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Merge pull request #1421 from julient31/gneb_spin

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Adding a GNEB implementation in the SPIN package
This commit is contained in:
Axel Kohlmeyer
2019-04-29 14:14:58 -04:00
committed by GitHub
parent ceff147fc0 97baee4931
commit f052509015
42 changed files with 4282 additions and 17 deletions
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1
doc/src/Commands_all.txt
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@ -83,6 +83,7 @@ An alphabetic list of all general LAMMPS commands.
"molecule"_molecule.html,
"ndx2group"_group2ndx.html,
"neb"_neb.html,
"neb_spin"_neb_spin.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,

1
doc/src/Commands_category.txt
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@ -116,6 +116,7 @@ Actions:
"minimize"_minimize.html,
"neb"_neb.html,
"neb_spin"_neb_spin.html,
"prd"_prd.html,
"rerun"_rerun.html,
"run"_run.html,

1
doc/src/Commands_fix.txt
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@ -107,6 +107,7 @@ OPT.
"mvv/edpd"_fix_mvv_dpd.html,
"mvv/tdpd"_fix_mvv_dpd.html,
"neb"_fix_neb.html,
"neb_spin"_fix_neb_spin.html,
"nph (ko)"_fix_nh.html,
"nph/asphere (o)"_fix_nph_asphere.html,
"nph/body"_fix_nph_body.html,

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\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
\omega_i^{\nu} =
(\nu - 1) \Delta \omega_i
{\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
, \nonumber
\end{equation}
\end{varwidth}
\end{document}

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\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
\vec{k}_i =
\frac{\vec{m}_i^I \times \vec{m}_i^F}{\left|\vec{m}_i^I
\times \vec{m}_i^F\right|}
%&{\rm ~if~}& \vec{m}_i^I \times \vec{m}_i^F
, \nonumber
\end{equation}
\end{varwidth}
\end{document}

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doc/src/Eqs/neb_spin_rodrigues_formula.tex Normal file
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\documentclass[preview]{standalone}
\usepackage{varwidth}
\usepackage[utf8x]{inputenc}
\usepackage{amsmath, amssymb, graphics, setspace}
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
\vec{m}_i^{\nu} = \vec{m}_i^{I} \cos(\omega_i^{\nu})
+ (\vec{k}_i \times \vec{m}_i^{I}) \sin(\omega_i^{\nu})
+ (1.0-\cos(\omega_i^{\nu})) \vec{k}_i (\vec{k}_i\cdot
\vec{m}_i^{I})
, \nonumber
\end{equation}
\end{varwidth}
\end{document}

1
doc/src/Howto_replica.txt
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@ -17,6 +17,7 @@ periodically.
These are the relevant commands:
"neb"_neb.html for nudged elastic band calculations
"neb_spin"_neb_spin.html for magnetic nudged elastic band calculations
"prd"_prd.html for parallel replica dynamics
"tad"_tad.html for temperature accelerated dynamics
"temper"_temper.html for parallel tempering

1
doc/src/Packages_details.txt
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@ -918,6 +918,7 @@ src/SPIN: filenames -> commands
"fix nve/spin"_fix_nve_spin.html
"fix precession/spin"_fix_precession_spin.html
"compute spin"_compute_spin.html
"neb/spin"_neb_spin.html
examples/SPIN :ul
:line

1
doc/src/commands_list.txt
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@ -67,6 +67,7 @@ Commands :h1
minimize
molecule
neb
neb_spin
neigh_modify
neighbor
newton

6
doc/src/fix_neb.txt
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@ -97,7 +97,7 @@ Note that in this case the specified {Kspring} is in force/distance
units.
With a value of {ideal}, the spring force is computed as suggested in
"(WeinenE)"_#WeinenE :
"(WeinanE)"_#WeinanE :
Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
@ -224,8 +224,8 @@ specified (no inter-replica force on the end replicas).
[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
9901-9904 (2000).
:link(WeinenE)
[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
:link(WeinanE)
[(WeinanE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
:link(Jonsson)
[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum

