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Commit2 JT 040819 

- finished doc (compiled and spell check)
- compiled with -Wall -Wextra, unused var. removed
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julient31 2019-04-08 11:08:06 -06:00
parent fcb4b75589
commit 57247142d2
5 changed files with 163 additions and 118 deletions
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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/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
@ -308,6 +309,7 @@ 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

175
doc/src/neb_spin.txt
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@ -47,7 +47,7 @@ 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: "(Bessarab)"_#Bessarab.
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
@ -78,11 +78,11 @@ 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 precessional motion is computed in the usual way due only
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 precess during the GNEB
Their magnetic spins can be allowed to evolve during the GNEB
minimization procedure.
The initial spin configuration for each of the replicas can be
@ -117,7 +117,8 @@ 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 "(Bessarab)"_#Bessarab.
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:
@ -142,7 +143,7 @@ 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 perpandicular to initial and final spins is chosen.
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
@ -177,14 +178,14 @@ 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
{ftol}, the same as for the "minimize"_minimize.html command.
{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 {ftol}
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 {ftol} include
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
@ -198,7 +199,7 @@ 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 spinsi involved (see equation (13) in "(Bessarab)"_#Bessarab).
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}.
@ -217,7 +218,7 @@ 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
"(Bessarab)"_#Bessarab. As before, the other replicas rearrange
"(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,
@ -227,37 +228,22 @@ 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
A few other settings in your input script are required or advised to
perform a NEB calculation. See the NOTE about the choice of timestep
at the beginning of this doc page.
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.
The minimizers in LAMMPS operate on all atoms in your system, even
non-NEB atoms, as defined above. To prevent non-NEB atoms from moving
during the minimization, you should use the "fix
setforce"_fix_setforce.html command to set the force on each of those
atoms to 0.0. This is not required, and may not even be desired in
some cases, but if those atoms move too far (e.g. because the initial
state of your system was not well-minimized), it can cause problems
for the NEB procedure.
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 damped dynamics "minimizers"_min_style.html, such as {quickmin}
and {fire}), adjust the position and velocity of the atoms via an
Euler integration step. Thus you must define an appropriate
"timestep"_timestep.html to use with NEB. As mentioned above, NEB
will often converge more quickly if you use a timestep about 10x
larger than you would normally use for dynamics simulations.
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 command containing atomic coordinates used
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
@ -266,130 +252,103 @@ 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 x1 y1 z1
ID2 x2 y2 z2
ID1 g1 x1 y1 z1 sx1 sy1 sz1
ID2 g2 x2 y2 z2 sx2 sy2 sz2
...
IDN xN yN zN :pre
IDN gN yN zN sxN syN szN :pre
The fields are the atom ID, followed by the x,y,z coordinates. The
lines can be listed in any order. Additional trailing information on
The 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 NEB calculation you do not need to specify
initial coordinates for very many atoms to produce differing starting
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 coordinates for atoms
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 NEB atoms in the group defined by the "fix
neb"_fix_neb.html command. Not every NEB atom need be in the file,
and non-NEB atoms can be listed 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 NEB calculation: energy
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 force per replica, the maximum
force per atom (in any replica), potential gradients in the initial,
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 force per replica" is the two-norm of the 3N-length force
vector for the atoms in each replica, maximized across replicas, which
is what the {ftol} setting is checking against. In this case, N is
all the atoms in each replica. The "maximum force per atom" is the
maximum force component of any atom in any replica. The potential
gradients are the two-norm of the 3N-length force vector solely due to
the interaction potential i.e. without adding in inter-replica
forces.
The "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 distances between its atoms and the preceding
replica's atoms, added to the RD of the preceding replica. The RD of
the first replica RD1 = 0.0; the RD of the final replica RDN = RDT,
the total reaction coordinate. The normalized RDs are divided by RDT,
so that they form a monotonically increasing sequence from zero to
one. When computing RD, N only includes the atoms being operated on by
the fix neb command.
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 "path angle" (pathangle) for
the replica i which is the angle between the 3N-length vectors (Ri-1 -
Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
aligned. "angletangrad" is the angle between the 3N-length tangent
vector and the 3N-length force vector at image i. The tangent vector
is calculated as in "(HenkelmanA)"_#HenkelmanA for all intermediate
replicas and at R2 - R1 and RM - RM-1 for the first and last replica,
respectively. "anglegrad" is the angle between the 3N-length energy
gradient vector of replica i and that of replica i+1. It is not
defined for the final replica and reads nan. gradV is the norm of the
energy gradient of image i. ReplicaForce is the two-norm of the
3N-length force vector (including nudging forces) for replica i.
MaxAtomForce is the maximum force component of any atom in replica i.
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. For instance
when the path angle becomes acute, the definition of tangent used in
the NEB calculation is questionable and the NEB cannot may diverge
"(Maras)"_#Maras2.
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
NEB calculation, these contain the thermodynamic output for each
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 NEB calculation, the final snapshot in
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 NEB
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.
There are 2 Python scripts provided in the tools/python directory,
neb_combine.py and neb_final.py, which are useful in analyzing output
from a NEB calculation. Assume a NEB simulation with M replicas, and
the NEB atoms labeled with a specific atom type.
The neb_combine.py script extracts atom coords for the NEB atoms from
all M dump files and creates a single dump file where each snapshot
contains the NEB atoms from all the replicas and one copy of non-NEB
atoms from the first replica (presumed to be identical in other
replicas). This can be visualized/animated to see how the NEB atoms
relax as the NEB calculation proceeds.
The neb_final.py script extracts the final snapshot from each of the M
dump files to create a single dump file with M snapshots. This can be
visualized to watch the system make its transition over the energy
barrier.
To illustrate, here are images from the final snapshot produced by the
neb_combine.py script run on the dump files produced by the two
example input scripts in examples/neb. Click on them to see a larger
image.
:image(JPG/hop1_small.jpg,JPG/hop1.jpg)
:image(JPG/hop2_small.jpg,JPG/hop2.jpg)
A c file script in provided in the examples/SPIN/gneb/interpolate
directory, that interpolates the MEP given the information provided
by the verbose output option (as detailed in Appendix D of
"(BessarabA)"_#BessarabA).
:line
@ -411,6 +370,6 @@ none
:line
:link(Bessarab)
[(Bessarab)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
:link(BessarabA)
[(BessarabA)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
335-347 (2015).

