ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

repair incorrect conversions on [*] expressions by txt2rst

Browse Source
This commit is contained in:
Axel Kohlmeyer
2020-01-22 13:00:28 -05:00
parent 37e8195b01
commit 8a1f893b43
14 changed files with 21 additions and 1505 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
doc/src/Howto_bash.rst
View File

@ -115,8 +115,8 @@ Files in Ubuntu on Windows
^^^^^^^^^^^^^^^^^^^^^^^^^^
When you launch "Bash on Ubuntu on Windows" you will start out in your Linux
user home directory /home/\ **username**\ . You can access your Windows user directory
using the /mnt/c/Users/\ **username** folder.
user home directory /home/[username]\ . You can access your Windows user directory
using the /mnt/c/Users/[username] folder.
Download LAMMPS
^^^^^^^^^^^^^^^

8
doc/src/compute_angle_local.rst
View File

@ -81,12 +81,12 @@ and output the statistics in various ways:
compute 1 all property/local aatom1 aatom2 aatom3 atype
compute 2 all angle/local eng theta v_cos v_cossq set theta t
dump 1 all local 100 tmp.dump c_1**\*** c_2**\***
dump 1 all local 100 tmp.dump c_1[*] c_2[*]
compute 3 all reduce ave c_2**\***
thermo_style custom step temp press c_3**\***
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*]
fix 10 all ave/histo 10 10 100 -1 1 20 c_2\ **3** mode vector file tmp.histo
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo
The :doc:`dump local <dump>` command will output the energy, angle,
cosine(angle), cosine\^2(angle) for every angle in the system. The

8
doc/src/compute_bond_local.rst
View File

@ -134,12 +134,12 @@ output the statistics in various ways:
compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local engpot dist v_dsq set dist d
dump 1 all local 100 tmp.dump c_1**\*** c_2**\***
dump 1 all local 100 tmp.dump c_1[*] c_2[*]
compute 3 all reduce ave c_2**\***
thermo_style custom step temp press c_3**\***
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*]
fix 10 all ave/histo 10 10 100 0 6 20 c_2\ **3** mode vector file tmp.histo
fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo
The :doc:`dump local <dump>` command will output the energy, distance,
distance\^2 for every bond in the system. The

8
doc/src/compute_chunk_spread_atom.rst
View File

@ -32,7 +32,7 @@ Examples
.. parsed-literal::
compute 1 all chunk/spread/atom mychunk c_com**\*** c_gyration
compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration
Description
"""""""""""
@ -109,7 +109,7 @@ with 3 columns:
.. parsed-literal::
compute com all com/chunk mychunk
compute 10 all chunk/spread/atom mychunk c_com[\*]
compute 10 all chunk/spread/atom mychunk c_com[*]
compute 10 all chunk/spread/atom mychunk c_com[1] c_com[2] c_com[3]
@ -125,8 +125,8 @@ to the bench/in.chain script.
compute cmol all chunk/atom molecule
compute com all com/chunk cmol
compute comchunk all chunk/spread/atom cmol c_com**\***
dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk**\***
compute comchunk all chunk/spread/atom cmol c_com[*]
dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk[*]
dump_modify 1 sort id
The same per-chunk data for each atom could be used to define per-atom

8
doc/src/compute_dihedral_local.rst
View File

@ -79,12 +79,12 @@ the system and output the statistics in various ways:
compute 1 all property/local datom1 datom2 datom3 datom4 dtype
compute 2 all dihedral/local phi v_cos v_cossq set phi p
dump 1 all local 100 tmp.dump c_1**\*** c_2**\***
dump 1 all local 100 tmp.dump c_1[*] c_2[*]
compute 3 all reduce ave c_2**\***
thermo_style custom step temp press c_3**\***
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*]
fix 10 all ave/histo 10 10 100 -1 1 20 c_2\ **2** mode vector file tmp.histo
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo
The :doc:`dump local <dump>` command will output the angle,
cosine(angle), cosine\^2(angle) for every dihedral in the system. The

4
doc/src/compute_displace_atom.rst
View File

@ -94,10 +94,10 @@ something like the following commands:
write_dump all custom tmp.dump id type x y z # see comment below
variable Dhop equal 0.6
variable check atom "c_dsp\ **4** > v_Dhop"
variable check atom "c_dsp[4] > v_Dhop"
compute dsp all displace/atom refresh check
dump 1 all custom 100 tmp.dump id type x y z
dump_modify 1 append yes thresh c_dsp\ **4** > $\ *Dhop* &
dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} &
refresh c_dsp delay 100
The :doc:`dump\_modify thresh <dump_modify>` command will only output

2
doc/src/fix_ave_chunk.rst
View File

@ -440,7 +440,7 @@ By default, these header lines are as follows:
In the first line, ID and name are replaced with the fix-ID and group
name. The second line describes the two values that are printed at
the first of each section of output. In the third line the values are
replaced with the appropriate value names, e.g. fx or c\_myCompute\ **2**\ .
replaced with the appropriate value names, e.g. fx or c\_myCompute[2].
The words in parenthesis only appear with corresponding columns if the
chunk style specified for the :doc:`compute chunk/atom <compute_chunk_atom>` command supports them. The OrigID