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Merge branch 'master' into chem_snap

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2020-06-15 12:20:48 -07:00
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commit 39aee089e7
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5
.github/CODEOWNERS vendored
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@ -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
@ -111,6 +113,7 @@ src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
src/min* @sjplimp @stanmoore1
src/utils.* @akohlmey @rbberger
# tools
tools/msi2lmp/* @akohlmey
@ -123,6 +126,8 @@ 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

4
.github/CONTRIBUTING.md vendored
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@ -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.

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.github/PULL_REQUEST_TEMPLATE.md vendored
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@ -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

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bench/FERMI/README
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@ -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.

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bench/FERMI/in.eam
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@ -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

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bench/FERMI/in.eam.titan
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@ -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

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bench/FERMI/in.lj
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@ -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

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bench/FERMI/in.lj.titan
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@ -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

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bench/FERMI/in.rhodo
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@ -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

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bench/FERMI/in.rhodo.scaled.titan
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@ -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

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bench/FERMI/in.rhodo.split.titan
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@ -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

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bench/POTENTIALS/Ni.meam
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@ -1,2 +0,0 @@
rc = 4.0
delr = 0.1

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bench/POTENTIALS/Ni.meam Symbolic link
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@ -0,0 +1 @@
../../potentials/Ni.meam

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bench/POTENTIALS/Si.sw
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@ -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

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bench/POTENTIALS/Si.sw Symbolic link
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@ -0,0 +1 @@
../../potentials/Si.sw

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bench/POTENTIALS/Si.tersoff
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@ -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

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bench/POTENTIALS/Si.tersoff Symbolic link
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@ -0,0 +1 @@
../../potentials/Si.tersoff

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bench/POTENTIALS/in.meam
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@ -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

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bench/POTENTIALS/in.reax
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@ -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

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bench/POTENTIALS/library.meam
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@ -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

1
bench/POTENTIALS/library.meam Symbolic link
View File

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

84
bench/POTENTIALS/log.16Mar18.meam.1
View File

@ -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

84
bench/POTENTIALS/log.16Mar18.meam.4
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@ -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

86
bench/POTENTIALS/log.16Mar18.reax.1
View File

@ -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

86
bench/POTENTIALS/log.16Mar18.reax.4
View File

@ -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

69
bench/POTENTIALS/reax_defs.h
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@ -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

19
cmake/CMakeLists.txt
View File

@ -420,13 +420,19 @@ 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
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
if(PKG_LIB STREQUAL mesont)
enable_language(Fortran)
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})
@ -625,6 +631,8 @@ 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})
@ -780,3 +788,6 @@ if(PKG_KSPACE)
endif()
endif()
endif()
if(BUILD_DOC)
message(STATUS "<<< Building HTML Manual >>>")
endif()

37
cmake/Modules/Documentation.cmake
View File

@ -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 ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
@ -25,11 +34,10 @@ if(BUILD_DOC)
)
# download mathjax distribution and unpack to folder "mathjax"
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
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}
)

12
cmake/Modules/LAMMPSUtils.cmake
View File

@ -96,9 +96,15 @@ function(FetchPotentials pkgfolder potfolder)
math(EXPR plusone "${blank}+1")
string(SUBSTRING ${line} 0 ${blank} pot)
string(SUBSTRING ${line} ${plusone} -1 sum)
message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${LAMMPS_POTENTIALS_DIR}/${pot}"
EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
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)

