Commit cce9fe4a authored by julient31's avatar julient31
Browse files

Commit2 JT 092118 

- created pair_spin_dipolar_cut
- real-space short-range calc of the spin dipolar interaction
- run and check valgrind ok
parent 407392f6

examples/SPIN/pppm_spin/in.spin.spin_dipolar_cut

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# hcp cobalt in a 3d periodic box



clear 

units	 	metal

atom_style 	spin



dimension 	3

boundary 	p p p



# necessary for the serial algorithm (sametag)

atom_modify 	map array 



lattice 	hcp 2.5071

region 		box block 0.0 8.0 0.0 8.0 0.0 8.0

create_box 	1 box

create_atoms 	1 box



# setting mass, mag. moments, and interactions for hcp cobalt



mass		1 58.93



#set 		group all spin/random 31 1.72

set 		group all spin 1.72 0.0 0.0 1.0 

velocity 	all create 100 4928459 rot yes dist gaussian



#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/long 8.0

pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/dipolar/cut 8.0

#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0

pair_coeff 	* * eam/alloy ../examples/SPIN/pppm_spin/Co_PurjaPun_2012.eam.alloy Co

pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567

pair_coeff 	* * spin/dipolar/cut long 8.0

#pair_coeff 	* * spin/long long 8.0



neighbor 	0.1 bin

neigh_modify 	every 10 check yes delay 20



#fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0

fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0

fix 		2 all langevin/spin 0.0 0.0 21

fix 		3 all nve/spin lattice yes



timestep	0.0001





compute 	out_mag    all compute/spin

compute 	out_pe     all pe

compute 	out_ke     all ke

compute 	out_temp   all temp



variable 	magz      equal c_out_mag[3]

variable 	magnorm   equal c_out_mag[4]

variable 	emag      equal c_out_mag[5]

variable 	tmag      equal c_out_mag[6]



thermo_style    custom step time v_magnorm v_emag temp etotal

thermo          10



compute 	outsp all property/atom spx spy spz sp fmx fmy fmz

dump 		100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]



#run 		20000

run 		10

src/SPIN/pair_spin_dipolar_cut.cpp

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/* ----------------------------------------------------------------------

   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

   www.cs.sandia.gov/~sjplimp/lammps.html

   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories



   Copyright (2003) Sandia Corporation.  Under the terms of Contract

   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

   certain rights in this software.  This software is distributed under

   the GNU General Public License.



   See the README file in the top-level LAMMPS directory.

------------------------------------------------------------------------- */



/* ------------------------------------------------------------------------

   Contributing authors: Julien Tranchida (SNL)

                         Aidan Thompson (SNL)



   Please cite the related publication:

   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).

   Massively parallel symplectic algorithm for coupled magnetic spin dynamics

   and molecular dynamics. Journal of Computational Physics.

------------------------------------------------------------------------- */



#include <cmath>

#include <cstdio>

#include <cstdlib>

#include <cstring>



#include "pair_spin_dipolar_cut.h"

#include "atom.h"

#include "comm.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "neigh_request.h"

#include "fix_nve_spin.h"

#include "force.h"

#include "kspace.h"

#include "math_const.h"

#include "memory.h"

#include "modify.h"

#include "error.h"

#include "update.h"





using namespace LAMMPS_NS;

using namespace MathConst;



#define EWALD_F   1.12837917

#define EWALD_P   0.3275911

#define A1        0.254829592

#define A2       -0.284496736

#define A3        1.421413741

#define A4       -1.453152027

#define A5        1.061405429



/* ---------------------------------------------------------------------- */



PairSpinDipolarCut::PairSpinDipolarCut(LAMMPS *lmp) : PairSpin(lmp),

lockfixnvespin(NULL)

{

  single_enable = 0;

  spinflag = 1;

  respa_enable = 0;

  no_virial_fdotr_compute = 1;

  lattice_flag = 0;



  hbar = force->hplanck/MY_2PI;		// eV/(rad.THz)

  mub = 5.78901e-5;                	// in eV/T

  mu_0 = 1.2566370614e-6;		// in T.m/A

  mub2mu0 = mub * mub * mu_0;		// in eV

  mub2mu0hbinv = mub2mu0 / hbar;	// in rad.THz



}



/* ----------------------------------------------------------------------

   free all arrays

------------------------------------------------------------------------- */



PairSpinDipolarCut::~PairSpinDipolarCut()