76
doc/src/fix_neb_spin.txt Normal file
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@ -0,0 +1,76 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix neb/spin command :h3
[Syntax:]
fix ID group-ID neb/spin Kspring :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
neb/spin = style name of this fix command :l
Kspring = spring constant for parallel nudging force
(force/distance units or force units, see parallel keyword) :pre,ule
[Examples:]
fix 1 active neb/spin 1.0
[Description:]
Add nudging forces to spins in the group for a multi-replica
simulation run via the "neb/spin"_neb_spin.html command to perform a
geodesic nudged elastic band (GNEB) calculation for finding the
transition state.
Hi-level explanations of GNEB are given with the
"neb/spin"_neb_spin.html command and on the
"Howto replica"_Howto_replica.html doc page.
The fix neb/spin command must be used with the "neb/spin" command and
defines how inter-replica nudging forces are computed. A GNEB
calculation is divided in two stages. In the first stage n replicas
are relaxed toward a MEP until convergence. In the second stage, the
climbing image scheme is enabled, so that the replica having the highest
energy relaxes toward the saddle point (i.e. the point of highest energy
along the MEP), and a second relaxation is performed.
The nudging forces are calculated as explained in
"(BessarabB)"_#BessarabB).
See this reference for more explanation about their expression.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output commands"_Howto_output.html.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
as invoked by the "minimize"_minimize.html command via the
"neb/spin"_neb_spin.html command.
[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.
[Related commands:]
"neb_spin"_neb_spin.html
[Default:]
none
:line
:link(BessarabB)
[(BessarabB)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
335-347 (2015).

2
doc/src/fix_precession_spin.txt
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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
[Description:]
Impose a force torque to each magnetic spin in the group.
This fix applies a precession torque to each magnetic spin in the group.
Style {zeeman} is used for the simulation of the interaction
between the magnetic spins in the defined group and an external

1
doc/src/fixes.txt
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@ -84,6 +84,7 @@ Fixes :h1
fix_msst
fix_mvv_dpd
fix_neb
fix_neb_spin
fix_nh
fix_nh_eff
fix_nh_uef

2
doc/src/lammps.book
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@ -179,6 +179,7 @@ min_spin.html
minimize.html
molecule.html
neb.html
neb_spin.html
neigh_modify.html
neighbor.html
newton.html
@ -309,6 +310,7 @@ fix_mscg.html
fix_msst.html
fix_mvv_dpd.html
fix_neb.html
fix_neb_spin.html
fix_nh.html
fix_nh_eff.html
fix_nph_asphere.html

