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finish updating docs for fixes using code-block plus a few other improvements

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This commit is contained in:
Axel Kohlmeyer
2020-03-11 11:44:21 -04:00
parent 5029bc9e1e
commit d0f57289fc
115 changed files with 234 additions and 208 deletions
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2
doc/src/fix_bond_break.rst
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@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 5 all bond/break 10 2 1.2
fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829

2
doc/src/fix_bond_create.rst
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@ -40,7 +40,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 5 all bond/create 10 1 2 0.8 1
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3

4
doc/src/fix_bond_react.rst
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@ -59,7 +59,7 @@ Examples
For unabridged example scripts and files, see examples/USER/reaction.
.. parsed-literal::
.. code-block:: LAMMPS
molecule mol1 pre_reacted_topology.txt
molecule mol2 post_reacted_topology.txt
@ -466,7 +466,7 @@ atoms currently involved in a reaction. For example, adding the
following command would add an additional thermostat to the group of
all currently-reacting atoms:
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1

4
doc/src/fix_bond_swap.rst
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@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all bond/swap 50 0.5 1.3 598934
@ -119,7 +119,7 @@ This fix computes a temperature each time it is invoked for use by the
Boltzmann criterion. To do this, the fix creates its own compute of
style *temp*\ , as if this command had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp all temp

6
doc/src/fix_box_relax.rst
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@ -32,7 +32,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all box/relax iso 0.0 vmax 0.001
fix 2 water box/relax aniso 0.0 dilate partial
@ -286,7 +286,7 @@ pressure, even though this is subsequently ignored by default. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp virial
@ -343,7 +343,7 @@ result in double-counting of the fix energy in the minimization
energy. Instead, the fix energy can be explicitly added to the
potential energy using one of these two variants:
.. parsed-literal::
.. code-block:: LAMMPS
variable emin equal pe+f_1

2
doc/src/fix_client_md.rst
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@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all client/md

2
doc/src/fix_cmap.rst
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@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix myCMAP all cmap ../potentials/cmap36.data
read_data proteinX.data fix myCMAP crossterm CMAP

2
doc/src/fix_colvars.rst
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@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide
fix abf all colvars colvars.inp tstat 1

2
doc/src/fix_controller.rst
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@ -33,7 +33,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall

14
doc/src/fix_deform.rst
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@ -81,7 +81,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all deform 1 x final 0.0 9.0 z final 0.0 5.0 units box
fix 1 all deform 1 x trate 0.1 y volume z volume
@ -280,12 +280,12 @@ Here is an example of using the *variable* style to perform the same
box deformation as the *wiggle* style formula listed above, where we
assume that the current timestep = 0.
.. parsed-literal::
.. code-block:: LAMMPS
variable A equal 5.0
variable Tp equal 10.0
variable displace equal "v_A \* sin(2\*PI \* step\*dt/v_Tp)"
variable rate equal "2\*PI\*v_A/v_Tp \* cos(2\*PI \* step\*dt/v_Tp)"
variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
fix 2 all deform 1 x variable v_displace v_rate remap v
For the *scale*\ , *vel*\ , *erate*\ , *trate*\ , *volume*\ , *wiggle*\ , and
@ -425,12 +425,12 @@ Here is an example of using the *variable* style to perform the same
box deformation as the *wiggle* style formula listed above, where we
assume that the current timestep = 0.
.. parsed-literal::
.. code-block:: LAMMPS
variable A equal 5.0
variable Tp equal 10.0
variable displace equal "v_A \* sin(2\*PI \* step\*dt/v_Tp)"
variable rate equal "2\*PI\*v_A/v_Tp \* cos(2\*PI \* step\*dt/v_Tp)"
variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
fix 2 all deform 1 xy variable v_displace v_rate remap v
----------

2
doc/src/fix_deposit.rst
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@ -65,7 +65,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8

2
doc/src/fix_dpd_energy.rst
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@ -19,7 +19,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all dpd/energy

