diff --git a/doc/src/JPG/balance_nonuniform_small.jpg b/doc/src/JPG/balance_nonuniform_small.jpg deleted file mode 100644 index c6df715727..0000000000 Binary files a/doc/src/JPG/balance_nonuniform_small.jpg and /dev/null differ diff --git a/doc/src/JPG/balance_rcb_small.jpg b/doc/src/JPG/balance_rcb_small.jpg deleted file mode 100644 index f61b2ea4e4..0000000000 Binary files a/doc/src/JPG/balance_rcb_small.jpg and /dev/null differ diff --git a/doc/src/JPG/balance_uniform_small.jpg b/doc/src/JPG/balance_uniform_small.jpg deleted file mode 100644 index 3e9ffc35b9..0000000000 Binary files a/doc/src/JPG/balance_uniform_small.jpg and /dev/null differ diff --git a/doc/src/JPG/dump1_small.jpg b/doc/src/JPG/dump1_small.jpg deleted file mode 100644 index 2ac2015d21..0000000000 Binary files a/doc/src/JPG/dump1_small.jpg and /dev/null differ diff --git a/doc/src/JPG/dump2_small.jpg b/doc/src/JPG/dump2_small.jpg deleted file mode 100644 index 9393ba613f..0000000000 Binary files a/doc/src/JPG/dump2_small.jpg and /dev/null differ diff --git a/doc/src/JPG/gran_funnel.png b/doc/src/JPG/gran_funnel.png deleted file mode 100644 index 8e26005f78..0000000000 Binary files a/doc/src/JPG/gran_funnel.png and /dev/null differ diff --git a/doc/src/JPG/gran_funnel_small.jpg b/doc/src/JPG/gran_funnel_small.jpg deleted file mode 100644 index 6e29803388..0000000000 Binary files a/doc/src/JPG/gran_funnel_small.jpg and /dev/null differ diff --git a/doc/src/JPG/gran_mixer.png b/doc/src/JPG/gran_mixer.png deleted file mode 100644 index 6ea7221241..0000000000 Binary files a/doc/src/JPG/gran_mixer.png and /dev/null differ diff --git a/doc/src/JPG/gran_mixer_small.jpg b/doc/src/JPG/gran_mixer_small.jpg deleted file mode 100644 index 7cc85d92bf..0000000000 Binary files a/doc/src/JPG/gran_mixer_small.jpg and /dev/null differ diff --git a/doc/src/JPG/hop1_small.jpg b/doc/src/JPG/hop1_small.jpg deleted file mode 100644 index 155a777485..0000000000 Binary files a/doc/src/JPG/hop1_small.jpg and /dev/null differ diff --git a/doc/src/JPG/hop2_small.jpg b/doc/src/JPG/hop2_small.jpg deleted file mode 100644 index a412408b83..0000000000 Binary files a/doc/src/JPG/hop2_small.jpg and /dev/null differ diff --git a/doc/src/JPG/saed_ewald_intersect_small.jpg b/doc/src/JPG/saed_ewald_intersect_small.jpg deleted file mode 100644 index 6dbe169848..0000000000 Binary files a/doc/src/JPG/saed_ewald_intersect_small.jpg and /dev/null differ diff --git a/doc/src/JPG/saed_mesh_small.jpg b/doc/src/JPG/saed_mesh_small.jpg deleted file mode 100644 index 4f936b3575..0000000000 Binary files a/doc/src/JPG/saed_mesh_small.jpg and /dev/null differ diff --git a/doc/src/JPG/screenshot_atomeye_small.jpg b/doc/src/JPG/screenshot_atomeye_small.jpg deleted file mode 100644 index 364a6ace4a..0000000000 Binary files a/doc/src/JPG/screenshot_atomeye_small.jpg and /dev/null differ diff --git a/doc/src/JPG/screenshot_gl_small.jpg b/doc/src/JPG/screenshot_gl_small.jpg deleted file mode 100644 index 8184cc8016..0000000000 Binary files a/doc/src/JPG/screenshot_gl_small.jpg and /dev/null differ diff --git a/doc/src/JPG/screenshot_pymol_small.jpg b/doc/src/JPG/screenshot_pymol_small.jpg deleted file mode 100644 index 237e8aed37..0000000000 Binary files a/doc/src/JPG/screenshot_pymol_small.jpg and /dev/null differ diff --git a/doc/src/JPG/screenshot_vmd_small.jpg b/doc/src/JPG/screenshot_vmd_small.jpg deleted file mode 100644 index 18a18b005b..0000000000 Binary files a/doc/src/JPG/screenshot_vmd_small.jpg and /dev/null differ diff --git a/doc/src/JPG/sinusoid_small.jpg b/doc/src/JPG/sinusoid_small.jpg deleted file mode 100644 index 1643d81698..0000000000 Binary files a/doc/src/JPG/sinusoid_small.jpg and /dev/null differ diff --git a/doc/src/JPG/xrd_mesh_small.jpg b/doc/src/JPG/xrd_mesh_small.jpg deleted file mode 100644 index 1c5241705f..0000000000 