Merge branch 'master' into compute_momentum
This commit is contained in:
Rupert Nash
@ -50,11 +50,11 @@ An alphabetic list of all general LAMMPS commands.
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"dump"_dump.html,
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"dump adios"_dump_adios.html,
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"dump image"_dump_image.html,
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||||
"dump_modify"_dump_modify.html,
|
||||
"dump movie"_dump_image.html,
|
||||
"dump netcdf"_dump_netcdf.html,
|
||||
"dump netcdf/mpiio"_dump_netcdf.html,
|
||||
"dump vtk"_dump_vtk.html,
|
||||
"dump_modify"_dump_modify.html,
|
||||
"dynamical_matrix"_dynamical_matrix.html,
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||||
"echo"_echo.html,
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||||
"fix"_fix.html,
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||||
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@ -222,6 +222,8 @@ OPT.
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"sph/rhosum"_pair_sph_rhosum.html,
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"sph/taitwater"_pair_sph_taitwater.html,
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"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
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"spin/dipole/cut"_pair_spin_dipole.html,
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"spin/dipole/long"_pair_spin_dipole.html,
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"spin/dmi"_pair_spin_dmi.html,
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"spin/exchange"_pair_spin_exchange.html,
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"spin/magelec"_pair_spin_magelec.html,
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15
doc/src/Eqs/angle_class2_p6.tex
Normal file
15
doc/src/Eqs/angle_class2_p6.tex
Normal file
@ -0,0 +1,15 @@
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\documentclass[12pt]{article}
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\pagestyle{empty}
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\begin{document}
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$$
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E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
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$$
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\end{document}
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%%% Local Variables:
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%%% mode: latex
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%%% TeX-master: t
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%%% End:
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||||
15
doc/src/Eqs/angle_cosine_buck6d.tex
Normal file
15
doc/src/Eqs/angle_cosine_buck6d.tex
Normal file
@ -0,0 +1,15 @@
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\documentclass[12pt]{article}
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\pagestyle{empty}
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\begin{document}
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$$
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E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
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$$
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\end{document}
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%%% Local Variables:
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%%% mode: latex
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%%% TeX-master: t
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||||
%%% End:
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||||
15
doc/src/Eqs/improper_inversion_harmonic.tex
Normal file
15
doc/src/Eqs/improper_inversion_harmonic.tex
Normal file
@ -0,0 +1,15 @@
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\documentclass[12pt]{article}
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||||
|
||||
\pagestyle{empty}
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\begin{document}
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|
||||
$$
|
||||
E = K \left(\theta - \theta_0\right)^2
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||||
$$
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||||
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\end{document}
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||||
%%% Local Variables:
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%%% mode: latex
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%%% TeX-master: t
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||||
%%% End:
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||||
18
doc/src/Eqs/pair_agni.tex
Normal file
18
doc/src/Eqs/pair_agni.tex
Normal file
@ -0,0 +1,18 @@
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\documentclass[12pt]{article}
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||||
|
||||
\pagestyle{empty}
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\begin{document}
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||||
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||||
\begin{eqnarray*}