{

  if (allocated) {

    memory->destroy(setflag);

    memory->destroy(cut_spin_long);

    memory->destroy(cutsq);

  }

}



/* ----------------------------------------------------------------------

   global settings

------------------------------------------------------------------------- */



void PairSpinDipolarCut::settings(int narg, char **arg)

{

  if (narg < 1 || narg > 2)

    error->all(FLERR,"Incorrect args in pair_style command");



  if (strcmp(update->unit_style,"metal") != 0)

    error->all(FLERR,"Spin simulations require metal unit style");



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

  

  // reset cutoffs that have been explicitly set

  

  if (allocated) {

    int i,j;

    for (i = 1; i <= atom->ntypes; i++) {

      for (j = i+1; j <= atom->ntypes; j++) {

        if (setflag[i][j]) {

          cut_spin_long[i][j] = cut_spin_long_global;

        }

      }

    }

  }



}



/* ----------------------------------------------------------------------

   set coeffs for one or more type pairs

------------------------------------------------------------------------- */



void PairSpinDipolarCut::coeff(int narg, char **arg)

{

  if (!allocated) allocate();

  

  // check if args correct



  if (strcmp(arg[2],"long") != 0)

    error->all(FLERR,"Incorrect args in pair_style command");

  if (narg < 1 || narg > 4)

    error->all(FLERR,"Incorrect args in pair_style command");

  

  int ilo,ihi,jlo,jhi;

  force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);

  force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);



  double spin_long_cut_one = force->numeric(FLERR,arg[3]);



  int count = 0;

  for (int i = ilo; i <= ihi; i++) {

    for (int j = MAX(jlo,i); j <= jhi; j++) {

      setflag[i][j] = 1;

      cut_spin_long[i][j] = spin_long_cut_one;

      count++;

    }

  }



  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");

}



/* ----------------------------------------------------------------------

   init specific to this pair style

------------------------------------------------------------------------- */



void PairSpinDipolarCut::init_style()

{

  if (!atom->sp_flag)

    error->all(FLERR,"Pair spin requires atom/spin style");

  

  // need a full neighbor list



  int irequest = neighbor->request(this,instance_me);

  neighbor->requests[irequest]->half = 0;

  neighbor->requests[irequest]->full = 1;

  

  // checking if nve/spin is a listed fix



  int ifix = 0;

  while (ifix < modify->nfix) {

    if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break;

    ifix++;

  }

  if (ifix == modify->nfix)

    error->all(FLERR,"pair/spin style requires nve/spin");



  // get the lattice_flag from nve/spin



  for (int i = 0; i < modify->nfix; i++) {

    if (strcmp(modify->fix[i]->style,"nve/spin") == 0) {

      lockfixnvespin = (FixNVESpin *) modify->fix[i];

      lattice_flag = lockfixnvespin->lattice_flag;

    }

  }



}



/* ----------------------------------------------------------------------

   init for one type pair i,j and corresponding j,i

------------------------------------------------------------------------- */



double PairSpinDipolarCut::init_one(int i, int j)

{

  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");

  

  cut_spin_long[j][i] = cut_spin_long[i][j];

  

  return cut_spin_long_global;

}



/* ----------------------------------------------------------------------

   extract the larger cutoff if "cut" or "cut_coul"

------------------------------------------------------------------------- */



void *PairSpinDipolarCut::extract(const char *str, int &dim)

{

  if (strcmp(str,"cut") == 0) {

    dim = 0;

    return (void *) &cut_spin_long_global;

  } else if (strcmp(str,"cut_coul") == 0) {

    dim = 0;

    return (void *) &cut_spin_long_global;

  } else if (strcmp(str,"ewald_order") == 0) {

    ewald_order = 0;

    ewald_order |= 1<<1;

    ewald_order |= 1<<3;

    dim = 0;

    return (void *) &ewald_order;

  } else if (strcmp(str,"ewald_mix") == 0) {

    dim = 0;

    return (void *) &mix_flag;

  }

  return NULL;

