Merge branch 'master' into zeeman-rework
This commit is contained in:
Axel Kohlmeyer
3
doc/src/Developer/.gitignore
vendored
Normal file
3
doc/src/Developer/.gitignore
vendored
Normal file
@ -0,0 +1,3 @@
|
||||
/developer.aux
|
||||
/developer.log
|
||||
/developer.toc
|
||||
198
doc/src/Developer/classes.fig
Normal file
198
doc/src/Developer/classes.fig
Normal file
@ -0,0 +1,198 @@
|
||||
#FIG 3.2 Produced by xfig version 3.2.5a
|
||||
Portrait
|
||||
Center
|
||||
Inches
|
||||
Letter
|
||||
100.00
|
||||
Single
|
||||
-2
|
||||
1200 2
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2232 1170 3540 1170 3540 1505 2232 1505 2232 1170
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2220 1830 3015 1830 3015 2219 2220 2219 2220 1830
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2226 3285 3300 3285 3300 3665 2226 3665 2226 3285
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2223 5190 3225 5190 3225 5525 2223 5525 2223 5190
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2232 7125 3090 7125 3090 7478 2232 7478 2232 7125
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2226 10230 3300 10230 3300 10565 2226 10565 2226 10230
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4026 10305 4980 10305 4980 10592 4026 10592 4026 10305
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4029 9900 5205 9900 5205 10250 4029 10250 4029 9900
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4038 9315 5370 9315 5370 9659 4038 9659 4038 9315
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4023 8955 4530 8955 4530 9278 4023 9278 4023 8955
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4029 8475 5190 8475 5190 8762 4029 8762 4029 8475
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4008 8115 5430 8115 5430 8408 4008 8408 4008 8115
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4026 7425 4995 7425 4995 7712 4026 7712 4026 7425
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4035 6720 4650 6720 4650 7025 4035 7025 4035 6720
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4044 7080 4830 7080 4830 7358 4044 7358 4044 7080
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4032 6105 5205 6105 5205 6419 4032 6419 4032 6105
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4026 5715 5115 5715 5115 6062 4026 6062 4026 5715
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4023 3585 4605 3585 4605 3872 4023 3872 4023 3585
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
3954 1680 5175 1680 5175 1997 3954 1997 3954 1680
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
1620 5235 2100 615
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
1605 5445 2070 10695
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3120 1935 3855 1800
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3150 2115 3765 2250
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3135 7230 3945 6840
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3150 7335 3945 8610
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
5265 8610 6195 8400
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
5280 8655 6180 8820
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3345 10290 3930 10020
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3360 10395 3930 10425
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3360 10455 3930 10755
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2193 360 3435 360 3435 647 2193 647 2193 360
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3398 3472 3923 3307
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3413 3601 3923 3721
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3285 2806 3870 2802
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3315 5372 3900 5368
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
6354 2280 7470 2280 7470 2585 6354 2585 6354 2280
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
6348 1875 7320 1875 7320 2222 6348 2222 6348 1875
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
3954 2070 5505 2070 5505 2372 3954 2372 3954 2070
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
5634 2137 6230 2045
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
5670 2310 6265 2418
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
3900 2640 5400 2640 5400 2975 3900 2975 3900 2640
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4038 3165 5385 3165 5385 3497 4038 3497 4038 3165
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4245 4110 5730 4110 5730 4499 4245 4499 4245 4110
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4233 4545 6390 4545 6390 4862 4233 4862 4233 4545
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4026 5190 5385 5190 5385 5525 4026 5525 4026 5190
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4038 7755 5310 7755 5310 8075 4038 8075 4038 7755
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
6270 8250 7365 8250 7365 8610 6270 8610 6270 8250
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
6273 8655 7380 8655 7380 8978 6273 8978 6273 8655
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
4041 10620 5985 10620 5985 10943 4041 10943 4041 10620
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2217 10830 3135 10830 3135 11156 2217 11156 2217 10830
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2229 9780 3240 9780 3240 10118 2229 10118 2229 9780
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2214 9015 3285 9015 3285 9362 2214 9362 2214 9015
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2208 5850 3420 5850 3420 6209 2208 6209 2208 5850
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2217 4275 3615 4275 3615 4634 2217 4634 2217 4275
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2235 2655 3150 2655 3150 3000 2235 3000 2235 2655
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
60 5115 1500 5115 1500 5610 60 5610 60 5115
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3486 6018 4011 5853
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3486 6129 3996 6249
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3361 9291 3991 9531
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3345 9129 4005 9099
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3691 4412 4216 4277
|
||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
||||
1 1 2.00 120.00 240.00
|
||||
3695 4561 4175 4711
|
||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
||||
2220 735 3129 735 3129 1043 2220 1043 2220 735
|
||||
4 0 1 50 -1 18 18 0.0000 4 225 1275 2265 1455 Universe\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 285 735 2265 2175 Input\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 225 780 2265 2925 Atom\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 285 1020 2265 3600 Update\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 285 1320 2265 4575 Neighbor\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 225 945 2265 5475 Comm\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 225 1110 2265 6150 Domain\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 225 810 2265 7425 Force\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 285 975 2265 9300 Modify\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 285 900 2265 10050 Group\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 285 990 2265 10500 Output\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 225 825 2265 11100 Timer\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 225 1170 3990 1950 Variable\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 225 1470 3990 2325 Command\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 285 1275 4065 3450 Integrate\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 225 525 4065 3825 Min\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 285 1230 4065 5475 Irregular\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 285 1020 4065 6000 Region\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 225 975 4065 6375 Lattice\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 225 435 4065 9225 Fix\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 285 1305 4065 9600 Compute\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 225 570 4065 6975 Pair\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 285 840 4065 7665 Angle\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 225 1215 4065 8010 Dihedral\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 285 1305 4065 8355 Improper\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 285 1095 4065 8700 KSpace\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 285 855 4065 10545 Dump\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 225 1815 4065 10890 WriteRestart\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 225 930 6315 8550 FFT3D\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 285 1005 6315 8925 Remap\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 225 885 6390 2175 Finish\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 285 1050 6390 2550 Special\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 225 1305 3990 2925 AtomVec\001
|
||||
4 0 4 50 -1 18 18 0.0000 4 225 765 4065 7320 Bond\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 225 1095 4065 10200 Thermo\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 285 1380 4305 4425 NeighList\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 285 2025 4305 4800 NeighRequest\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 285 1155 2250 600 Memory\001
|
||||
4 0 0 50 -1 18 18 0.0000 4 225 1305 120 5475 LAMMPS\001
|
||||
4 0 1 50 -1 18 18 0.0000 4 225 735 2265 1005 Error\001
|
||||
BIN
doc/src/Developer/classes.pdf
Normal file
BIN
doc/src/Developer/classes.pdf
Normal file
Binary file not shown.
699
doc/src/Developer/developer.tex
Normal file
699
doc/src/Developer/developer.tex
Normal file
@ -0,0 +1,699 @@
|
||||
\documentclass{article}
|
||||
\usepackage{graphicx}
|
||||
|
||||
\begin{document}
|
||||
|
||||
\centerline{\Large \bf LAMMPS Developer Guide}
|
||||
\centerline{\bf 23 Aug 2011}
|
||||
|
||||
\vspace{0.5in}
|
||||
|
||||
This document is a developer guide to the LAMMPS molecular dynamics
|
||||
package, whose WWW site is at lammps.sandia.gov. It describes the
|
||||
internal structure and algorithms of the code. Sections will be added
|
||||
as we have time, and in response to requests from developers and
|
||||
users.
|
||||
|
||||
\tableofcontents
|
||||
|
||||
\pagebreak
|
||||
\section{LAMMPS source files}
|
||||
|
||||
LAMMPS source files are in two directories of the distribution
|
||||
tarball. The src directory has the majority of them, all of which are
|
||||
C++ files (*.cpp and *.h). Many of these files are in the src
|
||||
directory itself. There are also dozens of ``packages'', which can be
|
||||
included or excluded when LAMMPS is built. See the
|
||||
doc/Section\_build.html section of the manual for more information
|
||||
about packages, or type ``make'' from within the src directory, which
|
||||
lists package-related commands, such as ``make package-status''. The
|
||||
source files for each package are in an all-uppercase sub-directory of
|
||||
src, like src/MOLECULE or src/USER-CUDA. If the package is currently
|
||||
installed, copies of the package source files will also exist in the
|
||||
src directory itself. The src/STUBS sub-directory is not a package
|
||||
but contains a dummy version of the MPI library, used when building a
|
||||
serial version of the code.
|
||||
|
||||
The lib directory also contains source code for external libraries,
|
||||
used by a few of the packages. Each sub-directory, like meam or gpu,
|
||||
contains the source files, some of which are in different languages
|
||||
such as Fortran. The files are compiled into libraries from within
|
||||
each sub-directory, e.g. performing a ``make'' in the lib/meam directory
|
||||
creates a libmeam.a file. These libraries are linked to during a
|
||||
LAMMPS build, if the corresponding package is installed.
|
||||
|
||||
LAMMPS C++ source files almost always come in pairs, such as run.cpp
|
||||
and run.h. The pair of files defines a C++ class, the Run class in
|
||||
this case, which contains the code invoked by the ``run'' command in a
|
||||
LAMMPS input script. As this example illustrates, source file and
|
||||
class names often have a one-to-one correspondence with a command used
|
||||
in a LAMMPS input script. Some source files and classes do not have a
|
||||
corresponding input script command, e.g. ``force.cpp'' and the Force
|
||||
class. They are discussed in the next section.
|
||||
|
||||
\pagebreak
|
||||
\section{Class hierarchy of LAMMPS}
|
||||
|
||||
Though LAMMPS has a lot of source files and classes, its class
|
||||
hierarchy is quite simple, as outlined in Fig \ref{fig:classes}. Each
|
||||
boxed name refers to a class and has a pair of associated source files
|
||||
in lammps/src, e.g. ``memory.cpp'' and ``memory.h''. More details on the
|
||||
class and its methods and data structures can be found by examining
|
||||
its *.h file.
|
||||
|
||||
LAMMPS (lammps.cpp/h) is the top-level class for the entire code. It
|
||||
holds an ``instance'' of LAMMPS and can be instantiated one or more
|
||||
times by a calling code. For example, the file src/main.cpp simply
|
||||
instantiates one instance of LAMMPS and passes it the input script.
|
||||
|
||||
The file src/library.cpp contains a C-style library interface to the
|
||||
LAMMPS class. See the lammps/couple and lammps/python directories for
|
||||
examples of simple programs that use LAMMPS through its library
|
||||
interface. A driver program can instantiate the LAMMPS class multiple
|
||||
times, e.g. to embed several atomistic simulation regions within a
|
||||
mesoscale or continuum simulation domain.
|
||||
|
||||
There are a dozen or so top-level classes within the LAMMPS class that
|
||||
are visible everywhere in the code. They are shaded blue in Fig
|
||||
\ref{fig:classes}. Thus any class can refer to the y-coordinate of
|
||||
local atom $I$ as atom$\rightarrow$x[i][1]. This visibility is
|
||||
enabled by a bit of cleverness in the Pointers class (see
|
||||
src/pointers.h) which every class inherits from.
|
||||
|
||||
There are a handful of virtual parent classes in LAMMPS that define
|
||||
what LAMMPS calls ``styles''. They are shaded red in Fig
|
||||
\ref{fig:classes}. Each of these are parents of a number of child
|
||||
classes that implement the interface defined by the parent class. For
|
||||
example, the fix style has around 100 child classes. They are the
|
||||
possible fixes that can be specified by the fix command in an input
|
||||
script, e.g. fix nve, fix shake, fix ave/time, etc. The corresponding
|
||||
classes are Fix (for the parent class), FixNVE, FixShake, FixAveTime,
|
||||
etc. The source files for these classes are easy to identify in the
|
||||
src directory, since they begin with the word ``fix'', e,g,
|
||||
fix\_nve.cpp, fix\_shake,cpp, fix\_ave\_time.cpp, etc.
|
||||
|
||||
The one exception is child class files for the ``command'' style. These
|
||||
implement specific commands in the input script that can be invoked
|
||||
before/after/between runs or which launch a simulation. Examples are
|
||||
the create\_box, minimize, run, and velocity commands which encode the
|
||||
CreateBox, Minimize, Run, and Velocity classes. The corresponding
|
||||
files are create\_box,cpp, minimize.cpp, run.cpp, and velocity.cpp.
|
||||
The list of command style files can be found by typing ``grep
|
||||
COMMAND\_CLASS *.h'' from within the src directory, since that word in
|
||||
the header file identifies the class as an input script command.
|
||||
Similar words can be grepped to list files for the other LAMMPS
|
||||
styles. E.g. ATOM\_CLASS, PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS,
|
||||
FIX\_CLASS, COMPUTE\_CLASS, DUMP\_CLASS, etc.
