Commit ccc8f29d authored by Steve Plimpton's avatar Steve Plimpton
Browse files

added support for USER-AWPMD package

parent b6374bac

src/USER-AWPMD/atom_vec_wavepacket.cpp

+17 −8
Original line number Diff line number Diff line
@@ -61,6 +61,20 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp) 
  setup_fields();

}



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

   set local copies of all grow ptrs used by this class, except defaults

   needed in replicate when 2 atom classes exist and it calls pack_restart()

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



void AtomVecWavepacket::grow_pointers()

{

  q = atom->q;

  spin = atom->spin;

  eradius = atom->eradius;

  ervel = atom->ervel;

  erforce = atom->erforce;

}



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

   clear extra forces starting at atom N

   nbytes = # of bytes to clear for a per-atom vector
@@ -68,7 +82,7 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp) 


void AtomVecWavepacket::force_clear(int n, size_t nbytes)

{

  memset(&atom->erforce[n],0,nbytes);

  memset(&erforce[n],0,nbytes);

}



/* ----------------------------------------------------------------------
@@ -78,7 +92,7 @@ void AtomVecWavepacket::force_clear(int n, size_t nbytes) 


void AtomVecWavepacket::create_atom_post(int ilocal)

{

  atom->q[ilocal] = 1.0;

  q[ilocal] = 1.0;

}



/* ----------------------------------------------------------------------
@@ -88,7 +102,7 @@ void AtomVecWavepacket::create_atom_post(int ilocal) 


void AtomVecWavepacket::data_atom_post(int ilocal)

{

  atom->ervel[ilocal] = 0.0;

  ervel[ilocal] = 0.0;

}



/* ----------------------------------------------------------------------
@@ -113,33 +127,28 @@ int AtomVecWavepacket::property_atom(char *name) 
void AtomVecWavepacket::pack_property_atom(int index, double *buf,

                                           int nvalues, int groupbit)

{

  int *mask = atom->mask;

  int nlocal = atom->nlocal;



  int n = 0;

  if (index == 0) {

    int *spin = atom->spin;

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

      if (mask[i] & groupbit) buf[n] = spin[i];

      else buf[n] = 0.0;

      n += nvalues;

    }

  } else if (index == 1) {

    double *eradius = atom->eradius;

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

      if (mask[i] & groupbit) buf[n] = eradius[i];

      else buf[n] = 0.0;

      n += nvalues;

    }

  } else if (index == 2) {

    double *ervel = atom->ervel;

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

      if (mask[i] & groupbit) buf[n] = ervel[i];

      else buf[n] = 0.0;

      n += nvalues;

    }

  } else if (index == 3) {

    double *erforce = atom->erforce;

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

      if (mask[i] & groupbit) buf[n] = erforce[i];

      else buf[n] = 0.0;

src/USER-AWPMD/atom_vec_wavepacket.h

+6 −0
Original line number Diff line number Diff line
@@ -27,11 +27,17 @@ namespace LAMMPS_NS { 
class AtomVecWavepacket : public AtomVec {

public:

  AtomVecWavepacket(class LAMMPS *);



  void grow_pointers();

  void force_clear(int, size_t);

  void create_atom_post(int);

  void data_atom_post(int);

  int property_atom(char *);

  void pack_property_atom(int, double *, int, int);



 private:

  int *spin;

  double *q,*eradius,*ervel,*erforce;

};



}

src/USER-AWPMD/pair_awpmd_cut.cpp

+13 −13
Original line number Diff line number Diff line
@@ -259,7 +259,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) 
      Vector_3 xx=Vector_3(x[i][0],x[i][1],x[i][2]);

      Vector_3 rv=m*Vector_3(v[i][0],v[i][1],v[i][2]);

      double pv=ermscale*m*atom->ervel[i];

      Vector_2 cc=Vector_2(atom->cs[2*i],atom->cs[2*i+1]);

      Vector_2 cc=Vector_2(atom->cs[i][0],atom->cs[i][1]);

      gmap[i]=wpmd->add_split(xx,rv,atom->eradius[i],pv,cc,1.,atom->q[i],i<nlocal ? atom->tag[i] : -atom->tag[i]);

