Merge branch 'master' into package-meamc
This commit is contained in:
Axel Kohlmeyer
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doc/src/Eqs/cnp_cutoff.jpg
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14
doc/src/Eqs/cnp_cutoff.tex
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doc/src/Eqs/cnp_cutoff.tex
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@ -0,0 +1,14 @@
|
||||
\documentclass[12pt,article]{article}
|
||||
|
||||
\usepackage{indentfirst}
|
||||
\usepackage{amsmath}
|
||||
|
||||
\begin{document}
|
||||
|
||||
\begin{eqnarray*}
|
||||
r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
|
||||
r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
|
||||
r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
|
||||
\end{eqnarray*}
|
||||
|
||||
\end{document}
|
||||
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doc/src/Eqs/cnp_cutoff2.jpg
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doc/src/Eqs/cnp_cutoff2.jpg
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12
doc/src/Eqs/cnp_cutoff2.tex
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doc/src/Eqs/cnp_cutoff2.tex
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@ -0,0 +1,12 @@
|
||||
\documentclass[12pt,article]{article}
|
||||
|
||||
\usepackage{indentfirst}
|
||||
\usepackage{amsmath}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
Rc + Rs > 2*{\rm cutoff}
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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doc/src/Eqs/cnp_eq.jpg
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9
doc/src/Eqs/cnp_eq.tex
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9
doc/src/Eqs/cnp_eq.tex
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@ -0,0 +1,9 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}} \vec{R}_{ik} + \vec{R}_{jk} |^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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@ -1,11 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
\begin{eqnarray*}
|
||||
F & = & F_{\mathrm{LJ}}(r) - F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
|
||||
E & = & E_{\mathrm{LJ}}(r) - E_{\mathrm{LJ}}(r_{\mathrm{c}}) + (r - r_{\mathrm{c}}) F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
|
||||
\mathrm{with} \qquad E_{\mathrm{LJ}}(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad \mathrm{and} \qquad F_{\mathrm{LJ}}(r) = - E^\prime_{\mathrm{LJ}}(r)
|
||||
\end{eqnarray*}
|
||||
|
||||
\end{document}
|
||||
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|
Before Width: | Height: | Size: 14 KiB After Width: | Height: | Size: 14 KiB |
@ -717,7 +717,7 @@ package"_Section_start.html#start_3.
|
||||
"phonon"_fix_phonon.html,
|
||||
"pimd"_fix_pimd.html,
|
||||
"qbmsst"_fix_qbmsst.html,
|
||||
"qeq/reax"_fix_qeq_reax.html,
|
||||
"qeq/reax (ko)"_fix_qeq_reax.html,
|
||||
"qmmm"_fix_qmmm.html,
|
||||
"qtb"_fix_qtb.html,
|
||||
"reax/c/bonds"_fix_reax_bonds.html,
|
||||
@ -831,6 +831,7 @@ package"_Section_start.html#start_3.
|
||||
|
||||
"ackland/atom"_compute_ackland_atom.html,
|
||||
"basal/atom"_compute_basal_atom.html,
|
||||
"cnp/atom"_compute_cnp_atom.html,
|
||||
"dpd"_compute_dpd.html,
|
||||
"dpd/atom"_compute_dpd_atom.html,
|
||||
"fep"_compute_fep.html,
|
||||
@ -963,7 +964,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
"lj/expand (gko)"_pair_lj_expand.html,
|
||||
"lj/gromacs (gko)"_pair_gromacs.html,
|
||||
"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
|
||||
"lj/long/coul/long (o)"_pair_lj_long.html,
|
||||
"lj/long/coul/long (io)"_pair_lj_long.html,
|
||||
"lj/long/dipole/long"_pair_dipole.html,
|
||||
"lj/long/tip4p/long"_pair_lj_long.html,
|
||||
"lj/smooth (o)"_pair_lj_smooth.html,
|
||||
@ -1038,7 +1039,6 @@ package"_Section_start.html#start_3.
|
||||
"lj/sdk (gko)"_pair_sdk.html,
|
||||
"lj/sdk/coul/long (go)"_pair_sdk.html,
|
||||
"lj/sdk/coul/msm (o)"_pair_sdk.html,
|
||||
"lj/sf (o)"_pair_lj_sf.html,
|
||||
"meam/c"_pair_meam.html,
|
||||
"meam/spline (o)"_pair_meam_spline.html,
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html,
|
||||
@ -1058,7 +1058,7 @@ package"_Section_start.html#start_3.
|
||||
"oxdna2/excv"_pair_oxdna2.html,
|
||||
"oxdna2/stk"_pair_oxdna2.html,
|
||||
"quip"_pair_quip.html,
|
||||
"reax/c (k)"_pair_reaxc.html,
|
||||
"reax/c (ko)"_pair_reaxc.html,
|
||||
"smd/hertz"_pair_smd_hertz.html,
|
||||
"smd/tlsph"_pair_smd_tlsph.html,
|
||||
"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
|
||||
@ -1226,7 +1226,7 @@ USER-OMP, t = OPT.
|
||||
"msm/cg (o)"_kspace_style.html,
|
||||
"pppm (go)"_kspace_style.html,
|
||||
"pppm/cg (o)"_kspace_style.html,
|
||||
"pppm/disp"_kspace_style.html,
|
||||
"pppm/disp (i)"_kspace_style.html,
|
||||
"pppm/disp/tip4p"_kspace_style.html,
|
||||
"pppm/stagger"_kspace_style.html,
|
||||
"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
|
||||
|
||||
@ -8890,6 +8890,14 @@ This is a requirement to use this potential. :dd
|
||||
|
||||
See the newton command. This is a restriction to use this potential. :dd
|
||||
|
||||
{Pair style vashishta/gpu requires atom IDs} :dt
|
||||
|
||||
This is a requirement to use this potential. :dd
|
||||
|
||||
{Pair style vashishta/gpu requires newton pair off} :dt
|
||||
|
||||
See the newton command. This is a restriction to use this potential. :dd
|
||||
|
||||
{Pair style tersoff/gpu requires atom IDs} :dt
|
||||
|
||||
This is a requirement to use the tersoff/gpu potential. :dd
|
||||
|
||||
@ -1503,7 +1503,7 @@ oxDNA model of Doye, Louis and Ouldridge at the University of Oxford.
|
||||
This includes Langevin-type rigid-body integrators with improved
|
||||
stability.
|
||||
|
||||
[Author:] Oliver Henrich (University of Edinburgh).
|
||||
[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
@ -2028,8 +2028,8 @@ algorithm to formulate single-particle constraint functions
|
||||
g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
|
||||
n = grad(g).
|
||||
|
||||
[Author:] Stefan Paquay (Eindhoven University of Technology (TU/e), The
|
||||
Netherlands)
|
||||
[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The
|
||||
Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
@ -30,8 +30,8 @@ Dihedral Styles: charmm, harmonic, opls :l
|
||||
Fixes: nve, npt, nvt, nvt/sllod :l
|
||||
Improper Styles: cvff, harmonic :l
|
||||
Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
|
||||
charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
|
||||
K-Space Styles: pppm :l
|
||||
charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, sw, tersoff :l
|
||||
K-Space Styles: pppm, pppm/disp :l
|
||||
:ule
|
||||
|
||||
[Speed-ups to expect:]
|
||||
@ -42,62 +42,88 @@ precision mode. Performance improvements are shown compared to
|
||||
LAMMPS {without using other acceleration packages} as these are
|
||||
under active development (and subject to performance changes). The
|
||||
measurements were performed using the input files available in
|
||||
the src/USER-INTEL/TEST directory. These are scalable in size; the
|
||||
results given are with 512K particles (524K for Liquid Crystal).
|
||||
Most of the simulations are standard LAMMPS benchmarks (indicated
|
||||
by the filename extension in parenthesis) with modifications to the
|
||||
run length and to add a warmup run (for use with offload
|
||||
benchmarks).
|
||||
the src/USER-INTEL/TEST directory with the provided run script.
|
||||
These are scalable in size; the results given are with 512K
|
||||
particles (524K for Liquid Crystal). Most of the simulations are
|
||||
standard LAMMPS benchmarks (indicated by the filename extension in
|
||||
parenthesis) with modifications to the run length and to add a
|
||||
warmup run (for use with offload benchmarks).
|
||||
|
||||
:c,image(JPG/user_intel.png)
|
||||
|
||||
Results are speedups obtained on Intel Xeon E5-2697v4 processors
|
||||
(code-named Broadwell) and Intel Xeon Phi 7250 processors
|
||||
(code-named Knights Landing) with "18 Jun 2016" LAMMPS built with
|
||||
Intel Parallel Studio 2016 update 3. Results are with 1 MPI task
|
||||
(code-named Knights Landing) with "June 2017" LAMMPS built with
|
||||
Intel Parallel Studio 2017 update 2. Results are with 1 MPI task
|
||||
per physical core. See {src/USER-INTEL/TEST/README} for the raw
|
||||
simulation rates and instructions to reproduce.