2
doc/src/fix_dpd_source.rst
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@ -33,7 +33,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all edpd/source sphere 0.0 0.0 0.0 5.0 0.01
fix 1 all edpd/source cuboid 0.0 0.0 0.0 20.0 10.0 10.0 -0.01

2
doc/src/fix_drag.rst
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@ -19,7 +19,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix center small-molecule drag 0.0 10.0 0.0 5.0 2.0

2
doc/src/fix_drude.rst
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@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all drude 1 1 0 1 0 2 2 2
fix 1 all drude C C N C N D D D

8
doc/src/fix_drude_transform.rst
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@ -19,7 +19,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 all drude/transform/direct
fix 1 all drude/transform/inverse
@ -132,7 +132,7 @@ acting on two distinct groups.
Example:
.. parsed-literal::
.. code-block:: LAMMPS
fix fDIRECT all drude/transform/direct
fix fNVT gCORES nvt temp 300.0 300.0 100
@ -157,7 +157,7 @@ pressure *thermo\_press*.
Example:
.. parsed-literal::
.. code-block:: LAMMPS
compute cTEMP_CORE gCORES temp/com
fix fDIRECT all drude/transform/direct
@ -176,7 +176,7 @@ In order to avoid the flying ice cube problem (irreversible transfer
of linear momentum to the center of mass of the system), you may need
to add a *fix momentum* command:
.. parsed-literal::
.. code-block:: LAMMPS
fix fMOMENTUM all momentum 100 linear 1 1 1

2
doc/src/fix_dt_reset.rst
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@ -30,7 +30,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 5 all dt/reset 10 1.0e-5 0.01 0.1
fix 5 all dt/reset 10 0.01 2.0 0.2 units box

2
doc/src/fix_efield.rst
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@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix kick external-field efield 1.0 0.0 0.0
fix kick external-field efield 0.0 0.0 v_oscillate

2
doc/src/fix_ehex.rst
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@ -31,7 +31,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
# Lennard-Jones, from examples/in.ehex.lj

2
doc/src/fix_electron_stopping.rst
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@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix el all electron/stopping 10.0 elstop-table.txt
fix el all electron/stopping 10.0 elstop-table.txt minneigh 3

2
doc/src/fix_enforce2d.rst
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@ -19,7 +19,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 5 all enforce2d

2
doc/src/fix_eos_cv.rst
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@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all eos/cv 0.01

2
doc/src/fix_eos_table.rst
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@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all eos/table linear eos.table 100000 KEYWORD

2
doc/src/fix_eos_table_rx.rst
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@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table
fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5

2
doc/src/fix_evaporate.rst
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@ -26,7 +26,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 solvent evaporate 1000 10 surface 49892
fix 1 solvent evaporate 1000 10 surface 38277 molecule yes

