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Fix whitespace

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This commit is contained in:
Richard Berger
2020-06-16 07:20:09 -04:00
parent 95e79b2347
commit 9d74984144
29 changed files with 200 additions and 200 deletions
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6
doc/github-development-workflow.md
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@ -25,10 +25,10 @@ In the interest of consistency, ONLY ONE of the core LAMMPS developers
should doing the merging itself. This is currently
[@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
If this assignment needs to be changed, it shall be done right after a
stable release. If the currently assigned developer cannot merge outstanding pull
requests in a timely manner, or in other extenuating circumstances,
stable release. If the currently assigned developer cannot merge outstanding pull
requests in a timely manner, or in other extenuating circumstances,
other core LAMMPS developers with merge rights can merge pull requests,
when necessary.
when necessary.
## Pull Requests

2
doc/include-file-conventions.md
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@ -65,7 +65,7 @@ Header files will typically contain the definition of a (single) class.
These header files should have as few include statements as possible.
This is particularly important for classes that implement a "style" and
thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
all be included in the auto-generated `"some_style.h"` files which
all be included in the auto-generated `"some_style.h"` files which
results in a high potential for direct or indirect symbol name clashes.
In the ideal case, the header would only include one file defining the

14
doc/src/compute_mesont.rst
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@ -26,23 +26,23 @@ Examples
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,
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
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
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.

2
doc/src/compute_orientorder_atom.rst
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@ -26,7 +26,7 @@ Syntax
*wl* value = yes or no
*wl/hat* value = yes or no
*components* value = ldegree
*chunksize* value = number of atoms in each pass
*chunksize* value = number of atoms in each pass
Examples
""""""""

2
doc/src/compute_property_atom.rst
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@ -64,7 +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
buckling = buckling flag used in mesoscopic simulation of nanotubes
.. parsed-literal::

6
doc/src/pair_mesont_tpm.rst
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@ -9,7 +9,7 @@ Syntax
.. parsed-literal::
pair_style mesont/tpm cut table_path BendingMode TPMType
pair_style mesont/tpm cut table_path BendingMode TPMType
* cut = the cutoff distance
* table_path = the path to the potential table
@ -114,7 +114,7 @@ study the thermal transport properties of carbon nanotube films
The methods for modeling of
the mechanical energy dissipation into heat (energy exchange between the
dynamic degrees of freedom of the mesoscopic model and the energy of atomic
vibrations that are not explicitly represented in the model)
vibrations that are not explicitly represented in the model)
:ref:`(Zhigilei10) <Zhigilei10>` and mesoscopic description of covalent cross-links
between nanotubes :ref:`(Banna) <Banna>` have also been developed but are not
included in this first release of the LAMMPS implementation of the force field.
@ -144,7 +144,7 @@ pair interactions.
The cutoff distance should be set to be at least :math:`max\left[2L,\sqrt{L^2/2+(2R+T_{cut})^2}\right]` ,
where L is the maximum segment length, R is the maximum tube radius, and
:math:`T_{cut}` = 10.2 A is the maximum distance between the surfaces of interacting
segments. Because of the use of extended chain concept at CNT ends, the recommended
segments. Because of the use of extended chain concept at CNT ends, the recommended
cutoff is 3L.
The MESONT-TABTP_10_10.xrs potential file provided with LAMMPS (see the

8
src/GPU/Install.sh
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@ -32,7 +32,7 @@ action fix_gpu.cpp
action fix_gpu.h
action gpu_extra.h
action pair_beck_gpu.cpp
action pair_beck_gpu.h
action pair_beck_gpu.h
action pair_born_coul_long_gpu.cpp pair_born_coul_long.cpp
action pair_born_coul_long_gpu.h pair_born_coul_long.cpp
action pair_born_coul_long_cs_gpu.cpp pair_born_coul_long_cs.cpp
@ -71,9 +71,9 @@ action pair_lj_sf_dipole_sf_gpu.cpp pair_lj_sf_dipole_sf.cpp
action pair_lj_sf_dipole_sf_gpu.h pair_lj_sf_dipole_sf.cpp
action pair_eam_alloy_gpu.cpp pair_eam.cpp
action pair_eam_alloy_gpu.h pair_eam.cpp
action pair_eam_fs_gpu.cpp pair_eam.cpp
action pair_eam_fs_gpu.cpp pair_eam.cpp
action pair_eam_fs_gpu.h pair_eam.cpp
action pair_eam_gpu.cpp pair_eam.cpp
action pair_eam_gpu.cpp pair_eam.cpp
action pair_eam_gpu.h pair_eam.cpp
action pair_gauss_gpu.cpp
action pair_gauss_gpu.h
@ -112,7 +112,7 @@ action pair_lj_sdk_coul_long_gpu.h pair_lj_sdk_coul_long.cpp
action pair_lj_sdk_gpu.cpp pair_lj_sdk.cpp
action pair_lj_sdk_gpu.h pair_lj_sdk.cpp
action pair_mie_cut_gpu.cpp
action pair_mie_cut_gpu.h
action pair_mie_cut_gpu.h
action pair_morse_gpu.cpp
action pair_morse_gpu.h
action pair_resquared_gpu.cpp pair_resquared.cpp

