Commit ccca80a6 authored by Steve Plimpton's avatar Steve Plimpton
Browse files

changes to enable atom_style hybrid to work

parent 4f6cb135

src/DIPOLE/atom_vec_dipole.cpp

+4 −4
Original line number Diff line number Diff line
@@ -35,21 +35,21 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp) 


  // strings with peratom variables to include in each AtomVec method

  // strings cannot contain fields in corresponding AtomVec default strings

  // order of fields in the string does not matter

  //   except fields_data_atom and fields_data_vel which must match data file

  // order of fields in a string does not matter

  // except: fields_data_atom & fields_data_vel must match data file



  fields_grow = (char *) "q mu";

  fields_copy = (char *) "q mu";

  fields_comm = (char *) "mu3";

  fields_comm_vel = (char *) "mu3";

  fields_reverse = NULL;

  fields_reverse = (char *) "";

  fields_border = (char *) "q mu";

  fields_border_vel = (char *) "q mu";

  fields_exchange = (char *) "q mu";

  fields_restart = (char *) "q mu";

  fields_create = (char *) "q mu";

  fields_data_atom = (char *) "id type q x mu3";

  fields_data_vel = NULL;

  fields_data_vel = (char *) "id v";



  setup_fields();

}

src/MOLECULE/atom_vec_angle.cpp

+18 −18
Original line number Diff line number Diff line
@@ -28,8 +28,8 @@ AtomVecAngle::AtomVecAngle(LAMMPS *lmp) : AtomVec(lmp) 


  // strings with peratom variables to include in each AtomVec method

  // strings cannot contain fields in corresponding AtomVec default strings

  // order of fields in the string does not matter

  //   except fields_data_atom and fields_data_vel which must match data file

  // order of fields in a string does not matter

  // except: fields_data_atom & fields_data_vel must match data file



  fields_grow = (char *) 

    "molecule num_bond bond_type bond_atom "
@@ -37,9 +37,9 @@ AtomVecAngle::AtomVecAngle(LAMMPS *lmp) : AtomVec(lmp) 
  fields_copy = (char *)

    "molecule num_bond bond_type bond_atom "

    "num_angle angle_type angle_atom1 angle_atom2 angle_atom3 nspecial special";

  fields_comm = NULL;

  fields_comm_vel = NULL;

  fields_reverse = NULL;

  fields_comm = (char *) "";

  fields_comm_vel = (char *) "";

  fields_reverse = (char *) "";

  fields_border = (char *) "molecule";

  fields_border_vel = (char *) "molecule";

  fields_exchange = (char *)
@@ -50,7 +50,7 @@ AtomVecAngle::AtomVecAngle(LAMMPS *lmp) : AtomVec(lmp) 
    "num_angle angle_type angle_atom1 angle_atom2 angle_atom3";

  fields_create = (char *) "molecule num_bond num_angle nspecial";

  fields_data_atom = (char *) "id molecule type x";

  fields_data_vel = NULL;

  fields_data_vel = (char *) "id v";



  setup_fields();
@@ -70,7 +70,7 @@ AtomVecAngle::~AtomVecAngle() 
   modify values for AtomVec::pack_restart() to pack

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



void AtomVecAngle::pack_restart_pre(int i)

void AtomVecAngle::pack_restart_pre(int ilocal)

{

  // insure negative vectors are needed length
@@ -93,19 +93,19 @@ void AtomVecAngle::pack_restart_pre(int i) 
  int **angle_type = atom->angle_type;



  int any_bond_negative = 0;

  for (int m = 0; m < num_bond[i]; m++) {

    if (bond_type[i][m] < 0) {

  for (int m = 0; m < num_bond[ilocal]; m++) {

    if (bond_type[ilocal][m] < 0) {

      bond_negative[m] = 1;

      bond_type[i][m] = -bond_type[i][m];

      bond_type[ilocal][m] = -bond_type[ilocal][m];

      any_bond_negative = 1;

    } else bond_negative[m] = 0;