34
doc/src/fix_external.rst
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@ -25,7 +25,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all external pf/callback 1 1
fix 1 all external pf/callback 100 1
@ -51,23 +51,25 @@ be used multiple times to update atom forces.
The callback function "foo" is invoked by the fix as:
.. parsed-literal::
.. code-block:: c++
foo(void \*ptr, bigint timestep, int nlocal, int \*ids, double \*\*x, double \*\*fexternal);
foo(void *ptr, bigint timestep, int nlocal, tagint *ids, double **x, double **fexternal);
The arguments are as follows:
* ptr = pointer provided by and simply passed back to external driver
* timestep = current LAMMPS timestep
* nlocal = # of atoms on this processor
* ids = list of atom IDs on this processor
* x = coordinates of atoms on this processor
* fexternal = forces to add to atoms on this processor
* *ptr* = pointer provided by and simply passed back to external driver
* *timestep* = current LAMMPS timestep
* *nlocal* = # of atoms on this processor
* *ids* = list of atom IDs on this processor
* *x* = coordinates of atoms on this processor
* *fexternal* = forces to add to atoms on this processor
Note that timestep is a "bigint" which is defined in src/lmptype.h,
typically as a 64-bit integer.
Fexternal are the forces returned by the driver program.
Note that *timestep* is a "bigint" which is defined in src/lmptype.h,
typically as a 64-bit integer. And *ids* is a pointer to type "tagint"
which is typically a 32-bit integer unless LAMMPS is compiled with
-DLAMMPS\_BIGBIG. For more info please see the :ref:`build settings
<size>` section of the manual. Finally, *fexternal* are the forces
returned by the driver program.
The fix has a set\_callback() method which the external driver can call
to pass a pointer to its foo() function. See the
@ -87,9 +89,9 @@ every *Napply* steps, similar to the way the :doc:`fix addforce <fix_addforce>`
The name of the public force array provided by the FixExternal
class is
.. parsed-literal::
.. code-block:: c++
double \*\*fexternal;
double **fexternal;
It is allocated by the FixExternal class as an (N,3) array where N is
the number of atoms owned by a processor. The 3 corresponds to the
@ -111,7 +113,7 @@ added forces. Otherwise the minimization will not converge correctly.
This can be done from the external driver by calling this public
method of the FixExternal class:
.. parsed-literal::
.. code-block:: c++
void set_energy(double eng);

2
doc/src/fix_ffl.rst
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@ -24,7 +24,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 boundary ffl 10 300 300 31415
fix 1 all ffl 100 500 500 9265 soft

2
doc/src/fix_filter_corotate.rst
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@ -24,7 +24,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3

2
doc/src/fix_flow_gauss.rst
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@ -31,7 +31,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix GD fluid flow/gauss 1 0 0
fix GD fluid flow/gauss 1 1 1 energy yes

2
doc/src/fix_freeze.rst
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@ -19,7 +19,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 2 bottom freeze

6
doc/src/fix_gcmc.rst
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@ -56,7 +56,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
@ -150,7 +150,7 @@ thermal equilibrium with the simulation cell. Also, it is important
that the temperature used by fix nvt be dynamic/dof, which can be
achieved as follows:
.. parsed-literal::
.. code-block:: LAMMPS
compute mdtemp mdatoms temp
compute_modify mdtemp dynamic/dof yes
@ -357,7 +357,7 @@ therefore, you will want to use the
current number of atoms is used as a normalizing factor each time
temperature is computed. A simple example of this is:
.. parsed-literal::
.. code-block:: LAMMPS
compute_modify thermo_temp dynamic yes

2
doc/src/fix_gld.rst
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@ -33,7 +33,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all gld 1.0 1.0 2 82885 pprony 0.5 1.0 1.0 2.0 frozen yes zero yes
fix 3 rouse gld 7.355 7.355 4 48823 pprony 107.1 0.02415 186.0 0.04294 428.6 0.09661 1714 0.38643

2
doc/src/fix_gle.rst
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@ -29,7 +29,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 boundary gle 6 300 300 31415 smart.A
fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C

2
doc/src/fix_gravity.rst
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@ -38,7 +38,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all gravity 1.0 chute 24.0
fix 1 all gravity v_increase chute 24.0

2
doc/src/fix_grem.rst
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@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix fxgREM all grem 400 -0.01 -30000 fxnpt
thermo_modify press fxgREM_press

6
doc/src/fix_halt.rst
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@ -34,7 +34,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 10 all halt 1 bondmax > 1.5
fix 10 all print 10 v_myCheck != 0 error soft
@ -86,7 +86,7 @@ computing some attribute of the current system. For example, the
following "bondmax" variable will calculate the same quantity as the
hstyle = bondmax option.
.. parsed-literal::
.. code-block:: LAMMPS
compute bdist all bond/local dist
compute bmax all reduce max c_bdist
@ -94,7 +94,7 @@ hstyle = bondmax option.
Thus these two versions of a fix halt command will do the same thing:
.. parsed-literal::
.. code-block:: LAMMPS
fix 10 all halt 1 bondmax > 1.5
fix 10 all halt 1 v_bondmax > 1.5