22
src/KOKKOS/Install.sh
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@ -31,7 +31,7 @@ action () {
KOKKOS_INSTALLED=0
if (test -e ../Makefile.package) then
KOKKOS_INSTALLED=`grep DLMP_KOKKOS ../Makefile.package | wc -l`
fi
fi
if (test $mode = 1) then
if (test $KOKKOS_INSTALLED = 0) then
@ -45,14 +45,14 @@ fi
# list of files with optional dependcies
action angle_charmm_kokkos.cpp angle_charmm.cpp
action angle_charmm_kokkos.cpp angle_charmm.cpp
action angle_charmm_kokkos.h angle_charmm.h
action angle_class2_kokkos.cpp angle_class2.cpp
action angle_class2_kokkos.cpp angle_class2.cpp
action angle_class2_kokkos.h angle_class2.h
action angle_cosine_kokkos.cpp angle_cosine.cpp
action angle_cosine_kokkos.cpp angle_cosine.cpp
action angle_cosine_kokkos.h angle_cosine.h
action angle_harmonic_kokkos.cpp angle_harmonic.cpp
action angle_harmonic_kokkos.h angle_harmonic.h
action angle_harmonic_kokkos.cpp angle_harmonic.cpp
action angle_harmonic_kokkos.h angle_harmonic.h
action atom_kokkos.cpp
action atom_kokkos.h
action atom_vec_angle_kokkos.cpp atom_vec_angle.cpp
@ -75,7 +75,7 @@ action atom_vec_molecular_kokkos.cpp atom_vec_molecular.cpp
action atom_vec_molecular_kokkos.h atom_vec_molecular.h
action atom_vec_sphere_kokkos.cpp atom_vec_sphere.cpp
action atom_vec_sphere_kokkos.h atom_vec_sphere.h
action bond_class2_kokkos.cpp bond_class2.cpp
action bond_class2_kokkos.cpp bond_class2.cpp
action bond_class2_kokkos.h bond_class2.h
action bond_fene_kokkos.cpp bond_fene.cpp
action bond_fene_kokkos.h bond_fene.h
@ -93,9 +93,9 @@ action compute_temp_kokkos.cpp
action compute_temp_kokkos.h
action dihedral_charmm_kokkos.cpp dihedral_charmm.cpp
action dihedral_charmm_kokkos.h dihedral_charmm.h
action dihedral_class2_kokkos.cpp dihedral_class2.cpp
action dihedral_class2_kokkos.cpp dihedral_class2.cpp
action dihedral_class2_kokkos.h dihedral_class2.h
action dihedral_harmonic_kokkos.cpp dihedral_harmonic.cpp
action dihedral_harmonic_kokkos.cpp dihedral_harmonic.cpp
action dihedral_harmonic_kokkos.h dihedral_harmonic.h
action dihedral_opls_kokkos.cpp dihedral_opls.cpp
action dihedral_opls_kokkos.h dihedral_opls.h
@ -109,7 +109,7 @@ action fix_deform_kokkos.h
action fix_enforce2d_kokkos.cpp
action fix_enforce2d_kokkos.h
action fix_eos_table_rx_kokkos.cpp fix_eos_table_rx.cpp
action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h
action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h
action fix_freeze_kokkos.cpp fix_freeze.cpp
action fix_freeze_kokkos.h fix_freeze.h
action fix_gravity_kokkos.cpp
@ -156,7 +156,7 @@ action fix_rx_kokkos.cpp fix_rx.cpp
action fix_rx_kokkos.h fix_rx.h
action gridcomm_kokkos.cpp gridcomm.cpp
action gridcomm_kokkos.h gridcomm.h
action improper_class2_kokkos.cpp improper_class2.cpp
action improper_class2_kokkos.cpp improper_class2.cpp
action improper_class2_kokkos.h improper_class2.h
action improper_harmonic_kokkos.cpp improper_harmonic.cpp
action improper_harmonic_kokkos.h improper_harmonic.h

8
src/Make.sh
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@ -1,4 +1,4 @@
# Make.sh = update Makefile.lib, Makefile.shlib, Makefile.list
# Make.sh = update Makefile.lib, Makefile.shlib, Makefile.list
# or style_*.h files
# Syntax: sh Make.sh style
# sh Make.sh Makefile.lib
@ -31,7 +31,7 @@ style () {
rm -f style_$3.h
touch style_$3.h
rm -f Obj_*/$4.d
if (test $5) then
if (test $5) then
rm -f Obj_*/$5.d
fi
rm -f Obj_*/lammps.d
@ -39,14 +39,14 @@ style () {
elif (test ! -e style_$3.h) then
mv style_$3.tmp style_$3.h
rm -f Obj_*/$4.d
if (test $5) then
if (test $5) then
rm -f Obj_*/$5.d
fi
rm -f Obj_*/lammps.d
elif (test "`diff --brief style_$3.h style_$3.tmp`" != "") then
mv style_$3.tmp style_$3.h
rm -f Obj_*/$4.d
if (test $5) then
if (test $5) then
rm -f Obj_*/$5.d
fi
rm -f Obj_*/lammps.d

