Merge remote-tracking branch 'origin/master' into refactor-reading

.github/CODEOWNERS

@@ -10,6 +10,7 @@ lib/molfile/*         @akohlmey
 lib/qmmm/*            @akohlmey
 lib/vtk/*             @rbberger
 lib/kim/*             @ellio167
+lib/mesont/*          @iafoss
 
 # whole packages
 src/COMPRESS/*        @akohlmey
@@ -25,6 +26,7 @@ src/USER-COLVARS/*    @giacomofiorin
 src/USER-INTEL/*      @wmbrownintel
 src/USER-MANIFOLD/*   @Pakketeretet2
 src/USER-MEAMC/*      @martok
+src/USER-MESONT/*     @iafoss
 src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
@@ -111,11 +113,14 @@ src/fix_nh.*              @athomps
 src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
 src/min*                  @sjplimp @stanmoore1
+src/utils.*               @akohlmey @rbberger
 
 # tools
 tools/msi2lmp/*       @akohlmey
 tools/emacs/*         @HaoZeke
 tools/singularity/*   @akohlmey @rbberger
+tools/code_standard/* @rbberger
+tools/valgrind/*      @akohlmey
 
 # tests
 unittest/*            @akohlmey @rbberger
@@ -123,6 +128,8 @@ unittest/*            @akohlmey @rbberger
 # cmake
 cmake/*               @junghans @rbberger
 cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
+cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
+cmake/presets/*.cmake @junghans @rbberger @akohlmey
 
 # python
 python/*              @rbberger

.github/CONTRIBUTING.md

@@ -75,7 +75,9 @@ Here is a checklist of steps you need to follow to submit a single file or user
 * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
 * You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file.  For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
 * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
-* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
+* For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree.
+* When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.).
+* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the <name>.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
 
 Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -34,6 +34,7 @@ By submitting this pull request, I agree, that my contribution will be included
 - [ ] The added/updated documentation is integrated and tested with the documentation build system
 - [ ] The feature has been verified to work with the conventional build system
 - [ ] The feature has been verified to work with the CMake based build system
+- [ ] Suitable tests have been added to the unittest tree.
 - [ ] A package specific README file has been included or updated
 - [ ] One or more example input decks are included
 

bench/FERMI/README

@@ -1,51 +0,0 @@
-These are input scripts used to run versions of several of the
-benchmarks in the top-level bench directory using the GPU accelerator
-package.  The results of running these scripts on two different machines
-(a desktop with 2 Tesla GPUs and the ORNL Titan supercomputer) are shown
-on the "GPU (Fermi)" section of the Benchmark page of the LAMMPS WWW
-site: lammps.sandia.gov/bench.
-
-Examples are shown below of how to run these scripts.  This assumes
-you have built 3 executables with the GPU package
-installed, e.g.
-
-lmp_linux_single
-lmp_linux_mixed
-lmp_linux_double
-
-------------------------------------------------------------------------
-
-To run on just CPUs (without using the GPU styles),
-do something like the following:
-
-mpirun -np 1 lmp_linux_double -v x 8 -v y 8 -v z 8 -v t 100 < in.lj
-mpirun -np 12 lmp_linux_double -v x 16 -v y 16 -v z 16 -v t 100 < in.eam
-
-The "xyz" settings determine the problem size.  The "t" setting
-determines the number of timesteps.
-
-These mpirun commands run on a single node.  To run on multiple
-nodes, scale up the "-np" setting.
-
-------------------------------------------------------------------------
-
-To run with the GPU package, do something like the following:
-
-mpirun -np 12 lmp_linux_single -sf gpu -v x 32 -v y 32 -v z 64 -v t 100 < in.lj
-mpirun -np 8 lmp_linux_mixed -sf gpu -pk gpu 2 -v x 32 -v y 32 -v z 64 -v t 100 < in.eam
-
-The "xyz" settings determine the problem size.  The "t" setting
-determines the number of timesteps.  The "np" setting determines how
-many MPI tasks (per node) the problem will run on.  The numeric
-argument to the "-pk" setting is the number of GPUs (per node); 1 GPU
-is the default.  Note that you can use more MPI tasks than GPUs (per
-node) with the GPU package.
-
-These mpirun commands run on a single node.  To run on multiple nodes,
-scale up the "-np" setting, and control the number of MPI tasks per
-node via a "-ppn" setting.
-
-------------------------------------------------------------------------
-
-If the script has "titan" in its name, it was run on the Titan
-supercomputer at ORNL.

bench/FERMI/in.eam

@@ -1,24 +0,0 @@
-# bulk Cu lattice
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		$t

bench/FERMI/in.eam.titan

@@ -1,37 +0,0 @@
-# bulk Cu lattice
-
-newton          off
-package         gpu force/neigh 0 0 1
-processors      * * * grid numa
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-
-pair_style	eam/gpu
-pair_coeff	1 1 Cu_u3.eam
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run             15
-run		100

bench/FERMI/in.lj

@@ -1,22 +0,0 @@
-# 3d Lennard-Jones melt
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 $x 0 $y 0 $z
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run		$t

bench/FERMI/in.lj.titan

@@ -1,35 +0,0 @@
-# 3d Lennard-Jones melt
-
-newton          off
-package         gpu force/neigh 0 0 1
-processors      * * * grid numa
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
-
-units		lj
-atom_style	atomic
-
-lattice		fcc 0.8442
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
-
-velocity	all create 1.44 87287 loop geom
-
-pair_style	lj/cut/gpu 2.5
-pair_coeff	1 1 1.0 1.0 2.5
-
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
-
-fix		1 all nve
-
-run             15
-run		100

bench/FERMI/in.rhodo

@@ -1,30 +0,0 @@
-# Rhodopsin model
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long 8.0 10.0 
-pair_modify     mix arithmetic 
-kspace_style    pppm 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-thermo_style    multi 
-timestep        2.0
-
-run		$t

bench/FERMI/in.rhodo.scaled.titan

@@ -1,39 +0,0 @@
-# Rhodopsin model
-
-newton          off
-package         gpu force/neigh 0 0 1
-processors      * * * grid numa
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long/gpu 8.0 ${cutoff}
-pair_modify     mix arithmetic 
-kspace_style    pppm/gpu 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-# thermo_style    multi 
-timestep        2.0
-
-run             15
-run		100

bench/FERMI/in.rhodo.split.titan

@@ -1,42 +0,0 @@
-# Rhodopsin model
-
-newton          off
-package         gpu force/neigh 0 0 1
-partition	yes 1 processors * * * grid twolevel ${grid} * * * &
-		part 1 2 multiple
-partition	yes 2 processors * * * part 1 2 multiple
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-units           real  
-neigh_modify    delay 5 every 1   
-
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long/gpu 8.0 ${cutoff}
-pair_modify     mix arithmetic 
-kspace_style    pppm/gpu 1e-4 
-
-read_data       data.rhodo
-
-replicate	$x $y $z
-
-fix             1 all shake 0.0001 5 0 m 1.0 a 232
-fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
-
-special_bonds   charmm
- 
-thermo          50
-# thermo_style    multi 
-timestep        2.0
-
-run_style       verlet/split
-run             15
-run		100

bench/POTENTIALS/Ni.meam

@@ -1,2 +0,0 @@
-rc = 4.0
-delr = 0.1

bench/POTENTIALS/Ni.meam

@@ -0,0 +1 @@
+../../potentials/Ni.meam

bench/POTENTIALS/Si.sw

@@ -1,17 +0,0 @@
-# Stillinger-Weber parameters for various elements and mixtures
-# multiple entries can be added to this file, LAMMPS reads the ones it needs
-# these entries are in LAMMPS "metal" units:
-#   epsilon = eV; sigma = Angstroms
-#   other quantities are unitless
-
-# format of a single entry (one or more lines):
-#   element 1, element 2, element 3, 
-#   epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
-
-# Here are the original parameters in metal units, for Silicon from:
-#
-# Stillinger and Weber,  Phys. Rev. B, v. 31, p. 5262, (1985)
-#
-
-Si Si Si 2.1683  2.0951  1.80  21.0  1.20  -0.333333333333
-         7.049556277  0.6022245584  4.0  0.0 0.0

bench/POTENTIALS/Si.sw

@@ -0,0 +1 @@
+../../potentials/Si.sw

bench/POTENTIALS/Si.tersoff

@@ -1,16 +0,0 @@
-# Tersoff parameters for various elements and mixtures
-# multiple entries can be added to this file, LAMMPS reads the ones it needs
-# these entries are in LAMMPS "metal" units:
-#   A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
-#   other quantities are unitless
-
-# This is the Si parameterization from a particular Tersoff paper:
-# J. Tersoff, PRB, 37, 6991 (1988) 
-# See the SiCGe.tersoff file for different Si variants.
-
-# format of a single entry (one or more lines):
-#   element 1, element 2, element 3, 
-#   m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
-
-Si  Si   Si  3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
-             0.33675  1.3258  95.373  3.0  0.2  3.2394  3264.7

bench/POTENTIALS/Si.tersoff

@@ -0,0 +1 @@
+../../potentials/Si.tersoff

bench/POTENTIALS/in.meam

@@ -1,24 +0,0 @@
-# bulk Ni in MEAM
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.52
-region		box block 0 20 0 20 0 20
-create_box	1 box
-create_atoms	1 box
-
-pair_style	meam
-pair_coeff	* * library.meam Ni4 Ni.meam Ni4
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    delay 5 every 1
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100

bench/POTENTIALS/in.reax

@@ -1,22 +0,0 @@
-# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
-
-units		real
-atom_style	charge
-
-read_data	data.reax
-
-#replicate	7 8 10
-replicate	7 8 5
-
-velocity	all create 300.0 9999
-
-pair_style	reax
-pair_coeff      * * ffield.reax 1 2 3 4
-
-timestep	0.1
-fix		2 all nve 
-
-thermo		10
-thermo_style	custom step temp ke pe pxx pyy pzz etotal
-
-run		100

bench/POTENTIALS/library.meam

@@ -1,162 +0,0 @@
-# meam data from vax files fcc,bcc,dia    11/4/92
-# elt        lat     z       ielement     atwt
-# alpha      b0      b1      b2           b3    alat    esub    asub
-# t0         t1              t2           t3            rozero  ibar
-
-'Sn5'       'dia'   4.      50           118.
-5.09        5.00   16.0    04.0          5.0  6.483   3.14     1.00
-1.0         2.00            5.756        -0.30         1.      0
-'Sn'        'dia'   4.      50           118.
-5.09        5.42    8.0     5.0          6.0  6.483   3.14     1.12
-1.0         3.0             5.707        +0.30         1.      0
-'Cu'        'fcc'   12.     29           63.54
-5.10570729  3.634   2.20    6            2.20  3.62    3.54    1.07
-1.0         3.13803254      2.49438711   2.95269237    1.      0
-'Ag'        'fcc'   12.     47           107.870
-5.89222008  4.456   2.20    6            2.20  4.08    2.85    1.06
-1.0         5.54097609      2.45015783   1.28843988    1.      0
-'Au'        'fcc'   12.     79           196.967
-6.34090112  5.449   2.20    6            2.20  4.07    3.93    1.04
-1.0         1.58956328      1.50776392   2.60609758    1.      0
-'Ni1'        'fcc'   12.     28           58.71
-4.99        2.45    2.20    6            2.20  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    0
-'Ni2'        'fcc'   12.     28           58.71
-4.99        2.45    2.20    6            2.20  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    3
-'Ni3'        'fcc'   12.     28           58.71
-4.99        2.45    1.50    6            1.50  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    3
-'Ni4'        'fcc'   12.     28           58.71
-4.99        2.45    1.50    6            1.50  3.52    4.45    1.10
-1.0         3.57            1.60         3.70           1.0    0
-'Ni'        'fcc'   12.     28           58.71
-4.99        2.64    1.50    4.50         1.50  3.52    4.45    1.10
-1.0         1.692           4.987        3.683          1.0    1 
-'Nix'        'fcc'   12.     28           58.71
-4.99        2.64    1.50    4.50         1.50  3.52    4.45    1.10
-1.0         0.00            0.000        3.683          1.0    1 
-'Ni'        'fcc'   12.     28           58.71
-4.99        3.25    0.80    4            1.50  3.52    4.45    1.07
-1.0         -4.052          13.14        3.786		1.0    1
-'Pd'        'fcc'   12.     46           106.4
-6.43230473  4.975   2.20    6            2.20  3.89    3.91    1.01
-1.0         2.33573516      1.38343023   4.47989049    1.      0
-'Pt'        'fcc'   12.     78           195.09
-6.44221724  4.673   2.20    6            2.20  3.92    5.77    1.04
-1.0         2.73335406      -1.3759593   3.29322278    1.      0
-'Al'        'fcc'   12.     13           26.9815
-4.61        2.21    2.20    6.0          2.20  4.05    3.58    1.07
-1.0         -1.78           -2.21        8.01          0.6     0
-'Al'        'fcc'   12.     13           26.9815
-4.69        1.56    4.00    5.5          0.60  4.05    3.36    1.09
-1.0         -0.251          -3.450       8.298         0.6     1
-'Al'        'fcc'   12.     13           26.9815
-4.69	    1.58    1.00    6.0          0.60  4.05    3.36    1.09
-1.0         -0.808          -2.614       8.298         0.6     1
-'Pb'        'fcc'   12.     82           207.19
-6.0564428   5.306   2.20    6            2.20  4.95    2.04    1.01
-1.0         2.74022352      3.06323991   1.2           1.      0
-'Rh'        'fcc'   12.     45           102.905
-6.0045385   1.131   1.00    2            1.00  3.8     5.75    1.05
-1.0         2.9900          4.60231784   4.8           1.      0
-'Ir'        'fcc'   12.     77           192.2
-6.52315787  1.13    1.00    2            1.00  3.84    6.93    1.05
-1.0         1.50000         8.09942666   4.8           1.      0
-'Li'        'bcc'   8.      3            6.939
-2.97244804  1.425   1.00    1.00169907   1.00  3.509   1.65    0.87
-1.0         0.26395017      0.44431129   -0.2          1.      0 
-'Na'        'bcc'   8.      11           22.9898
-3.64280541  2.313   1.00    1.00173951   1.00  4.291   1.13    0.9
-1.0         3.55398839      0.68807569   -0.2          1.      0
-'K'         'bcc'   8.      19           39.102
-3.90128376  2.687   1.00    1.00186667   1.00  5.344   0.94    0.92
-1.0         5.09756981      0.69413264   -0.2          1.      0
-'V'         'bcc'   8.      23           50.942
-4.83265262  4.113   1.00    1.00095022   1.00  3.04    5.3     1
-1.0         4.20161301      4.09946561   -1            1.      0
-'Nb'        'bcc'   8.      41           92.906
-4.79306197  4.374   1.00    1.00101441   1.00  3.301   7.47    1
-1.0         3.75762849      3.82514598   -1            1.      0
-'Ta'        'bcc'   8.      73           180.948
-4.89528669  3.709   1.00    1.00099783   1.00  3.303   8.09    0.99
-1.0         6.08617812      3.35255804   -2.9          1.      0
-'Cr'        'bcc'   8.      24           51.996
-5.12169218  3.224   1.00    1.00048646   1.00  2.885   4.1     0.94
-1.0         -0.207535       12.2600006   -1.9          1.      0
-'Mo'        'bcc'   8.      42           95.94
-5.84872871  4.481   1.00    1.00065204   1.00  3.15    6.81    0.99
-1.0         3.47727181      9.48582009   -2.9          1.      0
-'W'         'bcc'   8.      74           183.85
-5.62777409  3.978   1.00    1.00065894   1.00  3.165   8.66    0.98
-1.0         3.16353338      8.24586928   -2.7          1.      0
-'WL'	    'bcc'   8	    74	         183.85
-5.6831	    6.54    1	    1	         1     3.1639  8.66    0.4
-1	    -0.6	    0.3	         -8.7	       1       3
-'Fe'        'bcc'   8.      26           55.847
-5.07292627  2.935   1.00    1.00080073   1.00  2.866   4.29    0.89
-1.0         5.13579244      4.12042448   -2.7          1.      0
-'Si'        'dia'   4.      14           28.086
-4.87        4.8     4.8     4.8          4.8   5.431   4.63    1.
-1.0         3.30            5.105        -0.80         1.      1
-'Si97'        'dia'   4.      14           28.086
-4.87        4.4     5.5     5.5          5.5   5.431   4.63    1.
-1.0         3.13            4.47         -1.80         2.05    0
-'Si92'        'dia'   4.      14           28.086
-4.87        4.4     5.5     5.5          5.5   5.431   4.63    1.
-1.0         3.13            4.47        -1.80          2.35    0
-'Six'	    'dia'   4	    14	         28.086
-4.87	    4.4	    5.5	    5.5	         5.5   5.431   4.63    1.0
-1.0	    2.05            4.47         -1.8	       2.05     0
-'Sixb'	    'dia'   4	    14	         28.086
-4.87	    4.4	    5.5	    5.5	         5.5   5.431   4.63    1.0
-1.0	    2.05            4.47         -1.8	       2.5     0
-'Mg'       'hcp'   12.      12           24.305
-5.45        2.70    0.0     0.35         3.0   3.20    1.55    1.11
-1.0         8.00            04.1         -02.0         1.0     0
-'C'         'dia'   4.      6            12.0111
-4.38        4.10    4.200   5.00         3.00  3.567   7.37    1.000
-1.0         5.0             9.34         -1.00         2.25    1
-'C'         'dia'   4.      6            12.0111
-4.38        5.20    3.87    4.00         4.50  3.567   7.37    1.278
-1.0         15.             2.09         -6.00         2.5     1
-'C'         'dia'   4.      6            12.0111
-4.38        4.50    4.00    3.50         4.80  3.567   7.37    1.00
-1.0         10.5            1.54         -8.75         3.2     1 
-'C'         'dia'   4.      6            12.0111
-4.38        3.30    2.80    1.50         3.20  3.567   7.37    1.00 
-1.0         10.3            1.54         -8.80         2.5     1 
-'C'         'dia'   4.      6            12.0111
-4.38        4.60    3.45    4.00         4.20  3.567   7.37    1.061
-1.0         15.0            1.74         -8.00         2.5     1
-'C'         'dia'   4.      6            12.0111
-4.38        4.50    4.00    3.50         4.80  3.567   7.37    1.00
-1.0         10.5            1.54         -8.75         3.2     1
-'h'         'dim'   1.      1            1.0079
-2.96        2.70    3.5     3.4          3.4   0.74    2.235   2.27
-1.0         0.19            0.00         0.00          20.00    0
-'h'         'dim'   1.      1            1.0079
-2.96        2.00    4.0     4.0          0.0   0.74    2.235   1.00
-1.0         -0.60           -0.80        -0.0          01.0    1
-'H'         'dim'   1.      1            1.0079
-2.96        2.96    3.0     3.0          3.0   0.74    2.235   2.50
-1.0         0.20            -0.10        0.0           0.5     0
-'H'         'dim'   1.      1            1.0079
-2.96        2.0     3.0     4.0          0.0   0.74    2.225   1.00
-1.0         -0.5            -1.00        0.0           0.15    1
-'H'         'dim'   1.      1            1.0079
-2.96        2.00    2.0     2.0          2.0   0.74    2.235   1.00
-1.0         -0.60           -0.80        -0.0          01.0    2
-'Hni'       'dim'   1.      1            1.0079
-2.96        2.96    3.0     3.0          3.0   0.74    2.235   2.50
-1.0         0.2             -0.1         0.0           0.5     0
-'Hni'         'dim'   1.      1            1.0079
-2.96        2.96    3.0     2.0          3.0   0.74    2.235   36.4
-1.0         0.2             6.0         0.0           22.8     0
-'Vac'       'fcc'   12.     1            1.
-0           0       0.0     0            0.0   1E+08   0       1  
-0           0               0             0             1.     0
-'zz'        'zzz'   99.     1            1.
-0           0       0.0     0            0.0    0.     0.     0.
-0           0               0             0             1.     0
-                                 