|
||||
|
||||
\begin{figure}[htb]
|
||||
\begin{center}
|
||||
\includegraphics[height=4in]{classes.pdf}
|
||||
\end{center}
|
||||
\caption{Class hierarchy within LAMMPS source code.}
|
||||
\label{fig:classes}
|
||||
\end{figure}
|
||||
|
||||
More details on individual classes in Fig \ref{fig:classes} are as
|
||||
follows:
|
||||
|
||||
\begin{itemize}
|
||||
|
||||
\item The Memory class handles allocation of all large vectors and
|
||||
arrays.
|
||||
|
||||
\item The Error class prints all error and warning messages.
|
||||
|
||||
\item The Universe class sets up partitions of processors so that
|
||||
multiple simulations can be run, each on a subset of the processors
|
||||
allocated for a run, e.g. by the mpirun command.
|
||||
|
||||
\item The Input class reads an input script, stores variables, and
|
||||
invokes stand-alone commands that are child classes of the Command
|
||||
class.
|
||||
|
||||
\item As discussed above, the Command class is a parent class for
|
||||
certain input script commands that perform a one-time operation
|
||||
before/after/between simulations or which invoke a simulation. They
|
||||
are instantiated from within the Input class, invoked, then
|
||||
immediately destructed.
|
||||
|
||||
\item The Finish class is instantiated to print statistics to the
|
||||
screen after a simulation is performed, by commands like run and
|
||||
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
|
||||
several commands, like read\_data, read\_restart, and replicate.
|
||||
|
||||
\item The Atom class stores all per-atom arrays. More precisely, they
|
||||
are allocated and stored by the AtomVec class, and the Atom class
|
||||
simply stores a pointer to them. The AtomVec class is a parent
|
||||
class for atom styles, defined by the atom\_style command.
|
||||
|
||||
\item The Update class holds an integrator and a minimizer. The
|
||||
Integrate class is a parent style for the Verlet and rRESPA time
|
||||
integrators, as defined by the run\_style input command. The Min
|
||||
class is a parent style for various energy minimizers.
|
||||
|
||||
\item The Neighbor class builds and stores neighbor lists. The
|
||||
NeighList class stores a single list (for all atoms). The
|
||||
NeighRequest class is called by pair, fix, or compute styles when
|
||||
they need a particular kind of neighbor list.
|
||||
|
||||
\item The Comm class performs interprocessor communication, typically
|
||||
of ghost atom information. This usually involves MPI message
|
||||
exchanges with 6 neighboring processors in the 3d logical grid of
|
||||
processors mapped to the simulation box. Sometimes the Irregular
|
||||
class is used, when atoms may migrate to arbitrary processors.
|
||||
|
||||
\item The Domain class stores the simulation box geometry, as well as
|
||||
geometric Regions and any user definition of a Lattice. The latter
|
||||
are defined by region and lattice commands in an input script.
|
||||
|
||||
\item The Force class computes various forces between atoms. The Pair
|
||||
parent class is for non-bonded or pair-wise forces, which in LAMMPS
|
||||
lingo includes many-body forces such as the Tersoff 3-body
|
||||
potential. The Bond, Angle, Dihedral, Improper parent classes are
|
||||
styles for bonded interactions within a static molecular topology.
|
||||
The KSpace parent class is for computing long-range Coulombic
|
||||
interactions. One of its child classes, PPPM, uses the FFT3D and
|
||||
Remap classes to communicate grid-based information with neighboring
|
||||
processors.
|
||||
|
||||
\item The Modify class stores lists of Fix and Compute classes, both
|
||||
of which are parent styles.
|
||||
|
||||
\item The Group class manipulates groups that atoms are assigned to
|
||||
via the group command. It also computes various attributes of
|
||||
groups of atoms.
|
||||
|
||||
\item The Output class is used to generate 3 kinds of output from a
|
||||
LAMMPS simulation: thermodynamic information printed to the screen
|
||||
and log file, dump file snapshots, and restart files. These
|
||||
correspond to the Thermo, Dump, and WriteRestart classes
|
||||
respectively. The Dump class is a parent style.
|
||||
|
||||
\item The Timer class logs MPI timing information, output at the end
|
||||
of a run.
|
||||
|
||||
\end{itemize}
|
||||
|
||||
%%\pagebreak
|
||||
%%\section{Spatial decomposition and parallel operations}
|
||||
%%distributed memory
|
||||
%%Ref to JCP paper
|
||||
%%diagram of 3d grid of procs and spatial decomp
|
||||
%%6-way comm
|
||||
%%ghost atoms, PBC added when comm (in atom class)
|
||||
|
||||
%%\pagebreak
|
||||
%%\section{Fixes, computes, variables}
|
||||
%%fixes intercolate in timestep, store per-atom info
|
||||
%%computes based on current snapshot
|
||||
%%equal- and atom-style variables
|
||||
%%output they produce - see write-up in HowTo
|
||||
|
||||
\pagebreak
|
||||
\section{How a timestep works}
|
||||
|
||||
The first and most fundamental operation within LAMMPS to understand
|
||||
is how a timestep is structured. Timestepping is performed by the
|
||||
Integrate class within the Update class. Since Integrate is a parent
|
||||
class, corresponding to the run\_style input script command, it has
|
||||
child classes. In this section, the timestep implemented by the
|
||||
Verlet child class is described. A similar timestep is implemented by
|
||||
the Respa child class, for the rRESPA hierarchical timestepping
|
||||
method. The Min parent class performs energy minimization, so does
|
||||
not perform a literal timestep. But it has logic similar to what is
|
||||
described here, to compute forces and invoke fixes at each iteration
|
||||
of a minimization. Differences between time integration and
|
||||
minimization are highlighted at the end of this section.
|
||||
|
||||
The Verlet class is encoded in the src/verlet.cpp and verlet.h files.
|
||||
It implements the velocity-Verlet timestepping algorithm. The
|
||||
workhorse method is Verlet::run(), but first we highlight several
|
||||
other methods in the class.
|
||||
|
||||
\begin{itemize}
|
||||
|
||||
\item The init() method is called at the beginning of each dynamics
|
||||
run. It simply sets some internal flags, based on user settings in
|
||||
other parts of the code.
|
||||
|
||||
\item The setup() or setup\_minimal() methods are also called before
|
||||
each run. The velocity-Verlet method requires current forces be
|
||||
calculated before the first timestep, so these routines compute
|
||||
forces due to all atomic interactions, using the same logic that
|
||||
appears in the timestepping described next. A few fixes are also
|
||||
invoked, using the mechanism described in the next section. Various
|
||||
counters are also initialized before the run begins. The
|
||||
setup\_minimal() method is a variant that has a flag for performing
|
||||
less setup. This is used when runs are continued and information
|
||||
from the previous run is still valid. For example, if repeated
|
||||
short LAMMPS runs are being invoked, interleaved by other commands,
|
||||
via the ``pre no'' and ``every'' options of the run command, the
|
||||
setup\_minimal() method is used.
|
||||
|
||||
\item The force\_clear() method initializes force and other arrays to
|
||||
zero before each timestep, so that forces (torques, etc) can be
|
||||
accumulated.
|
||||
|
||||
\end{itemize}
|
||||
|
||||
Now for the Verlet::run() method. Its structure in hi-level pseudo
|
||||
code is shown in Fig \ref{fig:verlet}. In the actual code in
|
||||
src/verlet.cpp some of these operations are conditionally invoked.
|
||||
|
||||
\begin{figure}[htb]
|
||||
\begin{center}
|
||||
\begin{verbatim}
|
||||
loop over N timesteps:
|
||||
ev_set()
|
||||
|
||||
fix->initial_integrate()
|
||||
fix->post_integrate()
|
||||
|
||||
nflag = neighbor->decide()
|
||||
if nflag:
|
||||
fix->pre_exchange()
|
||||
domain->pbc()
|
||||
domain->reset_box()
|
||||
comm->setup()
|
||||
neighbor->setup_bins()
|
||||
comm->exchange()
|
||||
comm->borders()
|
||||
fix->pre_neighbor()
|
||||
neighbor->build()
|
||||
else
|
||||
comm->forward_comm()
|
||||
|
||||
force_clear()
|
||||
fix->pre_force()
|
||||
|
||||
pair->compute()
|
||||
bond->compute()
|
||||
angle->compute()
|
||||
dihedral->compute()
|
||||
improper->compute()
|
||||
kspace->compute()
|
||||
|
||||
comm->reverse_comm()
|
||||
|
||||
fix->post_force()
|
||||
fix->final_integrate()
|
||||
fix->end_of_step()
|
||||
|
||||
if any output on this step: output->write()
|
||||
\end{verbatim}
|
||||
\end{center}
|
||||
\caption{Pseudo-code for the Verlet::run() method.}
|
||||
\label{fig:verlet}
|
||||
\end{figure}
|
||||
|
||||
The ev\_set() method (in the parent Integrate class), sets two flags
|
||||
({\em eflag} and {\em vflag}) for energy and virial computation. Each
|
||||
flag encodes whether global and/or per-atom energy and virial should
|
||||
be calculated on this timestep, because some fix or variable or output
|
||||
will need it. These flags are passed to the various methods that
|
||||
compute particle interactions, so that they can skip the extra
|
||||
calculations if the energy and virial are not needed. See the
|
||||
comments with the Integrate::ev\_set() method which document the flag
|
||||
values.
|
||||
|
||||
At various points of the timestep, fixes are invoked,
|
||||
e.g. fix$\rightarrow$initial\_integrate(). In the code, this is
|
||||
actually done via the Modify class which stores all the Fix objects
|
||||
and lists of which should be invoked at what point in the timestep.
|
||||
Fixes are the LAMMPS mechanism for tailoring the operations of a
|
||||
timestep for a particular simulation. As described elsewhere
|
||||
(unwritten section), each fix has one or more methods, each of which
|
||||
is invoked at a specific stage of the timestep, as in Fig
|
||||
\ref{fig:verlet}. All the fixes defined in an input script with an
|
||||
initial\_integrate() method are invoked at the beginning of each
|
||||
timestep. Fix nve, nvt, npt are examples, since they perform the
|
||||
start-of-timestep velocity-Verlet integration to update velocities by
|
||||
a half-step, and coordinates by a full step. The post\_integrate()
|
||||
method is next. Only a few fixes use this, e.g. to reflect particles
|
||||
off box boundaries in the FixWallReflect class.
|
||||
|
||||
The decide() method in the Neighbor class determines whether neighbor
|
||||
lists need to be rebuilt on the current timestep. If not, coordinates
|
||||
of ghost atoms are acquired by each processor via the forward\_comm()
|
||||
method of the Comm class. If neighbor lists need to be built, several
|
||||
operations within the inner if clause of Fig \ref{fig:verlet} are
|
||||
first invoked. The pre\_exchange() method of any defined fixes is
|
||||
invoked first. Typically this inserts or deletes particles from the
|
||||
system.
|
||||
|
||||
Periodic boundary conditions are then applied by the Domain class via
|
||||
its pbc() method to remap particles that have moved outside the
|
||||
simulation box back into the box. Note that this is not done every
|
||||
timestep. but only when neighbor lists are rebuilt. This is so that
|
||||
each processor's sub-domain will have consistent (nearby) atom
|
||||
coordinates for its owned and ghost atoms. It is also why dumped atom
|
||||
coordinates can be slightly outside the simulation box.
|
||||
|
||||
The box boundaries are then reset (if needed) via the reset\_box()
|
||||
method of the Domain class, e.g. if box boundaries are shrink-wrapped
|
||||
to current particle coordinates. A change in the box size or shape
|
||||
requires internal information for communicating ghost atoms (Comm
|
||||
class) and neighbor list bins (Neighbor class) be updated. The
|
||||
setup() method of the Comm class and setup\_bins() method of the
|
||||
Neighbor class perform the update.
|
||||
|
||||
The code is now ready to migrate atoms that have left a processor's
|
||||
geometric sub-domain to new processors. The exchange() method of the
|
||||
Comm class performs this operation. The borders() method of the Comm
|
||||
class then identifies ghost atoms surrounding each processor's
|
||||
sub-domain and communicates ghost atom information to neighboring
|
||||
processors. It does this by looping over all the atoms owned by a
|
||||
processor to make lists of those to send to each neighbor processor.
|
||||
On subsequent timesteps, the lists are used by the
|
||||
Comm::forward\_comm() method.
|
||||
|
||||
Fixes with a pre\_neighbor() method are then called. These typically
|
||||
re-build some data structure stored by the fix that depends on the
|
||||
current atoms owned by each processor.
|
||||
|
||||
Now that each processor has a current list of its owned and ghost
|
||||
atoms, LAMMPS is ready to rebuild neighbor lists via the build()
|
||||
method of the Neighbor class. This is typically done by binning all
|
||||
owned and ghost atoms, and scanning a stencil of bins around each
|
||||
owned atom's bin to make a Verlet list of neighboring atoms within the
|
||||
force cutoff plus neighbor skin distance.
|
||||
|
||||
In the next portion of the timestep, all interaction forces between
|
||||
particles are computed, after zeroing the per-atom force vector via
|
||||
the force\_clear() method. If the newton flag is set to ``on'' by the
|
||||
newton command, forces on both owned and ghost atoms are calculated.