29
cmake/Modules/Packages/USER-SCAFACOS.cmake
View File

@ -14,6 +14,29 @@ endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
if(DOWNLOAD_SCAFACOS)
message(STATUS "ScaFaCoS download requested - we will build our own")
# create variables to pass our compiler flags along to the subsystem compile
# need to apply -fallow-argument-mismatch, if the fortran compiler supports it
include(CheckFortranCompilerFlag)
check_fortran_compiler_flag("-fallow-argument-mismatch" GNUFortran_ARGUMENT_MISMATCH_FLAG)
if(GNUFortran_ARGUMENT_MISMATCH_FLAG)
set(APPEND_Fortran_FLAG "-fallow-argument-mismatch")
endif()
if(CMAKE_Fortran_FLAGS)
set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${APPEND_Fortran_FLAG}")
else()
set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_${CMAKE_BUILD_TYPE}_FLAGS} ${APPEND_Fortran_FLAG}")
endif()
if(CMAKE_CXX_FLAGS)
set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
else()
set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS}")
endif()
if(CMAKE_C_FLAGS)
set(SCAFACOS_C_FLAGS "${CMAKE_C_FLAGS}")
else()
set(SCAFACOS_C_FLAGS "${CMAKE_C_${CMAKE_BUILD_TYPE}_FLAGS}")
endif()
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
@ -22,9 +45,9 @@ if(DOWNLOAD_SCAFACOS)
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
--with-internal-fftw --with-internal-pfft
--with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
FC=${CMAKE_MPI_Fortran_COMPILER}
CXX=${CMAKE_MPI_CXX_COMPILER}
CC=${CMAKE_MPI_C_COMPILER}
FC=${CMAKE_MPI_Fortran_COMPILER} FCFLAGS=${SCAFACOS_Fortran_FLAGS}
CXX=${CMAKE_MPI_CXX_COMPILER} CXXFLAGS=${SCAFACOS_CXX_FLAGS}
CC=${CMAKE_MPI_C_COMPILER} CFLAGS=${SCAFACOS_C_FLAGS}
F77=
BUILD_BYPRODUCTS
<INSTALL_DIR>/lib/libfcs.a

2
cmake/presets/all_off.cmake
View File

@ -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)

2
cmake/presets/all_on.cmake
View File

@ -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)

17
cmake/presets/download.cmake Normal file
View File

@ -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)

2
cmake/presets/mingw-cross.cmake
View File

@ -4,7 +4,7 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
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)

2
cmake/presets/nolib.cmake
View File

@ -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})

23
doc/src/Build_basics.rst
View File

@ -225,7 +225,7 @@ 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
@ -372,7 +372,8 @@ 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 +463,8 @@ 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 +491,8 @@ 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 +515,8 @@ 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 +525,8 @@ 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 +550,8 @@ 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 +559,8 @@ 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

10
doc/src/Build_development.rst
View File

@ -126,7 +126,7 @@ 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
@ -237,12 +237,12 @@ 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
reordering of operations).
of mis-compiled code (or an undesired large loss of precision due
to significant reordering of operations and thus less error cancellation).
Collect and visualize code coverage metrics
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

541
doc/src/Build_extras.rst
View File

File diff suppressed because it is too large Load Diff

88
doc/src/Build_link.rst
View File

@ -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
and how to extend it for your needs.
library <Howto_library>` page for a description of the interface
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
LAMMPS library is C++ code. You can display the currently applied
settings for building LAMMPS for the "serial" machine target by using
the command:
Note, that you need to link with ``g++`` instead of ``gcc`` even if you have
written your code in C, since LAMMPS itself is C++ code. You can display the
currently applied settings for building LAMMPS for the "serial" machine target
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

29
doc/src/Build_package.rst
View File

@ -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/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/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all 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/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default
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.

82
doc/src/Build_settings.rst
View File

@ -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
8-byte integers. The default setting of "smallbig" is almost always
adequate.
LAMMPS has a few integer data types which can be defined as either
4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
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
*catch* exceptions from within LAMMPS.
e.g. to Python. Of course, the calling code has to be set up to
*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.

1
doc/src/Commands_compute.rst
View File

@ -79,6 +79,7 @@ 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:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>`
* :doc:`msd/chunk <compute_msd_chunk>`

6
doc/src/Commands_input.rst
View File

@ -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
timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
timestep is used for the 2nd one.
simulations of 100 timesteps each. In the second case, the default
timestep (1.0 fs) is used for the first 100 step simulation and a 0.5 fs
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

3
doc/src/Commands_pair.rst
View File

@ -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>`
@ -180,6 +180,7 @@ 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:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`

2
doc/src/Developer/developer.tex
View File

@ -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

18
doc/src/Errors_debug.rst
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@ -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

22
doc/src/Errors_messages.rst
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@ -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.