2
doc/src/fix_heat.rst
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@ -26,7 +26,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 qin heat 1 1.0
fix 3 qin heat 10 v_flux

2
doc/src/fix_hyper_global.rst
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@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all hyper/global 1.0 0.3 0.8 300.0

4
doc/src/fix_hyper_local.rst
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@ -34,7 +34,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all hyper/local 1.0 0.3 0.8 300.0
fix 1 all hyper/local 1.0 0.3 0.8 300.0 bound 0.1 reset 0
@ -248,7 +248,7 @@ well for many solid-state systems.
pair\_style cutoff, which will typically be < *Dcut*\ . The :doc:`comm_modify cutoff <comm_modify>` command should be used to override the ghost
cutoff explicitly, e.g.
.. parsed-literal::
.. code-block:: LAMMPS
comm_modify cutoff 12.0

2
doc/src/fix_imd.rst
View File

@ -30,7 +30,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix vmd all imd 5678
fix comm all imd 8888 trate 5 unwrap on fscale 10.0

20
doc/src/fix_indent.rst
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@ -42,7 +42,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0
fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in
@ -62,9 +62,9 @@ must set one of those 3 keywords.
A spherical indenter exerts a force of magnitude
.. parsed-literal::
.. math::
F(r) = - K (r - R)\^2
F(r) = - K \left( r - R \right)^2
on each atom where *K* is the specified force constant, *r* is the
distance from the atom to the center of the indenter, and *R* is the
@ -117,27 +117,27 @@ then this variable definition will keep it's center at a relative
position in the simulation box, 1/4 of the way from the left edge to
the right edge, even if the box size changes:
.. parsed-literal::
.. code-block:: LAMMPS
variable x equal "xlo + 0.25\*lx"
variable x equal "xlo + 0.25*lx"
Similarly, either of these variable definitions will move the indenter
from an initial position at 2.5 at a constant velocity of 5:
.. parsed-literal::
.. code-block:: LAMMPS
variable x equal "2.5 + 5\*elaplong\*dt"
variable x equal "2.5 + 5*elaplong*dt"
variable x equal vdisplace(2.5,5)
If a spherical indenter's radius is specified as v\_r, then these
variable definitions will grow the size of the indenter at a specified
rate.
.. parsed-literal::
.. code-block:: LAMMPS
variable r0 equal 0.0
variable rate equal 1.0
variable r equal "v_r0 + step\*dt\*v_rate"
variable r equal "v_r0 + step*dt*v_rate"
If the *side* keyword is specified as *out*\ , which is the default,
then particles outside the indenter are pushed away from its outer
@ -171,7 +171,7 @@ lattice spacing, you can define K with a variable whose formula
contains *xlat*\ , *ylat*\ , *zlat* keywords of the
:doc:`thermo_style <thermo_style>` command, e.g.
.. parsed-literal::
.. code-block:: LAMMPS
variable k equal 100.0/xlat/xlat
fix 1 all indent $k sphere ...

6
doc/src/fix_ipi.rst
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@ -20,8 +20,10 @@ Syntax
Examples
""""""""
fix 1 all ipi my.server.com 12345
fix 1 all ipi mysocket 666 unix reset
.. code-block:: LAMMPS
fix 1 all ipi my.server.com 12345
fix 1 all ipi mysocket 666 unix reset
Description
"""""""""""

6
doc/src/fix_langevin_drude.rst
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@ -30,7 +30,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
@ -145,7 +145,7 @@ specify the Drude status of each atom type.
correctly. You must use the :doc:`comm_modify <comm_modify>` command to
enable this, e.g.
.. parsed-literal::
.. code-block:: LAMMPS
comm_modify vel yes
@ -220,7 +220,7 @@ command.
Usage example for rigid bodies in the NPT ensemble:
.. parsed-literal::
.. code-block:: LAMMPS
comm_modify vel yes
fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes

