Merge pull request #1421 from julient31/gneb_spin

Adding a GNEB implementation in the SPIN package

doc/src/Commands_all.txt

@@ -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,

doc/src/Commands_category.txt

@@ -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,

doc/src/Commands_fix.txt

@@ -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,

doc/src/Eqs/neb_spin_angle.tex

@@ -0,0 +1,15 @@
+\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}

doc/src/Eqs/neb_spin_k.tex

@@ -0,0 +1,16 @@
+\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}

doc/src/Eqs/neb_spin_rodrigues_formula.tex

@@ -0,0 +1,16 @@
+\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}

doc/src/Howto_replica.txt

@@ -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

doc/src/Packages_details.txt

@@ -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

doc/src/commands_list.txt

@@ -67,6 +67,7 @@ Commands :h1
    minimize
    molecule
    neb
+   neb_spin
    neigh_modify
    neighbor
    newton

doc/src/fix_neb.txt

@@ -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)
+:link(WeinanE)
-[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
+[(WeinanE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
 
 :link(Jonsson)
 [(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum

doc/src/fix_neb_spin.txt

@@ -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).

doc/src/fix_precession_spin.txt

@@ -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

doc/src/fixes.txt

@@ -84,6 +84,7 @@ Fixes :h1
    fix_msst
    fix_mvv_dpd
    fix_neb
+   fix_neb_spin
    fix_nh
    fix_nh_eff
    fix_nh_uef

doc/src/lammps.book

@@ -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

doc/src/neb_spin.txt

@@ -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).

doc/utils/sphinx-config/false_positives.txt

@@ -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

examples/SPIN/gneb/README

@@ -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. 

examples/SPIN/gneb/iron/final.iron_spin

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+

examples/SPIN/gneb/iron/in.gneb.iron

@@ -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

examples/SPIN/gneb/iron/initial.iron_spin

@@ -0,0 +1,82 @@
+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
+
+Masses
+
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+
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+
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examples/SPIN/gneb/skyrmion/final.skyrmion

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examples/SPIN/gneb/skyrmion/in.gneb.skyrmion

@@ -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

examples/SPIN/gneb/skyrmion/initial.skyrmion

@@ -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
+
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examples/SPIN/read_restart/in.spin.read_data

@@ -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

src/SPIN/README

@@ -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
 

src/SPIN/atom_vec_spin.cpp

@@ -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);

src/SPIN/fix_neb_spin.h

@@ -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.
+
+*/

src/SPIN/neb_spin.cpp

@@ -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);
+    }
+  }
+}

src/SPIN/neb_spin.h

@@ -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.
+
+*/

src/SPIN/pair_spin_dmi.cpp

@@ -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[0] -= (dmiy*spj[2] - dmiz*spj[1]);
-  fmi[1] -= (spj[2]*dmix - spj[0]*dmiz);
+  fmi[1] -= (dmiz*spj[0] - dmix*spj[2]);
-  fmi[2] -= (spj[0]*dmiy - spj[1]*dmix);
+  fmi[2] -= (dmix*spj[1] - dmiy*spj[0]);
 }
 
 /* ----------------------------------------------------------------------

src/SPIN/pair_spin_exchange.cpp

@@ -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
 

src/SPIN/pair_spin_magelec.cpp

@@ -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
 

src/SPIN/pair_spin_neel.cpp

@@ -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
 

tools/spin/interpolate_gneb/README

@@ -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. 

tools/spin/interpolate_gneb/interpolate.c

@@ -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;
+}

tools/spin/interpolate_gneb/neb_init.dat

@@ -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