8
doc/src/Errors_warnings.rst
View File

@ -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*

2
doc/src/Examples.rst
View File

@ -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.

2
doc/src/Howto_chunk.rst
View File

@ -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

32
doc/src/Howto_cmake.rst
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@ -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: TRUE (found version "3.1")
-- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (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: TRUE (found version "4.5")
-- Found JPEG: /usr/lib64/libjpeg.so (found version "62")
-- Found PNG: /usr/lib64/libpng.so (found version "1.6.37")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found GZIP: /usr/bin/gzip
-- Found FFMPEG: /usr/bin/ffmpeg
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found JPEG: /usr/lib64/libjpeg.so (found version "62")
-- Found PNG: /usr/lib64/libpng.so (found version "1.6.37")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found GZIP: /usr/bin/gzip
-- 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``
@ -438,7 +438,7 @@ the target name to the command. Example: ``cmake --build . --target all`` or
* - ``clean``
- remove all generated files
Choosing generators
-------------------

2
doc/src/Howto_coreshell.rst
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@ -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

2
doc/src/Howto_multiple.rst
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@ -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.

2
doc/src/Howto_restart.rst
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@ -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

6
doc/src/Howto_triclinic.rst
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@ -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

2
doc/src/Intro_nonfeatures.rst
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@ -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.

3
doc/src/Manual.rst
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@ -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

177
doc/src/Manual_build.rst
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@ -1,60 +1,62 @@
Building the LAMMPS manual
**************************
Depending on how you obtained LAMMPS, the doc directory has up
to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files
plus 2 e-book format files:
Depending on how you obtained LAMMPS and whether you have built the
manual yourself, this directory has a number of sub-directories and
files. Here is a list with descriptions:
.. code-block:: bash
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
utils # tools and settings for building the documentation
docenv # virtualenv for processing the manual sources
doctrees # temporary data from processing the manual
mathjax # code and fonts for rendering math in html
Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured
LAMMPS.epub # Manual in ePUB e-book format
LAMMPS.mobi # Manual in MOBI e-book format
lammps.1 # man page for the lammps command
msi2lmp.1 # man page for the msi2lmp command
README # brief info about the documentation
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
utils # tools and settings for building the documentation
lammps.1 # man page for the lammps command
msi2lmp.1 # man page for the msi2lmp command
Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured
LAMMPS.epub # Manual in ePUB e-book format
LAMMPS.mobi # Manual in MOBI e-book format
docenv # virtualenv folder for processing the manual sources
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
and the PDF files should be included.
If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
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"
or "make pdf". This requires various tools including Sphinx, git,
and the MathJax javascript library, which the build process will attempt
to download automatically into a virtual environment in the folder
doc/docenv and the folder mathjax, respectively, if not already available.
This download is required only once, unless you type "make clean-all".
After that, viewing and processing of the documentation can be done
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.
b. You can build the HTML or PDF files yourself, by typing ``make html``
or ``make pdf``. This requires various tools and files. Some of them
have to be installed (more on that below). For the rest the build
process will attempt to download and install them into a python
virtual environment and local folders. This download is required
only once, unless you type ``make clean-all``. After that, viewing and
processing of the documentation can be done without internet access.
----------
The generation of all documentation is managed by the Makefile in
the doc directory.
The generation of all documentation is managed by the Makefile in the
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
have to be installed. Here are instructions for common setups:
To run the HTML documentation build toolchain, python 3, git, doxygen,
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
files as the HTML tree. In addition it uses LaTeX to convert embedded
In addition to the tools needed for building the HTML format manual,
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 e-book readers, like Kindle, that cannot read ePUB), you
also need to have the 'ebook-convert' tool from the "calibre"
software installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
You first create the ePUB file and then convert it with 'make mobi'
On the Kindle readers in particular, you also have support for
PDF files, so you could download and view the PDF version as an alternative.
For converting the generated ePUB file to a MOBI format file (for e-book
readers, like Kindle, that cannot read ePUB), you also need to have the
``ebook-convert`` tool from the "calibre" software
installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
Typing ``make mobi`` will first create the ePUB file and then convert
it. On the Kindle readers in particular, you also have support for PDF
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