  }



  int any_angle_negative = 0;

  for (int m = 0; m < num_angle[i]; m++) {

    if (angle_type[i][m] < 0) {

  for (int m = 0; m < num_angle[ilocal]; m++) {

    if (angle_type[ilocal][m] < 0) {

      angle_negative[m] = 1;

      angle_type[i][m] = -angle_type[i][m];

      angle_type[ilocal][m] = -angle_type[ilocal][m];

      any_angle_negative = 1;

    } else angle_negative[m] = 0;

  }
@@ -115,22 +115,22 @@ void AtomVecAngle::pack_restart_pre(int i) 
   unmodify values packed by AtomVec::pack_restart()

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



void AtomVecAngle::pack_restart_post(int i)

void AtomVecAngle::pack_restart_post(int ilocal)

{

  // restore the flagged types to their negative values



  if (any_bond_negative) {

    int *num_bond = atom->num_bond;

    int **bond_type = atom->bond_type;

    for (int m = 0; m < num_bond[i]; m++)

      if (bond_negative[m]) bond_type[i][m] = -bond_type[i][m];

    for (int m = 0; m < num_bond[ilocal]; m++)

      if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];

  }



  if (any_angle_negative) {

    int *num_angle = atom->num_angle;

    int **angle_type = atom->angle_type;

    for (int m = 0; m < num_angle[i]; m++)

      if (angle_negative[m]) angle_type[i][m] = -angle_type[i][m];

    for (int m = 0; m < num_angle[ilocal]; m++)

      if (angle_negative[m]) angle_type[ilocal][m] = -angle_type[ilocal][m];

  }

}

src/MOLECULE/atom_vec_bond.cpp

+13 −13
Original line number Diff line number Diff line
@@ -28,16 +28,16 @@ AtomVecBond::AtomVecBond(LAMMPS *lmp) : AtomVec(lmp) 


  // strings with peratom variables to include in each AtomVec method

  // strings cannot contain fields in corresponding AtomVec default strings

  // order of fields in the string does not matter

  //   except fields_data_atom and fields_data_vel which must match data file

  // order of fields in a string does not matter

  // except: fields_data_atom & fields_data_vel must match data file



  fields_grow = (char *) 

    "molecule num_bond bond_type bond_atom nspecial special";

  fields_copy = (char *)

    "molecule num_bond bond_type bond_atom nspecial special";

  fields_comm = NULL;

  fields_comm_vel = NULL;

  fields_reverse = NULL;

  fields_comm = (char *) "";

  fields_comm_vel = (char *) "";

  fields_reverse = (char *) "";

  fields_border = (char *) "molecule";

  fields_border_vel = (char *) "molecule";

  fields_exchange = (char *)
@@ -45,7 +45,7 @@ AtomVecBond::AtomVecBond(LAMMPS *lmp) : AtomVec(lmp) 
  fields_restart = (char *) "molecule num_bond bond_type bond_atom";

  fields_create = (char *) "molecule num_bond nspecial";

  fields_data_atom = (char *) "id molecule type x";

  fields_data_vel = NULL;

  fields_data_vel = (char *) "id v";



  setup_fields();
@@ -64,7 +64,7 @@ AtomVecBond::~AtomVecBond() 
   modify values for AtomVec::pack_restart() to pack

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



void AtomVecBond::pack_restart_pre(int i)

void AtomVecBond::pack_restart_pre(int ilocal)

{

  // insure bond_negative vector is needed length
@@ -80,10 +80,10 @@ void AtomVecBond::pack_restart_pre(int i) 
  int **bond_type = atom->bond_type;



  any_bond_negative = 0;

  for (int m = 0; m < num_bond[i]; m++) {

    if (bond_type[i][m] < 0) {

  for (int m = 0; m < num_bond[ilocal]; m++) {

    if (bond_type[ilocal][m] < 0) {

      bond_negative[m] = 1;

      bond_type[i][m] = -bond_type[i][m];

      bond_type[ilocal][m] = -bond_type[ilocal][m];

      any_bond_negative = 1;

    } else bond_negative[m] = 0;

  }
@@ -93,15 +93,15 @@ void AtomVecBond::pack_restart_pre(int i) 
   unmodify values packed by AtomVec::pack_restart()

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



void AtomVecBond::pack_restart_post(int i)

void AtomVecBond::pack_restart_post(int ilocal)