bench/POTENTIALS/library.meam

@@ -0,0 +1 @@
+../../potentials/library.meam

bench/POTENTIALS/log.16Mar18.meam.1

@@ -1,84 +0,0 @@
-LAMMPS (16 Mar 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# bulk Ni in MEAM
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-  Time spent = 0.00186539 secs
-
-pair_style	meam
-WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
-pair_coeff	* * library.meam Ni4 Ni.meam Ni4
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    delay 5 every 1
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5
-  ghost atom cutoff = 5
-  binsize = 2.5, bins = 29 29 29
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair meam, perpetual, half/full from (1)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 55.91 | 55.91 | 55.91 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -142400            0   -135782.09     20259.18 
-      50    885.10702   -139411.51            0   -135750.54    32425.433 
-     100     895.5097    -139454.3            0    -135750.3    31804.187 
-Loop time of 30.6278 on 1 procs for 100 steps with 32000 atoms
-
-Performance: 1.410 ns/day, 17.015 hours/ns, 3.265 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 30.088     | 30.088     | 30.088     |   0.0 | 98.24
-Neigh   | 0.48914    | 0.48914    | 0.48914    |   0.0 |  1.60
-Comm    | 0.015916   | 0.015916   | 0.015916   |   0.0 |  0.05
-Output  | 0.00022554 | 0.00022554 | 0.00022554 |   0.0 |  0.00
-Modify  | 0.025481   | 0.025481   | 0.025481   |   0.0 |  0.08
-Other   |            | 0.009055   |            |       |  0.03
-
-Nlocal:    32000 ave 32000 max 32000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    13576 ave 13576 max 13576 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    780360 ave 780360 max 780360 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1560720
-Ave neighs/atom = 48.7725
-Neighbor list builds = 8
-Dangerous builds = 0
-Total wall time: 0:00:30

bench/POTENTIALS/log.16Mar18.meam.4

@@ -1,84 +0,0 @@
-LAMMPS (16 Mar 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# bulk Ni in MEAM
-
-units		metal
-atom_style	atomic
-
-lattice		fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region		box block 0 20 0 20 0 20
-create_box	1 box
-Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
-  1 by 2 by 2 MPI processor grid
-create_atoms	1 box
-Created 32000 atoms
-  Time spent = 0.000587463 secs
-
-pair_style	meam
-WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
-pair_coeff	* * library.meam Ni4 Ni.meam Ni4
-
-velocity	all create 1600.0 376847 loop geom
-
-neighbor	1.0 bin
-neigh_modify    delay 5 every 1
-
-fix		1 all nve
-
-timestep	0.005
-thermo		50
-
-run		100
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5
-  ghost atom cutoff = 5
-  binsize = 2.5, bins = 29 29 29
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair meam, perpetual, half/full from (1)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 17.41 | 17.41 | 17.41 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         1600      -142400            0   -135782.09     20259.18 
-      50    885.10702   -139411.51            0   -135750.54    32425.433 
-     100     895.5097    -139454.3            0    -135750.3    31804.187 
-Loop time of 8.21941 on 4 procs for 100 steps with 32000 atoms
-
-Performance: 5.256 ns/day, 4.566 hours/ns, 12.166 timesteps/s
-99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 8.0277     | 8.0384     | 8.0504     |   0.3 | 97.80
-Neigh   | 0.12555    | 0.12645    | 0.12713    |   0.2 |  1.54
-Comm    | 0.024279   | 0.036776   | 0.048389   |   4.5 |  0.45
-Output  | 9.4414e-05 | 0.00011903 | 0.00018597 |   0.0 |  0.00
-Modify  | 0.01252    | 0.012608   | 0.012795   |   0.1 |  0.15
-Other   |            | 0.005028   |            |       |  0.06
-
-Nlocal:    8000 ave 8045 max 7947 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-Nghost:    6066.75 ave 6120 max 6021 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Neighs:    195090 ave 196403 max 193697 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-FullNghs:  390180 ave 392616 max 387490 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-
-Total # of neighbors = 1560720
-Ave neighs/atom = 48.7725
-Neighbor list builds = 8
-Dangerous builds = 0
-Total wall time: 0:00:08

bench/POTENTIALS/log.16Mar18.reax.1

@@ -1,86 +0,0 @@
-LAMMPS (16 Mar 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
-
-units		real
-atom_style	charge
-
-read_data	data.reax
-  orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  58 atoms
-
-#replicate	7 8 10
-replicate	7 8 5
-  orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
-  1 by 1 by 1 MPI processor grid
-  16240 atoms
-  Time spent = 0.000834942 secs
-
-velocity	all create 300.0 9999
-
-pair_style	reax
-WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
-pair_coeff      * * ffield.reax 1 2 3 4
-
-timestep	0.1
-fix		2 all nve
-
-thermo		10
-thermo_style	custom step temp ke pe pxx pyy pzz etotal
-
-run		100
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 12 13 6
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair reax, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 115.8 | 115.8 | 115.8 Mbytes
-Step Temp KinEng PotEng Pxx Pyy Pzz TotEng 
-       0          300    14521.612   -1616144.2    22296.712   -29858.677    5721.0921   -1601622.5 
-      10    298.98728    14472.591   -1616093.9    21955.847   -24067.096     7389.148   -1601621.3 
-      20    294.76158    14268.045   -1615890.1    19179.258   -10513.494    10789.925     -1601622 
-      30    288.56967    13968.323   -1615591.2    13854.377      5833.02    13949.731   -1601622.9 
-      40    282.06725    13653.571   -1615278.2    6259.9845     19406.33    14947.939   -1601624.6 
-      50    274.84112    13303.787   -1614931.9   -2009.6832    26964.336    13346.855   -1601628.2 
-      60    266.20153    12885.585   -1614519.7   -8441.1641    28485.532    10195.429   -1601634.1 
-      70    259.17085    12545.262   -1614184.2   -11426.993    24941.516    6572.2953   -1601638.9 
-      80    259.73004     12572.33   -1614216.7   -10867.598    16928.461    3033.9021   -1601644.3 
-      90     269.2352    13032.431     -1614679   -7962.3129    4931.5317   -280.22164   -1601646.6 
-     100    280.67181    13586.024   -1615234.3   -3606.1519   -8769.8482   -2527.5887   -1601648.3 
-Loop time of 358.104 on 1 procs for 100 steps with 16240 atoms
-
-Performance: 0.002 ns/day, 9947.338 hours/ns, 0.279 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 358.07     | 358.07     | 358.07     |   0.0 | 99.99
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.01623    | 0.01623    | 0.01623    |   0.0 |  0.00
-Output  | 0.0013328  | 0.0013328  | 0.0013328  |   0.0 |  0.00
-Modify  | 0.012679   | 0.012679   | 0.012679   |   0.0 |  0.00
-Other   |            | 0.006895   |            |       |  0.00
-
-Nlocal:    16240 ave 16240 max 16240 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    32428 ave 32428 max 32428 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    6.69975e+06 ave 6.69975e+06 max 6.69975e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 6699752
-Ave neighs/atom = 412.546
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:06:02

bench/POTENTIALS/log.16Mar18.reax.4

@@ -1,86 +0,0 @@
-LAMMPS (16 Mar 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
-  using 1 OpenMP thread(s) per MPI task
-# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
-
-units		real
-atom_style	charge
-
-read_data	data.reax
-  orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  58 atoms
-
-#replicate	7 8 10
-replicate	7 8 5
-  orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
-  2 by 2 by 1 MPI processor grid
-  16240 atoms
-  Time spent = 0.000491619 secs
-
-velocity	all create 300.0 9999
-
-pair_style	reax
-WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
-pair_coeff      * * ffield.reax 1 2 3 4
-
-timestep	0.1
-fix		2 all nve
-
-thermo		10
-thermo_style	custom step temp ke pe pxx pyy pzz etotal
-
-run		100
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 12 13 6
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair reax, perpetual
-      attributes: half, newton off
-      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newtoff
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 35.58 | 35.68 | 35.77 Mbytes
-Step Temp KinEng PotEng Pxx Pyy Pzz TotEng 
-       0          300    14521.612   -1616144.1    22296.712   -29858.677    5721.0922   -1601622.5 
-      10    298.98728    14472.591   -1616093.8    21955.847   -24067.094     7389.149   -1601621.3 
-      20    294.76158    14268.044     -1615890    19179.258   -10513.494    10789.925     -1601622 
-      30    288.56967    13968.323   -1615591.2     13854.38    5833.0219    13949.731   -1601622.9 
-      40    282.06725    13653.571   -1615278.2     6259.981    19406.327    14947.938   -1601624.7 
-      50    274.84112    13303.787   -1614931.9   -2009.6844    26964.334    13346.855   -1601628.1 
-      60    266.20153    12885.585   -1614519.8   -8441.1628    28485.533    10195.428   -1601634.2 
-      70    259.17085    12545.262   -1614184.2   -11426.992    24941.517     6572.295     -1601639 
-      80    259.73004     12572.33   -1614216.8   -10867.596    16928.464    3033.9024   -1601644.5 
-      90     269.2352    13032.431     -1614679   -7962.3097    4931.5336   -280.21988   -1601646.5 
-     100    280.67181    13586.024   -1615234.3   -3606.1482   -8769.8463   -2527.5874   -1601648.3 
-Loop time of 97.054 on 4 procs for 100 steps with 16240 atoms
-
-Performance: 0.009 ns/day, 2695.944 hours/ns, 1.030 timesteps/s
-99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 94.83      | 95.764     | 96.883     |   9.2 | 98.67
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.16123    | 1.2801     | 2.2132     |  79.9 |  1.32
-Output  | 0.00056076 | 0.00066662 | 0.00095987 |   0.0 |  0.00
-Modify  | 0.0048354  | 0.0049006  | 0.0049515  |   0.1 |  0.01
-Other   |            | 0.004639   |            |       |  0.00
-
-Nlocal:    4060 ave 4080 max 4040 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    14972 ave 14992 max 14952 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    1.8135e+06 ave 1.82186e+06 max 1.80514e+06 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 7253988
-Ave neighs/atom = 446.674
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:01:38

bench/POTENTIALS/reax_defs.h

@@ -1,69 +0,0 @@
-#define PORTABLECOMMENTFLAG
-#ifndef PORTABLECOMMENTFLAG
-// This is just a way to have portable comments 
-// for both C++ and FORTRAN preprocessing.
- /* ///:EOH~                                                                 */
- /*                                                                          */
- /* This file contains array dimension parameters for all the main           */
- /* ReaxFF data structures, some of which need to be directly accessed       */
- /* by Grasp C++ functions. If they are set too small, the calculation       */
- /* will run out of allocated memory. If they are set too big, the machine   */
- /* will not be able to allocate enough memory.                              */
- /*                                                                          */
- 
- /*     NNEIGHMAXDEF =   Max number of neighbors / NATDEF                    */
- /*     NATDEF =         Max number of atoms                                 */
- /*     NATTOTDEF =      Max number of global atoms                          */
- /*     NSORTDEF =       Max number of atom types                            */
- /*     MBONDDEF =       Max number of bonds connected to one atom           */
- /*     NAVIBDEF =       for 2nd derivatives                                 */
- /*     NBOTYMDEF =      Max number of bond types                            */
- /*     NVATYMDEF =      Max number of valency angle types                   */
- /*     NTOTYMDEF =      Max number of torsion angle types                   */
- /*     NHBTYMDEF =      Max number of hydrogen bond types                   */
- /*     NODMTYMDEF =     Max number of off-diagonal Morse types              */
- /*     NBOALLMAXDEF =   Max number of all bonds                             */
- /*     NBOMAXDEF =      Max number of bonds                                 */
- /*     NHBMAXDEF =      Max number of  hydrogen bonds                       */
- /*     NVAMAXDEF =      Max number of valency angles                        */
- /*     NOPMAXDEF =      Max number of out of plane angles                   */
- /*     NTOMAXDEF =      Max number of torsion angles                        */
- /*     NPAMAXDEF =      Max number of general parameters in force field     */
- /*     NMOLMAXDEF =     Max number of molecules in system                   */
- /*     NMOLSETDEF =     Max number of molecules in training set             */
- /*     MRESTRADEF =     Max number of restraints                            */
- /*     MTREGDEF =       Max number of temperature regimes                   */
- /*     MTZONEDEF =      Max number of temperature zones                     */
- /*     MVREGDEF =       Max number of volume regimes                        */
- /*     MVZONEDEF =      Max number of volume zones                          */
- /*     MEREGDEF =       Max number of electric field regimes                */
- /*     MEZONEDEF =      Max number of electric field zones                  */
-#endif
-
-#define NNEIGHMAXDEF 200
-#define NATDEF 50000
-#define NATTOTDEF 1
-#define NSORTDEF 20
-#define MBONDDEF 20
-#define NAVIBDEF 50
-#define NBOTYMDEF 200
-#define NVATYMDEF 200
-#define NTOTYMDEF 200
-#define NHBTYMDEF 200
-#define NODMTYMDEF 20
-#define NBOALLMAXDEF 180000
-#define NBOMAXDEF 90000
-#define NHBMAXDEF 400000
-#define NVAMAXDEF 300000
-#define NOPMAXDEF 00010
-#define NTOMAXDEF 200000
-#define NPAMAXDEF 50
-#define NMOLMAXDEF 2000
-#define NMOLSETDEF 1500
-#define MRESTRADEF 100
-#define MTREGDEF 100
-#define MTZONEDEF 5
-#define MVREGDEF 100
-#define MVZONEDEF 6
-#define MEREGDEF 100
-#define MEZONEDEF 3

cmake/CMakeLists.txt

@@ -32,6 +32,12 @@ endif()
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
 
+# make sure LIBRARY_PATH is set if environment variable is set
+if (DEFINED ENV{LIBRARY_PATH})
+  list(APPEND CMAKE_LIBRARY_PATH "$ENV{LIBRARY_PATH}")
+  message(STATUS "Appending $ENV{LIBRARY_PATH} to CMAKE_LIBRARY_PATH: ${CMAKE_LIBRARY_PATH}")
+endif()
+
 include(LAMMPSUtils)
 
 get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)
@@ -51,7 +57,6 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 # compiler tests
 # these need ot be done early (before further tests).
 #####################################################################
-include(CheckCCompilerFlag)
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
@@ -64,28 +69,11 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
   endif()
 endif()
 
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-  set(CMAKE_TUNE_DEFAULT "-march=native")
-endif()
-
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
-  set(CMAKE_TUNE_DEFAULT "-march=native")
-endif()
-
 # we require C++11 without extensions
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
-# GNU compiler specific features for testing
-if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
-  mark_as_advanced(ENABLE_COVERAGE)
-  if(ENABLE_COVERAGE)
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
-  endif()
-endif()
-
 ########################################################################
 # User input options                                                   #
 ########################################################################
@@ -116,11 +104,11 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
 set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
-  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
+  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
-  REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
+  QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
   USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS
   USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
-  USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+  USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
   USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
   USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
   USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
@@ -197,13 +185,14 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
   target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 endif()
 
-option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
+option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING})
 if(LAMMPS_EXCEPTIONS)
   target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
 endif()
 
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
+pkg_depends(MLIAP SNAP)
 pkg_depends(MPIIO MPI)
 pkg_depends(USER-ATC MANYBODY)
 pkg_depends(USER-LB MPI)
@@ -242,6 +231,48 @@ if(BUILD_OMP)
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
+# Compiler specific features for testing
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
+  mark_as_advanced(ENABLE_COVERAGE)
+  if(ENABLE_COVERAGE)
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC --coverage)
+      target_link_options(lammps PUBLIC --coverage)
+    endif()
+  endif()
+endif()
+
+set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
+mark_as_advanced(ENABLE_SANITIZER)
+set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
+set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
+validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
+string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
+if(NOT ENABLE_SANITIZER STREQUAL "none")
+  if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+      target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+    endif()
+  else()
+    message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
+    set(ENABLE_SANITIZER "none")
+  endif()
+endif()
+
 if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   enable_language(C)
   find_package(LAPACK)
@@ -327,17 +358,10 @@ foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCD
   endif()
 endforeach()
 
-set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")
+set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
 separate_arguments(CMAKE_TUNE_FLAGS)
-include(CheckCXXCompilerFlag)
 foreach(_FLAG ${CMAKE_TUNE_FLAGS})
-  string(REGEX REPLACE "[=\"]" "" _FLAGX ${_FLAG})
+  target_compile_options(lammps PRIVATE ${_FLAG})
-  check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
-  if(COMPILER_SUPPORTS${_FLAGX})
-    target_compile_options(lammps PRIVATE ${_FLAG})
-  else()
-    message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
-  endif()
 endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
@@ -359,6 +383,15 @@ target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
 include(StyleHeaderUtils)
 RegisterStyles(${LAMMPS_SOURCE_DIR})
 
+########################################################
+# Fetch missing external files and archives for packages
+########################################################
+foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
+  if(PKG_${PKG})
+    FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
+  endif()
+endforeach()
+
 ##############################################
 # add sources of enabled packages
 ############################################
@@ -405,13 +438,19 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
   if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
-    file(GLOB_RECURSE ${PKG_LIB}_SOURCES
+    if(PKG_LIB STREQUAL mesont)
-      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
+      enable_language(Fortran)
-      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
+      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
+        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
+    else()
+      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
+        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
+        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
+    endif()
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
     set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
     target_link_libraries(lammps PRIVATE ${PKG_LIB})
@@ -610,6 +649,8 @@ install(
 ###############################################################################
 if(BUILD_SHARED_LIBS)
   if(CMAKE_VERSION VERSION_LESS 3.12)
+    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
+    set(Python_ADDITIONAL_VERSIONS 3.8 3.7 3.6 3.5)
     find_package(PythonInterp) # Deprecated since version 3.12
     if(PYTHONINTERP_FOUND)
         set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
@@ -661,6 +702,7 @@ endif()
 
 include(Testing)
 include(CodeCoverage)
+include(CodingStandard)
 
 ###############################################################################
 # Print package summary
@@ -765,3 +807,6 @@ if(PKG_KSPACE)
     endif()
   endif()
 endif()
+if(BUILD_DOC)
+  message(STATUS "<<< Building HTML Manual >>>")
+endif()

cmake/Modules/CodingStandard.cmake

@@ -0,0 +1,34 @@
+if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonInterp 3.5 QUIET) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+        set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
+        set(Python3_VERSION ${PYTHON_VERSION_STRING})
+    endif()
+else()
+    find_package(Python3 COMPONENTS Interpreter QUIET)
+endif()
+
+if (Python3_EXECUTABLE)
+    if(Python3_VERSION VERSION_GREATER_EQUAL 3.5)
+        add_custom_target(
+          check-whitespace
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Check for whitespace errors")
+        add_custom_target(
+          check-permissions
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Check for permission errors")
+        add_custom_target(
+          fix-whitespace
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Fix whitespace errors")
+        add_custom_target(
+          fix-permissions
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Fix permission errors")
+    endif()
+endif()

cmake/Modules/Documentation.cmake

@@ -2,10 +2,19 @@
 # Build documentation
 ###############################################################################
 option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
-if(BUILD_DOC)
-  find_package(PythonInterp 3 REQUIRED)
 