2
doc/src/Modify_fix.rst
View File

@ -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) |
+---------------------------+--------------------------------------------------------------------------------------------+

18
doc/src/Modify_kspace.rst
View File

@ -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 |
+---------------+----------------------------------------------+
| setup | computation before the 1st timestep of a run |
+---------------+----------------------------------------------+
| compute | every-timestep computation |
+---------------+----------------------------------------------+
| memory_usage | tally of memory usage |
+---------------+----------------------------------------------+
+---------------+------------------------------------------------+
| init | initialize the calculation before a run |
+---------------+------------------------------------------------+
| setup | computation before the first timestep of a run |
+---------------+------------------------------------------------+
| compute | every-timestep computation |
+---------------+------------------------------------------------+
| memory_usage | tally of memory usage |
+---------------+------------------------------------------------+

53
doc/src/Packages_details.rst
View File

@ -81,6 +81,7 @@ 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>`
@ -489,7 +490,7 @@ 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.
@ -1712,6 +1713,56 @@ 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:

2
doc/src/Packages_user.rst
View File

@ -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 |

9
doc/src/Python_library.rst
View File

@ -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:

2
doc/src/Python_test.rst
View File

@ -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::

8
doc/src/Run_options.rst
View File

@ -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
matched up with a specific set of processors in the 1st partition.
to insure that a specific Kspace processor (in the second partition) is
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

2
doc/src/angle_charmm.rst
View File

@ -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.

4
doc/src/angle_coeff.rst
View File

@ -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::

10
doc/src/angle_table.rst
View File

@ -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
the angle value (in degrees), the 3rd value is the energy (in energy
units), and the 4th is -dE/d(theta) (also in energy units). The 3rd
On each line, the first value is the index from 1 to N, the second value is
the angle value (in degrees), the third value is the energy (in energy
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

4
doc/src/atc_control_momentum.rst
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@ -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.

2
doc/src/atc_control_thermal.rst
View File

@ -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.

6
doc/src/atc_hardy_fields.rst
View File

@ -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
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy 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 : 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
""""""""

4
doc/src/atc_hardy_gradients.rst
View File

@ -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
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy 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 : 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

2
doc/src/atc_hardy_kernel.rst
View File

@ -25,7 +25,7 @@ Syntax
- *quartic_bar* : <half_width>
- *quartic_cylinder* : <radius>
- *quartic_sphere* : <radius>
Examples

4
doc/src/atc_hardy_rates.rst
View File

@ -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
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy 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 : 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

2
doc/src/atc_remove_species.rst
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@ -38,7 +38,7 @@ Related AtC commands
- :doc:`fix_modify AtC add_species <atc_add_species>`
- :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
- :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
Default
"""""""

2
doc/src/atc_set_reference_pe.rst
View File

@ -22,7 +22,7 @@ Examples
fix_modify AtC set reference_potential_energy
fix_modify AtC set reference_potential_energy -0.05
fix_modify AtC set reference_potential_energy myPEvalues
fix_modify AtC set reference_potential_energy myPEvalues
Description
"""""""""""