|
||||
|
||||
Pairwise forces are calculated first, which enables the global virial
|
||||
(if requested) to be calculated cheaply (at the end of the
|
||||
Pair::compute() method), by a dot product of atom coordinates and
|
||||
forces. By including owned and ghost atoms in the dot product, the
|
||||
effect of periodic boundary conditions is correctly accounted for.
|
||||
Molecular topology interactions (bonds, angles, dihedrals, impropers)
|
||||
are calculated next. The final contribution is from long-range
|
||||
Coulombic interactions, invoked by the KSpace class.
|
||||
|
||||
If the newton flag is on, forces on ghost atoms are communicated and
|
||||
summed back to their corresponding owned atoms. The reverse\_comm()
|
||||
method of the Comm class performs this operation, which is essentially
|
||||
the inverse operation of sending copies of owned atom coordinates to
|
||||
other processor's ghost atoms.
|
||||
|
||||
At this point in the timestep, the total force on each atom is known.
|
||||
Additional force constraints (external forces, SHAKE, etc) are applied
|
||||
by Fixes that have a post\_force() method. The second half of the
|
||||
velocity-Verlet integration is then performed (another half-step
|
||||
update of the velocities) via fixes like nve, nvt, npt.
|
||||
|
||||
At the end of the timestep, fixes that define an end\_of\_step()
|
||||
method are invoked. These typically perform a diagnostic calculation,
|
||||
e.g. the ave/time and ave/spatial fixes. The final operation of the
|
||||
timestep is to perform any requested output, via the write() method of
|
||||
the Output class. There are 3 kinds of LAMMPS output: thermodynamic
|
||||
output to the screen and log file, snapshots of atom data to a dump
|
||||
file, and restart files. See the thermo\_style, dump, and restart
|
||||
commands for more details.
|
||||
|
||||
The iteration performed by an energy minimization is similar to the
|
||||
dynamics timestep of Fig \ref{fig:verlet}. Forces are computed,
|
||||
neighbor lists are built as needed, atoms migrate to new processors,
|
||||
and atom coordinates and forces are communicated to neighboring
|
||||
processors. The only difference is what Fix class operations are
|
||||
invoked when. Only a subset of LAMMPS fixes are useful during energy
|
||||
minimization, as explained in their individual doc pages. The
|
||||
relevant Fix class methods are min\_pre\_exchange(),
|
||||
min\_pre\_force(), and min\_post\_force(). Each is invoked at the
|
||||
appropriate place within the minimization iteration. For example, the
|
||||
min\_post\_force() method is analogous to the post\_force() method for
|
||||
dynamics; it is used to alter or constrain forces on each atom, which
|
||||
affects the minimization procedure.
|
||||
|
||||
\pagebreak
|
||||
\section{Extending LAMMPS}
|
||||
|
||||
The Section\_modify.html file in the doc directory of
|
||||
the LAMMPS distribution gives an overview of how LAMMPS can
|
||||
be extended by writing new classes that derive from existing
|
||||
parent classes in LAMMPS. Here, some specific coding
|
||||
details are provided for writing a new fix.
|
||||
|
||||
\subsection{New fixes}
|
||||
|
||||
(this section provided by Kirill Lykov)
|
||||
\vspace{0.25cm}
|
||||
|
||||
Writing fixes is a flexible way of extending LAMMPS. Users can
|
||||
implement many things using fixes:
|
||||
|
||||
\begin{itemize}
|
||||
\item changing particles attributes (positions, velocities, forces, etc.).
|
||||
Example: FixFreeze.
|
||||
\item reading/writing data. Example: FixRestart.
|
||||
\item implementing boundary conditions. Example: FixWall.
|
||||
\item saving information about particles for future use (previous positions,
|
||||
for instance). Example: FixStoreState.
|
||||
\end{itemize}
|
||||
|
||||
All fixes are derived from class Fix and must have constructor with the
|
||||
signature: FixMine(class LAMMPS *, int, char **).
|
||||
|
||||
Every fix must be registered in LAMMPS by writing the following lines
|
||||
of code in the header before include guards:
|
||||
|
||||
\begin{center}
|
||||
\begin{verbatim}
|
||||
#ifdef FIX_CLASS
|
||||
FixStyle(your/fix/name,FixMine)
|
||||
#else
|
||||
\end{verbatim}
|
||||
\end{center}
|
||||
|
||||
Where ``your/fix/name'' is a name of your fix in the script and FixMine
|
||||
is the name of the class. This code allows LAMMPS to find your fix
|
||||
when it parses input script. In addition, your fix header must be
|
||||
included in the file ``style\_fix.h''. In case if you use LAMMPS make,
|
||||
this file is generated automatically - all files starting with prefix
|
||||
fix\_ are included, so call your header the same way. Otherwise, don't
|
||||
forget to add your include into ``style\_fix.h''.
|
||||
|
||||
Let's write a simple fix which will print average velocity at the end
|
||||
of each timestep. First of all, implement a constructor:
|
||||
|
||||
\begin{center}
|
||||
\begin{verbatim}
|
||||
FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
|
||||
: Fix(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 4)
|
||||
error->all(FLERR,"Illegal fix print command");
|
||||
|
||||
nevery = atoi(arg[3]);
|
||||
if (nevery <= 0)
|
||||
error->all(FLERR,"Illegal fix print command");
|
||||
}
|
||||
\end{verbatim}
|
||||
\end{center}
|
||||
|
||||
In the constructor you should parse your fix arguments which are
|
||||
specified in the script. All fixes have pretty the same syntax: fix
|
||||
[fix\_identifier] [group\_name] [fix\_name] [fix\_arguments]. The
|
||||
first 3 parameters are parsed by Fix class constructor, while
|
||||
[fix\_arguments] should be parsed by you. In our case, we need to
|
||||
specify how often we want to print an average velocity. For instance,
|
||||
once in 50 timesteps: fix 1 print/vel 50. There is a special variable
|
||||
in Fix class called nevery which specifies how often method
|
||||
end\_of\_step() is called. Thus all we need to do is just set it up.
|
||||
|
||||
The next method we need to implement is setmask():
|
||||
\begin{center}
|
||||
\begin{verbatim}
|
||||
int FixPrintVel::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= FixConst::END_OF_STEP;
|
||||
return mask;
|
||||
}
|
||||
\end{verbatim}
|
||||
\end{center}
|
||||
|
||||
Here user specifies which methods of your fix should be called during
|
||||
the execution. For instance, END\_OF\_STEP corresponds to the
|
||||
end\_of\_step() method. Overall, there are 8 most important methods,
|
||||
methods are called in predefined order during the execution of the
|
||||
verlet algorithm as was mentioned in the Section 3:
|
||||
|
||||
\begin{itemize}
|
||||
\item initial\_integrate()
|
||||
\item post\_integrate()
|
||||
\item pre\_exchange()
|
||||
\item pre\_neighbor()
|
||||
\item pre\_force()
|
||||
\item post\_force()
|
||||
\item final\_integrate()
|
||||
\item end\_of\_step()
|
||||
\end{itemize}
|
||||
|
||||
Fix developer must understand when he wants to execute his code. In
|
||||
case if we want to write FixPrintVel, we need only end\_of\_step():
|
||||
|
||||
\begin{center}
|
||||
\begin{verbatim}
|
||||
void FixPrintVel::end_of_step()
|
||||
{
|
||||
// for add3, scale3
|
||||
using namespace MathExtra;
|
||||
|
||||
double** v = atom->v;
|
||||
int nlocal = atom->nlocal;
|
||||
double localAvgVel[4]; // 4th element for particles count
|
||||
memset(localAvgVel, 0, 4 * sizeof(double));
|
||||
for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
|
||||
add3(localAvgVel, v[particleInd], localAvgVel);
|
||||
}
|
||||
localAvgVel[3] = nlocal;
|
||||
double globalAvgVel[4];
|
||||
memset(globalAvgVel, 0, 4 * sizeof(double));
|
||||
MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
|
||||
scale3(1.0 / globalAvgVel[3], globalAvgVel);
|
||||
if (comm->me == 0) {
|
||||
printf("\%e, \%e, \%e\n",
|
||||
globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
|
||||
}
|
||||
}
|
||||
\end{verbatim}
|
||||
\end{center}
|
||||
|
||||
In the code above, we use MathExtra routines defined in
|
||||
``math\_extra.h''. There are bunch of math functions to work with
|
||||
arrays of doubles as with math vectors.
|
||||
|
||||
In this code we use an instance of Atom class. This object is stored
|
||||
in the Pointers class (see ``pointers.h''). This object contains all
|
||||
global information about the simulation system. Data from Pointers
|
||||
class available to all classes inherited from it using protected
|
||||
inheritance. Hence when you write you own class, which is going to use
|
||||
LAMMPS data, don't forget to inherit from Pointers. When writing
|
||||
fixes we inherit from class Fix which is inherited from Pointers so
|
||||
there is no need to inherit from it directly.
|
||||
|
||||
The code above computes average velocity for all particles in the
|
||||
simulation. Yet you have one unused parameter in fix call from the
|
||||
script - [group\_name]. This parameter specifies the group of atoms
|
||||
used in the fix. So we should compute average for all particles in the
|
||||
simulation if group\_name == all, but it can be any group. The group
|
||||
information is specified by groupbit which is defined in class Fix:
|
||||
|
||||
\begin{center}
|
||||
\begin{verbatim}
|
||||
for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
|
||||
if (atom->mask[particleInd] & groupbit) {
|
||||
//Do all job here
|
||||
}
|
||||
}
|
||||
\end{verbatim}
|
||||
\end{center}
|
||||
|
||||
Class Atom encapsulates atoms positions, velocities, forces, etc. User
|
||||
can access them using particle index. Note, that particle indexes are
|
||||
usually changed every timestep because of sorting.
|
||||
|
||||
Lets consider another Fix example. We want to have a fix which stores
|
||||
atoms position from previous time step in your fix. The local atoms
|
||||
indexes will not be valid on the next iteration. In order to handle
|
||||
this situation there are several methods which should be implemented:
|
||||
|
||||
\begin{itemize}
|
||||
\item \verb|double memory_usage| - return how much memory fix uses
|
||||
\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays
|
||||
in your fix
|
||||
\item \verb|void copy_arrays(int i, int j, int delflag)| - copy i-th per-particle
|
||||
information to j-th. Used when atoms sorting is performed. if delflag is set
|
||||
and atom j owns a body, move the body information to atom i.
|
||||
\item \verb|void set_arrays(int i)| - sets i-th particle related information to zero
|
||||
\end{itemize}
|
||||
|
||||
Note, that if your class implements these methods, it must call add calls of
|
||||
add\_callback and delete\_callback to constructor and destructor:
|
||||
|
||||
\begin{center}
|
||||
\begin{verbatim}
|
||||
FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg) {
|
||||
//...
|
||||
atom->add_callback(0);
|
||||
}
|
||||
|
||||
FixSavePos::~FixSavePos() {
|
||||
atom->delete_callback(id, 0);
|
||||
}
|
||||
\end{verbatim}
|
||||
\end{center}
|
||||
|
||||
Since we want to store positions of atoms from previous timestep, we
|
||||
need to add double** x to the header file. Than add allocation code to
|
||||
constructor:
|
||||
|
||||
\verb|memory->create(this->x, atom->nmax, 3, "FixSavePos:x");|. Free memory
|
||||
at destructor: \verb|memory->destroy(x);|
|
||||
|
||||
Finally, implement mentioned methods:
|
||||
|
||||
\begin{center}
|
||||
\begin{verbatim}
|
||||
double FixSavePos::memory_usage()
|
||||
{
|
||||
int nmax = atom->nmax;
|
||||
double bytes = 0.0;
|
||||
bytes += nmax * 3 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
void FixSavePos::grow_arrays(int nmax)
|
||||
{
|
||||
memory->grow(this->x, nmax, 3, "FixSavePos:x");
|
||||
}
|
||||
|
||||
void FixSavePos::copy_arrays(int i, int j, int delflag)
|
||||
{
|
||||
memcpy(this->x[j], this->x[i], sizeof(double) * 3);
|
||||
}
|
||||
|
||||
void FixSavePos::set_arrays(int i)
|
||||
{
|
||||
memset(this->x[i], 0, sizeof(double) * 3);
|
||||
}
|
||||
|
||||
int FixSavePos::pack_exchange(int i, double *buf)
|
||||
{
|
||||
int m = 0;
|
||||
buf[m++] = x[i][0];
|
||||
buf[m++] = x[i][1];
|
||||
buf[m++] = x[i][2];
|
||||
|
||||
return m;
|
||||
}
|
||||
|
||||
int FixSavePos::unpack_exchange(int nlocal, double *buf)
|
||||
{
|
||||
int m = 0;
|
||||
x[nlocal][0] = buf[m++];
|
||||
x[nlocal][1] = buf[m++];
|
||||
x[nlocal][2] = buf[m++];
|
||||
|
||||
return m;
|
||||
}
|
||||
\end{verbatim}
|
||||
\end{center}
|
||||
|
||||
Now, a little bit about memory allocation. We used Memory class which
|
||||
is just a bunch of template functions for allocating 1D and 2D
|
||||
arrays. So you need to add include ``memory.h'' to have access to them.
|
||||
|
||||
Finally, if you need to write/read some global information used in
|
||||
your fix to the restart file, you might do it by setting flag
|
||||
restart\_global = 1 in the constructor and implementing methods void
|
||||
write\_restart(FILE *fp) and void restart(char *buf).