2
src/OPT/Install.sh
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@ -41,7 +41,7 @@ action pair_lj_cut_coul_long_opt.h pair_lj_cut_coul_long.cpp
action pair_lj_cut_opt.cpp
action pair_lj_cut_opt.h
action pair_lj_cut_tip4p_long_opt.cpp pair_lj_cut_tip4p_long.cpp
action pair_lj_cut_tip4p_long_opt.h pair_lj_cut_tip4p_long.cpp
action pair_lj_cut_tip4p_long_opt.h pair_lj_cut_tip4p_long.cpp
action pair_lj_long_coul_long_opt.cpp pair_lj_long_coul_long.cpp
action pair_lj_long_coul_long_opt.h pair_lj_long_coul_long.cpp
action pair_morse_opt.cpp

10
src/SPIN/README
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@ -1,5 +1,5 @@
The SPIN package enables coupled spin dynamics and molecular
dynamics simulations.
The SPIN package enables coupled spin dynamics and molecular
dynamics simulations.
The package provides the following features:
@ -12,11 +12,11 @@ atom in the system
* computing and outputting magnetic quantities
* minimizing the energy or total torque of a magnetic system
The different options provided by this package are explained in the
The different options provided by this package are explained in the
LAMMPS documentation.
Once you have successfully built LAMMPS with this package, you can test
it using one of the input files provided from the examples/SPIN dir.
Once you have successfully built LAMMPS with this package, you can test
it using one of the input files provided from the examples/SPIN dir.
For example:
./lmp_serial < lammps/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp

2
src/USER-ADIOS/Install.sh
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@ -52,7 +52,7 @@ if (test $1 = 1) then
"installation directory or adios2-config should be in PATH"
fi
if [ "$CONFIGSCRIPT" != "none" ]; then
if [ "$CONFIGSCRIPT" != "none" ]; then
ADIOS2_INC=`$CONFIGSCRIPT --cxx-flags`
ADIOS2_LIB=`$CONFIGSCRIPT --cxx-libs`

14
src/USER-ADIOS/README
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@ -1,16 +1,16 @@
This package provides the adios dump and read_dump styles.
See the doc page for the "dump adios" and "read_dump ... format adios" commands.
See the doc page for the "dump adios" and "read_dump ... format adios" commands.
These styles require having ADIOS 2.x itself installed on your system.
Configure LAMMPS with CMake
a. set the environment variable
ADIOS2_DIR
Configure LAMMPS with CMake
a. set the environment variable
ADIOS2_DIR
to the ADIOS 2.x installation path
b. use the cmake option
-D PKG_USER-ADIOS=yes
b. use the cmake option
-D PKG_USER-ADIOS=yes
The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory);
The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory);
If you need help, please submit a ticket at the OLCF ticket user support mentioning his name in the ticket.
https://www.olcf.ornl.gov/support/submit-ticket

4
src/USER-BOCS/README
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@ -1,7 +1,7 @@
This user package implements the pressure correction to the barostat as
This user package implements the pressure correction to the barostat as
outlined in:
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015).

44
src/USER-CGDNA/README.md
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@ -2,49 +2,49 @@ This package contains a LAMMPS implementation of coarse-grained
models of DNA, which can be used to model sequence-specific
DNA strands.
Please cite
Please cite
[![DOI](https://zenodo.org/badge/132764768.svg)](https://zenodo.org/badge/latestdoi/132764768)
as well as [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles
as well as [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles
in any publication that uses this package.
See the doc pages and [2,3,4,5,6] for the individual bond and pair styles.
See the doc pages and [2,3,4,5,6] for the individual bond and pair styles.
The packages contains also a new Langevin-type rigid-body integrator,
which has also its own doc page and is explained in [7].
[1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge,
"Coarse-grained simulation of DNA using LAMMPS",
"Coarse-grained simulation of DNA using LAMMPS",
Eur. Phys. J. E 41, 57 (2018).
[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
and thermodynamic properties of a coarse-grained DNA model",
J. Chem. Phys. 134, 085101 (2011).
[3] T.E. Ouldridge, "Coarse-grained modelling of DNA and DNA
[3] T.E. Ouldridge, "Coarse-grained modelling of DNA and DNA
self-assembly", DPhil. University of Oxford (2011).
[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., "Introducing
Improved structural properties and salt dependence into a coarse-grained
model of DNA", J. Chem. Phys. 142, 234901 (2015).
[5] P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level
[5] P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level
coarse-grained model of RNA", J. Chem. Phys. 140, 235102 (2014).
[6] P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent
[6] P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent
thermodynamics of a coarse-grained DNA model",
J. Chem. Phys. 137, 135101 (2012).
J. Chem. Phys. 137, 135101 (2012).
[7] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
[7] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
144114 (2015).
Example input and data files can be found in
/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/.
Python setup tools which create single straight or helical DNA or RNA
strands as well as DNA or RNA duplexes or arrays of duplexes can be
found in /examples/USER/cgdna/util/. A technical report with more
general information on the model, its implementation and performance
/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/.
Python setup tools which create single straight or helical DNA or RNA
strands as well as DNA or RNA duplexes or arrays of duplexes can be
found in /examples/USER/cgdna/util/. A technical report with more
general information on the model, its implementation and performance
as well as the structure of the data and input file can be found
in /doc/src/PDF/USER-CGDNA.pdf.
@ -65,7 +65,7 @@ oliver d o t henrich a t strath d o t ac d o t uk
** Bond styles provided by this package:
bond_oxdna_fene.cpp: backbone connectivity,
bond_oxdna_fene.cpp: backbone connectivity,
a modified FENE potential (see [2,3])
bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [4])
@ -86,20 +86,20 @@ pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides
pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides
pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp:
pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp:
corresponding pair styles in oxDNA2 (see [4])
pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp,
pair_oxrna2_xstk.cpp:
pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp,
pair_oxrna2_xstk.cpp:
corresponding pair styles in oxDNA2 (see [5])
pair_oxdna2_dh.cpp, pair_oxrna2_dh.cpp:
pair_oxdna2_dh.cpp, pair_oxrna2_dh.cpp:
Debye-Hueckel electrostatic interaction between backbone sites
** Fixes provided by this package:
fix_nve_dotc_langevin.cpp: fix for Langevin-type rigid body integrator "C"
in above Ref. [7]
in above Ref. [7]
fix_nve_dot.cpp: NVE-type rigid body integrator without noise

