Commit d66b07da authored by julient31's avatar julient31
Browse files

Commit2 JT 031419 

- commit before solo tests
parent 033a5c27

src/REPLICA/neb_spin.cpp

+6 −36
Original line number Diff line number Diff line
@@ -46,7 +46,6 @@ using namespace MathConst; 


#define MAXLINE 256

#define CHUNK 1024

//#define ATTRIBUTE_PERLINE 4

// 8 attributes: tag, spin norm, position (3), spin direction (3)

#define ATTRIBUTE_PERLINE 8
@@ -62,11 +61,9 @@ NEB_spin::NEB_spin(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in, 
         int n2steps_in, int nevery_in, double *buf_init, double *buf_final)

  : Pointers(lmp)

{

  //double delx,dely,delz;

  double delspx,delspy,delspz;



  etol = etol_in;

  //ftol = ftol_in;

  ttol = ftol_in;

  n1steps = n1steps_in;

  n2steps = n2steps_in;
@@ -98,17 +95,15 @@ NEB_spin::NEB_spin(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in, 
    spfinal[1] = buf_final[ii+1];

    spfinal[2] = buf_final[ii+2];



    // circular initialization

    // a better procedure may be developed



    initial_rotation(spinit,spfinal,fraction);



    sp[i][0] = spfinal[0];

    sp[i][1] = spfinal[1];

    sp[i][2] = spfinal[2];

    

    // adjust distance if pbc

    //domain->minimum_image(delx,dely,delz);

   

    // need to define a better procedure for circular initialization

    

    ii += 3;

  }

}
@@ -134,7 +129,6 @@ void NEB_spin::command(int narg, char **arg) 
  if (narg < 6) error->universe_all(FLERR,"Illegal NEB_spin command");



  etol = force->numeric(FLERR,arg[0]);

  //ftol = force->numeric(FLERR,arg[1]);

  ttol = force->numeric(FLERR,arg[1]);

  n1steps = force->inumeric(FLERR,arg[2]);

  n2steps = force->inumeric(FLERR,arg[3]);
@@ -143,7 +137,6 @@ void NEB_spin::command(int narg, char **arg) 
  // error checks



  if (etol < 0.0) error->all(FLERR,"Illegal NEB_spin command");

  //if (ftol < 0.0) error->all(FLERR,"Illegal NEB_spin command");

  if (ttol < 0.0) error->all(FLERR,"Illegal NEB_spin command");

  if (nevery <= 0) error->universe_all(FLERR,"Illegal NEB_spin command");

  if (n1steps % nevery || n2steps % nevery)
@@ -172,7 +165,6 @@ void NEB_spin::command(int narg, char **arg) 


  // process file-style setting to setup initial configs for all replicas



  // check what options are available

  if (strcmp(arg[5],"final") == 0) {

    if (narg != 7 && narg !=8) error->universe_all(FLERR,"Illegal NEB_spin command");

    infile = arg[6];
@@ -205,6 +197,7 @@ void NEB_spin::run() 
  MPI_Comm_split(uworld,color,0,&roots);



  // search for neb_spin fix, allocate it

  

  int ineb;

  for (ineb = 0; ineb < modify->nfix; ineb++)

    if (strcmp(modify->fix[ineb]->style,"neb/spin") == 0) break;
@@ -220,7 +213,6 @@ void NEB_spin::run() 


  update->whichflag = 2;

  update->etol = etol;

  //update->ftol = ftol;

  update->ftol = ttol;		// update->ftol is a torque tolerance

  update->multireplica = 1;
@@ -258,11 +250,6 @@ void NEB_spin::run() 
                "RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 "

                "ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "

                "... ReplicaTorqueN MaxAtomTorqueN\n");

        //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 MaxReplicaTorque MaxAtomTorque "

                "GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
@@ -424,7 +411,6 @@ void NEB_spin::readfile(char *file, int flag) 
  char *eof,*start,*next,*buf;

  char line[MAXLINE];

  double xx,yy,zz,delx,dely,delz;