18
doc/src/atc_time_integration.rst
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@ -33,11 +33,11 @@ Command to select the thermal or momentum time integration.
Options for thermal time integration:
*gear*
atomic velocity update with 2nd order Verlet, nodal temperature update
with 3rd or 4th order Gear, thermostats based on controlling power
atomic velocity update with second order Verlet, nodal temperature update
with third or fourth order Gear, thermostats based on controlling power
*fractional_step*
atomic velocity update with 2nd order Verlet, mixed nodal temperature
atomic velocity update with second order Verlet, mixed nodal temperature
update, 3/4 Gear for continuum and 2 Verlet for atomic contributions,
thermostats based on controlling discrete energy changes
@ -46,18 +46,18 @@ Options for thermal time integration:
Options for momentum time integration:
*verlet*
atomic velocity update with 2nd order Verlet, nodal temperature update
with 2nd order Verlet, kinetostats based on controlling force
atomic velocity update with second order Verlet, nodal temperature update
with second order Verlet, kinetostats based on controlling force
*fractional_step*
atomic velocity update with 2nd order Verlet, mixed nodal momentum
update, 2nd order Verlet for continuum and exact 2nd order Verlet for
atomic velocity update with second order Verlet, mixed nodal momentum
update, second order Verlet for continuum and exact second order Verlet for
atomic contributions, kinetostats based on controlling discrete
momentum changes
*gear*
atomic velocity update with 2nd order Verlet, nodal temperature update
with 3rd or 4th order Gear, kinetostats based on controlling power.
atomic velocity update with second order Verlet, nodal temperature update
with third or fourth order Gear, kinetostats based on controlling power.
---------

4
doc/src/atom_style.rst
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@ -103,6 +103,8 @@ quantities.
+--------------+-----------------------------------------------------+--------------------------------------+
| *mdpd* | density | mDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *mesont* | mass, radius, length, buckling, connections, tube id| mesoscopic nanotubes |
+--------------+-----------------------------------------------------+--------------------------------------+
| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
+--------------+-----------------------------------------------------+--------------------------------------+
| *peri* | mass, volume | mesoscopic Peridynamic models |
@ -347,6 +349,8 @@ dynamics (tDPD), respectively.
The *sph* style is part of the USER-SPH package for smoothed particle
hydrodynamics (SPH). See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
The *mesont* style is part of the USER-MESONT package.
The *spin* style is part of the SPIN package.
The *wavepacket* style is part of the USER-AWPMD package for the

4
doc/src/bond_coeff.rst
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@ -32,7 +32,7 @@ Bond 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 bond types. This takes the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of bond types,
then an asterisk with no numeric values means all types from 1 to N. A
@ -54,7 +54,7 @@ same format as the arguments of the bond_coeff command in an input
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 "Bond 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::

4
doc/src/bond_fene.rst
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@ -38,8 +38,8 @@ The *fene* bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd
term is attractive, the second Lennard-Jones term is repulsive. The
first term extends to :math:`R_0`, the maximum extent of the bond. The second
term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
The following coefficients must be defined for each bond type via the

4
doc/src/bond_fene_expand.rst
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@ -32,12 +32,12 @@ The *fene/expand* bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
term is attractive, the second Lennard-Jones term is repulsive.
The *fene/expand* bond style is similar to *fene* except that an extra
shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
effectively change the bead size of the bonded atoms. The first term
now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
now extends to :math:`R_0 + \Delta` and the second term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in

8
doc/src/bond_table.rst
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@ -74,7 +74,7 @@ parenthesized comments):
...
101 1.00 338.0000 -1352.0000
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
@ -109,9 +109,9 @@ equilibrium bond length, which is used, for example, by the :doc:`fix shake <fix
length is to the distance in the table with the lowest potential energy.
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
the bond length r (in distance units), the 3rd value is the energy (in
energy units), and the 4th is the force (in force units). The bond
On each line, the first value is the index from 1 to N, the second value is
the bond length r (in distance units), the third value is the energy (in
energy units), and the fourth is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the calculation is

8
doc/src/bond_write.rst
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@ -47,7 +47,13 @@ The file is written in the format used as input for the
:doc:`bond_style <bond_style>` *table* option with *keyword* as the
section name. Each line written to the file lists an index number
(1-N), a distance (in distance units), an energy (in energy units),
and a force (in force units).
and a force (in force units). In case a new file is created, the first
line will be a comment with a "DATE:" and "UNITS:" tag with the current
date and :doc:`units <units>` settings. For subsequent invocations of
the bond_write command for the same file, data will be appended and the
current units settings will be compared to the data from the header, if
present, and bond_write will refuse to add a table if the units are not
the same.
Restrictions
""""""""""""

