diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt index cd0fa23e85..94c6ee84fd 100644 --- a/doc/src/fix_neb.txt +++ b/doc/src/fix_neb.txt @@ -18,20 +18,19 @@ Kspring = parallel spring constant (force/distance units or force units) :l zero or more keyword/value pairs may be appended :l keyword = {nudg_style} or {perp} or {freend} or {freend_k_spring} :l {nudg_style} value = {neigh} or {idealpos} - {neigh} = the parallel nudging force is calculated from the distance to neighbouring replicas (in this case, Kspring is in force/distance units) + {neigh} = the parallel nudging force is calculated from the distances to neighbouring replicas (in this case, Kspring is in force/distance units) {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) {perp} value {none} or kspring2 {none} = no perpendicular spring force is applied + {kspring2} = spring constant for the perpendicular nudging force (in force/distance units) {freeend} value = {none} or {ini} or {final} or {finaleini} or {final2eini} - {none} = no nudging force is apply to the first and last replicas + {none} = no nudging force is applied to the first and last replicas {ini} = set the first replica to be a free end {final} = set the last replica to be a free end {finaleini} = set the last replica to be a free end and set its target energy as that of the first replica {final2eini} = same as {finaleini} plus prevent intermediate replicas to have a lower energy than the first replica - {freeend_kspring} value = kspring2 - kspring2 = spring constant of the perpendicular spring force (per distance units) -flag = set behavior for the end points - flag = + {freeend_kspring} value = kspring3 + kspring3 = spring constant of the perpendicular spring force (per distance units) :pre [Examples:] @@ -58,10 +57,10 @@ highest energy along the MEP). One purpose of the nudging forces is to keep the replicas equally spaced. During the NEB, the 3N-length vector of interatomic force Fi = -Grad(V) of replicas i is altered. For all intermediate replicas -(i.e. for 1 0 -:pre - -where E is the energy of the free end replica and ETarget is the -target energy. - -When the value {ini} ({final}) is used after the keyword {freeend}, -the first (last) replica is considered as a free end. The target -energy is set to the energy of the replica at starting of the NEB -calculation. When the value {finaleini} or {final2eini} is used the -last image is considered as a free end and the target energy is equal -to the energy of the first replica (which can evolve during the NEB -relaxation). With the value {finaleini}, when the initial path is too -far from the MEP, an intermediate repilica might relax "faster" and -get a lower energy than the last replica. The benefit of the free end -is then lost since this intermediate replica will relax toward a local -minima. This behavior can be prevented by using the value {final2eini} -which remove entirely the contribution of the gradient for all -intermediate replica which have a lower energy than the initial one -thus preventing these replicae to over-relax. After converging a NEB -with the {final2eini} value it is recommended to check that all -intermediate replica have a larger energy than the initial -replica. Finally note that if the last replica converges toward a -local minimum with a larger energy than the energy of the first -replica, a free end neb calculation with the value {finaleini} or -{final2eini} cannot reach the convergence criteria. - -:line - The keyword {nudg_style} allow to specify how to parallel nudging force is computed. With a value of idealpos, the spring force is computed as suggested in "(E)"_#E : @@ -159,6 +115,52 @@ when the angle Ri-1 Ri Ri+1 is accute. f(Ri-1 Ri R+1) is defined in :line +By default, the force acting on the first and last replicas is not +altered so that during the NEB relaxation, these ending replicas relax +toward local minima. However it is possible to use the key word +{freeend} to allow either the initial or the final replica to relax +toward a MEP while constraining its energy. The interatomic force Fi +for the free end image becomes : + +Fi = -Grad(V)+ (Grad(V) dot That + (E-ETarget)*kspring3) That, {when} Grad(V) dot That < 0 +Fi = -Grad(V)+ (Grad(V) dot That + (ETarget- E)*kspring3) That, {when} Grad(V) dot That > 0 +:pre + +where E is the energy of the free end replica and ETarget is the +target energy. + +When the value {ini} ({final}) is used after the keyword {freeend}, +the first (last) replica is considered as a free end. The target +energy is set to the energy of the replica at starting of the NEB +calculation. When the value {finaleini} or {final2eini} is used the +last image is considered as a free end and the target energy is equal +to the energy of the first replica (which can evolve during the NEB +relaxation). With the value {finaleini}, when the initial path is too +far from the MEP, an intermediate repilica might relax "faster" and +get a lower energy than the last replica. The benefit of the free end +is then lost since this intermediate replica will relax toward a local +minima. This behavior can be prevented by using the value {final2eini} +which remove entirely the contribution of the gradient for all +intermediate replica which have a lower energy than the initial one +thus preventing these replicae to over-relax. After converging a NEB +with the {final2eini} value it is recommended to check that all +intermediate replica have a larger energy than the initial +replica. Finally note that if the last replica converges toward a +local minimum with a larger energy than the energy of the first +replica, a free end neb calculation with the value {finaleini} or +{final2eini} cannot reach the convergence criteria. + +:line + + + +In the second stage of the NEB, the interatomic force Fi for the +climbing replica (which is the replica of highest energy) becomes: + +Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre + + + [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart