forked from lijiext/lammps
Merge pull request #490 from EmileMaras/NEB-Change
added several features to the NEB
This commit is contained in:
sjplimp
GitHub
commit
34cfc7bd51
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@ -10,68 +10,156 @@ fix neb command :h3
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[Syntax:]
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fix ID group-ID neb Kspring :pre
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fix ID group-ID neb Kspring keyword value :pre
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ID, group-ID are documented in "fix"_fix.html command
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neb = style name of this fix command
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Kspring = inter-replica spring constant (force/distance units) :ul
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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neb = style name of this fix command :l
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Kspring = parallel spring constant (force/distance units or force units) :l
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zero or more keyword/value pairs may be appended :l
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keyword = {nudg_style} or {perp} or {freend} or {freend_k_spring} :l
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{nudg_style} value = {neigh} or {idealpos}
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{neigh} = the parallel nudging force is calculated from the distances to neighbouring replicas (in this case, Kspring is in force/distance units)
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{idealpos} = the parallel nudging force is proportional to the distance between the replica and its interpolated ideal position (in this case Kspring is in force units)
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{perp} value {none} or kspring2
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{none} = no perpendicular spring force is applied
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{kspring2} = spring constant for the perpendicular nudging force (in force/distance units)
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{freeend} value = {none} or {ini} or {final} or {finaleini} or {final2eini}
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{none} = no nudging force is applied to the first and last replicas
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{ini} = set the first replica to be a free end
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{final} = set the last replica to be a free end
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{finaleini} = set the last replica to be a free end and set its target energy as that of the first replica
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{final2eini} = same as {finaleini} plus prevent intermediate replicas to have a lower energy than the first replica
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{freeend_kspring} value = kspring3
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kspring3 = spring constant of the perpendicular spring force (per distance units)
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:pre
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[Examples:]
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fix 1 active neb 10.0 :pre
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fix 1 active neb 10.0
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fix 2 all neb 1.0 perp 1.0 freeend final
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fix 1 all neb 1.0 nudg_style idealpos freeend final2eini freend_kspring 1:pre
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[Description:]
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Add inter-replica forces to atoms in the group for a multi-replica
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Add a nudging force to atoms in the group for a multi-replica
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simulation run via the "neb"_neb.html command to perform a nudged
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elastic band (NEB) calculation for transition state finding. Hi-level
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explanations of NEB are given with the "neb"_neb.html command and in
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"Section 6.5"_Section_howto.html#howto_5 of the manual. The fix
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neb command must be used with the "neb" command to define how
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inter-replica forces are computed.
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elastic band (NEB) calculation for finding the transition state.
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Hi-level explanations of NEB are given with the "neb"_neb.html command
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and in "Section_howto 5"_Section_howto.html#howto_5 of the manual.
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The fix neb command must be used with the "neb" command and defines
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how nudging inter-replica forces are computed. A NEB calculation is
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divided in two stages. In the first stage n replicas are relaxed
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toward a MEP and in a second stage, the climbing image scheme (see
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"(Henkelman2)"_#Henkelman2) is turned on so that the replica having
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the highest energy relaxes toward the saddle point (i.e. the point of
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highest energy along the MEP).
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Only the N atoms in the fix group experience inter-replica forces.
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Atoms in the two end-point replicas do not experience these forces,
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but those in intermediate replicas do. During the initial stage of
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NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
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on the atoms of each intermediate replica I is altered, as described
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in the "(Henkelman1)"_#Henkelman1 paper, to become:
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One purpose of the nudging forces is to keep the replicas equally
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spaced. During the NEB, the 3N-length vector of interatomic force Fi
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= -Grad(V) of replicas i is altered. For all intermediate replicas
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(i.e. for 1<i<n) but the climbing replica the force vector
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becomes:
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Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (| Ri+i - Ri | - | Ri - Ri-1 |) That :pre
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Fi = -Grad(V) + (Grad(V) dot That) That + Fnudgparallel + Fspringperp :pre
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Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
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coordinates of its neighbor replicas. That (t with a hat over it) is
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the unit "tangent" vector for replica I which is a function of Ri,
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Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
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roughly in the direction of (Ri+i - Ri-1); see the
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"(Henkelman1)"_#Henkelman1 paper for details.
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That is the unit "tangent" vector for replica i and is a function of
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Ri, Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
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roughly in the direction of (Ri+i - Ri-1) (see the
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"(Henkelman1)"_#Henkelman1 paper for details). Ri are the atomic
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coordinates of replica i; Ri-1 and Ri+1 are the coordinates of its
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neighbor replicas. The term (Grad(V) dot That) is used to remove the
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component of the gradient parallel to the path which would tend to
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distribute the replica unevenly along the path. Fnudgparallel is an
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artificial nudging force which is applied only in the tangent direction
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and which maintains the replicas equally spaced (see below for more
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information). Fspringperp is an optinal artificial spring which is
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applied only perpendicular to the tangent and which prevent the paths
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from forming too acute kinks (see below for more information).
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The first two terms in the above equation are the component of the
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interatomic forces perpendicular to the tangent vector. The last term
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is a spring force between replica I and its neighbors, parallel to the
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tangent vector direction with the specified spring constant {Kspring}.
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The keyword {nudg_style} allow to specify how to parallel
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nudging force is computed. With a value of idealpos, the spring
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force is computed as suggested in "(E)"_#E :
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Fnudgparallel=-{Kspring}* (RD-RDideal)/(2 meanDist) :pre
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The effect of the first two terms is to push the atoms of each replica
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toward the minimum energy path (MEP) of conformational states that
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transition over the energy barrier. The MEP for an energy barrier is
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defined as a sequence of 3N-dimensional states which cross the barrier
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at its saddle point, each of which has a potential energy gradient
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parallel to the MEP itself.
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where RD is the "reaction coordinate" see "neb"_neb.html section, and
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RDideal is the ideal RD for which all the images are equally spaced
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(i.e. RDideal = (i-1)*meanDist when the climbing image is off, where i
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is the replica number). The meanDist is the average distance between
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replicas.
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The effect of the last term is to push each replica away from its two
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neighbors in a direction along the MEP, so that the final set of
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states are equidistant from each other.
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When {nudg_style} has a value of neigh (or by default), the parallel
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nudging force is computed as in "(Henkelman1)"_#Henkelman1 by
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connecting each intermediate replica with the previous and the next
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image:
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During the second stage of NEB, the forces on the N atoms in the
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replica nearest the top of the energy barrier are altered so that it
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climbs to the top of the barrier and finds the saddle point. The
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forces on atoms in this replica are described in the
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"(Henkelman2)"_#Henkelman2 paper, and become:
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Fnudgparallel= {Kspring}* (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
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The parallel nudging force associated with the key word idealpos should
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usually be more efficient at keeping the images equally spaced.
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:line
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The keyword {perp} allows to add a spring force perpendicular to the
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path in order to prevent the path from becoming too kinky. It can
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improve significantly the convergence of the NEB when the resolution
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is poor (i.e. when too few images are used) (see "(Maras)"_#Maras1).
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The perpendicular spring force is given by
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Fspringperp = {Kspringperp} * f(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
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f(Ri-1 Ri R+1) is a smooth scalar function of the angle Ri-1 Ri
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Ri+1. It is equal to 0 when the path is straight and is equal to 1
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when the angle Ri-1 Ri Ri+1 is accute. f(Ri-1 Ri R+1) is defined in
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"(Jonsson)"_#Jonsson
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:line
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By default, the force acting on the first and last replicas is not
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altered so that during the NEB relaxation, these ending replicas relax
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toward local minima. However it is possible to use the key word
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{freeend} to allow either the initial or the final replica to relax
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toward a MEP while constraining its energy. The interatomic force Fi
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for the free end image becomes :
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Fi = -Grad(V)+ (Grad(V) dot That + (E-ETarget)*kspring3) That, {when} Grad(V) dot That < 0
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Fi = -Grad(V)+ (Grad(V) dot That + (ETarget- E)*kspring3) That, {when} Grad(V) dot That > 0
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:pre
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where E is the energy of the free end replica and ETarget is the
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target energy.
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When the value {ini} ({final}) is used after the keyword {freeend},
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the first (last) replica is considered as a free end. The target
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energy is set to the energy of the replica at starting of the NEB
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calculation. When the value {finaleini} or {final2eini} is used the
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last image is considered as a free end and the target energy is equal
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to the energy of the first replica (which can evolve during the NEB
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relaxation). With the value {finaleini}, when the initial path is too
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far from the MEP, an intermediate repilica might relax "faster" and
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get a lower energy than the last replica. The benefit of the free end
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is then lost since this intermediate replica will relax toward a local
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minima. This behavior can be prevented by using the value {final2eini}
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which remove entirely the contribution of the gradient for all
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intermediate replica which have a lower energy than the initial one
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thus preventing these replicae to over-relax. After converging a NEB
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with the {final2eini} value it is recommended to check that all
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intermediate replica have a larger energy than the initial
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replica. Finally note that if the last replica converges toward a
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local minimum with a larger energy than the energy of the first
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replica, a free end neb calculation with the value {finaleini} or
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{final2eini} cannot reach the convergence criteria.
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:line
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In the second stage of the NEB, the interatomic force Fi for the
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climbing replica (which is the replica of highest energy) becomes:
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Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre
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The inter-replica forces for the other replicas are unchanged from the
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first equation.
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[Restart, fix_modify, output, run start/stop, minimize info:]
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@ -96,7 +184,11 @@ for more info on packages.
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"neb"_neb.html
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[Default:] none
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[Default:]
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The option defaults are nudg_style = neigh, perp = none, freeend = none and freend_kspring = 1.
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:line
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:link(Henkelman1)
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[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
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@ -104,3 +196,15 @@ for more info on packages.
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:link(Henkelman2)
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[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
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9901-9904 (2000).
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:link(E)
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[(E)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002)
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:link(Jonsson)
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[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum
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Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti, and Coker
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World Scientific, Singapore, 1998, p. 385
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:link(Maras1)
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[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
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Comp Phys Comm, 205, 13-21 (2016)
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219
doc/src/neb.txt
219
doc/src/neb.txt
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@ -10,28 +10,31 @@ neb command :h3
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[Syntax:]
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neb etol ftol N1 N2 Nevery file-style arg :pre
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neb etol ftol N1 N2 Nevery file-style arg keyword :pre
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etol = stopping tolerance for energy (energy units) :ulb,l
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ftol = stopping tolerance for force (force units) :l
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N1 = max # of iterations (timesteps) to run initial NEB :l
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N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
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Nevery = print replica energies and reaction coordinates every this many timesteps :l
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file-style= {final} or {each} or {none} :l
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file-style = {final} or {each} or {none} :l
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{final} arg = filename
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filename = file with initial coords for final replica
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coords for intermediate replicas are linearly interpolated between first and last replica
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coords for intermediate replicas are linearly interpolated
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between first and last replica
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{each} arg = filename
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filename = unique filename for each replica (except first) with its initial coords
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{none} arg = no argument
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all replicas assumed to already have their initial coords :pre
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filename = unique filename for each replica (except first)
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with its initial coords
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{none} arg = no argument all replicas assumed to already have
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their initial coords :pre
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keyword = {verbose}
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:ule
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[Examples:]
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neb 0.1 0.0 1000 500 50 final coords.final
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neb 0.0 0.001 1000 500 50 each coords.initial.$i
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neb 0.0 0.001 1000 500 50 none :pre
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neb 0.0 0.001 1000 500 50 none verbose :pre
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[Description:]
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@ -43,8 +46,8 @@ NEB is a method for finding both the atomic configurations and height
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of the energy barrier associated with a transition state, e.g. for an
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atom to perform a diffusive hop from one energy basin to another in a
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coordinated fashion with its neighbors. The implementation in LAMMPS
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follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA,
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"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano3.
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follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA,
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"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2.
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Each replica runs on a partition of one or more processors. Processor
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partitions are defined at run-time using the -partition command-line
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@ -70,18 +73,17 @@ I.e. the simulation domain, the number of atoms, the interaction
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potentials, and the starting configuration when the neb command is
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issued should be the same for every replica.
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In a NEB calculation each atom in a replica is connected to the same
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atom in adjacent replicas by springs, which induce inter-replica
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forces. These forces are imposed by the "fix neb"_fix_neb.html
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command, which must be used in conjunction with the neb command. The
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group used to define the fix neb command defines the NEB atoms which
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are the only ones that inter-replica springs are applied to. If the
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group does not include all atoms, then non-NEB atoms have no
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inter-replica springs and the forces they feel and their motion is
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computed in the usual way due only to other atoms within their
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replica. Conceptually, the non-NEB atoms provide a background force
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field for the NEB atoms. They can be allowed to move during the NEB
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minimization procedure (which will typically induce different
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In a NEB calculation each replica is connected to other replicas by
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inter-replica nudging forces. These forces are imposed by the "fix
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neb"_fix_neb.html command, which must be used in conjunction with the
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neb command. The group used to define the fix neb command defines the
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NEB atoms which are the only ones that inter-replica springs are
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applied to. If the group does not include all atoms, then non-NEB
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atoms have no inter-replica springs and the forces they feel and their
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motion is computed in the usual way due only to other atoms within
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their replica. Conceptually, the non-NEB atoms provide a background
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force field for the NEB atoms. They can be allowed to move during the
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NEB minimization procedure (which will typically induce different
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coordinates for non-NEB atoms in different replicas), or held fixed
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using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
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Note that the "partition"_partition.html command can be used to invoke
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@ -93,33 +95,18 @@ specified in different manners via the {file-style} setting, as
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discussed below. Only atoms whose initial coordinates should differ
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from the current configuration need be specified.
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Conceptually, the initial configuration for the first replica should
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be a state with all the atoms (NEB and non-NEB) having coordinates on
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one side of the energy barrier. A perfect energy minimum is not
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required, since atoms in the first replica experience no spring forces
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from the 2nd replica. Thus the damped dynamics minimization will
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drive the first replica to an energy minimum if it is not already
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there. However, you will typically get better convergence if the
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initial state is already at a minimum. For example, for a system with
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a free surface, the surface should be fully relaxed before attempting
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a NEB calculation.
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Likewise, the initial configuration of the final replica should be a
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state with all the atoms (NEB and non-NEB) on the other side of the
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energy barrier. Again, a perfect energy minimum is not required,
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since the atoms in the last replica also experience no spring forces
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from the next-to-last replica, and thus the damped dynamics
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minimization will drive it to an energy minimum.
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Conceptually, the initial and final configurations for the first
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replica should be states on either side of an energy barrier.
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As explained below, the initial configurations of intermediate
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replicas can be atomic coordinates interpolated in a linear fashion
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between the first and last replicas. This is often adequate state for
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between the first and last replicas. This is often adequate for
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simple transitions. For more complex transitions, it may lead to slow
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convergence or even bad results if the minimum energy path (MEP, see
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below) of states over the barrier cannot be correctly converged to
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from such an initial configuration. In this case, you will want to
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generate initial states for the intermediate replicas that are
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geometrically closer to the MEP and read them in.
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from such an initial path. In this case, you will want to generate
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initial states for the intermediate replicas that are geometrically
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closer to the MEP and read them in.
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:line
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@ -135,10 +122,11 @@ is assigned to be a fraction of the distance. E.g. if there are 10
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replicas, the 2nd replica will assign a position that is 10% of the
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distance along a line between the starting and final point, and the
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9th replica will assign a position that is 90% of the distance along
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the line. Note that this procedure to produce consistent coordinates
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across all the replicas, the current coordinates need to be the same
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in all replicas. LAMMPS does not check for this, but invalid initial
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configurations will likely result if it is not the case.
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the line. Note that for this procedure to produce consistent
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coordinates across all the replicas, the current coordinates need to
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be the same in all replicas. LAMMPS does not check for this, but
|
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invalid initial configurations will likely result if it is not the
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case.
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NOTE: The "distance" between the starting and final point is
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calculated in a minimum-image sense for a periodic simulation box.
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@ -150,8 +138,8 @@ interpolation is outside the periodic box, the atom will be wrapped
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back into the box when the NEB calculation begins.
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For a {file-style} setting of {each}, a filename is specified which is
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assumed to be unique to each replica. This can be done by
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||||
using a variable in the filename, e.g.
|
||||
assumed to be unique to each replica. This can be done by using a
|
||||
variable in the filename, e.g.
|
||||
|
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variable i equal part
|
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neb 0.0 0.001 1000 500 50 each coords.initial.$i :pre
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|
@ -198,11 +186,10 @@ The minimizer tolerances for energy and force are set by {etol} and
|
|||
A non-zero {etol} means that the NEB calculation will terminate if the
|
||||
energy criterion is met by every replica. The energies being compared
|
||||
to {etol} do not include any contribution from the inter-replica
|
||||
forces, since these are non-conservative. A non-zero {ftol} means
|
||||
that the NEB calculation will terminate if the force criterion is met
|
||||
by every replica. The forces being compared to {ftol} include the
|
||||
inter-replica forces between an atom and its images in adjacent
|
||||
replicas.
|
||||
nudging forces, since these are non-conservative. A non-zero {ftol}
|
||||
means that the NEB calculation will terminate if the force criterion
|
||||
is met by every replica. The forces being compared to {ftol} include
|
||||
the inter-replica nudging forces.
|
||||
|
||||
The maximum number of iterations in each stage is set by {N1} and
|
||||
{N2}. These are effectively timestep counts since each iteration of
|
||||
|
|
@ -220,27 +207,27 @@ finding a good energy barrier. {N1} and {N2} must both be multiples
|
|||
of {Nevery}.
|
||||
|
||||
In the first stage of NEB, the set of replicas should converge toward
|
||||
the minimum energy path (MEP) of conformational states that transition
|
||||
over the barrier. The MEP for a barrier is defined as a sequence of
|
||||
3N-dimensional states that cross the barrier at its saddle point, each
|
||||
of which has a potential energy gradient parallel to the MEP itself.
|
||||
The replica states will also be roughly equally spaced along the MEP
|
||||
due to the inter-replica spring force added by the "fix
|
||||
neb"_fix_neb.html command.
|
||||
a minimum energy path (MEP) of conformational states that transition
|
||||
over a barrier. The MEP for a transition is defined as a sequence of
|
||||
3N-dimensional states, each of which has a potential energy gradient
|
||||
parallel to the MEP itself. The configuration of highest energy along
|
||||
a MEP corresponds to a saddle point. The replica states will also be
|
||||
roughly equally spaced along the MEP due to the inter-replica nugding
|
||||
force added by the "fix neb"_fix_neb.html command.
|
||||
|
||||
In the second stage of NEB, the replica with the highest energy
|
||||
is selected and the inter-replica forces on it are converted to a
|
||||
force that drives its atom coordinates to the top or saddle point of
|
||||
the barrier, via the barrier-climbing calculation described in
|
||||
In the second stage of NEB, the replica with the highest energy is
|
||||
selected and the inter-replica forces on it are converted to a force
|
||||
that drives its atom coordinates to the top or saddle point of the
|
||||
barrier, via the barrier-climbing calculation described in
|
||||
"(HenkelmanB)"_#HenkelmanB. As before, the other replicas rearrange
|
||||
themselves along the MEP so as to be roughly equally spaced.
|
||||
|
||||
When both stages are complete, if the NEB calculation was successful,
|
||||
one of the replicas should be an atomic configuration at the top or
|
||||
saddle point of the barrier, the potential energies for the set of
|
||||
replicas should represent the energy profile of the barrier along the
|
||||
MEP, and the configurations of the replicas should be a sequence of
|
||||
configurations along the MEP.
|
||||
the configurations of the replicas should be along (close to) the MEP
|
||||
and the replica with the highest energy should be an atomic
|
||||
configuration at (close to) the saddle point of the transition. The
|
||||
potential energies for the set of replicas represents the energy
|
||||
profile of the transition along the MEP.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -284,9 +271,9 @@ ID2 x2 y2 z2
|
|||
...
|
||||
IDN xN yN zN :pre
|
||||
|
||||
The fields are the atom ID, followed by the x,y,z coordinates.
|
||||
The lines can be listed in any order. Additional trailing information
|
||||
on the line is OK, such as a comment.
|
||||
The fields are the atom ID, followed by the x,y,z coordinates. The
|
||||
lines can be listed in any order. Additional trailing information on
|
||||
the line is OK, such as a comment.
|
||||
|
||||
Note that for a typical NEB calculation you do not need to specify
|
||||
initial coordinates for very many atoms to produce differing starting
|
||||
|
|
@ -310,38 +297,54 @@ this case), the print-out to the screen and master log.lammps file
|
|||
contains a line of output, printed once every {Nevery} timesteps. It
|
||||
contains the timestep, the maximum force per replica, the maximum
|
||||
force per atom (in any replica), potential gradients in the initial,
|
||||
final, and climbing replicas, the forward and backward energy barriers,
|
||||
the total reaction coordinate (RDT), and the normalized reaction
|
||||
coordinate and potential energy of each replica.
|
||||
final, and climbing replicas, the forward and backward energy
|
||||
barriers, the total reaction coordinate (RDT), and the normalized
|
||||
reaction coordinate and potential energy of each replica.