      // resetting for the case constraints were applied

      v[i][0]=rv[0]/m;
@@ -284,7 +284,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) 
    } else { // electron

      int iel=gmap[i];

      int s=spin[i] >0 ? 0 : 1;

      wpmd->get_wp_force(s,iel,(Vector_3 *)f[i],(Vector_3 *)(atom->vforce+3*i),atom->erforce+i,atom->ervelforce+i,(Vector_2 *)(atom->csforce+2*i));

      wpmd->get_wp_force(s,iel,(Vector_3 *)f[i],(Vector_3 *)(atom->vforce[i]),atom->erforce+i,atom->ervelforce+i,(Vector_2 *)(atom->csforce[i]));

    }

  }
@@ -671,11 +671,11 @@ void PairAWPMDCut::min_xf_get(int /* ignore */) 
  double *eradius = atom->eradius;

  double *erforce = atom->erforce;

  double **v=atom->v;

  double *vforce=atom->vforce;

  double **vforce=atom->vforce;

  double *ervel=atom->ervel;

  double *ervelforce=atom->ervelforce;

  double *cs=atom->cs;

  double *csforce=atom->csforce;

  double **cs=atom->cs;

  double **csforce=atom->csforce;



  int *spin = atom->spin;

  int nlocal = atom->nlocal;
@@ -686,14 +686,14 @@ void PairAWPMDCut::min_xf_get(int /* ignore */) 
      min_varforce[7*i] = eradius[i]*erforce[i];

      for(int j=0;j<3;j++){

        min_var[7*i+1+3*j] = v[i][j];

        min_varforce[7*i+1+3*j] = vforce[3*i+j];

        min_varforce[7*i+1+3*j] = vforce[i][j];

      }

      min_var[7*i+4] = ervel[i];

      min_varforce[7*i+4] = ervelforce[i];

      min_var[7*i+5] = cs[2*i];

      min_varforce[7*i+5] = csforce[2*i];

      min_var[7*i+6] = cs[2*i+1];

      min_varforce[7*i+6] = csforce[2*i+1];

      min_var[7*i+5] = cs[i][0];

      min_varforce[7*i+5] = csforce[i][0];

      min_var[7*i+6] = cs[i][1];

      min_varforce[7*i+6] = csforce[i][1];



    } else {

      for(int j=0;j<7;j++)
@@ -710,7 +710,7 @@ void PairAWPMDCut::min_x_set(int /* ignore */) 
  double *eradius = atom->eradius;

  double **v=atom->v;

  double *ervel=atom->ervel;

  double *cs=atom->cs;

  double **cs=atom->cs;



  int *spin = atom->spin;

  int nlocal = atom->nlocal;
@@ -721,8 +721,8 @@ void PairAWPMDCut::min_x_set(int /* ignore */) 
      for(int j=0;j<3;j++)

        v[i][j]=min_var[7*i+1+3*j];

      ervel[i]=min_var[7*i+4];

      cs[2*i]=min_var[7*i+5];

      cs[2*i+1]=min_var[7*i+6];

      cs[i][0]=min_var[7*i+5];

      cs[i][1]=min_var[7*i+6];

    }

  }

}

src/USER-SMD/atom_vec_smd.cpp

+1 −1
Original line number Diff line number Diff line
@@ -90,7 +90,7 @@ AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : AtomVec(lmp) 
    "x0 vest vfrac rmass radius contact_radius molecule e "

    "eff_plastic_strain eff_plastic_strain_rate smd_data_9 smd_stress damage";

  fields_data_atom = (char *) 

    "id type molecule vfrac rmass radius contact_radius x";

    "id type molecule vfrac rmass radius contact_radius x0 x";

  fields_data_vel = (char *) "id v";



  // set these array sizes based on defines

src/atom.cpp

+4 −4
Original line number Diff line number Diff line
@@ -134,8 +134,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) 


  spin = NULL;

  eradius = ervel = erforce = NULL;

  ervelforce = cs = csforce = NULL;

  vforce = NULL;

  ervelforce = NULL;

  cs = csforce = vforce = NULL;

  etag = NULL;



  // USER-DPD package
@@ -512,8 +512,8 @@ void Atom::peratom_create() 


  // USER-AWPMD package



  add_peratom("cs",&cs,DOUBLE,0);

  add_peratom("csforce",&csforce,DOUBLE,0);

  add_peratom("cs",&cs,DOUBLE,2);

  add_peratom("csforce",&csforce,DOUBLE,2);

  add_peratom("vforce",&vforce,DOUBLE,3);

  add_peratom("ervelforce",&ervelforce,DOUBLE,0);

  add_peratom("etag",&etag,INT,0);

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