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.8 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 16 KiB |
@ -1,12 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
\begin{eqnarray*}
|
||||
E & = & E_a + E_{bb} + E_{ba} \\
|
||||
E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\
|
||||
E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\
|
||||
E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0)
|
||||
\end{eqnarray*}
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.3 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K [1 + \cos(\theta)]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.2 KiB |
@ -1,15 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\pagestyle{empty}
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
|
||||
%%% Local Variables:
|
||||
%%% mode: latex
|
||||
%%% TeX-master: t
|
||||
%%% End:
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.5 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K [1 - \cos(\theta - \theta_0)]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.3 KiB |
@ -1,9 +0,0 @@
|
||||
\documentstyle[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.8 KiB |
@ -1,9 +0,0 @@
|
||||
\documentstyle[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 7.7 KiB |
@ -1,13 +0,0 @@
|
||||
\documentstyle[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E=-U_{min}
|
||||
\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
|
||||
\quad\mbox{with}\quad
|
||||
U(\theta,\theta_0)
|
||||
=-0.5 \left(1+\cos(\theta-\theta_0) \right)
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.2 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K [\cos(\theta) - \cos(\theta_0)]^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 7.8 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
\thispagestyle{empty}
|
||||
$$
|
||||
E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.9 KiB |
@ -1,10 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
\begin{eqnarray*}
|
||||
-\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\
|
||||
\vec{F_j} & = & -\vec{F_i} \\
|
||||
\end{eqnarray*}
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.6 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
\cos\gamma = \frac{\vec{\mu_j}\bullet\vec{r_{ij}}}{\mu_j\,r_{ij}}
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.6 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (\cos\gamma - \cos\gamma_0)^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.0 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\,
|
||||
\vec{r_{ij}} \times \vec{\mu_j}
|
||||
$$
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 4.5 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.7 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K [ 1.0 + c \cos ( n \theta) ]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.0 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (\theta - \theta_0)^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 9.0 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
\thispagestyle{empty}
|
||||
$$
|
||||
E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.1 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.0 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 8.1 KiB |
@ -1,11 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
|
||||
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
|
||||
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 11 KiB |
@ -1,13 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = -0.5 K R_0^2
|
||||
\ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] +
|
||||
4 \epsilon \left[ \left(\frac{\sigma}{\left(r -
|
||||
\Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r -
|
||||
\Delta\right)}\right)^6 \right] + \epsilon
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.1 KiB |
@ -1,10 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
\pagestyle{empty}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (r^2 - r_0^2)^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 1.8 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (r - r_0)^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.0 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.1 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.7 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
\thispagestyle{empty}
|
||||
$$
|
||||
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.5 KiB |
@ -1,10 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
% E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2
|
||||
E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.5 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.8 KiB |
@ -1,10 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
\pagestyle{empty}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 9.3 KiB |
@ -1,11 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 +
|
||||
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
|
||||
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
@ -32,12 +32,10 @@ install the `openkim-models` package
|
||||
|
||||
If you have problems with the installation you can post issues to
|
||||
`this link <conda_forge_lammps_>`_.
|
||||
|
||||
.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
|
||||
|
||||
Thanks to Jan Janssen (Max-Planck-Institut für Eisenforschung) for setting
|
||||
Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting
|
||||
up the Conda capability.
|
||||
|
||||
.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues
|
||||
|
||||
.. _openkim: https://openkim.org
|
||||
|
||||
@ -45,9 +43,6 @@ up the Conda capability.
|
||||
|
||||
.. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
|
||||
|
||||
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,22 +1,22 @@
|
||||
.. index:: angle\_style charmm
|
||||
.. index:: angle_style charmm
|
||||
|
||||
angle\_style charmm command
|
||||
===========================
|
||||
angle_style charmm command
|
||||
==========================
|
||||
|
||||
angle\_style charmm/intel command
|
||||
=================================
|
||||
angle_style charmm/intel command
|
||||
================================
|
||||
|
||||
angle\_style charmm/kk command
|
||||
angle_style charmm/kk command
|
||||
=============================
|
||||
|
||||
angle_style charmm/omp command
|
||||
==============================
|
||||
|
||||
angle\_style charmm/omp command
|
||||
===============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style charmm
|
||||
|
||||
@ -24,7 +24,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style charmm
|
||||
angle_coeff 1 300.0 107.0 50.0 3.0
|
||||
@ -34,12 +34,15 @@ Description
|
||||
|
||||
The *charmm* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_charmm.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
with an additional Urey\_Bradley term based on the distance *r* between
|
||||
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
|
||||
coefficients defined for each angle type.
|
||||
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`,
|
||||
:math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
|
||||
type.
|
||||
|
||||
See :ref:`(MacKerell) <angle-MacKerell>` for a description of the CHARMM force
|
||||
field.
|
||||
@ -49,13 +52,13 @@ The following coefficients must be defined for each angle type via the
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy/radian\^2)
|
||||
* theta0 (degrees)
|
||||
* K\_ub (energy/distance\^2)
|
||||
* r\_ub (distance)
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_{ub}` (energy/distance\^2)
|
||||
* :math:`r_{ub}` (distance)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
|
||||
|
||||
----------
|
||||
@ -108,8 +111,3 @@ Related commands
|
||||
|
||||
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
||||
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,22 +1,22 @@
|
||||
.. index:: angle\_style class2
|
||||
.. index:: angle_style class2
|
||||
|
||||
angle\_style class2 command
|
||||
===========================
|
||||
angle_style class2 command
|
||||
==========================
|
||||
|
||||
angle\_style class2/kk command
|
||||
angle_style class2/kk command
|
||||
=============================
|
||||
|
||||
angle_style class2/omp command
|
||||
==============================
|
||||
|
||||
angle\_style class2/omp command
|
||||
===============================
|
||||
|
||||
angle\_style class2/p6 command
|
||||
==============================
|
||||
angle_style class2/p6 command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style class2
|
||||
|
||||
@ -24,44 +24,49 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style class2
|
||||
angle_coeff \* 75.0
|
||||
angle_coeff * 75.0
|
||||
angle_coeff 1 bb 10.5872 1.0119 1.5228
|
||||
angle_coeff \* ba 3.6551 24.895 1.0119 1.5228
|
||||
angle_coeff * ba 3.6551 24.895 1.0119 1.5228
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *class2* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_class2.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
|
||||
bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
|
||||
E & = E_a + E_{bb} + E_{ba} \\
|
||||
E_a & = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4(\theta - \theta_0)^4 \\
|
||||
E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\
|
||||
E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0)
|
||||
|
||||
|
||||
where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a
|
||||
bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are
|
||||
the equilibrium bond lengths.
|
||||
|
||||
See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field.
|
||||
|
||||
Coefficients for the Ea, Ebb, and Eba formulas must be defined for
|
||||
Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for
|
||||
each angle type via the :doc:`angle\_coeff <angle_coeff>` command as in
|
||||
the example above, or in the data file or restart files read by the
|
||||
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
|
||||
commands.
|
||||
|
||||
These are the 4 coefficients for the Ea formula:
|
||||
These are the 4 coefficients for the :math:`E_a` formula:
|
||||
|
||||
* theta0 (degrees)
|
||||
* K2 (energy/radian\^2)
|
||||
* K3 (energy/radian\^3)
|
||||
* K4 (energy/radian\^4)
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_2` (energy/radian\^2)
|
||||
* :math:`K_3` (energy/radian\^3)
|
||||
* :math:`K_4` (energy/radian\^4)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of the various K are in per-radian.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of the various :math:`K` are in per-radian.
|
||||
|
||||
For the Ebb formula, each line in a :doc:`angle\_coeff <angle_coeff>`
|
||||
For the :math:`E_{bb}` formula, each line in a :doc:`angle\_coeff <angle_coeff>`
|
||||
command in the input script lists 4 coefficients, the first of which
|
||||
is "bb" to indicate they are BondBond coefficients. In a data file,
|
||||
these coefficients should be listed under a "BondBond Coeffs" heading
|
||||
@ -69,11 +74,11 @@ and you must leave out the "bb", i.e. only list 3 coefficients after
|
||||
the angle type.
|
||||
|
||||
* bb
|
||||
* M (energy/distance\^2)
|
||||
* r1 (distance)
|
||||
* r2 (distance)
|
||||
* :math:`M` (energy/distance\^2)
|
||||
* :math:`r_1` (distance)
|
||||
* :math:`r_2` (distance)
|
||||
|
||||
For the Eba formula, each line in a :doc:`angle\_coeff <angle_coeff>`
|
||||
For the :math:`E_{ba}` formula, each line in a :doc:`angle\_coeff <angle_coeff>`
|
||||
command in the input script lists 5 coefficients, the first of which
|
||||
is "ba" to indicate they are BondAngle coefficients. In a data file,
|
||||
these coefficients should be listed under a "BondAngle Coeffs" heading
|
||||
@ -81,13 +86,13 @@ and you must leave out the "ba", i.e. only list 4 coefficients after
|
||||
the angle type.
|
||||
|
||||
* ba
|
||||
* N1 (energy/distance\^2)
|
||||
* N2 (energy/distance\^2)
|
||||
* r1 (distance)
|
||||
* r2 (distance)
|
||||
* :math:`N_1` (energy/distance\^2)
|
||||
* :math:`N_2` (energy/distance\^2)
|
||||
* :math:`r_1` (distance)
|
||||
* :math:`r_2` (distance)
|
||||
|
||||
The theta0 value in the Eba formula is not specified, since it is the
|
||||
same value from the Ea formula.
|
||||
The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
|
||||
since it is the same value from the :math:`E_a` formula.
|
||||
|
||||
|
||||
----------
|
||||
@ -117,17 +122,19 @@ instructions on how to use the accelerated styles effectively.
|
||||
|
||||
The *class2/p6* angle style uses the *class2* potential expanded to sixth order:
|
||||
|
||||
.. image:: Eqs/angle_class2_p6.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
In this expanded term 6 coefficients for the Ea formula need to be set:
|
||||
E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
|
||||
|
||||
* theta0 (degrees)
|
||||
* K2 (energy/radian\^2)
|
||||
* K3 (energy/radian\^3)
|
||||
* K4 (energy/radian\^4)
|
||||
* K5 (energy/radian\^5)
|
||||
* K6 (energy/radian\^6)
|
||||
|
||||
In this expanded term 6 coefficients for the :math:`E_a` formula need to be set:
|
||||
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_2` (energy/radian\^2)
|
||||
* :math:`K_3` (energy/radian\^3)
|
||||
* :math:`K_4` (energy/radian\^4)
|
||||
* :math:`K_5` (energy/radian\^5)
|
||||
* :math:`K_6` (energy/radian\^6)
|
||||
|
||||
The bond-bond and bond-angle terms remain unchanged.
|
||||
|
||||
@ -160,8 +167,3 @@ Related commands
|
||||
|
||||
|
||||
**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: angle\_coeff
|
||||
.. index:: angle_coeff
|
||||
|
||||
angle\_coeff command
|
||||
====================
|
||||
angle_coeff command
|
||||
===================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_coeff N args
|
||||
|
||||
@ -18,11 +18,11 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_coeff 1 300.0 107.0
|
||||
angle_coeff \* 5.0
|
||||
angle_coeff 2\*10 5.0
|
||||
angle_coeff * 5.0
|
||||
angle_coeff 2*10 5.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -30,7 +30,7 @@ Description
|
||||
Specify the angle force field coefficients for one or more angle types.
|
||||
The number and meaning of the coefficients depends on the angle style.
|
||||
Angle coefficients can also be set in the data file read by the
|
||||
:doc:`read\_data <read_data>` command or in a restart file.
|
||||
: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
|
||||
@ -41,18 +41,18 @@ leading asterisk means all types from 1 to n (inclusive). A trailing
|
||||
asterisk means all types from n to N (inclusive). A middle asterisk
|
||||
means all types from m to n (inclusive).
|
||||
|
||||
Note that using an angle\_coeff command can override a previous setting
|
||||
Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting
|
||||
for the same angle type. For example, these commands set the coeffs
|
||||
for all angle types, then overwrite the coeffs for just angle type 2:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_coeff \* 200.0 107.0 1.2
|
||||
angle_coeff * 200.0 107.0 1.2
|
||||
angle_coeff 2 50.0 107.0
|
||||
|
||||
A line in a data file that specifies angle coefficients uses the exact
|
||||
same format as the arguments of the angle\_coeff command in an input
|
||||
same format as the arguments of the :doc:`angle_coeff <angle_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 "Angle Coeffs" section of a data file, the line that
|
||||
@ -63,7 +63,7 @@ corresponds to the 1st example above would be listed as
|
||||
|
||||
1 300.0 107.0
|
||||
|
||||
The :doc:`angle\_style class2 <angle_class2>` is an exception to this
|
||||
The :doc:`angle_style class2 <angle_class2>` is an exception to this
|
||||
rule, in that an additional argument is used in the input script to
|
||||
allow specification of the cross-term coefficients. See its
|
||||
doc page for details.
|
||||
@ -73,13 +73,13 @@ doc page for details.
|
||||
|
||||
|
||||
The list of all angle styles defined in LAMMPS is given on the
|
||||
:doc:`angle\_style <angle_style>` doc page. They are also listed in more
|
||||
:doc:`angle_style <angle_style>` doc page. They are also listed in more
|
||||
compact form on the :ref:`Commands angle <angle>` doc
|
||||
page.
|
||||
|
||||
On either of those pages, click on the style to display the formula it
|
||||
computes and its coefficients as specified by the associated
|
||||
angle\_coeff command.
|
||||
:doc:`angle_coeff <angle_coeff>` command.
|
||||
|
||||
|
||||
----------
|
||||
@ -90,8 +90,8 @@ Restrictions
|
||||
|
||||
|
||||
This command must come after the simulation box is defined by a
|
||||
:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`, or
|
||||
:doc:`create\_box <create_box>` command.
|
||||
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
|
||||
:doc:`create_box <create_box>` command.
|
||||
|
||||
An angle style must be defined before any angle coefficients are
|
||||
set, either in the input script or in a data file.
|
||||
@ -99,11 +99,6 @@ set, either in the input script or in a data file.