}



/* ---------------------------------------------------------------------- */



void PairSpinDipolarCut::compute(int eflag, int vflag)

{

  int i,j,ii,jj,inum,jnum,itype,jtype;  

  double rinv,r2inv,r3inv,rsq;

  double evdwl,ecoul;

  double xi[3],rij[3];

  double spi[4],spj[4],fi[3],fmi[3];

  double local_cut2;

  int *ilist,*jlist,*numneigh,**firstneigh;  



  evdwl = ecoul = 0.0;

  if (eflag || vflag) ev_setup(eflag,vflag);

  else evflag = vflag_fdotr = 0;



  double **x = atom->x;

  double **f = atom->f;

  double **fm = atom->fm;

  double **sp = atom->sp;	

  int *type = atom->type;  

  int nlocal = atom->nlocal;  

  int newton_pair = force->newton_pair;



  inum = list->inum;

  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;



  // computation of the exchange interaction

  // loop over atoms and their neighbors



  for (ii = 0; ii < inum; ii++) {

    i = ilist[ii];

    xi[0] = x[i][0];

    xi[1] = x[i][1];

    xi[2] = x[i][2];

    jlist = firstneigh[i];

    jnum = numneigh[i]; 

    spi[0] = sp[i][0]; 

    spi[1] = sp[i][1]; 

    spi[2] = sp[i][2];

    spi[3] = sp[i][3];

    itype = type[i];



    for (jj = 0; jj < jnum; jj++) {

      j = jlist[jj];

      j &= NEIGHMASK;

      jtype = type[j];



      spj[0] = sp[j][0]; 

      spj[1] = sp[j][1]; 

      spj[2] = sp[j][2]; 

      spj[3] = sp[j][3]; 



      fi[0] = fi[1] = fi[2] = 0.0;

      fmi[0] = fmi[1] = fmi[2] = 0.0;

     

      rij[0] = x[j][0] - xi[0];

      rij[1] = x[j][1] - xi[1];

      rij[2] = x[j][2] - xi[2];

      rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];



      local_cut2 = cut_spin_long[itype][jtype]*cut_spin_long[itype][jtype];



      if (rsq < local_cut2) {

        r2inv = 1.0/rsq;

        rinv = sqrt(r2inv);

	r3inv = r2inv*rinv;

	

	compute_dipolar(i,j,rij,fmi,spi,spj,r3inv);

	if (lattice_flag) compute_dipolar_mech(i,j,rij,fmi,spi,spj,r2inv);

      }



      // force accumulation



      f[i][0] += fi[0]; 

      f[i][1] += fi[1];  	  

      f[i][2] += fi[2];

      fm[i][0] += fmi[0];

      fm[i][1] += fmi[1];

      fm[i][2] += fmi[2];



      if (newton_pair || j < nlocal) {

	f[j][0] -= fi[0];	 

        f[j][1] -= fi[1];	  	  

        f[j][2] -= fi[2];

      }



      if (eflag) {

	if (rsq <= local_cut2) {

	  evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + 

	    spi[2]*fmi[2];

	  evdwl *= hbar;

	}

      } else evdwl = 0.0;





      if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,

	  evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);



    }

  }

}



/* ----------------------------------------------------------------------

   update the pair interaction fmi acting on the spin ii

   adding 1/r (for r in [0,rc]) contribution to the pair

   removing erf(r)/r (for r in [0,rc]) from the kspace force

------------------------------------------------------------------------- */



void PairSpinDipolarCut::compute_single_pair(int ii, double fmi[3])

{

  int i,j,jj,jnum,itype,jtype;  

  double rsq,rinv,r2inv,r3inv;

  double xi[3],rij[3];

  double spi[4],spj[4];

  double local_cut2;

  int *ilist,*jlist,*numneigh,**firstneigh;  



  double **x = atom->x;

  double **sp = atom->sp;	

  int *type = atom->type;  



  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;



  // computation of the exchange interaction

  // loop over neighbors of atom i

    

  i = ilist[ii];

  xi[0] = x[i][0];

  xi[1] = x[i][1];

  xi[2] = x[i][2];

  spi[0] = sp[i][0]; 

  spi[1] = sp[i][1]; 

  spi[2] = sp[i][2];

  spi[3] = sp[i][3];

  jlist = firstneigh[i];

  jnum = numneigh[i]; 

  itype = type[i];

