From 06511a6e77442fb1b2421c33202a7ddcd621987f Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 11 Jul 2024 19:17:09 -0400 Subject: [PATCH] couple more doc tweaks --- doc/src/Howto_chunk.rst | 16 ++++++++-------- doc/src/read_data.rst | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/src/Howto_chunk.rst b/doc/src/Howto_chunk.rst index 454e58cfa7..f8655b745d 100644 --- a/doc/src/Howto_chunk.rst +++ b/doc/src/Howto_chunk.rst @@ -148,14 +148,14 @@ Example calculations with chunks Here are examples using chunk commands to calculate various properties: -(1) Average velocity in each of 1000 2d spatial bins: +1. Average velocity in each of 1000 2d spatial bins: .. code-block:: LAMMPS compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out -(2) Temperature in each spatial bin, after subtracting a flow +2. Temperature in each spatial bin, after subtracting a flow velocity: .. code-block:: LAMMPS @@ -164,7 +164,7 @@ velocity: compute vbias all temp/profile 1 0 0 y 10 fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out -(3) Center of mass of each molecule: +3. Center of mass of each molecule: .. code-block:: LAMMPS @@ -172,7 +172,7 @@ velocity: compute myChunk all com/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector -(4) Total force on each molecule and ave/max across all molecules: +4. Total force on each molecule and ave/max across all molecules: .. code-block:: LAMMPS @@ -183,7 +183,7 @@ velocity: thermo 1000 thermo_style custom step temp v_xave v_xmax -(5) Histogram of cluster sizes: +5. Histogram of cluster sizes: .. code-block:: LAMMPS @@ -192,16 +192,16 @@ velocity: compute size all property/chunk cc1 count fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo -(6) An example for using a per-chunk value to apply per-atom forces to +6. An example for using a per-chunk value to apply per-atom forces to compress individual polymer chains (molecules) in a mixture, is explained on the :doc:`compute chunk/spread/atom ` command doc page. -(7) An example for using one set of per-chunk values for molecule +7. An example for using one set of per-chunk values for molecule chunks, to create a second set of micelle-scale chunks (clustered molecules, due to hydrophobicity), is explained on the :doc:`compute reduce/chunk ` command doc page. -(8) An example for using one set of per-chunk values (dipole moment +8. An example for using one set of per-chunk values (dipole moment vectors) for molecule chunks, spreading the values to each atom in each chunk, then defining a second set of chunks as spatial bins, and using the :doc:`fix ave/chunk ` command to calculate an diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index dd2f42e2a8..88060a105b 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -12,7 +12,7 @@ Syntax * file = name of data file to read in * zero or more keyword/arg pairs may be appended -* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *group* or *nocoeff* or *fix* +* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom* or *group* or *nocoeff* or *fix* .. parsed-literal::