Merge pull request #1421 from julient31/gneb_spin
Adding a GNEB implementation in the SPIN package
This commit is contained in:
Axel Kohlmeyer
@ -83,6 +83,7 @@ An alphabetic list of all general LAMMPS commands.
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"molecule"_molecule.html,
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"ndx2group"_group2ndx.html,
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"neb"_neb.html,
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"neb_spin"_neb_spin.html,
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"neigh_modify"_neigh_modify.html,
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"neighbor"_neighbor.html,
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"newton"_newton.html,
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@ -116,6 +116,7 @@ Actions:
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"minimize"_minimize.html,
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"neb"_neb.html,
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"neb_spin"_neb_spin.html,
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"prd"_prd.html,
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"rerun"_rerun.html,
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"run"_run.html,
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@ -107,6 +107,7 @@ OPT.
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"mvv/edpd"_fix_mvv_dpd.html,
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"mvv/tdpd"_fix_mvv_dpd.html,
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"neb"_fix_neb.html,
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"neb_spin"_fix_neb_spin.html,
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"nph (ko)"_fix_nh.html,
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"nph/asphere (o)"_fix_nph_asphere.html,
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"nph/body"_fix_nph_body.html,
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BIN
doc/src/Eqs/neb_spin_angle.jpg
Normal file
BIN
doc/src/Eqs/neb_spin_angle.jpg
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Binary file not shown.
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15
doc/src/Eqs/neb_spin_angle.tex
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15
doc/src/Eqs/neb_spin_angle.tex
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@ -0,0 +1,15 @@
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\documentclass[preview]{standalone}
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\usepackage{varwidth}
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\usepackage[utf8x]{inputenc}
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\usepackage{amsmath, amssymb, graphics, setspace}
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\begin{document}
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\begin{varwidth}{50in}
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\begin{equation}
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\omega_i^{\nu} =
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(\nu - 1) \Delta \omega_i
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{\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
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, \nonumber
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\end{equation}
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\end{varwidth}
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\end{document}
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BIN
doc/src/Eqs/neb_spin_k.jpg
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BIN
doc/src/Eqs/neb_spin_k.jpg
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Binary file not shown.
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16
doc/src/Eqs/neb_spin_k.tex
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16
doc/src/Eqs/neb_spin_k.tex
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@ -0,0 +1,16 @@
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\documentclass[preview]{standalone}
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\usepackage{varwidth}
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\usepackage[utf8x]{inputenc}
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\usepackage{amsmath, amssymb, graphics, setspace}
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\begin{document}
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\begin{varwidth}{50in}
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\begin{equation}
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\vec{k}_i =
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\frac{\vec{m}_i^I \times \vec{m}_i^F}{\left|\vec{m}_i^I
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\times \vec{m}_i^F\right|}
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%&{\rm ~if~}& \vec{m}_i^I \times \vec{m}_i^F
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, \nonumber
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\end{equation}
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\end{varwidth}
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\end{document}
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BIN
doc/src/Eqs/neb_spin_rodrigues_formula.jpg
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BIN
doc/src/Eqs/neb_spin_rodrigues_formula.jpg
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After Width: | Height: | Size: 20 KiB |
16
doc/src/Eqs/neb_spin_rodrigues_formula.tex
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16
doc/src/Eqs/neb_spin_rodrigues_formula.tex
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@ -0,0 +1,16 @@
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\documentclass[preview]{standalone}
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\usepackage{varwidth}
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\usepackage[utf8x]{inputenc}
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\usepackage{amsmath, amssymb, graphics, setspace}
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\begin{document}
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\begin{varwidth}{50in}
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\begin{equation}
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\vec{m}_i^{\nu} = \vec{m}_i^{I} \cos(\omega_i^{\nu})
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+ (\vec{k}_i \times \vec{m}_i^{I}) \sin(\omega_i^{\nu})
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+ (1.0-\cos(\omega_i^{\nu})) \vec{k}_i (\vec{k}_i\cdot
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\vec{m}_i^{I})
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, \nonumber
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\end{equation}
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\end{varwidth}
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\end{document}
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@ -17,6 +17,7 @@ periodically.
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These are the relevant commands:
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"neb"_neb.html for nudged elastic band calculations
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"neb_spin"_neb_spin.html for magnetic nudged elastic band calculations
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"prd"_prd.html for parallel replica dynamics
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"tad"_tad.html for temperature accelerated dynamics
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"temper"_temper.html for parallel tempering
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@ -918,6 +918,7 @@ src/SPIN: filenames -> commands
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"fix nve/spin"_fix_nve_spin.html
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"fix precession/spin"_fix_precession_spin.html
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"compute spin"_compute_spin.html
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"neb/spin"_neb_spin.html
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examples/SPIN :ul
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:line
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@ -67,6 +67,7 @@ Commands :h1
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minimize
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molecule
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neb
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neb_spin
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neigh_modify
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neighbor
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newton
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@ -97,7 +97,7 @@ Note that in this case the specified {Kspring} is in force/distance
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units.
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With a value of {ideal}, the spring force is computed as suggested in
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"(WeinenE)"_#WeinenE :
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"(WeinanE)"_#WeinanE :
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Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
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@ -224,8 +224,8 @@ specified (no inter-replica force on the end replicas).
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[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
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9901-9904 (2000).
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:link(WeinenE)
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[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
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:link(WeinanE)
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[(WeinanE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
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:link(Jonsson)
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[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum
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76
doc/src/fix_neb_spin.txt
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76
doc/src/fix_neb_spin.txt
Normal file
@ -0,0 +1,76 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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fix neb/spin command :h3
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[Syntax:]
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fix ID group-ID neb/spin Kspring :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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neb/spin = style name of this fix command :l
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Kspring = spring constant for parallel nudging force
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(force/distance units or force units, see parallel keyword) :pre,ule
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[Examples:]
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fix 1 active neb/spin 1.0
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[Description:]
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Add nudging forces to spins in the group for a multi-replica
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simulation run via the "neb/spin"_neb_spin.html command to perform a
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geodesic nudged elastic band (GNEB) calculation for finding the
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transition state.
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Hi-level explanations of GNEB are given with the
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"neb/spin"_neb_spin.html command and on the
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"Howto replica"_Howto_replica.html doc page.
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The fix neb/spin command must be used with the "neb/spin" command and
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defines how inter-replica nudging forces are computed. A GNEB
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calculation is divided in two stages. In the first stage n replicas
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are relaxed toward a MEP until convergence. In the second stage, the
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climbing image scheme is enabled, so that the replica having the highest
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energy relaxes toward the saddle point (i.e. the point of highest energy
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along the MEP), and a second relaxation is performed.
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The nudging forces are calculated as explained in
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"(BessarabB)"_#BessarabB).
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See this reference for more explanation about their expression.
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various "output commands"_Howto_output.html.
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No parameter of this fix can be used with the {start/stop} keywords of
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the "run"_run.html command.
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The forces due to this fix are imposed during an energy minimization,
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as invoked by the "minimize"_minimize.html command via the
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"neb/spin"_neb_spin.html command.
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[Restrictions:]
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This command can only be used if LAMMPS was built with the SPIN
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package. See the "Build package"_Build_package.html doc
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page for more info.
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[Related commands:]
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"neb_spin"_neb_spin.html
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[Default:]
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none
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:line
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:link(BessarabB)
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[(BessarabB)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
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335-347 (2015).
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@ -31,7 +31,7 @@ fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :p
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[Description:]
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Impose a force torque to each magnetic spin in the group.
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This fix applies a precession torque to each magnetic spin in the group.
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Style {zeeman} is used for the simulation of the interaction
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between the magnetic spins in the defined group and an external
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@ -84,6 +84,7 @@ Fixes :h1
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fix_msst
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fix_mvv_dpd
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fix_neb
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fix_neb_spin
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fix_nh
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fix_nh_eff
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fix_nh_uef
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@ -179,6 +179,7 @@ min_spin.html
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minimize.html
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molecule.html
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neb.html
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neb_spin.html
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neigh_modify.html
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neighbor.html
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newton.html
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@ -309,6 +310,7 @@ fix_mscg.html
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fix_msst.html
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fix_mvv_dpd.html
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fix_neb.html
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fix_neb_spin.html
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fix_nh.html
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fix_nh_eff.html
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fix_nph_asphere.html
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375
doc/src/neb_spin.txt
Normal file
375
doc/src/neb_spin.txt
Normal file
@ -0,0 +1,375 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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neb command :h3
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[Syntax:]
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neb/spin etol ttol N1 N2 Nevery file-style arg keyword :pre
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etol = stopping tolerance for energy (energy units) :ulb,l
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ttol = stopping tolerance for torque ( units) :l
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N1 = max # of iterations (timesteps) to run initial NEB :l
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N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
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Nevery = print replica energies and reaction coordinates every this many timesteps :l
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file-style = {final} or {each} or {none} :l
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{final} arg = filename
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filename = file with initial coords for final replica
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coords for intermediate replicas are linearly interpolated
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between first and last replica
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{each} arg = filename
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filename = unique filename for each replica (except first)
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with its initial coords
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{none} arg = no argument all replicas assumed to already have
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their initial coords :pre
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keyword = {verbose}
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:ule
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[Examples:]
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neb/spin 0.1 0.0 1000 500 50 final coords.final
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neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i
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neb/spin 0.0 0.001 1000 500 50 none verbose :pre
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[Description:]
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Perform a geodesic nudged elastic band (GNEB) calculation using multiple
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replicas of a system. Two or more replicas must be used; the first
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and last are the end points of the transition path.
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GNEB is a method for finding both the spin configurations and height
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of the energy barrier associated with a transition state, e.g.
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spins to perform a collective rotation from one energy basin to
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another.
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The implementation in LAMMPS follows the discussion in the
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following paper: "(BessarabA)"_#BessarabA.
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Each replica runs on a partition of one or more processors. Processor
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partitions are defined at run-time using the "-partition command-line
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switch"_Run_options.html. Note that if you have MPI installed, you
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can run a multi-replica simulation with more replicas (partitions)
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than you have physical processors, e.g you can run a 10-replica
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simulation on just one or two processors. You will simply not get the
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performance speed-up you would see with one or more physical
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processors per replica. See the "Howto replica"_Howto_replica.html
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doc page for further discussion.
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NOTE: As explained below, a GNEB calculation performs a damped dynamics
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minimization across all the replicas. The "spin"_min_spin.html
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style minimizer has to be defined in your input script.
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When a GNEB calculation is performed, it is assumed that each replica
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is running the same system, though LAMMPS does not check for this.
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I.e. the simulation domain, the number of magnetic atoms, the
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interaction potentials, and the starting configuration when the neb
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command is issued should be the same for every replica.
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In a GNEB calculation each replica is connected to other replicas by
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inter-replica nudging forces. These forces are imposed by the "fix
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neb/spin"_fix_neb_spin.html command, which must be used in conjunction
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with the neb command.
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The group used to define the fix neb/spin command defines the
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GNEB magnetic atoms which are the only ones that inter-replica springs
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are applied to.
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If the group does not include all magnetic atoms, then non-GNEB
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magnetic atoms have no inter-replica springs and the torques they feel
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and their precession motion is computed in the usual way due only
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to other magnetic atoms within their replica.
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Conceptually, the non-GNEB atoms provide a background force field for
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the GNEB atoms.
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Their magnetic spins can be allowed to evolve during the GNEB
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minimization procedure.
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The initial spin configuration for each of the replicas can be
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specified in different manners via the {file-style} setting, as
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discussed below. Only atomic spins whose initial coordinates should
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differ from the current configuration need to be specified.
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Conceptually, the initial and final configurations for the first
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replica should be states on either side of an energy barrier.
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As explained below, the initial configurations of intermediate
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replicas can be spin coordinates interpolated in a linear fashion
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between the first and last replicas. This is often adequate for
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simple transitions. For more complex transitions, it may lead to slow
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convergence or even bad results if the minimum energy path (MEP, see
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below) of states over the barrier cannot be correctly converged to
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from such an initial path. In this case, you will want to generate
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initial states for the intermediate replicas that are geometrically
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closer to the MEP and read them in.
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:line
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For a {file-style} setting of {final}, a filename is specified which
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contains atomic and spin coordinates for zero or more atoms, in the
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format described below.
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For each atom that appears in the file, the new coordinates are
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assigned to that atom in the final replica. Each intermediate replica
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also assigns a new spin to that atom in an interpolated manner.
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This is done by using the current direction of the spin at the starting
|
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point and the read-in direction as the final point.
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The "angular distance" between them is calculated, and the new direction
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is assigned to be a fraction of the angular distance.
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NOTE: The "angular distance" between the starting and final point is
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evaluated in the geodesic sense, as described in
|
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"(BessarabA)"_#BessarabA.
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NOTE: The angular interpolation between the starting and final point
|
||||
is achieved using Rodrigues formula:
|
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:c,image(Eqs/neb_spin_rodrigues_formula.jpg)
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where m_i^I is the initial spin configuration for the spin i,
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omega_i^nu is a rotation angle defined as:
|
||||
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||||
:c,image(Eqs/neb_spin_angle.jpg)
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|
||||
with nu the image number, Q the total number of images, and
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omega_i the total rotation between the initial and final spins.
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k_i defines a rotation axis such as:
|
||||
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:c,image(Eqs/neb_spin_k.jpg)
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||||
if the initial and final spins are not aligned.
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If the initial and final spins are aligned, then their cross
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||||
product is null, and the expression above does not apply.
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If they point toward the same direction, the intermediate images
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conserve the same orientation.
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If the initial and final spins are aligned, but point toward
|
||||
opposite directions, an arbitrary rotation vector belonging to
|
||||
the plane perpendicular to initial and final spins is chosen.
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||||
In this case, a warning message is displayed.
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||||
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For a {file-style} setting of {each}, a filename is specified which is
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||||
assumed to be unique to each replica.
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||||
See the "neb"_neb.html documentation page for more information about this
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||||
option.