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F_i^u & = & \sum_t^{N_t}\alpha_t \cdot \exp\left[-\frac{\left(d_{i,t}^u\right)^2}{2l^2}\right] \\
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d_{i,t}^u & = & \left|\left| V_i^u(\eta) - V_t^u(\eta) \right|\right| \\
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V_i^u(\eta) & = & \sum_{j \neq i}\frac{r^u_{ij}}{r_{ij}} \cdot e^{-\left(\frac{r_{ij}}{\eta} \right)^2} \cdot f_d\left(r_{ij}\right) \\
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f_d\left(r_{ij}\right) & = & \frac{1}{2} \left[\cos\left(\frac{\pi r_{ij}}{R_c}\right) + 1 \right]
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\end{eqnarray*}
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||||
|
||||
\end{document}
|
||||
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||||
%%% Local Variables:
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||||
%%% mode: latex
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||||
%%% TeX-master: t
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||||
%%% End:
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||||
@ -1,6 +1,7 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
\pagestyle{empty}
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||||
|
||||
\begin{eqnarray*}
|
||||
E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\
|
||||
15
doc/src/Eqs/pair_coul_gauss.tex
Normal file
15
doc/src/Eqs/pair_coul_gauss.tex
Normal file
@ -0,0 +1,15 @@
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\documentclass[12pt]{article}
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||||
|
||||
\pagestyle{empty}
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||||
\begin{document}
|
||||
|
||||
$$
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||||
E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c
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||||
$$
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||||
|
||||
\end{document}
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||||
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||||
%%% Local Variables:
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||||
%%% mode: latex
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%%% TeX-master: t
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||||
%%% End:
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@ -5890,6 +5890,11 @@ The element names in the ADP file do not match those requested. :dd
|
||||
|
||||
The element names in the EAM file do not match those requested. :dd
|
||||
|
||||
{Incorrect format of ... section in data file} :dt
|
||||
|
||||
Number or type of values per line in the given section of the data file
|
||||
is not consistent with the requirements for this section. :dd
|
||||
|
||||
{Incorrect format in COMB potential file} :dt
|
||||
|
||||
Incorrect number of words per line in the potential file. :dd
|
||||
|
||||
@ -15,7 +15,8 @@ Binaries are available for different versions of Linux:
|
||||
"Pre-built Fedora Linux executables"_#fedora
|
||||
"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
|
||||
"Pre-built OpenSuse Linux executables"_#opensuse
|
||||
"Gentoo Linux executable"_#gentoo :all(b)
|
||||
"Gentoo Linux executable"_#gentoo
|
||||
"Arch Linux build-script"_#arch :all(b)
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||||
|
||||
:line
|
||||
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||||
@ -168,3 +169,31 @@ for details.
|
||||
|
||||
Thanks to Nicolas Bock and Christoph Junghans (LANL) for setting up
|
||||
this Gentoo capability.
|
||||
|
||||
:line
|
||||
|
||||
Archlinux build-script :h4,link(arch)
|
||||
|
||||
LAMMPS is available via Arch's unofficial Arch User repository (AUR).
|
||||
|
||||
There are three scripts available, named lammps, lammps-beta and lammps-git.
|
||||
They respectively package the stable, patch and git releases.
|
||||
|
||||
To install, you will need to have the git package installed. You may use
|
||||
any of the above names in-place of lammps.
|
||||
|
||||
$ git clone https://aur.archlinux.org/lammps.git :pre
|
||||
$ cd lammps :pre
|
||||
$ makepkg -s :pre
|
||||
# makepkg -i :pre
|
||||
|
||||
To update, you may repeat the above, or change into the cloned directory,
|
||||
and execute the following, after which, if there are any changes, you may
|
||||
use makepkg as above.
|
||||
|
||||
$ git pull :pre
|
||||
|
||||
Alternatively, you may use an AUR helper to install these packages.
|
||||
|
||||
Note that the AUR provides build-scripts that download the source and
|
||||
the build the package on your machine.
|
||||
|
||||
|
Before Width: | Height: | Size: 21 KiB After Width: | Height: | Size: 21 KiB |
|
Before Width: | Height: | Size: 20 KiB After Width: | Height: | Size: 20 KiB |
@ -1,7 +1,7 @@
|
||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="18 Jun 2019 version">
|
||||
<META NAME="docnumber" CONTENT="19 Jul 2019 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
@ -21,7 +21,7 @@
|
||||
:line
|
||||
|
||||
LAMMPS Documentation :c,h1
|
||||
18 Jun 2019 version :c,h2
|
||||
19 Jul 2019 version :c,h2
|
||||
|
||||
"What is a LAMMPS version?"_Manual_version.html
|
||||
|
||||
|
||||
Binary file not shown.
@ -911,6 +911,8 @@ the usual manner via MD. Various pair, fix, and compute styles.