Binary files a/doc/src/JPG/xrd_mesh_small.jpg and /dev/null differ diff --git a/doc/src/Python_examples.rst b/doc/src/Python_examples.rst index 976358801e..6b444e40ed 100644 --- a/doc/src/Python_examples.rst +++ b/doc/src/Python_examples.rst @@ -80,16 +80,23 @@ See the python/README file for instructions on how to run them and the source code for individual scripts for comments about what they do. Here are screenshots of the vizplotgui_tool.py script in action for -different visualization package options. Click to see larger images: +different visualization package options: -.. image:: JPG/screenshot_gl_small.jpg - :target: JPG/screenshot_gl.jpg +.. |pyex1| image:: img/screenshot_gl.jpg + :width: 24% -.. image:: JPG/screenshot_atomeye_small.jpg - :target: JPG/screenshot_atomeye.jpg +.. |pyex2| image:: img/screenshot_atomeye.jpg + :width: 24% -.. image:: JPG/screenshot_pymol_small.jpg - :target: JPG/screenshot_pymol.jpg +.. |pyex3| image:: img/screenshot_pymol.jpg + :width: 24% + +.. |pyex4| image:: img/screenshot_vmd.jpg + :width: 24% + +|pyex1| |pyex2| |pyex3| |pyex4| + +.. raw:: html + + Click to see larger versions of the images. -.. image:: JPG/screenshot_vmd_small.jpg - :target: JPG/screenshot_vmd.jpg diff --git a/doc/src/balance.rst b/doc/src/balance.rst index 5873724924..fbf8c8fb5f 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -177,16 +177,16 @@ volume (area in 2d) assigned to each processor, as in the following 2d diagram where processor sub-domains are shown and particles are colored by the processor that owns them. -.. list-table:: +.. |balance1| image:: img/balance_uniform.jpg + :width: 32% - * - .. figure:: JPG/balance_uniform_small.jpg - :target: JPG/balance_uniform.jpg +.. |balance2| image:: img/balance_nonuniform.jpg + :width: 32% - - .. figure:: JPG/balance_nonuniform_small.jpg - :target: JPG/balance_nonuniform.jpg +.. |balance3| image:: img/balance_rcb.jpg + :width: 32% - - .. figure:: JPG/balance_rcb_small.jpg - :target: JPG/balance_rcb.jpg +|balance1| |balance2| |balance3| The leftmost diagram is the default partitioning of the simulation box across processors (one sub-box for each of 16 processors); the middle diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index cad4bc1b93..7ee5b91dab 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -68,8 +68,8 @@ reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire simulation domain or (b) manually using selected values as shown in the 2D diagram below. -.. image:: JPG/saed_mesh_small.jpg - :target: JPG/saed_mesh.jpg +.. image:: img/saed_mesh.jpg + :scale: 75% :align: center For a mesh defined by the simulation domain, a rectilinear grid is @@ -103,8 +103,8 @@ mesh and a *dR_Ewald* thick surface of the Ewald sphere. See the example 3D intensity data and the intersection of a [010] zone axis in the below image. -.. image:: JPG/saed_ewald_intersect_small.jpg - :target: JPG/saed_ewald_intersect.jpg +.. image:: img/saed_ewald_intersect.jpg + :scale: 75% :align: center The atomic scattering factors, fj, accounts for the reduction in diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index 29b1e9ebd0..29bb2d2d3b 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -71,8 +71,8 @@ reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire simulation domain or (b) manually using selected values as shown in the 2D diagram below. -.. image:: JPG/xrd_mesh_small.jpg - :target: JPG/xrd_mesh.jpg +.. image:: img/xrd_mesh.jpg + :scale: 75% :align: center For a mesh defined by the simulation domain, a rectilinear grid is diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index b58489f868..4239933721 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -257,8 +257,7 @@ individual lattice points being "above" or "below" the mathematical expression for the sinusoidal curve. If a finer