|
||||
|
||||
:line
|
||||
|
||||
[Accuracy and order of operations:]
|
||||
|
||||
In most molecular dynamics software, parallelization parameters
|
||||
(# of MPI, OpenMP, and vectorization) can change the results due
|
||||
to changing the order of operations with finite-precision
|
||||
calculations. The USER-INTEL package is deterministic. This means
|
||||
that the results should be reproducible from run to run with the
|
||||
{same} parallel configurations and when using determinstic
|
||||
libraries or library settings (MPI, OpenMP, FFT). However, there
|
||||
are differences in the USER-INTEL package that can change the
|
||||
order of operations compared to LAMMPS without acceleration:
|
||||
|
||||
Neighbor lists can be created in a different order :ulb,l
|
||||
Bins used for sorting atoms can be oriented differently :l
|
||||
The default stencil order for PPPM is 7. By default, LAMMPS will
|
||||
calculate other PPPM parameters to fit the desired acuracy with
|
||||
this order :l
|
||||
The {newton} setting applies to all atoms, not just atoms shared
|
||||
between MPI tasks :l
|
||||
Vectorization can change the order for adding pairwise forces :l
|
||||
:ule
|
||||
|
||||
The precision mode (described below) used with the USER-INTEL
|
||||
package can change the {accuracy} of the calculations. For the
|
||||
default {mixed} precision option, calculations between pairs or
|
||||
triplets of atoms are performed in single precision, intended to
|
||||
be within the inherent error of MD simulations. All accumulation
|
||||
is performed in double precision to prevent the error from growing
|
||||
with the number of atoms in the simulation. {Single} precision
|
||||
mode should not be used without appropriate validation.
|
||||
|
||||
:line
|
||||
|
||||
[Quick Start for Experienced Users:]
|
||||
|
||||
LAMMPS should be built with the USER-INTEL package installed.
|
||||
Simulations should be run with 1 MPI task per physical {core},
|
||||
not {hardware thread}.
|
||||
|
||||
For Intel Xeon CPUs:
|
||||
|
||||
Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
|
||||
If using {kspace_style pppm} in the input script, add "neigh_modify binsize cutoff" and "kspace_modify diff ad" to the input script for better
|
||||
performance. Cutoff should be roughly the neighbor list cutoff. By
|
||||
default the binsize is half the neighbor list cutoff. :l
|
||||
"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
|
||||
Set the environment variable KMP_BLOCKTIME=0 :l
|
||||
"-pk intel 0 omp $t -sf intel" added to LAMMPS command-line :l
|
||||
$t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
|
||||
For some of the simple 2-body potentials without long-range
|
||||
electrostatics, performance and scalability can be better with
|
||||
the "newton off" setting added to the input script :l
|
||||
If using {kspace_style pppm} in the input script, add
|
||||
"kspace_modify diff ad" for better performance :l
|
||||
:ule
|
||||
|
||||
For Intel Xeon Phi CPUs for simulations without {kspace_style
|
||||
pppm} in the input script :
|
||||
For Intel Xeon Phi CPUs:
|
||||
|
||||
Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
|
||||
Runs should be performed using MCDRAM. :l
|
||||
"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
|
||||
should be added to the LAMMPS command-line. Choice for best
|
||||
performance will depend on the simulation. :l
|
||||
Runs should be performed using MCDRAM. :ulb,l
|
||||
:ule
|
||||
|
||||
For Intel Xeon Phi CPUs for simulations with {kspace_style
|
||||
pppm} in the input script:
|
||||
For simulations using {kspace_style pppm} on Intel CPUs
|
||||
supporting AVX-512:
|
||||
|
||||
Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
|
||||
Runs should be performed using MCDRAM. :l
|
||||
Add "neigh_modify binsize 3" to the input script for better
|
||||
performance. :l
|
||||
Add "kspace_modify diff ad" to the input script for better
|
||||
performance. :l
|
||||
export KMP_AFFINITY=none :l
|
||||
"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
|
||||
-sf intel" added to LAMMPS command-line. Choice for best performance
|
||||
will depend on the simulation. :l
|
||||
Add "kspace_modify diff ad" to the input script :ulb,l
|
||||
The command-line option should be changed to
|
||||
"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
|
||||
threads minus 1. :l
|
||||
Do not use thread affinity (set KMP_AFFINITY=none) :l
|
||||
The "newton off" setting may provide better scalability :l
|
||||
:ule
|
||||
|
||||
For Intel Xeon Phi coprocessors (Offload):
|
||||
@ -169,6 +195,10 @@ cat /proc/cpuinfo :pre
|
||||
|
||||
[Building LAMMPS with the USER-INTEL package:]
|
||||
|
||||
NOTE: See the src/USER-INTEL/README file for additional flags that
|
||||
might be needed for best performance on Intel server processors
|
||||
code-named "Skylake".
|
||||
|
||||
The USER-INTEL package must be installed into the source directory:
|
||||
|
||||
make yes-user-intel :pre
|
||||
@ -322,8 +352,8 @@ follow in the input script.
|
||||
|
||||
NOTE: The USER-INTEL package will perform better with modifications
|
||||
to the input script when "PPPM"_kspace_style.html is used:
|
||||
"kspace_modify diff ad"_kspace_modify.html and "neigh_modify binsize
|
||||
3"_neigh_modify.html should be added to the input script.
|
||||
"kspace_modify diff ad"_kspace_modify.html should be added to the
|
||||
input script.
|
||||
|
||||
Long-Range Thread (LRT) mode is an option to the "package
|
||||
intel"_package.html command that can improve performance when using
|
||||
@ -342,6 +372,10 @@ would normally perform best with "-pk intel 0 omp 4", instead use
|
||||
environment variable "KMP_AFFINITY=none". LRT mode is not supported
|
||||
when using offload.
|
||||
|
||||
NOTE: Changing the "newton"_newton.html setting to off can improve
|
||||
performance and/or scalability for simple 2-body potentials such as
|
||||
lj/cut or when using LRT mode on processors supporting AVX-512.
|
||||
|
||||
Not all styles are supported in the USER-INTEL package. You can mix
|
||||
the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
|
||||
package or the "USER-OMP package"_accelerate_omp.html. Of course,
|
||||
@ -467,7 +501,7 @@ supported.
|
||||
|
||||
Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
|
||||
|
||||
Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l
|
||||
Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l
|
||||
|
||||
Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l
|
||||
:ule
|
||||
|
||||
@ -26,7 +26,7 @@ Define a computation that calculates the CNA (Common Neighbor
|
||||
Analysis) pattern for each atom in the group. In solid-state systems
|
||||
the CNA pattern is a useful measure of the local crystal structure
|
||||
around an atom. The CNA methodology is described in "(Faken)"_#Faken
|
||||
and "(Tsuzuki)"_#Tsuzuki.
|
||||
and "(Tsuzuki)"_#Tsuzuki1.
|
||||
|
||||
Currently, there are five kinds of CNA patterns LAMMPS recognizes:
|
||||
|
||||
@ -93,5 +93,5 @@ above.
|
||||
:link(Faken)
|
||||
[(Faken)] Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
|
||||
|
||||
:link(Tsuzuki)
|
||||
:link(Tsuzuki1)
|
||||
[(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
|
||||
|
||||
111
doc/src/compute_cnp_atom.txt
Normal file
111
doc/src/compute_cnp_atom.txt
Normal file
@ -0,0 +1,111 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
compute cnp/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID cnp/atom cutoff :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
cnp/atom = style name of this compute command
|
||||
cutoff = cutoff distance for nearest neighbors (distance units) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all cnp/atom 3.08 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the Common Neighborhood
|
||||
Parameter (CNP) for each atom in the group. In solid-state systems
|
||||
the CNP is a useful measure of the local crystal structure
|
||||
around an atom and can be used to characterize whether the
|
||||
atom is part of a perfect lattice, a local defect (e.g. a dislocation
|
||||
or stacking fault), or at a surface.
|
||||
|
||||
The value of the CNP parameter will be 0.0 for atoms not in the
|
||||
specified compute group. Note that normally a CNP calculation should
|
||||
only be performed on single component systems.
|
||||
|
||||
This parameter is computed using the following formula from
|
||||
"(Tsuzuki)"_#Tsuzuki2
|
||||
|
||||
:c,image(Eqs/cnp_eq.jpg)
|
||||
|
||||
where the index {j} goes over the {n}i nearest neighbors of atom
|
||||
{i}, and the index {k} goes over the {n}ij common nearest neighbors
|
||||
between atom {i} and atom {j}. Rik and Rjk are the vectors connecting atom
|
||||
{k} to atoms {i} and {j}. The quantity in the double sum is computed
|
||||
for each atom.
|
||||
|
||||
The CNP calculation is sensitive to the specified cutoff value.
|
||||
You should ensure that the appropriate nearest neighbors of an atom are
|
||||
found within the cutoff distance for the presumed crystal structure.
|
||||
E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
|
||||
neighbors for perfect BCC crystals. These formulas can be used to
|
||||
obtain a good cutoff distance:
|
||||
|
||||
:c,image(Eqs/cnp_cutoff.jpg)
|
||||
|
||||
where a is the lattice constant for the crystal structure concerned
|
||||
and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
|
||||
for HCP crystals.