4
doc/src/boundary.rst
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@ -76,9 +76,9 @@ atoms becomes less than 50.0. This can be useful if you start a
simulation with an empty box or if you wish to leave room on one side
of the box, e.g. for atoms to evaporate from a surface.
For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension
For triclinic (non-orthogonal) simulation boxes, if the second dimension
of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
enforced with the tilt factor offset. If the 1st dimension is
enforced with the tilt factor offset. If the first dimension is
shrink-wrapped, then the shrink wrapping is applied to the tilted box
face, to encompass the atoms. E.g. for a positive xy tilt, the xlo
and xhi faces of the box are planes tilting in the +y direction as y

2
doc/src/box.rst
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@ -38,7 +38,7 @@ skewed the triclinic box is; see the :doc:`Howto triclinic <Howto_triclinic>` do
boxes in LAMMPS.
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
than half the distance of the parallel box length, which is the first
dimension in the tilt factor (x for xz). If *tilt* is set to
*small*\ , which is the default, then an error will be
generated if a box is created which exceeds this limit. If *tilt*

1
doc/src/compute.rst
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@ -235,6 +235,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction
* :doc:`pe <compute_pe>` - potential energy
* :doc:`pe/atom <compute_pe_atom>` - potential energy for each atom
* :doc:`mesont <compute_mesont>` - Nanotube bending,stretching, and intertube energies
* :doc:`pe/mol/tally <compute_tally>` -
* :doc:`pe/tally <compute_tally>` -
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom

8
doc/src/compute_adf.rst
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@ -82,9 +82,9 @@ neighbor atom in each requested ADF.
is what is specified with the :doc:`neighbor <neighbor>` command.
The *itypeN*\ ,\ *jtypeN*\ ,\ *ktypeN* settings can be specified in one of two
ways. An explicit numeric value can be used, as in the 1st example
ways. An explicit numeric value can be used, as in the first example
above. Or a wild-card asterisk can be used to specify a range of atom
types as in the 2nd example above.
types as in the second example above.
This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
@ -92,12 +92,12 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A middle asterisk means all types from m to n
(inclusive).
If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the 1st example
If *itypeN*\ , *jtypeN*\ , and *ktypeN* are single values, as in the first example
above, this means that the ADF is computed where atoms of type *itypeN*
are the central atom, and neighbor atoms of type *jtypeN* and *ktypeN*
are forming the angle. If any of *itypeN*\ , *jtypeN*\ , or *ktypeN*
represent a range of values via
the wild-card asterisk, as in the 2nd example above, this means that the
the wild-card asterisk, as in the second example above, this means that the
ADF is computed where atoms of any of the range of types represented
by *itypeN* are the central atom, and the angle is formed by two neighbors,
one neighbor in the range of types represented by *jtypeN* and another neighbor

6
doc/src/compute_chunk_atom.rst
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@ -218,8 +218,8 @@ into ellipses.
The created bins (and hence the chunk IDs) are numbered consecutively
from 1 to the number of bins = *Nchunk*\ . For *bin2d* and *bin3d*\ , the
numbering varies most rapidly in the first dimension (which could be
x, y, or z), next rapidly in the 2nd dimension, and most slowly in the
3rd dimension. For *bin/sphere*\ , the bin with smallest radii is chunk
x, y, or z), next rapidly in the second dimension, and most slowly in the
third dimension. For *bin/sphere*\ , the bin with smallest radii is chunk
1 and the bni with largest radii is chunk Nchunk = *ncbin*\ . For
*bin/cylinder*\ , the numbering varies most rapidly in the dimension
along the cylinder axis and most slowly in the radial direction.
@ -614,7 +614,7 @@ Note that for the *bin/sphere* style, the radii *srmin* and *srmax* are
scaled by the lattice spacing or reduced value of the *x* dimension.
Note that for the *bin/cylinder* style, the radii *crmin* and *crmax*
are scaled by the lattice spacing or reduced value of the 1st
are scaled by the lattice spacing or reduced value of the first
dimension perpendicular to the cylinder axis. E.g. y for an x-axis
cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.