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||||
|
||||
src/SPIN: filenames -> commands
|
||||
"Howto spins"_Howto_spins.html
|
||||
"pair_style spin/dipole/cut"_pair_spin_dipole.html
|
||||
"pair_style spin/dipole/long"_pair_spin_dipole.html
|
||||
"pair_style spin/dmi"_pair_spin_dmi.html
|
||||
"pair_style spin/exchange"_pair_spin_exchange.html
|
||||
"pair_style spin/magelec"_pair_spin_magelec.html
|
||||
|
||||
@ -171,42 +171,40 @@ The individual style names on the "Commands
|
||||
compute"_Commands_compute.html doc page are followed by one or more of
|
||||
(g,i,k,o,t) to indicate which accelerated styles exist.
|
||||
|
||||
"ackland/atom"_compute_ackland_atom.html -
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||||
"ackland/atom"_compute_ackland_atom.html - determines the local lattice structure based on the Ackland formulation
|
||||
"adf"_compute_adf.html - angular distribution function of triples of atoms
|
||||
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
|
||||
"angle"_compute_angle.html -
|
||||
"angle/local"_compute_angle_local.html -
|
||||
"angle/local"_compute_bond_local.html - theta and energy of each angle
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||||
"angle"_compute_angle.html - energy of each angle sub-style
|
||||
"angle/local"_compute_angle_local.html - theta and energy of each angle
|
||||
"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
|
||||
"basal/atom"_compute_basal_atom.html -
|
||||
"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom
|
||||
"body/local"_compute_body_local.html - attributes of body sub-particles
|
||||
"bond"_compute_bond.html - values computed by a bond style
|
||||
"bond"_compute_bond.html - energy of each bond sub-style
|
||||
"bond/local"_compute_bond_local.html - distance and energy of each bond
|
||||
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
|
||||
"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
|
||||
"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
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||||
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
|
||||
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
|
||||
"cnp/atom"_compute_cnp_atom.html -
|
||||
"cnp/atom"_compute_cnp_atom.html - common neighborhood parameter (CNP) for each atom
|
||||
"com"_compute_com.html - center-of-mass of group of atoms
|
||||
"com/chunk"_compute_com_chunk.html - center-of-mass for each chunk
|
||||
"contact/atom"_compute_contact_atom.html - contact count for each spherical particle
|
||||
"coord/atom"_compute_coord_atom.html - coordination number for each atom
|
||||
"damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom
|
||||
"dihedral"_compute_dihedral.html -
|
||||
"dihedral"_compute_dihedral.html - energy of each dihedral sub-style
|
||||
"dihedral/local"_compute_dihedral_local.html - angle of each dihedral
|
||||
"dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom
|
||||
"dipole/chunk"_compute_dipole_chunk.html -
|
||||
"dipole/chunk"_compute_dipole_chunk.html - dipole vector and total dipole for each chunk
|
||||
"displace/atom"_compute_displace_atom.html - displacement of each atom
|
||||
"dpd"_compute_dpd.html -
|
||||
"dpd/atom"_compute_dpd_atom.html -
|
||||
"edpd/temp/atom"_compute_edpd_temp_atom.html -
|
||||
"entropy/atom"_compute_entropy_atom.html -
|
||||
"edpd/temp/atom"_compute_edpd_temp_atom.html - per-atom temperature for each eDPD particle in a group
|
||||
"entropy/atom"_compute_entropy_atom.html - pair entropy fingerprint of each atom
|
||||
"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
|
||||
"erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies
|
||||
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
|
||||
"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
|
||||
"erotate/sphere/atom"_compute_erotate_sphere_atom.html -
|
||||
"erotate/sphere/atom"_compute_erotate_sphere_atom.html - rotational energy for each spherical particle
|
||||
"event/displace"_compute_event_displace.html - detect event on atom displacement
|
||||
"fep"_compute_fep.html -
|
||||
"force/tally"_compute_tally.html -
|
||||
@ -218,17 +216,17 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
||||
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
|
||||
"heat/flux/tally"_compute_tally.html -
|
||||
"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
|
||||
"improper"_compute_improper.html -
|
||||