-  set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
+if(BUILD_DOC)
+  # Sphinx 3.x requires at least Python 3.5
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonInterp 3.5 REQUIRED)
+    set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv -p ${PYTHON_EXECUTABLE})
+  else()
+    find_package(Python3 REQUIRED COMPONENTS Interpreter)
+    if(Python3_VERSION VERSION_LESS 3.5)
+      message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
+    endif()
+    set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
+  endif()
 
   file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
@@ -25,11 +34,10 @@ if(BUILD_DOC)
   )
 
   # download mathjax distribution and unpack to folder "mathjax"
-  file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
+  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
-    "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
+    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
-    EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
+      "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
-
+      EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
-  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
     file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
@@ -37,11 +45,18 @@ if(BUILD_DOC)
   file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
   file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)
 
+  # for increased browser compatibility
+  if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js)
+    file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
+      "${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js")
+  endif()
+
   # note, this may run in parallel with other tasks, so we must not use multiple processes here
   add_custom_command(
     OUTPUT html
     DEPENDS ${DOC_SOURCES} docenv requirements.txt
     COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
+    COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
   )
 
   # copy selected image files to html output tree
@@ -56,17 +71,17 @@ if(BUILD_DOC)
   set(HTML_IMAGE_TARGETS "")
   foreach(_IMG ${HTML_EXTRA_IMAGES})
     string(PREPEND _IMG JPG/)
-    list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}")
+    list(APPEND HTML_IMAGE_TARGETS "${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}")
     add_custom_command(
       OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
-      DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} html/JPG
+      DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_CURRENT_BINARY_DIR}/html/JPG
       COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
     )
   endforeach()
 
   add_custom_target(
     doc ALL
-    DEPENDS html html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
+    DEPENDS html ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
     SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
   )
 

cmake/Modules/FindClangFormat.cmake

@@ -0,0 +1,46 @@
+# Find clang-format
+find_program(ClangFormat_EXECUTABLE NAMES clang-format
+                                          clang-format-10.0
+                                          clang-format-9.0
+                                          clang-format-8.0
+                                          clang-format-7.0
+                                          clang-format-6.0
+                                     DOC "clang-format executable")
+mark_as_advanced(ClangFormat_EXECUTABLE)
+
+if(ClangFormat_EXECUTABLE)
+  # find version
+  execute_process(COMMAND ${ClangFormat_EXECUTABLE} --version
+                  OUTPUT_VARIABLE clang_format_version
+                  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+
+  if(clang_format_version MATCHES "^clang-format version .*")
+    # Arch Linux
+    # clang-format version 10.0.0
+
+    # Ubuntu 18.04 LTS Output
+    # clang-format version 6.0.0-1ubuntu2 (tags/RELEASE_600/final)
+    string(REGEX REPLACE "clang-format version ([0-9.]+).*"
+                         "\\1"
+                         ClangFormat_VERSION
+                         "${clang_format_version}")
+  elseif(clang_format_version MATCHES ".*LLVM version .*")
+    # CentOS 7 Output
+    # LLVM (http://llvm.org/):
+    #   LLVM version 3.4.2
+    #   Optimized build.
+    #   Built Nov  1 2018 (15:06:24).
+    #   Default target: x86_64-redhat-linux-gnu
+    #   Host CPU: x86-64
+    string(REGEX REPLACE ".*LLVM version ([0-9.]+).*"
+                         "\\1"
+                         ClangFormat_VERSION
+                         "${clang_format_version}")
+  else()
+    set(ClangFormat_VERSION "0.0")
+  endif()
+endif()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(ClangFormat REQUIRED_VARS ClangFormat_EXECUTABLE VERSION_VAR ClangFormat_VERSION)

cmake/Modules/LAMMPSUtils.cmake

@@ -85,3 +85,26 @@ function(GenerateBinaryHeader varname outfile files)
         file(APPEND ${outfile} "const unsigned int ${varname}_size = sizeof(${varname});\n")
     endforeach()
 endfunction(GenerateBinaryHeader)
+
+# fetch missing potential files
+function(FetchPotentials pkgfolder potfolder)
+  if (EXISTS "${pkgfolder}/potentials.txt")
+    set(LAMMPS_POTENTIALS_URL "https://download.lammps.org/potentials")
+    file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
+    foreach(line ${linelist})
+      string(FIND ${line} " " blank)
+      math(EXPR plusone "${blank}+1")
+      string(SUBSTRING ${line} 0 ${blank} pot)
+      string(SUBSTRING ${line} ${plusone} -1 sum)
+      if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot})
+        file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
+      endif()
+      if(NOT sum STREQUAL oldsum)
+        message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
+        file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
+          EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
+        file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR})
+      endif()
+    endforeach()
+  endif()
+endfunction(FetchPotentials)

cmake/Modules/Packages/GPU.cmake

@@ -40,6 +40,17 @@ if(GPU_API STREQUAL "CUDA")
 
   set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
+  # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
+  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
+  if (GPU_LIB_OLD_CUBIN_HEADERS)
+    message(FATAL_ERROR "########################################################################\n"
+      "Found file(s) generated by the make-based build system in lib/gpu\n"
+      "Please run\n"
+      "  make -C ${LAMMPS_LIB_SOURCE_DIR}/gpu -f Makefile.serial clean\n"
+      "to remove\n"
+      "########################################################################")
+  endif()
+
   file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
@@ -53,33 +64,44 @@ if(GPU_API STREQUAL "CUDA")
 
   # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
   # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
-  set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
+  set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
   # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
-  if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
+  if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
-    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20] ")
   endif()
-  # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
+  # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
-  if(CUDA_VERSION VERSION_GREATER "4.9")
+  if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
-    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
+  endif()
+  # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
+  if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35]")
   endif()
   # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
-  if(CUDA_VERSION VERSION_GREATER "5.9")
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
-    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
   endif()
   # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
-  if(CUDA_VERSION VERSION_GREATER "7.9")
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
-    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
   endif()
   # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
-  if(CUDA_VERSION VERSION_GREATER "8.9")
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
-    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
   endif()
   # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
-  if(CUDA_VERSION VERSION_GREATER "9.9")
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
-    string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
+  endif()
+  # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
+  endif()
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+    message(WARNING "Unsupported CUDA version. Use at your own risk.")
   endif()
 
-  cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+  cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
           -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
@@ -115,7 +137,7 @@ if(GPU_API STREQUAL "CUDA")
 elseif(GPU_API STREQUAL "OPENCL")
   if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
     # download and unpack support binaries for compilation of windows binaries.
-    set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
+    set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
     file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
             EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
@@ -215,30 +237,41 @@ elseif(GPU_API STREQUAL "HIP")
 
     # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
     # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
-    set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH} ")
+    set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")
     # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
-    if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
+    if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") AND (CUDA_VERSION VERSION_LESS "9.0"))
-      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_20,code=[sm_20,compute_20]")
     endif()
-    # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
+    # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
-    if(CUDA_VERSION VERSION_GREATER "4.9")
+    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
-      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30]")
+    endif()
+    # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11.0
+    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
     endif()
     # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
-    if(CUDA_VERSION VERSION_GREATER "5.9")
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
-      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
     endif()
     # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
-    if(CUDA_VERSION VERSION_GREATER "7.9")
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
-      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
     endif()
     # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
-    if(CUDA_VERSION VERSION_GREATER "8.9")
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
-      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
     endif()
     # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
-    if(CUDA_VERSION VERSION_GREATER "9.9")
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
-      string(APPEND HIP_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
+    endif()
+    # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
+      string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
+    endif()
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+      message(WARNING "Unsupported CUDA version. Use at your own risk.")
     endif()
   endif()
 
@@ -257,10 +290,17 @@ elseif(GPU_API STREQUAL "HIP")
     if(HIP_PLATFORM STREQUAL "hcc")
         configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
 
-        add_custom_command(OUTPUT ${CUBIN_FILE}
+        if(HIP_COMPILER STREQUAL "clang")
-          VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
+          add_custom_command(OUTPUT ${CUBIN_FILE}
-          DEPENDS ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
-          COMMENT "Generating ${CU_NAME}.cubin")
+            DEPENDS ${CU_CPP_FILE}
+            COMMENT "Generating ${CU_NAME}.cubin")
+        else()
+          add_custom_command(OUTPUT ${CUBIN_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            DEPENDS ${CU_CPP_FILE}
+            COMMENT "Generating ${CU_NAME}.cubin")
+        endif()
     elseif(HIP_PLATFORM STREQUAL "nvcc")
         add_custom_command(OUTPUT ${CUBIN_FILE}
           VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}

cmake/Modules/Packages/USER-INTEL.cmake

@@ -77,7 +77,7 @@ else()
     foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
       check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
       if(COMPILER_SUPPORTS${_FLAG})
-	  target_compile_options(lammps PRIVATE ${_FLAG})
+          target_compile_options(lammps PRIVATE ${_FLAG})
       endif()
     endforeach()
   endif()

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -14,10 +14,16 @@ endif()
 option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
 if(DOWNLOAD_SCAFACOS)
   message(STATUS "ScaFaCoS download requested - we will build our own")
+
+  # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
+  file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
+          EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
+
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
     URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
     URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+    PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
                                              --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
                                              --with-internal-fftw --with-internal-pfft

cmake/Modules/Packages/USER-SMD.cmake

@@ -9,7 +9,7 @@ if(DOWNLOAD_EIGEN3)
   message(STATUS "Eigen3 download requested - we will build our own")
   include(ExternalProject)
   ExternalProject_Add(Eigen3_build
-    URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
+    URL https://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
     URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
   )

cmake/Modules/Testing.cmake

@@ -3,6 +3,21 @@
 ###############################################################################
 option(ENABLE_TESTING "Enable testing" OFF)
 if(ENABLE_TESTING)
+  find_program(VALGRIND_BINARY NAMES valgrind)
+  # generate custom suppression file
+  file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
+  file(GLOB VALGRIND_SUPPRESSION_FILES ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
+  foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
+    file(READ ${SUPP} SUPPRESSIONS)
+    file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
+  endforeach()
+  set(VALGRIND_DEFAULT_OPTIONS "--leak-check=full --show-leak-kinds=all --track-origins=yes --suppressions=${CMAKE_BINARY_DIR}/lammps.supp")
+
+  set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
+  set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
+
+  include(CTest)
+
   enable_testing()
   get_filename_component(LAMMPS_UNITTEST_DIR ${LAMMPS_SOURCE_DIR}/../unittest ABSOLUTE)
   get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)

cmake/presets/all_off.cmake

@@ -8,7 +8,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
         USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
         USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
         USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
+        USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
         USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
         USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
         USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)

cmake/presets/all_on.cmake

@@ -10,7 +10,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
         USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
         USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
         USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
+        USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
         USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
         USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
         USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)

cmake/presets/download.cmake

@@ -0,0 +1,17 @@
+# preset that turns on packages with automatic downloads of sources of potentials
+# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
+
+set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()
+
+set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_PLUMED ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" FORCE)
+

cmake/presets/mingw-cross.cmake

@@ -1,10 +1,10 @@
 set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                 GRANULAR KSPACE LATTE MANYBODY MC MISC MOLECULE OPT PERI
+                 GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
-                 POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+                 PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
                  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
                  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
                  USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
-                 USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
+                 USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
                  USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
                  USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
                  USER-YAFF)

cmake/presets/most.cmake

@@ -2,8 +2,8 @@
 # external libraries. Compared to all_on.cmake some more unusual packages
 # are removed. The resulting binary should be able to run most inputs.
 
-set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
-        DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
+        GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
         POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
         USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
         USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD

cmake/presets/nolib.cmake

@@ -3,7 +3,7 @@
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
         VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
-        USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
+        USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
         USER-SCAFACOS USER-SMD USER-VTK)
 
 foreach(PKG ${PACKAGES_WITH_LIB})

doc/github-development-workflow.md

@@ -25,10 +25,10 @@ In the interest of consistency, ONLY ONE of the core LAMMPS developers
 should doing the merging itself.  This is currently
 [@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
 If this assignment needs to be changed, it shall be done right after a
-stable release.  If the currently assigned developer cannot merge outstanding pull 
+stable release.  If the currently assigned developer cannot merge outstanding pull
-requests in a timely manner, or in other extenuating circumstances, 
+requests in a timely manner, or in other extenuating circumstances,
 other core LAMMPS developers with merge rights can merge pull requests,
-when necessary. 
+when necessary.
 
 ## Pull Requests
 

doc/include-file-conventions.md

@@ -65,7 +65,7 @@ Header files will typically contain the definition of a (single) class.
 These header files should have as few include statements as possible.
 This is particularly important for classes that implement a "style" and
 thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
-all be included in the auto-generated `"some_style.h"` files which 
+all be included in the auto-generated `"some_style.h"` files which
 results in a high potential for direct or indirect symbol name clashes.
 
 In the ideal case, the header would only include one file defining the

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "2 June 2020" "2020-06-02"
+.TH LAMMPS "30 June 2020" "2020-06-30"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_basics.rst

@@ -193,14 +193,17 @@ compiler and any :doc:`accelerator packages <Speed_packages>` you have
 included in the build.
 
 You can tell CMake to look for a specific compiler with setting CMake
-variable during configuration.  For a few common choices, there are also
+variables (listed below) during configuration.  For a few common
-presets in the ``cmake/presets`` folder.  For convenience, there is a
+choices, there are also presets in the ``cmake/presets`` folder.  For
-``CMAKE_TUNE_FLAGS`` variable that can be set to apply global compiler
+convenience, there is a ``CMAKE_TUNE_FLAGS`` variable that can be set to
-options.  More on that below, but you can also specify the corresponding
+apply global compiler options (applied to compilation only), to be used
-``CMAKE_*_FLAGS`` variables individually if you want to experiment with
+for adding compiler or host specific optimization flags in addition to
-alternate optimization flags.  You should specify all 3 compilers, so
+the "flags" variables listed below. You may also specify the
-that the (few) LAMMPS source files written in C or Fortran are built
+corresponding ``CMAKE_*_FLAGS`` variables individually, if you want to
-with a compiler consistent with the one used for the C++ files:
+experiment with alternate optimization flags.  You should specify all 3
+compilers, so that the (few) LAMMPS source files written in C or Fortran
+are built with a compiler consistent with the one used for the C++
+files:
 
 .. code-block:: bash
 
@@ -225,15 +228,11 @@ A few example command lines are:
 
 For compiling with the Clang/LLVM compilers a CMake preset is provided that
 can be loaded with `-C ../cmake/presets/clang.cmake`.  Similarly,
-`-C ../cmake/presets/intel.cmake` should switch the 
+`-C ../cmake/presets/intel.cmake` should switch the
 
 In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
 compiler flags to tune for optimal performance on given hosts. By
-default these are initialized to some compiler specific flags, to
+default this variable is empty.
-optimize the LAMMPS executable with optimizations and instructions
-available on the host where LAMMPS is compiled. For example, for Intel
-compilers this would be ``-xHost`` and for GNU compilers this would be
-``-march=native``. To turn these flags off, do ``-D CMAKE_TUNE_FLAGS=``.
 
 .. note::
 
@@ -372,7 +371,8 @@ it.  The build step will also create generic soft links, named
 ``liblammps.a`` and ``liblammps.so``\ , which point to the specific
 ``liblammps_machine.a/so`` files.
 
-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^
 
 Note that for creating a shared library, all the libraries it depends on
 must be compiled to be compatible with shared libraries.  This should be
@@ -462,7 +462,8 @@ tool.  The actual translation is then done via make commands.
 .. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
 .. _sphinx: https://sphinx-doc.org
 
-**Documentation make option**\ :
+Documentation make option
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The following make commands can be issued in the doc folder of the
 LAMMPS source distribution.
@@ -489,7 +490,8 @@ your system.
    current LAMMPS version (HTML and PDF files), from the website
    `download page <https://lammps.sandia.gov/download.html>`_.
 
-**CMake build option**\ :
+CMake build option
+^^^^^^^^^^^^^^^^^^
 
 It is also possible to create the HTML version of the manual within
 the :doc:`CMake build directory <Build_cmake>`.  The reason for this
@@ -512,7 +514,8 @@ Build LAMMPS tools
 Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
 using CMake or Make.
 
-**CMake build3**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -521,7 +524,8 @@ using CMake or Make.
 The generated binaries will also become part of the LAMMPS installation
 (see below).
 
-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -545,7 +549,8 @@ a globally visible place on your system, for others to access.  Note
 that you may need super-user privileges (e.g. sudo) if the directory
 you want to copy files to is protected.
 
-**CMake build**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -553,7 +558,8 @@ you want to copy files to is protected.
    make                        # perform make after CMake command
    make install                # perform the installation into prefix
 
-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 There is no "install" option in the ``src/Makefile`` for LAMMPS.  If
 you wish to do this you will need to first build LAMMPS, then manually

doc/src/Build_development.rst

@@ -8,8 +8,8 @@ useful during development, testing or debugging.
 
 .. _compilation:
 
-Verify compilation flags
+Monitor compilation flags
-------------------------
+-------------------------
 
 Sometimes it is necessary to verify the complete sequence of compilation flags
 generated by the CMake build. To enable a more verbose output during
@@ -19,7 +19,8 @@ compilation you can use the following option.
 
    -D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes
 
-Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+Another way of doing this without reconfiguration is calling make with
+variable VERBOSE set to 1:
 
 .. code-block:: bash
 
@@ -33,25 +34,27 @@ Address, Undefined Behavior, and Thread Sanitizer Support
 ---------------------------------------------------------
 
 Compilers such as GCC and Clang support generating instrumented binaries
-which use different sanitizer libraries to detect problems in code
+which use different sanitizer libraries to detect problems in the code
 during run-time. They can detect issues like:
 
  - `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_
  - `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_
  - `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_
 
-Please note that this kind of instrumentation usually comes with a small
+Please note that this kind of instrumentation usually comes with a
-performance hit (much less than using tools like `Valgrind
+performance hit (but much less than using tools like `Valgrind
-<https://valgrind.org>`_).  The to enable these features additional
+<https://valgrind.org>`_ with a more low level approach).  The to enable
-compiler flags need to be added to the compilation and linking stages.
+these features additional compiler flags need to be added to the
-This is most easily done through setting the ``CMAKE_TUNE_FLAGS``
+compilation and linking stages.  This is done through setting the
-variable during configuration. Examples:
+``ENABLE_SANITIZER`` variable during configuration. Examples:
 
 .. code-block:: bash
 
-   -D CMAKE_TUNE_FLAGS=-fsanitize=address    # enable address sanitizer / memory leak checker
+   -D ENABLE_SANITIZER=none       # no sanitizer active (default)
-   -D CMAKE_TUNE_FLAGS=-fsanitize=undefined  # enable undefined behavior sanitizer
+   -D ENABLE_SANITIZER=address    # enable address sanitizer / memory leak checker
-   -D CMAKE_TUNE_FLAGS=-fsanitize=thread     # enable thread sanitizer
+   -D ENABLE_SANITIZER=leak       # enable memory leak checker (only)
+   -D ENABLE_SANITIZER=undefined  # enable undefined behavior sanitizer
+   -D ENABLE_SANITIZER=thread     # enable thread sanitizer
 
 ----------
 
@@ -86,19 +89,21 @@ The output of this command will be looking something like this::
    [...]$ ctest
    Test project /home/akohlmey/compile/lammps/build-testing
          Start  1: MolPairStyle:hybrid-overlay
-    1/26 Test  #1: MolPairStyle:hybrid-overlay .........   Passed    0.02 sec
+   1/109 Test  #1: MolPairStyle:hybrid-overlay .........   Passed    0.02 sec
          Start  2: MolPairStyle:hybrid
-    2/26 Test  #2: MolPairStyle:hybrid .................   Passed    0.01 sec
+   2/109 Test  #2: MolPairStyle:hybrid .................   Passed    0.01 sec
          Start  3: MolPairStyle:lj_class2
     [...]
-         Start 25: AngleStyle:harmonic
+         Start 107: PotentialFileReader
-   25/26 Test #25: AngleStyle:harmonic .................   Passed    0.01 sec
+ 107/109 Test #107: PotentialFileReader ................   Passed    0.04 sec
-         Start 26: AngleStyle:zero
+         Start 108: EIMPotentialFileReader
-   26/26 Test #26: AngleStyle:zero .....................   Passed    0.01 sec
+ 108/109 Test #108: EIMPotentialFileReader .............   Passed    0.03 sec
-   
+         Start 109: TestSimpleCommands
+ 109/109 Test #109: TestSimpleCommands .................   Passed    0.02 sec
+
    100% tests passed, 0 tests failed out of 26
-   
+
-   Total Test time (real) =   0.27 sec
+   Total Test time (real) =  25.57 sec
 
 
 The ``ctest`` command has many options, the most important ones are:
@@ -117,6 +122,8 @@ The ``ctest`` command has many options, the most important ones are:
      - exclude subset of tests matching the regular expression <regex>
    * - -N
      - dry-run: display list of tests without running them
+   * - -T memcheck
+     - run tests with valgrind memory checker (if available)
 
 In its full implementation, the unit test framework will consist of multiple
 kinds of tests implemented in different programming languages (C++, C, Python,
@@ -126,7 +133,7 @@ in the next section.
 