34
src/USER-DIFFRACTION/README
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@ -1,41 +1,41 @@
This package contains the commands needed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
electron diffraction intensities based on kinematic diffraction
theory. Detailed discription of the computation can be found in the
following works:
Coleman, S.P., Spearot, D.E., Capolungo, L. (2013) Virtual
diffraction analysis of Ni [010] symmetric tilt grain boundaries,
Modelling and Simulation in Materials Science and Engineering, 21
Coleman, S.P., Spearot, D.E., Capolungo, L. (2013) Virtual
diffraction analysis of Ni [010] symmetric tilt grain boundaries,
Modelling and Simulation in Materials Science and Engineering, 21
055020. doi:10.1088/0965-0393/21/5/055020
Coleman, S.P., Sichani, M.M., Spearot, D.E. (2014) A computational
algorithm to produce virtual x-ray and electron diffraction patterns
from atomistic simulations, JOM, 66 (3), 408-416.
doi:10.1007/s11837-013-0829-3
Coleman, S.P., Sichani, M.M., Spearot, D.E. (2014) A computational
algorithm to produce virtual x-ray and electron diffraction patterns
from atomistic simulations, JOM, 66 (3), 408-416.
doi:10.1007/s11837-013-0829-3
Coleman, S.P., Pamidighantam, S. Van Moer, M., Wang, Y., Koesterke, L.
Spearot D.E (2014) Performance improvement and workflow development
of virtual diffraction calculations, XSEDE14,
Coleman, S.P., Pamidighantam, S. Van Moer, M., Wang, Y., Koesterke, L.
Spearot D.E (2014) Performance improvement and workflow development
of virtual diffraction calculations, XSEDE14,
doi:10.1145/2616498.2616552
---------------------------------
User-diffraction includes:
1) compute_xrd : calculate x-ray diffraction intensities as a
1) compute_xrd : calculate x-ray diffraction intensities as a
scattering angle (2theta)
2) compute_xrd_consts.h : coefficients used for x-ray atomic
scattering factors listed by element
3) compute saed : calculate 3D diffraction intensities for the
purpose of creating selected area electron
3) compute saed : calculate 3D diffraction intensities for the
purpose of creating selected area electron
diffraction patterns
4) compute_xrd_consts.h : coefficients used for electron atomic
scattering factors listed by element
3) fix saed/vtk : writes 3D diffraction intensity data calculated
3) fix saed/vtk : writes 3D diffraction intensity data calculated
with "compute saed" in vtk format
@ -48,8 +48,8 @@ examples/USER/diffraction.
AUTHOR INFORMATION:
The person who created this package is Shawn P. Coleman
(shawn.p.coleman8.ctr at mail.mil) while at the University of
The person who created this package is Shawn P. Coleman
(shawn.p.coleman8.ctr at mail.mil) while at the University of
Arkansas. Contact him directly if you have questions.
Co-Author: Douglas Spearot (University of Arkansas)