|
||||
|
||||
The "maximum force per replica" is
|
||||
the two-norm of the 3N-length force vector for the atoms in each
|
||||
replica, maximized across replicas, which is what the {ftol} setting
|
||||
is checking against. In this case, N is all the atoms in each
|
||||
replica. The "maximum force per atom" is the maximum force component
|
||||
of any atom in any replica. The potential gradients are the two-norm
|
||||
of the 3N-length force vector solely due to the interaction potential i.e.
|
||||
without adding in inter-replica forces. Note that inter-replica forces
|
||||
are zero in the initial and final replicas, and only affect
|
||||
the direction in the climbing replica. For this reason, the "maximum
|
||||
force per replica" is often equal to the potential gradient in the
|
||||
climbing replica. In the first stage of NEB, there is no climbing
|
||||
replica, and so the potential gradient in the highest energy replica
|
||||
is reported, since this replica will become the climbing replica
|
||||
in the second stage of NEB.
|
||||
The "maximum force per replica" is the two-norm of the 3N-length force
|
||||
vector for the atoms in each replica, maximized across replicas, which
|
||||
is what the {ftol} setting is checking against. In this case, N is
|
||||
all the atoms in each replica. The "maximum force per atom" is the
|
||||
maximum force component of any atom in any replica. The potential
|
||||
gradients are the two-norm of the 3N-length force vector solely due to
|
||||
the interaction potential i.e. without adding in inter-replica
|
||||
forces.
|
||||
|
||||
The "reaction coordinate" (RD) for each
|
||||
replica is the two-norm of the 3N-length vector of distances between
|
||||
its atoms and the preceding replica's atoms, added to the RD of the
|
||||
preceding replica. The RD of the first replica RD1 = 0.0;
|
||||
the RD of the final replica RDN = RDT, the total reaction coordinate.
|
||||
The normalized RDs are divided by RDT,
|
||||
so that they form a monotonically increasing sequence
|
||||
from zero to one. When computing RD, N only includes the atoms
|
||||
being operated on by the fix neb command.
|
||||
The "reaction coordinate" (RD) for each replica is the two-norm of the
|
||||
3N-length vector of distances between its atoms and the preceding
|
||||
replica's atoms, added to the RD of the preceding replica. The RD of
|
||||
the first replica RD1 = 0.0; the RD of the final replica RDN = RDT,
|
||||
the total reaction coordinate. The normalized RDs are divided by RDT,
|
||||
so that they form a monotonically increasing sequence from zero to
|
||||
one. When computing RD, N only includes the atoms being operated on by
|
||||
the fix neb command.
|
||||
|
||||
The forward (reverse) energy barrier is the potential energy of the highest
|
||||
replica minus the energy of the first (last) replica.
|
||||
The forward (reverse) energy barrier is the potential energy of the
|
||||
highest replica minus the energy of the first (last) replica.
|
||||
|
||||
Supplementary informations for all replicas can be printed out to the
|
||||
screen and master log.lammps file by adding the verbose keyword. These
|
||||
informations include the following. The "path angle" (pathangle) for
|
||||
the replica i which is the angle between the 3N-length vectors (Ri-1 -
|
||||
Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
|
||||
i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
|
||||
aligned. "angletangrad" is the angle between the 3N-length tangent
|
||||
vector and the 3N-length force vector at image i. The tangent vector
|
||||
is calculated as in "(HenkelmanA)"_#HenkelmanA for all intermediate
|
||||
replicas and at R2 - R1 and RM - RM-1 for the first and last replica,
|
||||
respectively. "anglegrad" is the angle between the 3N-length energy
|
||||
gradient vector of replica i and that of replica i+1. It is not
|
||||
defined for the final replica and reads nan. gradV is the norm of the
|
||||
energy gradient of image i. ReplicaForce is the two-norm of the
|
||||
3N-length force vector (including nudging forces) for replica i.
|
||||
MaxAtomForce is the maximum force component of any atom in replica i.
|
||||
|
||||
When a NEB calculation does not converge properly, these suplementary
|
||||
informations can help understanding what is going wrong. For instance
|
||||
when the path angle becomes accute the definition of tangent used in
|
||||
the NEB calculation is questionable and the NEB cannot may diverge
|
||||
"(Maras)"_#Maras2.
|
||||
|
||||
|
||||
When running on multiple partitions, LAMMPS produces additional log
|
||||
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
|
||||
|
|
@ -396,12 +399,16 @@ This command can only be used if LAMMPS was built with the REPLICA
|
|||
package. See the "Making LAMMPS"_Section_start.html#start_3 section
|
||||
for more info on packages.
|
||||
|
||||
:line
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"prd"_prd.html, "temper"_temper.html, "fix
|
||||
langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html
|
||||
"prd"_prd.html, "temper"_temper.html, "fix langevin"_fix_langevin.html,
|
||||
"fix viscous"_fix_viscous.html
|
||||
|
||||
[Default:] none
|
||||
[Default:]
|
||||
|
||||
none
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -414,3 +421,7 @@ langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html
|
|||
|
||||
:link(Nakano3)
|
||||
[(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008).
|
||||
|
||||
:link(Maras2)
|
||||
[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
|
||||
Comp Phys Comm, 205, 13-21 (2016)
|
||||
|
|
|
|||
|
|
@ -2,13 +2,19 @@ Run these examples as:
|
|||
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1freeend
|
||||
mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac
|
||||
|
||||
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1
|
||||
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2
|
||||
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1freeend
|
||||
mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac
|
||||
mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac
|
||||
|
||||
|
||||
Note that more than 4 replicas should be used for a precise estimate
|
||||
of the activation energy corresponding to a transition.
|
||||
|
||||
If you uncomment the dump command lines in the input scripts, you can
|
||||
create dump files to do visualization from via Python tools: (see
|
||||
lammps/tools/README and lammps/tools/python/README for more info on
|
||||
|
|
|
|||
|
|
@ -51,7 +51,7 @@ set group nebatoms type 3
|
|||
group nonneb subtract all nebatoms
|
||||
|
||||
fix 1 lower setforce 0.0 0.0 0.0
|
||||
fix 2 nebatoms neb 1.0
|
||||
fix 2 nebatoms neb 1.0 nudg_style idealpos
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo 100
|
||||
|
|
|
|||
|
|
@ -0,0 +1,56 @@
|
|||
# 2d NEB surface simulation, hop from surface to become adatom
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
atom_modify map array sort 0 0.0
|
||||
|
||||
variable u uloop 20
|
||||
|
||||
# create geometry with flat surface
|
||||
|
||||
lattice hex 0.9
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
|
||||
read_data initial.hop1freeend
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
group mobile subtract all lower
|
||||
set group lower type 2
|
||||
|
||||
timestep 0.05
|
||||
|
||||
# group of NEB atoms - either block or single atom ID 412
|
||||
|
||||
region surround block 10 18 17 20 0 0 units box
|
||||
group nebatoms region surround
|
||||
#group nebatoms id 412
|
||||
set group nebatoms type 3
|
||||
group nonneb subtract all nebatoms
|
||||
|
||||
fix 1 lower setforce 0.0 0.0 0.0
|
||||
fix 2 nebatoms neb 1.0 nudg_style idealpos freeend ini
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 nebatoms atom 10 dump.neb.$u
|
||||
#dump 2 nonneb atom 10 dump.nonneb.$u
|
||||
|
||||
# run NEB for 2000 steps or to force tolerance
|
||||
|
||||
min_style quickmin
|
||||
|
||||
neb 0.0 0.1 1000 1000 100 final final.hop1
|
||||
|
|
@ -53,7 +53,7 @@ set group nebatoms type 3
|
|||
group nonneb subtract all nebatoms
|
||||
|
||||
fix 1 lower setforce 0.0 0.0 0.0
|
||||
fix 2 nebatoms neb 1.0
|
||||
fix 2 nebatoms neb 1.0
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo 100
|
||||
|
|
|
|||
|
|
@ -66,7 +66,7 @@ minimize 1.0e-6 1.0e-4 1000 10000
|
|||
|
||||
reset_timestep 0
|
||||
|
||||
fix 1 all neb 1.0
|
||||
fix 1 all neb 1.0
|
||||
|
||||
thermo 100
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,860 @@
|
|||
LAMMPS data file via write_data, version 4 May 2017, timestep = 155
|
||||
|
||||
420 atoms
|
||||
3 atom types
|
||||
|
||||
0.0000000000000000e+00 2.2653923264628304e+01 xlo xhi
|
||||
2.1918578738841410e-01 1.9932852254455714e+01 ylo yhi
|
||||
-2.8317404080785380e-01 2.8317404080785380e-01 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
|
||||
Atoms # atomic
|
||||
|
||||
1 2 0.0000000000000000e+00 2.2114806707013038e-01 0.0000000000000000e+00 0 0 0
|
||||
2 2 5.6634808161570760e-01 1.1832938184587634e+00 0.0000000000000000e+00 0 0 0
|
||||
3 2 1.1326961632314152e+00 2.2114806707013018e-01 0.0000000000000000e+00 0 0 0