  

  for (jj = 0; jj < jnum; jj++) {

    j = jlist[jj];

    j &= NEIGHMASK;

    jtype = type[j];



    spj[0] = sp[j][0]; 

    spj[1] = sp[j][1]; 

    spj[2] = sp[j][2]; 

    spj[3] = sp[j][3]; 



    rij[0] = x[j][0] - xi[0];

    rij[1] = x[j][1] - xi[1];

    rij[2] = x[j][2] - xi[2];

    rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];



    local_cut2 = cut_spin_long[itype][jtype]*cut_spin_long[itype][jtype];



    if (rsq < local_cut2) {

      r2inv = 1.0/rsq;

      rinv = sqrt(r2inv);

      r3inv = r2inv*rinv;

      

      // compute dipolar interaction

      

      compute_dipolar(i,j,rij,fmi,spi,spj,r3inv);

    }

  }

  

  //fmi[0] *= mub2mu0hbinv;

  //fmi[1] *= mub2mu0hbinv;

  //fmi[2] *= mub2mu0hbinv;

}



/* ----------------------------------------------------------------------

   compute dipolar interaction between spins i and j

------------------------------------------------------------------------- */



void PairSpinDipolarCut::compute_dipolar(int i, int j, double rij[3], 

    double fmi[3], double spi[4], double spj[4], double r3inv)

{

  double sjdotr;

  double gigjri2,pre;



  sjdotr = spj[0]*rij[0] + spj[1]*rij[1] + spj[2]*rij[2];

  gigjri2 = (spi[3] * spj[3])*r3inv;

  pre = mub2mu0hbinv * gigjri2 / 4.0 / MY_PI;



  fmi[0] += pre * gigjri2 * (3.0 * sjdotr *rij[0] - spj[0]);

  fmi[1] += pre * gigjri2 * (3.0 * sjdotr *rij[1] - spj[1]);

  fmi[2] += pre * gigjri2 * (3.0 * sjdotr *rij[2] - spj[2]);

}



/* ----------------------------------------------------------------------

   compute the mechanical force due to the dipolar interaction between 

   atom i and atom j

------------------------------------------------------------------------- */



void PairSpinDipolarCut::compute_dipolar_mech(int i, int j, double rij[3],

    double fi[3], double spi[3], double spj[3], double r2inv)

{

  double sdots,sidotr,sjdotr,b2,b3;

  double gigjri4,bij,pre;



  gigjri4 = (spi[3] * spj[3])/r2inv/r2inv;

  sdots = spi[0]*spj[0] + spi[1]*spj[1] + spi[2]*spj[2];

  sidotr = spi[0]*rij[0] + spi[1]*rij[1] + spi[2]*rij[2];

  sjdotr = spj[0]*rij[0] + spj[1]*rij[1] + spj[2]*rij[2];



  bij = sdots - 5.0 * sidotr*sjdotr;

  pre = mub2mu0 * bij / 4.0 / MY_PI;

  fi[0] += pre * (rij[0] * bij + (sjdotr*spi[0] + sidotr*spj[0]));

  fi[1] += pre * (rij[1] * bij + (sjdotr*spi[1] + sidotr*spj[1]));

  fi[2] += pre * (rij[2] * bij + (sjdotr*spi[2] + sidotr*spj[2]));

}





/* ----------------------------------------------------------------------

   allocate all arrays

------------------------------------------------------------------------- */



void PairSpinDipolarCut::allocate()

{

  allocated = 1;

  int n = atom->ntypes;



  memory->create(setflag,n+1,n+1,"pair:setflag");

  for (int i = 1; i <= n; i++)

    for (int j = i; j <= n; j++)

      setflag[i][j] = 0;



  memory->create(cut_spin_long,n+1,n+1,"pair/spin/long:cut_spin_long");

  memory->create(cutsq,n+1,n+1,"pair/spin/long:cutsq");

}



/* ----------------------------------------------------------------------

   proc 0 writes to restart file

------------------------------------------------------------------------- */



void PairSpinDipolarCut::write_restart(FILE *fp)