"improper"_compute_improper.html - energy of each improper sub-style
|
||||
"improper/local"_compute_improper_local.html - angle of each improper
|
||||
"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
|
||||
"ke"_compute_ke.html - translational kinetic energy
|
||||
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
|
||||
"ke/atom/eff"_compute_ke_atom_eff.html -
|
||||
"ke/eff"_compute_ke_eff.html -
|
||||
"ke/atom/eff"_compute_ke_atom_eff.html - per-atom translational and radial kinetic energy in the electron force field model
|
||||
"ke/eff"_compute_ke_eff.html - kinetic energy of a group of nuclei and electrons in the electron force field model
|
||||
"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies
|
||||
"meso/e/atom"_compute_meso_e_atom.html -
|
||||
"meso/rho/atom"_compute_meso_rho_atom.html -
|
||||
"meso/t/atom"_compute_meso_t_atom.html -
|
||||
"meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
|
||||
"meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
|
||||
"meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
|
||||
"momentum"_compute_momentum.html - translational momentum
|
||||
"msd"_compute_msd.html - mean-squared displacement of group of atoms
|
||||
"msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
|
||||
@ -243,73 +241,72 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
||||
"pe/tally"_compute_tally.html -
|
||||
"plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
|
||||
"pressure"_compute_pressure.html - total pressure and pressure tensor
|
||||
"pressure/cylinder"_compute_pressure_cylinder.html -
|
||||
"pressure/uef"_compute_pressure_uef.html -
|
||||
"pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates
|
||||
"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field
|
||||
"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
|
||||
"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
|
||||
"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
|
||||
"ptm/atom"_compute_ptm_atom.html -
|
||||
"ptm/atom"_compute_ptm_atom.html - determines the local lattice structure based on the Polyhedral Template Matching method
|
||||
"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
|
||||
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
|
||||
"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
|
||||
"reduce/region"_compute_reduce.html - same as compute reduce, within a region
|
||||
"rigid/local"_compute_rigid_local.html - extract rigid body attributes
|
||||
"saed"_compute_saed.html -
|
||||
"saed"_compute_saed.html - electron diffraction intensity on a mesh of reciprocal lattice nodes
|
||||
"slice"_compute_slice.html - extract values from global vector or array
|
||||
"smd/contact/radius"_compute_smd_contact_radius.html -
|
||||
"smd/damage"_compute_smd_damage.html -
|
||||
"smd/damage"_compute_smd_damage.html - damage status of SPH particles in Smooth Mach Dynamics
|
||||
"smd/hourglass/error"_compute_smd_hourglass_error.html -
|
||||
"smd/internal/energy"_compute_smd_internal_energy.html -
|
||||
"smd/plastic/strain"_compute_smd_plastic_strain.html -
|
||||
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html -
|
||||
"smd/rho"_compute_smd_rho.html -
|
||||
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html -
|
||||
"smd/tlsph/dt"_compute_smd_tlsph_dt.html -
|
||||
"smd/internal/energy"_compute_smd_internal_energy.html - per-particle enthalpy in Smooth Mach Dynamics
|
||||
"smd/plastic/strain"_compute_smd_plastic_strain.html - equivalent plastic strain per particle in Smooth Mach Dynamics
|
||||
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - time rate of the equivalent plastic strain in Smooth Mach Dynamics
|
||||
"smd/rho"_compute_smd_rho.html - per-particle mass density in Smooth Mach Dynamics
|
||||
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - deformation gradient in Smooth Mach Dynamics
|
||||
"smd/tlsph/dt"_compute_smd_tlsph_dt.html - CFL-stable time increment per particle in Smooth Mach Dynamics
|
||||
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html -
|
||||
"smd/tlsph/shape"_compute_smd_tlsph_shape.html -
|
||||
"smd/tlsph/strain"_compute_smd_tlsph_strain.html -
|
||||
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html -
|
||||
"smd/tlsph/stress"_compute_smd_tlsph_stress.html -
|
||||
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
|
||||
"smd/tlsph/stress"_compute_smd_tlsph_stress.html - per-particle Cauchy stress tensor for SPH particles
|
||||
