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modified "package" related pages to point to USER-CAUCHY correctly

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This commit is contained in:
Ronald E. Miller
2018-11-30 12:54:18 -05:00
parent 01f47c4450
commit 7b64ed19be
2 changed files with 50 additions and 30 deletions
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79
doc/src/Packages_details.txt
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@ -68,6 +68,7 @@ as contained in the file name.
"USER-ATC"_#PKG-USER-ATC,
"USER-AWPMD"_#PKG-USER-AWPMD,
"USER-BOCS"_#PKG-USER-BOCS,
"USER-CAUCHY"_#PKG-USER-CAUCHY,
"USER-CGDNA"_#PKG-USER-CGDNA,
"USER-CGSDK"_#PKG-USER-CGSDK,
"USER-COLVARS"_#PKG-USER-COLVARS,
@ -203,7 +204,7 @@ available on your system.
[Author:] Axel Kohlmeyer (Temple U).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -284,7 +285,7 @@ also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
(Northwestern U) while at ORNL.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -352,7 +353,7 @@ API which the "pair_style kim"_pair_kim.html command uses. He
developed the pair style in collaboration with Valeriu Smirichinski (U
Minnesota).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -398,7 +399,7 @@ which was developed by Carter Edwards, Christian Trott, and others at
Sandia, and which is included in the LAMMPS distribution in
lib/kokkos.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -546,7 +547,7 @@ and user interface.
[Author:] Greg Wagner (Northwestern U) while at Sandia.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -679,7 +680,7 @@ system.
library was developed by Jacob Wagner in Greg Voth's group at the
University of Chicago.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -711,7 +712,7 @@ have styles optimized for CPU performance.
[Authors:] James Fischer (High Performance Technologies), David Richie,
and Vincent Natoli (Stone Ridge Technolgy).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -768,7 +769,7 @@ connections at hinge points.
[Author:] Rudra Mukherjee (JPL) while at RPI.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -800,7 +801,7 @@ shared library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not yet supported. See the
lib/python/README for more details.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -848,7 +849,7 @@ as bonds are created and destroyed.
[Author:] Aidan Thompson (Sandia).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1021,7 +1022,7 @@ system.
library was written by Chris Rycroft (Harvard U) while at UC Berkeley
and LBNL.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1048,7 +1049,7 @@ atomic information to continuum fields.
[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1075,7 +1076,7 @@ model.
[Author:] Ilya Valuev (JIHT, Russia).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1098,7 +1099,7 @@ This package provides "fix bocs"_fix_bocs.html, a modified version
of "fix npt"_fix_nh.html which includes 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).
@ -1120,6 +1121,26 @@ Example inputs are in the examples/USER/bocs folder.
:line
USER-CAUCHY package :link(PKG-USER-CAUCHY),h4
[Contents:]
This package provides a modified version of
"fix npt"_fix_nh.html which directly controls the Cauchy (true) stress
instead of the second Piola-Kirchhoff stress, as presented in:
R. E. Miller, E. B. Tadmor, J. S. Gibson, N. Bernstein, and F. Pavia,
“Molecular Dynamics at Constant Cauchy Stress,” J. Chem. Phys. 144, 184107 (2016).
[Authors:] R. E. Miller (Carleton University), F. Pavia and S. Pattamatta
[Supporting info:]
Example input is in the examples/USER/cauchy folder. Usage instructions are part of
the "fix npt"_fix_nh.html description.
:line
USER-CGDNA package :link(PKG-USER-CGDNA),h4
[Contents:]
@ -1183,7 +1204,7 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for
the NAMD MD code, but with portability in mind. Axel Kohlmeyer
(Temple U) provided the interface to LAMMPS.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1363,7 +1384,7 @@ system.
[Author:] Pierre de Buyl (KU Leuven) created both the package and the
H5MD format.
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1401,7 +1422,7 @@ NOTE: the USER-INTEL package contains styles that require using the
[Author:] Mike Brown (Intel).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1571,17 +1592,17 @@ USER-MOFFF package :link(PKG-USER-MOFFF),h4
[Contents:]
Pair, angle and improper styles needed to employ the MOF-FF
force field by Schmid and coworkers with LAMMPS.
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+"_MOFplus website.
:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
[Author:] Hendrik Heenen (Technical U of Munich),
[Author:] Hendrik Heenen (Technical U of Munich),
Rochus Schmid (Ruhr-University Bochum).
[Supporting info:]
@ -1622,7 +1643,7 @@ at
[Author:] Axel Kohlmeyer (Temple U).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1662,7 +1683,7 @@ tools:
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1706,7 +1727,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner:
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1784,7 +1805,7 @@ without changes to LAMMPS itself.
[Author:] Axel Kohlmeyer (Temple U).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1842,7 +1863,7 @@ on your system.
[Author:] Albert Bartok (Cambridge University)
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -1936,7 +1957,7 @@ specified as surface geometries from *.STL files.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -2062,7 +2083,7 @@ system.
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
[Install:]
[Install:]
This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
@ -2074,5 +2095,3 @@ src/USER-VTK: filenames -> commands
src/USER-VTK/README
lib/vtk/README
"dump vtk"_dump_vtk.html :ul

1
doc/src/Packages_user.txt
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@ -41,6 +41,7 @@ Package, Description, Doc page, Example, Library
"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
"USER-CAUCHY"_Packages_details.html#PKG-USER-CAUCHY, Cauchystat stress control, "fix npt/cauchy"_fix_nh.html, USER/cauchy, int
"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no
"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no
"USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int