 .. note::
 
-   This unit test framework is new and still under development.
+   The unit test framework is new and still under development.
    The coverage is only minimal and will be expanded over time.
    Tests styles of the same kind of style (e.g. pair styles or
    bond styles) are performed with the same executable using
@@ -193,8 +200,8 @@ In this particular case, 5 out of 6 sets of tests were conducted, the
 tests for the ``lj/cut/opt`` pair style was skipped, since the tests
 executable did not include it.  To learn what individual tests are performed,
 you (currently) need to read the source code.  You can use code coverage
-recording (see next section) to confirm how well the tests cover the individual
+recording (see next section) to confirm how well the tests cover the code
-source files.
+paths in the individual source files.
 
 The force style test programs have a common set of options:
 
@@ -211,6 +218,14 @@ The force style test programs have a common set of options:
    * - -v
      - verbose output: also print the executed LAMMPS commands
 
+The ``ctest`` tool has no mechanism to directly pass flags to the individual
+test programs, but a workaround has been implemented where these flags can be
+set in an environment variable ``TEST_ARGS``. Example:
+
+.. code-block:: bash
+
+   env TEST_ARGS=-s ctest -V -R BondStyle
+
 To add a test for a style that is not yet covered, it is usually best
 to copy a YAML file for a similar style to a new file, edit the details
 of the style (how to call it, how to set its coefficients) and then
@@ -237,12 +252,22 @@ and working.
      performed with automatically rescaled epsilon to account for
      additional loss of precision from code optimizations and different
      summation orders.
-   - When compiling with aggressive compiler optimization, some tests
+   - When compiling with (aggressive) compiler optimization, some tests
      are likely to fail.  It is recommended to inspect the individual
-     tests in detail to decide whether the specific error for a specific
+     tests in detail to decide, whether the specific error for a specific
      property is acceptable (it often is), or this may be an indication
-     of mis-compiled code (or undesired large of precision due to
+     of mis-compiled code (or an undesired large loss of precision due
-     reordering of operations).
+     to significant reordering of operations and thus less error cancellation).
+
+Tests for other components and utility functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Additional tests that validate utility functions or specific components
+of LAMMPS are implemented as standalone executable which may, or may not
+require creating a suitable LAMMPS instance.  These tests are more specific
+and do not require YAML format input files.  To add a test, either an
+existing source file needs to be extended or a new file added, which in turn
+requires additions to the ``CMakeLists.txt`` file in the source folder.
 
 Collect and visualize code coverage metrics
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -306,3 +331,23 @@ The images below illustrate how the data is presented.
              :target: JPG/coverage-file-branches.png
 
           Source page with branches
+
+Coding style utilities
+----------------------
+
+To aid with enforcing some of the coding style conventions in LAMMPS
+some additional build targets have been added. These require Python 3.5
+or later and will only work on Unix-like operating and file systems.
+The following options are available.
+
+.. code-block:: bash
+
+   make check-whitespace    # generate coverage report in HTML format
+   make fix-whitespace      # generate coverage report in XML format
+   make check-permissions   # delete folder with HTML format coverage report
+   make fix-permissions     # delete all collected coverage data and HTML output
+
+For the code in the ``unittest`` tree we are using the `clang-format`
+tool (Clang version 8.0 or later is required). If available, the source
+code files in the ``unittest`` tree can be updated to conform to the
+formatting settings using ``make format-tests``.

doc/src/Build_link.rst

@@ -1,12 +1,12 @@
 Link LAMMPS as a library to another code
 ========================================
 
-LAMMPS is designed as a library of C++ objects and can thus be
+LAMMPS is designed as a library of C++ objects that can be
 integrated into other applications including Python scripts.
 The files ``src/library.cpp`` and ``src/library.h`` define a
 C-style API for using LAMMPS as a library.  See the :doc:`Howto
-library <Howto_library>` doc page for a description of the interface
+library <Howto_library>` page for a description of the interface
-and how to extend it for your needs.
+and how to use it for your needs.
 
 The :doc:`Build basics <Build_basics>` doc page explains how to build
 LAMMPS as either a shared or static library.  This results in a file
@@ -31,18 +31,18 @@ the suffix ``.so.0`` (or some other number).
    communicator with a subset of MPI ranks to the function creating the
    LAMMPS instance.
 
-----------
+Link with LAMMPS as a static library
-
+------------------------------------
-**Link with LAMMPS as a static library**\ :
 
 The calling application can link to LAMMPS as a static library with
 compilation and link commands as in the examples shown below.  These
-are examples for a code written in C in the file *caller.c*.
+are examples for a code written in C in the file ``caller.c``.
 The benefit of linking to a static library is, that the resulting
 executable is independent of that library since all required
 executable code from the library is copied into the calling executable.
 
-*CMake build*\ :
+CMake build
+^^^^^^^^^^^
 
 This assumes that LAMMPS has been configured without setting a
 ``LAMMPS_MACHINE`` name, installed with "make install", and the
@@ -55,7 +55,8 @@ The commands to compile and link a coupled executable are then:
    mpicc -c -O $(pkgconf liblammps --cflags) caller.c
    mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
 
-*Traditional make*\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 This assumes that LAMMPS has been compiled in the folder
 ``${HOME}/lammps/src`` with "make mpi". The commands to compile and link
@@ -83,20 +84,20 @@ LAMMPS library without any optional packages that depend on libraries
 need to include all flags, libraries, and paths for the coupled
 executable, that are also required to link the LAMMPS executable.
 
-*CMake build*\ :
+CMake build
+^^^^^^^^^^^
 
 When using CMake, additional libraries with sources in the lib folder
 are built, but not included in ``liblammps.a`` and (currently) not
-installed with "make install" and not included in the *pkgconfig*
+installed with ``make install`` and not included in the ``pkgconfig``
 configuration file.  They can be found in the top level build folder,
 but you have to determine the necessary link flags manually.  It is
 therefore recommended to either use the traditional make procedure to
 build and link with a static library or build and link with a shared
 library instead.
 
-.. TODO: this needs to be updated to reflect that latest CMake changes after they are complete.
+Traditional make
-
+^^^^^^^^^^^^^^^^
-*Traditional make*\ :
 
 After you have compiled a static LAMMPS library using the conventional
 build system for example with "make mode=static serial". And you also
@@ -110,10 +111,10 @@ change to:
    g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
      -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs
 
-Note, that you need to link with "g++" instead of "gcc", since the
+Note, that you need to link with ``g++`` instead of ``gcc`` even if you have
-LAMMPS library is C++ code.  You can display the currently applied
+written your code in C, since LAMMPS itself is C++ code.  You can display the
-settings for building LAMMPS for the "serial" machine target by using
+currently applied settings for building LAMMPS for the "serial" machine target
-the command:
+by using the command:
 
 .. code-block:: bash
 
@@ -123,25 +124,24 @@ Which should output something like:
 
 .. code-block:: bash
 
-   # Compiler: 
+   # Compiler:
    CXX=g++
-   # Linker: 
+   # Linker:
    LD=g++
-   # Compilation: 
+   # Compilation:
    CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
-   # Linking: 
+   # Linking:
    LDFLAGS=-g -O
-   # Libraries: 
+   # Libraries:
    LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs
 
 From this you can gather the necessary paths and flags.  With
 makefiles for other *machine* configurations you need to do the
-equivalent and replace "serial" with the corresponding *machine* name
+equivalent and replace "serial" with the corresponding "machine" name
 of the makefile.
 
-----------
+Link with LAMMPS as a shared library
-
+------------------------------------
-**Link with LAMMPS as a shared library**\ :
 
 When linking to LAMMPS built as a shared library, the situation becomes
 much simpler, as all dependent libraries and objects are either included
@@ -151,7 +151,8 @@ linking the calling executable.  Only the *-I* flags are needed.  So the
 example case from above of the serial version static LAMMPS library with
 the POEMS package installed becomes:
 
-*CMake build*\ :
+CMake build
+^^^^^^^^^^^
 
 The commands with a shared LAMMPS library compiled with the CMake
 build process are the same as for the static library.
@@ -161,10 +162,11 @@ build process are the same as for the static library.
    mpicc -c -O $(pkgconf liblammps --cflags) caller.c
    mpicxx -o caller caller.o -$(pkgconf --libs)
 
-*Traditional make*\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 The commands with a shared LAMMPS library compiled with the
-traditional make build using "make mode=shared serial" becomes:
+traditional make build using ``make mode=shared serial`` becomes:
 
 .. code-block:: bash
 
@@ -231,29 +233,3 @@ If a required library is missing, you would get a 'not found' entry:
         libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
         /lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
 
-----------
-
-**Calling the LAMMPS library**\ :
-
-Either flavor of library (static or shared) allows one or more LAMMPS
-objects to be instantiated from the calling program. When used from a
-C++ program, most of the symbols and functions in LAMMPS are wrapped
-in a ``LAMMPS_NS`` namespace; you can safely use any of its classes and
-methods from within the calling code, as needed, and you will not incur
-conflicts with functions and variables in your code that share the name.
-This, however, does not extend to all additional libraries bundled with
-LAMMPS in the lib folder and some of the low-level code of some packages.
-
-To be compatible with C, Fortran, Python programs, the library has a simple
-C-style interface, provided in ``src/library.cpp`` and ``src/library.h``.
-
-See the :doc:`Python library <Python_library>` doc page for a
-description of the Python interface to LAMMPS, which wraps the C-style
-interface from a shared library through the `ctypes python module <ctypes_>`_.
-
-See the sample codes in ``examples/COUPLE/simple`` for examples of C++ and
-C and Fortran codes that invoke LAMMPS through its library interface.
-Other examples in the COUPLE directory use coupling ideas discussed on
-the :doc:`Howto couple <Howto_couple>` doc page.
-
-.. _ctypes: https://docs.python.org/3/library/ctypes.html

doc/src/Build_package.rst

@@ -45,7 +45,8 @@ packages:
 The mechanism for including packages is simple but different for CMake
 versus make.
 
-**CMake build**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: csh
 
@@ -72,7 +73,8 @@ once with CMake.
    invoke cmake.  CMake will give an error if that is not the case,
    indicating how you can un-install all packages in the src dir.
 
-**Traditional make**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -108,7 +110,8 @@ once with make.
    within the same command.  You can include or exclude multiple packages
    in a single make command, e.g. make yes-colloid no-manybody.
 
-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^
 
 Any package can be included or excluded in a LAMMPS build, independent
 of all other packages.  However, some packages include files derived
@@ -132,7 +135,7 @@ src directory.
 
 .. _cmake_presets:
 
-**CMake shortcuts for installing many packages**\ :
+CMake presets for installing many packages
 
 Instead of specifying all the CMake options via the command-line,
 CMake allows initializing its settings cache using script files.
@@ -148,13 +151,14 @@ one of them as a starting point and customize it to your needs.
 
 .. code-block:: bash
 
-    cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake  # enable just a few core packages
+    cmake -C ../cmake/presets/minimal.cmake  [OPTIONS] ../cmake  # enable just a few core packages
-    cmake -C ../cmake/presets/most.cmake    [OPTIONS] ../cmake  # enable most packages
+    cmake -C ../cmake/presets/most.cmake     [OPTIONS] ../cmake  # enable most packages
-    cmake -C ../cmake/presets/nolib.cmake   [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
+    cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake  # enable packages which download sources or potential files
-    cmake -C ../cmake/presets/clang.cmake   [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
+    cmake -C ../cmake/presets/nolib.cmake    [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
-    cmake -C ../cmake/presets/intel.cmake   [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
+    cmake -C ../cmake/presets/clang.cmake    [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
-    cmake -C ../cmake/presets/all_on.cmake  [OPTIONS] ../cmake  # enable all packages
+    cmake -C ../cmake/presets/intel.cmake    [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
-    cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake  # disable all packages
+    cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
+    cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
     mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross compilers
 
 .. note::
@@ -184,7 +188,8 @@ one of them as a starting point and customize it to your needs.
 
 ----------
 
-**Make shortcuts for installing many packages**\ :
+Make shortcuts for installing many packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The following commands are useful for managing package source files
 and their installation when building LAMMPS via traditional make.

doc/src/Build_settings.rst

@@ -44,7 +44,8 @@ require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
 
-**CMake variables**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -74,7 +75,12 @@ to assist:
    -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
    -D MKL_LIBRARIES=path
 
-**Makefile.machine settings**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
+
+To change the FFT library to be used and its options, you have to edit
+your machine Makefile. Below are examples how the makefile variables
+could be changed.
 
 .. code-block:: make
 
@@ -104,7 +110,8 @@ As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if
 the compiler can find the FFT header and library files in its default search path.
 You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link.
 
-**CMake and make info**\ :
+CMake build
+^^^^^^^^^^^
 
 The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
 distribution.  It is portable across all platforms.  Depending on the size
@@ -127,7 +134,7 @@ download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
 version 3.X; the legacy version 2.1.X is no longer supported.
 
 Building FFTW for your box should be as simple as ``./configure; make;
-make install``\ .  The install command typically requires root privileges
+make install``.  The install command typically requires root privileges
 (e.g. invoke it via sudo), unless you specify a local directory with
 the "--prefix" option of configure.  Type ``./configure --help`` to see
 various options.
@@ -169,20 +176,25 @@ ARRAY mode.
 
 .. _size:
 
-Size of LAMMPS data types
+Size of LAMMPS integer types
 ------------------------------------
 
-LAMMPS has a few integer data types which can be defined as 4-byte or
+LAMMPS has a few integer data types which can be defined as either
-8-byte integers.  The default setting of "smallbig" is almost always
+4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
-adequate.
+The default setting of "smallbig" is almost always adequate.
 
-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
    -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall
 
-**Makefile.machine setting**\ :
+Traditional build
+^^^^^^^^^^^^^^^^^
+
+If you want a setting different from the default, you need to edit your
+machine Makefile.
 
 .. code-block:: make
 
@@ -190,7 +202,8 @@ adequate.
 
 The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
 
-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^
 
 The default "smallbig" setting allows for simulations with:
 
@@ -251,7 +264,8 @@ PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
 outputs movie files in MPEG format.  Using these options requires the
 following settings:
 
-**CMake variables**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -276,7 +290,8 @@ variables:
    -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
    -D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable
 
-**Makefile.machine settings**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: make
 
@@ -295,7 +310,8 @@ with a list of graphics libraries to include in the link.  You must
 insure ffmpeg is in a directory where LAMMPS can find it at runtime,
 that is a directory in your PATH environment variable.
 
-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^
 
 Using ``ffmpeg`` to output movie files requires that your machine
 supports the "popen" function in the standard runtime library.
@@ -318,7 +334,8 @@ If this option is enabled, large files can be read or written with
 gzip compression by several LAMMPS commands, including
 :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
 
-**CMake variables**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -326,13 +343,15 @@ gzip compression by several LAMMPS commands, including
                             # default is yes if CMake can find gzip, else no
    -D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it
 
-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: make
 
    LMP_INC = -DLAMMPS_GZIP
 
-**CMake and make info**\ :
+CMake and make info
+^^^^^^^^^^^^^^^^^^^
 
 This option requires that your machine supports the "popen()" function
 in the standard runtime library and that a gzip executable can be
@@ -363,7 +382,8 @@ pointers that are aligned to 16-byte boundaries. Using SSE vector
 instructions efficiently, however, requires memory blocks being
 aligned on 64-byte boundaries.
 
-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
@@ -374,7 +394,8 @@ and revert to using the malloc() C-library function instead.  When
 compiling LAMMPS for Windows systems, malloc() will always be used
 and this setting ignored.
 
-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: make
 
@@ -398,13 +419,15 @@ types, the following setting will be needed.  It converts "long long"
 to a "long" data type, which should be the desired 8-byte integer on
 those systems:
 
-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
    -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)
 
-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: make
 
@@ -420,17 +443,26 @@ Exception handling when using LAMMPS as a library
 This setting is useful when external codes drive LAMMPS as a library.
 With this option enabled, LAMMPS errors do not kill the calling code.
 Instead, the call stack is unwound and control returns to the caller,
-e.g. to Python. Of course the calling code has to be set up to
+e.g. to Python. Of course, the calling code has to be set up to
-*catch* exceptions from within LAMMPS.
+*catch* exceptions thrown from within LAMMPS.
 
