Commit 60ebc08d authored by julient31's avatar julient31
Browse files

Commit JT 071719 

- added doc for read_data spin
- corrected an error in pack/unpack data hybrid
- added mask flags in fix_nve_spin::initial_integrate
- removed spin renormalization in min_spin (was causing a bug)
parent 0a90032b

doc/src/read_data.txt

+3 −0
Original line number Diff line number Diff line
@@ -565,6 +565,7 @@ molecular: atom-ID molecule-ID atom-type x y z 
peri: atom-ID atom-type volume density x y z

smd: atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z

sphere: atom-ID atom-type diameter density x y z

spin: atom-ID atom-type sp x y z spx spy spz

template: atom-ID molecule-ID template-index template-atom atom-type x y z

tri: atom-ID molecule-ID atom-type triangleflag density x y z

wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
@@ -595,6 +596,8 @@ mux,muy,muz = components of dipole moment of atom (dipole units) 
q = charge on atom (charge units)

rho = density (need units) for SPH particles

spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)

sp = norm of magnetic spin of atom (in number of Bohr magnetons)

spx,spy,spz = components of magnetic spin of atom (adim normalized vector)

template-atom = which atom within a template molecule the atom is

template-index = which molecule within the molecule template the atom is part of

theta = internal temperature of a DPD particle

src/SPIN/atom_vec_spin.cpp

+9 −9
Original line number Diff line number Diff line
@@ -263,10 +263,10 @@ int AtomVecSpin::pack_comm_hybrid(int n, int *list, double *buf) 
  m = 0;

  for (i = 0; i < n; i++) {

    j = list[i];

    buf[m++] = sp[j][3];

    buf[m++] = sp[j][0];

    buf[m++] = sp[j][1];

    buf[m++] = sp[j][2];

    buf[m++] = sp[j][3];

  }

  return m;

}
@@ -321,10 +321,10 @@ int AtomVecSpin::unpack_comm_hybrid(int n, int first, double *buf) 
  m = 0;

  last = first + n;

  for (i = first; i < last; i++) {

    sp[i][3] = buf[m++];

    sp[i][0] = buf[m++];

    sp[i][1] = buf[m++];

    sp[i][2] = buf[m++];

    sp[i][3] = buf[m++];

  }

  return m;

}
@@ -524,10 +524,10 @@ int AtomVecSpin::pack_border_hybrid(int n, int *list, double *buf) 
  m = 0;

  for (i = 0; i < n; i++) {

    j = list[i];

    buf[m++] = sp[j][3];

    buf[m++] = sp[j][0];

    buf[m++] = sp[j][1];

    buf[m++] = sp[j][2];

    buf[m++] = sp[j][3];

  }



  return m;
@@ -603,10 +603,10 @@ int AtomVecSpin::unpack_border_hybrid(int n, int first, double *buf) 
  m = 0;

  last = first + n;

  for (i = first; i < last; i++) {

    sp[i][3] = buf[m++];

    sp[i][0] = buf[m++];

    sp[i][1] = buf[m++];

    sp[i][2] = buf[m++];

    sp[i][3] = buf[m++];

  }



  return m;
@@ -894,10 +894,10 @@ void AtomVecSpin::pack_data(double **buf) 


int AtomVecSpin::pack_data_hybrid(int i, double *buf)

{

  buf[0] = sp[i][0];

  buf[1] = sp[i][1];

  buf[2] = sp[i][2];

  buf[3] = sp[i][3];

  buf[0] = sp[i][3];

  buf[1] = sp[i][0];

  buf[2] = sp[i][1];

  buf[3] = sp[i][2];

  return 4;

}
@@ -924,7 +924,7 @@ void AtomVecSpin::write_data(FILE *fp, int n, double **buf) 


int AtomVecSpin::write_data_hybrid(FILE *fp, double *buf)

{

  fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2],buf[3],buf[4]);

  fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2],buf[3]);

  return 4;

}

src/SPIN/fix_nve_spin.cpp

+41 −25
Original line number Diff line number Diff line
@@ -312,30 +312,38 @@ void FixNVESpin::initial_integrate(int /*vflag*/) 
      comm->forward_comm();

      int i = stack_foot[j];

      while (i >= 0) {

        if (mask[i] & groupbit) {

          ComputeInteractionsSpin(i);

          AdvanceSingleSpin(i);

          i = forward_stacks[i];

	}

      }

    }

    for (int j = nsectors-1; j >= 0; j--) {     // advance quarter s for nlocal

      comm->forward_comm();

      int i = stack_head[j];

      while (i >= 0) {

        if (mask[i] & groupbit) {

          ComputeInteractionsSpin(i);

          AdvanceSingleSpin(i);

          i = backward_stacks[i];

	}

      }

    }

  } else if (sector_flag == 0) {                // serial seq. update

    comm->forward_comm();                       // comm. positions of ghost atoms

    for (int i = 0; i < nlocal; i++){           // advance quarter s for nlocal

      if (mask[i] & groupbit) {

        ComputeInteractionsSpin(i);

        AdvanceSingleSpin(i);

      }

    }

    for (int i = nlocal-1; i >= 0; i--){        // advance quarter s for nlocal

      if (mask[i] & groupbit) {

        ComputeInteractionsSpin(i);

        AdvanceSingleSpin(i);

      }

    }

  } else error->all(FLERR,"Illegal fix NVE/spin command");



  // update x for all particles
@@ -357,30 +365,38 @@ void FixNVESpin::initial_integrate(int /*vflag*/) 
      comm->forward_comm();

      int i = stack_foot[j];

      while (i >= 0) {

        if (mask[i] & groupbit) {

          ComputeInteractionsSpin(i);

          AdvanceSingleSpin(i);

          i = forward_stacks[i];

	}

      }

    }

    for (int j = nsectors-1; j >= 0; j--) {     // advance quarter s for nlocal

      comm->forward_comm();

      int i = stack_head[j];

      while (i >= 0) {

        if (mask[i] & groupbit) {

          ComputeInteractionsSpin(i);

          AdvanceSingleSpin(i);

          i = backward_stacks[i];

	}

      }

    }

  } else if (sector_flag == 0) {                // serial seq. update

    comm->forward_comm();                       // comm. positions of ghost atoms

    for (int i = 0; i < nlocal; i++){           // advance quarter s for nlocal-1

      if (mask[i] & groupbit) {

        ComputeInteractionsSpin(i);

        AdvanceSingleSpin(i);

      }

    }

    for (int i = nlocal-1; i >= 0; i--){        // advance quarter s for nlocal-1

      if (mask[i] & groupbit) {

        ComputeInteractionsSpin(i);

        AdvanceSingleSpin(i);

      }

    }

  } else error->all(FLERR,"Illegal fix NVE/spin command");



}

src/SPIN/min_spin.cpp

+0 −6
Original line number Diff line number Diff line
@@ -287,12 +287,6 @@ void MinSpin::advance_spins(double dts) 


    // renormalization (check if necessary)



    msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];

    scale = 1.0/sqrt(msq);

    sp[i][0] *= scale;

    sp[i][1] *= scale;

    sp[i][2] *= scale;



    // no comm. to atoms with same tag

    // because no need for simplecticity

  }

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