375
doc/src/neb_spin.txt Normal file
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@ -0,0 +1,375 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
neb command :h3
[Syntax:]
neb/spin etol ttol N1 N2 Nevery file-style arg keyword :pre
etol = stopping tolerance for energy (energy units) :ulb,l
ttol = stopping tolerance for torque ( units) :l
N1 = max # of iterations (timesteps) to run initial NEB :l
N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
Nevery = print replica energies and reaction coordinates every this many timesteps :l
file-style = {final} or {each} or {none} :l
{final} arg = filename
filename = file with initial coords for final replica
coords for intermediate replicas are linearly interpolated
between first and last replica
{each} arg = filename
filename = unique filename for each replica (except first)
with its initial coords
{none} arg = no argument all replicas assumed to already have
their initial coords :pre
keyword = {verbose}
:ule
[Examples:]
neb/spin 0.1 0.0 1000 500 50 final coords.final
neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i
neb/spin 0.0 0.001 1000 500 50 none verbose :pre
[Description:]
Perform a geodesic nudged elastic band (GNEB) calculation using multiple
replicas of a system. Two or more replicas must be used; the first
and last are the end points of the transition path.
GNEB is a method for finding both the spin configurations and height
of the energy barrier associated with a transition state, e.g.
spins to perform a collective rotation from one energy basin to
another.
The implementation in LAMMPS follows the discussion in the
following paper: "(BessarabA)"_#BessarabA.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the "-partition command-line
switch"_Run_options.html. Note that if you have MPI installed, you
can run a multi-replica simulation with more replicas (partitions)
than you have physical processors, e.g you can run a 10-replica
simulation on just one or two processors. You will simply not get the
performance speed-up you would see with one or more physical
processors per replica. See the "Howto replica"_Howto_replica.html
doc page for further discussion.
NOTE: As explained below, a GNEB calculation performs a damped dynamics
minimization across all the replicas. The "spin"_min_spin.html
style minimizer has to be defined in your input script.
When a GNEB calculation is performed, it is assumed that each replica
is running the same system, though LAMMPS does not check for this.
I.e. the simulation domain, the number of magnetic atoms, the
interaction potentials, and the starting configuration when the neb
command is issued should be the same for every replica.
In a GNEB calculation each replica is connected to other replicas by
inter-replica nudging forces. These forces are imposed by the "fix
neb/spin"_fix_neb_spin.html command, which must be used in conjunction
with the neb command.
The group used to define the fix neb/spin command defines the
GNEB magnetic atoms which are the only ones that inter-replica springs
are applied to.
If the group does not include all magnetic atoms, then non-GNEB
magnetic atoms have no inter-replica springs and the torques they feel
and their precession motion is computed in the usual way due only
to other magnetic atoms within their replica.
Conceptually, the non-GNEB atoms provide a background force field for
the GNEB atoms.
Their magnetic spins can be allowed to evolve during the GNEB
minimization procedure.
The initial spin configuration for each of the replicas can be
specified in different manners via the {file-style} setting, as
discussed below. Only atomic spins whose initial coordinates should
differ from the current configuration need to be specified.
Conceptually, the initial and final configurations for the first
replica should be states on either side of an energy barrier.
As explained below, the initial configurations of intermediate
replicas can be spin coordinates interpolated in a linear fashion
between the first and last replicas. This is often adequate for
simple transitions. For more complex transitions, it may lead to slow
convergence or even bad results if the minimum energy path (MEP, see
below) of states over the barrier cannot be correctly converged to
from such an initial path. In this case, you will want to generate
initial states for the intermediate replicas that are geometrically
closer to the MEP and read them in.
:line
For a {file-style} setting of {final}, a filename is specified which
contains atomic and spin coordinates for zero or more atoms, in the
format described below.
For each atom that appears in the file, the new coordinates are
assigned to that atom in the final replica. Each intermediate replica
also assigns a new spin to that atom in an interpolated manner.
This is done by using the current direction of the spin at the starting
point and the read-in direction as the final point.
The "angular distance" between them is calculated, and the new direction
is assigned to be a fraction of the angular distance.
NOTE: The "angular distance" between the starting and final point is
evaluated in the geodesic sense, as described in
"(BessarabA)"_#BessarabA.
NOTE: The angular interpolation between the starting and final point
is achieved using Rodrigues formula:
:c,image(Eqs/neb_spin_rodrigues_formula.jpg)
where m_i^I is the initial spin configuration for the spin i,
omega_i^nu is a rotation angle defined as:
:c,image(Eqs/neb_spin_angle.jpg)
with nu the image number, Q the total number of images, and
omega_i the total rotation between the initial and final spins.
k_i defines a rotation axis such as:
:c,image(Eqs/neb_spin_k.jpg)
if the initial and final spins are not aligned.
If the initial and final spins are aligned, then their cross
product is null, and the expression above does not apply.
If they point toward the same direction, the intermediate images
conserve the same orientation.
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.
In this case, a warning message is displayed.
For a {file-style} setting of {each}, a filename is specified which is
assumed to be unique to each replica.
See the "neb"_neb.html documentation page for more information about this
option.
For a {file-style} setting of {none}, no filename is specified. Each
replica is assumed to already be in its initial configuration at the
time the neb command is issued. This allows each replica to define
its own configuration by reading a replica-specific data or restart or
dump file, via the "read_data"_read_data.html,
"read_restart"_read_restart.html, or "read_dump"_read_dump.html
commands. The replica-specific names of these files can be specified
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
must thus be in the correct initial configuration at the time the neb
command is issued.
:line
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).

9
doc/utils/sphinx-config/false_positives.txt
View File

@ -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
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@ -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.

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50
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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

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LAMMPS data file via write_data, version 4 Jan 2019, timestep = 0
32 atoms
1 atom types
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0.0000000000000000e+00 1.1465999999999999e+01 ylo yhi
0.0000000000000000e+00 2.8664999999999998e+00 zlo zhi
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examples/SPIN/gneb/skyrmion/final.skyrmion Normal file
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134 2.5 18.0 39.0 0.0 0.0 0.0 1.0
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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
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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
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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
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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
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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
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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
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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
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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
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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
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380 2.5 54.0 57.0 0.0 0.0 0.0 1.0
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382 2.5 57.0 3.0 0.0 0.0 0.0 1.0
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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
View 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
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@ -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
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2
examples/SPIN/read_restart/in.spin.read_data
View File

@ -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

5
src/SPIN/README
View File

@ -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

4
src/SPIN/atom_vec_spin.cpp
View File

@ -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
View File

File diff suppressed because it is too large Load Diff

112
src/SPIN/fix_neb_spin.h Normal file
View 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
View 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
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/* -*- 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.
*/

9
src/SPIN/pair_spin_dmi.cpp
View File

@ -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]);
}
/* ----------------------------------------------------------------------

5
src/SPIN/pair_spin_exchange.cpp
View File

@ -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

3
src/SPIN/pair_spin_magelec.cpp
View File

@ -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

3
src/SPIN/pair_spin_neel.cpp
View File

@ -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
View 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
View 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
View 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