16
src/USER-EFF/README
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@ -46,7 +46,7 @@ Chemistry and Chemical Engineering, 139-74
Phone: (626) 395-3591
e-mail: ajaramil@wag.caltech.edu
Co-Authors:
Co-Authors:
Julius Su (jsu@wag.caltech.edu)
William A. Goddard III (wag@wag.caltech.edu)
@ -57,11 +57,11 @@ LAMMPS architecture and for their help in customizing some of the
required LAMMPS core modules.
Version 01/2010: Special thanks to:
- Hai Xiao (Caltech) for reviewing the fixed-core implementation and
- Hai Xiao (Caltech) for reviewing the fixed-core implementation and
providing useful insights to improve it, and for his work on the effective core pseudopotential.
- Vaclav Cvicek (Caltech) for thoroughly revising the units, for finding a bug in the
- Vaclav Cvicek (Caltech) for thoroughly revising the units, for finding a bug in the
fix_langevin_eff radial scaling factors, and for suggesting changes to clean-up the code.
- Patrick Theofanis (Caltech) for providing an optimized set of parameters for the Si ECP
- Patrick Theofanis (Caltech) for providing an optimized set of parameters for the Si ECP
(default) and for providing basic cases.
- Qi An (Caltech) for providing feedback on usage, application cases, and testing.
@ -76,16 +76,16 @@ different eFF energy components (eke, epauli, ecoul and errestrain),
fixed radial scaling factors in the eff langevin thermostat.
12/2011: Added support for "zero" option in fix langevin/eff (see doc), and
adjusted fix_langevin_eff.cpp to correctly thermostat between nuclear and electronic dof
adjusted fix_langevin_eff.cpp to correctly thermostat between nuclear and electronic dof
(required additional scaling of friction term in the Langevin equations of motion).
Radial electron mass now scales as a function of system dimension.
Bug fixes:
(10-2011): Thanks to Christian Chenard-Lemire (U Montreal) for reporting a bug in the
fixed pair_eff_cut.cpp fixedcore-pseudocore interactions (an incorrect index and a missing
elec-core call to account for the 2 electrons from the fixed core.)
(12-2011): Corrected undefined natom variable in fix_langevin_eff (recent changes in
main fix_langevin class caused compilation error in user-eff).
elec-core call to account for the 2 electrons from the fixed core.)
(12-2011): Corrected undefined natom variable in fix_langevin_eff (recent changes in
main fix_langevin class caused compilation error in user-eff).
Corrected thermostat in fix langevin/eff as described in version 12/2011.

2
src/USER-FEP/README
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@ -17,6 +17,6 @@ Applied Physics/Theory of Polymers and Soft Matter,
Eindhoven University of Technology (TU/e), The Netherlands
Contact him in case of problems with this pair style.
Pair styles lj/class2/soft were contributed by Evangelos Voyiatzis at
Pair styles lj/class2/soft were contributed by Evangelos Voyiatzis at
Technical University of Darmstadt (e.voyiatzis at theo.chemie.tu-darmstadt.de)
Contact him in case of problems with these pair styles.

2
src/USER-INTEL/TEST/run_benchmarks.sh
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@ -6,7 +6,7 @@
# --------------------- MPI Launch Command
export MPI="mpirun"
export MPI="mpirun"
#export MPI="numactl -p 1 mpirun" # -- Systems w/ MCDRAM in flat mode
# ------------- Name and location of the LAMMPS binary

6
src/USER-LB/README
View File

@ -39,15 +39,15 @@ cdennist@uwo.ca
Fixes provided by this package:
fix_lb_fluid.cpp: fix used to create the lattice-Boltzmann fluid on a
fix_lb_fluid.cpp: fix used to create the lattice-Boltzmann fluid on a
grid covering the LAMMPS simulation domain.
fix_momentum_lb.cpp: fix used to subtract off the total (atom plus fluid)
fix_momentum_lb.cpp: fix used to subtract off the total (atom plus fluid)
linear momentum from the system.
fix_pc.cpp: integration algorithm for individual atoms.
fix_rigid_pc_sphere.cpp: integration algorithm for rigid spherical
fix_rigid_pc_sphere.cpp: integration algorithm for rigid spherical
collections of atoms.
fix_viscous_lb.cpp: fix to add the fluid force to the atoms when using a

