Commit 9a71efc5 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

fix neb bugfix from Emile Maras 

NEB was not working fine when using multiple proc
per replica and the keywords last/efirst or last/efirst/middle

I have corrected this in the enclosed fix_neb.cpp

I also slightly modified the nudging for this free end so that
it would be applied only when the target energy is larger than
the energy. Anyway if the target energy is lower than the energy,
the replica should relax toward the target energy without adding
any nudging.

I also modified the documentation according to this change.
parent 2f857c6e

doc/src/fix_neb.txt

+8 −9
Original line number Diff line number Diff line
@@ -138,17 +138,17 @@ By default, no additional forces act on the first and last replicas 
during the NEB relaxation, so these replicas simply relax toward their

respective local minima.  By using the key word {end}, additional

forces can be applied to the first and/or last replicas, to enable

them to relax toward a MEP while constraining their energy.

them to relax toward a MEP while constraining their energy E to the

target energy ETarget.



The interatomic force Fi for the specified replica becomes:

If ETarget>E, the interatomic force Fi for the specified replica becomes:



Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)*Kspring3) T',  {when} Grad(V) dot T' < 0

Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)*Kspring3) T', {when} Grad(V) dot T' > 0

:pre



where E is the current energy of the replica and ETarget is the target

energy.  The "spring" constant on the difference in energies is the

specified {Kspring3} value.

The "spring" constant on the difference in energies is the specified

{Kspring3} value.



When {estyle} is specified as {first}, the force is applied to the

first replica.  When {estyle} is specified as {last}, the force is
@@ -183,10 +183,9 @@ After converging a NEB calculation using an {estyle} of 
have a larger energy than the first replica. If this is not the case,

the path is probably not a MEP.



Finally, note that if the last replica converges toward a local

minimum which has a larger energy than the energy of the first

replica, a NEB calculation using an {estyle} of {last/efirst} or

{last/efirst/middle} cannot reach final convergence.

Finally, note that the last replica may never reach the target energy

if it is stuck in a local minima which has a larger energy than the

target energy.



[Restart, fix_modify, output, run start/stop, minimize info:]

src/REPLICA/fix_neb.cpp

+31 −28
Original line number Diff line number Diff line
@@ -298,12 +298,14 @@ void FixNEB::min_post_force(int vflag) 
  if (ireplica == 0) vIni=veng;



  if (FreeEndFinalWithRespToEIni) {

    if (me == 0) {

    if (cmode == SINGLE_PROC_DIRECT || cmode == SINGLE_PROC_MAP) {

      int procFirst;

      procFirst=universe->root_proc[0];

      MPI_Bcast(&vIni,1,MPI_DOUBLE,procFirst,uworld);

    }

    if (cmode == MULTI_PROC) {

    }else {

      if (me == 0)

        MPI_Bcast(&vIni,1,MPI_DOUBLE,0,rootworld);



      MPI_Bcast(&vIni,1,MPI_DOUBLE,0,world);

    }

  }
@@ -514,9 +516,10 @@ void FixNEB::min_post_force(int vflag) 
      MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);

      dot=dotall/tlen;



      if (veng<EFinalIni) {

        if (dot<0) prefactor = -dot - kspringFinal*(veng-EFinalIni);

        else prefactor = -dot + kspringFinal*(veng-EFinalIni);



      }

      for (int i = 0; i < nlocal; i++)

        if (mask[i] & groupbit) {

          f[i][0] += prefactor *tangent[i][0];
@@ -531,10 +534,10 @@ void FixNEB::min_post_force(int vflag) 
      double dotall;

      MPI_Allreduce(&dot,&dotall,1,MPI_DOUBLE,MPI_SUM,world);

      dot=dotall/tlen;



      if (veng<vIni) {

        if (dot<0) prefactor = -dot - kspringFinal*(veng-vIni);

        else prefactor = -dot + kspringFinal*(veng-vIni);



      }

      for (int i = 0; i < nlocal; i++)

        if (mask[i] & groupbit) {

          f[i][0] += prefactor *tangent[i][0];

CRA Git | Maintained and supported by SUSTech CRA and CCSE