2
doc/src/compute_coord_atom.rst
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@ -63,7 +63,7 @@ keywords are listed, a single coordination number is calculated, which
includes atoms of all types (same as the "\*" format, see below).
The *typeN* keywords can be specified in one of two ways. An explicit
numeric value can be used, as in the 2nd example above. Or a
numeric value can be used, as in the second example above. Or a
wild-card asterisk can be used to specify a range of atom types. This
takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of
atom types, then an asterisk with no numeric values means all types

2
doc/src/compute_displace_atom.rst
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@ -36,7 +36,7 @@ all effects due to atoms passing through periodic boundaries.
A vector of four quantities per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy +
The fourth component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy +
dz\*dz).
The displacement of an atom is from its original position at the time

2
doc/src/compute_fep.rst
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@ -224,7 +224,7 @@ the pair\_\*.cpp file associated with the potential.
Similar to the :doc:`pair_coeff <pair_coeff>` command, I and J can be
specified in one of two ways. Explicit numeric values can be used for
each, as in the 1st example above. I <= J is required. LAMMPS sets
each, as in the first example above. I <= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same
values. A wild-card asterisk can be used in place of or in conjunction
with the I,J arguments to set the coefficients for multiple pairs of

2
doc/src/compute_group_group.rst
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@ -64,7 +64,7 @@ If the *kspace* keyword is set to *yes*\ , which is not the default, and
if a :doc:`kspace_style <kspace_style>` is defined, then the interaction
energy will include a Kspace component which is the long-range
Coulombic energy between all the atoms in the first group and all the
atoms in the 2nd group. Likewise, the interaction force calculated by
atoms in the second group. Likewise, the interaction force calculated by
this compute will include the force on the compute group atoms due to
long-range Coulombic interactions with atoms in the specified group2.

56
doc/src/compute_mesont.rst Normal file
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@ -0,0 +1,56 @@
.. index:: compute mesont
compute mesont command
==========================
Syntax
""""""
.. parsed-literal::
compute ID group-ID mesont mode
* ID, group-ID are documented in :doc:`compute <compute>` command
* mesont = style name of the compute command
* mode = one of estretch, ebend, etube (see details below)
Examples
""""""""
.. parsed-literal::
compute 1 all mesont estretch
Description
"""""""""""
These computes define computations for the stretching (estretch), bending
(ebend), and intertube (etube) per-node (atom) and total energies. The
evaluated value is selected by a parameter passed to the compute: estretch,
ebend, etube.
**Output info:**
These computes calculate per-node (per-atom) vectors, which can be accessed by
any command that uses per-atom values from a compute as input, and global
scalars. See the :doc:`Howto output <Howto_output>` doc page for an overview of
LAMMPS output options.
The computed values are provided in energy :doc:`units <units>`.
Restrictions
""""""""""""
These computes are part of the USER-MESONT package. They are only enabled if
LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
doc page for more info. In addition, :doc:`mesont pair_style <pair_style>`
must be used.
Related commands
""""""""""""""""
:doc:`dump custom <dump>`
**Default:** none

2
doc/src/compute_msd.rst
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@ -38,7 +38,7 @@ parameter of mean-squared displacement, see the :doc:`compute msd/nongauss <comp
A vector of four quantities is calculated by this compute. The first 3
elements of the vector are the squared dx,dy,dz displacements, summed
and averaged over atoms in the group. The 4th element is the total
and averaged over atoms in the group. The fourth element is the total
squared displacement, i.e. (dx\*dx + dy\*dy + dz\*dz), summed and
averaged over atoms in the group.