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
|
||||
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html -
|
||||
"smd/ulsph/strain"_compute_smd_ulsph_strain.html -
|
||||
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
|
||||
"smd/ulsph/stress"_compute_smd_ulsph_stress.html -
|
||||
"smd/vol"_compute_smd_vol.html -
|
||||
"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
|
||||
"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics
|
||||
"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
|
||||
"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
|
||||
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
|
||||
"spin"_compute_spin.html -
|
||||
"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins
|
||||
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
|
||||
"stress/mop"_compute_stress_mop.html -
|
||||
"stress/mop/profile"_compute_stress_mop.html -
|
||||
"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
|
||||
"stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes
|
||||
"stress/tally"_compute_tally.html -
|
||||
"tdpd/cc/atom"_compute_tdpd_cc_atom.html -
|
||||
"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle
|
||||
"temp"_compute_temp.html - temperature of group of atoms
|
||||
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
|
||||
"temp/body"_compute_temp_body.html - temperature of body particles
|
||||
"temp/chunk"_compute_temp_chunk.html - temperature of each chunk
|
||||
"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
|
||||
"temp/cs"_compute_temp_cs.html -
|
||||
"temp/cs"_compute_temp_cs.html - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other
|
||||
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
|
||||
"temp/deform/eff"_compute_temp_deform_eff.html -
|
||||
"temp/drude"_compute_temp_drude.html -
|
||||
"temp/eff"_compute_temp_eff.html -
|
||||
"temp/deform/eff"_compute_temp_deform_eff.html - temperature excluding box deformation velocity in the electron force field model
|
||||
"temp/drude"_compute_temp_drude.html - temperature of Core-Drude pairs
|
||||
"temp/eff"_compute_temp_eff.html - temperature of a group of nuclei and electrons in the electron force field model
|
||||
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
|
||||
"temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
|
||||
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
|
||||
"temp/region"_compute_temp_region.html - temperature of a region of atoms
|
||||
"temp/region/eff"_compute_temp_region_eff.html -
|
||||
"temp/rotate"_compute_temp_rotate.html -
|
||||
"temp/region/eff"_compute_temp_region_eff.html - temperature of a region of nuclei and electrons in the electron force field model
|
||||
"temp/rotate"_compute_temp_rotate.html - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities
|
||||
"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
|
||||
"temp/uef"_compute_temp_uef.html -
|
||||
"temp/uef"_compute_temp_uef.html - kinetic energy tensor in the reference frame of an applied flow field
|
||||
"ti"_compute_ti.html - thermodynamic integration free energy values
|
||||
"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
|
||||
"vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms
|
||||
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
|
||||
"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom
|
||||
"xrd"_compute_xrd.html - :ul
|
||||
"xrd"_compute_xrd.html - x-ray diffraction intensity on a mesh of reciprocal lattice nodes :ul
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
||||
@ -57,8 +57,7 @@ Boolean expression is FALSE, then no commands are executed.
|
||||
The syntax for Boolean expressions is described below.
|
||||
|
||||
Each command (t1, f1, e1, etc) can be any valid LAMMPS input script
|
||||
command, except an "include"_include.html command, which is not
|
||||
allowed. If the command is more than one word, it must enclosed in
|
||||
command. If the command is more than one word, it must enclosed in
|
||||
quotes, so it will be treated as a single argument, as in the examples
|
||||
above.
|
||||
|
||||
|
||||
@ -27,7 +27,7 @@ The {fourier} improper style uses the following potential:
|
||||
where K is the force constant and omega is the angle between the IL
|
||||
axis and the IJK plane:
|
||||
|
||||
:c,image(Eqs/umbrella.jpg)
|
||||
:c,image(JPG/umbrella.jpg)
|
||||
|
||||
If all parameter (see bellow) is not zero, the all the three possible angles will taken in account.
