Unverified Commit 6745c377 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #1222 from lammps/doc-adjust3 

Some adjustments to the documentation for the per style listing pages
parents 4004b8f1 4434481c

doc/src/Run_options.txt

+28 −25
Original line number Diff line number Diff line
@@ -354,29 +354,31 @@ the LAMMPS simulation domain. 


:line



[-restart2data restartfile (remap) datafile keyword value ...] :link(restart2data)

[-restart2data restartfile \[remap\] datafile keyword value ...]

:link(restart2data)



Convert the restart file into a data file and immediately exit.  This

is the same operation as if the following 2-line input script were

run:



read_restart restartfile (remap)

read_restart restartfile \[remap\]

write_data datafile keyword value ... :pre



Note that the specified restartfile and/or datafile can have the

wild-card character "*".  The restartfile can also have the wild-card

The specified restartfile and/or datafile name may contain the wild-card

character "*".  The restartfile name may also contain the wild-card

character "%".  The meaning of these characters is explained on the

"read_restart"_read_restart.html and "write_data"_write_data.html doc

pages.  The use of "%" means that a parallel restart file can be read.

Note that a filename such as file.* will need to be enclosed in quotes

to avoid shell expansion of the "*" character.

Note that a filename such as file.* may need to be enclosed in quotes or

the "*" character prefixed with a backslash ("\") to avoid shell

expansion of the "*" character.



Note that following restartfile, the optional word "remap" can be

used.  This has the effect of adding it to the

"read_restart"_read_restart.html command, as explained on its doc

page.  This is useful if reading the restart file triggers an error

that atoms have been lost.  In that case, use of the remap flag should

allow the data file to still be produced.

Following restartfile argument, the optional word "remap" may be used.

This has the same effect like adding it to a

"read_restart"_read_restart.html command, and operates as explained on

its doc page.  This is useful if reading the restart file triggers an

error that atoms have been lost.  In that case, use of the remap flag

should allow the data file to still be produced.



The syntax following restartfile (or remap), namely
@@ -388,29 +390,30 @@ optional keyword/value settings. 


:line



[-restart2dump restartfile {remap} group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)

[-restart2dump restartfile \[remap\] group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)



Convert the restart file into a dump file and immediately exit.  This

is the same operation as if the following 2-line input script were

run:



read_restart restartfile (remap)

read_restart restartfile \[remap\]

write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre



Note that the specified restartfile and dumpfile can have wild-card

characters ("*","%") as explained on the

Note that the specified restartfile and dumpfile names may contain

wild-card characters ("*","%") as explained on the

"read_restart"_read_restart.html and "write_dump"_write_dump.html doc

pages.  The use of "%" means that a parallel restart file and/or

parallel dump file can be read and/or written.  Note that a filename

such as file.* will need to be enclosed in quotes to avoid shell

expansion of the "*" character.



Note that following restartfile, the optional word "remap" can be

used.  This has the effect as adding it to the

"read_restart"_read_restart.html command, as explained on its doc

page.  This is useful if reading the restart file triggers an error

that atoms have been lost.  In that case, use of the remap flag should

allow the dump file to still be produced.

such as file.* may need to be enclosed in quotes or the "*" character

prefixed with a backslash ("\") to avoid shell expansion of the "*"

character.



Note that following the restartfile argument, the optional word "remap"

can be used.  This has the effect as adding it to the

"read_restart"_read_restart.html command, as explained on its doc page.

This is useful if reading the restart file triggers an error that atoms

have been lost.  In that case, use of the remap flag should allow the

dump file to still be produced.



The syntax following restartfile (or remap), namely

doc/src/angle_coeff.txt

+6 −18
Original line number Diff line number Diff line
@@ -60,26 +60,14 @@ doc page for details. 


:line



Here is an alphabetic list of angle styles defined in LAMMPS.  Click on

the style to display the formula it computes and coefficients

specified by the associated "angle_coeff"_angle_coeff.html command.