2
doc/src/fix_latte.rst
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@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix dftb all latte NULL

2
doc/src/fix_lb_fluid.rst
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@ -50,7 +50,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce sphere1
fix 1 all lb/fluid 1 1 1.0 0.0009982071 setArea 1 1.144592082 dx 2.0 dm 0.3 trilinear noise 300.0 8979873

2
doc/src/fix_lb_momentum.rst
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@ -24,7 +24,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 sphere lb/momentum
fix 1 all lb/momentum linear 1 1 0

2
doc/src/fix_lb_pc.rst
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@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all lb/pc

2
doc/src/fix_lb_rigid_pc_sphere.rst
View File

@ -38,7 +38,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 spheres lb/rigid/pc/sphere
fix 1 all lb/rigid/pc/sphere force 1 0 0 innerNodes ForceAtoms

4
doc/src/fix_lb_viscous.rst
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@ -16,7 +16,9 @@ Syntax
Examples
""""""""
fix 1 flow lb/viscous
.. code-block:: LAMMPS
fix 1 flow lb/viscous
Description
"""""""""""

2
doc/src/fix_lineforce.rst
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@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix hold boundary lineforce 0.0 1.0 1.0

4
doc/src/fix_manifoldforce.rst
View File

@ -17,7 +17,9 @@ Syntax
Examples
""""""""
fix constrain all manifoldforce sphere 5.0
.. code-block:: LAMMPS
fix constrain all manifoldforce sphere 5.0
Description
"""""""""""

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

10
doc/src/fix_meso_move.rst
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@ -39,7 +39,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 boundary meso/move wiggle 3.0 0.0 0.0 1.0 units box
fix 2 boundary meso/move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
@ -107,7 +107,7 @@ Note that the *linear* style is identical to using the *variable*
style with an :doc:`equal-style variable <variable>` that uses the
vdisplace() function. E.g.
.. parsed-literal::
.. code-block:: LAMMPS
variable V equal 10.0
variable x equal vdisplace(0.0,$V)
@ -135,13 +135,13 @@ Note that the *wiggle* style is identical to using the *variable*
style with :doc:`equal-style variables <variable>` that use the
swiggle() and cwiggle() functions. E.g.
.. parsed-literal::
.. code-block:: LAMMPS
variable A equal 10.0
variable T equal 5.0
variable omega equal 2.0\*PI/$T
variable omega equal 2.0*PI/$T
variable x equal swiggle(0.0,$A,$T)
variable v equal v_omega\*($A-cwiggle(0.0,$A,$T))
variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
The *rotate* style rotates particles around a rotation axis *R* =

2
doc/src/fix_meso_stationary.rst
View File

@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 boundary meso/stationary

2
doc/src/fix_momentum.rst
View File

@ -32,7 +32,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all momentum 1 linear 1 1 0
fix 1 all momentum 1 linear 1 1 1 rescale

10
doc/src/fix_move.rst
View File

@ -39,7 +39,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
@ -102,7 +102,7 @@ Note that the *linear* style is identical to using the *variable*
style with an :doc:`equal-style variable <variable>` that uses the
vdisplace() function. E.g.
.. parsed-literal::
.. code-block:: LAMMPS
variable V equal 10.0
variable x equal vdisplace(0.0,$V)
@ -130,13 +130,13 @@ Note that the *wiggle* style is identical to using the *variable*
style with :doc:`equal-style variables <variable>` that use the
swiggle() and cwiggle() functions. E.g.
.. parsed-literal::
.. code-block:: LAMMPS
variable A equal 10.0
variable T equal 5.0
variable omega equal 2.0\*PI/$T
variable omega equal 2.0*PI/$T
variable x equal swiggle(0.0,$A,$T)
variable v equal v_omega\*($A-cwiggle(0.0,$A,$T))
variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
The *rotate* style rotates atoms around a rotation axis *R* =