|
||||
|
||||
|
||||
@ -28,7 +28,7 @@ where K is the force constant and omega is the angle evaluated for
|
||||
all three axis-plane combinations centered around the atom I. For
|
||||
the IL axis and the IJK plane omega looks as follows:
|
||||
|
||||
:c,image(Eqs/umbrella.jpg)
|
||||
:c,image(JPG/umbrella.jpg)
|
||||
|
||||
Note that the {inversion/harmonic} angle term evaluation differs to
|
||||
the "improper_umbrella"_improper_umbrella.html due to the cyclic
|
||||
|
||||
@ -29,7 +29,7 @@ commonly referred to as a classic inversion and used in the
|
||||
where K is the force constant and omega is the angle between the IL
|
||||
axis and the IJK plane:
|
||||
|
||||
:c,image(Eqs/umbrella.jpg)
|
||||
:c,image(JPG/umbrella.jpg)
|
||||
|
||||
If omega0 = 0 the potential term has a minimum for the planar
|
||||
structure. Otherwise it has two minima at +/- omega0, with a barrier
|
||||
|
||||
@ -648,6 +648,7 @@ pair_sph_lj.html
|
||||
pair_sph_rhosum.html
|
||||
pair_sph_taitwater.html
|
||||
pair_sph_taitwater_morris.html
|
||||
pair_spin_dipole.html
|
||||
pair_spin_dmi.html
|
||||
pair_spin_exchange.html
|
||||
pair_spin_magelec.html
|
||||
|
||||
@ -155,7 +155,7 @@ All of the lj/class2 pair styles write their information to "binary
|
||||
restart files"_restart.html, so pair_style and pair_coeff commands do
|
||||
not need to be specified in an input script that reads a restart file.
|
||||
|
||||
Only the {lj/class2} pair style support the use of the
|
||||
Only the {lj/class2} and {lj/class2/coul/long} pair styles support the use of the
|
||||
{inner}, {middle}, and {outer} keywords of the "run_style
|
||||
respa"_run_style.html command, meaning the pairwise forces can be
|
||||
partitioned by distance at different levels of the rRESPA hierarchy.
|
||||
|
||||
@ -46,7 +46,7 @@ Here, {r} is the radial distance between the donor (D) and acceptor
|
||||
(A) atoms and {theta} is the bond angle between the acceptor, the
|
||||
hydrogen (H) and the donor atoms:
|
||||
|
||||
:c,image(Eqs/dreiding_hbond.jpg)
|
||||
:c,image(JPG/dreiding_hbond.jpg)
|
||||
|
||||
These 3-body interactions can be defined for pairs of acceptor and
|
||||
donor atoms, based on atom types. For each donor/acceptor atom pair,
|
||||
|
||||
@ -147,7 +147,8 @@ asub = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre
|
||||
|
||||
The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
|
||||
standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b
|
||||
parameters are the standard beta parameters). The rozero parameter is
|
||||
parameters are the standard beta parameters). Note that only parameters
|
||||
normalized to t0 = 1.0 are supported. The rozero parameter is
|
||||
an element-dependent density scaling that weights the reference
|
||||
background density (see e.g. equation 4.5 in "(Gullet)"_#Gullet) and
|
||||
is typically 1.0 for single-element systems. The ibar parameter
|
||||
|
||||
@ -13,7 +13,8 @@ pair_modify command :h3
|
||||
pair_modify keyword values ... :pre
|
||||
|
||||
one or more keyword/value pairs may be listed :ulb,l
|
||||
keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or {tabinner/disp} or {tail} or {compute} :l
|
||||
keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner}
|
||||
or {tabinner/disp} or {tail} or {compute} or {nofdotr} :l
|
||||
{pair} values = sub-style N {special} which wt1 wt2 wt3
|
||||
or sub-style N {compute/tally} flag
|
||||
sub-style = sub-style of "pair hybrid"_pair_hybrid.html
|
||||
@ -33,7 +34,8 @@ keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or
|
||||
{tabinner/disp} value = cutoff
|
||||
cutoff = inner cutoff at which to begin table (distance units)
|
||||
{tail} value = {yes} or {no}
|
||||
{compute} value = {yes} or {no} :pre
|
||||
{compute} value = {yes} or {no}
|
||||
{nofdotr} :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
@ -212,6 +214,10 @@ a pair style will not work, because the
|
||||
"kspace_style"_kspace_style.html command requires a Kspace-compatible
|
||||
pair style be defined.