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_style <angle_style>`
|
||||
:doc:`angle_style <angle_style>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,19 +1,19 @@
|
||||
.. index:: angle\_style cosine
|
||||
.. index:: angle_style cosine
|
||||
|
||||
angle\_style cosine command
|
||||
===========================
|
||||
angle_style cosine command
|
||||
==========================
|
||||
|
||||
angle\_style cosine/omp command
|
||||
===============================
|
||||
|
||||
angle\_style cosine/kk command
|
||||
angle_style cosine/omp command
|
||||
==============================
|
||||
|
||||
angle_style cosine/kk command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine
|
||||
|
||||
@ -21,27 +21,29 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine
|
||||
angle_coeff \* 75.0
|
||||
angle_coeff * 75.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where K is defined for each angle type.
|
||||
E = K [1 + \cos(\theta)]
|
||||
|
||||
|
||||
where :math:`K` is defined for each angle type.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* :math:`K` (energy)
|
||||
|
||||
|
||||
----------
|
||||
@ -83,8 +85,3 @@ Related commands
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: angle\_style cosine/buck6d
|
||||
.. index:: angle_style cosine/buck6d
|
||||
|
||||
angle\_style cosine/buck6d command
|
||||
==================================
|
||||
angle_style cosine/buck6d command
|
||||
=================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/buck6d
|
||||
|
||||
@ -15,7 +15,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/buck6d
|
||||
angle_coeff 1 cosine/buck6d 1.978350 4 180.000000
|
||||
@ -25,22 +25,23 @@ Description
|
||||
|
||||
The *cosine/buck6d* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine_buck6d.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where K is the energy constant, n is the periodic multiplicity and
|
||||
Theta0 is the equilibrium angle.
|
||||
E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
|
||||
|
||||
where :math:`K` is the energy constant, :math:`n` is the periodic multiplicity and
|
||||
:math:`\theta_0` is the equilibrium angle.
|
||||
|
||||
The coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands in the following order:
|
||||
|
||||
* K (energy)
|
||||
* n
|
||||
* Theta0 (degrees)
|
||||
* :math:`K` (energy)
|
||||
* :math:`n`
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally.
|
||||
|
||||
Additional to the cosine term the *cosine/buck6d* angle style computes
|
||||
@ -73,8 +74,3 @@ Related commands
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: angle\_style cosine/delta
|
||||
.. index:: angle_style cosine/delta
|
||||
|
||||
angle\_style cosine/delta command
|
||||
=================================
|
||||
angle_style cosine/delta command
|
||||
================================
|
||||
|
||||
angle\_style cosine/delta/omp command
|
||||
=====================================
|
||||
angle_style cosine/delta/omp command
|
||||
====================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/delta
|
||||
|
||||
@ -18,31 +18,33 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/delta
|
||||
angle_coeff 2\*4 75.0 100.0
|
||||
angle_coeff 2*4 75.0 100.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine/delta* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine_delta.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
E = K [1 - \cos(\theta - \theta_0)]
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally.
|
||||
|
||||
|
||||
@ -85,8 +87,3 @@ Related commands
|
||||
:doc:`angle\_coeff <angle_coeff>`, :doc:`angle\_style cosine/squared <angle_cosine_squared>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: angle\_style cosine/periodic
|
||||
.. index:: angle_style cosine/periodic
|
||||
|
||||
angle\_style cosine/periodic command
|
||||
====================================
|
||||
angle_style cosine/periodic command
|
||||
===================================
|
||||
|
||||
angle\_style cosine/periodic/omp command
|
||||
========================================
|
||||
angle_style cosine/periodic/omp command
|
||||
=======================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/periodic
|
||||
|
||||
@ -18,24 +18,26 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/periodic
|
||||
angle_coeff \* 75.0 1 6
|
||||
angle_coeff * 75.0 1 6
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine/periodic* angle style uses the following potential, which
|
||||
is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
|
||||
particularly for organometallic systems where *n* = 4 might be used
|
||||
for an octahedral complex and *n* = 3 might be used for a trigonal
|
||||
particularly for organometallic systems where :math:`n` = 4 might be used
|
||||
for an octahedral complex and :math:`n` = 3 might be used for a trigonal
|
||||
center:
|
||||
|
||||
.. image:: Eqs/angle_cosine_periodic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where C, B and n are coefficients defined for each angle type.
|
||||
E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
|
||||
|
||||
|
||||
where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type.
|
||||
|
||||
See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
|
||||
|
||||
@ -44,13 +46,13 @@ The following coefficients must be defined for each angle type via the
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* C (energy)
|
||||
* B = 1 or -1
|
||||
* n = 1, 2, 3, 4, 5 or 6 for periodicity
|
||||
* :math:`C` (energy)
|
||||
* :math:`B` = 1 or -1
|
||||
* :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity
|
||||
|
||||
Note that the prefactor C is specified and not the overall force
|
||||
constant K = C / n\^2. When B = 1, it leads to a minimum for the
|
||||
linear geometry. When B = -1, it leads to a maximum for the linear
|
||||
Note that the prefactor :math:`C` is specified and not the overall force
|
||||
constant :math:`K = \frac{C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the
|
||||
linear geometry. When :math:`B = -1`, it leads to a maximum for the linear
|
||||
geometry.
|
||||
|
||||
|
||||
@ -104,8 +106,3 @@ Related commands
|
||||
|
||||
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
||||
(1990).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: angle\_style cosine/shift
|
||||
.. index:: angle_style cosine/shift
|
||||
|
||||
angle\_style cosine/shift command
|
||||
angle_style cosine/shift command
|
||||
=================================
|
||||
|
||||
angle\_style cosine/shift/omp command
|
||||
=====================================
|
||||
angle_style cosine/shift/omp command
|
||||
====================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/shift
|
||||
|
||||
@ -18,30 +18,33 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/shift
|
||||
angle_coeff \* 10.0 45.0
|
||||
angle_coeff * 10.0 45.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine/shift* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine_shift.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium angle. The potential is bounded
|
||||
between -Umin and zero. In the neighborhood of the minimum E=- Umin +
|
||||
Umin/4(theta-theta0)\^2 hence the spring constant is umin/2.
|
||||
E = -\frac{U_{\text{min}}}{2} \left[ 1 + \cos(\theta-\theta_0) \right]
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium angle. The potential is bounded
|
||||
between :math:`-U_{\text{min}}` and zero. In the neighborhood of the minimum
|
||||
:math:`E = - U_{\text{min}} + U_{\text{min}}/4(\theta - \theta_0)^2` hence
|
||||
the spring constant is :math:`\frac{U_{\text{min}}}{2}`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* umin (energy)
|
||||
* theta (angle)
|
||||
* :math:`U_{\text{min}}` (energy)
|
||||
* :math:`\theta` (angle)
|
||||
|
||||
|
||||
----------
|
||||
@ -83,8 +86,3 @@ Related commands
|
||||
:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: angle\_style cosine/shift/exp
|
||||
.. index:: angle_style cosine/shift/exp
|
||||
|
||||
angle\_style cosine/shift/exp command
|
||||
=====================================
|
||||
angle_style cosine/shift/exp command
|
||||
====================================
|
||||
|
||||
angle\_style cosine/shift/exp/omp command
|
||||
=========================================
|
||||
angle_style cosine/shift/exp/omp command
|
||||
========================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/shift/exp
|
||||
|
||||
@ -18,32 +18,33 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/shift/exp
|
||||
angle_coeff \* 10.0 45.0 2.0
|
||||
angle_coeff * 10.0 45.0 2.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine/shift/exp* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine_shift_exp.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where Umin, theta, and a are defined for each angle type.
|
||||
E = -U_{\text{min}} \frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad \text{with} \quad U(\theta,\theta_0) = -0.5 \left(1+\cos(\theta-\theta_0) \right)
|
||||
|
||||
The potential is bounded between [-Umin:0] and the minimum is
|
||||
located at the angle theta0. The a parameter can be both positive or
|
||||
where :math:`U_{\text{min}}`, :math:`\theta`, and :math:`a` are defined for each angle type.
|
||||
|
||||
The potential is bounded between :math:`[-U_{\text{min}}, 0]` and the minimum is
|
||||
located at the angle :math:`\theta_0`. The a parameter can be both positive or
|
||||
negative and is used to control the spring constant at the
|
||||
equilibrium.
|
||||
|
||||
The spring constant is given by k = A exp(A) Umin / [2 (Exp(a)-1)].
|
||||
For a > 3, k/Umin = a/2 to better than 5% relative error. For negative
|
||||
values of the a parameter, the spring constant is essentially zero,
|
||||
The spring constant is given by :math:`k = A \exp(A) U_{\text{min}} / [2 (\exp(a)-1)]`.
|
||||
For :math:`a > 3`, :math:`\frac{k}{U_{\text{min}}} = \frac{a}{2}` to better than 5% relative error. For negative
|
||||
values of the :math:`a` parameter, the spring constant is essentially zero,
|
||||
and anharmonic terms takes over. The potential is furthermore well
|
||||
behaved in the limit a -> 0, where it has been implemented to linear
|
||||
order in a for a < 0.001. In this limit the potential reduces to the
|
||||
behaved in the limit :math:`a \rightarrow 0`, where it has been implemented to linear
|
||||
order in :math:`a` for :math:`a < 0.001`. In this limit the potential reduces to the
|
||||
cosineshifted potential.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
@ -51,9 +52,9 @@ The following coefficients must be defined for each angle type via the
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* umin (energy)
|
||||
* theta (angle)
|
||||
* A (real number)
|
||||
* :math:`U_min` (energy)
|
||||
* :math:`\theta` (angle)
|
||||
* :math:`A` (real number)
|
||||
|
||||
|
||||
----------
|
||||
@ -97,8 +98,3 @@ Related commands
|
||||
:doc:`dihedral\_cosine\_shift\_exp <dihedral_cosine_shift_exp>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: angle\_style cosine/squared
|
||||
.. index:: angle_style cosine/squared
|
||||
|
||||
angle\_style cosine/squared command
|
||||
===================================
|
||||
angle_style cosine/squared command
|
||||
==================================
|
||||
|
||||
angle\_style cosine/squared/omp command
|
||||
=======================================
|
||||
angle_style cosine/squared/omp command
|
||||
======================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/squared
|
||||
|
||||
@ -18,31 +18,33 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cosine/squared
|
||||
angle_coeff 2\*4 75.0 100.0
|
||||
angle_coeff 2*4 75.0 100.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *cosine/squared* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_cosine_squared.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
E = K [\cos(\theta) - \cos(\theta_0)]^2
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally.