|
||||
4 2 1.6990442448471228e+00 1.1832938184587634e+00 0.0000000000000000e+00 0 0 0
|
||||
5 2 2.2653923264628304e+00 2.2114806707013032e-01 0.0000000000000000e+00 0 0 0
|
||||
6 2 2.8317404080785380e+00 1.1832938184587634e+00 0.0000000000000000e+00 0 0 0
|
||||
7 2 3.3980884896942456e+00 2.2114806707013024e-01 0.0000000000000000e+00 0 0 0
|
||||
8 2 3.9644365713099532e+00 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
9 2 4.5307846529256608e+00 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
10 2 5.0971327345413684e+00 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
11 2 5.6634808161570760e+00 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
12 2 6.2298288977727836e+00 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
13 2 6.7961769793884912e+00 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
14 2 7.3625250610041988e+00 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
15 2 7.9288731426199064e+00 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
16 2 8.4952212242356140e+00 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
17 2 9.0615693058513216e+00 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
18 2 9.6279173874670292e+00 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
19 2 1.0194265469082737e+01 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
20 2 1.0760613550698444e+01 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
21 2 1.1326961632314152e+01 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
22 2 1.1893309713929860e+01 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
23 2 1.2459657795545567e+01 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
24 2 1.3026005877161275e+01 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
25 2 1.3592353958776982e+01 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
26 2 1.4158702040392690e+01 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
27 2 1.4725050122008398e+01 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
28 2 1.5291398203624105e+01 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
29 2 1.5857746285239813e+01 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
30 2 1.6424094366855520e+01 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
31 2 1.6990442448471228e+01 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
32 2 1.7556790530086936e+01 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
33 2 1.8123138611702643e+01 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
34 2 1.8689486693318351e+01 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
35 2 1.9255834774934058e+01 2.2114806707013010e-01 0.0000000000000000e+00 0 0 0
|
||||
36 2 1.9822182856549766e+01 1.1832938184587636e+00 0.0000000000000000e+00 0 0 0
|
||||
37 2 2.0388530938165474e+01 2.2114806707013024e-01 0.0000000000000000e+00 0 0 0
|
||||
38 2 2.0954879019781181e+01 1.1832938184587634e+00 0.0000000000000000e+00 0 0 0
|
||||
39 2 2.1521227101396889e+01 2.2114806707013043e-01 0.0000000000000000e+00 0 0 0
|
||||
40 2 2.2087575183012596e+01 1.1832938184587634e+00 0.0000000000000000e+00 0 0 0
|
||||
41 2 5.5197595012095140e-17 2.1414943053865136e+00 0.0000000000000000e+00 0 0 0
|
||||
42 1 5.6653050195082300e-01 3.1000166664180786e+00 0.0000000000000000e+00 0 0 0
|
||||
43 2 1.1326961632314152e+00 2.1414943053865136e+00 0.0000000000000000e+00 0 0 0
|
||||
44 1 1.6992713312703549e+00 3.1000339212153092e+00 0.0000000000000000e+00 0 0 0
|
||||
45 2 2.2653923264628304e+00 2.1414943053865136e+00 0.0000000000000000e+00 0 0 0
|
||||
46 1 2.8319979330663916e+00 3.1000568858502824e+00 0.0000000000000000e+00 0 0 0
|
||||
47 2 3.3980884896942456e+00 2.1414943053865136e+00 0.0000000000000000e+00 0 0 0
|
||||
48 1 3.9647072056144004e+00 3.1000829051868171e+00 0.0000000000000000e+00 0 0 0
|
||||
49 2 4.5307846529256608e+00 2.1414943053865132e+00 0.0000000000000000e+00 0 0 0
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||||
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|
|
@ -27,24 +27,75 @@
|
|||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
using namespace MathConst;
|
||||
|
||||
enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg), id_pe(NULL), pe(NULL), xprev(NULL), xnext(NULL),
|
||||
tangent(NULL), xsend(NULL), xrecv(NULL), tagsend(NULL), tagrecv(NULL),
|
||||
xsendall(NULL), xrecvall(NULL), tagsendall(NULL), tagrecvall(NULL),
|
||||
counts(NULL), displacements(NULL)
|
||||
Fix(lmp, narg, arg),
|
||||
id_pe(NULL), pe(NULL), nlenall(NULL), xprev(NULL), xnext(NULL),
|
||||
fnext(NULL), springF(NULL), tangent(NULL), xsend(NULL), xrecv(NULL),
|
||||
fsend(NULL), frecv(NULL), tagsend(NULL), tagrecv(NULL),
|
||||
xsendall(NULL), xrecvall(NULL), fsendall(NULL), frecvall(NULL),
|
||||
tagsendall(NULL), tagrecvall(NULL), counts(NULL),
|
||||
displacements(NULL)
|
||||
{
|
||||
if (narg != 4) error->all(FLERR,"Illegal fix neb command");
|
||||
|
||||
NEBLongRange=false;
|
||||
StandardNEB=true;
|
||||
PerpSpring=FreeEndIni=FreeEndFinal=false;
|
||||
FreeEndFinalWithRespToEIni=FinalAndInterWithRespToEIni=false;
|
||||
|
||||
kspringPerp=0.0;
|
||||
kspring2=1.0;
|
||||
if (narg < 4)
|
||||
error->all(FLERR,"Illegal fix neb command, argument missing");
|
||||
|
||||
kspring = force->numeric(FLERR,arg[3]);
|
||||
if (kspring <= 0.0) error->all(FLERR,"Illegal fix neb command");
|
||||
if (kspring <= 0.0)
|
||||
error->all(FLERR,"Illegal fix neb command."
|
||||
" The spring force was not provided properly");
|
||||
|
||||
int iarg =4;
|
||||
while (iarg < narg) {
|
||||
if (strcmp (arg[iarg],"nudg_style")==0) {
|
||||
if (strcmp (arg[iarg+1],"idealpos")==0) {
|
||||
NEBLongRange = true;
|
||||
iarg+=2;}
|
||||
else if (strcmp (arg[iarg+1],"neigh")==0) {
|
||||
NEBLongRange = false;
|
||||
StandardNEB = true;
|
||||
iarg+=2;}
|
||||
else error->all(FLERR,"Illegal fix neb command. Unknown keyword");}
|
||||
else if (strcmp (arg[iarg],"perp")==0) {
|
||||
PerpSpring=true;
|
||||
kspringPerp = force->numeric(FLERR,arg[iarg+1]);
|
||||
if (kspringPerp < 0.0)
|
||||
error->all(FLERR,"Illegal fix neb command. "
|
||||
"The perpendicular spring force was not provided properly");
|
||||
iarg+=2;}
|
||||
else if (strcmp (arg[iarg],"freeend")==0) {
|
||||
if (strcmp (arg[iarg+1],"ini")==0)
|
||||
FreeEndIni=true;
|
||||
else if (strcmp (arg[iarg+1],"final")==0)
|
||||
FreeEndFinal=true;
|
||||
else if (strcmp (arg[iarg+1],"finaleini")==0)
|
||||
FreeEndFinalWithRespToEIni=true;
|
||||
else if (strcmp (arg[iarg+1],"final2eini")==0) {
|
||||
FinalAndInterWithRespToEIni=true;
|
||||
FreeEndFinalWithRespToEIni=true;}
|
||||
else if (strcmp (arg[iarg+1],"none")!=0) error->all(FLERR,"Illegal fix neb command. Unknown keyword");
|
||||
iarg+=2;}
|
||||
else if (strcmp (arg[iarg],"freeend_kspring")==0) {
|
||||
kspring2=force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg+=2; }
|
||||
else error->all(FLERR,"Illegal fix neb command. Unknown keyword");
|
||||
}
|
||||
|
||||
// nreplica = number of partitions
|
||||
// ireplica = which world I am in universe
|
||||
|
|
@ -62,7 +113,18 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
|
|||
else procprev = -1;
|
||||
if (ireplica < nreplica-1) procnext = universe->root_proc[ireplica+1];
|
||||
else procnext = -1;
|
||||
|
||||
uworld = universe->uworld;
|
||||
int *iroots = new int[nreplica];
|
||||
MPI_Group uworldgroup,rootgroup;
|
||||
if (NEBLongRange) {
|
||||
for (int i=0; i<nreplica; i++)
|
||||
iroots[i]=universe->root_proc[i];
|
||||
MPI_Comm_group(uworld, &uworldgroup);
|
||||
MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup);
|
||||
MPI_Comm_create(uworld, rootgroup, &rootworld);
|
||||
}
|
||||
delete[] iroots;
|
||||
|
||||
// create a new compute pe style
|
||||
// id = fix-ID + pe, compute group = all
|
||||
|
|
@ -81,15 +143,8 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
// initialize local storage
|
||||
|
||||
maxlocal = 0;
|
||||
ntotal = 0;
|
||||
|
||||
xprev = xnext = tangent = NULL;
|
||||
xsend = xrecv = NULL;
|
||||
tagsend = tagrecv = NULL;
|
||||
xsendall = xrecvall = NULL;
|
||||
tagsendall = tagrecvall = NULL;
|
||||
counts = displacements = NULL;
|
||||
maxlocal = -1;
|
||||
ntotal = -1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -102,19 +157,29 @@ FixNEB::~FixNEB()
|
|||
memory->destroy(xprev);
|
||||
memory->destroy(xnext);
|
||||
memory->destroy(tangent);
|
||||
|
||||
memory->destroy(fnext);
|
||||
memory->destroy(springF);
|
||||
memory->destroy(xsend);
|
||||
memory->destroy(xrecv);
|
||||
memory->destroy(fsend);
|
||||
memory->destroy(frecv);
|
||||
memory->destroy(tagsend);
|
||||
memory->destroy(tagrecv);
|
||||
|
||||
memory->destroy(xsendall);
|
||||
memory->destroy(xrecvall);
|
||||
memory->destroy(fsendall);
|
||||
memory->destroy(frecvall);
|
||||
memory->destroy(tagsendall);
|
||||
memory->destroy(tagrecvall);
|
||||
|
||||
memory->destroy(counts);
|
||||
memory->destroy(displacements);
|
||||
|
||||
if (NEBLongRange) {
|
||||
if (rootworld != MPI_COMM_NULL) MPI_Comm_free(&rootworld);
|
||||
memory->destroy(nlenall);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -148,7 +213,7 @@ void FixNEB::init()
|
|||
// comm mode for inter-replica exchange of coords