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||||
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||||
For a {file-style} setting of {none}, no filename is specified. Each
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||||
replica is assumed to already be in its initial configuration at the
|
||||
time the neb command is issued. This allows each replica to define
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||||
its own configuration by reading a replica-specific data or restart or
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dump file, via the "read_data"_read_data.html,
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"read_restart"_read_restart.html, or "read_dump"_read_dump.html
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commands. The replica-specific names of these files can be specified
|
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as in the discussion above for the {each} file-style. Also see the
|
||||
section below for how a NEB calculation can produce restart files, so
|
||||
that a long calculation can be restarted if needed.
|
||||
|
||||
NOTE: None of the {file-style} settings change the initial
|
||||
configuration of any atom in the first replica. The first replica
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||||
must thus be in the correct initial configuration at the time the neb
|
||||
command is issued.
|
||||
|
||||
:line
|
||||
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||||
A NEB calculation proceeds in two stages, each of which is a
|
||||
minimization procedure, performed via damped dynamics. To enable
|
||||
this, you must first define a damped spin dynamics
|
||||
"min_style"_min_style.html, using the {spin} style (see
|
||||
"min_spin"_min_spin.html for more information).
|
||||
The other styles cannot be used, since they relax the lattice
|
||||
degrees of freedom instead of the spins.
|
||||
|
||||
The minimizer tolerances for energy and force are set by {etol} and
|
||||
{ttol}, the same as for the "minimize"_minimize.html command.
|
||||
|
||||
A non-zero {etol} means that the GNEB 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
|
||||
nudging forces, since these are non-conservative. A non-zero {ttol}
|
||||
means that the GNEB calculation will terminate if the torque criterion
|
||||
is met by every replica. The torques being compared to {ttol} 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
|
||||
damped dynamics is like a single timestep in a dynamics
|
||||
"run"_run.html. During both stages, the potential energy of each
|
||||
replica and its normalized distance along the reaction path (reaction
|
||||
coordinate RD) will be printed to the screen and log file every
|
||||
{Nevery} timesteps. The RD is 0 and 1 for the first and last replica.
|
||||
For intermediate replicas, it is the cumulative angular distance
|
||||
(normalized by the total cumulative angular distance) between adjacent
|
||||
replicas, where "distance" is defined as the length of the 3N-vector of
|
||||
the geodesic distances in spin coordinates, with N the number of
|
||||
GNEB spins involved (see equation (13) in "(BessarabA)"_#BessarabA).
|
||||
These outputs allow you to monitor NEB's progress in
|
||||
finding a good energy barrier. {N1} and {N2} must both be multiples
|
||||
of {Nevery}.
|
||||
|
||||
In the first stage of GNEB, the set of replicas should converge toward
|
||||
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 spin 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 nudging force added by the
|
||||
"fix neb"_fix_neb.html command.
|
||||
|
||||
In the second stage of GNEB, the replica with the highest energy is
|
||||
selected and the inter-replica forces on it are converted to a force
|
||||
that drives its spin coordinates to the top or saddle point of the
|
||||
barrier, via the barrier-climbing calculation described in
|
||||
"(BessarabA)"_#BessarabA. As before, the other replicas rearrange
|
||||
themselves along the MEP so as to be roughly equally spaced.
|
||||
|
||||
When both stages are complete, if the GNEB calculation was successful,
|
||||
the configurations of the replicas should be along (close to) the MEP
|
||||
and the replica with the highest energy should be a spin
|
||||
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
|
||||
|
||||
An atom map must be defined which it is not by default for "atom_style
|
||||
atomic"_atom_style.html problems. The "atom_modify
|
||||
map"_atom_modify.html command can be used to do this.
|
||||
|
||||
An initial value can be defined for the timestep. Although, the {spin}
|
||||
minimization algorithm is an adaptive timestep methodology, so that
|
||||
this timestep is likely to evolve during the calculation.
|
||||
|
||||
The minimizers in LAMMPS operate on all spins in your system, even
|
||||
non-GNEB atoms, as defined above.
|
||||
|
||||
:line
|
||||
|
||||
Each file read by the neb/spin command containing spin coordinates used
|
||||
to initialize one or more replicas must be formatted as follows.
|
||||
|
||||
The file can be ASCII text or a gzipped text file (detected by a .gz
|
||||
suffix). The file can contain initial blank lines or comment lines
|
||||
starting with "#" which are ignored. The first non-blank, non-comment
|
||||
line should list N = the number of lines to follow. The N successive
|
||||
lines contain the following information:
|
||||
|
||||
ID1 g1 x1 y1 z1 sx1 sy1 sz1
|
||||
ID2 g2 x2 y2 z2 sx2 sy2 sz2
|
||||
...
|
||||
IDN gN yN zN sxN syN szN :pre
|
||||
|
||||
The fields are the atom ID, the norm of the associated magnetic spin,
|
||||
followed by the {x,y,z} coordinates and the {sx,sy,sz} spin 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 GNEB calculation you do not need to specify
|
||||
initial spin coordinates for very many atoms to produce differing starting
|
||||
and final replicas whose intermediate replicas will converge to the
|
||||
energy barrier. Typically only new spin coordinates for atoms
|
||||
geometrically near the barrier need be specified.
|
||||
|
||||
Also note there is no requirement that the atoms in the file
|
||||
correspond to the GNEB atoms in the group defined by the "fix
|
||||
neb"_fix_neb.html command. Not every GNEB atom need be in the file,
|
||||
and non-GNEB atoms can be listed in the file.
|
||||
|
||||
:line
|
||||
|
||||
Four kinds of output can be generated during a GNEB calculation: energy
|
||||
barrier statistics, thermodynamic output by each replica, dump files,
|
||||
and restart files.
|
||||
|
||||
When running with multiple partitions (each of which is a replica in
|
||||
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 torque per replica, the maximum
|
||||
torque 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.
|
||||
|
||||
The "maximum torque per replica" is the two-norm of the
|
||||
3N-length vector given by the cross product of a spin by its
|
||||
precession vector omega, in each replica, maximized across replicas,
|
||||
which is what the {ttol} setting is checking against. In this case, N is
|
||||
all the atoms in each replica. The "maximum torque per atom" is the
|
||||
maximum torque component of any atom in any replica. The potential
|
||||
gradients are the two-norm of the 3N-length magnetic precession vector
|
||||
solely due to the interaction potential i.e. without adding in
|
||||
inter-replica forces, and projected along the path tangent (as detailed
|
||||
in Appendix D of "(BessarabA)"_#BessarabA).
|
||||
|
||||
The "reaction coordinate" (RD) for each replica is the two-norm of the
|
||||
3N-length vector of geodesic distances between its spins and the preceding
|
||||
replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), 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 spins being operated on by the fix neb/spin command.
|
||||
|
||||
The forward (reverse) energy barrier is the potential energy of the
|
||||
highest replica minus the energy of the first (last) replica.
|
||||
|
||||
Supplementary information for all replicas can be printed out to the
|
||||
screen and master log.lammps file by adding the verbose keyword. This
|
||||
information include the following.
|
||||
The "GradVidottan" are the projections of the potential gradient for
|
||||
the replica i on its tangent vector (as detailed in Appendix D of
|
||||
"(BessarabA)"_#BessarabA).
|
||||
The "DNi" are the non normalized geodesic distances (see equation (13)
|
||||
of "(BessarabA)"_#BessarabA), between a replica i and the next replica
|
||||
i+1. For the last replica, this distance is not defined and a "NAN"
|
||||
value is the corresponding output.
|
||||
|
||||
When a NEB calculation does not converge properly, the supplementary
|
||||
information can help understanding what is going wrong.
|
||||
|
||||
When running on multiple partitions, LAMMPS produces additional log
|
||||
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
|
||||
GNEB calculation, these contain the thermodynamic output for each
|
||||
replica.
|
||||
|
||||
If "dump"_dump.html commands in the input script define a filename
|
||||
that includes a {universe} or {uloop} style "variable"_variable.html,
|
||||
then one dump file (per dump command) will be created for each
|
||||
replica. At the end of the GNEB calculation, the final snapshot in
|
||||
each file will contain the sequence of snapshots that transition the
|
||||
system over the energy barrier. Earlier snapshots will show the
|
||||
convergence of the replicas to the MEP.
|
||||
|
||||
Likewise, "restart"_restart.html filenames can be specified with a
|
||||
{universe} or {uloop} style "variable"_variable.html, to generate
|
||||
restart files for each replica. These may be useful if the GNEB
|
||||
calculation fails to converge properly to the MEP, and you wish to
|
||||
restart the calculation from an intermediate point with altered
|
||||
parameters.
|
||||
|
||||
A c file script in provided in the tool/spin/interpolate_gneb
|
||||
directory, that interpolates the MEP given the information provided
|
||||
by the verbose output option (as detailed in Appendix D of
|
||||
"(BessarabA)"_#BessarabA).
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command can only be used if LAMMPS was built with the SPIN
|
||||
package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
:line
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"min/spin"_min_spin.html, "fix neb/spin"_fix_neb_spin.html
|
||||
|
||||
[Default:]
|
||||
|
||||
none
|
||||
|
||||
:line
|
||||
|
||||
:link(BessarabA)
|
||||
[(BessarabA)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
|
||||
335-347 (2015).
|
||||
@ -200,6 +200,7 @@ Berkowitz
|
||||
berlin
|
||||
Berne
|
||||
Bertotti
|
||||
Bessarab
|
||||
Beutler
|
||||
bgq
|
||||
Bh
|
||||
@ -592,6 +593,7 @@ Dmax
|
||||
dmg
|
||||
dmi
|
||||
dnf
|
||||
DNi
|
||||
Dobson
|
||||
Dodds
|
||||
dodgerblue
|
||||
@ -963,6 +965,8 @@ gmail
|
||||
gmake
|
||||
gmask
|
||||
Gmask
|
||||
gneb
|
||||
GNEB
|
||||
googlemail
|
||||
Gordan
|
||||
GPa
|
||||
@ -2368,6 +2372,7 @@ rNEMD
|
||||
ro
|
||||
Rochus
|
||||
Rockett
|
||||
Rodrigues
|
||||
Rohart
|
||||
Ronchetti
|
||||
Rosati
|
||||
@ -2772,6 +2777,7 @@ tt
|
||||
Tt
|
||||
TThis
|
||||
ttm
|
||||
ttol
|
||||
tu
|
||||
Tuckerman
|
||||
tue
|
||||
@ -2844,6 +2850,7 @@ utsa
|
||||
Uttormark
|
||||
uvm
|
||||
uwo
|
||||
Uzdin
|
||||
vacf
|
||||
valent
|
||||
Valeriu
|
||||
@ -2943,7 +2950,7 @@ wB
|
||||
Wbody
|
||||
webpage
|
||||
Weckner
|
||||
WeinenE
|
||||
WeinanE
|
||||
Wennberg
|
||||
Westview
|
||||
wget
|
||||
|
||||
13
examples/SPIN/gneb/README
Normal file
13
examples/SPIN/gneb/README
Normal file
@ -0,0 +1,13 @@
|
||||
Perform geodesic NEB calculations for spin configurations.
|
||||
The two examples are:
|
||||
- the magnetic switching of an iron nanoisland
|
||||
- the collapse of a magnetic skyrmion
|
||||
|
||||
Run those examples as:
|
||||
|
||||
mpirun -np 3 lmp_mpi -in in.gneb.iron -partition 3x1
|
||||
|
||||
You should be able to use any number of replicas >= 3.
|
||||
|
||||
In the interpolate/ directory, a c routine is provided to
|
||||
interpolate the MEP.
|
||||
68
examples/SPIN/gneb/iron/final.iron_spin
Normal file
68
examples/SPIN/gneb/iron/final.iron_spin
Normal file
@ -0,0 +1,68 @@
|
||||
32
|
||||
1 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
2 2.2000000000000002e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
3 2.2000000000000002e+00 2.8664999999999998e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
4 2.2000000000000002e+00 4.2997499999999995e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
5 2.2000000000000002e+00 5.7329999999999997e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
6 2.2000000000000002e+00 7.1662499999999998e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
7 2.2000000000000002e+00 8.5994999999999990e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
8 2.2000000000000002e+00 1.0032750000000000e+01 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
9 2.2000000000000002e+00 0.0000000000000000e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
10 2.2000000000000002e+00 2.8664999999999998e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
11 2.2000000000000002e+00 5.7329999999999997e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
12 2.2000000000000002e+00 8.5994999999999990e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
13 2.2000000000000002e+00 1.4332499999999999e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
14 2.2000000000000002e+00 4.2997499999999995e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
15 2.2000000000000002e+00 7.1662499999999998e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
16 2.2000000000000002e+00 1.0032750000000000e+01 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
17 2.2000000000000002e+00 0.0000000000000000e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
18 2.2000000000000002e+00 1.4332499999999999e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
19 2.2000000000000002e+00 2.8664999999999998e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
20 2.2000000000000002e+00 4.2997499999999995e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
21 2.2000000000000002e+00 5.7329999999999997e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
22 2.2000000000000002e+00 7.1662499999999998e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
23 2.2000000000000002e+00 8.5994999999999990e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
24 2.2000000000000002e+00 1.0032750000000000e+01 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
25 2.2000000000000002e+00 0.0000000000000000e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
26 2.2000000000000002e+00 2.8664999999999998e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
27 2.2000000000000002e+00 5.7329999999999997e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
28 2.2000000000000002e+00 8.5994999999999990e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
29 2.2000000000000002e+00 1.4332499999999999e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
30 2.2000000000000002e+00 4.2997499999999995e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
31 2.2000000000000002e+00 7.1662499999999998e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
32 2.2000000000000002e+00 1.0032750000000000e+01 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
50
examples/SPIN/gneb/iron/in.gneb.iron
Normal file
50
examples/SPIN/gneb/iron/in.gneb.iron
Normal file
@ -0,0 +1,50 @@