lattice were used, the sinusoid would appear to be "smoother". Also note the use of the "xlat" and "ylat" :doc:`thermo_style ` keywords which -converts lattice spacings to distance. Click on the image for a -larger version. +converts lattice spacings to distance. .. code-block:: LAMMPS @@ -275,10 +274,14 @@ larger version. create_atoms 1 box var v set x xx set y yy write_dump all atom sinusoid.lammpstrj -.. image:: JPG/sinusoid_small.jpg - :target: JPG/sinusoid.jpg +.. image:: img/sinusoid.jpg + :scale: 50% :align: center +.. raw:: html + + Click on the image for a larger version. + The *rotate* keyword allows specification of the orientation at which molecules are inserted. The axis of rotation is determined by the rotation vector (Rx,Ry,Rz) that goes through the diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index d222c208ac..396f1eeb2d 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -116,19 +116,17 @@ script to generate the images/movie. Here are two sample images, rendered as 1024x1024 JPEG files. -.. raw:: html - - Click to see the full-size images: - -.. |dump1| image:: JPG/dump1_small.jpg - :target: JPG/dump1.jpg +.. |dump1| image:: img/dump1.jpg :width: 48% -.. |dump2| image:: JPG/dump2_small.jpg - :target: JPG/dump2.jpg +.. |dump2| image:: img/dump2.jpg :width: 48% |dump1| |dump2| +.. raw:: html + + Click to see the full-size images: + Only atoms in the specified group are rendered in the image. The :doc:`dump_modify region and thresh ` commands can also alter what atoms are included in the image. diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index b92644fcd9..0753794aa7 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -156,16 +156,16 @@ assigned to each processor, as in the following 2d diagram where processor sub-domains are shown and atoms are colored by the processor that owns them. -.. list-table:: +.. |balance1| image:: img/balance_uniform.jpg + :width: 32% - * - .. figure:: JPG/balance_uniform_small.jpg - :target: JPG/balance_uniform.jpg +.. |balance2| image:: img/balance_nonuniform.jpg + :width: 32% - - .. figure:: JPG/balance_nonuniform_small.jpg - :target: JPG/balance_nonuniform.jpg +.. |balance3| image:: img/balance_rcb.jpg + :width: 32% - - .. figure:: JPG/balance_rcb_small.jpg - :target: JPG/balance_rcb.jpg +|balance1| |balance2| |balance3| The leftmost diagram is the default partitioning of the simulation box across processors (one sub-box for each of 16 processors); the middle diff --git a/doc/src/fix_wall_gran_region.rst b/doc/src/fix_wall_gran_region.rst index ecf850f11e..5d40bdd639 100644 --- a/doc/src/fix_wall_gran_region.rst +++ b/doc/src/fix_wall_gran_region.rst @@ -63,17 +63,22 @@ granular particles when they are close enough to touch the wall. See the :doc:`fix wall/region ` and :doc:`fix wall/gran ` commands for related kinds of walls for non-granular particles and simpler wall geometries, respectively. -Here are snapshots of example models using this command. -Corresponding input scripts can be found in examples/granregion. -Click on the images to see a bigger picture. Movies of these -simulations are `here on the Movies page `_ of the LAMMPS -web site. +Here are snapshots of example models using this command. Corresponding +input scripts can be found in examples/granregion. Movies of these +simulations are `here on the Movies page `_ +of the LAMMPS web site. -.. image:: JPG/gran_funnel_small.jpg - :target: JPG/gran_funnel.png +.. |wallgran1| image:: img/gran_funnel.png + :width: 48% -.. image:: JPG/gran_mixer_small.jpg - :target: JPG/gran_mixer.png +.. |wallgran2| image:: img/gran_mixer.png + :width: 48% + +|wallgran1| |wallgran2| + +.. raw:: html + + Click on the images to see a bigger picture. ---------- diff --git a/doc/src/JPG/balance_nonuniform.jpg b/doc/src/img/balance_nonuniform.jpg similarity