-**CMake variable**\ :
+CMake build
+^^^^^^^^^^^
 
 .. code-block:: bash
 
    -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
 
-**Makefile.machine setting**\ :
+Traditional make
+^^^^^^^^^^^^^^^^
 
 .. code-block:: make
 
    LMP_INC = -DLAMMPS_EXCEPTIONS
+
+.. note::
+
+   When LAMMPS is running in parallel, it is not always possible to
+   cleanly recover from an exception since not all parallel ranks may
+   throw an exception and thus other MPI ranks may get stuck waiting for
+   messages from the ones with errors.

doc/src/Commands_all.rst

@@ -46,13 +46,6 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`dimension <dimension>`
    * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
-   * :doc:`dump atom/adios <dump_adios>`
-   * :doc:`dump custom/adios <dump_adios>`
-   * :doc:`dump image <dump_image>`
-   * :doc:`dump movie <dump_image>`
-   * :doc:`dump netcdf <dump_netcdf>`
-   * :doc:`dump netcdf/mpiio <dump_netcdf>`
-   * :doc:`dump vtk <dump_vtk>`
    * :doc:`dump_modify <dump_modify>`
    * :doc:`dynamical_matrix <dynamical_matrix>`
    * :doc:`echo <echo>`
@@ -108,7 +101,8 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`region <region>`
    * :doc:`replicate <replicate>`
    * :doc:`rerun <rerun>`
-   * :doc:`reset_ids <reset_ids>`
+   * :doc:`reset_atom_ids <reset_atom_ids>`
+   * :doc:`reset_mol_ids <reset_mol_ids>`
    * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`
    * :doc:`run <run>`

doc/src/Commands_compute.rst

@@ -79,6 +79,8 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`ke/atom/eff <compute_ke_atom_eff>`
    * :doc:`ke/eff <compute_ke_eff>`
    * :doc:`ke/rigid <compute_ke_rigid>`
+   * :doc:`mesont <compute_mesont>`
+   * :doc:`mliap <compute_mliap>`
    * :doc:`momentum <compute_momentum>`
    * :doc:`msd <compute_msd>`
    * :doc:`msd/chunk <compute_msd_chunk>`
@@ -121,6 +123,7 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
    * :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
    * :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
+   * :doc:`smd/ulsph/effm <compute_smd_ulsph_effm>`
    * :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
    * :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
    * :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`

doc/src/Commands_fix.rst

@@ -42,6 +42,7 @@ OPT.
    * :doc:`bocs <fix_bocs>`
    * :doc:`bond/break <fix_bond_break>`
    * :doc:`bond/create <fix_bond_create>`
+   * :doc:`bond/create/angle <fix_bond_create>`
    * :doc:`bond/react <fix_bond_react>`
    * :doc:`bond/swap <fix_bond_swap>`
    * :doc:`box/relax <fix_box_relax>`
@@ -147,6 +148,7 @@ OPT.
    * :doc:`oneway <fix_oneway>`
    * :doc:`orient/bcc <fix_orient>`
    * :doc:`orient/fcc <fix_orient>`
+   * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`

doc/src/Commands_input.rst

@@ -31,9 +31,9 @@ does something different than this sequence:
    run      100
 
 In the first case, the specified timestep (0.5 fs) is used for two
-simulations of 100 timesteps each.  In the 2nd case, the default
+simulations of 100 timesteps each.  In the second case, the default
-timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
+timestep (1.0 fs) is used for the first 100 step simulation and a 0.5 fs
-timestep is used for the 2nd one.
+timestep is used for the second one.
 
 (2) Some commands are only valid when they follow other commands.  For
 example you cannot set the temperature of a group of atoms until atoms

doc/src/Commands_pair.rst

@@ -78,7 +78,7 @@ OPT.
    * :doc:`coul/long/soft (o) <pair_fep_soft>`
    * :doc:`coul/msm (o) <pair_coul>`
    * :doc:`coul/slater/cut <pair_coul_slater>`
-   * :doc:`coul/slater/long <pair_coul_slater>`   
+   * :doc:`coul/slater/long <pair_coul_slater>`
    * :doc:`coul/shield <pair_coul_shield>`
    * :doc:`coul/streitz <pair_coul>`
    * :doc:`coul/wolf (ko) <pair_coul>`
@@ -136,22 +136,22 @@ OPT.
    * :doc:`lj/class2/soft <pair_fep_soft>`
    * :doc:`lj/cubic (go) <pair_lj_cubic>`
    * :doc:`lj/cut (gikot) <pair_lj>`
-   * :doc:`lj/cut/coul/cut (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
-   * :doc:`lj/cut/coul/debye (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
-   * :doc:`lj/cut/coul/dsf (gko) <pair_lj>`
+   * :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
-   * :doc:`lj/cut/coul/long (gikot) <pair_lj>`
+   * :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/long/cs <pair_cs>`
    * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
-   * :doc:`lj/cut/coul/msm (go) <pair_lj>`
+   * :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
-   * :doc:`lj/cut/coul/wolf (o) <pair_lj>`
+   * :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
    * :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
    * :doc:`lj/cut/dipole/long (g) <pair_dipole>`
    * :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/cut/soft (o) <pair_fep_soft>`
    * :doc:`lj/cut/thole/long (o) <pair_thole>`
-   * :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
+   * :doc:`lj/cut/tip4p/cut (o) <pair_lj_cut_tip4p>`
-   * :doc:`lj/cut/tip4p/long (got) <pair_lj>`
+   * :doc:`lj/cut/tip4p/long (got) <pair_lj_cut_tip4p>`
    * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/expand (gko) <pair_lj_expand>`
    * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
@@ -180,8 +180,10 @@ OPT.
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mesocnt <pair_mesocnt>`
+   * :doc:`mesont/tpm <pair_mesont_tpm>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
+   * :doc:`mliap <pair_mliap>`
    * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
@@ -227,7 +229,6 @@ OPT.
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (k) <pair_snap>`
-   * :doc:`snap (k) <pair_snap>`
    * :doc:`soft (go) <pair_soft>`
    * :doc:`sph/heatconduction <pair_sph_heatconduction>`
    * :doc:`sph/idealgas <pair_sph_idealgas>`

doc/src/Developer/developer.tex

@@ -142,7 +142,7 @@ follows:
   minimize.
 
 \item The Special class walks the bond topology of a molecular system
-  to find 1st, 2nd, 3rd neighbors of each atom.  It is invoked by
+  to find first, second, third neighbors of each atom.  It is invoked by
   several commands, like read\_data, read\_restart, and replicate.
 
 \item The Atom class stores all per-atom arrays.  More precisely, they

doc/src/Errors_debug.rst

@@ -23,7 +23,7 @@ We use it to show how to identify the origin of a segmentation fault.
      double *special_lj = force->special_lj;
      int newton_pair = force->newton_pair;
   +  double comx = 0.0;
-   
+
      inum = list->inum;
      ilist = list->ilist;
   @@ -134,8 +135,10 @@ void PairLJCut::compute(int eflag, int vflag)
@@ -31,7 +31,7 @@ We use it to show how to identify the origin of a segmentation fault.
          }
        }
   -  }
-   
+
   +    comx += atom->rmass[i]*x[i][0]; /* BUG */
   +  }
   +  printf("comx = %g\n",comx);
@@ -42,7 +42,7 @@ After recompiling LAMMPS and running the input you should get something like thi
 
 .. code-block:
 
-   $ ./lmp -in in.melt 
+   $ ./lmp -in in.melt
    LAMMPS (19 Mar 2020)
    OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
      using 1 OpenMP thread(s) per MPI task
@@ -98,11 +98,11 @@ drop back to the GDB prompt.
      Unit style    : lj
      Current step  : 0
      Time step     : 0.005
-   
+
    Program received signal SIGSEGV, Segmentation fault.
    0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
    139      comx += atom->rmass[i]*x[i][0]; /* BUG */
-   (gdb) 
+   (gdb)
 
 Now typing the command "where" will show the stack of functions starting from
 the current function back to "main()".
@@ -119,7 +119,7 @@ the current function back to "main()".
    #4  0x0000000000410ad3 in LAMMPS_NS::Input::execute_command (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:864
    #5  0x00000000004111fb in LAMMPS_NS::Input::file (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:229
    #6  0x000000000040933a in main (argc=<optimized out>, argv=<optimized out>) at /home/akohlmey/compile/lammps/src/main.cpp:65
-   (gdb) 
+   (gdb)
 
 You can also print the value of variables and see if there is anything
 unexpected.  Segmentation faults, for example, commonly happen when a
@@ -189,12 +189,12 @@ the console are not mixed.
 
 .. code-block::
 
-   $ valgrind ./lmp -in in.melt 
+   $ valgrind ./lmp -in in.melt
    ==1933642== Memcheck, a memory error detector
    ==1933642== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
    ==1933642== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
    ==1933642== Command: ./lmp -in in.melt
-   ==1933642== 
+   ==1933642==
    LAMMPS (19 Mar 2020)
    OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
      using 1 OpenMP thread(s) per MPI task
@@ -228,7 +228,7 @@ the console are not mixed.
    ==1933642==    by 0x4111FA: LAMMPS_NS::Input::file() (input.cpp:229)
    ==1933642==    by 0x409339: main (main.cpp:65)
    ==1933642==  Address 0x0 is not stack'd, malloc'd or (recently) free'd
-   ==1933642== 
+   ==1933642==
 
 As you can see, the stack trace information is similar to that obtained
 from GDB. In addition you get a more specific hint about what cause the

doc/src/Errors_messages.rst

@@ -381,7 +381,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    are defined.
 
 *Bond atom missing in box size check*
-   The 2nd atoms needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
@@ -391,7 +391,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    the atoms are too far apart to make a valid bond.
 
 *Bond atom missing in image check*
-   The 2nd atom in a particular bond is missing on this processor.
+   The second atom in a particular bond is missing on this processor.
    Typically this is because the pairwise cutoff is set too short or the
    bond has blown apart and an atom is too far away.
 
@@ -401,12 +401,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    are too far apart to make a valid bond.
 
 *Bond atoms %d %d missing on proc %d at step %ld*
-   The 2nd atom needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
 *Bond atoms missing on proc %d at step %ld*
-   The 2nd atom needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
@@ -1374,7 +1374,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    template does not qualify.
 
 *Cannot use fix box/relax on a 2nd non-periodic dimension*
-   When specifying an off-diagonal pressure component, the 2nd of the two
+   When specifying an off-diagonal pressure component, the second of the two
    dimensions must be periodic.  E.g. if the xy component is specified,
    then the y dimension must be periodic.
 
@@ -1388,7 +1388,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    also keyword tri or xy, this is wrong.
 
 *Cannot use fix box/relax with tilt factor scaling on a 2nd non-periodic dimension*
-   When specifying scaling on a tilt factor component, the 2nd of the two
+   When specifying scaling on a tilt factor component, the second of the two
    dimensions must be periodic.  E.g. if the xy component is specified,
    then the y dimension must be periodic.
 
@@ -1429,7 +1429,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    This would be changing the same box dimension twice.
 
 *Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension*
-   When specifying an off-diagonal pressure component, the 2nd of the two
+   When specifying an off-diagonal pressure component, the second of the two
    dimensions must be periodic.  E.g. if the xy component is specified,
    then the y dimension must be periodic.
 
@@ -1447,13 +1447,13 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Self-explanatory.
 
 *Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension*
-   The 2nd dimension in the barostatted tilt factor must be periodic.
+   The second dimension in the barostatted tilt factor must be periodic.
 
 *Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension*
-   The 2nd dimension in the barostatted tilt factor must be periodic.
+   The second dimension in the barostatted tilt factor must be periodic.
 
 *Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension*
-   The 2nd dimension in the barostatted tilt factor must be periodic.
+   The second dimension in the barostatted tilt factor must be periodic.
 
 *Cannot use fix pour rigid and not molecule*
    Self-explanatory.
@@ -7192,7 +7192,7 @@ keyword to allow for additional bonds to be formed
    does not exist.
 
 *Replacing a fix, but new style != old style*
-   A fix ID can be used a 2nd time, but only if the style matches the
+   A fix ID can be used a second time, but only if the style matches the
    previous fix.  In this case it is assumed you with to reset a fix's
    parameters.  This error may mean you are mistakenly re-using a fix ID
    when you do not intend to.

doc/src/Errors_warnings.rst

@@ -43,17 +43,17 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    Self-explanatory.
 
 *Bond atom missing in box size check*
-   The 2nd atoms needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
 *Bond atom missing in image check*
-   The 2nd atom in a particular bond is missing on this processor.
+   The second atom in a particular bond is missing on this processor.
    Typically this is because the pairwise cutoff is set too short or the
    bond has blown apart and an atom is too far away.
 
 *Bond atoms missing at step %ld*
-   The 2nd atom needed to compute a particular bond is missing on this
+   The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
@@ -486,7 +486,7 @@ This will most likely cause errors in kinetic fluctuations.
    a new style.
 
 *No Kspace calculation with verlet/split*
-   The 2nd partition performs a kspace calculation so the kspace_style
+   The second partition performs a kspace calculation so the kspace_style
    command must be used.
 
 *No automatic unit conversion to XTC file format conventions possible for units lj*

doc/src/Examples.rst

@@ -163,7 +163,7 @@ Here is how you can run and visualize one of the sample problems:
 
 Running the simulation produces the files *dump.indent* and
 *log.lammps*\ .  You can visualize the dump file of snapshots with a
-variety of 3rd-party tools highlighted on the
+variety of third-party tools highlighted on the
 `Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
 web site.
 

doc/src/Howto_bioFF.rst

@@ -102,8 +102,8 @@ documentation for the formula it computes.
 * :doc:`pair_style <pair_buck>` buck/coul/cut
 * :doc:`pair_style <pair_buck>` buck/coul/long
 * :doc:`pair_style <pair_lj>` lj/cut
-* :doc:`pair_style <pair_lj>` lj/cut/coul/cut
+* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/cut
-* :doc:`pair_style <pair_lj>` lj/cut/coul/long
+* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/long
 
 * :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/lj
 * :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/morse

doc/src/Howto_body.rst

@@ -9,13 +9,15 @@ surface meshes of discrete points, collections of sub-particles,
 deformable objects, etc.  Note that other kinds of finite-size
 spherical and aspherical particles are also supported by LAMMPS, such
 as spheres, ellipsoids, line segments, and triangles, but they are
-simpler entities that body particles.  See the :doc:`Howto spherical <Howto_spherical>` doc page for a general overview of all
+simpler entities than body particles.  See the :doc:`Howto spherical
-these particle types.
+<Howto_spherical>` doc page for a general overview of all these
+particle types.
 
 Body particles are used via the :doc:`atom_style body <atom_style>`
 command.  It takes a body style as an argument.  The current body
 styles supported by LAMMPS are as follows.  The name in the first
-column is used as the *bstyle* argument for the :doc:`atom_style body <atom_style>` command.
+column is used as the *bstyle* argument for the :doc:`atom_style body
+<atom_style>` command.
 
 +----------------------+---------------------------------------------------+
 | *nparticle*          | rigid body with N sub-particles                   |
@@ -30,8 +32,9 @@ thus how they can be used to compute pairwise body/body or
 bond/non-body (point particle) interactions.  More details of each
 style are described below.
 
-More styles may be added in the future.  See the :doc:`Modify body <Modify_body>` doc page for details on how to add a new body
+More styles may be added in the future.  See the :doc:`Modify body
-style to the code.
+<Modify_body>` doc page for details on how to add a new body style to
+the code.
 
 ----------
 
@@ -55,10 +58,10 @@ interactions, building neighbor lists, migrating particles between
 processors, output of particles to a dump file, etc.  This means that
 interactions between pairs of bodies or between a body and non-body
 (point) particle need to be encoded in an appropriate pair style.  If
-such a pair style were to mimic the :doc:`fix rigid <fix_rigid>` model,
+such a pair style were to mimic the :doc:`fix rigid <fix_rigid>`
-it would need to loop over the entire collection of interactions
+model, it would need to loop over the entire collection of
-between pairs of simple particles within the two bodies, each time a
+interactions between pairs of simple particles within the two bodies,
-single body/body interaction was computed.
+each time a single body/body interaction was computed.
 
 Thus it only makes sense to use body particles and develop such a pair
 style, when particle/particle interactions are more complex than what
@@ -160,27 +163,6 @@ of the body particle.
 The :doc:`pair_style body/nparticle <pair_body_nparticle>` command can be used
 with this body style to compute body/body and body/non-body interactions.
 
-For output purposes via the :doc:`compute body/local <compute_body_local>` and :doc:`dump local <dump>`
-commands, this body style produces one datum for each of the N
-sub-particles in a body particle.  The datum has 3 values:
-
-.. parsed-literal::
-
-   1 = x position of sub-particle
-   2 = y position of sub-particle
-   3 = z position of sub-particle
-
-These values are the current position of the sub-particle within the
-simulation domain, not a displacement from the center-of-mass (COM) of
-the body particle itself.  These values are calculated using the
-current COM and orientation of the body particle.
-
-For images created by the :doc:`dump image <dump_image>` command, if the
-*body* keyword is set, then each body particle is drawn as a
-collection of spheres, one for each sub-particle.  The size of each
-sphere is determined by the *bflag1* parameter for the *body* keyword.
-The *bflag2* argument is ignored.
-
 ----------
 
 **Specifics of body style rounded/polygon:**
@@ -208,7 +190,7 @@ The Nmin and Nmax arguments are used to bound the size of data
 structures used internally by each particle.
 
 When the :doc:`read_data <read_data>` command reads a data file for this
-body style, the following information must be provided for each entry
+body style, the following information must be provided for each body
 in the *Bodies* section of the data file:
 
 .. parsed-literal::
@@ -219,21 +201,25 @@ in the *Bodies* section of the data file:
    x1 y1 z1
    ...
    xN yN zN
-   i j j k k ...
    diameter
 
-where M = 6 + 3\*N + 2\*N + 1, and N is the number of vertices in the
+where M = 6 + 3\*N + 1, and N is the number of vertices in the body
-body particle.
+particle.
 
 The integer line has a single value N.  The floating point line(s)
-list 6 moments of inertia followed by the coordinates of the N
+list 6 moments of inertia, followed by the coordinates of the N
 vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by
-2N vertex indices corresponding to the end points of the N edges,
+a diameter value = the rounded diameter of the circle that surrounds
-followed by a single diameter value = the rounded diameter of the
+each vertex. The diameter value can be different for each body
-circle that surrounds each vertex. The diameter value can be different
+particle. These floating-point values can be listed on as many lines
-for each body particle. These floating-point values can be listed on
+as you wish; see the :doc:`read_data <read_data>` command for more
-as many lines as you wish; see the :doc:`read_data <read_data>` command
+details.
-for more details.
+
+.. note::
+
+  It is important that the vertices for each polygonal body particle be
+  listed in order around its perimeter, so that edges can be inferred.
+  LAMMPS does not check that this is the case.
 
 The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
 values consistent with the current orientation of the rigid body
@@ -260,10 +246,6 @@ is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
    -0.7071 0.7071 0
    0.7071 0.7071 0
    0.7071 -0.7071 0
-   0 1
-   1 2
-   2 3
-   3 0
    1.0
 
 A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends
@@ -345,8 +327,10 @@ in the *Bodies* section of the data file:
    1 2 3 4
    diameter
 
-where M = 6 + 3\*N + 2\*E + 4\*F + 1, and N is the number of vertices in
+where M = 6 + 3\*N + 2\*E + 4\*F + 1, and N is the number of vertices
-the body particle, E = number of edges, F = number of faces.
+in the body particle, E = number of edges, F = number of faces.  For N
+= 1 or 2, the format is simpler.  E and F are ignored and no edges or
+faces are listed, so that M = 6 + 3\*N + 1.
 
 The integer line has three values: number of vertices (N), number of
 edges (E) and number of faces (F). The floating point line(s) list 6
@@ -356,16 +340,26 @@ the end points of the E edges, then 4\*F vertex indices defining F
 faces.  The last value is the diameter value = the rounded diameter of
 the sphere that surrounds each vertex. The diameter value can be
 different for each body particle. These floating-point values can be
-listed on as many lines as you wish; see the
+listed on as many lines as you wish; see the :doc:`read_data
-:doc:`read_data <read_data>` command for more details.  Because the
+<read_data>` command for more details.
-maximum number of vertices per face is hard-coded to be 4
-(i.e. quadrilaterals), faces with more than 4 vertices need to be
-split into triangles or quadrilaterals.  For triangular faces, the
-last vertex index should be set to -1.
 
-The ordering of the 4 vertices within a face should follow
+Note that vertices are numbered from 0 to N-1 inclusive.  The order of
-the right-hand rule so that the normal vector of the face points
+the 2 vertices in each edge does not matter.  Faces can be triangles
-outwards from the center of mass.
+or quadrilaterals.  In both cases 4 vertices must be specified.  For a
+triangle the 4th vertex is -1.  The 4 vertices within each triangle or
+quadrilateral face should be ordered by the right-hand rule so that
+the normal vector of the face points outwards from the center of mass.
+For polyhedron with faces with more than 4 vertices, you should split
+the complex face into multiple simple faces, each of which is a
+triangle or quadrilateral.
+
+.. note::
+
+  If a face is a quadrilateral then its 4 vertices must be co-planar.
+  LAMMPS does not check that this is the case.  If you have a quad-face
+  of a polyhedron that is not planar (e.g. a cube whose vertices have
+  been randomly displaced), then you should represent the single quad
+  face as two triangle faces instead.
 
