[pull] develop from lammps:develop

cmake/presets/lammps-gui.cmake

@@ -0,0 +1,74 @@
+set(WIN_PACKAGES
+  AMOEBA
+  ASPHERE
+  BODY
+  BPM
+  BROWNIAN
+  CG-DNA
+  CG-SPICA
+  CLASS2
+  COLLOID
+  COLVARS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMMAND
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GRAPHICS
+  GRANULAR
+  INTERLAYER
+  KSPACE
+  LEPTON
+  MACHDYN
+  MANYBODY
+  MC
+  MEAM
+  MISC
+  ML-IAP
+  ML-POD
+  ML-SNAP
+  ML-UF3
+  MOFFF
+  MOLECULE
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  QEQ
+  QTB
+  REACTION
+  REAXFF
+  RHEO
+  RIGID
+  SHOCK
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  YAFF)
+
+foreach(PKG ${WIN_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()
+
+set(BUILD_SHARED_LIBS ON CACHE BOOL "" FORCE)
+set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
+set(USE_INTERNAL_LINALG ON CACHE BOOL "" FORCE)
+set(FFT KISS CACHE STRING "" FORCE)
+set(BUILD_MPI OFF CACHE BOOL "" FORCE)
+set(BUILD_TOOLS OFF CACHE BOOL "" FORCE)
+set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")

doc/src/Errors_details.rst

@@ -142,11 +142,24 @@ contacts or bad geometries (for the given force styles in use) leading
 to forces that can no longer be represented as numbers.  Those will show
 as "NaN" or "Inf".  On most machines, the program will continue, but
 there is no way to recover from it and those NaN or Inf values will
-propagate.  So-called :doc:`"soft-core" potentials <pair_fep_soft>` or
-the :doc:`"soft" repulsive-only pair style <pair_soft>` are less prone
-for this behavior (depending on the settings in use) and can be used at
-the beginning of a simulation.  Also, single precision numbers can
-overflow much faster, so for the GPU, KOKKOS, or INTEL package it may be
+propagate.
+
+If the "NaN" or "Inf" appears in the first simulation step, the most
+common cause is overlapping atoms.  Note that when atoms are *very*
+close, this cannot be seen when visualizing the geometry, since the
+atoms are effectively sitting on top of each other.  A good test is to
+insert a command like :doc:`delete_atoms 0.1 all all <delete_atoms>` and
+then monitor the output to see how many atoms are deleted, if any.  A
+non-zero number would be an indication of overlapping atoms. Note that
+atoms can also overlap through periodic boundaries when the box
+dimensions are too small (e.g. determined by min/max position of atoms
+without padding).
+
+So-called :doc:`"soft-core" potentials <pair_fep_soft>` or the
+:doc:`"soft" repulsive-only pair style <pair_soft>` are less prone for
+this behavior (depending on the settings in use) and can be used at the
+beginning of a simulation.  Also, single precision numbers can overflow
+much faster, so for the GPU, KOKKOS, or INTEL package it may be
 beneficial to run with double precision initially before switching to
 mixed or single precision for faster execution when the system has
 relaxed.

doc/src/Packages_details.rst

@@ -263,6 +263,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
 * :doc:`pair_style gayberne <pair_gayberne>`
 * :doc:`pair_style resquared <pair_resquared>`
 * :doc:`pair_style ylz <pair_ylz>`
+* :doc:`pair_style line/lj <pair_line_lj>`
+* :doc:`pair_style tri/lj <pair_tri_lj>`
 * `doc/PDF/pair_gayberne_extra.pdf <PDF/pair_gayberne_extra.pdf>`_
 * `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
 * ``examples/ASPHERE``