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
# setting mass, mag. moments, and interactions for bcc iron
|
||||
# (mass not necessary for fixed lattice calculation)
|
||||
|
||||
read_data initial.iron_spin
|
||||
mass 1 55.845
|
||||
|
||||
pair_style spin/exchange 3.5
|
||||
pair_coeff * * exchange 3.4 0.02726 0.2171 1.841
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.0001 1.0 0.0 0.0
|
||||
fix_modify 1 energy yes
|
||||
fix 3 all neb/spin 1.0
|
||||
|
||||
timestep 0.0001
|
||||
thermo 100
|
||||
|
||||
compute out_mag all spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magx equal c_out_mag[1]
|
||||
variable magy equal c_out_mag[2]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time v_magx v_magz v_magnorm etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
variable u universe 1 2 3 4
|
||||
dump 1 all custom 200 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
min_style spin
|
||||
min_modify alpha_damp 1.0 discrete_factor 10.0
|
||||
neb/spin 1.0e-12 1.0e-12 200000 100000 1000 final final.iron_spin verbose
|
||||
82
examples/SPIN/gneb/iron/initial.iron_spin
Normal file
82
examples/SPIN/gneb/iron/initial.iron_spin
Normal file
@ -0,0 +1,82 @@
|
||||
LAMMPS data file via write_data, version 4 Jan 2019, timestep = 0
|
||||
|
||||
32 atoms
|
||||
1 atom types
|
||||
|
||||
0.0000000000000000e+00 1.1465999999999999e+01 xlo xhi
|
||||
0.0000000000000000e+00 1.1465999999999999e+01 ylo yhi
|
||||
0.0000000000000000e+00 2.8664999999999998e+00 zlo zhi
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|
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Masses
|
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|
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1 55.845
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|
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Atoms # spin
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Velocities
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401
examples/SPIN/gneb/skyrmion/final.skyrmion
Normal file
401
examples/SPIN/gneb/skyrmion/final.skyrmion
Normal file
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400
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2 2.5 0.0 3.0 0.0 0.0 0.0 1.0
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3 2.5 0.0 6.0 0.0 0.0 0.0 1.0
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4 2.5 0.0 9.0 0.0 0.0 0.0 1.0
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5 2.5 0.0 12.0 0.0 0.0 0.0 1.0
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6 2.5 0.0 15.0 0.0 0.0 0.0 1.0
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7 2.5 0.0 18.0 0.0 0.0 0.0 1.0
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8 2.5 0.0 21.0 0.0 0.0 0.0 1.0
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9 2.5 0.0 24.0 0.0 0.0 0.0 1.0
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10 2.5 0.0 27.0 0.0 0.0 0.0 1.0
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11 2.5 0.0 30.0 0.0 0.0 0.0 1.0
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15 2.5 0.0 42.0 0.0 0.0 0.0 1.0
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20 2.5 0.0 57.0 0.0 0.0 0.0 1.0
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22 2.5 3.0 3.0 0.0 0.0 0.0 1.0
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23 2.5 3.0 6.0 0.0 0.0 0.0 1.0
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24 2.5 3.0 9.0 0.0 0.0 0.0 1.0
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25 2.5 3.0 12.0 0.0 0.0 0.0 1.0
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26 2.5 3.0 15.0 0.0 0.0 0.0 1.0
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27 2.5 3.0 18.0 0.0 0.0 0.0 1.0
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28 2.5 3.0 21.0 0.0 0.0 0.0 1.0
|
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29 2.5 3.0 24.0 0.0 0.0 0.0 1.0
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30 2.5 3.0 27.0 0.0 0.0 0.0 1.0
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31 2.5 3.0 30.0 0.0 0.0 0.0 1.0
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32 2.5 3.0 33.0 0.0 0.0 0.0 1.0
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33 2.5 3.0 36.0 0.0 0.0 0.0 1.0
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35 2.5 3.0 42.0 0.0 0.0 0.0 1.0
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36 2.5 3.0 45.0 0.0 0.0 0.0 1.0
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38 2.5 3.0 51.0 0.0 0.0 0.0 1.0
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39 2.5 3.0 54.0 0.0 0.0 0.0 1.0
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40 2.5 3.0 57.0 0.0 0.0 0.0 1.0
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41 2.5 6.0 0.0 0.0 0.0 0.0 1.0
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42 2.5 6.0 3.0 0.0 0.0 0.0 1.0
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43 2.5 6.0 6.0 0.0 0.0 0.0 1.0
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44 2.5 6.0 9.0 0.0 0.0 0.0 1.0
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45 2.5 6.0 12.0 0.0 0.0 0.0 1.0
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46 2.5 6.0 15.0 0.0 0.0 0.0 1.0
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47 2.5 6.0 18.0 0.0 0.0 0.0 1.0
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51 2.5 6.0 30.0 0.0 0.0 0.0 1.0
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52 2.5 6.0 33.0 0.0 0.0 0.0 1.0
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53 2.5 6.0 36.0 0.0 0.0 0.0 1.0
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54 2.5 6.0 39.0 0.0 0.0 0.0 1.0
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55 2.5 6.0 42.0 0.0 0.0 0.0 1.0
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56 2.5 6.0 45.0 0.0 0.0 0.0 1.0
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57 2.5 6.0 48.0 0.0 0.0 0.0 1.0
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58 2.5 6.0 51.0 0.0 0.0 0.0 1.0
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59 2.5 6.0 54.0 0.0 0.0 0.0 1.0
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60 2.5 6.0 57.0 0.0 0.0 0.0 1.0
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62 2.5 9.0 3.0 0.0 0.0 0.0 1.0
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63 2.5 9.0 6.0 0.0 0.0 0.0 1.0
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64 2.5 9.0 9.0 0.0 0.0 0.0 1.0
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65 2.5 9.0 12.0 0.0 0.0 0.0 1.0
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66 2.5 9.0 15.0 0.0 0.0 0.0 1.0
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67 2.5 9.0 18.0 0.0 0.0 0.0 1.0
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68 2.5 9.0 21.0 0.0 0.0 0.0 1.0
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69 2.5 9.0 24.0 0.0 0.0 0.0 1.0
|
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70 2.5 9.0 27.0 0.0 0.0 0.0 1.0
|
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71 2.5 9.0 30.0 0.0 0.0 0.0 1.0
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72 2.5 9.0 33.0 0.0 0.0 0.0 1.0
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80 2.5 9.0 57.0 0.0 0.0 0.0 1.0
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81 2.5 12.0 0.0 0.0 0.0 0.0 1.0
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82 2.5 12.0 3.0 0.0 0.0 0.0 1.0
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93 2.5 12.0 36.0 0.0 0.0 0.0 1.0
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97 2.5 12.0 48.0 0.0 0.0 0.0 1.0
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129 2.5 18.0 24.0 0.0 0.0 0.0 1.0
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130 2.5 18.0 27.0 0.0 0.0 0.0 1.0
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131 2.5 18.0 30.0 0.0 0.0 0.0 1.0
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132 2.5 18.0 33.0 0.0 0.0 0.0 1.0
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133 2.5 18.0 36.0 0.0 0.0 0.0 1.0
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134 2.5 18.0 39.0 0.0 0.0 0.0 1.0
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135 2.5 18.0 42.0 0.0 0.0 0.0 1.0
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147 2.5 21.0 18.0 0.0 0.0 0.0 1.0
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|
||||
161 2.5 24.0 0.0 0.0 0.0 0.0 1.0
|
||||
162 2.5 24.0 3.0 0.0 0.0 0.0 1.0
|
||||
163 2.5 24.0 6.0 0.0 0.0 0.0 1.0
|
||||
164 2.5 24.0 9.0 0.0 0.0 0.0 1.0
|
||||
165 2.5 24.0 12.0 0.0 0.0 0.0 1.0
|
||||
166 2.5 24.0 15.0 0.0 0.0 0.0 1.0
|
||||
167 2.5 24.0 18.0 0.0 0.0 0.0 1.0
|
||||
168 2.5 24.0 21.0 0.0 0.0 0.0 1.0
|
||||
169 2.5 24.0 24.0 0.0 0.0 0.0 1.0
|
||||
170 2.5 24.0 27.0 0.0 0.0 0.0 1.0
|
||||
171 2.5 24.0 30.0 0.0 0.0 0.0 1.0
|
||||
172 2.5 24.0 33.0 0.0 0.0 0.0 1.0
|
||||
173 2.5 24.0 36.0 0.0 0.0 0.0 1.0
|
||||
174 2.5 24.0 39.0 0.0 0.0 0.0 1.0
|
||||
175 2.5 24.0 42.0 0.0 0.0 0.0 1.0
|
||||
176 2.5 24.0 45.0 0.0 0.0 0.0 1.0
|
||||
177 2.5 24.0 48.0 0.0 0.0 0.0 1.0
|
||||
178 2.5 24.0 51.0 0.0 0.0 0.0 1.0
|
||||
179 2.5 24.0 54.0 0.0 0.0 0.0 1.0
|
||||
180 2.5 24.0 57.0 0.0 0.0 0.0 1.0
|
||||
181 2.5 27.0 0.0 0.0 0.0 0.0 1.0
|
||||
182 2.5 27.0 3.0 0.0 0.0 0.0 1.0
|
||||
183 2.5 27.0 6.0 0.0 0.0 0.0 1.0
|
||||
184 2.5 27.0 9.0 0.0 0.0 0.0 1.0
|
||||
185 2.5 27.0 12.0 0.0 0.0 0.0 1.0
|
||||
186 2.5 27.0 15.0 0.0 0.0 0.0 1.0
|
||||
187 2.5 27.0 18.0 0.0 0.0 0.0 1.0
|
||||
188 2.5 27.0 21.0 0.0 0.0 0.0 1.0
|
||||
189 2.5 27.0 24.0 0.0 0.0 0.0 1.0
|
||||
190 2.5 27.0 27.0 0.0 0.0 0.0 1.0
|
||||
191 2.5 27.0 30.0 0.0 0.0 0.0 1.0
|
||||
192 2.5 27.0 33.0 0.0 0.0 0.0 1.0
|
||||
193 2.5 27.0 36.0 0.0 0.0 0.0 1.0
|
||||
194 2.5 27.0 39.0 0.0 0.0 0.0 1.0
|
||||
195 2.5 27.0 42.0 0.0 0.0 0.0 1.0
|
||||
196 2.5 27.0 45.0 0.0 0.0 0.0 1.0
|
||||
197 2.5 27.0 48.0 0.0 0.0 0.0 1.0
|
||||
198 2.5 27.0 51.0 0.0 0.0 0.0 1.0
|
||||
199 2.5 27.0 54.0 0.0 0.0 0.0 1.0
|
||||
200 2.5 27.0 57.0 0.0 0.0 0.0 1.0
|
||||
201 2.5 30.0 0.0 0.0 0.0 0.0 1.0
|
||||
202 2.5 30.0 3.0 0.0 0.0 0.0 1.0
|
||||
203 2.5 30.0 6.0 0.0 0.0 0.0 1.0
|
||||
204 2.5 30.0 9.0 0.0 0.0 0.0 1.0
|
||||
205 2.5 30.0 12.0 0.0 0.0 0.0 1.0
|
||||
206 2.5 30.0 15.0 0.0 0.0 0.0 1.0
|
||||
207 2.5 30.0 18.0 0.0 0.0 0.0 1.0
|
||||
208 2.5 30.0 21.0 0.0 0.0 0.0 1.0
|
||||
209 2.5 30.0 24.0 0.0 0.0 0.0 1.0
|
||||
210 2.5 30.0 27.0 0.0 0.0 0.0 1.0
|
||||
211 2.5 30.0 30.0 0.0 0.0 0.0 1.0
|
||||
212 2.5 30.0 33.0 0.0 0.0 0.0 1.0
|
||||
213 2.5 30.0 36.0 0.0 0.0 0.0 1.0
|
||||
214 2.5 30.0 39.0 0.0 0.0 0.0 1.0
|
||||
215 2.5 30.0 42.0 0.0 0.0 0.0 1.0
|
||||
216 2.5 30.0 45.0 0.0 0.0 0.0 1.0
|
||||
217 2.5 30.0 48.0 0.0 0.0 0.0 1.0
|
||||
218 2.5 30.0 51.0 0.0 0.0 0.0 1.0
|
||||
219 2.5 30.0 54.0 0.0 0.0 0.0 1.0
|
||||
220 2.5 30.0 57.0 0.0 0.0 0.0 1.0
|
||||
221 2.5 33.0 0.0 0.0 0.0 0.0 1.0
|
||||
222 2.5 33.0 3.0 0.0 0.0 0.0 1.0
|
||||
223 2.5 33.0 6.0 0.0 0.0 0.0 1.0
|
||||
224 2.5 33.0 9.0 0.0 0.0 0.0 1.0
|
||||
225 2.5 33.0 12.0 0.0 0.0 0.0 1.0
|
||||
226 2.5 33.0 15.0 0.0 0.0 0.0 1.0
|
||||
227 2.5 33.0 18.0 0.0 0.0 0.0 1.0
|
||||
228 2.5 33.0 21.0 0.0 0.0 0.0 1.0
|
||||
229 2.5 33.0 24.0 0.0 0.0 0.0 1.0
|
||||
230 2.5 33.0 27.0 0.0 0.0 0.0 1.0
|
||||
231 2.5 33.0 30.0 0.0 0.0 0.0 1.0
|
||||
232 2.5 33.0 33.0 0.0 0.0 0.0 1.0
|
||||
233 2.5 33.0 36.0 0.0 0.0 0.0 1.0
|
||||
234 2.5 33.0 39.0 0.0 0.0 0.0 1.0
|
||||
235 2.5 33.0 42.0 0.0 0.0 0.0 1.0
|
||||
236 2.5 33.0 45.0 0.0 0.0 0.0 1.0
|
||||
237 2.5 33.0 48.0 0.0 0.0 0.0 1.0
|
||||
238 2.5 33.0 51.0 0.0 0.0 0.0 1.0
|
||||
239 2.5 33.0 54.0 0.0 0.0 0.0 1.0
|
||||
240 2.5 33.0 57.0 0.0 0.0 0.0 1.0
|
||||
241 2.5 36.0 0.0 0.0 0.0 0.0 1.0
|
||||
242 2.5 36.0 3.0 0.0 0.0 0.0 1.0
|
||||
243 2.5 36.0 6.0 0.0 0.0 0.0 1.0
|
||||
244 2.5 36.0 9.0 0.0 0.0 0.0 1.0
|
||||
245 2.5 36.0 12.0 0.0 0.0 0.0 1.0
|
||||
246 2.5 36.0 15.0 0.0 0.0 0.0 1.0
|
||||
247 2.5 36.0 18.0 0.0 0.0 0.0 1.0
|
||||
248 2.5 36.0 21.0 0.0 0.0 0.0 1.0
|
||||
249 2.5 36.0 24.0 0.0 0.0 0.0 1.0
|
||||
250 2.5 36.0 27.0 0.0 0.0 0.0 1.0
|
||||
251 2.5 36.0 30.0 0.0 0.0 0.0 1.0
|
||||
252 2.5 36.0 33.0 0.0 0.0 0.0 1.0
|
||||
253 2.5 36.0 36.0 0.0 0.0 0.0 1.0
|
||||
254 2.5 36.0 39.0 0.0 0.0 0.0 1.0
|
||||
255 2.5 36.0 42.0 0.0 0.0 0.0 1.0
|
||||
256 2.5 36.0 45.0 0.0 0.0 0.0 1.0
|
||||
257 2.5 36.0 48.0 0.0 0.0 0.0 1.0
|
||||
258 2.5 36.0 51.0 0.0 0.0 0.0 1.0
|
||||
259 2.5 36.0 54.0 0.0 0.0 0.0 1.0
|
||||
260 2.5 36.0 57.0 0.0 0.0 0.0 1.0
|
||||
261 2.5 39.0 0.0 0.0 0.0 0.0 1.0
|
||||
262 2.5 39.0 3.0 0.0 0.0 0.0 1.0
|
||||
263 2.5 39.0 6.0 0.0 0.0 0.0 1.0
|
||||
264 2.5 39.0 9.0 0.0 0.0 0.0 1.0
|
||||
265 2.5 39.0 12.0 0.0 0.0 0.0 1.0
|
||||
266 2.5 39.0 15.0 0.0 0.0 0.0 1.0
|
||||
267 2.5 39.0 18.0 0.0 0.0 0.0 1.0
|
||||
268 2.5 39.0 21.0 0.0 0.0 0.0 1.0
|
||||
269 2.5 39.0 24.0 0.0 0.0 0.0 1.0
|
||||
270 2.5 39.0 27.0 0.0 0.0 0.0 1.0
|
||||
271 2.5 39.0 30.0 0.0 0.0 0.0 1.0
|
||||
272 2.5 39.0 33.0 0.0 0.0 0.0 1.0
|
||||
273 2.5 39.0 36.0 0.0 0.0 0.0 1.0
|
||||
274 2.5 39.0 39.0 0.0 0.0 0.0 1.0
|
||||
275 2.5 39.0 42.0 0.0 0.0 0.0 1.0
|
||||
276 2.5 39.0 45.0 0.0 0.0 0.0 1.0
|
||||
277 2.5 39.0 48.0 0.0 0.0 0.0 1.0
|
||||
278 2.5 39.0 51.0 0.0 0.0 0.0 1.0
|
||||
279 2.5 39.0 54.0 0.0 0.0 0.0 1.0
|
||||
280 2.5 39.0 57.0 0.0 0.0 0.0 1.0
|
||||
281 2.5 42.0 0.0 0.0 0.0 0.0 1.0
|
||||
282 2.5 42.0 3.0 0.0 0.0 0.0 1.0
|
||||
283 2.5 42.0 6.0 0.0 0.0 0.0 1.0
|
||||
284 2.5 42.0 9.0 0.0 0.0 0.0 1.0
|
||||
285 2.5 42.0 12.0 0.0 0.0 0.0 1.0
|
||||
286 2.5 42.0 15.0 0.0 0.0 0.0 1.0
|
||||
287 2.5 42.0 18.0 0.0 0.0 0.0 1.0
|
||||
288 2.5 42.0 21.0 0.0 0.0 0.0 1.0
|
||||
289 2.5 42.0 24.0 0.0 0.0 0.0 1.0
|
||||
290 2.5 42.0 27.0 0.0 0.0 0.0 1.0
|
||||
291 2.5 42.0 30.0 0.0 0.0 0.0 1.0
|
||||
292 2.5 42.0 33.0 0.0 0.0 0.0 1.0
|
||||
293 2.5 42.0 36.0 0.0 0.0 0.0 1.0
|
||||
294 2.5 42.0 39.0 0.0 0.0 0.0 1.0
|
||||
295 2.5 42.0 42.0 0.0 0.0 0.0 1.0
|
||||
296 2.5 42.0 45.0 0.0 0.0 0.0 1.0
|
||||
297 2.5 42.0 48.0 0.0 0.0 0.0 1.0
|
||||
298 2.5 42.0 51.0 0.0 0.0 0.0 1.0
|
||||
299 2.5 42.0 54.0 0.0 0.0 0.0 1.0
|
||||
300 2.5 42.0 57.0 0.0 0.0 0.0 1.0
|
||||
301 2.5 45.0 0.0 0.0 0.0 0.0 1.0
|
||||
302 2.5 45.0 3.0 0.0 0.0 0.0 1.0
|
||||
303 2.5 45.0 6.0 0.0 0.0 0.0 1.0
|
||||
304 2.5 45.0 9.0 0.0 0.0 0.0 1.0
|
||||
305 2.5 45.0 12.0 0.0 0.0 0.0 1.0
|
||||
306 2.5 45.0 15.0 0.0 0.0 0.0 1.0
|
||||
307 2.5 45.0 18.0 0.0 0.0 0.0 1.0
|
||||
308 2.5 45.0 21.0 0.0 0.0 0.0 1.0
|
||||
309 2.5 45.0 24.0 0.0 0.0 0.0 1.0
|
||||
310 2.5 45.0 27.0 0.0 0.0 0.0 1.0
|
||||
311 2.5 45.0 30.0 0.0 0.0 0.0 1.0
|
||||
312 2.5 45.0 33.0 0.0 0.0 0.0 1.0
|
||||
313 2.5 45.0 36.0 0.0 0.0 0.0 1.0
|
||||
314 2.5 45.0 39.0 0.0 0.0 0.0 1.0
|
||||
315 2.5 45.0 42.0 0.0 0.0 0.0 1.0
|
||||
316 2.5 45.0 45.0 0.0 0.0 0.0 1.0
|
||||
317 2.5 45.0 48.0 0.0 0.0 0.0 1.0
|
||||
318 2.5 45.0 51.0 0.0 0.0 0.0 1.0
|
||||
319 2.5 45.0 54.0 0.0 0.0 0.0 1.0
|
||||
320 2.5 45.0 57.0 0.0 0.0 0.0 1.0
|
||||
321 2.5 48.0 0.0 0.0 0.0 0.0 1.0
|
||||
322 2.5 48.0 3.0 0.0 0.0 0.0 1.0
|
||||
323 2.5 48.0 6.0 0.0 0.0 0.0 1.0
|
||||
324 2.5 48.0 9.0 0.0 0.0 0.0 1.0
|
||||
325 2.5 48.0 12.0 0.0 0.0 0.0 1.0
|
||||
326 2.5 48.0 15.0 0.0 0.0 0.0 1.0
|
||||
327 2.5 48.0 18.0 0.0 0.0 0.0 1.0
|
||||
328 2.5 48.0 21.0 0.0 0.0 0.0 1.0
|
||||
329 2.5 48.0 24.0 0.0 0.0 0.0 1.0
|
||||
330 2.5 48.0 27.0 0.0 0.0 0.0 1.0
|
||||
331 2.5 48.0 30.0 0.0 0.0 0.0 1.0
|
||||
332 2.5 48.0 33.0 0.0 0.0 0.0 1.0
|
||||
333 2.5 48.0 36.0 0.0 0.0 0.0 1.0
|
||||
334 2.5 48.0 39.0 0.0 0.0 0.0 1.0
|
||||
335 2.5 48.0 42.0 0.0 0.0 0.0 1.0
|
||||
336 2.5 48.0 45.0 0.0 0.0 0.0 1.0
|
||||
337 2.5 48.0 48.0 0.0 0.0 0.0 1.0
|
||||
338 2.5 48.0 51.0 0.0 0.0 0.0 1.0
|
||||
339 2.5 48.0 54.0 0.0 0.0 0.0 1.0
|
||||
340 2.5 48.0 57.0 0.0 0.0 0.0 1.0
|
||||
341 2.5 51.0 0.0 0.0 0.0 0.0 1.0
|
||||
342 2.5 51.0 3.0 0.0 0.0 0.0 1.0
|
||||