|
||||
|
||||
if (nreplica == nprocs_universe &&
|
||||
nebatoms == atom->natoms && atom->sortfreq == 0)
|
||||
nebatoms == atom->natoms && atom->sortfreq == 0)
|
||||
cmode = SINGLE_PROC_DIRECT;
|
||||
else if (nreplica == nprocs_universe) cmode = SINGLE_PROC_MAP;
|
||||
else cmode = MULTI_PROC;
|
||||
|
|
@ -158,11 +223,13 @@ void FixNEB::init()
|
|||
if (atom->natoms > MAXSMALLINT) error->all(FLERR,"Too many atoms for NEB");
|
||||
ntotal = atom->natoms;
|
||||
|
||||
if (atom->nlocal > maxlocal) reallocate();
|
||||
if (atom->nmax > maxlocal) reallocate();
|
||||
|
||||
if (MULTI_PROC && counts == NULL) {
|
||||
memory->create(xsendall,ntotal,3,"neb:xsendall");
|
||||
memory->create(xrecvall,ntotal,3,"neb:xrecvall");
|
||||
memory->create(fsendall,ntotal,3,"neb:fsendall");
|
||||
memory->create(frecvall,ntotal,3,"neb:frecvall");
|
||||
memory->create(tagsendall,ntotal,"neb:tagsendall");
|
||||
memory->create(tagrecvall,ntotal,"neb:tagrecvall");
|
||||
memory->create(counts,nprocs,"neb:counts");
|
||||
|
|
@ -185,19 +252,15 @@ void FixNEB::min_setup(int vflag)
|
|||
|
||||
void FixNEB::min_post_force(int vflag)
|
||||
{
|
||||
double vprev,vnext,vmax,vmin;
|
||||
double delx,dely,delz;
|
||||
double delta1[3],delta2[3];
|
||||
double vprev,vnext;
|
||||
double delxp,delyp,delzp,delxn,delyn,delzn;
|
||||
double vIni=0.0;
|
||||
|
||||
// veng = PE of this replica
|
||||
// vprev,vnext = PEs of adjacent replicas
|
||||
// only proc 0 in each replica communicates
|
||||
vprev=vnext=veng=pe->compute_scalar();
|
||||
|
||||
vprev = vnext = veng = pe->compute_scalar();
|
||||
|
||||
if (ireplica < nreplica-1 && me == 0)
|
||||
if (ireplica < nreplica-1 && me ==0)
|
||||
MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
|
||||
if (ireplica > 0 && me == 0)
|
||||
if (ireplica > 0 && me ==0)
|
||||
MPI_Recv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,MPI_STATUS_IGNORE);
|
||||
|
||||
if (ireplica > 0 && me == 0)
|
||||
|
|
@ -210,116 +273,177 @@ void FixNEB::min_post_force(int vflag)
|
|||
MPI_Bcast(&vnext,1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
|
||||
// communicate atoms to/from adjacent replicas to fill xprev,xnext
|
||||
if (FreeEndFinal && (update->ntimestep == 0)) EFinalIni = veng;
|
||||
|
||||
if (ireplica == 0) vIni=veng;
|
||||
|
||||
if (FreeEndFinalWithRespToEIni) {
|
||||
if (me == 0) {
|
||||
int procFirst;
|
||||
procFirst=universe->root_proc[0];
|
||||
MPI_Bcast(&vIni,1,MPI_DOUBLE,procFirst,uworld);
|
||||
}
|
||||
if (cmode == MULTI_PROC) {
|
||||
MPI_Bcast(&vIni,1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
if (FreeEndIni && ireplica == 0) {
|
||||
if (me == 0 )
|
||||
if (update->ntimestep == 0) {
|
||||
EIniIni = veng;
|
||||
if (cmode == MULTI_PROC)
|
||||
MPI_Bcast(&EIniIni,1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
|
||||
// communicate atoms to/from adjacent replicas to fill xprev,xnext
|
||||
inter_replica_comm();
|
||||
|
||||
// trigger potential energy computation on next timestep
|
||||
|
||||
pe->addstep(update->ntimestep+1);
|
||||
|
||||
// compute norm of GradV for log output
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
double dot = 0.0;
|
||||
double prefactor = 0.0;
|
||||
|
||||
double **f = atom->f;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double fsq = 0.0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
fsq += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
|
||||
//calculating separation between images
|
||||
|
||||
MPI_Allreduce(&fsq,&gradvnorm,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
gradvnorm = sqrt(gradvnorm);
|
||||
|
||||
// first or last replica has no change to forces, just return
|
||||
|
||||
if (ireplica == 0 || ireplica == nreplica-1) {
|
||||
plen = nlen = 0.0;
|
||||
return;
|
||||
}
|
||||
|
||||
// tangent = unit tangent vector in 3N space
|
||||
// based on delta vectors between atoms and their images in adjacent replicas
|
||||
// use one or two delta vecs to compute tangent,
|
||||
// depending on relative PEs of 3 replicas
|
||||
// see Henkelman & Jonsson 2000 paper, eqs 8-11
|
||||
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
|
||||
if (vnext > veng && veng > vprev) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
tangent[i][0] = xnext[i][0] - x[i][0];
|
||||
tangent[i][1] = xnext[i][1] - x[i][1];
|
||||
tangent[i][2] = xnext[i][2] - x[i][2];
|
||||
domain->minimum_image(tangent[i]);
|
||||
}
|
||||
} else if (vnext < veng && veng < vprev) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
tangent[i][0] = x[i][0] - xprev[i][0];
|
||||
tangent[i][1] = x[i][1] - xprev[i][1];
|
||||
tangent[i][2] = x[i][2] - xprev[i][2];
|
||||
domain->minimum_image(tangent[i]);
|
||||
}
|
||||
} else {
|
||||
vmax = MAX(fabs(vnext-veng),fabs(vprev-veng));
|
||||
vmin = MIN(fabs(vnext-veng),fabs(vprev-veng));
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
delta1[0] = xnext[i][0] - x[i][0];
|
||||
delta1[1] = xnext[i][1] - x[i][1];
|
||||
delta1[2] = xnext[i][2] - x[i][2];
|
||||
domain->minimum_image(delta1);
|
||||
delta2[0] = x[i][0] - xprev[i][0];
|
||||
delta2[1] = x[i][1] - xprev[i][1];
|
||||
delta2[2] = x[i][2] - xprev[i][2];
|
||||
domain->minimum_image(delta2);
|
||||
if (vnext > vprev) {
|
||||
tangent[i][0] = vmax*delta1[0] + vmin*delta2[0];
|
||||
tangent[i][1] = vmax*delta1[1] + vmin*delta2[1];
|
||||
tangent[i][2] = vmax*delta1[2] + vmin*delta2[2];
|
||||
} else {
|
||||
tangent[i][0] = vmin*delta1[0] + vmax*delta2[0];
|
||||
tangent[i][1] = vmin*delta1[1] + vmax*delta2[1];
|
||||
tangent[i][2] = vmin*delta1[2] + vmax*delta2[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// tlen,plen,nlen = lengths of tangent, prev, next vectors
|
||||
|
||||
double tlen = 0.0;
|
||||
plen = 0.0;
|
||||
nlen = 0.0;
|
||||
double tlen = 0.0;
|
||||
double gradnextlen = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
tlen += tangent[i][0]*tangent[i][0] + tangent[i][1]*tangent[i][1] +
|
||||
tangent[i][2]*tangent[i][2];
|
||||
dotgrad = gradlen = dotpath = dottangrad = 0.0;
|
||||
|
||||
delx = x[i][0] - xprev[i][0];
|
||||
dely = x[i][1] - xprev[i][1];
|
||||
delz = x[i][2] - xprev[i][2];
|
||||
domain->minimum_image(delx,dely,delz);
|
||||
plen += delx*delx + dely*dely + delz*delz;
|
||||
if (ireplica == nreplica-1) {
|
||||
|
||||
delx = xnext[i][0] - x[i][0];
|
||||
dely = xnext[i][1] - x[i][1];
|
||||
delz = xnext[i][2] - x[i][2];
|
||||
domain->minimum_image(delx,dely,delz);
|
||||
nlen += delx*delx + dely*dely + delz*delz;
|
||||
}
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
delxp = x[i][0] - xprev[i][0];
|
||||
delyp = x[i][1] - xprev[i][1];
|
||||
delzp = x[i][2] - xprev[i][2];
|
||||
domain->minimum_image(delxp,delyp,delzp);
|
||||
plen += delxp*delxp + delyp*delyp + delzp*delzp;
|
||||
dottangrad += delxp* f[i][0]+ delyp*f[i][1]+delzp*f[i][2];
|
||||
gradlen += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
|
||||
if (FreeEndFinal||FreeEndFinalWithRespToEIni) {
|
||||
tangent[i][0]=delxp;
|
||||
tangent[i][1]=delyp;
|
||||
tangent[i][2]=delzp;
|
||||
tlen += tangent[i][0]*tangent[i][0]
|
||||
+ tangent[i][1]*tangent[i][1] + tangent[i][2]*tangent[i][2];
|
||||
dot += f[i][0]*tangent[i][0]
|
||||
+ f[i][1]*tangent[i][1] + f[i][2]*tangent[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
double lenall;
|
||||
MPI_Allreduce(&tlen,&lenall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
tlen = sqrt(lenall);
|
||||
} else if (ireplica == 0) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
delxn = xnext[i][0] - x[i][0];
|
||||
delyn = xnext[i][1] - x[i][1];
|
||||
delzn = xnext[i][2] - x[i][2];
|
||||
domain->minimum_image(delxn,delyn,delzn);
|
||||
nlen += delxn*delxn + delyn*delyn + delzn*delzn;
|
||||
gradnextlen += fnext[i][0]*fnext[i][0]
|
||||
+ fnext[i][1]*fnext[i][1] +fnext[i][2] * fnext[i][2];
|
||||
dotgrad += f[i][0]*fnext[i][0]
|
||||
+ f[i][1]*fnext[i][1] + f[i][2]*fnext[i][2];
|
||||
dottangrad += delxn*f[i][0]+ delyn*f[i][1] + delzn*f[i][2];
|
||||
gradlen += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
|
||||
if (FreeEndIni) {
|
||||
tangent[i][0]=delxn;
|
||||
tangent[i][1]=delyn;
|
||||
tangent[i][2]=delzn;
|
||||
tlen += tangent[i][0]*tangent[i][0]
|
||||
+ tangent[i][1]*tangent[i][1] + tangent[i][2]*tangent[i][2];
|
||||
dot += f[i][0]*tangent[i][0]
|
||||
+ f[i][1]*tangent[i][1] + f[i][2]*tangent[i][2];
|
||||
}
|
||||
}
|
||||
} else {
|
||||
|
||||
MPI_Allreduce(&plen,&lenall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
plen = sqrt(lenall);
|
||||
// not the first or last replica
|
||||
|
||||
MPI_Allreduce(&nlen,&lenall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
nlen = sqrt(lenall);
|
||||
double vmax = MAX(fabs(vnext-veng),fabs(vprev-veng));
|
||||
double vmin = MIN(fabs(vnext-veng),fabs(vprev-veng));
|
||||
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
delxp = x[i][0] - xprev[i][0];
|
||||
delyp = x[i][1] - xprev[i][1];
|
||||
delzp = x[i][2] - xprev[i][2];
|
||||
domain->minimum_image(delxp,delyp,delzp);
|
||||
plen += delxp*delxp + delyp*delyp + delzp*delzp;
|
||||
|
||||
delxn = xnext[i][0] - x[i][0];
|
||||