doc/src/dump_image.rst

@@ -56,7 +56,7 @@ Syntax
          level = mesh refinement level, value between 1 (low resolution) and 6 (ultra high resolution)
          width = diameter of wireframe edges (distance units) (ignored for triangles)
        *body* = color bflag1 bflag2
-         color = *type* or *index*
+         color = *type* or *index* or *atom*
          bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
        *compute* = computeID color cflag1 cflag2
          computeID = ID of computes that generates objects to draw
@@ -181,9 +181,10 @@ Syntax
          color = name of color for simulation box lines and processor subdomain lines
        *subboxtrans* arg = transparency
          transparency = transparency for simulation subbox lines (value between 0 (invisible) and 1 (fully opaque))
-       *color* args = name R G B
+       *color* args = name R G B *or* name hex
          name = name of color
          R,G,B = red/green/blue numeric values from 0.0 to 1.0
+         hex = 24-bit RGB color in hexadecimal
        *ccolor* args = computeID color
          computeID = ID of the compute
          color = name of color for image objects provided by this compute when using "const" color style
@@ -218,6 +219,7 @@ Examples
 
    labelmap atom 1 C 2 H 3 O 4 N
    dump_modify 1 acolor C gray acolor H white acolor O red acolor N blue
+   dump_modify 1 color gray80 0.8 0.8 0.8 color gray20 0x333333
 
 Description
 """""""""""
@@ -585,25 +587,34 @@ is used to define body particles with internal state
 body style.  If this keyword is not used, such particles will be drawn
 as spheres, the same as if they were regular atoms.
 
-The :doc:`Howto body <Howto_body>` page describes the body styles
-LAMMPS currently supports, and provides more details as to the kind of
-body particles they represent and how they are drawn by this dump
-image command.  For all the body styles, individual atoms can be
-either a body particle or a usual point (non-body) particle.  Non-body
-particles will be drawn the same way they would be as a regular atom.
-The *bflag1* and *bflag2* settings are numerical values which are
-passed to the body style to affect how the drawing of a body particle
-is done.  See the :doc:`Howto body <Howto_body>` page for a
-description of what these parameters mean for each body style.
+The :doc:`Howto body <Howto_body>` page describes the body styles LAMMPS
+currently supports, and provides more details as to the kind of body
+particles they represent and how they are drawn by this dump image
+command.  For all the body styles, individual atoms can be either a body
+particle or a usual point (non-body) particle.  Non-body particles will
+be drawn the same way they would be as a regular atom.  The *bflag1* and
+*bflag2* settings are numerical values which are passed to the body
+style to affect how the drawing of a body particle is done.  See the
+:doc:`Howto body <Howto_body>` page for a description of what these
+parameters mean for each body style.
 
 .. versionchanged:: 11Feb2026
 
-The there are currently two supported settings for the *color* value:
-*type*, or *index*.  With the *type* setting the body particles will be
-colored according to the atom type of the particle.  With the *index*
-setting the coloring follows the body index instead.  For both settings,
-the value (type or index) is mapped to the colors of atom types.  The
-list of colors is by default as follows:
+   added *index* color style
+
+.. versionchanged:: TBD
+
+   added *atom* color style
+
+The there are currently three supported settings for the *color* value:
+*type*, *index*, or *atom*.  With the *atom* setting, the color follows
+the coloring selected for coloring atoms (including using color maps).
+With the *type* setting the body particles will be colored according to
+the atom type of the particle.  With the *index* setting the coloring
+follows the body index instead.  For both settings, the value (type or
+index) is mapped to the colors of atom types thus the coloring style for
+atoms **must** be set to *type*.  The list of colors is by default as
+follows:
 
 * type 1 = red
 * type 2 = green
@@ -614,9 +625,9 @@ list of colors is by default as follows:
 
 and repeats itself for types > 6.  This list can by changed with the
 :doc:`dump_modify acolor <dump_image>` command.  If more different
-colors than atom types are desired, the number of atom types must be
-increased when using either the :doc:`create_box <create_box>` or the
-:doc:`read_data <read_data>` command.
+colors than atom types are desired, the *number of atom types* must be
+*increased* correspondingly when using either the :doc:`create_box
+<create_box>` or the :doc:`read_data <read_data>` command.
 