 The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
 values consistent with the current orientation of the rigid body
@@ -421,8 +415,8 @@ by circles of diameter 0.5, is specified as follows:
 
 .. parsed-literal::
 
-   1 1 13
+   1 3 13
-   2
+   2 1 1
    0 1.33333 1.33333 0 0 0
    -2 0 0
    2 0 0
@@ -432,27 +426,34 @@ A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
 
 .. parsed-literal::
 
-   1 1 10
+   1 3 10
-   1
+   1 1 1
    0.9 0.9 0.9 0 0 0
    0 0 0
    3.0
 
-The :doc:`pair_style body/rounded/polhedron <pair_body_rounded_polyhedron>` command can
+The number of edges and faces for a rod or sphere must be listed,
-be used with this body style to compute body/body interactions.  The
+but is ignored.
-:doc:`fix wall/body/polyhedron <fix_wall_body_polygon>` command can be
+
-used with this body style to compute the interaction of body particles
+The :doc:`pair_style body/rounded/polhedron
-with a wall.
+<pair_body_rounded_polyhedron>` command can be used with this body
+style to compute body/body interactions.  The :doc:`fix
+wall/body/polyhedron <fix_wall_body_polygon>` command can be used with
+this body style to compute the interaction of body particles with a
+wall.
 
 ----------
 
-For output purposes via the :doc:`compute body/local <compute_body_local>` and :doc:`dump local <dump>`
+**Output specifics for all body styles:**
-commands, this body style produces one datum for each of the N
+
-sub-particles in a body particle.  The datum has 3 values:
+For the :doc:`compute body/local <compute_body_local>` and :doc:`dump
+local <dump>` commands, all 3 of the body styles described on his page
+produces one datum for each of the N vertices (of sub-particles) in a
+body particle.  The datum has 3 values:
 
 .. parsed-literal::
 
-   1 = x position of vertex
+   1 = x position of vertex (or sub-particle)
    2 = y position of vertex
    3 = z position of vertex
 
@@ -461,15 +462,29 @@ simulation domain, not a displacement from the center-of-mass (COM) of
 the body particle itself.  These values are calculated using the
 current COM and orientation of the body particle.
 
-For images created by the :doc:`dump image <dump_image>` command, if the
+The :doc:`dump image <dump_image>` command and its *body* keyword can
-*body* keyword is set, then each body particle is drawn as a polygon
+be used to render body particles.
-consisting of N line segments.  Note that the line segments are drawn
+
-between the N vertices, which does not correspond exactly to the
+For the *nparticle* body style, each body is drawn as a
-physical extent of the body (because the :doc:`pair_style rounded/polygon <pair_body_rounded_polygon>` defines finite-size
+collection of spheres, one for each sub-particle.  The size of each
-spheres at those point and the line segments between the spheres are
+sphere is determined by the *bflag1* parameter for the *body* keyword.
-tangent to the spheres).  The drawn diameter of each line segment is
+The *bflag2* argument is ignored.
-determined by the *bflag1* parameter for the *body* keyword.  The
+
-*bflag2* argument is ignored.
+For the *rounded/polygon* body style, each body is drawn as a polygon
+with N line segments.  For the *rounded/polyhedron* body style, each
+face of each body is drawn as a polygon with N line segments.  The
+drawn diameter of each line segment is determined by the *bflag1*
+parameter for the *body* keyword.  The *bflag2* argument is ignored.
+
+Note that for both the *rounded/polygon* and *rounded/polyhedron*
+styles, line segments are drawn between the pairs of vertices.
+Depending on the diameters of the line segments this may be slightly
+different than the physical extent of the body as calculated by the
+:doc:`pair_style rounded/polygon <pair_body_rounded_polygon>` or
+:doc:`pair_style rounded/polyhedron <pair_body_rounded_polyhedron>`
+commands.  Conceptually, the pair styles define the surface of a 2d or
+3d body by lines or planes that are tangent to the finite-size spheres
+of specified diameter which are placed on each vertex position.
 
 ----------
 

doc/src/Howto_chunk.rst

@@ -197,7 +197,7 @@ compress individual polymer chains (molecules) in a mixture, is
 explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
 
 (7) An example for using one set of per-chunk values for molecule
-chunks, to create a 2nd set of micelle-scale chunks (clustered
+chunks, to create a second set of micelle-scale chunks (clustered
 molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce <compute_reduce_chunk>` command doc page.
 
 (8) An example for using one set of per-chunk values (dipole moment

doc/src/Howto_cmake.rst

@@ -114,19 +114,19 @@ summary screen will look like this:
    -- Detecting CXX compiler ABI info - done
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
-   -- Found Git: /usr/bin/git (found version "2.25.2") 
+   -- Found Git: /usr/bin/git (found version "2.25.2")
    -- Running check for auto-generated files from make-based build system
-   -- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1") 
+   -- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1")
-   -- Found MPI: TRUE (found version "3.1")  
+   -- Found MPI: TRUE (found version "3.1")
    -- Looking for C++ include omp.h
    -- Looking for C++ include omp.h - found
-   -- Found OpenMP_CXX: -fopenmp (found version "4.5") 
+   -- Found OpenMP_CXX: -fopenmp (found version "4.5")
-   -- Found OpenMP: TRUE (found version "4.5")  
+   -- Found OpenMP: TRUE (found version "4.5")
-   -- Found JPEG: /usr/lib64/libjpeg.so (found version "62") 
+   -- Found JPEG: /usr/lib64/libjpeg.so (found version "62")
-   -- Found PNG: /usr/lib64/libpng.so (found version "1.6.37") 
+   -- Found PNG: /usr/lib64/libpng.so (found version "1.6.37")
-   -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") 
+   -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-   -- Found GZIP: /usr/bin/gzip  
+   -- Found GZIP: /usr/bin/gzip
-   -- Found FFMPEG: /usr/bin/ffmpeg  
+   -- Found FFMPEG: /usr/bin/ffmpeg
    -- Performing Test COMPILER_SUPPORTS-ffast-math
    -- Performing Test COMPILER_SUPPORTS-ffast-math - Success
    -- Performing Test COMPILER_SUPPORTS-march=native
@@ -143,7 +143,7 @@ summary screen will look like this:
     * JPEG
     * PNG
     * ZLIB
-   
+
    -- <<< Build configuration >>>
       Build type:       RelWithDebInfo
       Install path:     /home/akohlmey/.local
@@ -157,7 +157,7 @@ summary screen will look like this:
          Options:       -ffast-math;-march=native
    -- <<< Linker flags: >>>
    -- Executable name:  lmp
-   -- Static library flags:    
+   -- Static library flags:
    -- <<< MPI flags >>>
    -- MPI includes:     /usr/include/mpich-x86_64
    -- MPI libraries:    /usr/lib64/mpich/lib/libmpicxx.so;/usr/lib64/mpich/lib/libmpi.so;
@@ -291,7 +291,7 @@ Some common CMake variables
 
 .. list-table::
    :header-rows: 1
-   
+
    * - Variable
      - Description
    * - ``CMAKE_INSTALL_PREFIX``
@@ -313,13 +313,13 @@ Some common CMake variables
      - Fortran compiler to be used for compilation (default: system specific, ``gfortran`` on Linux)
    * - ``CXX_COMPILER_LAUNCHER``
      - tool to launch the C++ compiler, e.g. ``ccache`` or ``distcc`` for faster compilation (default: empty)
-       
+
 Some common LAMMPS specific variables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. list-table::
    :header-rows: 1
-   
+
    * - Variable
      - Description
    * - ``BUILD_MPI``
@@ -331,7 +331,7 @@ Some common LAMMPS specific variables
    * - ``BUILD_DOC``
      - include building the HTML format documentation for packaging/installing (default: ``off``)
    * - ``CMAKE_TUNE_FLAGS``
-     - common compiler flags, for optimization or instrumentation (default: compiler specific)
+     - common compiler flags, for optimization or instrumentation (default:)
    * - ``LAMMPS_MACHINE``
      - when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
    * - ``LAMMPS_EXCEPTIONS``
@@ -438,7 +438,7 @@ the target name to the command. Example: ``cmake --build . --target all`` or
    * - ``clean``
      - remove all generated files
 
-   
+
 Choosing generators
 -------------------
 

doc/src/Howto_coreshell.rst

@@ -119,7 +119,7 @@ non-polarized ions (ions without an attached satellite particle).  The
 groups, one for the core atoms, another for the shell atoms.
 Non-polarized ions which might also be included in the treated system
 should not be included into either of these groups, they are taken
-into account by the *group-ID* (2nd argument) of the compute.  The
+into account by the *group-ID* (second argument) of the compute.  The
 groups can be defined using the :doc:`group *type*\ <group>` command.
 Note that to perform thermostatting using this definition of
 temperature, the :doc:`fix modify temp <fix_modify>` command should be

doc/src/Howto_multiple.rst

@@ -91,4 +91,4 @@ With these modifications, the 8 simulations of each script would run
 on the 3 partitions one after the other until all were finished.
 Initially, 3 simulations would be started simultaneously, one on each
 partition.  When one finished, that partition would then start
-the 4th simulation, and so forth, until all 8 were completed.
+the fourth simulation, and so forth, until all 8 were completed.

doc/src/Howto_output.rst

@@ -3,13 +3,15 @@ Output from LAMMPS (thermo, dumps, computes, fixes, variables)
 
 There are four basic kinds of LAMMPS output:
 
-* :doc:`Thermodynamic output <thermo_style>`, which is a list
+* :doc:`Thermodynamic output <thermo_style>`, which is a list of
-  of quantities printed every few timesteps to the screen and logfile.
+  quantities printed every few timesteps to the screen and logfile.
 * :doc:`Dump files <dump>`, which contain snapshots of atoms and various
   per-atom values and are written at a specified frequency.
-* Certain fixes can output user-specified quantities to files: :doc:`fix ave/time <fix_ave_time>` for time averaging, :doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and :doc:`fix print <fix_print>` for single-line output of
+* Certain fixes can output user-specified quantities to files:
-  :doc:`variables <variable>`.  Fix print can also output to the
+  :doc:`fix ave/time <fix_ave_time>` for time averaging,
-  screen.
+  :doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and
+  :doc:`fix print <fix_print>` for single-line output of
+  :doc:`variables <variable>`.  Fix print can also output to the screen.
 * :doc:`Restart files <restart>`.
 
 A simulation prints one set of thermodynamic output and (optionally)
@@ -41,7 +43,7 @@ to output and the kind of data they operate on and produce:
 .. _global:
 
 Global/per-atom/local data
----------------------------------------
+--------------------------
 
 Various output-related commands work with three different styles of
 data: global, per-atom, or local.  A global datum is one or more
@@ -54,7 +56,7 @@ bond distances.
 .. _scalar:
 
 Scalar/vector/array data
--------------------------------------
+------------------------
 
 Global, per-atom, and local datums can each come in three kinds: a
 single scalar value, a vector of values, or a 2d array of values.  The
@@ -81,10 +83,27 @@ the dimension twice (array -> scalar).  Thus a command that uses
 scalar values as input can typically also process elements of a vector
 or array.
 
+.. _disambiguation:
+
+Disambiguation
+--------------
+
+Some computes and fixes produce data in multiple styles, e.g. a global
+scalar and a per-atom vector. Usually the context in which the input
+script references the data determines which style is meant. Example: if
+a compute provides both a global scalar and a per-atom vector, the
+former will be accessed by using ``c_ID`` in an equal-style variable,
+while the latter will be accessed by using ``c_ID`` in an atom-style
+variable.  Note that atom-style variable formulas can also access global
+scalars, but in this case it is not possible to do directly because of
+the ambiguity.  Instead, an equal-style variable can be defined which
+accesses the global scalar, and that variable used in the atom-style
+variable formula in place of ``c_ID``.
+
 .. _thermo:
 
 Thermodynamic output
----------------------------------
+--------------------
 
 The frequency and format of thermodynamic output is set by the
 :doc:`thermo <thermo>`, :doc:`thermo_style <thermo_style>`, and
@@ -112,7 +131,7 @@ intensive result.
 .. _dump:
 
 Dump file output
----------------------------
+----------------
 
 Dump file output is specified by the :doc:`dump <dump>` and
 :doc:`dump_modify <dump_modify>` commands.  There are several
@@ -138,7 +157,7 @@ command.
 .. _fixoutput:
 
 Fixes that write output files
----------------------------------------------
+-----------------------------
 
 Several fixes take various quantities as input and can write output
 files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
@@ -192,7 +211,7 @@ from normal thermodynamic or dump file output.
 .. _computeoutput:
 
 Computes that process output quantities
------------------------------------------------------------
+---------------------------------------
 
 The :doc:`compute reduce <compute_reduce>` and :doc:`compute reduce/region <compute_reduce>` commands take one or more per-atom
 or local vector quantities as inputs and "reduce" them (sum, min, max,
@@ -219,7 +238,7 @@ output commands.
 .. _fixprocoutput:
 
 Fixes that process output quantities
---------------------------------------------------------
+------------------------------------
 
 The :doc:`fix vector <fix_vector>` command can create global vectors as
 output from global scalars as input, accumulating them one element at
@@ -244,7 +263,7 @@ The output of this fix can be used as input to other output commands.
 .. _compute:
 
 Computes that generate values to output
------------------------------------------------------
+---------------------------------------
 
 Every :doc:`compute <compute>` in LAMMPS produces either global or
 per-atom or local values.  The values can be scalars or vectors or
@@ -257,7 +276,7 @@ without the word "atom" or "local" produce global values.
 .. _fix:
 
 Fixes that generate values to output
-----------------------------------------------
+------------------------------------
 
 Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or
 local values which can be accessed by other commands.  The values can
@@ -269,7 +288,7 @@ describes them.
 .. _variable:
 
 Variables that generate values to output
--------------------------------------------------------
+----------------------------------------
 
 :doc:`Variables <variable>` defined in an input script can store one or
 more strings.  But equal-style, vector-style, and atom-style or
@@ -284,7 +303,7 @@ commands described in this section.
 .. _table:
 
 Summary table of output options and data flow between commands
---------------------------------------------------------------------------
+--------------------------------------------------------------
 
 This table summarizes the various commands that can be used for
 generating output from LAMMPS.  Each command produces output data of

doc/src/Howto_restart.rst

@@ -28,7 +28,7 @@ scripts are based on.  If that script had the line
 added to it, it would produce 2 binary restart files (tmp.restart.50
 and tmp.restart.100) as it ran.
 
-This script could be used to read the 1st restart file and re-run the
+This script could be used to read the first restart file and re-run the
 last 50 timesteps:
 
 .. code-block:: LAMMPS

doc/src/Howto_tip4p.rst

@@ -11,11 +11,11 @@ angle style of *harmonic* or *charmm* should also be used.
 A TIP4P model is run with LAMMPS using either this command
 for a cutoff model:
 
-* :doc:`pair_style lj/cut/tip4p/cut <pair_lj>`
+* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
 
 or these two commands for a long-range model:
 
-* :doc:`pair_style lj/cut/tip4p/long <pair_lj>`
+* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
 * :doc:`kspace_style pppm/tip4p <kspace_style>`
 
 For both models, the bond lengths and bond angles should be held fixed
@@ -95,7 +95,7 @@ typically best in an efficiency sense to use a LJ cutoff >= Coulomb
 cutoff + 2\*(OM distance), to shrink the size of the neighbor list.
 This leads to slightly larger cost for the long-range calculation, so
 you can test the trade-off for your model.  The OM distance and the LJ
-and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj>` command.
+and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.
 
 Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
 

doc/src/Howto_triclinic.rst

@@ -85,7 +85,7 @@ where *V* is the volume of the box, **X** is the original vector quantity and
 **x** is the vector in the LAMMPS basis.
 
 There is no requirement that a triclinic box be periodic in any
-dimension, though it typically should be in at least the 2nd dimension
+dimension, though it typically should be in at least the second dimension
 of the tilt (y in xy) if you want to enforce a shift in periodic
 boundary conditions across that boundary.  Some commands that work
 with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap
@@ -120,7 +120,7 @@ The 9 parameters, as well as lx,ly,lz, can be output via the
 To avoid extremely tilted boxes (which would be computationally
 inefficient), LAMMPS normally requires that no tilt factor can skew
 the box more than half the distance of the parallel box length, which
-is the 1st dimension in the tilt factor (x for xz).  This is required
+is the first dimension in the tilt factor (x for xz).  This is required
 both when the simulation box is created, e.g. via the
 :doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands,
 as well as when the box shape changes dynamically during a simulation,
@@ -137,7 +137,7 @@ limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
 command), then the box is "flipped" to an equivalent shape with a tilt
 factor within the bounds, so the run can continue.  See the :doc:`fix deform <fix_deform>` doc page for further details.
 
-One exception to this rule is if the 1st dimension in the tilt
+One exception to this rule is if the first dimension in the tilt
 factor (x for xy) is non-periodic.  In that case, the limits on the
 tilt factor are not enforced, since flipping the box in that dimension
 does not change the atom positions due to non-periodicity.  In this

doc/src/Install_linux.rst

@@ -21,8 +21,14 @@ Pre-built Ubuntu Linux executables
 A pre-built LAMMPS executable suitable for running on the latest
 Ubuntu Linux versions, can be downloaded as a Debian package.  This
 allows you to install LAMMPS with a single command, and stay
-up-to-date with the current version of LAMMPS by simply updating your
+up-to-date with the current stable version of LAMMPS by simply updating
-operating system.
+your operating system.  Please note, that the repository below offers
+two LAMMPS packages, ``lammps-daily`` and ``lammps-stable``.  The
+LAMMPS developers recommend to use the ``lammps-stable`` package for
+any production simulations.  The ``lammps-daily`` package is built
+from the LAMMPS development sources, and those versions may have known
+issues and bugs when new features are added and the software has not
+undergone full release testing.
 
 To install the appropriate personal-package archives (PPAs), do the
 following once:
@@ -37,16 +43,16 @@ To install LAMMPS do the following once:
 
 .. code-block:: bash
 
-   $ sudo apt-get install lammps-daily
+   $ sudo apt-get install lammps-stable
 
-This downloads an executable named ``lmp_daily`` to your box, which
+This downloads an executable named ``lmp_stable`` to your box, which
 can then be used in the usual way to run input scripts:
 
 .. code-block:: bash
 
-   $ lmp_daily -in in.lj
+   $ lmp_stable -in in.lj
 
-To update LAMMPS to the most current version, do the following:
+To update LAMMPS to the most current stable version, do the following:
 
 .. code-block:: bash
 
@@ -58,25 +64,25 @@ To get a copy of the current documentation and examples:
 
 .. code-block:: bash
 
-   $ sudo apt-get install lammps-daily-doc
+   $ sudo apt-get install lammps-stable-doc
 
 which will download the doc files in
-``/usr/share/doc/lammps-daily-doc/doc`` and example problems in
+``/usr/share/doc/lammps-stable-doc/doc`` and example problems in
 ``/usr/share/doc/lammps-doc/examples``.
 