delyn = xnext[i][1] - x[i][1];
|
||||
delzn = xnext[i][2] - x[i][2];
|
||||
domain->minimum_image(delxn,delyn,delzn);
|
||||
|
||||
if (vnext > veng && veng > vprev) {
|
||||
tangent[i][0]=delxn;
|
||||
tangent[i][1]=delyn;
|
||||
tangent[i][2]=delzn;
|
||||
} else if (vnext < veng && veng < vprev) {
|
||||
tangent[i][0]=delxp;
|
||||
tangent[i][1]=delyp;
|
||||
tangent[i][2]=delzp;
|
||||
} else {
|
||||
if (vnext > vprev) {
|
||||
tangent[i][0] = vmax*delxn + vmin*delxp;
|
||||
tangent[i][1] = vmax*delyn + vmin*delyp;
|
||||
tangent[i][2] = vmax*delzn + vmin*delzp;
|
||||
} else {
|
||||
tangent[i][0] = vmin*delxn + vmax*delxp;
|
||||
tangent[i][1] = vmin*delyn + vmax*delyp;
|
||||
tangent[i][2] = vmin*delzn + vmax*delzp;
|
||||
}
|
||||
}
|
||||
|
||||
nlen += delxn*delxn + delyn*delyn + delzn*delzn;
|
||||
tlen += tangent[i][0]*tangent[i][0]
|
||||
+ tangent[i][1]*tangent[i][1] + tangent[i][2]*tangent[i][2];
|
||||
gradlen += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
|
||||
dotpath += delxp*delxn + delyp*delyn + delzp*delzn;
|
||||
dottangrad += tangent[i][0]* f[i][0]
|
||||
+ tangent[i][1]*f[i][1] + tangent[i][2]*f[i][2];
|
||||
gradnextlen += fnext[i][0]*fnext[i][0]
|
||||
+ fnext[i][1]*fnext[i][1] +fnext[i][2] * fnext[i][2];
|
||||
dotgrad += f[i][0]*fnext[i][0]
|
||||
+ f[i][1]*fnext[i][1] + f[i][2]*fnext[i][2];
|
||||
|
||||
springF[i][0]=kspringPerp*(delxn-delxp);
|
||||
springF[i][1]=kspringPerp*(delyn-delyp);
|
||||
springF[i][2]=kspringPerp*(delzn-delzp);
|
||||
}
|
||||
}
|
||||
|
||||
#define BUFSIZE 8
|
||||
double bufin[BUFSIZE], bufout[BUFSIZE];
|
||||
bufin[0] = nlen;
|
||||
bufin[1] = plen;
|
||||
bufin[2] = tlen;
|
||||
bufin[3] = gradlen;
|
||||
bufin[4] = gradnextlen;
|
||||
bufin[5] = dotpath;
|
||||
bufin[6] = dottangrad;
|
||||
bufin[7] = dotgrad;
|
||||
MPI_Allreduce(bufin,bufout,BUFSIZE,MPI_DOUBLE,MPI_SUM,world);
|
||||
nlen = sqrt(bufout[0]);
|
||||
plen = sqrt(bufout[1]);
|
||||
tlen = sqrt(bufout[2]);
|
||||
gradlen = sqrt(bufout[3]);
|
||||
gradnextlen = sqrt(bufout[4]);
|
||||
dotpath = bufout[5];
|
||||
dottangrad = bufout[6];
|
||||
dotgrad = bufout[7];
|
||||
|
||||
// normalize tangent vector
|
||||
|
||||
|
|
@ -333,37 +457,158 @@ void FixNEB::min_post_force(int vflag)
|
|||
}
|
||||
}
|
||||
|
||||
// reset force on each atom in this replica
|
||||
// regular NEB for all replicas except rclimber does hill-climbing NEB
|
||||
// currently have F = -Grad(V) = -Grad(V)_perp - Grad(V)_parallel
|
||||
// want F = -Grad(V)_perp + Fspring for regular NEB
|
||||
// thus Fdelta = Grad(V)_parallel + Fspring for regular NEB
|
||||
// want F = -Grad(V) + 2 Grad(V)_parallel for hill-climbing NEB
|
||||
// thus Fdelta = 2 Grad(V)_parallel for hill-climbing NEB
|
||||
// Grad(V)_parallel = (Grad(V) . utan) * utangent = -(F . utan) * utangent
|
||||
// Fspring = k (nlen - plen) * utangent
|
||||
// see Henkelman & Jonsson 2000 paper, eqs 3,4,12
|
||||
// see Henkelman & Jonsson 2000a paper, eq 5
|
||||
// first or last replica has no change to forces, just return
|
||||
|
||||
double dot = 0.0;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit)
|
||||
dot += f[i][0]*tangent[i][0] + f[i][1]*tangent[i][1] +
|
||||
f[i][2]*tangent[i][2];
|
||||
if(ireplica>0 && ireplica<nreplica-1)
|
||||
dottangrad = dottangrad/(tlen*gradlen);
|
||||
if (ireplica == 0)
|
||||
dottangrad = dottangrad/(nlen*gradlen);
|
||||
if (ireplica == nreplica-1)
|
||||
dottangrad = dottangrad/(plen*gradlen);
|
||||
if (ireplica < nreplica-1)
|
||||
dotgrad = dotgrad /(gradlen*gradnextlen);
|
||||
|
||||
|
||||
if (FreeEndIni && ireplica == 0) {
|
||||
if (tlen > 0.0) {
|
||||
double dotall;
|
||||
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
dot=dotall/tlen;
|
||||
|
||||
if (dot<0) prefactor = -dot - kspring2*(veng-EIniIni);
|
||||
else prefactor = -dot + kspring2*(veng-EIniIni);
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
f[i][0] += prefactor *tangent[i][0];
|
||||
f[i][1] += prefactor *tangent[i][1];
|
||||
f[i][2] += prefactor *tangent[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (FreeEndFinal && ireplica == nreplica -1) {
|
||||
if (tlen > 0.0) {
|
||||
double dotall;
|
||||
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
dot=dotall/tlen;
|
||||
|
||||
if (dot<0) prefactor = -dot - kspring2*(veng-EFinalIni);
|
||||
else prefactor = -dot + kspring2*(veng-EFinalIni);
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
f[i][0] += prefactor *tangent[i][0];
|
||||
f[i][1] += prefactor *tangent[i][1];
|
||||
f[i][2] += prefactor *tangent[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (FreeEndFinalWithRespToEIni&&ireplica == nreplica -1) {
|
||||
if (tlen > 0.0) {
|
||||
double dotall;
|
||||
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
dot=dotall/tlen;
|
||||
|
||||
if (dot<0) prefactor = -dot - kspring2*(veng-vIni);
|
||||
else prefactor = -dot + kspring2*(veng-vIni);
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
f[i][0] += prefactor *tangent[i][0];
|
||||
f[i][1] += prefactor *tangent[i][1];
|
||||
f[i][2] += prefactor *tangent[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
double lentot = 0;
|
||||
double meanDist,idealPos,lenuntilIm,lenuntilClimber;
|
||||
lenuntilClimber=0;
|
||||
if (NEBLongRange) {
|
||||
if (cmode == SINGLE_PROC_DIRECT || cmode == SINGLE_PROC_MAP) {
|
||||
MPI_Allgather(&nlen,1,MPI_DOUBLE,&nlenall[0],1,MPI_DOUBLE,uworld);
|
||||
} else {
|
||||
if (me == 0)
|
||||
MPI_Allgather(&nlen,1,MPI_DOUBLE,&nlenall[0],1,MPI_DOUBLE,rootworld);
|
||||
MPI_Bcast(nlenall,nreplica,MPI_DOUBLE,0,world);
|
||||
}
|
||||
|
||||
lenuntilIm = 0;
|
||||
for (int i = 0; i < ireplica; i++)
|
||||
lenuntilIm += nlenall[i];
|
||||
|
||||
for (int i = 0; i < nreplica; i++)
|
||||
lentot += nlenall[i];
|
||||
|
||||
meanDist = lentot/(nreplica -1);
|
||||
|
||||
if (rclimber>0) {
|
||||
for (int i = 0; i < rclimber; i++)
|
||||
lenuntilClimber += nlenall[i];
|
||||
double meanDistBeforeClimber = lenuntilClimber/rclimber;
|
||||
double meanDistAfterClimber =
|
||||
(lentot-lenuntilClimber)/(nreplica-rclimber-1);
|
||||
if (ireplica<rclimber)
|
||||
idealPos = ireplica * meanDistBeforeClimber;
|
||||
else
|
||||
idealPos = lenuntilClimber+ (ireplica-rclimber)*meanDistAfterClimber;
|
||||
} else idealPos = ireplica * meanDist;
|
||||
}
|
||||
|
||||
if (ireplica == 0 || ireplica == nreplica-1) return ;
|
||||
|
||||
double AngularContr;
|
||||
dotpath = dotpath/(plen*nlen);
|
||||
AngularContr = 0.5 *(1+cos(MY_PI * dotpath));
|
||||
|
||||
double dotSpringTangent;
|
||||
dotSpringTangent=0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dot += f[i][0]*tangent[i][0]
|
||||
+ f[i][1]*tangent[i][1] + f[i][2]*tangent[i][2];
|
||||
dotSpringTangent += springF[i][0]*tangent[i][0]
|
||||
+springF[i][1]*tangent[i][1]+springF[i][2]*tangent[i][2];}
|
||||
}
|
||||
|
||||
double dotSpringTangentall;
|
||||
MPI_Allreduce(&dotSpringTangent,&dotSpringTangentall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
dotSpringTangent=dotSpringTangentall;
|
||||
double dotall;
|
||||
MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
dot=dotall;
|
||||
|
||||
double prefactor;
|
||||
if (ireplica == rclimber) prefactor = -2.0*dotall;
|
||||
else prefactor = -dotall + kspring*(nlen-plen);
|
||||
if (ireplica == rclimber) prefactor = -2.0*dot;
|
||||
else {
|
||||
if (NEBLongRange) {
|
||||
prefactor = -dot - kspring*(lenuntilIm-idealPos)/(2*meanDist);
|
||||
} else if (StandardNEB) {
|
||||
prefactor = -dot + kspring*(nlen-plen);
|
||||
}
|
||||
|
||||
if (FinalAndInterWithRespToEIni&& veng<vIni) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
f[i][0] = 0;
|
||||
f[i][1] = 0;
|
||||
f[i][2] = 0;
|
||||
}
|
||||
prefactor = kspring*(nlen-plen);
|
||||
AngularContr=0;
|
||||
}
|
||||
}
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
f[i][0] += prefactor*tangent[i][0];
|
||||
f[i][1] += prefactor*tangent[i][1];
|
||||
f[i][2] += prefactor*tangent[i][2];
|
||||
f[i][0] += prefactor*tangent[i][0]
|
||||
+AngularContr*(springF[i][0] -dotSpringTangent*tangent[i][0]);
|
||||
f[i][1] += prefactor*tangent[i][1]
|
||||
+ AngularContr*(springF[i][1] - dotSpringTangent*tangent[i][1]);
|
||||
f[i][2] += prefactor*tangent[i][2]
|
||||
+ AngularContr*(springF[i][2] - dotSpringTangent*tangent[i][2]);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -373,6 +618,7 @@ void FixNEB::min_post_force(int vflag)
|
|||
replicas 0 and N-1 send but do not receive any atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
void FixNEB::inter_replica_comm()
|
||||
{
|
||||
int i,m;
|
||||
|
|
@ -382,9 +628,10 @@ void FixNEB::inter_replica_comm()
|
|||
|
||||
// reallocate memory if necessary
|
||||
|
||||
if (atom->nlocal > maxlocal) reallocate();
|
||||
if (atom->nmax > maxlocal) reallocate();
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
tagint *tag = atom->tag;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
|
@ -395,7 +642,7 @@ void FixNEB::inter_replica_comm()
|
|||
// -----------------------------------------------------
|
||||
|
||||
// single proc per replica
|
||||
// all atoms are NEB atoms and no atom sorting is enabled
|
||||