|
||||
|
||||
|
||||
@ -85,8 +87,3 @@ Related commands
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: angle\_style cross
|
||||
.. index:: angle_style cross
|
||||
|
||||
angle\_style cross command
|
||||
angle_style cross command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cross
|
||||
|
||||
@ -15,7 +15,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style cross
|
||||
angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0
|
||||
@ -26,13 +26,14 @@ Description
|
||||
The *cross* angle style uses a potential that couples the bond stretches of
|
||||
a bend with the angle stretch of that bend:
|
||||
|
||||
.. image:: Eqs/angle_cross.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where r12,0 is the rest value of the bond length between atom 1 and 2,
|
||||
r32,0 is the rest value of the bond length between atom 2 and 2,
|
||||
and theta0 is the rest value of the angle. KSS is the force constant of
|
||||
the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants
|
||||
E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
|
||||
|
||||
where :math:`r_{12,0}` is the rest value of the bond length between atom 1 and 2,
|
||||
:math:`r_{32,0}` is the rest value of the bond length between atom 3 and 2,
|
||||
and :math:`\theta_0` is the rest value of the angle. :math:`K_{SS}` is the force constant of
|
||||
the bond stretch-bond stretch term and :math:`K_{BS0}` and :math:`K_{BS1}` are the force constants
|
||||
of the bond stretch-angle stretch terms.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
@ -40,15 +41,15 @@ The following coefficients must be defined for each angle type via the
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* KSS (energy/distance\^2)
|
||||
* KBS0 (energy/distance/rad)
|
||||
* KBS1 (energy/distance/rad)
|
||||
* r12,0 (distance)
|
||||
* r32,0 (distance)
|
||||
* theta0 (degrees)
|
||||
* :math:`K_{SS}` (energy/distance\^2)
|
||||
* :math:`K_{BS0}` (energy/distance/rad)
|
||||
* :math:`K_{BS1}` (energy/distance/rad)
|
||||
* :math:`r_{12,0}` (distance)
|
||||
* :math:`r_{32,0}` (distance)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of KBS0 and KBS1 are in energy/distance/radian.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
@ -64,12 +65,3 @@ Related commands
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: angle\_style dipole
|
||||
.. index:: angle_style dipole
|
||||
|
||||
angle\_style dipole command
|
||||
===========================
|
||||
angle_style dipole command
|
||||
==========================
|
||||
|
||||
angle\_style dipole/omp command
|
||||
===============================
|
||||
angle_style dipole/omp command
|
||||
==============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style dipole
|
||||
|
||||
@ -18,7 +18,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style dipole
|
||||
angle_coeff 6 2.1 180.0
|
||||
@ -28,53 +28,63 @@ Description
|
||||
|
||||
The *dipole* angle style is used to control the orientation of a dipolar
|
||||
atom within a molecule :ref:`(Orsi) <Orsi>`. Specifically, the *dipole* angle
|
||||
style restrains the orientation of a point dipole mu\_j (embedded in atom
|
||||
'j') with respect to a reference (bond) vector r\_ij = r\_i - r\_j, where 'i'
|
||||
is another atom of the same molecule (typically, 'i' and 'j' are also
|
||||
covalently bonded).
|
||||
style restrains the orientation of a point dipole :math:`\mu_j` (embedded in atom
|
||||
:math:`j`) with respect to a reference (bond) vector
|
||||
:math:`\vec{r_{ij}} = \vec{r_i} - \vec{r_j}`, where :math:`i` is another atom of
|
||||
the same molecule (typically, :math:`i` and :math:`j` are also covalently bonded).
|
||||
|
||||
It is convenient to define an angle gamma between the 'free' vector mu\_j
|
||||
and the reference (bond) vector r\_ij:
|
||||
It is convenient to define an angle gamma between the 'free' vector :math:`\vec{\mu_j}`
|
||||
and the reference (bond) vector :math:`\vec{r_{ij}}`:
|
||||
|
||||
.. math::
|
||||
|
||||
\cos\gamma = \frac{\vec{\mu_j}\cdot\vec{r_{ij}}}{\mu_j\,r_{ij}}
|
||||
|
||||
.. image:: Eqs/angle_dipole_gamma.jpg
|
||||
:align: center
|
||||
|
||||
The *dipole* angle style uses the potential:
|
||||
|
||||
.. image:: Eqs/angle_dipole_potential.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where K is a rigidity constant and gamma0 is an equilibrium (reference)
|
||||
E = K (\cos\gamma - \cos\gamma_0)^2
|
||||
|
||||
|
||||
where :math:`K` is a rigidity constant and gamma0 is an equilibrium (reference)
|
||||
angle.
|
||||
|
||||
The torque on the dipole can be obtained by differentiating the
|
||||
potential using the 'chain rule' as in appendix C.3 of
|
||||
:ref:`(Allen) <Allen1>`:
|
||||
|
||||
.. image:: Eqs/angle_dipole_torque.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
Example: if gamma0 is set to 0 degrees, the torque generated by
|
||||
\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\, \vec{r_{ij}} \times \vec{\mu_j}
|
||||
|
||||
|
||||
Example: if :math:`\gamma_0` is set to 0 degrees, the torque generated by
|
||||
the potential will tend to align the dipole along the reference
|
||||
direction defined by the (bond) vector r\_ij (in other words, mu\_j is
|
||||
restrained to point towards atom 'i').
|
||||
direction defined by the (bond) vector :math:`\vec{r_{ij}}` (in other words, :math:`\vec{\mu_j}` is
|
||||
restrained to point towards atom :math:`i`).
|
||||
|
||||
The dipolar torque T\_j must be counterbalanced in order to conserve
|
||||
The dipolar torque :math:`\vec{T_j}` must be counterbalanced in order to conserve
|
||||
the local angular momentum. This is achieved via an additional force
|
||||
couple generating a torque equivalent to the opposite of T\_j:
|
||||
couple generating a torque equivalent to the opposite of :math:`\vec{T_j}`:
|
||||
|
||||
.. image:: Eqs/angle_dipole_couple.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where F\_i and F\_j are applied on atoms i and j, respectively.
|
||||
-\vec{T_j} & = \vec{r_{ij}} \times \vec{F_i} \\
|
||||
\vec{F_j} & = -\vec{F_i}
|
||||
|
||||
|
||||
where :math:`\vec{F_i}` and :math:`\vec{F_j}` are applied on atoms :math:`i`
|
||||
and :math:`j`, respectively.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* gamma0 (degrees)
|
||||
* :math:`K` (energy)
|
||||
* :math:`\gamma_0` (degrees)
|
||||
|
||||
|
||||
----------
|
||||
@ -108,17 +118,17 @@ page for more info.
|
||||
|
||||
.. note::
|
||||
|
||||
In the "Angles" section of the data file, the atom ID 'j'
|
||||
In the "Angles" section of the data file, the atom ID :math:`j`
|
||||
defining the direction of the dipole vector to restrain must come
|
||||
before the atom ID of the reference atom 'i'. A third atom ID 'k' must
|
||||
before the atom ID of the reference atom :math:`i`. A third atom ID :math:`k` must
|
||||
also be provided to comply with the requirement of a valid angle
|
||||
definition. This atom ID k should be chosen to be that of an atom
|
||||
bonded to atom 'i' to avoid errors with "lost angle atoms" when running
|
||||
definition. This atom ID :math:`k` should be chosen to be that of an atom
|
||||
bonded to atom :math:`i` to avoid errors with "lost angle atoms" when running
|
||||
in parallel. Since the LAMMPS code checks for valid angle definitions,
|
||||
cannot use the same atom ID of either 'i' or 'j' (this was allowed
|
||||
cannot use the same atom ID of either :math:`i` or :math:`j` (this was allowed
|
||||
and recommended with older LAMMPS versions).
|
||||
|
||||
The "newton" command for intramolecular interactions must be "on"
|
||||
The :doc:`newton <newton>` command for intramolecular interactions must be "on"
|
||||
(which is the default except when using some accelerator packages).
|
||||
|
||||
This angle style should not be used with SHAKE.
|
||||
@ -147,8 +157,3 @@ lipid membranes, PloS ONE 6(12): e28637, 2011.
|
||||
|
||||
**(Allen)** Allen & Tildesley, Computer Simulation of Liquids,
|
||||
Clarendon Press, Oxford, 1987.
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,42 +1,46 @@
|
||||
.. index:: angle\_style fourier
|
||||
.. index:: angle_style fourier
|
||||
|
||||
angle\_style fourier command
|
||||
============================
|
||||
angle_style fourier command
|
||||
===========================
|
||||
|
||||
angle\_style fourier/omp command
|
||||
================================
|
||||
angle_style fourier/omp command
|
||||
===============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style fourier
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
angle\_style fourier
|
||||
angle\_coeff 75.0 1.0 1.0 1.0
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style fourier
|
||||
angle_coeff 75.0 1.0 1.0 1.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *fourier* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_fourier.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ]
|
||||
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* C0 (real)
|
||||
* C1 (real)
|
||||
* C2 (real)
|
||||
* :math:`K` (energy)
|
||||
* :math:`C_0` (real)
|
||||
* :math:`C_1` (real)
|
||||
* :math:`C_2` (real)
|
||||
|
||||
|
||||
----------
|
||||
@ -78,8 +82,3 @@ Related commands
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,41 +1,45 @@
|
||||
.. index:: angle\_style fourier/simple
|
||||
.. index:: angle_style fourier/simple
|
||||
|
||||
angle\_style fourier/simple command
|
||||
===================================
|
||||
angle_style fourier/simple command
|
||||
==================================
|
||||
|
||||
angle\_style fourier/simple/omp command
|
||||
=======================================
|
||||
angle_style fourier/simple/omp command
|
||||
======================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style fourier/simple
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
angle\_style fourier/simple
|
||||
angle\_coeff 100.0 -1.0 1.0
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style fourier/simple
|
||||
angle_coeff 100.0 -1.0 1.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *fourier/simple* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_fourier_simple.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = K [ 1.0 + c \cos ( n \theta) ]
|
||||
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy)
|
||||
* c (real)
|
||||
* n (real)
|
||||
* :math:`K` (energy)
|
||||
* :math:`c` (real)
|
||||
* :math:`n` (real)
|
||||
|
||||
|
||||
----------
|
||||
@ -77,8 +81,3 @@ Related commands
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,22 +1,22 @@
|
||||
.. index:: angle\_style harmonic
|
||||
.. index:: angle_style harmonic
|
||||
|
||||
angle\_style harmonic command
|
||||
=============================
|
||||
angle_style harmonic command
|
||||
============================
|
||||
|
||||
angle\_style harmonic/intel command
|
||||
===================================
|
||||
angle_style harmonic/intel command
|
||||
==================================
|
||||
|
||||
angle\_style harmonic/kk command
|
||||
angle_style harmonic/kk command
|
||||
===============================
|
||||
|
||||
angle_style harmonic/omp command
|
||||
================================
|
||||
|
||||
angle\_style harmonic/omp command
|
||||
=================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style harmonic
|
||||
|
||||
@ -24,7 +24,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style harmonic
|
||||
angle_coeff 1 300.0 107.0
|
||||
@ -34,22 +34,24 @@ Description
|
||||
|
||||
The *harmonic* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_harmonic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
E = K (\theta - \theta_0)^2
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy/radian\^2)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
|
||||
|
||||
----------
|
||||
@ -91,8 +93,3 @@ Related commands
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: angle\_style hybrid
|
||||
.. index:: angle_style hybrid
|
||||
|
||||
angle\_style hybrid command
|
||||
===========================
|
||||
angle_style hybrid command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style hybrid style1 style2 ...
|
||||
|
||||
@ -17,11 +17,11 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style hybrid harmonic cosine
|
||||
angle_coeff 1 harmonic 80.0 30.0
|
||||
angle_coeff 2\* cosine 50.0
|
||||
angle_coeff 2* cosine 50.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -31,19 +31,19 @@ simulation. An angle style is assigned to each angle type. For
|
||||
example, angles in a polymer flow (of angle type 1) could be computed
|
||||
with a *harmonic* potential and angles in the wall boundary (of angle
|
||||
type 2) could be computed with a *cosine* potential. The assignment
|
||||
of angle type to style is made via the :doc:`angle\_coeff <angle_coeff>`
|
||||
of angle type to style is made via the :doc:`angle_coeff <angle_coeff>`
|
||||
command or in the data file.
|
||||
|
||||
In the angle\_coeff commands, the name of an angle style must be added
|
||||
In the :doc:`angle_coeff <angle_coeff>` commands, the name of an angle style must be added
|
||||
after the angle type, with the remaining coefficients being those
|
||||
appropriate to that style. In the example above, the 2 angle\_coeff
|
||||
commands set angles of angle type 1 to be computed with a *harmonic*
|
||||
potential with coefficients 80.0, 30.0 for K, theta0. All other angle
|
||||
types (2-N) are computed with a *cosine* potential with coefficient
|
||||
50.0 for K.
|
||||
potential with coefficients 80.0, 30.0 for :math:`K`, :math:`\theta_0`. All other angle
|
||||
types :math:`(2 - N)` are computed with a *cosine* potential with coefficient
|
||||
50.0 for :math:`K`.
|
||||
|
||||
If angle coefficients are specified in the data file read via the
|
||||
:doc:`read\_data <read_data>` command, then the same rule applies.
|
||||
:doc:`read_data <read_data>` command, then the same rule applies.
|
||||
E.g. "harmonic" or "cosine", must be added after the angle type, for each
|
||||
line in the "Angle Coeffs" section, e.g.
|
||||
|
||||
@ -77,7 +77,7 @@ input script, since BondBond (or BondAngle) coefficients need not be
|
||||
specified at all for angle types that are not *class2*\ .
|
||||
|
||||
An angle style of *none* with no additional coefficients can be used
|
||||
in place of an angle style, either in a input script angle\_coeff
|
||||
in place of an angle style, either in a input script :doc:`angle_coeff <angle_coeff>`
|
||||
command or in the data file, if you desire to turn off interactions
|
||||
for specific angle types.
|
||||
|
||||
@ -95,16 +95,11 @@ for more info.
|
||||
|
||||
Unlike other angle styles, the hybrid angle style does not store angle
|
||||
coefficient info for individual sub-styles in a :doc:`binary restart files <restart>`. Thus when restarting a simulation from a restart
|
||||
file, you need to re-specify angle\_coeff commands.
|
||||
file, you need to re-specify :doc:`angle_coeff <angle_coeff>` commands.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: angle\_style mm3
|
||||
.. index:: angle_style mm3
|
||||
|
||||
angle\_style mm3 command
|
||||
========================
|
||||
angle_style mm3 command
|
||||
=======================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style mm3
|
||||
|
||||
@ -15,7 +15,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style mm3
|
||||
angle_coeff 1 100.0 107.0
|
||||
@ -26,23 +26,25 @@ Description
|
||||
The *mm3* angle style uses the potential that is anharmonic in the angle
|
||||
as defined in :ref:`(Allinger) <mm3-allinger1989>`
|
||||
|
||||
.. image:: Eqs/angle_mm3.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. The anharmonic prefactors have units deg\^(-n), for example
|
||||
-0.014 deg\^(-1), 5.6(10)\^(-5) deg\^(-2), ...
|
||||
E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example
|
||||
:math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ...