|
||||
|
||||
Also note that since the CNP calculation in LAMMPS uses the neighbors
|
||||
of an owned atom to find the nearest neighbors of a ghost atom, the
|
||||
following relation should also be satisfied:
|
||||
|
||||
:c,image(Eqs/cnp_cutoff2.jpg)
|
||||
|
||||
where Rc is the cutoff distance of the potential, Rs is the skin
|
||||
distance as specified by the "neighbor"_neighbor.html command, and
|
||||
cutoff is the argument used with the compute cnp/atom command. LAMMPS
|
||||
will issue a warning if this is not the case.
|
||||
|
||||
The neighbor list needed to compute this quantity is constructed each
|
||||
time the calculation is performed (e.g. each time a snapshot of atoms
|
||||
is dumped). Thus it can be inefficient to compute/dump this quantity
|
||||
too frequently or to have multiple compute/dump commands, each with a
|
||||
{cnp/atom} style.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a per-atom vector, which can be accessed by
|
||||
any command that uses per-atom values from a compute as input. See
|
||||
"Section 6.15"_Section_howto.html#howto_15 for an overview of
|
||||
LAMMPS output options.
|
||||
|
||||
The per-atom vector values will be real positive numbers. Some typical CNP
|
||||
values:
|
||||
|
||||
FCC lattice = 0.0
|
||||
BCC lattice = 0.0
|
||||
HCP lattice = 4.4 :pre
|
||||
|
||||
FCC (111) surface ~ 13.0
|
||||
FCC (100) surface ~ 26.5
|
||||
FCC dislocation core ~ 11 :pre
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute cna/atom"_compute_cna_atom.html
|
||||
"compute centro/atom"_compute_centro_atom.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Tsuzuki2)
|
||||
[(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
|
||||
@ -17,6 +17,7 @@ Computes :h1
|
||||
compute_chunk_atom
|
||||
compute_cluster_atom
|
||||
compute_cna_atom
|
||||
compute_cnp_atom
|
||||
compute_com
|
||||
compute_com_chunk
|
||||
compute_contact_atom
|
||||
|
||||
@ -16,7 +16,8 @@ dump-ID = ID of dump to modify :ulb,l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
these keywords apply to various dump styles :l
|
||||
keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
|
||||
{append} arg = {yes} or {no}
|
||||
{append} arg = {yes} or {no} or {at} N
|
||||
N = index of frame written upon first dump
|
||||
{buffer} arg = {yes} or {no}
|
||||
{element} args = E1 E2 ... EN, where N = # of atom types
|
||||
E1,...,EN = element name, e.g. C or Fe or Ga
|
||||
@ -41,6 +42,7 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
|
||||
{region} arg = region-ID or "none"
|
||||
{scale} arg = {yes} or {no}
|
||||
{sfactor} arg = coordinate scaling factor (> 0.0)
|
||||
{thermo} arg = {yes} or {no}
|
||||
{tfactor} arg = time scaling factor (> 0.0)
|
||||
{sort} arg = {off} or {id} or N or -N
|
||||
off = no sorting of per-atom lines within a snapshot
|
||||
@ -139,12 +141,13 @@ and {dcd}. It also applies only to text output files, not to binary
|
||||
or gzipped or image/movie files. If specified as {yes}, then dump
|
||||
snapshots are appended to the end of an existing dump file. If
|
||||
specified as {no}, then a new dump file will be created which will
|
||||
overwrite an existing file with the same name. This keyword can only
|
||||
take effect if the dump_modify command is used after the
|
||||
"dump"_dump.html command, but before the first command that causes
|
||||
dump snapshots to be output, e.g. a "run"_run.html or
|
||||
"minimize"_minimize.html command. Once the dump file has been opened,
|
||||
this keyword has no further effect.
|
||||
overwrite an existing file with the same name. If the {at} option is present
|
||||
({netcdf} only), then the frame to append to can be specified. Negative values
|
||||
are counted from the end of the file. This keyword can only take effect if the
|
||||
dump_modify command is used after the "dump"_dump.html command, but before the
|
||||
first command that causes dump snapshots to be output, e.g. a "run"_run.html or
|
||||
"minimize"_minimize.html command. Once the dump file has been opened, this
|
||||
keyword has no further effect.
|
||||
|
||||
:line
|
||||
|
||||
@ -413,6 +416,13 @@ most effective when the typical magnitude of position data is between
|
||||
|
||||
:line
|
||||
|
||||
The {thermo} keyword ({netcdf} only) triggers writing of "thermo"_thermo.html
|
||||
information to the dump file alongside per-atom data. The data included in the
|
||||
dump file is identical to the data specified by
|
||||
"thermo_style"_thermo_style.html.
|
||||
|
||||
:line
|
||||
|
||||
The {region} keyword only applies to the dump {custom}, {cfg},
|
||||
{image}, and {movie} styles. If specified, only atoms in the region
|
||||
will be written to the dump file or included in the image/movie. Only
|
||||
|
||||
@ -24,7 +24,7 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
|
||||
[Examples:]
|
||||
|
||||
dump 1 all netcdf 100 traj.nc type x y z vx vy vz
|
||||
dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press
|
||||
dump_modify 1 append yes at -1 thermo yes
|
||||
dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre
|
||||
|
||||
[Description:]
|
||||
@ -44,7 +44,7 @@ rank.
|
||||
NetCDF files can be directly visualized via the following tools:
|
||||
|
||||
Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
|
||||
all of the above extensions. :ule,b
|
||||
all extensions of this dump style. :ule,b
|
||||
|
||||
VMD (http://www.ks.uiuc.edu/Research/vmd/). :l
|
||||
|
||||
@ -52,15 +52,9 @@ AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
|
||||
contains a NetCDF reader that is not present in the standard
|
||||
distribution of AtomEye. :l,ule
|
||||
|
||||
In addition to per-atom data, global data can be included in the dump
|
||||
file, which are the kinds of values output by the
|
||||
"thermo_style"_thermo_style.html command . See "Section howto
|
||||
6.15"_Section_howto.html#howto_15 for an explanation of per-atom
|
||||
versus global data. The global output written into the dump file can
|
||||
be from computes, fixes, or variables, by prefixing the compute/fix ID
|
||||
or variable name with "c_" or "f_" or "v_" respectively, as in the
|
||||
example above. These global values are specified via the "dump_modify
|
||||
global"_dump_modify.html command.
|
||||
In addition to per-atom data, "thermo"_thermo.html data can be included in the
|
||||
dump file. The data included in the dump file is identical to the data specified
|
||||
by "thermo_style"_thermo_style.html.
|
||||
|
||||
:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
|
||||
:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
|
||||
|
||||
@ -47,7 +47,7 @@ keyword = {scale} or {reset} :l
|
||||
fix 1 all adapt 1 pair soft a 1 1 v_prefactor
|
||||
fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
|
||||
fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
|
||||
fix 1 all adapt 10 atom diameter v_size
|
||||
fix 1 all adapt 10 atom diameter v_size :pre
|
||||
|
||||
variable ramp_up equal "ramp(0.01,0.5)"
|
||||
fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre
|
||||
|
||||
@ -565,8 +565,10 @@ more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
This fix will restore the initial box settings from "binary restart
|
||||
files"_restart.html, which allows the fix to be properly continue
|
||||
deformation, when using the start/stop options of the "run"_run.html
|
||||
command. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various "output
|
||||
commands"_Section_howto.html#howto_15.
|
||||
|
||||
@ -10,68 +10,183 @@ fix neb command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID neb Kspring :pre
|
||||
fix ID group-ID neb Kspring keyword value :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
neb = style name of this fix command
|
||||
Kspring = inter-replica spring constant (force/distance units) :ul
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
neb = style name of this fix command :l
|
||||
Kspring = spring constant for parallel nudging force (force/distance units or force units, see parallel keyword) :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {parallel} or {perp} or {end} :l
|
||||
{parallel} value = {neigh} or {ideal}
|
||||
{neigh} = parallel nudging force based on distance to neighbor replicas (Kspring = force/distance units)
|
||||
{ideal} = parallel nudging force based on interpolated ideal position (Kspring = force units)
|
||||
{perp} value = {Kspring2}
|
||||
{Kspring2} = spring constant for perpendicular nudging force (force/distance units)
|
||||
{end} values = estyle Kspring3
|
||||
{estyle} = {first} or {last} or {last/efirst} or {last/efirst/middle}
|
||||
{first} = apply force to first replica
|
||||
{last} = apply force to last replica
|
||||
{last/efirst} = apply force to last replica and set its target energy to that of first replica
|
||||
{last/efirst/middle} = same as {last/efirst} plus prevent middle replicas having lower energy than first replica
|
||||
{Kspring3} = spring constant for target energy term (1/distance units) :pre,ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 active neb 10.0 :pre
|
||||
fix 1 active neb 10.0
|
||||
fix 2 all neb 1.0 perp 1.0 end last
|
||||
fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0
|
||||
fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Add inter-replica forces to atoms in the group for a multi-replica
|
||||
Add nudging forces to atoms in the group for a multi-replica
|
||||
simulation run via the "neb"_neb.html command to perform a nudged
|
||||
elastic band (NEB) calculation for transition state finding. Hi-level
|
||||
explanations of NEB are given with the "neb"_neb.html command and in
|
||||
"Section 6.5"_Section_howto.html#howto_5 of the manual. The fix
|
||||
neb command must be used with the "neb" command to define how
|
||||
inter-replica forces are computed.