Note that there are also additional angle styles submitted by users

which are included in the LAMMPS distribution.  The full list of all

angle styles is on the "Commands bond"_Commands_bond.html#angle doc

The list of all angle styles defined in LAMMPS is given on the

"angle_style"_angle_style.html doc page.  They are also listed in more

compact form on the "Commands angle"_Commands_bond.html#angle doc

page.



"angle_style none"_angle_none.html - turn off angle interactions

"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul



"angle_style charmm"_angle_charmm.html - CHARMM angle

"angle_style class2"_angle_class2.html - COMPASS (class 2) angle

"angle_style cosine"_angle_cosine.html - cosine angle potential

"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential

"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle

"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential

"angle_style harmonic"_angle_harmonic.html - harmonic angle

"angle_style table"_angle_table.html - tabulated by angle :ul

On either of those pages, click on the style to display the formula it

computes and its coefficients as specified by the associated

angle_coeff command.



:line

doc/src/angle_style.txt

+9 −4
Original line number Diff line number Diff line
@@ -57,10 +57,15 @@ Here is an alphabetic list of angle styles defined in LAMMPS. Click on 
the style to display the formula it computes and coefficients

specified by the associated "angle_coeff"_angle_coeff.html command.



Note that there are also additional angle styles submitted by users

which are included in the LAMMPS distribution.  The full list of all

angle styles are is on the "Commands bond"_Commands_bond.html#angle

doc page.

Click on the style to display the formula it computes, any additional

arguments specified in the angle_style command, and coefficients

specified by the associated "angle_coeff"_angle_coeff.html command.



There are also additional accelerated pair styles included in the

LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.

The individual style names on the "Commands

angle"_Commands_bond.html#angle doc page are followed by one or more

of (g,i,k,o,t) to indicate which accelerated styles exist.



"none"_angle_none.html - turn off angle interactions

"zero"_angle_zero.html - topology but no interactions

doc/src/bond_coeff.txt

+7 −19
Original line number Diff line number Diff line
@@ -56,25 +56,13 @@ corresponds to the 1st example above would be listed as 


:line



Here is an alphabetic list of bond styles defined in LAMMPS.  Click on

the style to display the formula it computes and coefficients

specified by the associated "bond_coeff"_bond_coeff.html command.



Note that here are also additional bond styles submitted by users

which are included in the LAMMPS distribution.  The full list of all

bond styles is on the "Commands bond"_Commands_bond.html doc page.



"bond_style none"_bond_none.html - turn off bonded interactions

"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul



"bond_style class2"_bond_class2.html - COMPASS (class 2) bond

"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond

"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles

"bond_style harmonic"_bond_harmonic.html - harmonic bond

"bond_style morse"_bond_morse.html - Morse bond

"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond

"bond_style quartic"_bond_quartic.html - breakable quartic bond

"bond_style table"_bond_table.html - tabulated by bond length :ul

The list of all bond styles defined in LAMMPS is given on the

"bond_style"_bond_style.html doc page.  They are also listed in more

compact form on the "Commands bond"_Commands_bond.html doc page.



On either of those pages, click on the style to display the formula it

computes and its coefficients as specified by the associated

bond_coeff command.



:line

doc/src/bond_style.txt

+10 −4
Original line number Diff line number Diff line
@@ -65,9 +65,15 @@ Here is an alphabetic list of bond styles defined in LAMMPS. Click on 
the style to display the formula it computes and coefficients

specified by the associated "bond_coeff"_bond_coeff.html command.



Note that there are also additional bond styles submitted by users

which are included in the LAMMPS distribution.  The full list of all

bond styles is on the "Commands bond"_Commands_bond.html doc page.

Click on the style to display the formula it computes, any additional

arguments specified in the bond_style command, and coefficients

specified by the associated "bond_coeff"_bond_coeff.html command.



There are also additional accelerated pair styles included in the

LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.

The individual style names on the "Commands bond"_Commands_bond.html

doc page are followed by one or more of (g,i,k,o,t) to indicate which

accelerated styles exist.



"none"_bond_none.html - turn off bonded interactions

"zero"_bond_zero.html - topology but no interactions

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