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy/radian\^2)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
@ -58,12 +60,3 @@ Related commands
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: angle\_style none
|
||||
.. index:: angle_style none
|
||||
|
||||
angle\_style none command
|
||||
=========================
|
||||
angle_style none command
|
||||
========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style none
|
||||
|
||||
@ -15,7 +15,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style none
|
||||
|
||||
@ -24,23 +24,19 @@ Description
|
||||
|
||||
Using an angle style of none means angle forces and energies are not
|
||||
computed, even if triplets of angle atoms were listed in the data file
|
||||
read by the :doc:`read\_data <read_data>` command.
|
||||
read by the :doc:`read_data <read_data>` command.
|
||||
|
||||
See the :doc:`angle\_style zero <angle_zero>` command for a way to
|
||||
See the :doc:`angle_style zero <angle_zero>` command for a way to
|
||||
calculate angle statistics, but compute no angle interactions.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_style zero <angle_zero>`
|
||||
:doc:`angle_style zero <angle_zero>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: angle\_style quartic
|
||||
.. index:: angle_style quartic
|
||||
|
||||
angle\_style quartic command
|
||||
============================
|
||||
angle_style quartic command
|
||||
===========================
|
||||
|
||||
angle\_style quartic/omp command
|
||||
================================
|
||||
angle_style quartic/omp command
|
||||
===============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style quartic
|
||||
|
||||
@ -18,7 +18,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style quartic
|
||||
angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
|
||||
@ -28,24 +28,26 @@ Description
|
||||
|
||||
The *quartic* angle style uses the potential
|
||||
|
||||
.. image:: Eqs/angle_quartic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle, and K is a
|
||||
prefactor. Note that the usual 1/2 factor is included in K.
|
||||
E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
|
||||
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* theta0 (degrees)
|
||||
* K2 (energy/radian\^2)
|
||||
* K3 (energy/radian\^3)
|
||||
* K4 (energy/radian\^4)
|
||||
* :math:`\theta_0` (degrees)
|
||||
* :math:`K_2` (energy/radian\^2)
|
||||
* :math:`K_3` (energy/radian\^3)
|
||||
* :math:`K_4` (energy/radian\^4)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
|
||||
|
||||
----------
|
||||
@ -87,8 +89,3 @@ Related commands
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: angle\_style sdk
|
||||
.. index:: angle_style sdk
|
||||
|
||||
angle\_style sdk command
|
||||
========================
|
||||
angle_style sdk command
|
||||
=======================
|
||||
|
||||
angle\_style sdk/omp command
|
||||
============================
|
||||
angle_style sdk/omp command
|
||||
===========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style sdk
|
||||
|
||||
@ -20,7 +20,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style sdk
|
||||
angle_coeff 1 300.0 107.0
|
||||
@ -30,25 +30,27 @@ Description
|
||||
|
||||
The *sdk* angle style is a combination of the harmonic angle potential,
|
||||
|
||||
.. image:: Eqs/angle_harmonic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where theta0 is the equilibrium value of the angle and K a prefactor,
|
||||
E = K (\theta - \theta_0)^2
|
||||
|
||||
|
||||
where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a prefactor,
|
||||
with the *repulsive* part of the non-bonded *lj/sdk* pair style
|
||||
between the atoms 1 and 3. This angle potential is intended for
|
||||
coarse grained MD simulations with the CMM parameterization using the
|
||||
:doc:`pair\_style lj/sdk <pair_sdk>`. Relative to the pair\_style
|
||||
*lj/sdk*\ , however, the energy is shifted by *epsilon*\ , to avoid sudden
|
||||
jumps. Note that the usual 1/2 factor is included in K.
|
||||
jumps. Note that the usual 1/2 factor is included in :math:`K`.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above:
|
||||
|
||||
* K (energy/radian\^2)
|
||||
* theta0 (degrees)
|
||||
* :math:`K` (energy/radian\^2)
|
||||
* :math:`\theta_0` (degrees)
|
||||
|
||||
Theta0 is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of K are in energy/radian\^2.
|
||||
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
|
||||
internally; hence the units of :math:`K` are in energy/radian\^2.
|
||||
The also required *lj/sdk* parameters will be extracted automatically
|
||||
from the pair\_style.
|
||||
|
||||
@ -93,8 +95,3 @@ Related commands
|
||||
:doc:`pair\_style lj/sdk/coul/long <pair_sdk>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: angle\_style
|
||||
.. index:: angle_style
|
||||
|
||||
angle\_style command
|
||||
====================
|
||||
angle_style command
|
||||
===================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style style
|
||||
|
||||
@ -17,7 +17,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style harmonic
|
||||
angle_style charmm
|
||||
@ -29,19 +29,19 @@ Description
|
||||
Set the formula(s) LAMMPS uses to compute angle interactions between
|
||||
triplets of atoms, which remain in force for the duration of the
|
||||
simulation. The list of angle triplets is read in by a
|
||||
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>` command
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` command
|
||||
from a data or restart file.
|
||||
|
||||
Hybrid models where angles are computed using different angle
|
||||
potentials can be setup using the *hybrid* angle style.
|
||||
|
||||
The coefficients associated with a angle style can be specified in a
|
||||
data or restart file or via the :doc:`angle\_coeff <angle_coeff>` command.
|
||||
data or restart file or via the :doc:`angle_coeff <angle_coeff>` command.
|
||||
|
||||
All angle potentials store their coefficient data in binary restart
|
||||
files which means angle\_style and :doc:`angle\_coeff <angle_coeff>`
|
||||
files which means angle_style and :doc:`angle_coeff <angle_coeff>`
|
||||
commands do not need to be re-specified in an input script that
|
||||
restarts a simulation. See the :doc:`read\_restart <read_restart>`
|
||||
restarts a simulation. See the :doc:`read_restart <read_restart>`
|
||||
command for details on how to do this. The one exception is that
|
||||
angle\_style *hybrid* only stores the list of sub-styles in the restart
|
||||
file; angle coefficients need to be re-specified.
|
||||
@ -49,7 +49,7 @@ file; angle coefficients need to be re-specified.
|
||||
.. note::
|
||||
|
||||
When both an angle and pair style is defined, the
|
||||
:doc:`special\_bonds <special_bonds>` command often needs to be used to
|
||||
:doc:`special_bonds <special_bonds>` command often needs to be used to
|
||||
turn off (or weight) the pairwise interaction that would otherwise
|
||||
exist between 3 bonded atoms.
|
||||
|
||||
@ -62,11 +62,11 @@ between the 3 atoms in the angle.
|
||||
|
||||
Here is an alphabetic list of angle styles defined in LAMMPS. Click on
|
||||
the style to display the formula it computes and coefficients
|
||||
specified by the associated :doc:`angle\_coeff <angle_coeff>` command.
|
||||
specified by the associated :doc:`angle_coeff <angle_coeff>` command.
|
||||
|
||||
Click on the style to display the formula it computes, any additional
|
||||
arguments specified in the angle\_style command, and coefficients
|
||||
specified by the associated :doc:`angle\_coeff <angle_coeff>` command.
|
||||
specified by the associated :doc:`angle_coeff <angle_coeff>` command.
|
||||
|
||||
There are also additional accelerated pair styles included in the
|
||||
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
|
||||
@ -115,17 +115,12 @@ individual bond potentials tell if it is part of a package.
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: angle\_style table
|
||||
.. index:: angle_style table
|
||||
|
||||
angle\_style table command
|
||||
==========================
|
||||
angle_style table command
|
||||
=========================
|
||||
|
||||
angle\_style table/omp command
|
||||
==============================
|
||||
angle_style table/omp command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style table style N
|
||||
|
||||
@ -21,7 +21,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style table linear 1000
|
||||
angle_coeff 3 file.table ENTRY1
|
||||
@ -31,7 +31,7 @@ Description
|
||||
|
||||
Style *table* creates interpolation tables of length *N* from angle
|
||||
potential and derivative values listed in a file(s) as a function of
|
||||
angle The files are read by the :doc:`angle\_coeff <angle_coeff>`
|
||||
angle The files are read by the :doc:`angle_coeff <angle_coeff>`
|
||||
command.
|
||||
|
||||
The interpolation tables are created by fitting cubic splines to the
|
||||
@ -50,7 +50,7 @@ find the appropriate set of coefficients which are used to evaluate a
|
||||
cubic polynomial which computes the energy or derivative.
|
||||
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle\_coeff <angle_coeff>` command as in the example above.
|
||||
:doc:`angle_coeff <angle_coeff>` command as in the example above.
|
||||
|
||||
* filename
|
||||
* keyword
|
||||
@ -85,13 +85,13 @@ A section begins with a non-blank line whose 1st character is not a
|
||||
between sections. The first line begins with a keyword which
|
||||
identifies the section. The line can contain additional text, but the
|
||||
initial text must match the argument specified in the
|
||||
:doc:`angle\_coeff <angle_coeff>` command. The next line lists (in any
|
||||
:doc:`angle_coeff <angle_coeff>` command. The next line lists (in any
|
||||
order) one or more parameters for the table. Each parameter is a
|
||||
keyword followed by one or more numeric values.
|
||||
|
||||
The parameter "N" is required and its value is the number of table
|
||||
entries that follow. Note that this may be different than the *N*
|
||||
specified in the :doc:`angle\_style table <angle_style>` command. Let
|
||||
specified in the :doc:`angle_style table <angle_style>` command. Let
|
||||
Ntable = *N* in the angle\_style command, and Nfile = "N" in the
|
||||
tabulated file. What LAMMPS does is a preliminary interpolation by
|
||||
creating splines using the Nfile tabulated values as nodal points. It
|
||||
@ -176,11 +176,6 @@ for more info.
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_coeff <angle_coeff>`
|
||||
:doc:`angle_coeff <angle_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: angle\_style zero
|
||||
.. index:: angle_style zero
|
||||
|
||||
angle\_style zero command
|
||||
=========================
|
||||
angle_style zero command
|
||||
========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style zero *nocoeff*
|
||||
|
||||
@ -15,12 +15,12 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
angle_style zero
|
||||
angle_style zero nocoeff
|
||||
angle_coeff \*
|
||||
angle_coeff \* 120.0
|
||||
angle_coeff *
|
||||
angle_coeff * 120.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -32,14 +32,14 @@ other commands.
|
||||
As an example, the :doc:`compute angle/local <compute_angle_local>`
|
||||
command can be used to compute the theta values for the list of
|
||||
triplets of angle atoms listed in the data file read by the
|
||||
:doc:`read\_data <read_data>` command. If no angle style is defined,
|
||||
:doc:`read_data <read_data>` command. If no angle style is defined,
|
||||
this command cannot be used.
|
||||
|
||||
The optional *nocoeff* flag allows to read data files with AngleCoeff
|
||||
section for any angle style. Similarly, any angle\_coeff commands
|
||||
section for any angle style. Similarly, any :doc:`angle_coeff <angle_coeff>` commands
|
||||
will only be checked for the angle type number and the rest ignored.
|
||||
|
||||
Note that the :doc:`angle\_coeff <angle_coeff>` command must be used for
|
||||
Note that the :doc:`angle_coeff <angle_coeff>` command must be used for
|
||||
all angle types. If specified, there can be only one value, which is
|
||||
going to be used to assign an equilibrium angle, e.g. for use with
|
||||
:doc:`fix shake <fix_shake>`.
|
||||
@ -51,11 +51,6 @@ Restrictions
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle\_style none <angle_none>`
|
||||
:doc:`angle_style none <angle_none>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: atom\_modify
|
||||
.. index:: atom_modify
|
||||
|
||||
atom\_modify command
|
||||
====================
|
||||
atom_modify command
|
||||
===================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
atom_modify keyword values ...
|
||||
|
||||
@ -29,7 +29,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
atom_modify map yes
|
||||
atom_modify map hash sort 10000 2.0
|
||||
@ -188,8 +188,3 @@ defined, sorting will be turned off.