343 2.5 51.0 6.0 0.0 0.0 0.0 1.0
|
||||
344 2.5 51.0 9.0 0.0 0.0 0.0 1.0
|
||||
345 2.5 51.0 12.0 0.0 0.0 0.0 1.0
|
||||
346 2.5 51.0 15.0 0.0 0.0 0.0 1.0
|
||||
347 2.5 51.0 18.0 0.0 0.0 0.0 1.0
|
||||
348 2.5 51.0 21.0 0.0 0.0 0.0 1.0
|
||||
349 2.5 51.0 24.0 0.0 0.0 0.0 1.0
|
||||
350 2.5 51.0 27.0 0.0 0.0 0.0 1.0
|
||||
351 2.5 51.0 30.0 0.0 0.0 0.0 1.0
|
||||
352 2.5 51.0 33.0 0.0 0.0 0.0 1.0
|
||||
353 2.5 51.0 36.0 0.0 0.0 0.0 1.0
|
||||
354 2.5 51.0 39.0 0.0 0.0 0.0 1.0
|
||||
355 2.5 51.0 42.0 0.0 0.0 0.0 1.0
|
||||
356 2.5 51.0 45.0 0.0 0.0 0.0 1.0
|
||||
357 2.5 51.0 48.0 0.0 0.0 0.0 1.0
|
||||
358 2.5 51.0 51.0 0.0 0.0 0.0 1.0
|
||||
359 2.5 51.0 54.0 0.0 0.0 0.0 1.0
|
||||
360 2.5 51.0 57.0 0.0 0.0 0.0 1.0
|
||||
361 2.5 54.0 0.0 0.0 0.0 0.0 1.0
|
||||
362 2.5 54.0 3.0 0.0 0.0 0.0 1.0
|
||||
363 2.5 54.0 6.0 0.0 0.0 0.0 1.0
|
||||
364 2.5 54.0 9.0 0.0 0.0 0.0 1.0
|
||||
365 2.5 54.0 12.0 0.0 0.0 0.0 1.0
|
||||
366 2.5 54.0 15.0 0.0 0.0 0.0 1.0
|
||||
367 2.5 54.0 18.0 0.0 0.0 0.0 1.0
|
||||
368 2.5 54.0 21.0 0.0 0.0 0.0 1.0
|
||||
369 2.5 54.0 24.0 0.0 0.0 0.0 1.0
|
||||
370 2.5 54.0 27.0 0.0 0.0 0.0 1.0
|
||||
371 2.5 54.0 30.0 0.0 0.0 0.0 1.0
|
||||
372 2.5 54.0 33.0 0.0 0.0 0.0 1.0
|
||||
373 2.5 54.0 36.0 0.0 0.0 0.0 1.0
|
||||
374 2.5 54.0 39.0 0.0 0.0 0.0 1.0
|
||||
375 2.5 54.0 42.0 0.0 0.0 0.0 1.0
|
||||
376 2.5 54.0 45.0 0.0 0.0 0.0 1.0
|
||||
377 2.5 54.0 48.0 0.0 0.0 0.0 1.0
|
||||
378 2.5 54.0 51.0 0.0 0.0 0.0 1.0
|
||||
379 2.5 54.0 54.0 0.0 0.0 0.0 1.0
|
||||
380 2.5 54.0 57.0 0.0 0.0 0.0 1.0
|
||||
381 2.5 57.0 0.0 0.0 0.0 0.0 1.0
|
||||
382 2.5 57.0 3.0 0.0 0.0 0.0 1.0
|
||||
383 2.5 57.0 6.0 0.0 0.0 0.0 1.0
|
||||
384 2.5 57.0 9.0 0.0 0.0 0.0 1.0
|
||||
385 2.5 57.0 12.0 0.0 0.0 0.0 1.0
|
||||
386 2.5 57.0 15.0 0.0 0.0 0.0 1.0
|
||||
387 2.5 57.0 18.0 0.0 0.0 0.0 1.0
|
||||
388 2.5 57.0 21.0 0.0 0.0 0.0 1.0
|
||||
389 2.5 57.0 24.0 0.0 0.0 0.0 1.0
|
||||
390 2.5 57.0 27.0 0.0 0.0 0.0 1.0
|
||||
391 2.5 57.0 30.0 0.0 0.0 0.0 1.0
|
||||
392 2.5 57.0 33.0 0.0 0.0 0.0 1.0
|
||||
393 2.5 57.0 36.0 0.0 0.0 0.0 1.0
|
||||
394 2.5 57.0 39.0 0.0 0.0 0.0 1.0
|
||||
395 2.5 57.0 42.0 0.0 0.0 0.0 1.0
|
||||
396 2.5 57.0 45.0 0.0 0.0 0.0 1.0
|
||||
397 2.5 57.0 48.0 0.0 0.0 0.0 1.0
|
||||
398 2.5 57.0 51.0 0.0 0.0 0.0 1.0
|
||||
399 2.5 57.0 54.0 0.0 0.0 0.0 1.0
|
||||
400 2.5 57.0 57.0 0.0 0.0 0.0 1.0
|
||||
47
examples/SPIN/gneb/skyrmion/in.gneb.skyrmion
Normal file
47
examples/SPIN/gneb/skyrmion/in.gneb.skyrmion
Normal file
@ -0,0 +1,47 @@
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style spin
|
||||
|
||||
# necessary for the serial algorithm (sametag)
|
||||
atom_modify map array
|
||||
|
||||
# setting mass, mag. moments, and interactions for bcc iron
|
||||
# (mass not necessary for fixed lattice calculation)
|
||||
|
||||
read_data initial.skyrmion
|
||||
mass 1 55.845
|
||||
|
||||
pair_style hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
|
||||
pair_coeff * * spin/exchange exchange 3.1 0.01593 0.06626915552 1.211
|
||||
pair_coeff * * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0
|
||||
fix_modify 1 energy yes
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
fix 3 all neb/spin 1.0
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
compute out_mag all spin
|
||||
variable magx equal c_out_mag[1]
|
||||
variable magy equal c_out_mag[2]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time v_magx v_magz v_magnorm etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
variable u universe 1 2 3 4
|
||||
dump 1 all custom 1 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3]
|
||||
|
||||
min_style spin
|
||||
min_modify alpha_damp 1.0 discrete_factor 10.0
|
||||
neb/spin 1.0e-9 1.0e-9 10000 10000 10 final final.skyrmion
|
||||
818
examples/SPIN/gneb/skyrmion/initial.skyrmion
Normal file
818
examples/SPIN/gneb/skyrmion/initial.skyrmion
Normal file
@ -0,0 +1,818 @@
|
||||
LAMMPS data file via write_data, version 28 Feb 2019, timestep = 6
|
||||
|
||||
400 atoms
|
||||
1 atom types
|
||||
|
||||
0.0000000000000000e+00 6.0000000000000000e+01 xlo xhi
|
||||
0.0000000000000000e+00 6.0000000000000000e+01 ylo yhi
|
||||
0.0000000000000000e+00 3.0000000000000000e+00 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 55.845
|
||||
|
||||
Atoms # spin
|
||||
|
||||
1 1 2.5000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -3.9693242391277868e-03 -3.9693242391277929e-03 9.9998424434096433e-01 0 0 0
|
||||
21 1 2.5000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.1868011343002482e-02 -4.8145058779812530e-03 9.9991798205648519e-01 0 0 0
|
||||
41 1 2.5000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.9561861499557517e-02 -6.5828744882500201e-03 9.9978697697966845e-01 0 0 0
|
||||
61 1 2.5000000000000000e+00 9.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -2.6644762521588476e-02 -9.3989438861432541e-03 9.9960077855311480e-01 0 0 0
|
||||
81 1 2.5000000000000000e+00 1.2000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -3.2364838887478299e-02 -1.3362272507461704e-02 9.9938679542868891e-01 0 0 0
|
||||
101 1 2.5000000000000000e+00 1.5000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -3.5634992015801843e-02 -1.8429703183501425e-02 9.9919492261750509e-01 0 0 0
|
||||
121 1 2.5000000000000000e+00 1.8000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -3.5235119566844247e-02 -2.4270277420221115e-02 9.9908430073895971e-01 0 0 0
|
||||
141 1 2.5000000000000000e+00 2.1000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -3.0237916900163156e-02 -3.0163850736159143e-02 9.9908748890690546e-01 0 0 0
|
||||
161 1 2.5000000000000000e+00 2.4000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -2.0551704657275890e-02 -3.5058787503171429e-02 9.9917391321755789e-01 0 0 0
|
||||
181 1 2.5000000000000000e+00 2.7000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 -7.2971667669136115e-03 -3.7860607272964066e-02 9.9925638640646097e-01 0 0 0
|
||||
201 1 2.5000000000000000e+00 3.0000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 7.2971667669136028e-03 -3.7860607272964066e-02 9.9925638640646086e-01 0 0 0
|
||||
221 1 2.5000000000000000e+00 3.3000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 2.0551704657275901e-02 -3.5058787503171443e-02 9.9917391321755789e-01 0 0 0
|
||||
241 1 2.5000000000000000e+00 3.6000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 3.0237916900163156e-02 -3.0163850736159153e-02 9.9908748890690535e-01 0 0 0
|
||||
261 1 2.5000000000000000e+00 3.9000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 3.5235119566844234e-02 -2.4270277420221108e-02 9.9908430073895960e-01 0 0 0
|
||||
281 1 2.5000000000000000e+00 4.2000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 3.5634992015801829e-02 -1.8429703183501414e-02 9.9919492261750498e-01 0 0 0
|
||||
301 1 2.5000000000000000e+00 4.5000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 3.2364838887478306e-02 -1.3362272507461704e-02 9.9938679542868891e-01 0 0 0
|
||||
321 1 2.5000000000000000e+00 4.8000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 2.6644762521588494e-02 -9.3989438861432611e-03 9.9960077855311491e-01 0 0 0
|
||||
341 1 2.5000000000000000e+00 5.1000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 1.9561861499557517e-02 -6.5828744882500201e-03 9.9978697697966856e-01 0 0 0
|
||||
361 1 2.5000000000000000e+00 5.4000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 1.1868011343002482e-02 -4.8145058779812547e-03 9.9991798205648508e-01 0 0 0
|
||||
381 1 2.5000000000000000e+00 5.7000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00 3.9693242391277929e-03 -3.9693242391277937e-03 9.9998424434096445e-01 0 0 0
|
||||
2 1 2.5000000000000000e+00 0.0000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 -4.8145058779812512e-03 -1.1868011343002475e-02 9.9991798205648519e-01 0 0 0
|
||||
22 1 2.5000000000000000e+00 3.0000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 -1.4489047587394138e-02 -1.4489047587394138e-02 9.9979004545955574e-01 0 0 0
|
||||
42 1 2.5000000000000000e+00 6.0000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 -2.4184841732588187e-02 -2.0009637034407928e-02 9.9950723251816487e-01 0 0 0
|
||||
62 1 2.5000000000000000e+00 9.0000000000000000e+00 3.0000000000000000e+00 0.0000000000000000e+00 -3.3534698701154796e-02 -2.8894018478272422e-02 9.9901979944303421e-01 0 0 0
|
||||
82 1 2.5000000000000000e+00 1.2000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -4.1631298256624205e-02 -4.1569375222726884e-02 9.9826791095830603e-01 0 0 0
|
||||
102 1 2.5000000000000000e+00 1.5000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -4.6947676140268457e-02 -5.8031121465001792e-02 9.9721026100143129e-01 0 0 0
|
||||
122 1 2.5000000000000000e+00 1.8000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -4.7535409319668050e-02 -7.7312985281705895e-02 9.9587302763336383e-01 0 0 0
|
||||
142 1 2.5000000000000000e+00 2.1000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -4.1653952417990837e-02 -9.7059251840902777e-02 9.9440658177630958e-01 0 0 0
|
||||
162 1 2.5000000000000000e+00 2.4000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -2.8752729368399305e-02 -1.1365104497068100e-01 9.9310458690459180e-01 0 0 0
|
||||
182 1 2.5000000000000000e+00 2.7000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 -1.0293413501576094e-02 -1.2321728304286263e-01 9.9232633079951105e-01 0 0 0
|
||||
202 1 2.5000000000000000e+00 3.0000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 1.0293413501576086e-02 -1.2321728304286261e-01 9.9232633079951116e-01 0 0 0
|
||||
222 1 2.5000000000000000e+00 3.3000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 2.8752729368399291e-02 -1.1365104497068100e-01 9.9310458690459180e-01 0 0 0
|
||||
242 1 2.5000000000000000e+00 3.6000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 4.1653952417990824e-02 -9.7059251840902777e-02 9.9440658177630958e-01 0 0 0
|
||||
262 1 2.5000000000000000e+00 3.9000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 4.7535409319668057e-02 -7.7312985281705895e-02 9.9587302763336383e-01 0 0 0
|
||||
282 1 2.5000000000000000e+00 4.2000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 4.6947676140268443e-02 -5.8031121465001792e-02 9.9721026100143140e-01 0 0 0
|
||||
302 1 2.5000000000000000e+00 4.5000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 4.1631298256624191e-02 -4.1569375222726877e-02 9.9826791095830592e-01 0 0 0
|
||||
322 1 2.5000000000000000e+00 4.8000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 3.3534698701154809e-02 -2.8894018478272433e-02 9.9901979944303410e-01 0 0 0
|
||||
342 1 2.5000000000000000e+00 5.1000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 2.4184841732588204e-02 -2.0009637034407945e-02 9.9950723251816487e-01 0 0 0
|
||||
362 1 2.5000000000000000e+00 5.4000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 1.4489047587394149e-02 -1.4489047587394138e-02 9.9979004545955585e-01 0 0 0
|
||||
382 1 2.5000000000000000e+00 5.7000000000000000e+01 3.0000000000000000e+00 0.0000000000000000e+00 4.8145058779812547e-03 -1.1868011343002482e-02 9.9991798205648519e-01 0 0 0
|
||||
3 1 2.5000000000000000e+00 0.0000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 -6.5828744882500158e-03 -1.9561861499557527e-02 9.9978697697966856e-01 0 0 0
|
||||
23 1 2.5000000000000000e+00 3.0000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 -2.0009637034407932e-02 -2.4184841732588200e-02 9.9950723251816498e-01 0 0 0
|
||||
43 1 2.5000000000000000e+00 6.0000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 -3.4047077037887570e-02 -3.4047077037887577e-02 9.9884012388887977e-01 0 0 0
|
||||
63 1 2.5000000000000000e+00 9.0000000000000000e+00 6.0000000000000000e+00 0.0000000000000000e+00 -4.8498220596720307e-02 -5.0241530269051260e-02 9.9755887607457838e-01 0 0 0
|
||||
83 1 2.5000000000000000e+00 1.2000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -6.2196104012276265e-02 -7.3954811425103587e-02 9.9532021506285684e-01 0 0 0
|
||||
103 1 2.5000000000000000e+00 1.5000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -7.2649992877525826e-02 -1.0567933713226435e-01 9.9174283775491956e-01 0 0 0
|
||||
123 1 2.5000000000000000e+00 1.8000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -7.6126593015943808e-02 -1.4398087111736477e-01 9.8664798717073865e-01 0 0 0
|
||||
143 1 2.5000000000000000e+00 2.1000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -6.8709104650143085e-02 -1.8428174194944069e-01 9.8046891767268973e-01 0 0 0
|
||||
163 1 2.5000000000000000e+00 2.4000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -4.8457456104349643e-02 -2.1884669159068457e-01 9.7455528346405618e-01 0 0 0
|
||||
183 1 2.5000000000000000e+00 2.7000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 -1.7543173966404597e-02 -2.3902270727461428e-01 9.7085548999544657e-01 0 0 0
|
||||
203 1 2.5000000000000000e+00 3.0000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 1.7543173966404587e-02 -2.3902270727461422e-01 9.7085548999544646e-01 0 0 0
|
||||
223 1 2.5000000000000000e+00 3.3000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 4.8457456104349608e-02 -2.1884669159068454e-01 9.7455528346405618e-01 0 0 0
|
||||
243 1 2.5000000000000000e+00 3.6000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 6.8709104650143044e-02 -1.8428174194944069e-01 9.8046891767268962e-01 0 0 0
|
||||
263 1 2.5000000000000000e+00 3.9000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 7.6126593015943766e-02 -1.4398087111736474e-01 9.8664798717073865e-01 0 0 0
|
||||
283 1 2.5000000000000000e+00 4.2000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 7.2649992877525826e-02 -1.0567933713226434e-01 9.9174283775491956e-01 0 0 0
|
||||
303 1 2.5000000000000000e+00 4.5000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 6.2196104012276258e-02 -7.3954811425103573e-02 9.9532021506285673e-01 0 0 0
|
||||
323 1 2.5000000000000000e+00 4.8000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 4.8498220596720307e-02 -5.0241530269051260e-02 9.9755887607457838e-01 0 0 0
|
||||
343 1 2.5000000000000000e+00 5.1000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 3.4047077037887577e-02 -3.4047077037887577e-02 9.9884012388887966e-01 0 0 0
|
||||
363 1 2.5000000000000000e+00 5.4000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 2.0009637034407942e-02 -2.4184841732588211e-02 9.9950723251816498e-01 0 0 0
|
||||
383 1 2.5000000000000000e+00 5.7000000000000000e+01 6.0000000000000000e+00 0.0000000000000000e+00 6.5828744882500201e-03 -1.9561861499557531e-02 9.9978697697966856e-01 0 0 0
|
||||
4 1 2.5000000000000000e+00 0.0000000000000000e+00 9.0000000000000000e+00 0.0000000000000000e+00 -9.3989438861432524e-03 -2.6644762521588497e-02 9.9960077855311480e-01 0 0 0
|
||||
24 1 2.5000000000000000e+00 3.0000000000000000e+00 9.0000000000000000e+00 0.0000000000000000e+00 -2.8894018478272426e-02 -3.3534698701154803e-02 9.9901979944303410e-01 0 0 0
|
||||
44 1 2.5000000000000000e+00 6.0000000000000000e+00 9.0000000000000000e+00 0.0000000000000000e+00 -5.0241530269051232e-02 -4.8498220596720286e-02 9.9755887607457827e-01 0 0 0
|
||||
64 1 2.5000000000000000e+00 9.0000000000000000e+00 9.0000000000000000e+00 0.0000000000000000e+00 -7.3771080474423129e-02 -7.3771080474423115e-02 9.9454293792237669e-01 0 0 0
|
||||
84 1 2.5000000000000000e+00 1.2000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 -9.8127311868331568e-02 -1.1214098437153223e-01 9.8883539089662387e-01 0 0 0
|
||||
104 1 2.5000000000000000e+00 1.5000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 -1.1922421797550638e-01 -1.6561310406555055e-01 9.7895755046370747e-01 0 0 0