index 100% rename from doc/src/JPG/balance_nonuniform.jpg rename to doc/src/img/balance_nonuniform.jpg diff --git a/doc/src/JPG/balance_rcb.jpg b/doc/src/img/balance_rcb.jpg similarity index 100% rename from doc/src/JPG/balance_rcb.jpg rename to doc/src/img/balance_rcb.jpg diff --git a/doc/src/JPG/balance_uniform.jpg b/doc/src/img/balance_uniform.jpg similarity index 100% rename from doc/src/JPG/balance_uniform.jpg rename to doc/src/img/balance_uniform.jpg diff --git a/doc/src/JPG/dump1.jpg b/doc/src/img/dump1.jpg similarity index 100% rename from doc/src/JPG/dump1.jpg rename to doc/src/img/dump1.jpg diff --git a/doc/src/JPG/dump2.jpg b/doc/src/img/dump2.jpg similarity index 100% rename from doc/src/JPG/dump2.jpg rename to doc/src/img/dump2.jpg diff --git a/doc/src/img/gran_funnel.png b/doc/src/img/gran_funnel.png new file mode 100644 index 0000000000..b5d0008f9b Binary files /dev/null and b/doc/src/img/gran_funnel.png differ diff --git a/doc/src/img/gran_mixer.png b/doc/src/img/gran_mixer.png new file mode 100644 index 0000000000..d37e17a5f7 Binary files /dev/null and b/doc/src/img/gran_mixer.png differ diff --git a/doc/src/JPG/hop1.jpg b/doc/src/img/hop1.jpg similarity index 100% rename from doc/src/JPG/hop1.jpg rename to doc/src/img/hop1.jpg diff --git a/doc/src/JPG/hop2.jpg b/doc/src/img/hop2.jpg similarity index 100% rename from doc/src/JPG/hop2.jpg rename to doc/src/img/hop2.jpg diff --git a/doc/src/JPG/saed_ewald_intersect.jpg b/doc/src/img/saed_ewald_intersect.jpg similarity index 100% rename from doc/src/JPG/saed_ewald_intersect.jpg rename to doc/src/img/saed_ewald_intersect.jpg diff --git a/doc/src/JPG/saed_mesh.jpg b/doc/src/img/saed_mesh.jpg similarity index 100% rename from doc/src/JPG/saed_mesh.jpg rename to doc/src/img/saed_mesh.jpg diff --git a/doc/src/JPG/screenshot_atomeye.jpg b/doc/src/img/screenshot_atomeye.jpg similarity index 100% rename from doc/src/JPG/screenshot_atomeye.jpg rename to doc/src/img/screenshot_atomeye.jpg diff --git a/doc/src/JPG/screenshot_gl.jpg b/doc/src/img/screenshot_gl.jpg similarity index 100% rename from doc/src/JPG/screenshot_gl.jpg rename to doc/src/img/screenshot_gl.jpg diff --git a/doc/src/JPG/screenshot_pymol.jpg b/doc/src/img/screenshot_pymol.jpg similarity index 100% rename from doc/src/JPG/screenshot_pymol.jpg rename to doc/src/img/screenshot_pymol.jpg diff --git a/doc/src/JPG/screenshot_vmd.jpg b/doc/src/img/screenshot_vmd.jpg similarity index 100% rename from doc/src/JPG/screenshot_vmd.jpg rename to doc/src/img/screenshot_vmd.jpg diff --git a/doc/src/JPG/sinusoid.jpg b/doc/src/img/sinusoid.jpg similarity index 100% rename from doc/src/JPG/sinusoid.jpg rename to doc/src/img/sinusoid.jpg diff --git a/doc/src/JPG/xrd_mesh.jpg b/doc/src/img/xrd_mesh.jpg similarity index 100% rename from doc/src/JPG/xrd_mesh.jpg rename to doc/src/img/xrd_mesh.jpg diff --git a/doc/src/neb.rst b/doc/src/neb.rst index e2c7fac51b..fdccdf3d9f 100644 --- a/doc/src/neb.rst +++ b/doc/src/neb.rst @@ -392,14 +392,20 @@ barrier. To illustrate, here are images from the final snapshot produced by the neb_combine.py script run on the dump files produced by the two -example input scripts in examples/neb. Click on them to see a larger -image. +example input scripts in examples/neb. -.. image:: JPG/hop1_small.jpg - :target: JPG/hop1.jpg -.. image:: JPG/hop2_small.jpg - :target: JPG/hop2.jpg +.. |neb1| image:: img/hop1.jpg + :width: 48% + +.. |neb2| image:: img/hop2.jpg + :width: 48% + +|neb1| |neb2| + +.. raw:: html + + Click on them to see a larger image. ---------- diff --git a/doc/src/pair_extep.rst b/doc/src/pair_extep.rst index 8e5bc3ac9f..417a837265 100644 --- a/doc/src/pair_extep.rst +++ b/doc/src/pair_extep.rst @@ -33,7 +33,7 @@ none Related commands """""""""""""""" -"pair_tersoff" pair_tersoff.html +`pair_tersoff ` **Default:** none