// all atoms are NEB atoms and no atom sorting
|
||||
// direct comm of x -> xprev and x -> xnext
|
||||
|
||||
if (cmode == SINGLE_PROC_DIRECT) {
|
||||
|
|
@ -404,13 +651,18 @@ void FixNEB::inter_replica_comm()
|
|||
if (ireplica < nreplica-1)
|
||||
MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld);
|
||||
if (ireplica > 0) MPI_Wait(&request,MPI_STATUS_IGNORE);
|
||||
|
||||
if (ireplica < nreplica-1)
|
||||
MPI_Irecv(xnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request);
|
||||
if (ireplica > 0)
|
||||
MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld);
|
||||
if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE);
|
||||
|
||||
if (ireplica < nreplica-1)
|
||||
MPI_Irecv(fnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request);
|
||||
if (ireplica > 0)
|
||||
MPI_Send(f[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld);
|
||||
if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE);
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
|
|
@ -427,6 +679,9 @@ void FixNEB::inter_replica_comm()
|
|||
xsend[m][0] = x[i][0];
|
||||
xsend[m][1] = x[i][1];
|
||||
xsend[m][2] = x[i][2];
|
||||
fsend[m][0] = f[i][0];
|
||||
fsend[m][1] = f[i][1];
|
||||
fsend[m][2] = f[i][2];
|
||||
m++;
|
||||
}
|
||||
|
||||
|
|
@ -448,13 +703,14 @@ void FixNEB::inter_replica_comm()
|
|||
xprev[m][2] = xrecv[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
if (ireplica < nreplica-1) {
|
||||
MPI_Irecv(xrecv[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
|
||||
MPI_Irecv(frecv[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
|
||||
MPI_Irecv(tagrecv,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld,&requests[1]);
|
||||
}
|
||||
if (ireplica > 0) {
|
||||
MPI_Send(xsend[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
|
||||
MPI_Send(fsend[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
|
||||
MPI_Send(tagsend,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld);
|
||||
}
|
||||
|
||||
|
|
@ -465,6 +721,9 @@ void FixNEB::inter_replica_comm()
|
|||
xnext[m][0] = xrecv[i][0];
|
||||
xnext[m][1] = xrecv[i][1];
|
||||
xnext[m][2] = xrecv[i][2];
|
||||
fnext[m][0] = frecv[i][0];
|
||||
fnext[m][1] = frecv[i][1];
|
||||
fnext[m][2] = frecv[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -484,6 +743,9 @@ void FixNEB::inter_replica_comm()
|
|||
xsend[m][0] = x[i][0];
|
||||
xsend[m][1] = x[i][1];
|
||||
xsend[m][2] = x[i][2];
|
||||
fsend[m][0] = f[i][0];
|
||||
fsend[m][1] = f[i][1];
|
||||
fsend[m][2] = f[i][2];
|
||||
m++;
|
||||
}
|
||||
|
||||
|
|
@ -496,12 +758,17 @@ void FixNEB::inter_replica_comm()
|
|||
for (i = 0; i < nprocs; i++) counts[i] *= 3;
|
||||
for (i = 0; i < nprocs-1; i++)
|
||||
displacements[i+1] = displacements[i] + counts[i];
|
||||
if (xsend)
|
||||
if (xsend) {
|
||||
MPI_Gatherv(xsend[0],3*m,MPI_DOUBLE,
|
||||
xsendall[0],counts,displacements,MPI_DOUBLE,0,world);
|
||||
else
|
||||
MPI_Gatherv(fsend[0],3*m,MPI_DOUBLE,
|
||||
fsendall[0],counts,displacements,MPI_DOUBLE,0,world);
|
||||
} else {
|
||||
MPI_Gatherv(NULL,3*m,MPI_DOUBLE,
|
||||
xsendall[0],counts,displacements,MPI_DOUBLE,0,world);
|
||||
MPI_Gatherv(NULL,3*m,MPI_DOUBLE,
|
||||
fsendall[0],counts,displacements,MPI_DOUBLE,0,world);
|
||||
}
|
||||
|
||||
if (ireplica > 0 && me == 0) {
|
||||
MPI_Irecv(xrecvall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld,&requests[0]);
|
||||
|
|
@ -530,11 +797,13 @@ void FixNEB::inter_replica_comm()
|
|||
|
||||
if (ireplica < nreplica-1 && me == 0) {
|
||||
MPI_Irecv(xrecvall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
|
||||
MPI_Irecv(frecvall[0],3*nebatoms,MPI_DOUBLE,procnext,0,uworld,&requests[0]);
|
||||
MPI_Irecv(tagrecvall,nebatoms,MPI_LMP_TAGINT,procnext,0,uworld,
|
||||
&requests[1]);
|
||||
}
|
||||
if (ireplica > 0 && me == 0) {
|
||||
MPI_Send(xsendall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
|
||||
MPI_Send(fsendall[0],3*nebatoms,MPI_DOUBLE,procprev,0,uworld);
|
||||
MPI_Send(tagsendall,nebatoms,MPI_LMP_TAGINT,procprev,0,uworld);
|
||||
}
|
||||
|
||||
|
|
@ -543,6 +812,7 @@ void FixNEB::inter_replica_comm()
|
|||
|
||||
MPI_Bcast(tagrecvall,nebatoms,MPI_INT,0,world);
|
||||
MPI_Bcast(xrecvall[0],3*nebatoms,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(frecvall[0],3*nebatoms,MPI_DOUBLE,0,world);
|
||||
|
||||
for (i = 0; i < nebatoms; i++) {
|
||||
m = atom->map(tagrecvall[i]);
|
||||
|
|
@ -550,10 +820,14 @@ void FixNEB::inter_replica_comm()
|
|||
xnext[m][0] = xrecvall[i][0];
|
||||
xnext[m][1] = xrecvall[i][1];
|
||||
xnext[m][2] = xrecvall[i][2];
|
||||
fnext[m][0] = frecvall[i][0];
|
||||
fnext[m][1] = frecvall[i][1];
|
||||
fnext[m][2] = frecvall[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
reallocate xprev,xnext,tangent arrays if necessary
|
||||
reallocate communication arrays if necessary
|
||||
|
|
@ -561,27 +835,37 @@ void FixNEB::inter_replica_comm()
|
|||
|
||||
void FixNEB::reallocate()
|
||||
{
|
||||
maxlocal = atom->nmax;
|
||||
|
||||
memory->destroy(xprev);
|
||||
memory->destroy(xnext);
|
||||
memory->destroy(tangent);
|
||||
|
||||
if (cmode != SINGLE_PROC_DIRECT) {
|
||||
memory->destroy(xsend);
|
||||
memory->destroy(xrecv);
|
||||
memory->destroy(tagsend);
|
||||
memory->destroy(tagrecv);
|
||||
}
|
||||
|
||||
maxlocal = atom->nmax;
|
||||
memory->destroy(fnext);
|
||||
memory->destroy(springF);
|
||||
|
||||
memory->create(xprev,maxlocal,3,"neb:xprev");
|
||||
memory->create(xnext,maxlocal,3,"neb:xnext");
|
||||
memory->create(tangent,maxlocal,3,"neb:tangent");
|
||||
memory->create(fnext,maxlocal,3,"neb:fnext");
|
||||
memory->create(springF,maxlocal,3,"neb:springF");
|
||||
|
||||
if (cmode != SINGLE_PROC_DIRECT) {
|
||||
memory->destroy(xsend);
|
||||
memory->destroy(fsend);
|
||||
memory->destroy(xrecv);
|
||||
memory->destroy(frecv);
|
||||
memory->destroy(tagsend);
|
||||
memory->destroy(tagrecv);
|
||||
memory->create(xsend,maxlocal,3,"neb:xsend");
|
||||
memory->create(fsend,maxlocal,3,"neb:fsend");
|
||||
memory->create(xrecv,maxlocal,3,"neb:xrecv");
|
||||
memory->create(frecv,maxlocal,3,"neb:frecv");
|
||||
memory->create(tagsend,maxlocal,"neb:tagsend");
|
||||
memory->create(tagrecv,maxlocal,"neb:tagrecv");
|
||||
}
|
||||
|
||||
if (NEBLongRange) {
|
||||
memory->destroy(nlenall);
|
||||
memory->create(nlenall,nreplica,"neb:nlenall");
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -26,9 +26,8 @@ namespace LAMMPS_NS {
|
|||
|
||||
class FixNEB : public Fix {
|
||||
public:
|
||||
double veng,plen,nlen;
|
||||
double veng,plen,nlen,dotpath,dottangrad,gradlen,dotgrad;
|
||||
int rclimber;
|
||||
double gradvnorm;
|
||||
|
||||
FixNEB(class LAMMPS *, int, char **);
|
||||
~FixNEB();
|
||||
|
|
@ -39,27 +38,32 @@ class FixNEB : public Fix {
|
|||
|
||||
private:
|
||||
int me,nprocs,nprocs_universe;
|
||||
double kspring;
|
||||
double kspring,kspring2,kspringPerp,EIniIni,EFinalIni;
|
||||
bool StandardNEB,NEBLongRange,PerpSpring,FreeEndIni,FreeEndFinal;
|
||||
bool FreeEndFinalWithRespToEIni,FinalAndInterWithRespToEIni;
|
||||
int ireplica,nreplica;
|
||||
int procnext,procprev;
|
||||
int cmode;
|
||||
MPI_Comm uworld;
|
||||
MPI_Comm rootworld;
|
||||
|
||||
|
||||
char *id_pe;
|
||||
class Compute *pe;
|
||||
|
||||
int nebatoms; // # of active NEB atoms
|
||||
int nebatoms;
|
||||
int ntotal; // total # of atoms, NEB or not
|
||||
int maxlocal; // size of xprev,xnext,tangent arrays
|
||||
|
||||
double **xprev,**xnext; // coords of my owned atoms in neighbor replicas
|
||||
double **tangent; // work vector for inter-replica forces
|
||||
|
||||
double *nlenall;
|
||||
double **xprev,**xnext,**fnext,**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
|
||||
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
|
||||
tagint *tagsendall,*tagrecvall; // ditto for atom IDs
|
||||
|
||||
int *counts,*displacements; // used for MPI_Gather
|
||||
|
|
|
|||
|
|
@ -37,8 +37,10 @@
|
|||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define MAXLINE 256
|
||||
#define CHUNK 1024
|
||||
|
|
@ -143,17 +145,19 @@ void NEB::command(int narg, char **arg)
|
|||
// process file-style setting to setup initial configs for all replicas
|
||||
|
||||
if (strcmp(arg[5],"final") == 0) {
|
||||
if (narg != 7) error->universe_all(FLERR,"Illegal NEB command");
|
||||
if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB command");
|
||||
infile = arg[6];
|
||||
readfile(infile,0);
|
||||
} else if (strcmp(arg[5],"each") == 0) {
|
||||
if (narg != 7) error->universe_all(FLERR,"Illegal NEB command");
|
||||
if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB command");
|
||||
infile = arg[6];
|
||||
readfile(infile,1);
|
||||
} else if (strcmp(arg[5],"none") == 0) {
|
||||
if (narg != 6) error->universe_all(FLERR,"Illegal NEB command");
|
||||
if (narg != 6 && narg !=7) error->universe_all(FLERR,"Illegal NEB command");
|
||||
} else error->universe_all(FLERR,"Illegal NEB command");
|
||||
|
||||
verbose=false;
|
||||
if (strcmp(arg[narg-1],"verbose") == 0) verbose=true;
|
||||
// run the NEB calculation
|
||||
|
||||
run();
|
||||
|
|
@ -178,8 +182,9 @@ void NEB::run()
|
|||
if (ineb == modify->nfix) error->all(FLERR,"NEB requires use of fix neb");