2
doc/src/fix_mscg.rst
View File

@ -29,7 +29,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all mscg 1
fix 1 all mscg 1 range name A B

2
doc/src/fix_mvv_dpd.rst
View File

@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all mvv/dpd
fix 1 all mvv/dpd 0.5

2
doc/src/fix_neb.rst
View File

@ -34,7 +34,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 active neb 10.0
fix 2 all neb 1.0 perp 1.0 end last

4
doc/src/fix_neb_spin.rst
View File

@ -21,7 +21,9 @@ Syntax
Examples
""""""""
fix 1 active neb/spin 1.0
.. code-block:: LAMMPS
fix 1 active neb/spin 1.0
Description
"""""""""""

16
doc/src/fix_nh.rst
View File

@ -84,7 +84,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nvt temp 300.0 300.0 100.0
fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
@ -153,9 +153,9 @@ by the velocity/position update portion of the integration.
via using an :doc:`immediate variable <variable>` expression accessing
the thermo property 'dt', which is the length of the time step. Example:
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nvt temp 300.0 300.0 $(100.0\*dt)
fix 1 all nvt temp 300.0 300.0 $(100.0*dt)
----------
@ -437,11 +437,15 @@ style "temp" and "pressure", as if one of these sets of commands had
been issued:
For fix nvt:
compute fix-ID\_temp group-ID temp
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp
For fix npt and fix nph:
.. code-block:: LAMMPS
For fix npt and fix nph:
compute fix-ID_temp all temp
compute fix-ID_press all pressure fix-ID_temp

2
doc/src/fix_nh_eff.rst
View File

@ -45,7 +45,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nvt/eff temp 300.0 300.0 0.1
fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0

12
doc/src/fix_nh_uef.rst
View File

@ -32,7 +32,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005
fix biax_nvt all nvt/uef temp 400 400 100 erate 0.000005 0.000005
@ -116,7 +116,7 @@ pressure (Pxx+Pyy)/2 will be controlled.
This example command will control the total hydrostatic pressure under
uniaxial tension:
.. parsed-literal::
.. code-block:: LAMMPS
fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz
@ -124,7 +124,7 @@ This example command will control the average stress in compression
directions, which would typically correspond to free surfaces under
drawing with uniaxial tension:
.. parsed-literal::
.. code-block:: LAMMPS
fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy
@ -140,14 +140,14 @@ method.
For example, the following commands will work:
.. parsed-literal::
.. code-block:: LAMMPS
fix f3 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 y 1 1 5 erate -0.5 -0.5
fix f4 all npt/uef temp 0.7 0.7 0.5 z 1 1 5 erate 0.5 0.5
The following commands will not work:
.. parsed-literal::
.. code-block:: LAMMPS
fix f5 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 1 1 5 erate -0.5 -0.5
fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5
@ -159,7 +159,7 @@ this, it creates its own computes of style "temp/uef" and
"pressure/uef", as if one of these two sets of commands had been
issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp/uef
compute fix-ID_press group-ID pressure/uef fix-ID_temp

4
doc/src/fix_nph_asphere.rst
View File

@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nph/asphere iso 0.0 0.0 1000.0
fix 2 all nph/asphere x 5.0 5.0 1000.0
@ -61,7 +61,7 @@ This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp all temp/asphere
compute fix-ID_press all pressure fix-ID_temp

4
doc/src/fix_nph_body.rst
View File

@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nph/body iso 0.0 0.0 1000.0
fix 2 all nph/body x 5.0 5.0 1000.0
@ -58,7 +58,7 @@ This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/body" and
"pressure", as if these commands had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp all temp/body
compute fix-ID_press all pressure fix-ID_temp