|
||||
elastic band (NEB) calculation for finding the transition state.
|
||||
Hi-level explanations of NEB are given with the "neb"_neb.html command
|
||||
and in "Section_howto 5"_Section_howto.html#howto_5 of the manual.
|
||||
The fix neb command must be used with the "neb" command and defines
|
||||
how inter-replica nudging forces are computed. A NEB calculation is
|
||||
divided in two stages. In the first stage n replicas are relaxed
|
||||
toward a MEP until convergence. In the second stage, the climbing
|
||||
image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the
|
||||
replica having the highest energy relaxes toward the saddle point
|
||||
(i.e. the point of highest energy along the MEP), and a second
|
||||
relaxation is performed.
|
||||
|
||||
Only the N atoms in the fix group experience inter-replica forces.
|
||||
Atoms in the two end-point replicas do not experience these forces,
|
||||
but those in intermediate replicas do. During the initial stage of
|
||||
NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
|
||||
on the atoms of each intermediate replica I is altered, as described
|
||||
in the "(Henkelman1)"_#Henkelman1 paper, to become:
|
||||
A key purpose of the nudging forces is to keep the replicas equally
|
||||
spaced. During the NEB calculation, the 3N-length vector of
|
||||
interatomic force Fi = -Grad(V) for each replica I is altered. For
|
||||
all intermediate replicas (i.e. for 1 < I < N, except the climbing
|
||||
replica) the force vector becomes:
|
||||
|
||||
Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (| Ri+i - Ri | - | Ri - Ri-1 |) That :pre
|
||||
Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fnudge_perp :pre
|
||||
|
||||
Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
|
||||
coordinates of its neighbor replicas. That (t with a hat over it) is
|
||||
the unit "tangent" vector for replica I which is a function of Ri,
|
||||
T' is the unit "tangent" vector for replica I and is a function of Ri,
|
||||
Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
|
||||
roughly in the direction of (Ri+i - Ri-1); see the
|
||||
"(Henkelman1)"_#Henkelman1 paper for details.
|
||||
"(Henkelman1)"_#Henkelman1 paper for details. Ri are the atomic
|
||||
coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its
|
||||
neighbor replicas. The term (Grad(V) dot T') is used to remove the
|
||||
component of the gradient parallel to the path which would tend to
|
||||
distribute the replica unevenly along the path. Fnudge_parallel is an
|
||||
artificial nudging force which is applied only in the tangent
|
||||
direction and which maintains the equal spacing between replicas (see
|
||||
below for more information). Fnudge_perp is an optional artificial
|
||||
spring which is applied in a direction perpendicular to the tangent
|
||||
direction and which prevent the paths from forming acute kinks (see
|
||||
below for more information).
|
||||
|
||||
The first two terms in the above equation are the component of the
|
||||
interatomic forces perpendicular to the tangent vector. The last term
|
||||
is a spring force between replica I and its neighbors, parallel to the
|
||||
tangent vector direction with the specified spring constant {Kspring}.
|
||||
In the second stage of the NEB calculation, the interatomic force Fi
|
||||
for the climbing replica (the replica of highest energy after the
|
||||
first stage) is changed to:
|
||||
|
||||
The effect of the first two terms is to push the atoms of each replica
|
||||
toward the minimum energy path (MEP) of conformational states that
|
||||
transition over the energy barrier. The MEP for an energy barrier is
|
||||
defined as a sequence of 3N-dimensional states which cross the barrier
|
||||
at its saddle point, each of which has a potential energy gradient
|
||||
parallel to the MEP itself.
|
||||
Fi = -Grad(V) + 2 (Grad(V) dot T') T' :pre
|
||||
|
||||
The effect of the last term is to push each replica away from its two
|
||||
neighbors in a direction along the MEP, so that the final set of
|
||||
states are equidistant from each other.
|
||||
and the relaxation procedure is continued to a new converged MEP.
|
||||
|
||||
During the second stage of NEB, the forces on the N atoms in the
|
||||
replica nearest the top of the energy barrier are altered so that it
|
||||
climbs to the top of the barrier and finds the saddle point. The
|
||||
forces on atoms in this replica are described in the
|
||||
"(Henkelman2)"_#Henkelman2 paper, and become:
|
||||
:line
|
||||
|
||||
Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre
|
||||
The keyword {parallel} specifies how the parallel nudging force is
|
||||
computed. With a value of {neigh}, the parallel nudging force is
|
||||
computed as in "(Henkelman1)"_#Henkelman1 by connecting each
|
||||
intermediate replica with the previous and the next image:
|
||||
|
||||
The inter-replica forces for the other replicas are unchanged from the
|
||||
first equation.
|
||||
Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
|
||||
|
||||
Note that in this case the specified {Kspring) is in force/distance
|
||||
units.
|
||||
|
||||
With a value of {ideal}, the spring force is computed as suggested in
|
||||
"(WeinenE)"_#WeinenE :
|
||||
|
||||
Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
|
||||
|
||||
where RD is the "reaction coordinate" see "neb"_neb.html section, and
|
||||
RDideal is the ideal RD for which all the images are equally spaced.
|
||||
I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
|
||||
I is the replica number). The meanDist is the average distance
|
||||
between replicas. Note that in this case the specified {Kspring) is
|
||||
in force units.
|
||||
|
||||
Note that the {ideal} form of nudging can often be more effective at
|
||||
keeping the replicas equally spaced.
|
||||
|
||||
:line
|
||||
|
||||
The keyword {perp} specifies if and how a perpendicual nudging force
|
||||
is computed. It adds a spring force perpendicular to the path in
|
||||
order to prevent the path from becoming too kinky. It can
|
||||
significantly improve the convergence of the NEB calculation when the
|
||||
resolution is poor. I.e. when few replicas are used; see
|
||||
"(Maras)"_#Maras1 for details.
|
||||
|
||||
The perpendicular spring force is given by
|
||||
|
||||
Fnudge_perp = {Kspring2} * F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
|
||||
|
||||
where {Kspring2} is the specified value. F(Ri-1 Ri R+1) is a smooth
|
||||
scalar function of the angle Ri-1 Ri Ri+1. It is equal to 0.0 when
|
||||
the path is straight and is equal to 1 when the angle Ri-1 Ri Ri+1 is
|
||||
acute. F(Ri-1 Ri R+1) is defined in "(Jonsson)"_#Jonsson.
|
||||
|
||||
If {Kspring2} is set to 0.0 (the default) then no perpendicular spring
|
||||
force is added.
|
||||
|
||||
:line
|
||||
|
||||
By default, no additional forces act on the first and last replicas
|
||||
during the NEB relaxation, so these replicas simply relax toward their
|
||||
respective local minima. By using the key word {end}, additional
|
||||
forces can be applied to the first and/or last replicas, to enable
|
||||
them to relax toward a MEP while constraining their energy.
|
||||
|
||||
The interatomic force Fi for the specified replica becomes:
|
||||
|
||||
Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)*Kspring3) T', {when} Grad(V) dot T' < 0
|
||||
Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)*Kspring3) T', {when} Grad(V) dot T' > 0
|
||||
:pre
|
||||
|
||||
where E is the current energy of the replica and ETarget is the target
|
||||
energy. The "spring" constant on the difference in energies is the
|
||||
specified {Kspring3} value.
|
||||
|
||||
When {estyle} is specified as {first}, the force is applied to the
|
||||
first replica. When {estyle} is specified as {last}, the force is
|
||||
applied to the last replica. Note that the {end} keyword can be used
|
||||
twice to add forces to both the first and last replicas.
|
||||
|
||||
For both these {estyle} settings, the target energy {ETarget} is set
|
||||
to the initial energy of the replica (at the start of the NEB
|
||||
calculation).
|
||||
|
||||
If the {estyle} is specified as {last/efirst} or {last/efirst/middle},
|
||||
force is applied to the last replica, but the target energy {ETarget}
|
||||
is continuously set to the energy of the first replica, as it evolves
|
||||
during the NEB relaxation.
|
||||
|
||||
The difference between these two {estyle} options is as follows. When
|
||||
{estyle} is specified as {last/efirst}, no change is made to the
|
||||
inter-replica force applied to the intermediate replicas (neither
|
||||
first or last). If the initial path is too far from the MEP, an
|
||||
intermediate repilica may relax "faster" and reach a lower energy than
|
||||
the last replica. In this case the intermediate replica will be
|
||||
relaxing toward its own local minima. This behavior can be prevented
|
||||
by specifying {estyle} as {last/efirst/middle} which will alter the
|
||||
inter-replica force applied to intermediate replicas by removing the
|
||||
contribution of the gradient to the inter-replica force. This will
|
||||
only be done if a particular intermediate replica has a lower energy
|
||||
than the first replica. This should effectively prevent the
|
||||
intermediate replicas from over-relaxing.
|
||||
|
||||
After converging a NEB calculation using an {estyle} of
|
||||
{last/efirst/middle}, you should check that all intermediate replicas
|
||||
have a larger energy than the first replica. If this is not the case,
|
||||
the path is probably not a MEP.
|
||||
|
||||
Finally, note that if the last replica converges toward a local
|
||||
minimum which has a larger energy than the energy of the first
|
||||
replica, a NEB calculation using an {estyle} of {last/efirst} or
|
||||
{last/efirst/middle} cannot reach final convergence.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
@ -96,7 +211,12 @@ for more info on packages.