|
||||
|
||||
The {nofdotr} keyword allows to disable an optimization that computes
|
||||
the global stress tensor from the total forces and atom positions rather
|
||||
than from summing forces between individual pairs of atoms.
|
||||
|
||||
:line
|
||||
|
||||
The {special} keyword allows to override the 1-2, 1-3, and 1-4
|
||||
|
||||
@ -23,9 +23,11 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs
|
||||
style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
|
||||
args = list of arguments for these particular styles :ul
|
||||
|
||||
{oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
{oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
xi = temperature-independent coefficient in stacking strength
|
||||
kappa = coefficient of linear temperature dependence in stacking strength
|
||||
{oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
|
||||
@ -34,7 +36,7 @@ args = list of arguments for these particular styles :ul
|
||||
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
@ -62,7 +64,7 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty
|
||||
{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
|
||||
"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)
|
||||
Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
|
||||
and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
|
||||
When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
|
||||
or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
|
||||
@ -24,10 +24,12 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/
|
||||
style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
|
||||
args = list of arguments for these particular styles :ul
|
||||
|
||||
{oxdna2/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
{oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
{oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
xi = temperature-independent coefficient in stacking strength
|
||||
kappa = coefficient of linear temperature dependence in stacking strength
|
||||
{oxdna2/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
|
||||
{oxdna2/dh} args = T rhos qeff
|
||||
@ -39,7 +41,7 @@ args = list of arguments for these particular styles :ul
|
||||
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
@ -68,8 +70,8 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st
|
||||
{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
|
||||
"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),
|
||||
the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients
|
||||
Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
|
||||
the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three coefficients
|
||||
after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
|
||||
e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
||||
@ -81,9 +81,3 @@ currently supported.
|
||||
"fix nve/spin"_fix_nve_spin.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Allen2)
|
||||
[(Allen)] Allen and Tildesley, Computer Simulation of Liquids,
|
||||
Clarendon Press, Oxford, 1987.
|
||||
|
||||
@ -284,6 +284,8 @@ accelerated styles exist.
|
||||
"sph/rhosum"_pair_sph_rhosum.html -
|
||||
"sph/taitwater"_pair_sph_taitwater.html -
|
||||
"sph/taitwater/morris"_pair_sph_taitwater_morris.html -
|
||||
"spin/dipole/cut"_pair_spin_dipole.html -
|
||||
"spin/dipole/long"_pair_spin_dipole.html -
|
||||
"spin/dmi"_pair_spin_dmi.html -
|
||||
"spin/exchange"_pair_spin_exchange.html -
|
||||
"spin/magelec"_pair_spin_magelec.html -
|
||||
|
||||
@ -105,6 +105,7 @@ Pair Styles :h1
|
||||
pair_sph_rhosum
|
||||
pair_sph_taitwater
|
||||
pair_sph_taitwater_morris
|
||||
pair_spin_dipole
|
||||
pair_spin_dmi
|
||||
pair_spin_exchange
|
||||
pair_spin_magelec
|
||||
|
||||
@ -565,6 +565,7 @@ molecular: atom-ID molecule-ID atom-type x y z
|
||||
peri: atom-ID atom-type volume density x y z
|
||||
smd: atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z
|
||||
sphere: atom-ID atom-type diameter density x y z
|
||||
spin: atom-ID atom-type sp x y z spx spy spz
|
||||
template: atom-ID molecule-ID template-index template-atom atom-type x y z
|
||||
tri: atom-ID molecule-ID atom-type triangleflag density x y z
|
||||
wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
|
||||
@ -595,6 +596,8 @@ mux,muy,muz = components of dipole moment of atom (dipole units)
|
||||
q = charge on atom (charge units)
|
||||
rho = density (need units) for SPH particles
|
||||
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
|
||||
sp = norm of magnetic spin of atom (in number of Bohr magnetons)
|
||||
spx,spy,spz = components of magnetic spin of atom (adim normalized vector)
|
||||
template-atom = which atom within a template molecule the atom is
|
||||
template-index = which molecule within the molecule template the atom is part of
|
||||
theta = internal temperature of a DPD particle
|
||||
|
||||
Reference in New Issue
Block a user