84
src/USER-MESONT/README
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@ -1,19 +1,19 @@
USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon
nanotubes (CNTs). The model is based on a coarse-grained representation
of CNTs as "flexible cylinders" consisting of a variable number of
segments. Internal interactions within a CNT 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
USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon
nanotubes (CNTs). The model is based on a coarse-grained representation
of CNTs as "flexible cylinders" consisting of a variable number of
segments. Internal interactions within a CNT 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 was created by Maxim Shugaev (mvs9t@virginia.edu)
This package was created by Maxim Shugaev (mvs9t@virginia.edu)
at the University of Virginia.
The Fortran library implementing basic level functions describing stretching,
The Fortran library implementing basic level functions describing stretching,
bending, and intertube components of the mesoscopic CNT force field, used
by this package is developed by Alexey N. Volkov (avolkov1@ua.edu)
by this package is developed by Alexey N. Volkov (avolkov1@ua.edu)
at the University of Alabama.
--
@ -21,69 +21,69 @@ at the University of Alabama.
The following commands are contained in this package:
atom_style mesont
This command enables mesont atom_style containing variables used for
This command enables mesont atom_style containing variables used for
further commands in USER-MESONT.
pair_style mesont/tpm cut table_path BendingMode TPMType
This command activates a pair_style describing CNT mesoscopic tubular
potential model (TPM) force field. "cut" is cutoff distance that should
be set to be at least max(2.0*L, sqrt(L^2/2 + (2.0*R + Tcut)^2)),
where L is the maximum segment length, R is the maximum tube radius,
and Tcut = 10.2 A is the maximum distance between surfaces of interacting
pair_style mesont/tpm cut table_path BendingMode TPMType
This command activates a pair_style describing CNT mesoscopic tubular
potential model (TPM) force field. "cut" is cutoff distance that should
be set to be at least max(2.0*L, sqrt(L^2/2 + (2.0*R + Tcut)^2)),
where L is the maximum segment length, R is the maximum tube radius,
and Tcut = 10.2 A is the maximum distance between surfaces of interacting
segments. However, the recommended cutoff is 3L.
compute mesont
This command allows evaluation of per atom and total values of stretching,
bending, and intertube interaction components of energies. Use the following
This command allows evaluation of per atom and total values of stretching,
bending, and intertube interaction components of energies. Use the following
flags: 'estretch', 'ebend', 'etube'.
--
References:
L. V. Zhigilei, C. Wei, and D. Srivastava, Mesoscopic model for dynamic
L. V. Zhigilei, C. Wei, and D. Srivastava, Mesoscopic model for dynamic
simulations of carbon nanotubes, Phys. Rev. B 71, 165417, 2005.
A. N. Volkov and L. V. Zhigilei, Structural stability of carbon nanotube
A. N. Volkov and L. V. Zhigilei, Structural stability of carbon nanotube
films: The role of bending buckling, ACS Nano 4, 6187-6195, 2010.
A. N. Volkov, K. R. Simov, and L. V. Zhigilei, Mesoscopic model for simulation
of CNT-based materials, Proceedings of the ASME International Mechanical
Engineering Congress and Exposition (IMECE2008), ASME paper IMECE2008-68021,
A. N. Volkov, K. R. Simov, and L. V. Zhigilei, Mesoscopic model for simulation
of CNT-based materials, Proceedings of the ASME International Mechanical
Engineering Congress and Exposition (IMECE2008), ASME paper IMECE2008-68021,
2008.
A. N. Volkov and L. V. Zhigilei, Mesoscopic interaction potential for carbon
nanotubes of arbitrary length and orientation, J. Phys. Chem. C 114, 5513-5531,
A. N. Volkov and L. V. Zhigilei, Mesoscopic interaction potential for carbon
nanotubes of arbitrary length and orientation, J. Phys. Chem. C 114, 5513-5531,
2010.
B. K. Wittmaack, A. H. Banna, A. N. Volkov, L. V. Zhigilei, Mesoscopic
modeling of structural self-organization of carbon nanotubes into vertically
B. K. Wittmaack, A. H. Banna, A. N. Volkov, L. V. Zhigilei, Mesoscopic
modeling of structural self-organization of carbon nanotubes into vertically
aligned networks of nanotube bundles, Carbon 130, 69-86, 2018.
B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Mesoscopic modeling of the
uniaxial compression and recovery of vertically aligned carbon nanotube
B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Mesoscopic modeling of the
uniaxial compression and recovery of vertically aligned carbon nanotube
forests, Compos. Sci. Technol. 166, 66-85, 2018.
B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Phase transformation as the
mechanism of mechanical deformation of vertically aligned carbon nanotube
B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Phase transformation as the
mechanism of mechanical deformation of vertically aligned carbon nanotube
arrays: Insights from mesoscopic modeling, Carbon 143, 587-597, 2019.
A. N. Volkov and L. V. Zhigilei, Scaling laws and mesoscopic modeling of
thermal conductivity in carbon nanotube materials, Phys. Rev. Lett. 104,
A. N. Volkov and L. V. Zhigilei, Scaling laws and mesoscopic modeling of
thermal conductivity in carbon nanotube materials, Phys. Rev. Lett. 104,
215902, 2010.
A. N. Volkov, T. Shiga, D. Nicholson, J. Shiomi, and L. V. Zhigilei, Effect
of bending buckling of carbon nanotubes on thermal conductivity of carbon
A. N. Volkov, T. Shiga, D. Nicholson, J. Shiomi, and L. V. Zhigilei, Effect
of bending buckling of carbon nanotubes on thermal conductivity of carbon
nanotube materials, J. Appl. Phys. 111, 053501, 2012.
A. N. Volkov and L. V. Zhigilei, Heat conduction in carbon nanotube materials:
Strong effect of intrinsic thermal conductivity of carbon nanotubes, Appl.
A. N. Volkov and L. V. Zhigilei, Heat conduction in carbon nanotube materials:
Strong effect of intrinsic thermal conductivity of carbon nanotubes, Appl.
Phys. Lett. 101, 043113, 2012.
W. M. Jacobs, D. A. Nicholson, H. Zemer, A. N. Volkov, and L. V. Zhigilei,
Acoustic energy dissipation and thermalization in carbon nanotubes: Atomistic
W. M. Jacobs, D. A. Nicholson, H. Zemer, A. N. Volkov, and L. V. Zhigilei,
Acoustic energy dissipation and thermalization in carbon nanotubes: Atomistic
modeling and mesoscopic description, Phys. Rev. B 86, 165414, 2012.
A. N. Volkov and A. H. Banna, Mesoscopic computational model of covalent
cross-links and mechanisms of load transfer in cross-linked carbon nanotube
A. N. Volkov and A. H. Banna, Mesoscopic computational model of covalent
cross-links and mechanisms of load transfer in cross-linked carbon nanotube
films with continuous networks of bundles, Comp. Mater. Sci. 176, 109410, 2020.