|
||||
|
||||
fneb = (FixNEB *) modify->fix[ineb];
|
||||
nall = 4;
|
||||
memory->create(all,nreplica,nall,"neb:all");
|
||||
if (verbose) numall =7;
|
||||
else numall = 4;
|
||||
memory->create(all,nreplica,numall,"neb:all");
|
||||
rdist = new double[nreplica];
|
||||
|
||||
// initialize LAMMPS
|
||||
|
|
@ -195,9 +200,11 @@ void NEB::run()
|
|||
error->all(FLERR,"NEB requires damped dynamics minimizer");
|
||||
|
||||
// setup regular NEB minimization
|
||||
FILE *uscreen = universe->uscreen;
|
||||
FILE *ulogfile = universe->ulogfile;
|
||||
|
||||
if (me_universe == 0 && universe->uscreen)
|
||||
fprintf(universe->uscreen,"Setting up regular NEB ...\n");
|
||||
if (me_universe == 0 && uscreen)
|
||||
fprintf(uscreen,"Setting up regular NEB ...\n");
|
||||
|
||||
update->beginstep = update->firststep = update->ntimestep;
|
||||
update->endstep = update->laststep = update->firststep + n1steps;
|
||||
|
|
@ -209,16 +216,33 @@ void NEB::run()
|
|||
update->minimize->setup();
|
||||
|
||||
if (me_universe == 0) {
|
||||
if (universe->uscreen)
|
||||
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc "
|
||||
"EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
|
||||
if (universe->ulogfile)
|
||||
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc "
|
||||
"EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
|
||||
if (uscreen) {
|
||||
if (verbose) {
|
||||
fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
|
||||
"RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 "
|
||||
"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
|
||||
"... ReplicaForceN MaxAtomForceN\n");
|
||||
} else {
|
||||
fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
|
||||
"RDN PEN\n");
|
||||
}
|
||||
}
|
||||
|
||||
if (ulogfile) {
|
||||
if (verbose) {
|
||||
fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
|
||||
"RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 "
|
||||
"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
|
||||
"... ReplicaForceN MaxAtomForceN\n");
|
||||
} else {
|
||||
fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
|
||||
"RDN PEN\n");
|
||||
}
|
||||
}
|
||||
}
|
||||
print_status();
|
||||
|
||||
|
|
@ -257,14 +281,14 @@ void NEB::run()
|
|||
// setup climbing NEB minimization
|
||||
// must reinitialize minimizer so it re-creates its fix MINIMIZE
|
||||
|
||||
if (me_universe == 0 && universe->uscreen)
|
||||
fprintf(universe->uscreen,"Setting up climbing ...\n");
|
||||
if (me_universe == 0 && uscreen)
|
||||
fprintf(uscreen,"Setting up climbing ...\n");
|
||||
|
||||
if (me_universe == 0) {
|
||||
if (universe->uscreen)
|
||||
fprintf(universe->uscreen,"Climbing replica = %d\n",top+1);
|
||||
if (universe->ulogfile)
|
||||
fprintf(universe->ulogfile,"Climbing replica = %d\n",top+1);
|
||||
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;
|
||||
|
|
@ -279,16 +303,34 @@ void NEB::run()
|
|||
update->minimize->setup();
|
||||
|
||||
if (me_universe == 0) {
|
||||
if (universe->uscreen)
|
||||
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc "
|
||||
"EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
|
||||
if (universe->ulogfile)
|
||||
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc "
|
||||
"EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
|
||||
if (uscreen)
|
||||
if (verbose) {
|
||||
fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN "
|
||||
"pathangle1 angletangrad1 anglegrad1 gradV1 "
|
||||
"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
|
||||
"... ReplicaForceN MaxAtomForceN\n");
|
||||
} else {
|
||||
fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc "
|
||||
"EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
|
||||
}
|
||||
if (ulogfile)
|
||||
if (verbose) {
|
||||
fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN "
|
||||
"pathangle1 angletangrad1 anglegrad1 gradV1 "
|
||||
"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
|
||||
"... ReplicaForceN MaxAtomForceN\n");
|
||||
} else {
|
||||
fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
|
||||
"GradV0 GradV1 GradVc "
|
||||
"EBF EBR RDT "
|
||||
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
|
||||
}
|
||||
}
|
||||
print_status();
|
||||
|
||||
|
|
@ -321,16 +363,16 @@ void NEB::run()
|
|||
/* ----------------------------------------------------------------------
|
||||
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
|
||||
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
|
||||
each replica (except first) opens file and reads it
|
||||
each replica stores coords
|
||||
initial replica does nothing
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void NEB::readfile(char *file, int flag)
|
||||
|
|
@ -539,16 +581,29 @@ void NEB::print_status()
|
|||
double fmaxatom;
|
||||
MPI_Allreduce(&fnorminf,&fmaxatom,1,MPI_DOUBLE,MPI_MAX,roots);
|
||||
|
||||
double one[4];
|
||||
if (verbose) {
|
||||
freplica = new double[nreplica];
|
||||
MPI_Allgather(&fnorm2,1,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[numall];
|
||||
one[0] = fneb->veng;
|
||||
one[1] = fneb->plen;
|
||||
one[2] = fneb->nlen;
|
||||
one[nall-1] = fneb->gradvnorm;
|
||||
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,nall,MPI_DOUBLE,&all[0][0],nall,MPI_DOUBLE,roots);
|
||||
MPI_Bcast(&all[0][0],nall*nreplica,MPI_DOUBLE,0,world);
|
||||
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++)
|
||||
|
|
@ -588,26 +643,56 @@ void NEB::print_status()
|
|||
}
|
||||
|
||||
if (me_universe == 0) {
|
||||
if (universe->uscreen) {
|
||||
fprintf(universe->uscreen,BIGINT_FORMAT " %12.8g %12.8g ",
|
||||
const double todeg=180.0/MY_PI;
|
||||
FILE *uscreen = universe->uscreen;
|
||||
FILE *ulogfile = universe->ulogfile;
|
||||
if (uscreen) {
|
||||
fprintf(uscreen,BIGINT_FORMAT " %12.8g %12.8g ",
|
||||
update->ntimestep,fmaxreplica,fmaxatom);
|
||||
fprintf(universe->uscreen,"%12.8g %12.8g %12.8g ",
|
||||
fprintf(uscreen,"%12.8g %12.8g %12.8g ",
|
||||
gradvnorm0,gradvnorm1,gradvnormc);
|
||||
fprintf(universe->uscreen,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
|
||||
fprintf(uscreen,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
|
||||
for (int i = 0; i < nreplica; i++)
|
||||
fprintf(universe->uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
|
||||
fprintf(universe->uscreen,"\n");
|
||||
fprintf(uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
|
||||
if (verbose) {
|
||||
fprintf(uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
|
||||
NAN,180-acos(all[0][5])*todeg,180-acos(all[0][6])*todeg,
|
||||
all[0][3],freplica[0],fmaxatomInRepl[0]);
|
||||
for (int i = 1; i < nreplica-1; i++)
|
||||
fprintf(uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
|
||||
180-acos(all[i][4])*todeg,180-acos(all[i][5])*todeg,
|
||||
180-acos(all[i][6])*todeg,all[i][3],freplica[i],
|
||||
fmaxatomInRepl[i]);
|
||||
fprintf(uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
|
||||
NAN,180-acos(all[nreplica-1][5])*todeg,NAN,all[nreplica-1][3],
|
||||
freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
|
||||
}
|
||||
fprintf(uscreen,"\n");
|
||||
}
|
||||
if (universe->ulogfile) {
|
||||
fprintf(universe->ulogfile,BIGINT_FORMAT " %12.8g %12.8g ",
|
||||
|
||||
if (ulogfile) {
|
||||
fprintf(ulogfile,BIGINT_FORMAT " %12.8g %12.8g ",
|
||||
update->ntimestep,fmaxreplica,fmaxatom);
|
||||
fprintf(universe->ulogfile,"%12.8g %12.8g %12.8g ",
|
||||
fprintf(ulogfile,"%12.8g %12.8g %12.8g ",
|
||||
gradvnorm0,gradvnorm1,gradvnormc);
|
||||
fprintf(universe->ulogfile,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
|
||||
fprintf(ulogfile,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
|
||||
for (int i = 0; i < nreplica; i++)
|
||||
fprintf(universe->ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
|
||||
fprintf(universe->ulogfile,"\n");
|
||||
fflush(universe->ulogfile);
|
||||
fprintf(ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
|
||||
if (verbose) {
|
||||
fprintf(ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
|
||||
NAN,180-acos(all[0][5])*todeg,180-acos(all[0][6])*todeg,
|
||||
all[0][3],freplica[0],fmaxatomInRepl[0]);
|
||||
for (int i = 1; i < nreplica-1; i++)
|
||||
fprintf(ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
|
||||
180-acos(all[i][4])*todeg,180-acos(all[i][5])*todeg,
|
||||
180-acos(all[i][6])*todeg,all[i][3],freplica[i],
|
||||
fmaxatomInRepl[i]);
|
||||
fprintf(ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
|
||||
NAN,180-acos(all[nreplica-1][5])*todeg,NAN,all[nreplica-1][3],
|
||||
freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
|
||||
}
|
||||
fprintf(ulogfile,"\n");
|
||||
fflush(ulogfile);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -38,6 +38,7 @@ class NEB : protected Pointers {
|
|||
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;
|
||||
|
|
@ -49,9 +50,11 @@ class NEB : protected Pointers {
|
|||
char *infile; // name of file containing final state
|
||||
|
||||
class FixNEB *fneb;
|
||||
int nall; // per-replica dimension of array all
|
||||
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);
|
||||
void open(char *);
|
||||
|
|
|
|||
Loading…
Reference in New Issue