|
||||
124 1 2.5000000000000000e+00 1.8000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 -1.2975986317850730e-01 -2.3284022614534144e-01 9.6381938504912923e-01 0 0 0
|
||||
144 1 2.5000000000000000e+00 2.1000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 -1.2090775615411226e-01 -3.0602867088565672e-01 9.4431338394504205e-01 0 0 0
|
||||
164 1 2.5000000000000000e+00 2.4000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 -8.7191355151399766e-02 -3.7026717261459724e-01 9.2482424734154478e-01 0 0 0
|
||||
184 1 2.5000000000000000e+00 2.7000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 -3.1922103301157183e-02 -4.0821375936870385e-01 9.1232806927272614e-01 0 0 0
|
||||
204 1 2.5000000000000000e+00 3.0000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 3.1922103301157155e-02 -4.0821375936870385e-01 9.1232806927272625e-01 0 0 0
|
||||
224 1 2.5000000000000000e+00 3.3000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 8.7191355151399724e-02 -3.7026717261459718e-01 9.2482424734154478e-01 0 0 0
|
||||
244 1 2.5000000000000000e+00 3.6000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 1.2090775615411219e-01 -3.0602867088565661e-01 9.4431338394504194e-01 0 0 0
|
||||
264 1 2.5000000000000000e+00 3.9000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 1.2975986317850724e-01 -2.3284022614534142e-01 9.6381938504912912e-01 0 0 0
|
||||
284 1 2.5000000000000000e+00 4.2000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 1.1922421797550635e-01 -1.6561310406555052e-01 9.7895755046370747e-01 0 0 0
|
||||
304 1 2.5000000000000000e+00 4.5000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 9.8127311868331568e-02 -1.1214098437153228e-01 9.8883539089662398e-01 0 0 0
|
||||
324 1 2.5000000000000000e+00 4.8000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 7.3771080474423129e-02 -7.3771080474423142e-02 9.9454293792237669e-01 0 0 0
|
||||
344 1 2.5000000000000000e+00 5.1000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 5.0241530269051253e-02 -4.8498220596720314e-02 9.9755887607457827e-01 0 0 0
|
||||
364 1 2.5000000000000000e+00 5.4000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 2.8894018478272443e-02 -3.3534698701154816e-02 9.9901979944303410e-01 0 0 0
|
||||
384 1 2.5000000000000000e+00 5.7000000000000000e+01 9.0000000000000000e+00 0.0000000000000000e+00 9.3989438861432611e-03 -2.6644762521588494e-02 9.9960077855311480e-01 0 0 0
|
||||
5 1 2.5000000000000000e+00 0.0000000000000000e+00 1.2000000000000000e+01 0.0000000000000000e+00 -1.3362272507461699e-02 -3.2364838887478299e-02 9.9938679542868880e-01 0 0 0
|
||||
25 1 2.5000000000000000e+00 3.0000000000000000e+00 1.2000000000000000e+01 0.0000000000000000e+00 -4.1569375222726863e-02 -4.1631298256624198e-02 9.9826791095830603e-01 0 0 0
|
||||
45 1 2.5000000000000000e+00 6.0000000000000000e+00 1.2000000000000000e+01 0.0000000000000000e+00 -7.3954811425103559e-02 -6.2196104012276245e-02 9.9532021506285673e-01 0 0 0
|
||||
65 1 2.5000000000000000e+00 9.0000000000000000e+00 1.2000000000000000e+01 0.0000000000000000e+00 -1.1214098437153225e-01 -9.8127311868331554e-02 9.8883539089662398e-01 0 0 0
|
||||
85 1 2.5000000000000000e+00 1.2000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 -1.5508313718777630e-01 -1.5508313718777628e-01 9.7565282817198595e-01 0 0 0
|
||||
105 1 2.5000000000000000e+00 1.5000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 -1.9646003525323200e-01 -2.3830565311068275e-01 9.5111191257590177e-01 0 0 0
|
||||
125 1 2.5000000000000000e+00 1.8000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 -2.2234110900479689e-01 -3.4758786972735528e-01 9.1090455266450188e-01 0 0 0
|
||||
145 1 2.5000000000000000e+00 2.1000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 -2.1357380845070773e-01 -4.7013886220911955e-01 8.5636188529416402e-01 0 0 0
|
||||
165 1 2.5000000000000000e+00 2.4000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 -1.5692234237038313e-01 -5.7886257432716870e-01 8.0018341554190886e-01 0 0 0
|
||||
185 1 2.5000000000000000e+00 2.7000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 -5.7920936211537863e-02 -6.4295931380698856e-01 7.6370706814669809e-01 0 0 0
|
||||
205 1 2.5000000000000000e+00 3.0000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 5.7920936211537793e-02 -6.4295931380698856e-01 7.6370706814669809e-01 0 0 0
|
||||
225 1 2.5000000000000000e+00 3.3000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 1.5692234237038311e-01 -5.7886257432716881e-01 8.0018341554190908e-01 0 0 0
|
||||
245 1 2.5000000000000000e+00 3.6000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 2.1357380845070767e-01 -4.7013886220911949e-01 8.5636188529416413e-01 0 0 0
|
||||
265 1 2.5000000000000000e+00 3.9000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 2.2234110900479689e-01 -3.4758786972735528e-01 9.1090455266450188e-01 0 0 0
|
||||
285 1 2.5000000000000000e+00 4.2000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 1.9646003525323205e-01 -2.3830565311068283e-01 9.5111191257590177e-01 0 0 0
|
||||
305 1 2.5000000000000000e+00 4.5000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 1.5508313718777633e-01 -1.5508313718777636e-01 9.7565282817198595e-01 0 0 0
|
||||
325 1 2.5000000000000000e+00 4.8000000000000000e+01 1.2000000000000000e+01 0.0000000000000000e+00 1.1214098437153229e-01 -9.8127311868331610e-02 9.8883539089662398e-01 0 0 0
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36 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
56 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
76 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
96 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
116 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
136 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
156 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
176 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
196 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
216 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
236 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
256 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
276 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
296 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
316 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
336 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
356 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
376 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
396 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
37 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
57 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
77 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
97 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
117 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
137 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
157 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
177 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
197 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
217 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
237 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
257 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
277 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
297 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
317 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
337 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
357 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
377 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
397 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
38 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
58 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
78 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
98 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
118 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
138 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
158 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
178 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
198 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
218 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
238 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
258 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
278 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
298 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
318 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
338 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
358 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
378 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
398 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
39 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
59 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
79 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
99 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
119 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
139 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
159 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
179 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
199 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
219 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
239 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
259 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
279 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
299 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
319 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
339 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
359 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
379 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
399 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
40 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
60 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
80 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
100 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
120 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
140 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
160 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
180 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
200 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
220 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
240 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
260 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
280 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
300 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
320 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
340 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
360 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
380 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
400 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
@ -40,6 +40,6 @@ thermo_style custom step time v_magnorm v_emag v_tmag temp etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
compute outsp all property/atom spx spy spz sp fmx fmy fmz
|
||||
dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
dump 1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
|
||||
|
||||
run 100
|
||||
|
||||
@ -8,6 +8,8 @@ atom in the system
|
||||
* integrating the equations of motion for the coupled spin-lattice system
|
||||
* implementing magnetic pair interactions and magnetic forces
|
||||
* thermostating and applying a transverse damping to the magnetic spins
|
||||
* minimizing spin configurations with an adaptive timestep scheme
|
||||
* performing geodesic NEB calculations
|
||||
* computing and outputing magnetic quantities
|
||||
* minimizing the energy or total torque of a magnetic system
|
||||
|
||||
@ -15,7 +17,8 @@ The different options provided by this package are explained in the
|
||||
LAMMPS documentation.
|
||||
|
||||
Once you have successfully built LAMMPS with this package, you can test
|
||||
it using one of the input files provided from the examples/SPIN dir:
|
||||
it using one of the input files provided from the examples/SPIN dir.
|
||||
For example:
|
||||
|
||||
./lmp_serial < lammps/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
|
||||
|
||||
|
||||
@ -943,6 +943,10 @@ bigint AtomVecSpin::memory_usage()
|
||||
return bytes;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
clear all forces (mech and mag)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecSpin::force_clear(int /*n*/, size_t nbytes)
|
||||
{
|
||||
memset(&atom->f[0][0],0,3*nbytes);
|
||||
|
||||
1014
src/SPIN/fix_neb_spin.cpp
Normal file
1014
src/SPIN/fix_neb_spin.cpp
Normal file
File diff suppressed because it is too large
Load Diff
112
src/SPIN/fix_neb_spin.h
Normal file
112
src/SPIN/fix_neb_spin.h
Normal file
@ -0,0 +1,112 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(neb/spin,FixNEBSpin)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NEB_SPIN_H
|
||||
#define LMP_FIX_NEB_SPIN_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNEBSpin : public Fix {
|
||||
public:
|
||||
double veng,plen,nlen,dotpath,dottangrad,gradlen,dotgrad;
|
||||
int rclimber;
|
||||
|
||||
FixNEBSpin(class LAMMPS *, int, char **);
|
||||
~FixNEBSpin();
|
||||
int setmask();
|
||||
void init();
|
||||
void min_setup(int);
|
||||
void min_post_force(int);
|
||||
|
||||
private:
|
||||
int me,nprocs,nprocs_universe;
|
||||
double kspring,kspringIni,kspringFinal,kspringPerp,EIniIni,EFinalIni;
|
||||
bool StandardNEB,NEBLongRange,PerpSpring,FreeEndIni,FreeEndFinal;
|
||||
bool FreeEndFinalWithRespToEIni,FinalAndInterWithRespToEIni;
|
||||
bool SpinLattice;
|
||||
int ireplica,nreplica;
|
||||
int procnext,procprev;
|
||||
int cmode;
|
||||
MPI_Comm uworld;
|
||||
MPI_Comm rootworld;
|
||||
|
||||
|
||||
char *id_pe;
|
||||
class Compute *pe;
|
||||
|
||||
int nebatoms;
|
||||
int ntotal; // total # of atoms, NEB or not
|
||||
int maxlocal; // size of xprev,xnext,tangent arrays
|
||||
double *nlenall;
|
||||
double **xprev,**xnext,**fnext;
|
||||
double **spprev,**spnext,**fmnext;
|
||||
double **springF;
|
||||
double **tangent;
|
||||
double **xsend,**xrecv; // coords to send/recv to/from other replica
|
||||
double **fsend,**frecv; // coords to send/recv to/from other replica
|
||||
double **spsend,**sprecv; // sp to send/recv to/from other replica
|
||||
double **fmsend,**fmrecv; // fm to send/recv to/from other replica
|
||||
tagint *tagsend,*tagrecv; // ditto for atom IDs
|
||||
|
||||
// info gathered from all procs in my replica
|
||||
double **xsendall,**xrecvall; // coords to send/recv to/from other replica
|
||||
double **fsendall,**frecvall; // force to send/recv to/from other replica
|
||||
double **spsendall,**sprecvall; // sp to send/recv to/from other replica
|
||||
double **fmsendall,**fmrecvall; // fm to send/recv to/from other replica
|
||||
tagint *tagsendall,*tagrecvall; // ditto for atom IDs
|
||||
|
||||
int *counts,*displacements; // used for MPI_Gather
|
||||
|
||||
double geodesic_distance(double *, double *);
|
||||
void inter_replica_comm();
|
||||
void reallocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Potential energy ID for fix neb does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Too many active GNEB atoms
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Too many atoms for GNEB
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
U: Atom count changed in fix neb
|
||||
|
||||
This is not allowed in a GNEB calculation.