{

  write_restart_settings(fp);



  int i,j;

  for (i = 1; i <= atom->ntypes; i++) {

    for (j = i; j <= atom->ntypes; j++) {

      fwrite(&setflag[i][j],sizeof(int),1,fp);

      if (setflag[i][j]) {

	fwrite(&cut_spin_long[i][j],sizeof(int),1,fp);

      }

    }

  }

}



/* ----------------------------------------------------------------------

   proc 0 reads from restart file, bcasts

------------------------------------------------------------------------- */



void PairSpinDipolarCut::read_restart(FILE *fp)

{

  read_restart_settings(fp);



  allocate();



  int i,j;

  int me = comm->me;

  for (i = 1; i <= atom->ntypes; i++) {

    for (j = i; j <= atom->ntypes; j++) {

      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);

      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);

      if (setflag[i][j]) {

	if (me == 0) {

	  fread(&cut_spin_long[i][j],sizeof(int),1,fp);

	}

	MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world);

      }

    }

  }

}



/* ----------------------------------------------------------------------

   proc 0 writes to restart file

------------------------------------------------------------------------- */



void PairSpinDipolarCut::write_restart_settings(FILE *fp)

{

  fwrite(&cut_spin_long_global,sizeof(double),1,fp);

  fwrite(&mix_flag,sizeof(int),1,fp);

}



/* ----------------------------------------------------------------------

   proc 0 reads from restart file, bcasts

------------------------------------------------------------------------- */



void PairSpinDipolarCut::read_restart_settings(FILE *fp)

{

  if (comm->me == 0) {

    fread(&cut_spin_long_global,sizeof(double),1,fp);

    fread(&mix_flag,sizeof(int),1,fp);

  }

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

  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);

}

src/SPIN/pair_spin_dipolar_cut.h

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/* -*- c++ -*- ----------------------------------------------------------

   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

   www.cs.sandia.gov/~sjplimp/lammps.html

   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories



   Copyright (2003) Sandia Corporation.  Under the terms of Contract

   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

   certain rights in this software.  This software is distributed under

   the GNU General Public License.



   See the README file in the top-level LAMMPS directory.

------------------------------------------------------------------------- */



#ifdef PAIR_CLASS



PairStyle(spin/dipolar/cut,PairSpinDipolarCut)



#else



#ifndef LMP_PAIR_SPIN_DIPOLAR_CUT_H

#define LMP_PAIR_SPIN_DIPOLAR_CUT_H



#include "pair_spin.h"



namespace LAMMPS_NS {



class PairSpinDipolarCut : public PairSpin {

 public:

  double cut_coul;

  double **sigma;



  PairSpinDipolarCut(class LAMMPS *);

  ~PairSpinDipolarCut();

  void settings(int, char **);

  void coeff(int, char **);

  double init_one(int, int);

  void init_style();

  void *extract(const char *, int &); 

  

  void compute(int, int);

  void compute_single_pair(int, double *);



  void compute_dipolar(int, int, double *, double *, double *, 

      double *, double);

  void compute_dipolar_mech(int, int, double *, double *, double *, 

      double *, double);



  void write_restart(FILE *);

  void read_restart(FILE *);

  void write_restart_settings(FILE *);

  void read_restart_settings(FILE *);

  

  double cut_spin_long_global;	// global long cutoff distance 



 protected:

  double hbar;	 		// reduced Planck's constant

  double mub;			// Bohr's magneton

  double mu_0;			// vacuum permeability

  double mub2mu0;		// prefactor for mech force

  double mub2mu0hbinv;		// prefactor for mag force



  double **cut_spin_long;	// cutoff distance long



  double g_ewald;

  int ewald_order;



  int lattice_flag;			// flag for mech force computation

  class FixNVESpin *lockfixnvespin;	// ptr for setups



  void allocate();

};



}



#endif

#endif



/* ERROR/WARNING messages:



E: Incorrect args in pair_style command



Self-explanatory.



E: Incorrect args for pair coefficients



Self-explanatory.  Check the input script or data file.



E: Pair dipole/long requires atom attributes q, mu, torque



The atom style defined does not have these attributes.



E: Cannot (yet) use 'electron' units with dipoles



This feature is not yet supported.



E: Pair style requires a KSpace style



No kspace style is defined.



*/

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