 ----------
 
@@ -1125,12 +1136,22 @@ dump_modify color option.
 
 ----------
 
+.. versionchanged:: TBD
+
+   add support for entering colors in hexadecimal
+
 The *color* keyword allows definition of a new color name, in addition
 to the 140-predefined colors (see below), and associates three
 red/green/blue RGB values with that color name.  The color name can
 then be used with any other dump_modify keyword that takes a color
-name as a value.  The RGB values should each be floating point values
-between 0.0 and 1.0 inclusive.
+name as a value.  The RGB values should be either specified as three
+floating point values between 0.0 and 1.0 inclusive or as a single
+24-bit hexadecimal number. The following two commands are equivalent.
+
+.. code-block:: LAMMPS
+
+   dump_modify 1 color mygray 0.431 0.498 0.502
+   dump_modify 1 color mygray 0x6e7f80
 
 When a color name is converted to RGB values, the user-defined color
 names are searched first, then the 140 pre-defined color names.  This

examples/GRAPHICS/README

@@ -21,7 +21,8 @@ Here is a list of the inputs and which graphics features they demonstrate
 
 - in.peptide-hbonds:        peptide with surrounding water molecules
                             visualize donated and accepted hydrogen bonds
-                            https://youtube.com/shorts/1QEjIITapwQ
+                            overlay graphics from image without background
+                            https://youtube.com/shorts/Q6KBE08AG8c
 
 - in.obstacle-lines         trajectory lines with obstacle flow example
                             https://youtu.be/9HEsGaOsdik

examples/GRAPHICS/in.breakable

@@ -86,7 +86,7 @@ fix labels all graphics/labels  500 text "LAMMPS Tutorial 2 - Stretching CNT usi
                                     text "Atoms with bonds  1: $(c_count[1])  2: $(c_count[2])  3: $(c_count[3])  4: $(c_count[4])" &
                                     32.5 7.5 5.0 size 24 fontcolor white backcolor silver
 
-dump viz all image 500 breakable.*.png c_nbond type size 1600 300 zoom 12.5 shiny 0.2 autobond 1.8 0.4 &
+dump viz all image 500 breakable.*.ppm c_nbond type size 1600 300 zoom 12.5 shiny 0.2 autobond 1.8 0.4 &
         adiam 0.8 box no 0.01 view 0 90 fsaa yes ssao yes 1325123 0.6 axes yes 0.5 0.1 &
         fix arrows const 0 0  fix labels const 0 0 fix vel const 0 0
 

examples/GRAPHICS/in.cubes-and-pyramids

@@ -45,9 +45,9 @@ thermo       1000
 variable progress equal step/v_steps
 fix pbar all graphics/objects ${out} progbar 3 4 y 24.0 12.0 -1.4 30.0 0.5 v_progress 10
 
-dump         2 all image ${out} cubes-and-pyramids.*.png type type size 600 600 shiny 0.4 &
+dump         2 all image ${out} cubes-and-pyramids.*.ppm type type size 600 600 shiny 0.4 &
                          box yes 0.025 axes no 0.5 0.1 zoom 1.5 view 80 0 fsaa yes ssao yes 315123 0.4 &
-                         body type 0.2 3 fix pbar type 0 0
+                         body atom 0.2 3 fix pbar type 0 0
 #            set cylinder diameter--^  ^-- set viz style (1 only faces, 2 cylinders, 3 both)
 dump_modify  2 pad 6 backcolor darkgray backcolor2 gray boxcolor white &
                      acolor 1 steelblue acolor 2 orange  acolor 3 slategray  acolor 4 red

examples/GRAPHICS/in.obstacle-lines

@@ -1,70 +1,70 @@
 # 2d LJ obstacle flow
 
-dimension	2
-boundary	p s p
+dimension       2
+boundary        p s p
 
-atom_style	atomic
-neighbor	0.3 bin
-neigh_modify	delay 5
+atom_style      atomic
+neighbor        0.3 bin
+neigh_modify    delay 5
 