|
||||
|
||||
*/
|
||||
853
src/SPIN/neb_spin.cpp
Normal file
853
src/SPIN/neb_spin.cpp
Normal file
@ -0,0 +1,853 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ------------------------------------------------------------------------
|
||||
Contributing authors: Julien Tranchida (SNL)
|
||||
|
||||
Please cite the related publication:
|
||||
Bessarab, P. F., Uzdin, V. M., & Jónsson, H. (2015).
|
||||
Method for finding mechanism and activation energy of magnetic transitions,
|
||||
applied to skyrmion and antivortex annihilation.
|
||||
Computer Physics Communications, 196, 335-347.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h
|
||||
// due to OpenMPI bug which sets INT64_MAX via its mpi.h
|
||||
// before lmptype.h can set flags to insure it is done correctly
|
||||
|
||||
#include "lmptype.h"
|
||||
#include <mpi.h>
|
||||
#include <cmath>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "neb_spin.h"
|
||||
#include "citeme.h"
|
||||
#include "compute.h"
|
||||
#include "force.h"
|
||||
#include "universe.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "min.h"
|
||||
#include "modify.h"
|
||||
#include "fix.h"
|
||||
#include "fix_neb_spin.h"
|
||||
#include "output.h"
|
||||
#include "thermo.h"
|
||||
#include "finish.h"
|
||||
#include "timer.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "math_const.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
static const char cite_neb_spin[] =
|
||||
"neb/spin command:\n\n"
|
||||
"@article{bessarab2015method,\n"
|
||||
"title={Method for finding mechanism and activation energy of "
|
||||
"magnetic transitions, applied to skyrmion and antivortex "
|
||||
"annihilation},\n"
|
||||
"author={Bessarab, P.F. and Uzdin, V.M. and J{\'o}nsson, H.},\n"
|
||||
"journal={Computer Physics Communications},\n"
|
||||
"volume={196},\n"
|
||||
"pages={335--347},\n"
|
||||
"year={2015},\n"
|
||||
"publisher={Elsevier}\n"
|
||||
"doi={10.1016/j.cpc.2015.07.001}\n"
|
||||
"}\n\n";
|
||||
|
||||
#define MAXLINE 256
|
||||
#define CHUNK 1024
|
||||
// 8 attributes: tag, spin norm, position (3), spin direction (3)
|
||||
#define ATTRIBUTE_PERLINE 8
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
NEBSpin::NEBSpin(LAMMPS *lmp) : Pointers(lmp) {
|
||||
if (lmp->citeme) lmp->citeme->add(cite_neb_spin);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
NEBSpin::~NEBSpin()
|
||||
{
|
||||
MPI_Comm_free(&roots);
|
||||
memory->destroy(all);
|
||||
delete [] rdist;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
perform NEBSpin on multiple replicas
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NEBSpin::command(int narg, char **arg)
|
||||
{
|
||||
if (domain->box_exist == 0)
|
||||
error->all(FLERR,"NEBSpin command before simulation box is defined");
|
||||
|
||||
if (narg < 6) error->universe_all(FLERR,"Illegal NEBSpin command");
|
||||
|
||||
etol = force->numeric(FLERR,arg[0]);
|
||||
ttol = force->numeric(FLERR,arg[1]);
|
||||
n1steps = force->inumeric(FLERR,arg[2]);
|
||||
n2steps = force->inumeric(FLERR,arg[3]);
|
||||
nevery = force->inumeric(FLERR,arg[4]);
|
||||
|
||||
// error checks
|
||||
|
||||
if (etol < 0.0) error->all(FLERR,"Illegal NEBSpin command");
|
||||
if (ttol < 0.0) error->all(FLERR,"Illegal NEBSpin command");
|
||||
if (nevery <= 0) error->universe_all(FLERR,"Illegal NEBSpin command");
|
||||
if (n1steps % nevery || n2steps % nevery)
|
||||
error->universe_all(FLERR,"Illegal NEBSpin command");
|
||||
|
||||
// replica info
|
||||
|
||||
nreplica = universe->nworlds;
|
||||
ireplica = universe->iworld;
|
||||
me_universe = universe->me;
|
||||
uworld = universe->uworld;
|
||||
MPI_Comm_rank(world,&me);
|
||||
|
||||
// check metal units and spin atom/style
|
||||
|
||||
if (!atom->sp_flag)
|
||||
error->all(FLERR,"neb/spin requires atom/spin style");
|
||||
if (strcmp(update->unit_style,"metal") != 0)
|
||||
error->all(FLERR,"neb/spin simulation requires metal unit style");
|
||||
|
||||
// error checks
|
||||
|
||||
if (nreplica == 1) error->all(FLERR,"Cannot use NEBSpin with a single replica");
|
||||
if (atom->map_style == 0)
|
||||
error->all(FLERR,"Cannot use NEBSpin unless atom map exists");
|
||||
|
||||
// process file-style setting to setup initial configs for all replicas
|
||||
|
||||
if (strcmp(arg[5],"final") == 0) {
|
||||
if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEBSpin command");
|
||||
infile = arg[6];
|
||||
readfile(infile,0);
|
||||
} else if (strcmp(arg[5],"each") == 0) {
|
||||
if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEBSpin command");
|
||||
infile = arg[6];
|
||||
readfile(infile,1);
|
||||
} else if (strcmp(arg[5],"none") == 0) {
|
||||
if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEBSpin command");
|
||||
} else error->universe_all(FLERR,"Illegal NEBSpin command");
|
||||
|
||||
verbose=false;
|
||||
if (strcmp(arg[narg-1],"verbose") == 0) verbose=true;
|
||||
|
||||
run();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
run NEBSpin on multiple replicas
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NEBSpin::run()
|
||||
{
|
||||
// create MPI communicator for root proc from each world
|
||||
|
||||
int color;
|
||||
if (me == 0) color = 0;
|
||||
else color = 1;
|
||||
MPI_Comm_split(uworld,color,0,&roots);
|
||||
|
||||
// search for neb_spin fix, allocate it
|
||||
|
||||
int ineb;
|
||||
for (ineb = 0; ineb < modify->nfix; ineb++)
|
||||
if (strcmp(modify->fix[ineb]->style,"neb/spin") == 0) break;
|
||||
if (ineb == modify->nfix) error->all(FLERR,"NEBSpin requires use of fix neb/spin");
|
||||
|
||||
fneb = (FixNEBSpin *) modify->fix[ineb];
|
||||
if (verbose) numall =7;
|
||||
else numall = 4;
|
||||
memory->create(all,nreplica,numall,"neb:all");
|
||||
rdist = new double[nreplica];
|
||||
|
||||
// initialize LAMMPS
|
||||
|
||||
update->whichflag = 2;
|
||||
update->etol = etol;
|
||||
update->ftol = ttol; // update->ftol is a torque tolerance
|
||||
update->multireplica = 1;
|
||||
|
||||
lmp->init();
|
||||
|
||||
// check if correct minimizer is setup
|
||||
|
||||
if (update->minimize->searchflag)
|
||||
error->all(FLERR,"NEBSpin requires damped dynamics minimizer");
|
||||
if (strcmp(update->minimize_style,"spin") != 0)
|
||||
error->all(FLERR,"NEBSpin requires spin minimizer");
|
||||
|
||||
// setup regular NEBSpin minimization
|
||||
|
||||
FILE *uscreen = universe->uscreen;
|
||||
FILE *ulogfile = universe->ulogfile;
|
||||
|
||||
if (me_universe == 0 && uscreen)
|
||||
fprintf(uscreen,"Setting up regular NEBSpin ...\n");
|
||||
|
||||
update->beginstep = update->firststep = update->ntimestep;
|
||||
update->endstep = update->laststep = update->firststep + n1steps;
|
||||
update->nsteps = n1steps;
|
||||
update->max_eval = n1steps;
|
||||
if (update->laststep < 0)
|
||||
error->all(FLERR,"Too many timesteps for NEBSpin");
|
||||
|
||||
update->minimize->setup();
|
||||
|
||||
if (me_universe == 0) {
|
||||
if (uscreen) {
|
||||
if (verbose) {
|
||||
fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN "
|
||||
"GradV0dottan DN0 ... GradVNdottan DNN\n");
|
||||
} else {
|
||||
fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
|
||||
"RDN PEN\n");
|
||||
}
|
||||
}
|
||||
|
||||
if (ulogfile) {
|
||||
if (verbose) {
|
||||
fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN "
|
||||
"GradV0dottan DN0 ... GradVNdottan DNN\n");
|
||||
} else {
|
||||
fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
|
||||
"RDN PEN\n");
|
||||
}
|
||||
}
|
||||
}
|
||||
print_status();
|
||||
|
||||
// perform regular NEBSpin for n1steps or until replicas converge
|
||||
// retrieve PE values from fix NEBSpin and print every nevery iterations
|
||||
// break out of while loop early if converged
|
||||
// damped dynamic min styles insure all replicas converge together
|
||||
|
||||
timer->init();
|
||||
timer->barrier_start();
|
||||
|
||||
while (update->minimize->niter < n1steps) {
|
||||
update->minimize->run(nevery);
|
||||
print_status();
|
||||
if (update->minimize->stop_condition) break;
|
||||
}
|
||||
|
||||
timer->barrier_stop();
|
||||
|
||||
update->minimize->cleanup();
|
||||
|
||||
Finish finish(lmp);
|
||||
finish.end(1);
|
||||
|
||||
// switch fix NEBSpin to climbing mode
|
||||
// top = replica that becomes hill climber
|
||||
|
||||
double vmax = all[0][0];
|
||||
int top = 0;
|
||||
for (int m = 1; m < nreplica; m++)
|
||||
if (vmax < all[m][0]) {
|
||||
vmax = all[m][0];
|
||||
top = m;
|
||||
}
|
||||
|
||||
// setup climbing NEBSpin minimization
|
||||
// must reinitialize minimizer so it re-creates its fix MINIMIZE
|
||||
|
||||
if (me_universe == 0 && uscreen)
|
||||
fprintf(uscreen,"Setting up climbing ...\n");
|
||||
|
||||
if (me_universe == 0) {
|
||||
if (uscreen)
|
||||
fprintf(uscreen,"Climbing replica = %d\n",top+1);
|
||||
if (ulogfile)
|
||||
fprintf(ulogfile,"Climbing replica = %d\n",top+1);
|
||||
}
|
||||
|
||||
update->beginstep = update->firststep = update->ntimestep;
|
||||
update->endstep = update->laststep = update->firststep + n2steps;
|
||||
update->nsteps = n2steps;
|
||||
update->max_eval = n2steps;
|
||||
if (update->laststep < 0)
|
||||
error->all(FLERR,"Too many timesteps");
|
||||
|
||||
update->minimize->init();
|
||||
fneb->rclimber = top;
|
||||
update->minimize->setup();
|
||||
|
||||
if (me_universe == 0) {
|
||||
if (uscreen) {
|
||||
if (verbose) {
|
||||
fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN "
|
||||
"GradV0dottan DN0... GradVNdottan DNN\n");
|
||||
} else {
|
||||
fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
|
||||
"GradV0 GradV1 GradVc "
|
||||
"EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
|
||||
}
|
||||
}
|
||||
if (ulogfile) {
|
||||
if (verbose) {
|
||||
fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN "
|
||||
"GradV0dottan DN0 ... GradVNdottan DNN\n");
|
||||
} else {
|
||||
fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
|
||||
"GradV0 GradV1 GradVc "
|
||||
"EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
|
||||
}
|
||||
}
|
||||
}
|
||||
print_status();
|
||||
|
||||
// perform climbing NEBSpin for n2steps or until replicas converge
|
||||
// retrieve PE values from fix NEBSpin and print every nevery iterations
|
||||
// break induced if converged
|
||||
// damped dynamic min styles insure all replicas converge together
|
||||
|
||||
timer->init();
|
||||
timer->barrier_start();
|
||||
|
||||
while (update->minimize->niter < n2steps) {
|
||||
update->minimize->run(nevery);
|
||||
print_status();
|
||||
if (update->minimize->stop_condition) break;
|
||||
}
|
||||
|
||||
timer->barrier_stop();
|
||||
|
||||
update->minimize->cleanup();
|
||||
|
||||
finish.end(1);
|
||||
|
||||
update->whichflag = 0;
|
||||
update->multireplica = 0;
|
||||
update->firststep = update->laststep = 0;
|
||||
update->beginstep = update->endstep = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
read initial config atom coords from file
|
||||
flag = 0
|
||||
only first replica opens file and reads it
|
||||
first replica bcasts lines to all replicas
|
||||
final replica stores coords
|
||||
intermediate replicas interpolate from coords
|
||||
new coord = replica fraction between current and final state
|
||||
initial replica does nothing
|
||||
flag = 1
|
||||
each replica (except first) opens file and reads it
|
||||
each replica stores coords
|
||||
initial replica does nothing
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NEBSpin::readfile(char *file, int flag)
|
||||
{
|
||||
int i,j,m,nchunk,eofflag,nlines;
|
||||
tagint tag;
|
||||
char *eof,*start,*next,*buf;
|
||||
char line[MAXLINE];
|
||||
double xx,yy,zz;
|
||||
double musp,spx,spy,spz;
|
||||
|
||||
if (me_universe == 0 && screen)
|
||||
fprintf(screen,"Reading NEBSpin coordinate file(s) ...\n");
|
||||
|
||||
// flag = 0, universe root reads header of file, bcast to universe
|
||||
// flag = 1, each replica's root reads header of file, bcast to world
|
||||
// but explicitly skip first replica
|
||||
|
||||
if (flag == 0) {
|
||||
if (me_universe == 0) {
|
||||
open(file);
|
||||
while (1) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of neb/spin file");
|
||||
start = &line[strspn(line," \t\n\v\f\r")];
|
||||
if (*start != '\0' && *start != '#') break;
|
||||
}
|
||||
sscanf(line,"%d",&nlines);
|
||||
}
|
||||
MPI_Bcast(&nlines,1,MPI_INT,0,uworld);
|
||||
|
||||
} else {
|
||||
if (me == 0) {
|
||||
if (ireplica) {
|
||||
open(file);
|
||||
while (1) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of neb/spin file");
|
||||
start = &line[strspn(line," \t\n\v\f\r")];
|
||||
if (*start != '\0' && *start != '#') break;
|
||||
}
|
||||
sscanf(line,"%d",&nlines);
|
||||
} else nlines = 0;
|
||||
}
|
||||
MPI_Bcast(&nlines,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
char *buffer = new char[CHUNK*MAXLINE];
|
||||
char **values = new char*[ATTRIBUTE_PERLINE];
|
||||
|
||||
double fraction = ireplica/(nreplica-1.0);
|
||||
|
||||
double **x = atom->x;
|
||||
double **sp = atom->sp;
|
||||
double spinit[3],spfinal[3];
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// loop over chunks of lines read from file
|
||||
// two versions of read_lines_from_file() for world vs universe bcast
|
||||
// count # of atom coords changed so can check for invalid atom IDs in file
|
||||
|
||||
int ncount = 0;
|
||||
|
||||
int temp_flag,rot_flag;
|
||||
temp_flag = rot_flag = 0;
|
||||
int nread = 0;
|
||||
while (nread < nlines) {
|
||||
nchunk = MIN(nlines-nread,CHUNK);
|
||||
if (flag == 0)
|
||||
eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer);
|
||||
else
|
||||
eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
|
||||
if (eofflag) error->all(FLERR,"Unexpected end of neb/spin file");
|
||||
|
||||
buf = buffer;
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
int nwords = atom->count_words(buf);
|
||||
*next = '\n';
|
||||
|
||||
if (nwords != ATTRIBUTE_PERLINE)
|
||||
error->all(FLERR,"Incorrect atom format in neb/spin file");
|
||||
|
||||
// loop over lines of atom coords
|
||||
// tokenize the line into values
|
||||
|
||||