  // spin quantities

  double musp,spx,spy,spz;



  if (me_universe == 0 && screen)
@@ -469,7 +455,6 @@ void NEB_spin::readfile(char *file, int flag) 
  double fraction = ireplica/(nreplica-1.0);



  double **x = atom->x;

  // spin quantities

  double **sp = atom->sp;

  double spinit[3],spfinal[3];

  int nlocal = atom->nlocal;
@@ -540,9 +525,6 @@ void NEB_spin::readfile(char *file, int flag) 
	  spfinal[1] = spy;

	  spfinal[2] = spz;



	  // to be used it atomic displacements with pbc

	  //domain->minimum_image(delx,dely,delz);



	  // interpolate intermediate spin states



	  initial_rotation(spinit,spfinal,fraction);
@@ -609,11 +591,10 @@ void NEB_spin::initial_rotation(double *spi, double *sploc, double fraction) 
{

  

  // implementing initial rotation using atan2

  // this is not a sufficient routine, 

  // we need more accurate verifications



  // this may not be a sufficient routine, need more accurate verifications



  // initial, final and inter ang. values 

  

  double itheta,iphi,ftheta,fphi,ktheta,kphi;

  double spix,spiy,spiz,spfx,spfy,spfz;

  double spkx,spky,spkz,iknorm;
@@ -648,7 +629,6 @@ void NEB_spin::initial_rotation(double *spi, double *sploc, double fraction) 
  sploc[0] = spkx;

  sploc[1] = spky;

  sploc[2] = spkz;

  

}



/* ----------------------------------------------------------------------
@@ -692,9 +672,6 @@ void NEB_spin::open(char *file) 


void NEB_spin::print_status()

{

  

  //double fnorm2 = sqrt(update->minimize->fnorm_sqr());

  

  int nlocal = atom->nlocal;

  double tx,ty,tz;

  double tnorm2,local_norm_inf,temp_inf;
@@ -709,20 +686,14 @@ void NEB_spin::print_status() 
    ty = (fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]);

    tz = (fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]);

    tnorm2 += tx*tx + ty*ty + tz*tz;



    temp_inf = MAX(fabs(tx),fabs(ty));

    temp_inf = MAX(fabs(tz),temp_inf);

    local_norm_inf = MAX(temp_inf,local_norm_inf);



  }



  double fmaxreplica;

  //MPI_Allreduce(&fnorm2,&fmaxreplica,1,MPI_DOUBLE,MPI_MAX,roots);

  MPI_Allreduce(&tnorm2,&fmaxreplica,1,MPI_DOUBLE,MPI_MAX,roots);

  

  //double fnorminf = update->minimize->fnorm_inf();

  //double fmaxatom;

  //MPI_Allreduce(&fnorminf,&fmaxatom,1,MPI_DOUBLE,MPI_MAX,roots);

  double fnorminf = 0.0;

  MPI_Allreduce(&local_norm_inf,&fnorminf,1,MPI_DOUBLE,MPI_MAX,world);

  double fmaxatom;
@@ -730,7 +701,6 @@ void NEB_spin::print_status() 


  if (verbose) {

    freplica = new double[nreplica];

    //MPI_Allgather(&fnorm2,1,MPI_DOUBLE,&freplica[0],1,MPI_DOUBLE,roots);

    MPI_Allgather(&tnorm2,1,MPI_DOUBLE,&freplica[0],1,MPI_DOUBLE,roots);

    fmaxatomInRepl = new double[nreplica];

    MPI_Allgather(&fnorminf,1,MPI_DOUBLE,&fmaxatomInRepl[0],1,MPI_DOUBLE,roots);

src/REPLICA/neb_spin.h

+0 −1
Original line number Diff line number Diff line
@@ -14,7 +14,6 @@ 
#ifdef COMMAND_CLASS



CommandStyle(neb/spin,NEB_spin)

//CommandStyle(neb,NEB_spin)



#else

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