|
||||
|
||||
|
||||
**(Meloni)** Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: atom\_style
|
||||
.. index:: atom_style
|
||||
|
||||
atom\_style command
|
||||
===================
|
||||
atom_style command
|
||||
==================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
atom_style style args
|
||||
|
||||
@ -33,7 +33,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
atom_style atomic
|
||||
atom_style bond
|
||||
@ -371,8 +371,3 @@ atom\_style atomic
|
||||
|
||||
**(Grime)** Grime and Voth, to appear in J Chem Theory & Computation
|
||||
(2014).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,19 +1,19 @@
|
||||
.. index:: bond\_style class2
|
||||
.. index:: bond_style class2
|
||||
|
||||
bond\_style class2 command
|
||||
==========================
|
||||
bond_style class2 command
|
||||
=========================
|
||||
|
||||
bond\_style class2/omp command
|
||||
==============================
|
||||
|
||||
bond\_style class2/kk command
|
||||
bond_style class2/omp command
|
||||
=============================
|
||||
|
||||
bond_style class2/kk command
|
||||
============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style class2
|
||||
|
||||
@ -21,7 +21,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style class2
|
||||
bond_coeff 1 1.0 100.0 80.0 80.0
|
||||
@ -31,10 +31,12 @@ Description
|
||||
|
||||
The *class2* bond style uses the potential
|
||||
|
||||
.. image:: Eqs/bond_class2.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where r0 is the equilibrium bond distance.
|
||||
E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
|
||||
|
||||
|
||||
where :math:`r_0` is the equilibrium bond distance.
|
||||
|
||||
See :ref:`(Sun) <bond-Sun>` for a description of the COMPASS class2 force field.
|
||||
|
||||
@ -43,10 +45,10 @@ The following coefficients must be defined for each bond type via the
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* R0 (distance)
|
||||
* K2 (energy/distance\^2)
|
||||
* K3 (energy/distance\^3)
|
||||
* K4 (energy/distance\^4)
|
||||
* :math:`r_0` (distance)
|
||||
* :math:`K_2` (energy/distance\^2)
|
||||
* :math:`K_3` (energy/distance\^3)
|
||||
* :math:`K_4` (energy/distance\^4)
|
||||
|
||||
|
||||
----------
|
||||
@ -98,8 +100,3 @@ Related commands
|
||||
|
||||
|
||||
**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
.. index:: bond\_coeff
|
||||
.. index:: bond_coeff
|
||||
|
||||
bond\_coeff command
|
||||
===================
|
||||
bond_coeff command
|
||||
==================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_coeff N args
|
||||
|
||||
@ -18,11 +18,11 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_coeff 5 80.0 1.2
|
||||
bond_coeff \* 30.0 1.5 1.0 1.0
|
||||
bond_coeff 1\*4 30.0 1.5 1.0 1.0
|
||||
bond_coeff * 30.0 1.5 1.0 1.0
|
||||
bond_coeff 1*4 30.0 1.5 1.0 1.0
|
||||
bond_coeff 1 harmonic 200.0 1.0
|
||||
|
||||
Description
|
||||
@ -47,9 +47,9 @@ for the same bond type. For example, these commands set the coeffs
|
||||
for all bond types, then overwrite the coeffs for just bond type 2:
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_coeff \* 100.0 1.2
|
||||
bond_coeff * 100.0 1.2
|
||||
bond_coeff 2 200.0 1.2
|
||||
|
||||
A line in a data file that specifies bond coefficients uses the exact
|
||||
@ -97,8 +97,3 @@ Related commands
|
||||
:doc:`bond\_style <bond_style>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,22 +1,22 @@
|
||||
.. index:: bond\_style fene
|
||||
.. index:: bond_style fene
|
||||
|
||||
bond\_style fene command
|
||||
========================
|
||||
bond_style fene command
|
||||
=======================
|
||||
|
||||
bond\_style fene/intel command
|
||||
==============================
|
||||
bond_style fene/intel command
|
||||
=============================
|
||||
|
||||
bond\_style fene/kk command
|
||||
bond_style fene/kk command
|
||||
==========================
|
||||
|
||||
bond_style fene/omp command
|
||||
===========================
|
||||
|
||||
bond\_style fene/omp command
|
||||
============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style fene
|
||||
|
||||
@ -24,7 +24,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style fene
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0
|
||||
@ -34,24 +34,26 @@ Description
|
||||
|
||||
The *fene* bond style uses the potential
|
||||
|
||||
.. image:: Eqs/bond_fene.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
|
||||
|
||||
|
||||
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 R0, the maximum extent of the bond. The 2nd
|
||||
term is cutoff at 2\^(1/6) sigma, the minimum of the LJ potential.
|
||||
first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd
|
||||
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
|
||||
:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy/distance\^2)
|
||||
* R0 (distance)
|
||||
* epsilon (energy)
|
||||
* sigma (distance)
|
||||
* :math:`K` (energy/distance\^2)
|
||||
* :math:`R_0` (distance)
|
||||
* :math:`\epsilon` (energy)
|
||||
* :math:`\sigma` (distance)
|
||||
|
||||
|
||||
----------
|
||||
@ -107,8 +109,3 @@ Related commands
|
||||
|
||||
|
||||
**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: bond\_style fene/expand
|
||||
.. index:: bond_style fene/expand
|
||||
|
||||
bond\_style fene/expand command
|
||||
===============================
|
||||
bond_style fene/expand command
|
||||
==============================
|
||||
|
||||
bond\_style fene/expand/omp command
|
||||
===================================
|
||||
bond_style fene/expand/omp command
|
||||
==================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style fene/expand
|
||||
|
||||
@ -18,7 +18,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style fene/expand
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
|
||||
@ -28,29 +28,30 @@ Description
|
||||
|
||||
The *fene/expand* bond style uses the potential
|
||||
|
||||
.. image:: Eqs/bond_fene_expand.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
E = -0.5 K R_0^2 \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + 4 \epsilon \left[ \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^6 \right] + \epsilon
|
||||
|
||||
|
||||
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.
|
||||
|
||||
The *fene/expand* bond style is similar to *fene* except that an extra
|
||||
shift factor of delta (positive or negative) is added to *r* to
|
||||
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 R0 + delta and the 2nd term is cutoff at 2\^(1/6) sigma
|
||||
+ delta.
|
||||
now extends to :math:`R_0 + \Delta` and the 2nd 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
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy/distance\^2)
|
||||
* R0 (distance)
|
||||
* epsilon (energy)
|
||||
* sigma (distance)
|
||||
* delta (distance)
|
||||
* :math:`K` (energy/distance\^2)
|
||||
* :math:`R_0` (distance)
|
||||
* :math:`\epsilon` (energy)
|
||||
* :math:`\sigma` (distance)
|
||||
* :math:`\Delta` (distance)
|
||||
|
||||
|
||||
----------
|
||||
@ -106,8 +107,3 @@ Related commands
|
||||
|
||||
|
||||
**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: bond\_style gromos
|
||||
.. index:: bond_style gromos
|
||||
|
||||
bond\_style gromos command
|
||||
==========================
|
||||
bond_style gromos command
|
||||
=========================
|
||||
|
||||
bond\_style gromos/omp command
|
||||
==============================
|
||||
bond_style gromos/omp command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style gromos
|
||||
|
||||
@ -18,7 +18,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style gromos
|
||||
bond_coeff 5 80.0 1.2
|
||||
@ -28,19 +28,21 @@ Description
|
||||
|
||||
The *gromos* bond style uses the potential
|
||||
|
||||
.. image:: Eqs/bond_gromos.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where r0 is the equilibrium bond distance. Note that the usual 1/4
|
||||
factor is included in K.
|
||||
E = K (r^2 - r_0^2)^2
|
||||
|
||||
|
||||
where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/4
|
||||
factor is included in :math:`K`.
|
||||
|
||||
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
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy/distance\^4)
|
||||
* r0 (distance)
|
||||
* :math:`K` (energy/distance\^4)
|
||||
* :math:`r_0` (distance)
|
||||
|
||||
|
||||
----------
|
||||
@ -82,8 +84,3 @@ Related commands
|
||||
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,22 +1,22 @@
|
||||
.. index:: bond\_style harmonic
|
||||
.. index:: bond_style harmonic
|
||||
|
||||
bond\_style harmonic command
|
||||
============================
|
||||
bond_style harmonic command
|
||||
===========================
|
||||
|
||||
bond\_style harmonic/intel command
|
||||
==================================
|
||||
bond_style harmonic/intel command
|
||||
=================================
|
||||
|
||||
bond\_style harmonic/kk command
|
||||
bond_style harmonic/kk command
|
||||
==============================
|
||||
|
||||
bond_style harmonic/omp command
|
||||
===============================
|
||||
|
||||
bond\_style harmonic/omp command
|
||||
================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style harmonic
|
||||
|
||||
@ -24,7 +24,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 5 80.0 1.2
|
||||
@ -34,19 +34,21 @@ Description
|
||||
|
||||
The *harmonic* bond style uses the potential
|
||||
|
||||
.. image:: Eqs/bond_harmonic.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where r0 is the equilibrium bond distance. Note that the usual 1/2
|
||||
factor is included in K.
|
||||
E = K (r - r_0)^2
|
||||
|
||||
|
||||
where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/2
|
||||
factor is included in :math:`K`.
|
||||
|
||||
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
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* K (energy/distance\^2)
|
||||
* r0 (distance)
|
||||
* :math:`K` (energy/distance\^2)
|
||||
* :math:`r_0` (distance)
|
||||
|
||||
|
||||
----------
|
||||
@ -88,8 +90,3 @@ Related commands
|
||||
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: bond\_style harmonic/shift
|
||||
.. index:: bond_style harmonic/shift
|
||||
|
||||
bond\_style harmonic/shift command
|
||||
==================================
|
||||
bond_style harmonic/shift command
|
||||
=================================
|
||||
|
||||
bond\_style harmonic/shift/omp command
|
||||
======================================
|
||||
bond_style harmonic/shift/omp command
|
||||
=====================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style harmonic/shift
|
||||
|
||||
@ -18,7 +18,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style harmonic/shift
|
||||
bond_coeff 5 10.0 0.5 1.0
|
||||
@ -29,23 +29,25 @@ Description
|
||||
The *harmonic/shift* bond style is a shifted harmonic bond that uses
|
||||
the potential
|
||||
|
||||
.. image:: Eqs/bond_harmonic_shift.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where r0 is the equilibrium bond distance, and rc the critical distance.
|
||||
The potential is -Umin at r0 and zero at rc. The spring constant is
|
||||
k = Umin / [ 2 (r0-rc)\^2].
|
||||
E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
|
||||
|
||||
|
||||
where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance.
|
||||
The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is
|
||||
:math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
|
||||
|
||||
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
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* Umin (energy)
|
||||
* :math:`U_{\text{min}}` (energy)
|
||||
|
||||
* r0 (distance)
|
||||
* :math:`r_0` (distance)
|
||||
|
||||
* rc (distance)
|
||||
* :math:`r_c` (distance)
|
||||
|
||||
|
||||
----------
|
||||
@ -88,8 +90,3 @@ Related commands
|
||||
:doc:`bond\_harmonic <bond_harmonic>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
@ -1,16 +1,16 @@
|
||||
.. index:: bond\_style harmonic/shift/cut
|
||||
.. index:: bond_style harmonic/shift/cut
|
||||
|
||||
bond\_style harmonic/shift/cut command
|
||||
======================================
|
||||
bond_style harmonic/shift/cut command
|
||||
=====================================
|
||||
|
||||
bond\_style harmonic/shift/cut/omp command
|
||||
==========================================
|
||||
bond_style harmonic/shift/cut/omp command
|
||||
=========================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style harmonic/shift/cut
|
||||
|
||||
@ -18,7 +18,7 @@ Examples
|
||||
""""""""
|
||||
|
||||
|
||||
.. parsed-literal::
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
bond_style harmonic/shift/cut
|
||||
bond_coeff 5 10.0 0.5 1.0
|
||||
@ -29,21 +29,23 @@ Description
|
||||
The *harmonic/shift/cut* bond style is a shifted harmonic bond that
|
||||
uses the potential
|
||||
|
||||
.. image:: Eqs/bond_harmonic_shift_cut.jpg
|
||||
:align: center
|
||||
.. math::
|
||||
|
||||
where r0 is the equilibrium bond distance, and rc the critical distance.
|
||||
The bond potential is zero for distances r > rc. The potential is -Umin
|
||||
at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)\^2].
|
||||
E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
|
||||
|
||||
|
||||
where :math:`r_0` is the equilibrium bond distance, and rc the critical distance.
|
||||
The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}`
|
||||
at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
|
||||
|
||||
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
|
||||
the data file or restart files read by the :doc:`read\_data <read_data>`
|
||||
or :doc:`read\_restart <read_restart>` commands:
|
||||
|
||||
* Umin (energy)
|
||||
* r0 (distance)
|
||||
* rc (distance)
|
||||
* :math:`U_{\text{min}}` (energy)
|
||||
* :math:`r_0` (distance)
|
||||
* :math:`r_c` (distance)
|
||||
|
||||
|
||||
----------
|
||||
@ -87,8 +89,3 @@ Related commands
|
||||
:doc:`bond\_harmonic\_shift <bond_harmonic_shift>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Commands_all.html
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user