for (i = 0; i < nchunk; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
|
||||
values[0] = strtok(buf," \t\n\r\f");
|
||||
for (j = 1; j < nwords; j++)
|
||||
values[j] = strtok(NULL," \t\n\r\f");
|
||||
|
||||
// adjust spin coord based on replica fraction
|
||||
// for flag = 0, interpolate for intermediate and final replicas
|
||||
// for flag = 1, replace existing coord with new coord
|
||||
// ignore image flags of final x
|
||||
// for interpolation:
|
||||
// new x is displacement from old x via minimum image convention
|
||||
// if final x is across periodic boundary:
|
||||
// new x may be outside box
|
||||
// will be remapped back into box when simulation starts
|
||||
// its image flags will then be adjusted
|
||||
|
||||
tag = ATOTAGINT(values[0]);
|
||||
m = atom->map(tag);
|
||||
if (m >= 0 && m < nlocal) {
|
||||
ncount++;
|
||||
musp = atof(values[1]);
|
||||
xx = atof(values[2]);
|
||||
yy = atof(values[3]);
|
||||
zz = atof(values[4]);
|
||||
spx = atof(values[5]);
|
||||
spy = atof(values[6]);
|
||||
spz = atof(values[7]);
|
||||
|
||||
if (flag == 0) {
|
||||
|
||||
spinit[0] = sp[m][0];
|
||||
spinit[1] = sp[m][1];
|
||||
spinit[2] = sp[m][2];
|
||||
spfinal[0] = spx;
|
||||
spfinal[1] = spy;
|
||||
spfinal[2] = spz;
|
||||
|
||||
// interpolate intermediate spin states
|
||||
|
||||
sp[m][3] = musp;
|
||||
if (fraction == 0.0) {
|
||||
sp[m][0] = spinit[0];
|
||||
sp[m][1] = spinit[1];
|
||||
sp[m][2] = spinit[2];
|
||||
} else if (fraction == 1.0) {
|
||||
sp[m][0] = spfinal[0];
|
||||
sp[m][1] = spfinal[1];
|
||||
sp[m][2] = spfinal[2];
|
||||
} else {
|
||||
temp_flag = initial_rotation(spinit,spfinal,fraction);
|
||||
rot_flag = MAX(temp_flag,rot_flag);
|
||||
sp[m][0] = spfinal[0];
|
||||
sp[m][1] = spfinal[1];
|
||||
sp[m][2] = spfinal[2];
|
||||
}
|
||||
} else {
|
||||
sp[m][3] = musp;
|
||||
x[m][0] = xx;
|
||||
x[m][1] = yy;
|
||||
x[m][2] = zz;
|
||||
sp[m][0] = spx;
|
||||
sp[m][1] = spy;
|
||||
sp[m][2] = spz;
|
||||
}
|
||||
}
|
||||
|
||||
buf = next + 1;
|
||||
}
|
||||
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
// warning message if one or more couples (spi,spf) were aligned
|
||||
// this breaks Rodrigues' formula, and an arbitrary rotation
|
||||
// vector has to be chosen
|
||||
|
||||
if ((rot_flag > 0) && (comm->me == 0))
|
||||
error->warning(FLERR,"arbitrary initial rotation of one or more spin(s)");
|
||||
|
||||
// check that all atom IDs in file were found by a proc
|
||||
|
||||
if (flag == 0) {
|
||||
int ntotal;
|
||||
MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,uworld);
|
||||
if (ntotal != nreplica*nlines)
|
||||
error->universe_all(FLERR,"Invalid atom IDs in neb/spin file");
|
||||
} else {
|
||||
int ntotal;
|
||||
MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,world);
|
||||
if (ntotal != nlines)
|
||||
error->all(FLERR,"Invalid atom IDs in neb/spin file");
|
||||
}
|
||||
|
||||
// clean up
|
||||
|
||||
delete [] buffer;
|
||||
delete [] values;
|
||||
|
||||
if (flag == 0) {
|
||||
if (me_universe == 0) {
|
||||
if (compressed) pclose(fp);
|
||||
else fclose(fp);
|
||||
}
|
||||
} else {
|
||||
if (me == 0 && ireplica) {
|
||||
if (compressed) pclose(fp);
|
||||
else fclose(fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
initial configuration of intermediate spins using Rodrigues' formula
|
||||
interpolates between initial (spi) and final (stored in sploc)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int NEBSpin::initial_rotation(double *spi, double *sploc, double fraction)
|
||||
{
|
||||
|
||||
// no interpolation for initial and final replica
|
||||
|
||||
if (fraction == 0.0 || fraction == 1.0) return 0;
|
||||
|
||||
int rot_flag = 0;
|
||||
double kx,ky,kz;
|
||||
double spix,spiy,spiz,spfx,spfy,spfz;
|
||||
double kcrossx,kcrossy,kcrossz,knormsq;
|
||||
double kdots;
|
||||
double spkx,spky,spkz;
|
||||
double sidotsf,omega,iknorm,isnorm;
|
||||
|
||||
spix = spi[0];
|
||||
spiy = spi[1];
|
||||
spiz = spi[2];
|
||||
|
||||
spfx = sploc[0];
|
||||
spfy = sploc[1];
|
||||
spfz = sploc[2];
|
||||
|
||||
kx = spiy*spfz - spiz*spfy;
|
||||
ky = spiz*spfx - spix*spfz;
|
||||
kz = spix*spfy - spiy*spfx;
|
||||
|
||||
knormsq = kx*kx+ky*ky+kz*kz;
|
||||
sidotsf = spix*spfx + spiy*spfy + spiz*spfz;
|
||||
|
||||
// if knormsq == 0.0, init and final spins are aligned
|
||||
// Rodrigues' formula breaks, needs to define another axis k
|
||||
|
||||
if (knormsq == 0.0) {
|
||||
if (sidotsf > 0.0) { // spins aligned and in same direction
|
||||
return 0;
|
||||
} else if (sidotsf < 0.0) { // spins aligned and in opposite directions
|
||||
|
||||
// defining a rotation axis
|
||||
// first guess, k = spi x [100]
|
||||
// second guess, k = spi x [010]
|
||||
|
||||
if (spiy*spiy + spiz*spiz != 0.0) { // spin not along [100]
|
||||
kx = 0.0;
|
||||
ky = spiz;
|
||||
kz = -spiy;
|
||||
knormsq = ky*ky + kz*kz;
|
||||
} else if (spix*spix + spiz*spiz != 0.0) { // spin not along [010]
|
||||
kx = -spiz;
|
||||
ky = 0.0;
|
||||
kz = spix;
|
||||
knormsq = kx*kx + kz*kz;
|
||||
} else error->all(FLERR,"Incorrect initial rotation operation");
|
||||
rot_flag = 1;
|
||||
}
|
||||
}
|
||||
|
||||
// knormsq should not be 0
|
||||
|
||||
if (knormsq == 0.0)
|
||||
error->all(FLERR,"Incorrect initial rotation operation");
|
||||
|
||||
// normalize k vector
|
||||
|
||||
iknorm = 1.0/sqrt(knormsq);
|
||||
kx *= iknorm;
|
||||
ky *= iknorm;
|
||||
kz *= iknorm;
|
||||
|
||||
// calc. k x spi and total rotation angle
|
||||
|
||||
kcrossx = ky*spiz - kz*spiy;
|
||||
kcrossy = kz*spix - kx*spiz;
|
||||
kcrossz = kx*spiy - ky*spix;
|
||||
|
||||
kdots = kx*spix + ky*spiz + kz*spiz;
|
||||
|
||||
omega = acos(sidotsf);
|
||||
omega *= fraction;
|
||||
|
||||
// apply Rodrigues' formula
|
||||
|
||||
spkx = spix*cos(omega);
|
||||
spky = spiy*cos(omega);
|
||||
spkz = spiz*cos(omega);
|
||||
|
||||
spkx += kcrossx*sin(omega);
|
||||
spky += kcrossy*sin(omega);
|
||||
spkz += kcrossz*sin(omega);
|
||||
|
||||
spkx += kx*kdots*(1.0-cos(omega));
|
||||
spky += ky*kdots*(1.0-cos(omega));
|
||||
spkz += kz*kdots*(1.0-cos(omega));
|
||||
|
||||
// normalizing resulting spin vector
|
||||
|
||||
isnorm = 1.0/sqrt(spkx*spkx+spky*spky+spkz*spkz);
|
||||
if (isnorm == 0.0)
|
||||
error->all(FLERR,"Incorrect initial rotation operation");
|
||||
|
||||
spkx *= isnorm;
|
||||
spky *= isnorm;
|
||||
spkz *= isnorm;
|
||||
|
||||
// returns rotated spin
|
||||
|
||||
sploc[0] = spkx;
|
||||
sploc[1] = spky;
|
||||
sploc[2] = spkz;
|
||||
|
||||
return rot_flag;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
universe proc 0 opens NEBSpin data file
|
||||
test if gzipped
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NEBSpin::open(char *file)
|
||||
{
|
||||
compressed = 0;
|
||||
char *suffix = file + strlen(file) - 3;
|
||||
if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1;
|
||||
if (!compressed) fp = fopen(file,"r");
|
||||
else {
|
||||
#ifdef LAMMPS_GZIP
|
||||
char gunzip[128];
|
||||
snprintf(gunzip,128,"gzip -c -d %s",file);
|
||||
|
||||
#ifdef _WIN32
|
||||
fp = _popen(gunzip,"rb");
|
||||
#else
|
||||
fp = popen(gunzip,"r");
|
||||
#endif
|
||||
|
||||
#else
|
||||
error->one(FLERR,"Cannot open gzipped file");
|
||||
#endif
|
||||
}
|
||||
|
||||
if (fp == NULL) {
|
||||
char str[128];
|
||||
snprintf(str,128,"Cannot open file %s",file);
|
||||
error->one(FLERR,str);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
query fix NEBSpin for info on each replica
|
||||
universe proc 0 prints current NEBSpin status
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NEBSpin::print_status()
|
||||
{
|
||||
int nlocal = atom->nlocal;
|
||||
double tx,ty,tz;
|
||||
double tnorm2,local_norm_inf,temp_inf;
|
||||
double **sp = atom->sp;
|
||||
double **fm = atom->fm;
|
||||
|
||||
// calc. magnetic torques
|
||||
|
||||
tnorm2 = local_norm_inf = temp_inf = 0.0;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
tx = (fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]);
|
||||
ty = (fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]);
|
||||
tz = (fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]);
|
||||
tnorm2 += tx*tx + ty*ty + tz*tz;
|
||||
temp_inf = MAX(fabs(tx),fabs(ty));
|
||||
temp_inf = MAX(fabs(tz),temp_inf);
|
||||
local_norm_inf = MAX(temp_inf,local_norm_inf);
|
||||
}
|
||||
|
||||
double fmaxreplica;
|
||||
MPI_Allreduce(&tnorm2,&fmaxreplica,1,MPI_DOUBLE,MPI_MAX,roots);
|
||||
|
||||
double fnorminf = 0.0;
|
||||
MPI_Allreduce(&local_norm_inf,&fnorminf,1,MPI_DOUBLE,MPI_MAX,world);
|
||||
double fmaxatom;
|
||||
MPI_Allreduce(&fnorminf,&fmaxatom,1,MPI_DOUBLE,MPI_MAX,roots);
|
||||
|
||||
if (verbose) {
|
||||
freplica = new double[nreplica];
|
||||
MPI_Allgather(&tnorm2,1,MPI_DOUBLE,&freplica[0],1,MPI_DOUBLE,roots);
|
||||
fmaxatomInRepl = new double[nreplica];
|
||||
MPI_Allgather(&fnorminf,1,MPI_DOUBLE,&fmaxatomInRepl[0],1,MPI_DOUBLE,roots);
|
||||
}
|
||||
|
||||
double one[7];
|
||||
one[0] = fneb->veng;
|
||||
one[1] = fneb->plen;
|
||||
one[2] = fneb->nlen;
|
||||
one[3] = fneb->gradlen;
|
||||
|
||||
if (verbose) {
|
||||
one[4] = fneb->dotpath;
|
||||
one[5] = fneb->dottangrad;
|
||||
one[6] = fneb->dotgrad;
|
||||
}
|
||||
|
||||
if (output->thermo->normflag) one[0] /= atom->natoms;
|
||||
if (me == 0)
|
||||
MPI_Allgather(one,numall,MPI_DOUBLE,&all[0][0],numall,MPI_DOUBLE,roots);
|
||||
MPI_Bcast(&all[0][0],numall*nreplica,MPI_DOUBLE,0,world);
|
||||
|
||||
rdist[0] = 0.0;
|
||||
for (int i = 1; i < nreplica; i++)
|
||||
rdist[i] = rdist[i-1] + all[i][1];
|
||||
double endpt = rdist[nreplica-1] = rdist[nreplica-2] + all[nreplica-2][2];
|
||||
for (int i = 1; i < nreplica; i++)
|
||||
rdist[i] /= endpt;
|
||||
|
||||
// look up GradV for the initial, final, and climbing replicas
|
||||
// these are identical to fnorm2, but to be safe we
|
||||
// take them straight from fix_neb
|
||||
|
||||
double gradvnorm0, gradvnorm1, gradvnormc;
|
||||
|
||||
int irep;
|
||||
irep = 0;
|
||||
gradvnorm0 = all[irep][3];
|
||||
irep = nreplica-1;
|
||||
gradvnorm1 = all[irep][3];
|
||||
irep = fneb->rclimber;
|
||||
if (irep > -1) {
|
||||
gradvnormc = all[irep][3];
|
||||
ebf = all[irep][0]-all[0][0];
|
||||
ebr = all[irep][0]-all[nreplica-1][0];
|
||||
} else {
|
||||
double vmax = all[0][0];
|
||||
int top = 0;
|
||||
for (int m = 1; m < nreplica; m++)
|
||||
if (vmax < all[m][0]) {
|
||||
vmax = all[m][0];
|
||||
top = m;
|
||||
}
|
||||
irep = top;
|
||||
gradvnormc = all[irep][3];
|
||||
ebf = all[irep][0]-all[0][0];
|
||||
ebr = all[irep][0]-all[nreplica-1][0];
|
||||
}
|
||||
|
||||
if (me_universe == 0) {
|
||||
FILE *uscreen = universe->uscreen;
|
||||
FILE *ulogfile = universe->ulogfile;
|
||||
if (uscreen) {
|
||||
fprintf(uscreen,BIGINT_FORMAT " %12.8g %12.8g ",
|
||||
update->ntimestep,fmaxreplica,fmaxatom);
|
||||
fprintf(uscreen,"%12.8g %12.8g %12.8g ",
|
||||
gradvnorm0,gradvnorm1,gradvnormc);
|
||||
fprintf(uscreen,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
|
||||
for (int i = 0; i < nreplica; i++)
|
||||
fprintf(uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
|
||||
if (verbose) {
|
||||
for (int i = 0; i < nreplica-1; i++)
|
||||
fprintf(uscreen,"%12.8g %12.8g ",all[i][2],all[i][5]);
|
||||
fprintf(uscreen,"%12.8g %12.8g ",NAN,all[nreplica-1][5]);
|
||||
}
|
||||
fprintf(uscreen,"\n");
|
||||
}
|
||||
|
||||
if (ulogfile) {
|
||||
fprintf(ulogfile,BIGINT_FORMAT " %12.8g %12.8g ",
|
||||
update->ntimestep,fmaxreplica,fmaxatom);
|
||||
fprintf(ulogfile,"%12.8g %12.8g %12.8g ",
|
||||
gradvnorm0,gradvnorm1,gradvnormc);
|
||||
fprintf(ulogfile,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
|
||||
for (int i = 0; i < nreplica; i++)
|
||||
fprintf(ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
|
||||
if (verbose) {
|
||||
for (int i = 0; i < nreplica-1; i++)
|
||||
fprintf(ulogfile,"%12.8g %12.8g ",all[i][2],all[i][5]);
|
||||
fprintf(ulogfile,"%12.8g %12.8g ",NAN,all[nreplica-1][5]);
|
||||
}
|
||||
fprintf(ulogfile,"\n");
|
||||
fflush(ulogfile);
|
||||
}
|
||||
}
|
||||
}
|
||||
137
src/SPIN/neb_spin.h
Normal file
137
src/SPIN/neb_spin.h
Normal file
@ -0,0 +1,137 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMMAND_CLASS
|
||||
|
||||
CommandStyle(neb/spin,NEBSpin)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_NEB_SPIN_H
|
||||
#define LMP_NEB_SPIN_H
|
||||
|
||||
#include <cstdio>
|
||||
#include "pointers.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class NEBSpin : protected Pointers {
|
||||
public:
|
||||
NEBSpin(class LAMMPS *);
|
||||
~NEBSpin();
|
||||
void command(int, char **); // process neb/spin command
|
||||
void run(); // run NEBSpin
|
||||
|
||||
double ebf,ebr; // forward and reverse energy barriers
|
||||
|
||||
private:
|
||||
int me,me_universe; // my proc ID in world and universe
|
||||
int ireplica,nreplica;
|
||||
bool verbose;
|
||||
MPI_Comm uworld;
|
||||
MPI_Comm roots; // MPI comm with 1 root proc from each world
|
||||
FILE *fp;
|
||||
int compressed;
|
||||
double etol; // energy tolerance convergence criterion
|
||||
double ttol; // torque tolerance convergence criterion
|
||||
int n1steps, n2steps; // number of steps in stage 1 and 2
|
||||
int nevery; // output interval
|
||||
char *infile; // name of file containing final state
|
||||
|
||||
class FixNEBSpin *fneb;
|
||||
int numall; // per-replica dimension of array all
|
||||
double **all; // PE,plen,nlen,gradvnorm from each replica
|
||||
double *rdist; // normalize reaction distance, 0 to 1
|
||||
double *freplica; // force on an image
|
||||
double *fmaxatomInRepl; // force on an image
|
||||
|
||||
void readfile(char *, int);
|
||||
int initial_rotation(double *, double *, double);
|
||||
void open(char *);
|
||||
void print_status();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: NEBSpin command before simulation box is defined
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Cannot use NEBSpin with a single replica
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot use NEBSpin unless atom map exists
|
||||
|
||||
Use the atom_modify command to create an atom map.