 # create geometry
 
-lattice		hex 0.7
-region		box block 0 40 0 10 -0.25 0.25
-create_box	4 box
-create_atoms	1 box
+lattice         hex 0.7
+region          box block 0 40 0 10 -0.25 0.25
+create_box      4 box
+create_atoms    1 box
 
-mass		* 1.0
+mass            * 1.0
 
 # LJ potentials
 
-pair_style	lj/cut 1.12246
-pair_coeff	* * 1.0 1.0 1.12246
+pair_style      lj/cut 1.12246
+pair_coeff      * * 1.0 1.0 1.12246
 
 # define groups
 
-region	        1 block INF INF INF 1.25 INF INF
-group		lower region 1
-region		2 block INF INF 8.75 INF INF INF
-group		upper region 2
-group		boundary union lower upper
-group		flow subtract all boundary
+region          1 block INF INF INF 1.25 INF INF
+group           lower region 1
+region          2 block INF INF 8.75 INF INF INF
+group           upper region 2
+group           boundary union lower upper
+group           flow subtract all boundary
 
-set		group lower type 2
-set		group upper type 3
+set             group lower type 2
+set             group upper type 3
 
 # initial velocities
 
-compute	        mobile flow temp
-velocity	flow create 1.0 482748 temp mobile
-fix		1 all nve
-fix		2 flow temp/rescale 200 1.0 1.0 0.02 1.0
-fix_modify	2 temp mobile
+compute         mobile flow temp
+velocity        flow create 1.0 482748 temp mobile
+fix             1 all nve
+fix             2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify      2 temp mobile
 
 # Poiselle flow
 
-velocity	boundary set 0.0 0.0 0.0
-fix		3 lower setforce 0.0 0.0 0.0
-fix		4 upper setforce 0.0 NULL 0.0
-fix		5 upper aveforce 0.0 -0.5 0.0
-fix		6 flow addforce 1.0 0.0 0.0
+velocity        boundary set 0.0 0.0 0.0
+fix             3 lower setforce 0.0 0.0 0.0
+fix             4 upper setforce 0.0 NULL 0.0
+fix             5 upper aveforce 0.0 -0.5 0.0
+fix             6 flow addforce 1.0 0.0 0.0
 
 # 2 obstacles
 
-region		void1 sphere 10 4 0 3
-delete_atoms	region void1
-region		void2 sphere 20 7 0 3
-delete_atoms	region void2
+region          void1 sphere 10 4 0 3
+delete_atoms    region void1
+region          void2 sphere 20 7 0 3
+delete_atoms    region void2
 
-fix		7 flow indent 100 sphere 10 4 0 4
-fix		8 flow indent 100 sphere 20 7 0 4
-fix		9 all enforce2d
+fix             7 flow indent 100 sphere 10 4 0 4
+fix             8 flow indent 100 sphere 20 7 0 4
+fix             9 all enforce2d
 
 # Run
 
-timestep	0.003
-thermo		1000
-thermo_modify	temp mobile
+timestep        0.003
+thermo          1000
+thermo_modify   temp mobile
 
 # select atoms to trace and assign atom type 4 so they have a different color (yellow)                
 region   trace block 2 3 1.25 8.75 INF INF
@@ -74,8 +74,8 @@ set      group trace type 4
 # create trajectory lines by averaging positions over 10 MD steps each 10 steps apart
 fix      lines trace graphics/lines 10 10 100 25
 # visualize the trace in silver with a diameter of 0.6 which is half of that of the atoms
-dump     viz   all image 100 obstacle-*.png type type size 800 600 zoom 2.5 center s 0.50 0.7 0 &
+dump     viz   all image 100 obstacle-*.ppm type type size 800 600 zoom 2.5 center s 0.50 0.7 0 &
                                            shiny 0.5 fsaa yes box no 0.025 fix lines const 1 0.6
 dump_modify  viz  pad 6 backcolor darkgray adiam * 1.2 fcolor lines silver
 
-run		30000
+run             30000