 To get a copy of the current potentials files:
 
 .. code-block:: bash
 
-   $ sudo apt-get install lammps-daily-data
+   $ sudo apt-get install lammps-stable-data
 
 which will download the potentials files to
-``/usr/share/lammps-daily/potentials``.  The ``lmp_daily`` binary is
+``/usr/share/lammps-stable/potentials``.  The ``lmp_stable`` binary is
 hard-coded to look for potential files in this directory (it does not
 use the `LAMMPS_POTENTIALS` environment variable, as described
 in :doc:`pair_coeff <pair_coeff>` command).
 
-The ``lmp_daily`` binary is built with the :ref:`KIM package <kim>` which
+The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which
 results in the above command also installing the `kim-api` binaries when LAMMPS
 is installed.  In order to use potentials from `openkim.org <openkim_>`_, you
 can install the `openkim-models` package
@@ -89,9 +95,9 @@ To un-install LAMMPS, do the following:
 
 .. code-block:: bash
 
-   $ sudo apt-get remove lammps-daily
+   $ sudo apt-get remove lammps-stable
 
-Please use ``lmp_daily -help`` to see which compilation options, packages,
+Please use ``lmp_stable -help`` to see which compilation options, packages,
 and styles are included in the binary.
 
 Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this

doc/src/Intro_nonfeatures.rst

@@ -34,7 +34,7 @@ Here are suggestions on how to perform these tasks:
   molecular builder that will generate complex molecular models.  See
   the :doc:`Tools <Tools>` doc page for details on tools packaged with
   LAMMPS.  The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website
-  describes a variety of 3rd party tools for this task.  Furthermore,
+  describes a variety of third party tools for this task.  Furthermore,
   some LAMMPS internal commands allow to reconstruct, or selectively add
   topology information, as well as provide the option to insert molecule
   templates instead of atoms for building bulk molecular systems.

doc/src/Manual.rst

@@ -32,11 +32,12 @@ a brief description of the basic code structure of LAMMPS.
 
 ----------
 
-Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands>` since it gives quick access to a doc page for
+Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands_all>` since it gives quick access to a doc page for
 every LAMMPS command.
 
 .. _lws: https://lammps.sandia.gov
 
+.. _user_documentation:
 .. toctree::
    :maxdepth: 2
    :numbered: 3

doc/src/Manual_build.rst

@@ -1,60 +1,62 @@
 Building the LAMMPS manual
 **************************
 
-Depending on how you obtained LAMMPS, the doc directory has up
+Depending on how you obtained LAMMPS and whether you have built the
-to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files
+manual yourself, this directory has a number of sub-directories and
-plus 2 e-book format files:
+files. Here is a list with descriptions:
 
 .. code-block:: bash
 
-   src             # content files for LAMMPS documentation
+   README           # brief info about the documentation
-   html            # HTML version of the LAMMPS manual (see html/Manual.html)
+   src              # content files for LAMMPS documentation
-   utils           # tools and settings for building the documentation
+   html             # HTML version of the LAMMPS manual (see html/Manual.html)
-   docenv          # virtualenv for processing the manual sources
+   utils            # tools and settings for building the documentation
-   doctrees        # temporary data from processing the manual
+   lammps.1         # man page for the lammps command
-   mathjax         # code and fonts for rendering math in html
+   msi2lmp.1        # man page for the msi2lmp command
-   Manual.pdf      # large PDF version of entire manual
+   Manual.pdf       # large PDF version of entire manual
-   Developer.pdf   # small PDF with info about how LAMMPS is structured
+   Developer.pdf    # small PDF with info about how LAMMPS is structured
-   LAMMPS.epub     # Manual in ePUB e-book format
+   LAMMPS.epub      # Manual in ePUB e-book format
-   LAMMPS.mobi     # Manual in MOBI e-book format
+   LAMMPS.mobi      # Manual in MOBI e-book format
-   lammps.1        # man page for the lammps command
+   docenv           # virtualenv folder for processing the manual sources
-   msi2lmp.1       # man page for the msi2lmp command
+   doctrees         # temporary data from processing the manual
+   mathjax          # code and fonts for rendering math in html
+   doxygen          # doxygen configuration and output
+   .gitignore       # list of files and folders to be ignored by git
+   doxygen-warn.log # logfile with warnings from running doxygen
+   github-development-workflow.md   # notes on the LAMMPS development workflow
+   include-file-conventions.md      # notes on LAMMPS' include file conventions
 
-If you downloaded LAMMPS as a tarball from the web site, the html folder
+If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
-and the PDF files should be included.
+the html folder and the PDF files should be included.
 
 If you downloaded LAMMPS from the public git repository, then the HTML
 and PDF files are not included.  Instead you need to create them, in one
 of two ways:
 
 a. You can "fetch" the current HTML and PDF files from the LAMMPS web
-   site.  Just type "make fetch".  This should download a html_www
+   site.  Just type ``make fetch``.  This should download a html_www
    directory and Manual_www.pdf/Developer_www.pdf files.  Note that if
    new LAMMPS features have been added more recently than the date of
    your LAMMPS version, the fetched documentation will include those
    changes (but your source code will not, unless you update your local
    repository).
 
-b. You can build the HTML or PDF files yourself, by typing "make html"
+b. You can build the HTML or PDF files yourself, by typing ``make html``
-   or "make pdf".  This requires various tools including Sphinx, git,
+   or ``make pdf``.  This requires various tools and files.  Some of them
-   and the MathJax javascript library, which the build process will attempt
+   have to be installed (more on that below). For the rest the build
-   to download automatically into a virtual environment in the folder
+   process will attempt to download and install them into a python
-   doc/docenv and the folder mathjax, respectively, if not already available.
+   virtual environment and local folders.  This download is required
-   This download is required only once, unless you type "make clean-all".
+   only once, unless you type ``make clean-all``.  After that, viewing and
-   After that, viewing and  processing of the documentation can be done
+   processing of the documentation can be done without internet access.
-   without internet access.  To generate the PDF version of the manual,
-   the PDFLaTeX software and several LaTeX packages are required as well.
-   However, those cannot be installed automatically at the moment.
 
 ----------
 
-The generation of all documentation is managed by the Makefile in
+The generation of all documentation is managed by the Makefile in the
-the doc directory.
+doc directory. The following documentation related make commands are
+available:
 
 .. code-block:: bash
 
-   Documentation Build Options:
-
    make html          # generate HTML in html dir using Sphinx
    make pdf           # generate 2 PDF files (Manual.pdf,Developer.pdf)
                       #   in doc dir via htmldoc and pdflatex
@@ -62,8 +64,10 @@ the doc directory.
                       #   as a tarball and unpack into html dir and 2 PDFs
    make epub          # generate LAMMPS.epub in ePUB format using Sphinx
    make mobi          # generate LAMMPS.mobi in MOBI format using ebook-convert
+
    make clean         # remove intermediate RST files created by HTML build
    make clean-all     # remove entire build folder and any cached data
+
    make anchor_check  # check for duplicate anchor labels
    make style_check   # check for complete and consistent style lists
    make package_check # check for complete and consistent package lists
@@ -74,29 +78,30 @@ the doc directory.
 Installing prerequisites for HTML build
 =======================================
 
-To run the HTML documentation build toolchain, Python 3 and virtualenv
+To run the HTML documentation build toolchain, python 3, git, doxygen,
-have to be installed.  Here are instructions for common setups:
+and virtualenv have to be installed locally.  Here are instructions for
+common setups:
 
 Ubuntu
 ------
 
 .. code-block:: bash
 
-   sudo apt-get install python-virtualenv
+   sudo apt-get install python-virtualenv git doxygen
 
 Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x)
 ------------------------------------------------------------------------------------
 
 .. code-block:: bash
 
-   sudo yum install python3-virtualenv
+   sudo yum install python3-virtualenv git doxygen
 
 Fedora (since version 22)
 -------------------------
 
 .. code-block:: bash
 
-   sudo dnf install python3-virtualenv
+   sudo dnf install python3-virtualenv git doxygen
 
 MacOS X
 -------
@@ -120,22 +125,92 @@ Once Python 3 is installed, open a Terminal and type
 
 This will install virtualenv from the Python Package Index.
 
-----------
+Installing prerequisites for PDF build
+======================================
 
-Installing prerequisites for epub build
+In addition to the tools needed for building the HTML format manual,
-=======================================
+a working LaTeX installation with support for PDFLaTeX and a selection
+of LaTeX styles/packages are required.
 
-ePUB
+Installing prerequisites for e-book reader builds
-----
+=================================================
 
-Same as for HTML. This uses mostly the same tools and configuration
+In addition to the tools needed for building the HTML format manual,
-files as the HTML tree. In addition it uses LaTeX to convert embedded
+a working LaTeX installation with a few add-on LaTeX packages
+as well as the ``dvipng`` tool are required to convert embedded
 math expressions transparently into embedded images.
 
-For converting the generated ePUB file to a MOBI format file
+For converting the generated ePUB file to a MOBI format file (for e-book
-(for e-book readers, like Kindle, that cannot read ePUB), you
+readers, like Kindle, that cannot read ePUB), you also need to have the
-also need to have the 'ebook-convert' tool from the "calibre"
+``ebook-convert`` tool from the "calibre" software
-software installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
+installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
-You first create the ePUB file and then convert it with 'make mobi'
+Typing ``make mobi`` will first create the ePUB file and then convert
-On the Kindle readers in particular, you also have support for
+it.  On the Kindle readers in particular, you also have support for PDF
-PDF files, so you could download and view the PDF version as an alternative.
+files, so you could download and view the PDF version as an alternative.
+
+
+Instructions for Developers
+===========================
+
+When adding new styles or options to the LAMMPS code, corresponding
+documentation is required and either existing files in the ``src``
+folder need to be updated or new files added. These files are written
+in `reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
+
+Before contributing any documentation, please check that both the HTML
+and the PDF format documentation can translate without errors. Please also
+check the output to the console for any warnings or problems.  There will
+be multiple tests run automatically:
+
+- A test for correctness of all anchor labels and their references
+
+- A test that all LAMMPS packages (= folders with sources in
+  ``lammps/src``) are documented and listed.  A typical warning shows
+  the name of the folder with the suspected new package code and the
+  documentation files where they need to be listed:
+
+  .. parsed-literal::
+
+     Found 33 standard and 41 user packages
+     Standard package NEWPACKAGE missing in Packages_standard.rst
+     Standard package NEWPACKAGE missing in Packages_details.rst
+
+- A test that only standard, printable ASCII text characters are used.
+  This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
+  thus prints all offending lines with filename and line number
+  prepended to the screen.  Special characters like the Angstrom
+  :math:`\mathrm{\mathring{A}}` should be typeset with embedded math
+  (like this ``:math:`\mathrm{\mathring{A}}```\ ).
+
+- A test whether all styles are documented and listed in their
+  respective overview pages.  A typical output with warnings looks like this:
+
+  .. parsed-literal::
+
+     Parsed style names w/o suffixes from C++ tree in ../src:
+        Angle styles:      21    Atom styles:       24
+        Body styles:        3    Bond styles:       17
+        Command styles:    41    Compute styles:   143
+        Dihedral styles:   16    Dump styles:       26
+        Fix styles:       223    Improper styles:   13
+        Integrate styles:   4    Kspace styles:     15
+        Minimize styles:    9    Pair styles:      234
+        Reader styles:      4    Region styles:      8
+     Compute style entry newcomp is missing or incomplete in Commands_compute.rst
+     Compute style entry newcomp is missing or incomplete in compute.rst
+     Fix style entry newfix is missing or incomplete in Commands_fix.rst
+     Fix style entry newfix is missing or incomplete in fix.rst
+     Pair style entry new is missing or incomplete in Commands_pair.rst
+     Pair style entry new is missing or incomplete in pair_style.rst
+     Found 6 issue(s) with style lists
+
+
+In addition, there is the option to run a spellcheck on the entire
+manual with ``make spelling``.  This requires `a library called enchant
+<https://github.com/AbiWord/enchant>`_.  To avoid printing out *false
+positives* (e.g. keywords, names, abbreviations) those can be added to
+the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
+
+.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
+
+.. _lws: https://lammps.sandia.gov

doc/src/Modify_contribute.rst

@@ -1,37 +1,51 @@
 Submitting new features for inclusion in LAMMPS
 ===============================================
 
-We encourage users to submit new features or modifications for LAMMPS
+We encourage users to submit new features or modifications for LAMMPS to
-to `the core developers <https://lammps.sandia.gov/authors.html>`_ so they
+`the core developers <https://lammps.sandia.gov/authors.html>`_ so they
-can be added to the LAMMPS distribution. The preferred way to manage
+can be added to the LAMMPS distribution. The preferred way to manage and
-and coordinate this is as of Fall 2016 via the LAMMPS project on
+coordinate this is via the LAMMPS project on `GitHub
-`GitHub <https://github.com/lammps/lammps>`_. An alternative is to
+<https://github.com/lammps/lammps>`_.  Please see the :doc:`GitHub
-contact the LAMMPS developers or the indicated developer of a package
+Tutorial <Howto_github>` for a demonstration on how to do that.  An
-or feature directly and send in your contribution via e-mail.
+alternative is to contact the LAMMPS developers or the indicated
+developer of a package or feature directly and send in your contribution
+via e-mail, but that can add a significant delay on getting your
+contribution included, depending on how busy the developer is you
+contact, how complex a task it would be to integrate that code, and how
+many - if any - changes are required before the code can be included.
 
-For any larger modifications or programming project, you are
+For any larger modifications or programming project, you are encouraged
-encouraged to contact the LAMMPS developers ahead of time, in order to
+to contact the LAMMPS developers ahead of time, in order to discuss
-discuss implementation strategies and coding guidelines, that will
+implementation strategies and coding guidelines, that will make it
-make it easier to integrate your contribution and result in less work
+easier to integrate your contribution and result in less work for
-for everybody involved. You are also encouraged to search through the
+everybody involved. You are also encouraged to search through the list
-list of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_ and submit a new issue
+of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_
-for a planned feature, so you would not duplicate the work of others
+and submit a new issue for a planned feature, so you would not duplicate
-(and possibly get scooped by them) or have your work duplicated by
+the work of others (and possibly get scooped by them) or have your work
-others.
+duplicated by others.
 
-How quickly your contribution will be integrated depends largely on
+For informal communication with (some of) the LAMMPS developers you may
-how much effort it will cause to integrate and test it, how much it
+ask to join the `LAMMPS developers on Slack <https://lammps.slack.com>`_.
-requires changes to the core codebase, and of how much interest it is
+This slack work space is by invitation only. Thus for access, please
-to the larger LAMMPS community.  Please see below for a checklist of
+send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
-typical requirements. Once you have prepared everything, see the
+you are working on.  Only discussions related to LAMMPS development are
-:doc:`Using GitHub with LAMMPS Howto <Howto_github>` doc page for instructions on how to
+tolerated, so this is **NOT** for people that look for help with compiling,
-submit your changes or new files through a GitHub pull request. If you
+installing, or using LAMMPS. Please contact the `lammps-users mailing
-prefer to submit patches or full files, you should first make certain,
+list <https://lammps.sandia.gov>`_ for those purposes instead.
-that your code works correctly with the latest patch-level version of
+
-LAMMPS and contains all bug fixes from it. Then create a gzipped tar
+How quickly your contribution will be integrated depends largely on how
-file of all changed or added files or a corresponding patch file using
+much effort it will cause to integrate and test it, how much it requires
-'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
+changes to the core codebase, and of how much interest it is to the
-compression, as this works well on all platforms.
+larger LAMMPS community.  Please see below for a checklist of typical
+requirements. Once you have prepared everything, see the :doc:`Using
+GitHub with LAMMPS Howto <Howto_github>` doc page for instructions on
+how to submit your changes or new files through a GitHub pull
+request. If you prefer to submit patches or full files, you should first
+make certain, that your code works correctly with the latest patch-level
+version of LAMMPS and contains all bug fixes from it. Then create a
+gzipped tar file of all changed or added files or a corresponding patch
+file using 'diff -u' or 'diff -c' and compress it with gzip. Please only
+use gzip compression, as this works well on all platforms.
 
 If the new features/files are broadly useful we may add them as core
 files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`.  Else we will add them as a

doc/src/Modify_fix.rst

@@ -27,7 +27,7 @@ derived class.  See fix.h for details.
 +---------------------------+--------------------------------------------------------------------------------------------+
 | setup_pre_force           | called before force computation in setup (optional)                                        |
 +---------------------------+--------------------------------------------------------------------------------------------+
-| setup                     | called immediately before the 1st timestep and after forces are computed (optional)        |
+| setup                     | called immediately before the first timestep and after forces are computed (optional)      |
 +---------------------------+--------------------------------------------------------------------------------------------+
 | min_setup_pre_force       | like setup_pre_force, but for minimizations instead of MD runs (optional)                  |
 +---------------------------+--------------------------------------------------------------------------------------------+

doc/src/Modify_kspace.rst

@@ -10,12 +10,12 @@ Ewald.cpp is an example of computing K-space interactions.
 Here is a brief description of methods you define in your new derived
 class.  See kspace.h for details.
 
-+---------------+----------------------------------------------+
++---------------+------------------------------------------------+
-| init          | initialize the calculation before a run      |
+| init          | initialize the calculation before a run        |
-+---------------+----------------------------------------------+
++---------------+------------------------------------------------+
-| setup         | computation before the 1st timestep of a run |
+| setup         | computation before the first timestep of a run |
-+---------------+----------------------------------------------+
++---------------+------------------------------------------------+
-| compute       | every-timestep computation                   |
+| compute       | every-timestep computation                     |
-+---------------+----------------------------------------------+
++---------------+------------------------------------------------+
-| memory_usage  | tally of memory usage                        |
+| memory_usage  | tally of memory usage                          |
-+---------------+----------------------------------------------+
++---------------+------------------------------------------------+

doc/src/Packages_details.rst

@@ -44,6 +44,7 @@ page gives those details.
    * :ref:`MC <PKG-MC>`
    * :ref:`MESSAGE <PKG-MESSAGE>`
    * :ref:`MISC <PKG-MISC>`
+   * :ref:`MLIAP <PKG-MLIAP>`
    * :ref:`MOLECULE <PKG-MOLECULE>`
    * :ref:`MPIIO <PKG-MPIIO>`
    * :ref:`MSCG <PKG-MSCG>`
@@ -81,6 +82,7 @@ page gives those details.
    * :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
    * :ref:`USER-MEAMC <PKG-USER-MEAMC>`
    * :ref:`USER-MESODPD <PKG-USER-MESODPD>`
+   * :ref:`USER-MESONT <PKG-USER-MESONT>`
    * :ref:`USER-MGPT <PKG-USER-MGPT>`
    * :ref:`USER-MISC <PKG-USER-MISC>`
    * :ref:`USER-MOFFF <PKG-USER-MOFFF>`
@@ -304,7 +306,8 @@ gpu" or "-suffix gpu" :doc:`command-line switches <Run_options>`.  See
 also the :ref:`KOKKOS <PKG-KOKKOS>` package, which has GPU-enabled styles.
 
 **Authors:** Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
-(Northwestern U) while at ORNL.
+(Northwestern U) while at ORNL and later. AMD HIP support by Evgeny
+Kuznetsov, Vladimir Stegailov, and Vsevolod Nikolskiy (HSE University).
 
 **Install:**
 
@@ -489,7 +492,7 @@ interactions.  These include Ewald, particle-particle particle-mesh
 
 Building with this package requires a 1d FFT library be present on
 your system for use by the PPPM solvers.  This can be the KISS FFT
-library provided with LAMMPS, 3rd party libraries like FFTW, or a
+library provided with LAMMPS, third party libraries like FFTW, or a
 vendor-supplied FFT library.  See the :doc:`Build settings <Build_settings>` doc page for details on how to select
 different FFT options for your LAMPMS build.
 
