From d13ec0d09871c794b634970e4d38ca2a44fa985c Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:27:08 -0500 Subject: [PATCH] Update docs: bond_quartic --- doc/src/Eqs/bond_quartic.jpg | Bin 9554 -> 0 bytes doc/src/Eqs/bond_quartic.tex | 11 ---- doc/src/bond_quartic.rst | 64 ++++++++++---------- doc/txt/bond_quartic.txt | 112 ----------------------------------- 4 files changed, 34 insertions(+), 153 deletions(-) delete mode 100644 doc/src/Eqs/bond_quartic.jpg delete mode 100644 doc/src/Eqs/bond_quartic.tex delete mode 100644 doc/txt/bond_quartic.txt diff --git a/doc/src/Eqs/bond_quartic.jpg b/doc/src/Eqs/bond_quartic.jpg deleted file mode 100644 index 9d092883b2ee55c75d9222a41836ed259ec6cc41..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 9554 zcmd6NcTkhT+imD5B}9}O2vw9Oy%!NBAP82P6oJrtks7*mLhsTP6_F;rgeEN@9fZ(3 zgc1UT4goH|`R2~t@4q{D=H9tyXLfdG-`U-F-e=Bxp7ZSWFZk8n>B_^W0nSDkF zAi5cn5R;ISQ<9KV0B)YX8Iys?DeiF6i{4dvMR||QOicQT>&IXQM()>oZmFZ@RW;(O zAz!{$@V?beN*i0co(53+pKCyr^IMB_1hurv1jSWM-{Qg%q?UX^;d&JbQ7WU71pDif{ex z9}b%2e8$_1{IG{zo?$P{Q^o|_MkXpv_P8un<7bM8dtdq12b=$UbvW4 za3x0O6abVLC;+2>E5^~5s%(K%mrXaSysfVRwDKf@-wDLo78SQDv+gdh@|&nQlF zXIAb=ehR(JenA^6yLv~nhee3+COalvZ*{lGT_AN;fBO~M!R=Y((EB2wSHnL2G}u!e z$L%}1cX<0~Ht(5?rz)>o*G!to(Q0m26m`;be4A!A=8lH)>vGD-|2@PgZ|Q6cd|&9s z1&-o`h^%J^`Uq)s~=w1blt79I+Oy4ACH z+5+PB&I$^&uhr;zNz=Wzv*C~Rq2=m`C z)d1F=$*n0O#DBr5gN+TFefHo!9h%0~(GDA%F4a2S8yYp$ zCsonlIuuuP+tD+}?q34=@f5VQ^VoLad4kocaf zjrU#*C@$u<;Ex!C`PR?qg`jE$lD4mc**n&E9@3+;ECP5v=-d4vO!7hM$3

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When monomers with sigma = epsilon = -1.0 are used, the following choice of parameters gives a quartic -potential that looks nearly like the FENE potential: K = 1200, B1 = --0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters -can be specified using the :doc:`bond\_coeff ` command, but -you will need to choose them carefully so they form a suitable bond -potential. +coarse-grained polymer chains. When monomers with :math:`\sigma = \epsilon = 1.0` +are used, the following choice of parameters gives a quartic potential that +looks nearly like the FENE potential: -Rc is the cutoff length at which the bond potential goes smoothly to a -local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks" +.. math:: + + K &= 1200 \\ + B_1 &= -0.55 \\ + B_2 &= 0.25 \\ + R_c &= 1.3 \\ + U_0 &= 34.6878 + +Different parameters can be specified using the :doc:`bond_coeff ` +command, but you will need to choose them carefully so they form a suitable +bond potential. + +:math:`R_c` is the cutoff length at which the bond potential goes smoothly to a +local maximum. If a bond length ever becomes :math:`> R_c`, LAMMPS "breaks" the bond, which means two things. First, the bond potential is turned off by setting its type to 0, and is no longer computed. Second, a pairwise interaction between the two atoms is turned on, since they @@ -75,7 +84,7 @@ Note that when bonds are dumped to a file via the :doc:`dump local ` comma status of broken bonds or permanently delete them, e.g.: -.. parsed-literal:: +.. code-block:: LAMMPS delete_bonds all stats delete_bonds all bond 0 remove @@ -124,8 +133,3 @@ Related commands :doc:`bond\_coeff `, :doc:`delete\_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_quartic.txt b/doc/txt/bond_quartic.txt deleted file mode 100644 index b7b1ee4ce6..0000000000 --- a/doc/txt/bond_quartic.txt +++ /dev/null @@ -1,112 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -bond_style quartic command :h3 -bond_style quartic/omp command :h3 - -[Syntax:] - -bond_style quartic :pre - -[Examples:] - -bond_style quartic -bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 :pre - -[Description:] - -The {quartic} bond style uses the potential - -:c,image(Eqs/bond_quartic.jpg) - -to define a bond that can be broken as the simulation proceeds (e.g. -due to a polymer being stretched). The sigma and epsilon used in the -LJ portion of the formula are both set equal to 1.0 by LAMMPS. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^4) -B1 (distance) -B2 (distance) -Rc (distance) -U0 (energy) :ul - -This potential was constructed to mimic the FENE bond potential for -coarse-grained polymer chains. When monomers with sigma = epsilon = -1.0 are used, the following choice of parameters gives a quartic -potential that looks nearly like the FENE potential: K = 1200, B1 = --0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters -can be specified using the "bond_coeff"_bond_coeff.html command, but -you will need to choose them carefully so they form a suitable bond -potential. - -Rc is the cutoff length at which the bond potential goes smoothly to a -local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks" -the bond, which means two things. First, the bond potential is turned -off by setting its type to 0, and is no longer computed. Second, a -pairwise interaction between the two atoms is turned on, since they -are no longer bonded. - -LAMMPS does the second task via a computational sleight-of-hand. It -subtracts the pairwise interaction as part of the bond computation. -When the bond breaks, the subtraction stops. For this to work, the -pairwise interaction must always be computed by the -"pair_style"_pair_style.html command, whether the bond is broken or -not. This means that "special_bonds"_special_bonds.html must be set -to 1,1,1, as indicated as a restriction below. - -Note that when bonds are dumped to a file via the "dump -local"_dump.html command, bonds with type 0 are not included. The -"delete_bonds"_delete_bonds.html command can also be used to query the -status of broken bonds or permanently delete them, e.g.: - -delete_bonds all stats -delete_bonds all bond 0 remove :pre - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -The {quartic} style requires that "special_bonds"_special_bonds.html -parameters be set to 1,1,1. Three- and four-body interactions (angle, -dihedral, etc) cannot be used with {quartic} bonds. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none