{

  // restore the flagged types to their negative values



  if (any_bond_negative) {

    int *num_bond = atom->num_bond;

    int **bond_type = atom->bond_type;

    for (int m = 0; m < num_bond[i]; m++)

      if (bond_negative[m]) bond_type[i][m] = -bond_type[i][m];

    for (int m = 0; m < num_bond[ilocal]; m++)

      if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];

  }

}

src/MOLECULE/atom_vec_full.cpp

+30 −28
Original line number Diff line number Diff line
@@ -28,8 +28,8 @@ AtomVecFull::AtomVecFull(LAMMPS *lmp) : AtomVec(lmp) 


  // strings with peratom variables to include in each AtomVec method

  // strings cannot contain fields in corresponding AtomVec default strings

  // order of fields in the string does not matter

  //   except fields_data_atom and fields_data_vel which must match data file

  // order of fields in a string does not matter

  // except: fields_data_atom & fields_data_vel must match data file



  fields_grow = (char *) 

    "q molecule num_bond bond_type bond_atom "
@@ -47,9 +47,9 @@ AtomVecFull::AtomVecFull(LAMMPS *lmp) : AtomVec(lmp) 
    "num_improper improper_type improper_atom1 improper_atom2 "

    "improper_atom3 improper_atom4 "

    "nspecial special";

  fields_comm = NULL;

  fields_comm_vel = NULL;

  fields_reverse = NULL;

  fields_comm = (char *) "";

  fields_comm_vel = (char *) "";

  fields_reverse = (char *) "";

  fields_border = (char *) "q molecule";

  fields_border_vel = (char *) "q molecule";

  fields_exchange = (char *)
@@ -70,7 +70,7 @@ AtomVecFull::AtomVecFull(LAMMPS *lmp) : AtomVec(lmp) 
  fields_create = (char *) 

    "q molecule num_bond num_angle num_dihedral num_improper nspecial";

  fields_data_atom = (char *) "id molecule type q x";

  fields_data_vel = NULL;

  fields_data_vel = (char *) "id v";



  setup_fields();
@@ -92,7 +92,7 @@ AtomVecFull::~AtomVecFull() 
   modify values for AtomVec::pack_restart() to pack

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



void AtomVecFull::pack_restart_pre(int i)

void AtomVecFull::pack_restart_pre(int ilocal)

{

  // insure negative vectors are needed length
@@ -129,37 +129,37 @@ void AtomVecFull::pack_restart_pre(int i) 
  int **improper_type = atom->improper_type;



  int any_bond_negative = 0;

  for (int m = 0; m < num_bond[i]; m++) {

    if (bond_type[i][m] < 0) {

  for (int m = 0; m < num_bond[ilocal]; m++) {

    if (bond_type[ilocal][m] < 0) {

      bond_negative[m] = 1;

      bond_type[i][m] = -bond_type[i][m];

      bond_type[ilocal][m] = -bond_type[ilocal][m];

      any_bond_negative = 1;

    } else bond_negative[m] = 0;

  }



  int any_angle_negative = 0;

  for (int m = 0; m < num_angle[i]; m++) {

    if (angle_type[i][m] < 0) {

  for (int m = 0; m < num_angle[ilocal]; m++) {

    if (angle_type[ilocal][m] < 0) {

      angle_negative[m] = 1;

      angle_type[i][m] = -angle_type[i][m];

      angle_type[ilocal][m] = -angle_type[ilocal][m];

      any_angle_negative = 1;

    } else angle_negative[m] = 0;

  }



  int any_dihedral_negative = 0;

  for (int m = 0; m < num_dihedral[i]; m++) {

    if (dihedral_type[i][m] < 0) {

  for (int m = 0; m < num_dihedral[ilocal]; m++) {

    if (dihedral_type[ilocal][m] < 0) {

      dihedral_negative[m] = 1;

      dihedral_type[i][m] = -dihedral_type[i][m];

      dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];

      any_dihedral_negative = 1;

    } else dihedral_negative[m] = 0;