26
src/USER-MGPT/README
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@ -1,17 +1,17 @@
This package contains a fast implementation for LAMMPS of quantum-based
MGPT multi-ion potentials. The MGPT or model GPT method derives from
first-principles DFT-based generalized pseudopotential theory (GPT)
through a series of systematic approximations valid for mid-period
This package contains a fast implementation for LAMMPS of quantum-based
MGPT multi-ion potentials. The MGPT or model GPT method derives from
first-principles DFT-based generalized pseudopotential theory (GPT)
through a series of systematic approximations valid for mid-period
transition metals with nearly half-filled d bands. The MGPT method
was originally developed by John Moriarty at Lawrence Livermore
was originally developed by John Moriarty at Lawrence Livermore
National Lab (LLNL).
In the general matrix representation of MGPT, which can also be applied
to f-band actinide metals, the multi-ion potentials are evaluated on the
fly during a simulation through d- or f-state matrix multiplication, and
the forces that move the ions are determined analytically. The mgpt
In the general matrix representation of MGPT, which can also be applied
to f-band actinide metals, the multi-ion potentials are evaluated on the
fly during a simulation through d- or f-state matrix multiplication, and
the forces that move the ions are determined analytically. The mgpt
pair style in this package calculates forces and energies using an
optimized matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
optimized matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
See the doc page for the pair_style mgpt command for full details on
using this package in LAMMPS. In particular, the user should note that
@ -22,10 +22,10 @@ steps to perform constant-volume calculations and simulations. It is
strongly recommended that the user work through and understand these
examples before proceeding to more complex simulations.
Specific MGPT potential data for the transition metals tantalum
Specific MGPT potential data for the transition metals tantalum
(Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), and
vanadium (V6.1 potentials) are contained in the LAMMPS "potentials"
directory. It is expected that MGPT potentials for additional
vanadium (V6.1 potentials) are contained in the LAMMPS "potentials"
directory. It is expected that MGPT potentials for additional
materials will be added over time.
The persons who created the USER-MGPT package are Tomas Oppelstrup

22
src/USER-MOFFF/README
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@ -1,32 +1,32 @@
This Package implements pair, angle and improper styles needed to employ
the MOF-FF force field by Schmid and coworkers with LAMMPS.
This Package implements pair, angle and improper styles needed to employ
the MOF-FF force field by Schmid and coworkers with LAMMPS.
MOF-FF is a first principles derived force field with the primary aim
to simulate MOFs and related porous framework materials, using spherical
to simulate MOFs and related porous framework materials, using spherical
Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
2013, 250, 1128-1141.
For the usage of MOF-FF see the example in the example directory as
For the usage of MOF-FF see the example in the example directory as
well as the "MOF+" website (https://www.mofplus.org/content/show/MOF-FF).
The package provides the following features:
The package provides the following features:
* a dispersion damped Buckhingham potential with spherical Gaussian type
* a dispersion damped Buckhingham potential with spherical Gaussian type
charges (dsf and long-range treatment of charges)
* a modified angle/class2 including 6th order polynomial
* a modified angle/cosine style which adds a dispersion damped Buckhingham
* a modified angle/cosine style which adds a dispersion damped Buckhingham
1-3 interaction analog to the dihedral/charmm style
* an improper style following the Wilson-Decius definition of the
* an improper style following the Wilson-Decius definition of the
out-of-plane angle
See the file doc/drude_tutorial.html for getting started.
See the doc pages for "pair_style buck6d/coul/gauss", "anlge_style class2",
See the doc pages for "pair_style buck6d/coul/gauss", "anlge_style class2",
"angle_style cosine/buck6d", and "improper_style inversion/harmonic"
commands to get started. Also see the above mentioned website and
commands to get started. Also see the above mentioned website and
literature for further documentation about the force field.
There are example scripts for using this force field in examples/USER/mofff.
The creators of this package are Hendrik Heenen (hendrik.heenen at mytum.de)
and Rochus Schmid (rochus.schmid at rub.de). Contact them directly if you
and Rochus Schmid (rochus.schmid at rub.de). Contact them directly if you
have questions.