|
||||
|
||||
"neb"_neb.html
|
||||
|
||||
[Default:] none
|
||||
[Default:]
|
||||
|
||||
The option defaults are nudge = neigh, perp = 0.0, ends is not
|
||||
specified (no inter-replica force on the end replicas).
|
||||
|
||||
:line
|
||||
|
||||
:link(Henkelman1)
|
||||
[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
|
||||
@ -104,3 +224,15 @@ for more info on packages.
|
||||
:link(Henkelman2)
|
||||
[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
|
||||
9901-9904 (2000).
|
||||
|
||||
:link(WeinenE)
|
||||
[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
|
||||
|
||||
:link(Jonsson)
|
||||
[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum
|
||||
Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti,
|
||||
and Coker World Scientific, Singapore, 1998, p 385.
|
||||
|
||||
:link(Maras1)
|
||||
[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
|
||||
Comp Phys Comm, 205, 13-21 (2016).
|
||||
|
||||
@ -8,17 +8,19 @@
|
||||
|
||||
fix qeq/reax command :h3
|
||||
fix qeq/reax/kk command :h3
|
||||
fix qeq/reax/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params :pre
|
||||
fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
qeq/reax = style name of this fix command
|
||||
Nevery = perform QEq every this many steps
|
||||
cutlo,cuthi = lo and hi cutoff for Taper radius
|
||||
tolerance = precision to which charges will be equilibrated
|
||||
params = reax/c or a filename :ul
|
||||
params = reax/c or a filename
|
||||
args = {dual} (optional) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
@ -59,6 +61,10 @@ potential file, except that eta is defined here as twice the eta value
|
||||
in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
|
||||
of this fix are hard-coded to be A, eV, and electronic charge.
|
||||
|
||||
The optional {dual} keyword allows to perform the optimization
|
||||
of the S and T matrices in parallel. This is only supported for
|
||||
the {qeq/reax/omp} style. Otherwise they are processed separately.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
|
||||
@ -31,11 +31,12 @@ bodystyle = {single} or {molecule} or {group} :l
|
||||
groupID1, groupID2, ... = list of N group IDs :pre
|
||||
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
|
||||
keyword = {langevin} or {reinit} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
|
||||
{langevin} values = Tstart Tstop Tperiod seed
|
||||
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
|
||||
Tdamp = temperature damping parameter (time units)
|
||||
seed = random number seed to use for white noise (positive integer)
|
||||
{reinit} = {yes} or {no}
|
||||
{temp} values = Tstart Tstop Tdamp
|
||||
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
|
||||
Tdamp = temperature damping parameter (time units)
|
||||
@ -68,10 +69,10 @@ keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {coup
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 clump rigid single
|
||||
fix 1 clump rigid single reinit yes
|
||||
fix 1 clump rigid/small molecule
|
||||
fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
|
||||
fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
|
||||
fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0 reinit no
|
||||
fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
|
||||
fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
|
||||
fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
|
||||
@ -87,7 +88,12 @@ means that each timestep the total force and torque on each rigid body
|
||||
is computed as the sum of the forces and torques on its constituent
|
||||
particles. The coordinates, velocities, and orientations of the atoms
|
||||
in each body are then updated so that the body moves and rotates as a
|
||||
single entity.
|
||||
single entity. This is implemented by creating internal data structures
|
||||
for each rigid body and performing time integration on these data
|
||||
structures. Positions, velocities, and orientations of the constituent
|
||||
particles are regenerated from the rigid body data structures in every
|
||||
time step. This restricts which operations and fixes can be applied to
|
||||
rigid bodies. See below for a detailed discussion.
|
||||
|
||||
Examples of large rigid bodies are a colloidal particle, or portions
|
||||
of a biomolecule such as a protein.
|
||||
@ -148,8 +154,9 @@ differences may accumulate to produce divergent trajectories.
|
||||
|
||||
NOTE: You should not update the atoms in rigid bodies via other
|
||||
time-integration fixes (e.g. "fix nve"_fix_nve.html, "fix
|
||||
nvt"_fix_nh.html, "fix npt"_fix_nh.html), or you will be integrating
|
||||
their motion more than once each timestep. When performing a hybrid
|
||||
nvt"_fix_nh.html, "fix npt"_fix_nh.html, "fix move"_fix_move.html),
|
||||
or you will have conflicting updates to positions and velocities
|
||||
resulting in unphysical behavior in most cases. When performing a hybrid
|
||||
simulation with some atoms in rigid bodies, and some not, a separate
|
||||
time integration fix like "fix nve"_fix_nve.html or "fix
|
||||
nvt"_fix_nh.html should be used for the non-rigid particles.
|
||||
@ -165,23 +172,29 @@ setting the force on them to 0.0 (via the "fix
|
||||
setforce"_fix_setforce.html command), and integrating them as usual
|
||||
(e.g. via the "fix nve"_fix_nve.html command).
|
||||
|
||||
NOTE: The aggregate properties of each rigid body are calculated one
|
||||
time at the start of the first simulation run after these fixes are
|
||||
specified. The properties include the position and velocity of the
|
||||
center-of-mass of the body, its moments of inertia, and its angular
|
||||
momentum. This is done using the properties of the constituent atoms
|
||||
of the body at that point in time (or see the {infile} keyword
|
||||
option). Thereafter, changing properties of individual atoms in the
|
||||
body will have no effect on a rigid body's dynamics, unless they
|
||||
affect the "pair_style"_pair_style.html interactions that individual
|
||||
particles are part of. For example, you might think you could
|
||||
displace the atoms in a body or add a large velocity to each atom in a
|
||||
body to make it move in a desired direction before a 2nd run is
|
||||
IMPORTANT NOTE: The aggregate properties of each rigid body are
|
||||
calculated at the start of a simulation run and are maintained in
|
||||
internal data structures. The properties include the position and
|
||||
velocity of the center-of-mass of the body, its moments of inertia, and
|
||||
its angular momentum. This is done using the properties of the
|
||||
constituent atoms of the body at that point in time (or see the {infile}
|
||||
keyword option). Thereafter, changing these properties of individual
|
||||
atoms in the body will have no effect on a rigid body's dynamics, unless
|
||||
they effect any computation of per-atom forces or torques. If the
|
||||
keyword {reinit} is set to {yes} (the default), the rigid body data
|
||||
structures will be recreated at the beginning of each {run} command;
|
||||
if the keyword {reinit} is set to {no}, the rigid body data structures
|
||||
will be built only at the very first {run} command and maintained for
|
||||
as long as the rigid fix is defined. For example, you might think you
|
||||
could displace the atoms in a body or add a large velocity to each atom
|
||||
in a body to make it move in a desired direction before a 2nd run is
|
||||
performed, using the "set"_set.html or
|
||||
"displace_atoms"_displace_atoms.html or "velocity"_velocity.html
|
||||
command. But these commands will not affect the internal attributes
|
||||
of the body, and the position and velocity of individual atoms in the
|
||||
body will be reset when time integration starts.
|
||||
commands. But these commands will not affect the internal attributes
|
||||
of the body unless {reinit} is set to {yes}. With {reinit} set to {no}
|
||||
(or using the {infile} option, which implies {reinit} {no}) the position
|
||||
and velocity of individual atoms in the body will be reset when time
|
||||
integration starts again.
|
||||
|
||||
:line
|
||||
|
||||
@ -401,6 +414,14 @@ couple none :pre
|
||||
|
||||
The keyword/value option pairs are used in the following ways.
|
||||
|
||||
The {reinit} keyword determines, whether the rigid body properties
|
||||
are reinitialized between run commands. With the option {yes} (the
|
||||
default) this is done, with the option {no} this is not done. Turning
|
||||
off the reinitialization can be helpful to protect rigid bodies against
|
||||
unphysical manipulations between runs or when properties cannot be
|
||||
easily recomputed (e.g. when read from a file). When using the {infile}
|
||||
keyword, the {reinit} option is automatically set to {no}.
|
||||
|
||||
The {langevin} and {temp} and {tparam} keywords perform thermostatting
|
||||
of the rigid bodies, altering both their translational and rotational
|
||||
degrees of freedom. What is meant by "temperature" of a collection of
|
||||
@ -778,7 +799,7 @@ exclude, "fix shake"_fix_shake.html
|
||||
|
||||
The option defaults are force * on on on and torque * on on on,
|
||||
meaning all rigid bodies are acted on by center-of-mass force and
|
||||
torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3.
|
||||
torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3, reinit = yes.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -308,7 +308,8 @@ The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
|
||||
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
|
||||
yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
|
||||
(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
|
||||
split = 0, tol = 1.0e-6, and disp/auto = no.
|
||||
split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order =
|
||||
order/disp = 7.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -33,12 +33,16 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/gpu} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/intel} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/kk} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/cg/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/disp/intel} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/tip4p/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/stagger} value = accuracy
|
||||
|
||||
@ -301,6 +301,7 @@ compute_centro_atom.html
|
||||
compute_chunk_atom.html
|
||||
compute_cluster_atom.html
|
||||
compute_cna_atom.html
|
||||
compute_cnp_atom.html
|
||||
compute_com.html
|
||||
compute_com_chunk.html
|
||||
compute_contact_atom.html
|
||||
@ -446,7 +447,6 @@ pair_lj96.html
|
||||
pair_lj_cubic.html
|
||||
pair_lj_expand.html
|
||||
pair_lj_long.html
|
||||
pair_lj_sf.html
|
||||
pair_lj_smooth.html
|
||||
pair_lj_smooth_linear.html
|
||||
pair_lj_soft.html
|
||||
|
||||
@ -24,8 +24,9 @@ to the relevant fixes.