8
src/SPIN/fix_neb_spin.cpp
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@ -310,7 +310,6 @@ void FixNEB_spin::min_post_force(int /*vflag*/)
int nlocal = atom->nlocal;
int *mask = atom->mask;
double **x = atom->x;
double **sp = atom->sp;
double dot = 0.0;
double prefactor = 0.0;
@ -322,7 +321,8 @@ void FixNEB_spin::min_post_force(int /*vflag*/)
nlen = 0.0;
double tlen = 0.0;
double gradnextlen = 0.0;
double delndots, delpdots;
double delndots = 0.0;
double delpdots = 0.0;
dotgrad = gradlen = dotpath = dottangrad = 0.0;
@ -584,10 +584,7 @@ void FixNEB_spin::min_post_force(int /*vflag*/)
if (ireplica == 0 || ireplica == nreplica-1) return ;
double AngularContr;
dotpath = dotpath/(plen*nlen);
AngularContr = 0.5 *(1+cos(MY_PI * dotpath));
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@ -620,7 +617,6 @@ void FixNEB_spin::min_post_force(int /*vflag*/)
fm[i][2] = 0;
}
prefactor = kspring*(nlen-plen);
AngularContr=0;
}
}

20
src/SPIN/neb_spin.cpp
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@ -88,7 +88,6 @@ NEB_spin::NEB_spin(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in,
int n2steps_in, int nevery_in, double *buf_init, double *buf_final)
: Pointers(lmp)
{
double delspx,delspy,delspz;
etol = etol_in;
ttol = ftol_in;
@ -450,7 +449,7 @@ void NEB_spin::readfile(char *file, int flag)
tagint tag;
char *eof,*start,*next,*buf;
char line[MAXLINE];
double xx,yy,zz,delx,dely,delz;
double xx,yy,zz;
double musp,spx,spy,spz;
if (me_universe == 0 && screen)
@ -701,6 +700,20 @@ int NEB_spin::initial_rotation(double *spi, double *sploc, double fraction)
}
}
// knormsq should not be 0 anymore
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;
@ -710,7 +723,7 @@ int NEB_spin::initial_rotation(double *spi, double *sploc, double fraction)
omega = acos(sidotsf);
omega *= fraction;
// applying Rodrigues' formula
// apply Rodrigues' formula
spkx = spix*cos(omega);
spky = spiy*cos(omega);
@ -873,7 +886,6 @@ void NEB_spin::print_status()
}
if (me_universe == 0) {
const double todeg=180.0/MY_PI;
FILE *uscreen = universe->uscreen;
FILE *ulogfile = universe->ulogfile;
if (uscreen) {