2
doc/src/compute_msd_chunk.rst
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@ -36,7 +36,7 @@ they can be used to measure properties of a system.
Four quantities are calculated by this compute for each chunk. The
first 3 quantities are the squared dx,dy,dz displacements of the
center-of-mass. The 4th component is the total squared displacement,
center-of-mass. The fourth component is the total squared displacement,
i.e. (dx\*dx + dy\*dy + dz\*dz) of the center-of-mass. These
calculations include all effects due to atoms passing through periodic
boundaries.

4
doc/src/compute_msd_nongauss.rst
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@ -39,7 +39,7 @@ element of the vector is the total squared dx,dy,dz displacements
drsquared = (dx\*dx + dy\*dy + dz\*dz) of atoms, and the second is the
fourth power of these displacements drfourth = (dx\*dx + dy\*dy +
dz\*dz)\*(dx\*dx + dy\*dy + dz\*dz), summed and averaged over atoms in the
group. The 3rd component is the nonGaussian diffusion parameter NGP =
group. The third component is the nonGaussian diffusion parameter NGP =
3\*drfourth/(5\*drsquared\*drsquared), i.e.
.. math::
@ -68,7 +68,7 @@ page for an overview of LAMMPS output options.
The vector values are "intensive". The first vector value will be in
distance\^2 :doc:`units <units>`, the second is in distance\^4 units, and
the 3rd is dimensionless.
the third is dimensionless.
Restrictions
""""""""""""

2
doc/src/compute_property_atom.rst
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@ -30,6 +30,7 @@ Syntax
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z,
nbonds,
buckling,
vfrac, s0,
spin, eradius, ervel, erforce,
rho, drho, e, de, cv,
@ -63,6 +64,7 @@ Syntax
end12x, end12y, end12z = end points of line segment
corner123x, corner123y, corner123z = corner points of triangle
nbonds = number of bonds assigned to an atom
buckling = buckling flag used in mesoscopic simulation of nanotubes
.. parsed-literal::

2
doc/src/compute_property_chunk.rst
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@ -63,7 +63,7 @@ chunkID. This means that the original chunk IDs (e.g. molecule IDs)
will have been compressed to remove chunk IDs with no atoms assigned
to them. Thus a compressed chunk ID of 3 may correspond to an original
chunk ID (molecule ID in this case) of 415. The *id* attribute will
then be 415 for the 3rd chunk.
then be 415 for the third chunk.
The *coordN* attributes can only be used if a *binning* style was used
in the :doc:`compute chunk/atom <compute_chunk_atom>` command referenced

6
doc/src/compute_rdf.rst
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@ -97,7 +97,7 @@ listed, then a separate histogram is generated for each
*itype*\ ,\ *jtype* pair.
The *itypeN* and *jtypeN* settings can be specified in one of two
ways. An explicit numeric value can be used, as in the 4th example
ways. An explicit numeric value can be used, as in the fourth example
above. Or a wild-card asterisk can be used to specify a range of atom
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
number of atom types, then an asterisk with no numeric values means
@ -106,11 +106,11 @@ all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A middle asterisk means all types from m to n
(inclusive).
If both *itypeN* and *jtypeN* are single values, as in the 4th example
If both *itypeN* and *jtypeN* are single values, as in the fourth example
above, this means that a g(r) is computed where atoms of type *itypeN*
are the central atom, and atoms of type *jtypeN* are the distribution
atom. If either *itypeN* and *jtypeN* represent a range of values via
the wild-card asterisk, as in the 5th example above, this means that a
the wild-card asterisk, as in the fifth example above, this means that a
g(r) is computed where atoms of any of the range of types represented
by *itypeN* are the central atom, and atoms of any of the range of
types represented by *jtypeN* are the distribution atom.

2
doc/src/compute_temp_cs.rst
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@ -49,7 +49,7 @@ respective group IDs, which can be defined using the
must be the same and there should be one bond defined between a pair
of atoms in the two groups. 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
these groups, they are taken into account by the *group-ID* (second
argument) of the compute.
The temperature is calculated by the formula KE = dim/2 N k T, where

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