46
src/USER-PLUMED/README
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@ -1,43 +1,43 @@
This package implements the "fix plumed" command, which can be used
in a LAMMPS input script.
The fix allows enhanced sampling methods such as umbrella sampling and
metadynamics to be used. Furthermore, PLUMED can be used to perform a
The fix allows enhanced sampling methods such as umbrella sampling and
metadynamics to be used. Furthermore, PLUMED can be used to perform a
wide range of analyses on trajectories on the fly as they are generated.
The package uses the "PLUMED" library, whose source code is not included
in the LAMMPS source code distribution. The files in the USER-PLUMED package
folder implement an interface between LAMMPS and PLUMED, that are written
in the LAMMPS source code distribution. The files in the USER-PLUMED package
folder implement an interface between LAMMPS and PLUMED, that are written
and maintained by Gareth Tribello (gareth.tribello@gmail.com).
PLUMED must instead be downloaded and compiled separately to LAMMPS. This building
and compiling of PLUMED can be done before or after the building of LAMMPS as LAMMPS
can call PLUMED as a dynamic library. There is also the possibility to link PLUEMD
statically. In this case a copy of PLUMED must be downloaded into the lib/plumed
directory. This copy of PLUMED will then always be linked into the code at compile
time.
PLUMED must instead be downloaded and compiled separately to LAMMPS. This building
and compiling of PLUMED can be done before or after the building of LAMMPS as LAMMPS
can call PLUMED as a dynamic library. There is also the possibility to link PLUEMD
statically. In this case a copy of PLUMED must be downloaded into the lib/plumed
directory. This copy of PLUMED will then always be linked into the code at compile
time.
However you decide to link PLUMED (statically or dynamically) you must run the command:
make yes-user-plumed
before compiling LAMMPS in order to enable the module. In addition, if you have chosen to
link PLUMED dynamically you must ensure that PLUMED is in your
PATH when running a LAMMPS calculation that takes advantage of PLUMED. If
PLUMED is linked as a runtime library and if PLUMED is not in the PATH an error will be returned whenever LAMMPS encounters
the fix plumed command in its input. To be clear, however, a LAMMPS executable that was dynamically linked with PLUMED will run
even if PLUMED is not in the path if as long as the input does not contain a fix
before compiling LAMMPS in order to enable the module. In addition, if you have chosen to
link PLUMED dynamically you must ensure that PLUMED is in your
PATH when running a LAMMPS calculation that takes advantage of PLUMED. If
PLUMED is linked as a runtime library and if PLUMED is not in the PATH an error will be returned whenever LAMMPS encounters
the fix plumed command in its input. To be clear, however, a LAMMPS executable that was dynamically linked with PLUMED will run
even if PLUMED is not in the path if as long as the input does not contain a fix
plumed command.
If you wish to statically link PLUMED you must download PLUMED to the /lib/plumed directory before compiling LAMMPS. You can
download a tar ball into that directory or you can clone the plumed2 repository from github there. Once you have created a
directory containing a distribution of PLUMED within /lib/plumed you then must build PLUMED within that directory by issuing
the usual commands. It is worth noting that we have provided a script that will download and build PLUMED for you with
If you wish to statically link PLUMED you must download PLUMED to the /lib/plumed directory before compiling LAMMPS. You can
download a tar ball into that directory or you can clone the plumed2 repository from github there. Once you have created a
directory containing a distribution of PLUMED within /lib/plumed you then must build PLUMED within that directory by issuing
the usual commands. It is worth noting that we have provided a script that will download and build PLUMED for you with
a minimal set of options. To run this script you need to issue the following command:
make lib-plumed args="-b"
in the src directory.
in the src directory.
More info about the PLUMED library can be found at:
@ -55,8 +55,8 @@ M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Don
Comp. Phys. Comm. 180, 1961 (2009)
https://doi.org/10.1016/j.cpc.2009.05.011
Instructions explaining how to use PLUMED and LAMMPS in tandem can be found on the PLUMED website, which also gives
numerous example scripts for PLUMED as well as citations to articles that dcoment the various methods that are
Instructions explaining how to use PLUMED and LAMMPS in tandem can be found on the PLUMED website, which also gives
numerous example scripts for PLUMED as well as citations to articles that dcoment the various methods that are
implemented within PLUMED.
There are also example scripts for using this package in the folder

2
src/USER-QUIP/README
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@ -1,6 +1,6 @@
This package provides the pair_style quip command. This pair style
provides an interface to the QUIP/libAtoms library, which includes a
variety of interatomic potentials, including Gaussian Approximation
variety of interatomic potentials, including Gaussian Approximation
Potential (GAP) models.
See lib/quip/README for more information on how to build LAMMPS

2
src/USER-SCAFACOS/Install.sh
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@ -46,7 +46,7 @@ if (test $1 = 1) then
elif (test $1 = 0) then
if (test -e ../Makefile.package) then
if (test -e ../Makefile.package) then
sed -i -e 's/`.*scafacos.*` //' ../Makefile.package
sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package
fi

6
src/USER-SPH/README
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@ -1,13 +1,13 @@
This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:
* Tait, ideal gas, Lennard-Jones equation of states, full support for
* Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state
* plain or Monaghans XSPH integration of the equations of motion
* density continuity or density summation to propagate the density field
* commands to set internal energy and density of particles from the
* commands to set internal energy and density of particles from the
input script
* output commands to access internal energy and density for dumping and
* output commands to access internal energy and density for dumping and
thermo output
See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started.

2
src/USER-TALLY/README
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@ -7,7 +7,7 @@ users have asked for such a facility over time.
The currently provided compute styles are mostly meant as a
demonstration for how to use this facility and provide an
alternative approach to using features like compute group/group
or compute heat/flux. Its application is limited to pairwise
or compute heat/flux. Its application is limited to pairwise
additive potentials that use the standard Pair::ev_tally()
method to accumulate energy (and virial).

4
src/VORONOI/README
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@ -20,8 +20,8 @@ you can test it using an input file from the examples dir:
./lmp_serial < lammps/examples/voronoi/in.voronoi | grep '^TEST_'
The output should conclude with 'TEST_DONE' and every line should
report an error of 0%.
The output should conclude with 'TEST_DONE' and every line should
report an error of 0%.
== Credits and license ==