|
||||
{manifold} @ {parameters} @ {equation} @ {description}
|
||||
cylinder @ R @ x^2 + y^2 - R^2 = 0 @ Cylinder along z-axis, axis going through (0,0,0)
|
||||
cylinder_dent @ R l a @ x^2 + y^2 - r(z)^2 = 0, r(x) = R if | z | > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise @ A cylinder with a dent around z = 0
|
||||
dumbbell @ a A B c @ -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell @
|
||||
dumbbell @ a A B c @ -( x^2 + y^2 ) + (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell
|
||||
ellipsoid @ a b c @ (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 @ An ellipsoid
|
||||
gaussian_bump @ A l rc1 rc2 @ if( x < rc1) -z + A * exp( -x^2 / (2 l^2) ); else if( x < rc2 ) -z + a + b*x + c*x^2 + d*x^3; else z @ A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0.
|
||||
plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with normal (a,b,c) going through point (x0,y0,z0)
|
||||
plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x.
|
||||
sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R
|
||||
|
||||
219
doc/src/neb.txt
219
doc/src/neb.txt
@ -10,28 +10,31 @@ neb command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
neb etol ftol N1 N2 Nevery file-style arg :pre
|
||||
neb etol ftol N1 N2 Nevery file-style arg keyword :pre
|
||||
|
||||
etol = stopping tolerance for energy (energy units) :ulb,l
|
||||
ftol = stopping tolerance for force (force units) :l
|
||||
N1 = max # of iterations (timesteps) to run initial NEB :l
|
||||
N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
|
||||
Nevery = print replica energies and reaction coordinates every this many timesteps :l
|
||||
file-style= {final} or {each} or {none} :l
|
||||
file-style = {final} or {each} or {none} :l
|
||||
{final} arg = filename
|
||||
filename = file with initial coords for final replica
|
||||
coords for intermediate replicas are linearly interpolated between first and last replica
|
||||
coords for intermediate replicas are linearly interpolated
|
||||
between first and last replica
|
||||
{each} arg = filename
|
||||
filename = unique filename for each replica (except first) with its initial coords
|
||||
{none} arg = no argument
|
||||
all replicas assumed to already have their initial coords :pre
|
||||
filename = unique filename for each replica (except first)
|
||||
with its initial coords
|
||||
{none} arg = no argument all replicas assumed to already have
|
||||
their initial coords :pre
|
||||
keyword = {verbose}
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
neb 0.1 0.0 1000 500 50 final coords.final
|
||||
neb 0.0 0.001 1000 500 50 each coords.initial.$i
|
||||
neb 0.0 0.001 1000 500 50 none :pre
|
||||
neb 0.0 0.001 1000 500 50 none verbose :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -43,8 +46,8 @@ NEB is a method for finding both the atomic configurations and height
|
||||
of the energy barrier associated with a transition state, e.g. for an
|
||||
atom to perform a diffusive hop from one energy basin to another in a
|
||||
coordinated fashion with its neighbors. The implementation in LAMMPS
|
||||
follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA,
|
||||
"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano3.
|
||||
follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA,
|
||||
"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2.
|
||||
|
||||
Each replica runs on a partition of one or more processors. Processor
|
||||
partitions are defined at run-time using the -partition command-line
|
||||
@ -70,18 +73,17 @@ I.e. the simulation domain, the number of atoms, the interaction
|
||||
potentials, and the starting configuration when the neb command is
|
||||
issued should be the same for every replica.
|
||||
|
||||
In a NEB calculation each atom in a replica is connected to the same
|
||||
atom in adjacent replicas by springs, which induce inter-replica
|
||||
forces. These forces are imposed by the "fix neb"_fix_neb.html
|
||||
command, which must be used in conjunction with the neb command. The
|
||||
group used to define the fix neb command defines the NEB atoms which
|
||||
are the only ones that inter-replica springs are applied to. If the
|
||||
group does not include all atoms, then non-NEB atoms have no
|
||||
inter-replica springs and the forces they feel and their motion is
|
||||
computed in the usual way due only to other atoms within their
|
||||
replica. Conceptually, the non-NEB atoms provide a background force
|
||||
field for the NEB atoms. They can be allowed to move during the NEB
|
||||
minimization procedure (which will typically induce different
|
||||
In a NEB calculation each replica is connected to other replicas by
|
||||
inter-replica nudging forces. These forces are imposed by the "fix
|
||||
neb"_fix_neb.html command, which must be used in conjunction with the
|
||||
neb command. The group used to define the fix neb command defines the
|
||||
NEB atoms which are the only ones that inter-replica springs are
|
||||
applied to. If the group does not include all atoms, then non-NEB
|
||||
atoms have no inter-replica springs and the forces they feel and their
|
||||
motion is computed in the usual way due only to other atoms within
|
||||
their replica. Conceptually, the non-NEB atoms provide a background
|
||||
force field for the NEB atoms. They can be allowed to move during the
|
||||
NEB minimization procedure (which will typically induce different
|
||||
coordinates for non-NEB atoms in different replicas), or held fixed
|
||||
using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
|
||||
Note that the "partition"_partition.html command can be used to invoke
|
||||
@ -93,33 +95,18 @@ specified in different manners via the {file-style} setting, as
|
||||
discussed below. Only atoms whose initial coordinates should differ
|
||||
from the current configuration need be specified.
|
||||
|
||||
Conceptually, the initial configuration for the first replica should
|
||||
be a state with all the atoms (NEB and non-NEB) having coordinates on
|
||||
one side of the energy barrier. A perfect energy minimum is not
|
||||
required, since atoms in the first replica experience no spring forces
|
||||
from the 2nd replica. Thus the damped dynamics minimization will
|
||||
drive the first replica to an energy minimum if it is not already
|
||||
there. However, you will typically get better convergence if the
|
||||
initial state is already at a minimum. For example, for a system with
|
||||
a free surface, the surface should be fully relaxed before attempting
|
||||
a NEB calculation.
|
||||
|
||||
Likewise, the initial configuration of the final replica should be a
|
||||
state with all the atoms (NEB and non-NEB) on the other side of the
|
||||
energy barrier. Again, a perfect energy minimum is not required,
|
||||
since the atoms in the last replica also experience no spring forces
|
||||
from the next-to-last replica, and thus the damped dynamics
|
||||
minimization will drive it to an energy minimum.
|
||||
Conceptually, the initial and final configurations for the first
|
||||
replica should be states on either side of an energy barrier.
|
||||
|
||||
As explained below, the initial configurations of intermediate
|
||||
replicas can be atomic coordinates interpolated in a linear fashion
|
||||
between the first and last replicas. This is often adequate state for
|
||||
between the first and last replicas. This is often adequate for
|
||||
simple transitions. For more complex transitions, it may lead to slow
|
||||
convergence or even bad results if the minimum energy path (MEP, see
|
||||
below) of states over the barrier cannot be correctly converged to
|
||||
from such an initial configuration. In this case, you will want to
|
||||
generate initial states for the intermediate replicas that are
|
||||
geometrically closer to the MEP and read them in.
|
||||
from such an initial path. In this case, you will want to generate
|
||||
initial states for the intermediate replicas that are geometrically
|
||||
closer to the MEP and read them in.
|
||||
|
||||
:line
|
||||
|
||||
@ -135,10 +122,11 @@ is assigned to be a fraction of the distance. E.g. if there are 10
|
||||
replicas, the 2nd replica will assign a position that is 10% of the
|
||||
distance along a line between the starting and final point, and the
|
||||
9th replica will assign a position that is 90% of the distance along
|
||||
the line. Note that this procedure to produce consistent coordinates
|
||||
across all the replicas, the current coordinates need to be the same
|
||||
in all replicas. LAMMPS does not check for this, but invalid initial
|
||||
configurations will likely result if it is not the case.
|
||||
the line. Note that for this procedure to produce consistent
|
||||
coordinates across all the replicas, the current coordinates need to
|
||||
be the same in all replicas. LAMMPS does not check for this, but
|
||||
invalid initial configurations will likely result if it is not the
|
||||
case.
|
||||
|
||||
NOTE: The "distance" between the starting and final point is
|
||||
calculated in a minimum-image sense for a periodic simulation box.
|
||||
@ -150,8 +138,8 @@ interpolation is outside the periodic box, the atom will be wrapped
|
||||
back into the box when the NEB calculation begins.
|
||||
|
||||
For a {file-style} setting of {each}, a filename is specified which is
|
||||
assumed to be unique to each replica. This can be done by
|
||||
using a variable in the filename, e.g.
|
||||
assumed to be unique to each replica. This can be done by using a
|
||||
variable in the filename, e.g.