@@ -651,6 +654,29 @@ listing, "ls src/MISC", to see the list of commands.
 
 ----------
 
+.. _PKG-MLIAP:
+
+MLIAP package
+-------------
+
+**Contents:**
+
+A general interface for machine-learning interatomic potentials.
+
+**Install:**
+
+To use this package, also the :ref:`SNAP package<PKG-SNAP>` needs to be installed.
+
+**Author:** Aidan Thompson (Sandia).
+
+**Supporting info:**
+
+* src/MLIAP: filenames -> commands
+* :doc:`pair_style mliap <pair_mliap>`
+* examples/mliap
+
+----------
+
 .. _PKG-MOLECULE:
 
 MOLECULE package
@@ -1712,6 +1738,56 @@ algorithm.
 * examples/USER/mesodpd
 * https://lammps.sandia.gov/movies.html#mesodpd
 
+* examples/USER/meso
+* http://lammps.sandia.gov/movies.html#mesodpd
+
+----------
+
+.. _PKG-USER-MESONT:
+
+USER-MESONT package
+-------------------
+
+**Contents:**
+
+USER-MESONT is a LAMMPS package for simulation of nanomechanics of
+nanotubes (NTs). The model is based on a coarse-grained representation
+of NTs as "flexible cylinders" consisting of a variable number of
+segments. Internal interactions within a NT and the van der Waals
+interaction between the tubes are described by a mesoscopic force field
+designed and parameterized based on the results of atomic-level
+molecular dynamics simulations. The description of the force field is
+provided in the papers listed below. This package contains two
+independent implementations of this model: :doc:`pair_style mesocnt
+<pair_mesocnt>` is a (minimal) C++ implementation, and :doc:`pair_style
+mesont/tpm <pair_mesont_tpm>` is a more general and feature rich
+implementation based on a Fortran library in the ``lib/mesont`` folder.
+
+**Download of potential files:**
+
+The potential files for these pair styles are *very* large and thus
+are not included in the regular downloaded packages of LAMMPS or the
+git repositories.  Instead, they will be automatically downloaded
+from a web server when the package is installed for the first time.
+
+**Authors of the *mesont* styles:**
+
+Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia)
+
+**Author of the *mesocnt* pair style:**
+Philipp Kloza (U Cambridge)
+
+**Supporting info:**
+
+* src/USER-MESONT: filenames -> commands
+* src/USER-MESONT/README
+* :doc:`atom_style mesont <atom_style>`
+* :doc:`pair_style mesont/tpm <pair_mesont_tpm>`
+* :doc:`compute mesont <compute_mesont>`
+* :doc:`pair_style mesocnt <pair_mesocnt>`
+* examples/USER/mesont
+* tools/mesont
+
 ----------
 
 .. _PKG-USER-MOFFF:

doc/src/Packages_standard.rst

@@ -59,6 +59,8 @@ package:
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`MISC <PKG-MISC>`           | miscellaneous single-file commands   | n/a                                                | no                                                   | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`MLIAP <PKG-MLIAP>`         | multiple machine learning potentials | :doc:`pair_style mliap <pair_mliap>`               | mliap                                                | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`MOLECULE <PKG-MOLECULE>`   | molecular system force fields        | :doc:`Howto bioFF <Howto_bioFF>`                   | peptide                                              | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`MPIIO <PKG-MPIIO>`         | MPI parallel I/O dump and restart    | :doc:`dump <dump>`                                 | n/a                                                  | no      |

doc/src/Packages_user.rst

@@ -67,6 +67,8 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-MESODPD <PKG-USER-MESODPD>`         | mesoscale DPD models                                            | :doc:`pair_style edpd <pair_mesodpd>`                                         | USER/mesodpd                                         | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`USER-MESONT <PKG-USER-MESONT>`           | mesoscopic tubular potential model for nanotubes                | pair style :doc:`mesont/tpm <pair_mesont_tpm>`, :doc:`mesocnt <pair_mesocnt>` | USER/mesont                                          | int     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-MGPT <PKG-USER-MGPT>`               | fast MGPT multi-ion potentials                                  | :doc:`pair_style mgpt <pair_mgpt>`                                            | USER/mgpt                                            | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-MISC <PKG-USER-MISC>`               | single-file contributions                                       | USER-MISC/README                                                              | USER/misc                                            | no      |

doc/src/Python_library.rst

@@ -254,12 +254,3 @@ following steps:
 * You should now be able to invoke the new interface function from a
   Python script.
 
-----------
-
-.. autoclass:: lammps.lammps
-   :members:
-   :no-undoc-members:
-
-.. autoclass:: lammps.NeighList
-   :members:
-   :no-undoc-members:

doc/src/Python_test.rst

@@ -10,7 +10,7 @@ and type:
    >>> lmp = lammps()
 
 If you get no errors, you're ready to use LAMMPS from Python.  If the
-2nd command fails, the most common error to see is
+second command fails, the most common error to see is
 
 .. parsed-literal::
 

doc/src/Run_options.rst

@@ -324,17 +324,17 @@ physical processors is done by MPI before LAMMPS begins.  It may be
 useful in some cases to alter the rank order.  E.g. to insure that
 cores within each node are ranked in a desired order.  Or when using
 the :doc:`run_style verlet/split <run_style>` command with 2 partitions
-to insure that a specific Kspace processor (in the 2nd partition) is
+to insure that a specific Kspace processor (in the second partition) is
-matched up with a specific set of processors in the 1st partition.
+matched up with a specific set of processors in the first partition.
 See the :doc:`Speed tips <Speed_tips>` doc page for more details.
 
 If the keyword *nth* is used with a setting *N*\ , then it means every
 Nth processor will be moved to the end of the ranking.  This is useful
 when using the :doc:`run_style verlet/split <run_style>` command with 2
 partitions via the -partition command-line switch.  The first set of
-processors will be in the first partition, the 2nd set in the 2nd
+processors will be in the first partition, the second set in the second
 partition.  The -reorder command-line switch can alter this so that
-the 1st N procs in the 1st partition and one proc in the 2nd partition
+the first N procs in the first partition and one proc in the second partition
 will be ordered consecutively, e.g. as the cores on one physical node.
 This can boost performance.  For example, if you use "-reorder nth 4"
 and "-partition 9 3" and you are running on 12 processors, the

doc/src/Speed_gpu.rst

@@ -50,6 +50,10 @@ but this can be overridden using the device option of the :doc:`package <package
 command. run lammps/lib/gpu/ocl_get_devices to get a list of available
 platforms and devices with a suitable ICD available.
 
+To compute and use this package in HIP mode, you have to have the AMD ROCm
+software installed. Versions of ROCm older than 3.5 are currently deprecated
+by AMD.
+
 **Building LAMMPS with the GPU package:**
 
 See the :ref:`Build extras <gpu>` doc page for
@@ -88,7 +92,7 @@ GPUs/node to 1.
 
 Using the "-pk" switch explicitly allows for setting of the number of
 GPUs/node to use and additional options.  Its syntax is the same as
-same as the "package gpu" command.  See the :doc:`package <package>`
+the "package gpu" command.  See the :doc:`package <package>`
 command doc page for details, including the default values used for
 all its options if it is not specified.
 

doc/src/Speed_intel.rst

@@ -138,10 +138,10 @@ For Intel Xeon Phi co-processors (Offload):
 
 **Required hardware/software:**
 
+When using Intel compilers version 16.0 or later is required.
+
 In order to use offload to co-processors, an Intel Xeon Phi
-co-processor and an Intel compiler are required. For this, the
+co-processor and an Intel compiler are required.
-recommended version of the Intel compiler is 14.0.1.106 or
-versions 15.0.2.044 and higher.
 
 Although any compiler can be used with the USER-INTEL package,
 currently, vectorization directives are disabled by default when

doc/src/angle_charmm.rst

@@ -37,7 +37,7 @@ The *charmm* angle style uses the potential
    E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2
 
 with an additional Urey_Bradley term based on the distance :math:`r` between
-the 1st and 3rd atoms in the angle.  :math:`K`, :math:`\theta_0`,
+the first and third atoms in the angle.  :math:`K`, :math:`\theta_0`,
 :math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
 type.
 
@@ -49,13 +49,14 @@ The following coefficients must be defined for each angle type via the
 the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
-* :math:`K` (energy/radian\^2)
+* :math:`K` (energy)
 * :math:`\theta_0` (degrees)
 * :math:`K_{ub}` (energy/distance\^2)
 * :math:`r_{ub}` (distance)
 
-:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
-internally; hence the units of :math:`K` are in energy/radian\^2.
+radians internally; hence :math:`K` is effectively energy per
+radian\^2.
 
 ----------
 

doc/src/angle_class2.rst

@@ -41,27 +41,29 @@ The *class2* angle style uses the potential
    E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\
    E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0)
 
-where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a
+where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond
-bond-angle term.  :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are
+term, and :math:`E_{ba}` is a bond-angle term.  :math:`\theta_0` is
-the equilibrium bond lengths.
+the equilibrium angle and :math:`r_1` and :math:`r_2` are the
+equilibrium bond lengths.
 
 See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field.
 
-Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for
+Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}`
-each angle type via the :doc:`angle_coeff <angle_coeff>` command as in
+formulas must be defined for each angle type via the :doc:`angle_coeff
-the example above, or in the data file or restart files read by the
+<angle_coeff>` command as in the example above, or in the data file or
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+restart files read by the :doc:`read_data <read_data>` or
-commands.
+:doc:`read_restart <read_restart>` commands.
 
 These are the 4 coefficients for the :math:`E_a` formula:
 
 * :math:`\theta_0` (degrees)
-* :math:`K_2` (energy/radian\^2)
+* :math:`K_2` (energy)
-* :math:`K_3` (energy/radian\^3)
+* :math:`K_3` (energy)
-* :math:`K_4` (energy/radian\^4)
+* :math:`K_4` (energy)
 
-:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
-internally; hence the units of the various :math:`K` are in per-radian.
+radians internally; hence the various :math:`K` are effectively energy
+per radian\^2 or radian\^3 or radian\^4.
 
 For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
 command in the input script lists 4 coefficients, the first of which
@@ -122,11 +124,15 @@ The *class2/p6* angle style uses the *class2* potential expanded to sixth order:
 In this expanded term 6 coefficients for the :math:`E_a` formula need to be set:
 
 * :math:`\theta_0` (degrees)
-* :math:`K_2` (energy/radian\^2)
+* :math:`K_2` (energy)
-* :math:`K_3` (energy/radian\^3)
+* :math:`K_3` (energy)
-* :math:`K_4` (energy/radian\^4)
+* :math:`K_4` (energy)
-* :math:`K_5` (energy/radian\^5)
+* :math:`K_5` (energy)
-* :math:`K_6` (energy/radian\^6)
+* :math:`K_6` (energy)
+
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
+radians internally; hence the various :math:`K` are effectively energy
+per radian\^2 or radian\^3 or radian\^4 or radian\^5 or radian\^6.
 
 The bond-bond and bond-angle terms remain unchanged.
 

doc/src/angle_coeff.rst

@@ -31,7 +31,7 @@ Angle coefficients can also be set in the data file read by the
 :doc:`read_data <read_data>` command or in a restart file.
 
 N can be specified in one of two ways.  An explicit numeric value can
-be used, as in the 1st example above.  Or a wild-card asterisk can be
+be used, as in the first example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple angle types.  This takes the
 form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of angle types,
 then an asterisk with no numeric values means all types from 1 to N.  A
@@ -53,7 +53,7 @@ same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in
 script, except that wild-card asterisks should not be used since
 coefficients for all N types must be listed in the file.  For example,
 under the "Angle Coeffs" section of a data file, the line that
-corresponds to the 1st example above would be listed as
+corresponds to the first example above would be listed as
 
 .. parsed-literal::
 

doc/src/angle_cross.rst

@@ -40,14 +40,15 @@ the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
 * :math:`K_{SS}` (energy/distance\^2)
-* :math:`K_{BS0}` (energy/distance/rad)
+* :math:`K_{BS0}` (energy/distance)
-* :math:`K_{BS1}` (energy/distance/rad)
+* :math:`K_{BS1}` (energy/distance)
 * :math:`r_{12,0}` (distance)
 * :math:`r_{32,0}` (distance)
 * :math:`\theta_0` (degrees)
 
-:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
-internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian.
+radians internally; hence the :math:`K_{BS0}` and :math:`K_{BS1}` are
+effectively energy/distance per radian.
 
 Restrictions
 """"""""""""

doc/src/angle_harmonic.rst

@@ -44,11 +44,12 @@ The following coefficients must be defined for each angle type via the
 the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
-* :math:`K` (energy/radian\^2)
+* :math:`K` (energy)
 * :math:`\theta_0` (degrees)
 
-:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
-internally; hence the units of :math:`K` are in energy/radian\^2.
+radians internally; hence :math:`K` is effectively energy per
+radian\^2.
 
 ----------
 
@@ -61,11 +62,13 @@ produce the same results, except for round-off and precision issues.
 
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with those packages.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+by including their suffix, or you can use the :doc:`-suffix
-:doc:`suffix <suffix>` command in your input script.
+command-line switch <Run_options>` when you invoke LAMMPS, or you can
+use the :doc:`suffix <suffix>` command in your input script.
 
 See the :doc:`Speed packages <Speed_packages>` doc page for more
 instructions on how to use the accelerated styles effectively.

doc/src/angle_mm3.rst

@@ -28,20 +28,22 @@ as defined in :ref:`(Allinger) <mm3-allinger1989>`
 
    E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
 
-where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
+where :math:`\theta_0` is the equilibrium value of the angle, and
-prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example
+:math:`K` is a prefactor. The anharmonic prefactors have units
-:math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ...
+:math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6
+\cdot 10^{-5} \deg^{-2}`, ...
 
 The following coefficients must be defined for each angle type via the
 :doc:`angle_coeff <angle_coeff>` command as in the example above, or in
 the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
-* :math:`K` (energy/radian\^2)
+* :math:`K` (energy)
 * :math:`\theta_0` (degrees)
 
-:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
-internally; hence the units of :math:`K` are in energy/radian\^2.
+radians internally; hence :math:`K` is effectively energy per
+radian\^2.
 
 Restrictions
 """"""""""""

doc/src/angle_quartic.rst

@@ -39,12 +39,13 @@ the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
 * :math:`\theta_0` (degrees)
-* :math:`K_2` (energy/radian\^2)
+* :math:`K_2` (energy)
-* :math:`K_3` (energy/radian\^3)
+* :math:`K_3` (energy)
-* :math:`K_4` (energy/radian\^4)
+* :math:`K_4` (energy)
 
-:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
-internally; hence the units of :math:`K` are in energy/radian\^2.
+radians internally; hence the various :math:`K` are effectively energy
+per radian\^2 or radian\^3 or radian\^4.
 
 ----------
 

doc/src/angle_sdk.rst

@@ -44,13 +44,15 @@ is included in :math:`K`.
 The following coefficients must be defined for each angle type via the
 :doc:`angle_coeff <angle_coeff>` command as in the example above:
 
-* :math:`K` (energy/radian\^2)
+* :math:`K` (energy)
 * :math:`\theta_0` (degrees)
 
-:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
+:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
-internally; hence the units of :math:`K` are in energy/radian\^2.
+radians internally; hence :math:`K` is effectively energy per
-The also required *lj/sdk* parameters will be extracted automatically
+radian\^2.
-from the pair_style.
+
+The required *lj/sdk* parameters are extracted automatically from the
+pair_style.
 
 ----------
 
@@ -63,7 +65,8 @@ produce the same results, except for round-off and precision issues.
 
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with those packages.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the

doc/src/angle_table.rst

@@ -75,7 +75,7 @@ parenthesized comments):
    ...
    181 180.0 0.0 0.0
 
-A section begins with a non-blank line whose 1st character is not a
+A section begins with a non-blank line whose first character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.  The first line begins with a keyword which
 identifies the section.  The line can contain additional text, but the
@@ -99,7 +99,7 @@ is in the tabulated file (with effectively no preliminary
 interpolation), you should set Ntable = Nfile.
 
 The "FP" parameter is optional.  If used, it is followed by two values
-fplo and fphi, which are the 2nd derivatives at the innermost and
+fplo and fphi, which are the second derivatives at the innermost and
 outermost angle settings.  These values are needed by the spline
 construction routines.  If not specified by the "FP" parameter, they
 are estimated (less accurately) by the first two and last two
@@ -110,9 +110,9 @@ equilibrium angle value, which is used, for example, by the :doc:`fix shake <fix
 set to 180.0.
 
 Following a blank line, the next N lines list the tabulated values.
-On each line, the 1st value is the index from 1 to N, the 2nd value is
+On each line, the first value is the index from 1 to N, the second value is
-the angle value (in degrees), the 3rd value is the energy (in energy
+the angle value (in degrees), the third value is the energy (in energy
-units), and the 4th is -dE/d(theta) (also in energy units).  The 3rd
+units), and the fourth is -dE/d(theta) (also in energy units).  The third
 term is the energy of the 3-atom configuration for the specified
 angle.  The last term is the derivative of the energy with respect to
 the angle (in degrees, not radians).  Thus the units of the last term

doc/src/atc_control_momentum.rst

@@ -15,7 +15,7 @@ Syntax
    fix_modify AtC control momentum glc_velocity
    fix_modify AtC control momentum hoover
    fix_modify AtC control momentum flux [faceset face_set_id, interpolate]
-   
+
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
 * control = name of the AtC sub-command
 * physics_type = *thermal* or *momentum*
@@ -52,7 +52,7 @@ the finite element temperature.  *flux* is a similar mode, but rather
 adds energy to the atoms based on conservation of energy.
 
 *correction_max_iterations* sets the maximum number of iterations to
-compute the 2nd order in time correction term for lambda with the
+compute the second order in time correction term for lambda with the
 fractional step method. The method uses the same tolerance as the
 controller's matrix solver.
 

doc/src/atc_control_thermal.rst

@@ -56,7 +56,7 @@ adds energy to the atoms based on conservation of energy. *hoover* and
 atoms.
 
 *correction_max_iterations* sets the maximum number of iterations to
-compute the 2nd order in time correction term for lambda with the
+compute the second order in time correction term for lambda with the
 fractional step method. The method uses the same tolerance as the
 controller's matrix solver.
 

doc/src/atc_hardy_fields.rst

@@ -25,8 +25,8 @@ Syntax
   - temperature : temperature derived from the relative atomic kinetic energy
   - kinetic_temperature : temperature derived from the full kinetic energy
   - number_density : simple kernel estimation of number of atoms per unit volume
-  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
+  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
-  - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
+  - transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
   - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
   - potential_energy : potential energy per unit volume
   - kinetic_energy : kinetic energy per unit volume
@@ -37,7 +37,7 @@ Syntax
   - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_
   - vacancy_concentration : volume fraction of vacancy content
   - type_concentration : volume fraction of a specific atom type
-  
+
 Examples
 """"""""
 

doc/src/atc_hardy_gradients.rst

@@ -23,8 +23,8 @@ Syntax
   - temperature : temperature derived from the relative atomic kinetic energy
   - kinetic_temperature : temperature derived from the full kinetic energy
   - number_density : simple kernel estimation of number of atoms per unit volume
-  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
+  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
-  - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
+  - transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
   - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
   - potential_energy : potential energy per unit volume
   - kinetic_energy : kinetic energy per unit volume