corrected the fix_neb documentation
This commit is contained in:
Emile Maras
@ -18,20 +18,19 @@ 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 distance to neighbouring replicas (in this case, Kspring is in force/distance units)
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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 apply to the first and last replicas
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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 = kspring2
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kspring2 = spring constant of the perpendicular spring force (per distance units)
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flag = set behavior for the end points
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flag =
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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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@ -58,10 +57,10 @@ highest energy along the MEP).
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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) except for the climbing replica the force vector
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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 + Fspringparallel + Fspringperp :pre
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Fi = -Grad(V) + (Grad(V) dot That) That + Fnudgparallel + Fspringperp :pre
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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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@ -70,56 +69,13 @@ roughly in the direction of (Ri+i - Ri-1) (see the
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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. Fspringparallel is an
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artificial spring force which is applied only in the tangent direction
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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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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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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) That, {when} Grad(V) dot That < 0
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Fi = -Grad(V)+ (Grad(V) dot That + ETarget- E) 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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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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@ -159,6 +115,52 @@ when the angle Ri-1 Ri Ri+1 is accute. f(Ri-1 Ri R+1) is defined in
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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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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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