4
doc/src/fix_nph_sphere.rst
View File

@ -26,7 +26,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nph/sphere iso 0.0 0.0 1000.0
fix 2 all nph/sphere x 5.0 5.0 1000.0
@ -74,7 +74,7 @@ This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/sphere" and
"pressure", as if these commands had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp all temp/sphere
compute fix-ID_press all pressure fix-ID_temp

4
doc/src/fix_nphug.rst
View File

@ -44,7 +44,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0
fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
@ -120,7 +120,7 @@ This fix computes a temperature and pressure at each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if one of these two sets of commands had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp

4
doc/src/fix_npt_asphere.rst
View File

@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
@ -69,7 +69,7 @@ This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp all temp/asphere
compute fix-ID_press all pressure fix-ID_temp

4
doc/src/fix_npt_body.rst
View File

@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all npt/body temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 2 all npt/body temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
@ -66,7 +66,7 @@ This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/body" and
"pressure", as if these commands had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp all temp/body
compute fix-ID_press all pressure fix-ID_temp

6
doc/src/fix_npt_cauchy.rst
View File

@ -54,7 +54,9 @@ Syntax
Examples
""""""""
fix 1 water npt/cauchy temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
.. code-block:: LAMMPS
fix 1 water npt/cauchy temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
Description
"""""""""""
@ -379,7 +381,7 @@ This fix compute a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if one of these sets of commands had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp all temp
compute fix-ID_press all pressure fix-ID_temp

4
doc/src/fix_npt_sphere.rst
View File

@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
@ -82,7 +82,7 @@ This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/sphere" and
"pressure", as if these commands had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp all temp/sphere
compute fix-ID_press all pressure fix-ID_temp

2
doc/src/fix_nve.rst
View File

@ -25,7 +25,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve

2
doc/src/fix_nve_asphere.rst
View File

@ -19,7 +19,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/asphere

4
doc/src/fix_nve_asphere_noforce.rst
View File

@ -16,7 +16,9 @@ Syntax
Examples
""""""""
fix 1 all nve/asphere/noforce
.. code-block:: LAMMPS
fix 1 all nve/asphere/noforce
Description
"""""""""""

2
doc/src/fix_nve_awpmd.rst
View File

@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/awpmd

2
doc/src/fix_nve_body.rst
View File

@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/body

2
doc/src/fix_nve_dot.rst
View File

@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/dot

2
doc/src/fix_nve_eff.rst
View File

@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/eff

2
doc/src/fix_nve_limit.rst
View File

@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/limit 0.1

2
doc/src/fix_nve_line.rst
View File

@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/line

4
doc/src/fix_nve_manifold_rattle.rst
View File

@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/manifold/rattle 1e-4 10 sphere 5.0
fix step all nve/manifold/rattle 1e-8 100 ellipsoid 2.5 2.5 5.0 every 25
@ -55,7 +55,7 @@ write a script.
The manifold args may be equal-style variables, like so:
.. parsed-literal::
.. code-block:: LAMMPS
variable R equal "ramp(5.0,3.0)"
fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R

2
doc/src/fix_nve_noforce.rst
View File

@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 wall nve/noforce

2
doc/src/fix_nve_sphere.rst
View File

@ -31,7 +31,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/sphere
fix 1 all nve/sphere update dipole

4
doc/src/fix_nve_spin.rst
View File

@ -23,7 +23,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 all nve/spin lattice moving
fix 1 all nve/spin lattice frozen
@ -64,7 +64,7 @@ info.
To use the spin algorithm, it is necessary to define a map with
the atom\_modify command. Typically, by adding the command:
.. parsed-literal::
.. code-block:: LAMMPS
atom_modify map array

2
doc/src/fix_nve_tri.rst
View File

@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nve/tri

2
doc/src/fix_nvk.rst
View File

@ -16,7 +16,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nvk

4
doc/src/fix_nvt_asphere.rst
View File

@ -20,7 +20,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nvt/asphere temp 300.0 300.0 100.0
fix 1 all nvt/asphere temp 300.0 300.0 100.0 drag 0.2
@ -53,7 +53,7 @@ This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/asphere", as if this command
had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp/asphere