  }



  int any_improper_negative = 0;

  for (int m = 0; m < num_improper[i]; m++) {

    if (improper_type[i][m] < 0) {

  for (int m = 0; m < num_improper[ilocal]; m++) {

    if (improper_type[ilocal][m] < 0) {

      improper_negative[m] = 1;

      improper_type[i][m] = -improper_type[i][m];

      improper_type[ilocal][m] = -improper_type[ilocal][m];

      any_improper_negative = 1;

    } else improper_negative[m] = 0;

  }
@@ -169,36 +169,38 @@ void AtomVecFull::pack_restart_pre(int i) 
   unmodify values packed by AtomVec::pack_restart()

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



void AtomVecFull::pack_restart_post(int i)

void AtomVecFull::pack_restart_post(int ilocal)

{

  // restore the flagged types to their negative values



  if (any_bond_negative) {

    int *num_bond = atom->num_bond;

    int **bond_type = atom->bond_type;

    for (int m = 0; m < num_bond[i]; m++)

      if (bond_negative[m]) bond_type[i][m] = -bond_type[i][m];

    for (int m = 0; m < num_bond[ilocal]; m++)

      if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];

  }



  if (any_angle_negative) {

    int *num_angle = atom->num_angle;

    int **angle_type = atom->angle_type;

    for (int m = 0; m < num_angle[i]; m++)

      if (angle_negative[m]) angle_type[i][m] = -angle_type[i][m];

    for (int m = 0; m < num_angle[ilocal]; m++)

      if (angle_negative[m]) angle_type[ilocal][m] = -angle_type[ilocal][m];

  }



  if (any_dihedral_negative) {

    int *num_dihedral = atom->num_dihedral;

    int **dihedral_type = atom->dihedral_type;

    for (int m = 0; m < num_dihedral[i]; m++)

      if (dihedral_negative[m]) dihedral_type[i][m] = -dihedral_type[i][m];

    for (int m = 0; m < num_dihedral[ilocal]; m++)

      if (dihedral_negative[m]) 

        dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];

  }



  if (any_improper_negative) {

    int *num_improper = atom->num_improper;

    int **improper_type = atom->improper_type;

    for (int m = 0; m < num_improper[i]; m++)

      if (improper_negative[m]) improper_type[i][m] = -improper_type[i][m];

    for (int m = 0; m < num_improper[ilocal]; m++)

      if (improper_negative[m]) 

        improper_type[ilocal][m] = -improper_type[ilocal][m];

  }

}

src/MOLECULE/atom_vec_molecular.cpp

+30 −28
Original line number Diff line number Diff line
@@ -28,8 +28,8 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp) : AtomVec(lmp) 


  // strings with peratom variables to include in each AtomVec method

  // strings cannot contain fields in corresponding AtomVec default strings

  // order of fields in the string does not matter

  //   except fields_data_atom and fields_data_vel which must match data file

  // order of fields in a string does not matter

  // except: fields_data_atom & fields_data_vel must match data file



  fields_grow = (char *) 

    "molecule num_bond bond_type bond_atom "
@@ -47,9 +47,9 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp) : AtomVec(lmp) 
    "num_improper improper_type improper_atom1 improper_atom2 "

    "improper_atom3 improper_atom4 "

    "nspecial special";

  fields_comm = NULL;

  fields_comm_vel = NULL;

  fields_reverse = NULL;

  fields_comm = (char *) "";

  fields_comm_vel = (char *) "";

  fields_reverse = (char *) "";

  fields_border = (char *) "molecule";

  fields_border_vel = (char *) "molecule";

  fields_exchange = (char *)
@@ -70,7 +70,7 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp) : AtomVec(lmp) 
  fields_create = (char *) 

    "molecule num_bond num_angle num_dihedral num_improper nspecial";

  fields_data_atom = (char *) "id molecule type x";

  fields_data_vel = NULL;

  fields_data_vel = (char *) "id v";



  setup_fields();
@@ -92,7 +92,7 @@ AtomVecMolecular::~AtomVecMolecular() 
   modify values for AtomVec::pack_restart() to pack

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



void AtomVecMolecular::pack_restart_pre(int i)

void AtomVecMolecular::pack_restart_pre(int ilocal)