|
||||
|
||||
E: NEBSpin requires use of fix neb
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: NEBSpin requires damped dynamics minimizer
|
||||
|
||||
Use a different minimization style.
|
||||
|
||||
E: Too many timesteps for NEBSpin
|
||||
|
||||
You must use a number of timesteps that fit in a 32-bit integer
|
||||
for NEBSpin.
|
||||
|
||||
E: Too many timesteps
|
||||
|
||||
The cumulative timesteps must fit in a 64-bit integer.
|
||||
|
||||
E: Unexpected end of neb/spin file
|
||||
|
||||
A read operation from the file failed.
|
||||
|
||||
E: Incorrect atom format in neb/spin file
|
||||
|
||||
The number of fields per line is not what expected.
|
||||
|
||||
E: Invalid atom IDs in neb/spin file
|
||||
|
||||
An ID in the file was not found in the system.
|
||||
|
||||
E: Cannot open gzipped file
|
||||
|
||||
LAMMPS was compiled without support for reading and writing gzipped
|
||||
files through a pipeline to the gzip program with -DLAMMPS_GZIP.
|
||||
|
||||
E: Cannot open file %s
|
||||
|
||||
The specified file cannot be opened. Check that the path and name are
|
||||
correct. If the file is a compressed file, also check that the gzip
|
||||
executable can be found and run.
|
||||
|
||||
U: Can only use NEBSpin with 1-processor replicas
|
||||
|
||||
This is current restriction for NEBSpin as implemented in LAMMPS.
|
||||
|
||||
U: Cannot use NEBSpin with atom_modify sort enabled
|
||||
|
||||
This is current restriction for NEBSpin implemented in LAMMPS.
|
||||
|
||||
*/
|
||||
@ -171,10 +171,11 @@ void PairSpinDmi::init_style()
|
||||
int ifix = 0;
|
||||
while (ifix < modify->nfix) {
|
||||
if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
|
||||
if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break;
|
||||
ifix++;
|
||||
}
|
||||
if ((ifix == modify->nfix) && (comm->me == 0))
|
||||
error->warning(FLERR,"Using pair/spin style without nve/spin");
|
||||
error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin");
|
||||
|
||||
// get the lattice_flag from nve/spin
|
||||
|
||||
@ -430,9 +431,9 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double
|
||||
dmiy = eij[2]*v_dmx[itype][jtype] - eij[0]*v_dmz[itype][jtype];
|
||||
dmiz = eij[0]*v_dmy[itype][jtype] - eij[1]*v_dmx[itype][jtype];
|
||||
|
||||
fmi[0] -= (spj[1]*dmiz - spj[2]*dmiy);
|
||||
fmi[1] -= (spj[2]*dmix - spj[0]*dmiz);
|
||||
fmi[2] -= (spj[0]*dmiy - spj[1]*dmix);
|
||||
fmi[0] -= (dmiy*spj[2] - dmiz*spj[1]);
|
||||
fmi[1] -= (dmiz*spj[0] - dmix*spj[2]);
|
||||
fmi[2] -= (dmix*spj[1] - dmiy*spj[0]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -153,15 +153,16 @@ void PairSpinExchange::init_style()
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
|
||||
// checking if nve/spin is a listed fix
|
||||
// checking if nve/spin or neb/spin are a listed fix
|
||||
|
||||
int ifix = 0;
|
||||
while (ifix < modify->nfix) {
|
||||
if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
|
||||
if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break;
|
||||
ifix++;
|
||||
}
|
||||
if ((ifix == modify->nfix) && (comm->me == 0))
|
||||
error->warning(FLERR,"Using pair/spin style without nve/spin");
|
||||
error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin");
|
||||
|
||||
// get the lattice_flag from nve/spin
|
||||
|
||||
|
||||
@ -164,10 +164,11 @@ void PairSpinMagelec::init_style()
|
||||
int ifix = 0;
|
||||
while (ifix < modify->nfix) {
|
||||
if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
|
||||
if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break;
|
||||
ifix++;
|
||||
}
|
||||
if ((ifix == modify->nfix) && (comm->me == 0))
|
||||
error->warning(FLERR,"Using pair/spin style without nve/spin");
|
||||
error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin");
|
||||
|
||||
// get the lattice_flag from nve/spin
|
||||
|
||||
|
||||
@ -171,10 +171,11 @@ void PairSpinNeel::init_style()
|
||||
int ifix = 0;
|
||||
while (ifix < modify->nfix) {
|
||||
if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;
|
||||
if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break;
|
||||
ifix++;
|
||||
}
|
||||
if ((ifix == modify->nfix) && (comm->me == 0))
|
||||
error->warning(FLERR,"Using pair/spin style without nve/spin");
|
||||
error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin");
|
||||
|
||||
// get the lattice_flag from nve/spin
|
||||
|
||||
|
||||
31
tools/spin/interpolate_gneb/README
Normal file
31
tools/spin/interpolate_gneb/README
Normal file
@ -0,0 +1,31 @@
|
||||
Interpolate.x tries to perform a cubic polynomial interpolation
|
||||
of the MEP.
|
||||
|
||||
Compile the program with:
|
||||
gcc interpolate.c -o interpolate.x
|
||||
|
||||
and then run it as:
|
||||
./interpolate.x
|
||||
|
||||
Enter N-1 (with N the number of replica).
|
||||
The program reads the "neb_init.dat", in which you need to
|
||||
replace the current values by your GNEB outputs.
|
||||
|
||||
Each line corresponds to a replica, and has to respectively
|
||||
contain:
|
||||
|
||||
Reac. coords /tab/ pot. energy /tab/ fm dot tangent /tab/
|
||||
geodesic dist to next replica
|
||||
|
||||
All those information can be provided by the verbose output of
|
||||
a neb/spin calculation
|
||||
|
||||
The progam outputs the interpolation result, and the
|
||||
interpolated MEP in "interpolation_result.dat".
|
||||
|
||||
This code is a courtesy of Aleksei Ivanov, University of
|
||||
Iceland.
|
||||
For more explanation about this calculation, see Appendix D
|
||||
of the following reference:
|
||||
Bessarab, P. F., Uzdin, V. M., & Jónsson, H. (2015).
|
||||
Computer Physics Communications, 196, 335-347.
|
||||
106
tools/spin/interpolate_gneb/interpolate.c
Normal file
106
tools/spin/interpolate_gneb/interpolate.c
Normal file
@ -0,0 +1,106 @@
|
||||
/* ------------------------------------------------------------------------
|
||||
Provide some explanation here
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ------------------------------------------------------------------------
|
||||
This program is a courtesy of Aleksei Ivanov (Univ. of Iceland)
|
||||
Contributing authors: Aleksei Ivanov (Univ. of Iceland),
|
||||
Julien Tranchida (SNL)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <stdio.h>
|
||||
#include <string.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
// calculate cubic coefficients
|
||||
|
||||
void count_coefficient(double *V, double *F, double *R, double *a, double *b,
|
||||
double *c,double *d,int M){
|
||||
/* R = square of distance between images*/
|
||||
/* V = energy of images */
|
||||
/* F = projection of real real forces along the path? */
|
||||
int i;
|
||||
for(i = 0; i < M ; i++) {
|
||||
a[i] = ( -2.0*(V[i+1]-V[i])/R[i] - F[i] - F[i+1] ) / (R[i]*R[i]);
|
||||
//a[i] = ( -2.0*(V[i+1]-V[i])/sqrt(R[i]) - F[i] - F[i+1] ) / R[i];
|
||||
b[i] = ( 3.0*(V[i+1]-V[i]) + (2.0*F[i]+F[i+1])*R[i] ) / (R[i]*R[i]);
|
||||
//b[i] = ( 3.0*(V[i+1]-V[i]) + (2.0*F[i]+F[i+1])*sqrt(R[i]) ) / R[i];
|
||||
c[i] = -F[i];
|
||||
d[i] = V[i];
|
||||
}
|
||||
}
|
||||
|
||||
// cubic spline
|
||||
|
||||
double spline(double a,double b,double c,double d,double x) {
|
||||
return (a*x*x*x + b*x*x + c*x + d);
|
||||
}
|
||||
|
||||
int main() {
|
||||
int M=0; // M+1 = number of images
|
||||
double *fmdottan; // projection of real forces on tangent path
|
||||
double *coords; // initial value of reaction coords
|
||||
double *V; // energy of images
|
||||
double *dist; // square of the distance between images
|
||||
double *a, *b, *c, *d ; // coefficients of cubic functions
|
||||
double x; // reaction coordinate
|
||||
double A,B; // additional variables for rnd
|
||||
double length = 0.0;
|
||||
int i,j;
|
||||
FILE *data;
|
||||
|
||||
printf("Enter M = number of images - 1 \n");
|
||||
scanf("%d",&M);
|
||||
|
||||
// allocating and initializing tables
|
||||
|
||||
a = calloc(M,sizeof(double)); // cubic coefficients
|
||||
b = calloc(M,sizeof(double));
|
||||
c = calloc(M,sizeof(double));
|
||||
d = calloc(M,sizeof(double));
|
||||
V = calloc((M+1),sizeof(double)); // energies
|
||||
coords = calloc((M+1),sizeof(double)); // reaction coordinates
|
||||
fmdottan = calloc((M+1),sizeof(double)); // fm dot tangent
|
||||
dist = calloc(M+1,sizeof(double)); // distance between images
|
||||
|
||||
// reading input file
|
||||
|
||||
if((data=fopen("neb_init.dat","r")) == NULL) {
|
||||
printf("Incorrect input file name.");
|
||||
return 0;
|
||||
}
|
||||
|
||||
for(j=0; j < M+1; j++) {
|
||||
fscanf(data,"%lf\t%lf\t%lf\t%lf\n",&coords[j],&V[j],&fmdottan[j],&dist[j]);
|
||||
length += dist[j];
|
||||
printf("%lf %lf %lf %lf\n",coords[j],V[j],fmdottan[j],dist[j]);
|
||||
}
|
||||
|
||||
if( (fclose(data)) == 0) {
|
||||
printf("Data stored, input file closed.\n ");
|
||||
}
|
||||
|
||||
// calculate value of coefficients
|
||||
|
||||
count_coefficient(V,fmdottan,dist,a,b,c,d,M);
|
||||
|
||||
// plot result of the interpolation
|
||||
|
||||
if( ( data=fopen("interpolation_result.dat","w") )== NULL) {
|
||||
printf("Interpolation file could not be open.");
|
||||
return 0;
|
||||
}
|
||||
|
||||
A = B = 0.0;
|
||||
for(i = 0; i < M ; i++) {
|
||||
B += dist[i];
|
||||
printf("%13le\n",B);
|
||||
for(j = 0; j <= 1000; j++) {
|
||||
x = dist[i]*1.0e-3*j;
|
||||
fprintf(data,"%13lf\t%13le\n",(x+A)/length,spline(a[i],b[i],c[i],d[i],x));
|
||||
}
|
||||
A += dist[i];
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
8
tools/spin/interpolate_gneb/neb_init.dat
Normal file
8
tools/spin/interpolate_gneb/neb_init.dat
Normal file
@ -0,0 +1,8 @@
|
||||
0.0000000 -3.915271 3.4995081e-17 2.4573077
|
||||
0.14285714 -3.9148148 -0.00059075739 2.4573077
|
||||
0.28571429 -3.9136926 -0.00072315767 2.4573077
|
||||
0.42857143 -3.9127883 -0.0003191228 2.4573265
|
||||
0.57142857 -3.9127883 0.0003191228 2.4403341
|
||||
0.71428571 -3.9136926 0.00072315767 2.4044093
|
||||
0.85714286 -3.9148148 0.00059075739 2.3766041
|
||||
1.0000000 -3.915271 -4.1231828e-17 0.0000000
|
||||
Reference in New Issue
Block a user