Commit a8eb3ff7 authored by jrgissing's avatar jrgissing
Browse files

consolidate per-atom property fixes into one

parent 38ce56f2

src/USER-MISC/fix_bond_react.cpp

+85 −132
Original line number Diff line number Diff line
@@ -63,8 +63,6 @@ Fix(lmp, narg, arg) 
{

  fix1 = NULL;

  fix2 = NULL;

  fix3 = NULL;

  fix4 = NULL;



  if (narg < 8) error->all(FLERR,"Illegal fix bond/react command 0.0");
@@ -284,9 +282,6 @@ Fix(lmp, narg, arg) 


  id_fix1 = NULL;

  id_fix2 = NULL;

  id_fix3 = NULL;

  id_fix4 = NULL;



}



/* ---------------------------------------------------------------------- */
@@ -354,12 +349,6 @@ FixBondReact::~FixBondReact() 
  if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2);

  delete [] id_fix2;



  if (id_fix3 == NULL && modify->nfix) modify->delete_fix(id_fix3);

  delete [] id_fix3;



  if (id_fix4 == NULL && modify->nfix) modify->delete_fix(id_fix4);

  delete [] id_fix4;



  delete [] guess_branch;

  delete [] pioneer_count;
@@ -386,29 +375,31 @@ void FixBondReact::post_constructor() 
{



  //let's add the limit_tags per-atom property fix

    //these are recently reacted atoms being relaxed

    int len = strlen("limit_tags") + 1;

  int len = strlen("per_atom_props") + 1;

  id_fix2 = new char[len];

    strcpy(id_fix2,"limit_tags"); //note: this is purposefully same as property 'name'

  strcpy(id_fix2,"per_atom_props");



  int ifix = modify->find_fix(id_fix2);

  if (ifix == -1) {

      char **newarg = new char*[6];

      newarg[0] = (char *) "limit_tags";

    char **newarg = new char*[8];

    newarg[0] = (char *) "per_atom_props";

    newarg[1] = (char *) "all"; // group ID is ignored

    newarg[2] = (char *) "property/atom";

    newarg[3] = (char *) "i_limit_tags";

      newarg[4] = (char *) "ghost";

      newarg[5] = (char *) "yes";

      modify->add_fix(6,newarg);

    newarg[4] = (char *) "i_statted_tags";

    newarg[5] = (char *) "i_react_tags";

    newarg[6] = (char *) "ghost";

    newarg[7] = (char *) "yes";

    modify->add_fix(8,newarg);

    fix2 = modify->fix[modify->nfix-1];

    delete [] newarg;

  }



  // limit_tags: these are recently reacted atoms being relaxed

  // per-atom properties already initialized to zero (not in group)

  // let's do it anyway for clarity

  int flag;

    int index = atom->find_custom(id_fix2,flag);

  int index = atom->find_custom("limit_tags",flag); //here's where error would happen

  int *i_limit_tags = atom->ivector[index];



  for (int i = 0; i < atom->nlocal; i++)
@@ -428,35 +419,15 @@ void FixBondReact::post_constructor() 
    delete [] newarg;

  }



    //let's add the statted_tags per-atom property fix

    //this are atoms subjec to the system-wide thermostat

    len = strlen("statted_tags") + 1;

    id_fix3 = new char[len];

    strcpy(id_fix3,"statted_tags"); //note: this is purposefully same as property 'name'



    ifix = modify->find_fix(id_fix3);

    if (ifix == -1) {

      char **newarg = new char*[6];

      newarg[0] = (char *) "statted_tags";

      newarg[1] = (char *) "all"; // group ID is ignored

      newarg[2] = (char *) "property/atom";

      newarg[3] = (char *) "i_statted_tags";

      newarg[4] = (char *) "ghost";

      newarg[5] = (char *) "yes";

      modify->add_fix(6,newarg);

      fix3 = modify->fix[modify->nfix-1];

      delete [] newarg;

    }



  // on to statted_tags (system-wide thermostat)

  // intialize per-atom statted_flags to 1

    index = atom->find_custom(id_fix3,flag);

  index = atom->find_custom("statted_tags",flag);

  int *i_statted_tags = atom->ivector[index];



  for (int i = 0; i < atom->nlocal; i++)

    i_statted_tags[i] = 1;



  if (stabilization_flag == 1) {



    // create exclude_group if not already existing

    if (group->find(exclude_group) == -1) {

      group->find_or_create(exclude_group);
@@ -491,29 +462,11 @@ void FixBondReact::post_constructor() 


  }



    //let's add the react_tags per-atom property fix

    //this per-atom property is the ID of the 'react' argument which recently caused atom to react

  //react_tags: this per-atom property is the ID of the 'react' argument which recently caused atom to react