{

  // insure negative vectors are needed length
@@ -129,37 +129,37 @@ void AtomVecMolecular::pack_restart_pre(int i) 
  int **improper_type = atom->improper_type;



  int any_bond_negative = 0;

  for (int m = 0; m < num_bond[i]; m++) {

    if (bond_type[i][m] < 0) {

  for (int m = 0; m < num_bond[ilocal]; m++) {

    if (bond_type[ilocal][m] < 0) {

      bond_negative[m] = 1;

      bond_type[i][m] = -bond_type[i][m];

      bond_type[ilocal][m] = -bond_type[ilocal][m];

      any_bond_negative = 1;

    } else bond_negative[m] = 0;

  }



  int any_angle_negative = 0;

  for (int m = 0; m < num_angle[i]; m++) {

    if (angle_type[i][m] < 0) {

  for (int m = 0; m < num_angle[ilocal]; m++) {

    if (angle_type[ilocal][m] < 0) {

      angle_negative[m] = 1;

      angle_type[i][m] = -angle_type[i][m];

      angle_type[ilocal][m] = -angle_type[ilocal][m];

      any_angle_negative = 1;

    } else angle_negative[m] = 0;

  }



  int any_dihedral_negative = 0;

  for (int m = 0; m < num_dihedral[i]; m++) {

    if (dihedral_type[i][m] < 0) {

  for (int m = 0; m < num_dihedral[ilocal]; m++) {

    if (dihedral_type[ilocal][m] < 0) {

      dihedral_negative[m] = 1;

      dihedral_type[i][m] = -dihedral_type[i][m];

      dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];

      any_dihedral_negative = 1;

    } else dihedral_negative[m] = 0;

  }



  int any_improper_negative = 0;

  for (int m = 0; m < num_improper[i]; m++) {

    if (improper_type[i][m] < 0) {

  for (int m = 0; m < num_improper[ilocal]; m++) {

    if (improper_type[ilocal][m] < 0) {

      improper_negative[m] = 1;

      improper_type[i][m] = -improper_type[i][m];

      improper_type[ilocal][m] = -improper_type[ilocal][m];

      any_improper_negative = 1;

    } else improper_negative[m] = 0;

  }
@@ -169,36 +169,38 @@ void AtomVecMolecular::pack_restart_pre(int i) 
   unmodify values packed by AtomVec::pack_restart()

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



void AtomVecMolecular::pack_restart_post(int i)

void AtomVecMolecular::pack_restart_post(int ilocal)

{

  // restore the flagged types to their negative values



  if (any_bond_negative) {

    int *num_bond = atom->num_bond;

    int **bond_type = atom->bond_type;

    for (int m = 0; m < num_bond[i]; m++)

      if (bond_negative[m]) bond_type[i][m] = -bond_type[i][m];

    for (int m = 0; m < num_bond[ilocal]; m++)

      if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];

  }



  if (any_angle_negative) {

    int *num_angle = atom->num_angle;

    int **angle_type = atom->angle_type;

    for (int m = 0; m < num_angle[i]; m++)

      if (angle_negative[m]) angle_type[i][m] = -angle_type[i][m];

    for (int m = 0; m < num_angle[ilocal]; m++)

      if (angle_negative[m]) angle_type[ilocal][m] = -angle_type[ilocal][m];

  }



  if (any_dihedral_negative) {

    int *num_dihedral = atom->num_dihedral;

    int **dihedral_type = atom->dihedral_type;

    for (int m = 0; m < num_dihedral[i]; m++)

      if (dihedral_negative[m]) dihedral_type[i][m] = -dihedral_type[i][m];

    for (int m = 0; m < num_dihedral[ilocal]; m++)

      if (dihedral_negative[m]) 

        dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];

  }



  if (any_improper_negative) {

    int *num_improper = atom->num_improper;

    int **improper_type = atom->improper_type;

    for (int m = 0; m < num_improper[i]; m++)

      if (improper_negative[m]) improper_type[i][m] = -improper_type[i][m];

    for (int m = 0; m < num_improper[ilocal]; m++)

      if (improper_negative[m]) 

        improper_type[ilocal][m] = -improper_type[ilocal][m];

  }

}

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