|
||||
|
||||
variable i equal part
|
||||
neb 0.0 0.001 1000 500 50 each coords.initial.$i :pre
|
||||
@ -198,11 +186,10 @@ The minimizer tolerances for energy and force are set by {etol} and
|
||||
A non-zero {etol} means that the NEB calculation will terminate if the
|
||||
energy criterion is met by every replica. The energies being compared
|
||||
to {etol} do not include any contribution from the inter-replica
|
||||
forces, since these are non-conservative. A non-zero {ftol} means
|
||||
that the NEB calculation will terminate if the force criterion is met
|
||||
by every replica. The forces being compared to {ftol} include the
|
||||
inter-replica forces between an atom and its images in adjacent
|
||||
replicas.
|
||||
nudging forces, since these are non-conservative. A non-zero {ftol}
|
||||
means that the NEB calculation will terminate if the force criterion
|
||||
is met by every replica. The forces being compared to {ftol} include
|
||||
the inter-replica nudging forces.
|
||||
|
||||
The maximum number of iterations in each stage is set by {N1} and
|
||||
{N2}. These are effectively timestep counts since each iteration of
|
||||
@ -220,27 +207,27 @@ finding a good energy barrier. {N1} and {N2} must both be multiples
|
||||
of {Nevery}.
|
||||
|
||||
In the first stage of NEB, the set of replicas should converge toward
|
||||
the minimum energy path (MEP) of conformational states that transition
|
||||
over the barrier. The MEP for a barrier is defined as a sequence of
|
||||
3N-dimensional states that cross the barrier at its saddle point, each
|
||||
of which has a potential energy gradient parallel to the MEP itself.
|
||||
The replica states will also be roughly equally spaced along the MEP
|
||||
due to the inter-replica spring force added by the "fix
|
||||
neb"_fix_neb.html command.
|
||||
a minimum energy path (MEP) of conformational states that transition
|
||||
over a barrier. The MEP for a transition is defined as a sequence of
|
||||
3N-dimensional states, each of which has a potential energy gradient
|
||||
parallel to the MEP itself. The configuration of highest energy along
|
||||
a MEP corresponds to a saddle point. The replica states will also be
|
||||
roughly equally spaced along the MEP due to the inter-replica nugding
|
||||
force added by the "fix neb"_fix_neb.html command.
|
||||
|
||||
In the second stage of NEB, the replica with the highest energy
|
||||
is selected and the inter-replica forces on it are converted to a
|
||||
force that drives its atom coordinates to the top or saddle point of
|
||||
the barrier, via the barrier-climbing calculation described in
|
||||
In the second stage of NEB, the replica with the highest energy is
|
||||
selected and the inter-replica forces on it are converted to a force
|
||||
that drives its atom coordinates to the top or saddle point of the
|
||||
barrier, via the barrier-climbing calculation described in
|
||||
"(HenkelmanB)"_#HenkelmanB. As before, the other replicas rearrange
|
||||
themselves along the MEP so as to be roughly equally spaced.
|
||||
|
||||
When both stages are complete, if the NEB calculation was successful,
|
||||
one of the replicas should be an atomic configuration at the top or
|
||||
saddle point of the barrier, the potential energies for the set of
|
||||
replicas should represent the energy profile of the barrier along the
|
||||
MEP, and the configurations of the replicas should be a sequence of
|
||||
configurations along the MEP.
|
||||
the configurations of the replicas should be along (close to) the MEP
|
||||
and the replica with the highest energy should be an atomic
|
||||
configuration at (close to) the saddle point of the transition. The
|
||||
potential energies for the set of replicas represents the energy
|
||||
profile of the transition along the MEP.
|
||||
|
||||
:line
|
||||
|
||||
@ -284,9 +271,9 @@ ID2 x2 y2 z2
|
||||
...
|
||||
IDN xN yN zN :pre
|
||||
|
||||
The fields are the atom ID, followed by the x,y,z coordinates.
|
||||
The lines can be listed in any order. Additional trailing information
|
||||
on the line is OK, such as a comment.
|
||||
The fields are the atom ID, followed by the x,y,z coordinates. The
|
||||
lines can be listed in any order. Additional trailing information on
|
||||
the line is OK, such as a comment.
|
||||
|
||||
Note that for a typical NEB calculation you do not need to specify
|
||||
initial coordinates for very many atoms to produce differing starting
|
||||
@ -310,38 +297,54 @@ this case), the print-out to the screen and master log.lammps file
|
||||
contains a line of output, printed once every {Nevery} timesteps. It
|
||||
contains the timestep, the maximum force per replica, the maximum
|
||||
force per atom (in any replica), potential gradients in the initial,
|
||||
final, and climbing replicas, the forward and backward energy barriers,
|
||||
the total reaction coordinate (RDT), and the normalized reaction
|
||||
coordinate and potential energy of each replica.
|
||||
final, and climbing replicas, the forward and backward energy
|
||||
barriers, the total reaction coordinate (RDT), and the normalized
|
||||
reaction coordinate and potential energy of each replica.
|
||||
|
||||
The "maximum force per replica" is
|
||||
the two-norm of the 3N-length force vector for the atoms in each
|
||||
replica, maximized across replicas, which is what the {ftol} setting
|
||||
is checking against. In this case, N is all the atoms in each
|
||||
replica. The "maximum force per atom" is the maximum force component
|
||||
of any atom in any replica. The potential gradients are the two-norm
|
||||
of the 3N-length force vector solely due to the interaction potential i.e.
|
||||
without adding in inter-replica forces. Note that inter-replica forces
|
||||
are zero in the initial and final replicas, and only affect
|
||||
the direction in the climbing replica. For this reason, the "maximum
|
||||
force per replica" is often equal to the potential gradient in the
|
||||
climbing replica. In the first stage of NEB, there is no climbing
|
||||
replica, and so the potential gradient in the highest energy replica
|
||||
is reported, since this replica will become the climbing replica
|
||||
in the second stage of NEB.
|
||||
The "maximum force per replica" is the two-norm of the 3N-length force
|
||||
vector for the atoms in each replica, maximized across replicas, which
|
||||
is what the {ftol} setting is checking against. In this case, N is
|
||||
all the atoms in each replica. The "maximum force per atom" is the
|
||||
maximum force component of any atom in any replica. The potential
|
||||
gradients are the two-norm of the 3N-length force vector solely due to
|
||||
the interaction potential i.e. without adding in inter-replica
|
||||
forces.
|
||||
|
||||
The "reaction coordinate" (RD) for each
|
||||
replica is the two-norm of the 3N-length vector of distances between
|
||||
its atoms and the preceding replica's atoms, added to the RD of the
|
||||
preceding replica. The RD of the first replica RD1 = 0.0;
|
||||
the RD of the final replica RDN = RDT, the total reaction coordinate.
|
||||
The normalized RDs are divided by RDT,
|
||||
so that they form a monotonically increasing sequence
|
||||
from zero to one. When computing RD, N only includes the atoms
|
||||
being operated on by the fix neb command.
|
||||
The "reaction coordinate" (RD) for each replica is the two-norm of the
|
||||
3N-length vector of distances between its atoms and the preceding
|
||||
replica's atoms, added to the RD of the preceding replica. The RD of
|
||||
the first replica RD1 = 0.0; the RD of the final replica RDN = RDT,
|
||||
the total reaction coordinate. The normalized RDs are divided by RDT,
|
||||
so that they form a monotonically increasing sequence from zero to
|
||||
one. When computing RD, N only includes the atoms being operated on by
|
||||
the fix neb command.
|
||||
|
||||
The forward (reverse) energy barrier is the potential energy of the highest
|
||||
replica minus the energy of the first (last) replica.
|
||||
The forward (reverse) energy barrier is the potential energy of the
|
||||
highest replica minus the energy of the first (last) replica.
|
||||
|
||||
Supplementary informations for all replicas can be printed out to the
|
||||
screen and master log.lammps file by adding the verbose keyword. These
|
||||
informations include the following. The "path angle" (pathangle) for
|
||||
the replica i which is the angle between the 3N-length vectors (Ri-1 -
|
||||
Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
|
||||
i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
|
||||
aligned. "angletangrad" is the angle between the 3N-length tangent
|
||||
vector and the 3N-length force vector at image i. The tangent vector
|
||||
is calculated as in "(HenkelmanA)"_#HenkelmanA for all intermediate
|
||||
replicas and at R2 - R1 and RM - RM-1 for the first and last replica,
|
||||
respectively. "anglegrad" is the angle between the 3N-length energy
|
||||
gradient vector of replica i and that of replica i+1. It is not
|
||||
defined for the final replica and reads nan. gradV is the norm of the
|
||||
energy gradient of image i. ReplicaForce is the two-norm of the
|
||||
3N-length force vector (including nudging forces) for replica i.
|
||||
MaxAtomForce is the maximum force component of any atom in replica i.
|
||||
|
||||
When a NEB calculation does not converge properly, these suplementary
|
||||
informations can help understanding what is going wrong. For instance
|
||||
when the path angle becomes accute the definition of tangent used in
|
||||
the NEB calculation is questionable and the NEB cannot may diverge
|
||||
"(Maras)"_#Maras2.
|
||||
|
||||
|
||||
When running on multiple partitions, LAMMPS produces additional log
|
||||
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
|
||||
@ -396,12 +399,16 @@ This command can only be used if LAMMPS was built with the REPLICA
|
||||
package. See the "Making LAMMPS"_Section_start.html#start_3 section
|
||||
for more info on packages.
