclose a variable formula in double
quotes if it contains variables preceded by $ signs. For example,
.. parsed-literal::
.. code-block:: LAMMPS
variable vratio equal "${vfinal}/${v0}"
@ -1309,7 +1309,7 @@ timestep of the preceding run, e.g. by thermodynamic output.
One way to get around this problem is to perform a 0-timestep run
before using the variable. For example, these commands
.. parsed-literal::
.. code-block:: LAMMPS
variable t equal temp
print "Initial temperature = $t"
@ -1321,7 +1321,7 @@ a compute for calculating the temperature to be invoked.
However, this sequence of commands would be fine:
.. parsed-literal::
.. code-block:: LAMMPS
run 0
variable t equal temp
@ -1355,7 +1355,7 @@ a 0-timestep run before printing the variable has the desired effect.
way to detect this has occurred. Consider the following sequence of
commands:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff 1 1 1.0 1.0
run 1000
@ -1381,7 +1381,7 @@ the system is up-to-date. For example, this sequence of commands
would print a potential energy that reflected the changed pairwise
coefficient:
.. parsed-literal::
.. code-block:: LAMMPS
pair_coeff 1 1 1.0 1.0
run 1000

6
doc/src/velocity.rst
View File

@ -51,7 +51,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
velocity all create 300.0 4928459 rot yes dist gaussian
velocity border set NULL 4.0 v_vz sum yes units box
@ -148,7 +148,7 @@ discussed on the :doc:`Howto thermostat <Howto_thermostat>` doc page.
If this keyword is not specified, *create* and *scale* calculate
temperature using a compute that is defined internally as follows:
.. parsed-literal::
.. code-block:: LAMMPS
compute velocity_temp group-ID temp
@ -246,7 +246,7 @@ temperature than desired. A workaround for this is to perform a :doc:`run 0 <ru
properly, and then rescale the temperature to the desired value before
performing a simulation. For example:
.. parsed-literal::
.. code-block:: LAMMPS
velocity all create 300.0 12345
run 0 # temperature may not be 300K