4
doc/src/fix_nvt_body.rst
View File

@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nvt/body temp 300.0 300.0 100.0
fix 1 all nvt/body temp 300.0 300.0 100.0 drag 0.2
@ -50,7 +50,7 @@ This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/body", as if this command
had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp/body

4
doc/src/fix_nvt_manifold_rattle.rst
View File

@ -32,7 +32,9 @@ Syntax
Examples
""""""""
fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0
.. code-block:: LAMMPS
fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0
Description
"""""""""""

4
doc/src/fix_nvt_sllod.rst
View File

@ -23,7 +23,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nvt/sllod temp 300.0 300.0 100.0
fix 1 all nvt/sllod temp 300.0 300.0 100.0 drag 0.2
@ -85,7 +85,7 @@ This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/deform", as if this command had
been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp/deform

2
doc/src/fix_nvt_sllod_eff.rst
View File

@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1
fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2

4
doc/src/fix_nvt_sphere.rst
View File

@ -27,7 +27,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all nvt/sphere temp 300.0 300.0 100.0
fix 1 all nvt/sphere temp 300.0 300.0 100.0 disc
@ -67,7 +67,7 @@ This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/sphere", as if this command
had been issued:
.. parsed-literal::
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp/sphere

2
doc/src/fix_oneway.rst
View File

@ -19,7 +19,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ions oneway 10 semi -x
fix all oneway 1 left -z

2
doc/src/fix_orient.rst
View File

@ -22,7 +22,7 @@ fix orient/bcc command
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec
fix gb all orient/bcc 0 1 2.882 0.001 0.25 0.75 ngb.left ngb.right

2
doc/src/fix_phonon.rst
View File

@ -41,7 +41,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all phonon 20 5000 200000 map.in LJ1D sysdim 1
fix 1 all phonon 20 5000 200000 map.in EAM3D

10
doc/src/fix_pimd.rst
View File

@ -26,7 +26,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 1 all pimd method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
@ -128,14 +128,14 @@ To run a PIMD simulation with M quasi-beads in each ring polymer using
N MPI tasks for each partition's domain-decomposition, you would use P
= MxN processors (cores) and run the simulation as follows:
.. parsed-literal::
.. code-block:: bash
mpirun -np P lmp_mpi -partition MxN -in script
Note that in the LAMMPS input script for a multi-partition simulation,
it is often very useful to define a :doc:`uloop-style variable <variable>` such as
.. parsed-literal::
.. code-block:: LAMMPS
variable ibead uloop M pad
@ -143,7 +143,7 @@ where M is the number of quasi-beads (partitions) used in the
calculation. The uloop variable can then be used to manage I/O
related tasks for each of the partitions, e.g.
.. parsed-literal::
.. code-block:: LAMMPS
dump dcd all dcd 10 system_${ibead}.dcd
restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
@ -163,7 +163,7 @@ To avoid this, users can simply initialize velocities with different
random number seeds assigned to each partition, as defined by the
uloop variable, e.g.
.. parsed-literal::
.. code-block:: LAMMPS
velocity all create 300.0 1234${ibead} rot yes dist gaussian

2
doc/src/fix_planeforce.rst
View File

@ -17,7 +17,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix hold boundary planeforce 1.0 0.0 0.0

4
doc/src/fix_plumed.rst
View File

@ -22,7 +22,9 @@ Syntax
Examples
""""""""
fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
.. code-block:: LAMMPS
fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
Description
"""""""""""

2
doc/src/fix_poems.rst
View File

@ -22,7 +22,7 @@ Syntax:
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 fluid poems group clump1 clump2 clump3
fix 3 fluid poems file cluster.list

2
doc/src/fix_pour.rst
View File

@ -63,7 +63,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix 3 all pour 1000 2 29494 region myblock
fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam range 0.9 1.1

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