|
||||
|
||||
:line
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"prd"_prd.html, "temper"_temper.html, "fix
|
||||
langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html
|
||||
"prd"_prd.html, "temper"_temper.html, "fix langevin"_fix_langevin.html,
|
||||
"fix viscous"_fix_viscous.html
|
||||
|
||||
[Default:] none
|
||||
[Default:]
|
||||
|
||||
none
|
||||
|
||||
:line
|
||||
|
||||
@ -414,3 +421,7 @@ langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html
|
||||
|
||||
:link(Nakano3)
|
||||
[(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008).
|
||||
|
||||
:link(Maras2)
|
||||
[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
|
||||
Comp Phys Comm, 205, 13-21 (2016)
|
||||
|
||||
@ -7,6 +7,7 @@
|
||||
:line
|
||||
|
||||
pair_style lj/long/coul/long command :h3
|
||||
pair_style lj/long/coul/long/intel command :h3
|
||||
pair_style lj/long/coul/long/omp command :h3
|
||||
pair_style lj/long/coul/long/opt command :h3
|
||||
pair_style lj/long/tip4p/long command :h3
|
||||
|
||||
@ -1,114 +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,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
pair_style lj/sf command :h3
|
||||
pair_style lj/sf/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style lj/sf cutoff :pre
|
||||
|
||||
cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style lj/sf 2.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.0 3.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {lj/sf} computes a truncated and force-shifted LJ interaction
|
||||
(Shifted Force Lennard-Jones), so that both the potential and the
|
||||
force go continuously to zero at the cutoff "(Toxvaerd)"_#Toxvaerd:
|
||||
|
||||
:c,image(Eqs/pair_lj_sf.jpg)
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands, or by mixing as described below:
|
||||
|
||||
epsilon (energy units)
|
||||
sigma (distance units)
|
||||
cutoff (distance units) :ul
|
||||
|
||||
The last coefficient is optional. If not specified, the global
|
||||
LJ cutoff specified in the pair_style command is used.
|
||||
|
||||
: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 in "Section 5"_Section_accelerate.html
|
||||
of the manual. 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 "Making
|
||||
LAMMPS"_Section_start.html#start_3 section 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"_Section_start.html#start_7 when you invoke LAMMPS, or you can
|
||||
use the "suffix"_suffix.html command in your input script.
|
||||
|
||||
See "Section 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma
|
||||
coefficients and cutoff distance for this pair style can be mixed.
|
||||
Rin is a cutoff value and is mixed like the cutoff. The
|
||||
default mix value is {geometric}. See the "pair_modify" command for
|
||||
details.
|
||||
|
||||
The "pair_modify"_pair_modify.html shift option is not relevant for
|
||||
this pair style, since the pair interaction goes to 0.0 at the cutoff.
|
||||
|
||||
The "pair_modify"_pair_modify.html table option is not relevant
|
||||
for this pair style.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
tail option for adding long-range tail corrections to energy and
|
||||
pressure, since the energy of the pair interaction is smoothed to 0.0
|
||||
at the cutoff.
|
||||
|
||||
This pair style writes its 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.
|
||||
|
||||
This pair style can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. It does not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This pair style is part of the USER-MISC package. It is only enabled
|
||||
if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Toxvaerd)
|
||||
[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).
|
||||
@ -11,26 +11,26 @@ pair_style lj/smooth/linear/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style lj/smooth/linear Rc :pre
|
||||
pair_style lj/smooth/linear cutoff :pre
|
||||
|
||||
Rc = cutoff for lj/smooth/linear interactions (distance units) :ul
|
||||
cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style lj/smooth/linear 5.456108274435118
|
||||
pair_coeff * * 0.7242785984051078 2.598146797350056
|
||||
pair_coeff 1 1 20.0 1.3 9.0 :pre
|
||||
pair_style lj/smooth/linear 2.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 0.3 3.0 9.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {lj/smooth/linear} computes a LJ interaction that combines the
|
||||
standard 12/6 Lennard-Jones function and subtracts a linear term that
|
||||
includes the cutoff distance Rc, as in this formula:
|
||||
Style {lj/smooth/linear} computes a truncated and force-shifted LJ
|
||||
interaction (aka Shifted Force Lennard-Jones) that combines the
|
||||
standard 12/6 Lennard-Jones function and subtracts a linear term based
|
||||
on the cutoff distance, so that both, the potential and the force, go
|
||||
continuously to zero at the cutoff Rc "(Toxvaerd)"_#Toxvaerd:
|
||||
|
||||
:c,image(Eqs/pair_lj_smooth_linear.jpg)
|
||||
|
||||
At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
@ -41,8 +41,8 @@ epsilon (energy units)
|
||||
sigma (distance units)
|
||||
cutoff (distance units) :ul
|
||||
|
||||
The last coefficient is optional. If not specified, the global value
|
||||
for Rc is used.
|
||||
The last coefficient is optional. If not specified, the global
|
||||
LJ cutoff specified in the pair_style command is used.
|
||||
|
||||
:line
|
||||
|
||||
@ -76,10 +76,11 @@ and cutoff distance can be mixed. The default mix value is geometric.
|
||||
See the "pair_modify" command for details.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
shift option for the energy of the pair interaction.
|
||||
shift option for the energy of the pair interaction, since it goes
|
||||
to 0.0 at the cutoff by construction.
|
||||
|
||||
The "pair_modify"_pair_modify.html table option is not relevant for
|
||||
this pair style.
|
||||
The "pair_modify"_pair_modify.html table option is not relevant
|
||||
for this pair style.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
tail option for adding long-range tail corrections to energy and
|
||||
@ -103,3 +104,8 @@ This pair style can only be used via the {pair} keyword of the
|
||||
"pair_coeff"_pair_coeff.html, "pair lj/smooth"_pair_lj_smooth.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Toxvaerd)
|
||||
[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).
|
||||
|
||||
@ -8,6 +8,7 @@
|
||||
|
||||
pair_style reax/c command :h3
|
||||
pair_style reax/c/kk command :h3
|
||||
pair_style reax/c/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
||||
@ -7,6 +7,7 @@
|
||||
:line
|
||||
|
||||
pair_style vashishta command :h3
|
||||
pair_style vashishta/gpu command :h3
|
||||
pair_style vashishta/omp command :h3
|
||||
pair_style vashishta/kk command :h3
|
||||
pair_style vashishta/table command :h3
|
||||
|
||||
@ -49,7 +49,6 @@ Pair Styles :h1
|
||||
pair_lj_cubic
|
||||
pair_lj_expand
|
||||
pair_lj_long
|
||||
pair_lj_sf
|
||||
pair_lj_smooth
|
||||
pair_lj_smooth_linear
|
||||
pair_lj_soft
|
||||
|
||||
@ -80,6 +80,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
|
||||
value can be an atom-style variable (see below)
|
||||
{image} nx ny nz
|
||||
nx,ny,nz = which periodic image of the simulation box the atom is in
|
||||
any of nx,ny,nz can be an atom-style variable (see below)
|
||||
{bond} value = bond type for all bonds between selected atoms
|
||||
{angle} value = angle type for all angles between selected atoms
|
||||
{dihedral} value = dihedral type for all dihedrals between selected atoms
|
||||
@ -363,9 +364,8 @@ A value of -1 means subtract 1 box length to get the true value.
|
||||
LAMMPS updates these flags as atoms cross periodic boundaries during
|
||||
the simulation. The flags can be output with atom snapshots via the
|
||||
"dump"_dump.html command. If a value of NULL is specified for any of
|
||||
nx,ny,nz, then the current image value for that dimension is
|
||||
unchanged. For non-periodic dimensions only a value of 0 can be
|
||||
specified. This keyword does not allow use of atom-style variables.
|
||||
nx,ny,nz, then the current image value for that dimension is unchanged.
|
||||
For non-periodic dimensions only a value of 0 can be specified.
|
||||
This command can be useful after a system has been equilibrated and
|
||||
atoms have diffused one or more box lengths in various directions.
|
||||
This command can then reset the image values for atoms so that they
|
||||
|
||||
@ -65,7 +65,13 @@ sense to define permanent bonds between atoms that interact via these
|
||||
potentials, though such bonds may exist elsewhere in your system,
|
||||
e.g. when using the "pair_style hybrid"_pair_hybrid.html command.
|
||||
Thus LAMMPS ignores special_bonds settings when manybody potentials
|
||||
are calculated.
|
||||
are calculated. Please note, that the existence of explicit bonds
|
||||
for atoms that are described by a manybody potential will alter the
|
||||
neigborlist and thus can render the computation of those interactions
|
||||
invalid, since those pairs are not only used to determine direct
|
||||
pairwise interactions but also neighbors of neighbors and more.
|
||||
The recommended course of action is to remove such bonds, or - if
|
||||
that is not possible - use a special bonds setting of 1.0 1.0 1.0.
|
||||
|
||||
NOTE: Unlike some commands in LAMMPS, you cannot use this command
|
||||
multiple times in an incremental fashion: e.g. to first set the LJ
|
||||
|
||||
Reference in New Issue
Block a user