  //so that atoms which wander between processors may be released to global thermostat at the proper time

    len = strlen("react_tags") + 1;

    id_fix4 = new char[len];

    strcpy(id_fix4,"react_tags"); //note: this is purposefully same as property 'name'



    ifix = modify->find_fix(id_fix4);

    if (ifix == -1) { //ifix

      char **newarg = new char*[6];

      newarg[0] = (char *) "react_tags";

      newarg[1] = (char *) "all"; // group ID is ignored

      newarg[2] = (char *) "property/atom";

      newarg[3] = (char *) "i_react_tags";

      newarg[4] = (char *) "ghost";

      newarg[5] = (char *) "yes";

      modify->add_fix(6,newarg);

      fix4 = modify->fix[modify->nfix-1];

      delete [] newarg;

    }



  //per-atom values initalized to 0

    index = atom->find_custom(id_fix4,flag);

  index = atom->find_custom("react_tags",flag);

  int *i_react_tags = atom->ivector[index];



  for (int i = 0; i < atom->nlocal; i++)
@@ -679,7 +632,7 @@ void FixBondReact::post_integrate() 


  // per-atom property indicating if in bond/react master group

  int flag;

  int index1 = atom->find_custom(id_fix2,flag);

  int index1 = atom->find_custom("limit_tags",flag);

  int *i_limit_tags = atom->ivector[index1];



  int i,j;
@@ -1077,7 +1030,7 @@ void FixBondReact::make_a_guess() 


  // per-atom property indicating if in bond/react master group

  int flag;

  int index1 = atom->find_custom(id_fix2,flag);

  int index1 = atom->find_custom("limit_tags",flag);

  int *i_limit_tags = atom->ivector[index1];



  if (status == GUESSFAIL && avail_guesses == 0) {
@@ -1696,13 +1649,13 @@ void FixBondReact::limit_bond(int limit_bond_mode) 
  // this will be a new per-atom property!



  int flag;

  int index1 = atom->find_custom(id_fix2,flag);

  int index1 = atom->find_custom("limit_tags",flag);

  int *i_limit_tags = atom->ivector[index1];



  int index2 = atom->find_custom(id_fix3,flag);

  int index2 = atom->find_custom("statted_tags",flag);

  int *i_statted_tags = atom->ivector[index2];



  int index3 = atom->find_custom(id_fix4,flag);

  int index3 = atom->find_custom("react_tags",flag);

  int *i_react_tags = atom->ivector[index3];



  for (int i = 0; i < temp_limit_num; i++) {
@@ -1725,15 +1678,15 @@ void FixBondReact::unlimit_bond() 
{

  //let's now unlimit in terms of i_limit_tags

  //we just run through all nlocal, looking for > limit_duration

  //then we return i_limit_tag to -1 (which removes from dynamic group)

  //then we return i_limit_tag to 0 (which removes from dynamic group)

  int flag;

  int index1 = atom->find_custom(id_fix2,flag);

  int index1 = atom->find_custom("limit_tags",flag);

  int *i_limit_tags = atom->ivector[index1];



  int index2 = atom->find_custom(id_fix3,flag); // statted_tags

  int index2 = atom->find_custom("statted_tags",flag);

  int *i_statted_tags = atom->ivector[index2];



  int index3 = atom->find_custom(id_fix4,flag); // statted_tags

  int index3 = atom->find_custom("react_tags",flag);

  int *i_react_tags = atom->ivector[index3];



  int num2unlimit = 0;

src/USER-MISC/fix_bond_react.h

+5 −7
Original line number Diff line number Diff line
@@ -75,10 +75,10 @@ class FixBondReact : public Fix { 


  class Molecule *onemol; // pre-reacted molecule template

  class Molecule *twomol; // post-reacted molecule template

  Fix *fix1;              // used to relax reaction sites

  Fix *fix2;              // used to indicate relaxing atoms

  Fix *fix3;              // used to indicate system-wide thermostat

  Fix *fix4;              // indicates to which 'react' atom belongs

  Fix *fix1;              // nve/limit used to relax reaction sites

  Fix *fix2;              // properties/atom used to indicate 1) indicate relaxing atoms

                          //                                  2) system-wide thermostat

                          //                                  3) to which 'react' atom belongs

  class RanMars **random;

  class NeighList *list;
@@ -86,9 +86,7 @@ class FixBondReact : public Fix { 
  int *limit_duration; // indicates how long to relax

  char *nve_limit_xmax; // indicates max distance allowed to move when relaxing

  char *id_fix1; // id of internally created fix nve/limit

  char *id_fix2; // id of internally created fix per-atom property (recently reacted)

  char *id_fix3; // id of internally created fix per-atom property (system-wide thermostat)

  char *id_fix4; // id of internally created fix per-atom property (ID of 'react' argument)

  char *id_fix2; // id of internally created fix per-atom properties

  char *master_group; // group containing relaxing atoms from all fix rxns

  char *exclude_group; // group for system-wide thermostat

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