Unverified Commit f46ba326 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #2195 from jrgissing/bond/react-reformat 

Bond/react reformat
parents 51174d4a 3044d83c

src/USER-REACTION/fix_bond_react.cpp

+27 −62
Original line number Original line Diff line number Diff line
@@ -19,6 +19,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) 
#include <mpi.h>

#include <mpi.h>

#include <cmath>

#include <cmath>

#include <cstring>

#include <cstring>

#include <string>

#include "update.h"

#include "update.h"

#include "modify.h"

#include "modify.h"

#include "respa.h"

#include "respa.h"
@@ -41,6 +42,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) 
#include "error.h"

#include "error.h"

#include "input.h"

#include "input.h"

#include "variable.h"

#include "variable.h"

#include "fmt/format.h"





#include <algorithm>

#include <algorithm>
@@ -575,17 +577,11 @@ FixBondReact::~FixBondReact() 
  delete [] set;

  delete [] set;





  if (group) {

  if (group) {

    char **newarg;

    group->assign(std::string(master_group) + " delete");

    newarg = new char*[2];

    newarg[0] = master_group;

    newarg[1] = (char *) "delete";

    group->assign(2,newarg);

    if (stabilization_flag == 1) {

    if (stabilization_flag == 1) {

      newarg[0] = exclude_group;

      group->assign(std::string(exclude_group) + " delete");

      group->assign(2,newarg);

      delete [] exclude_group;

      delete [] exclude_group;

    }

    }

    delete [] newarg;

  }

  }

}

}
@@ -608,59 +604,38 @@ it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group 




void FixBondReact::post_constructor()

void FixBondReact::post_constructor()

{

{

  int len;

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

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

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

  std::string cmd = std::string("bond_react_props_internal");

  id_fix2 = new char[len];

  id_fix2 = new char[cmd.size()+1];

  strcpy(id_fix2,"bond_react_props_internal");

  strcpy(id_fix2,cmd.c_str());





  int ifix = modify->find_fix(id_fix2);

  int ifix = modify->find_fix(id_fix2);

  if (ifix == -1) {

  if (ifix == -1) {

    char **newarg = new char*[7];

    cmd += std::string(" all property/atom i_limit_tags i_react_tags ghost yes");

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

    modify->add_fix(cmd);

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

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

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

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

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

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

    modify->add_fix(7,newarg);

    delete [] newarg;

  }

  }





  // create master_group if not already existing

  // create master_group if not already existing

  // NOTE: limit_tags and react_tags automaticaly intitialized to zero (unless read from restart)

  // NOTE: limit_tags and react_tags automaticaly intitialized to zero (unless read from restart)

  group->find_or_create(master_group);

  group->find_or_create(master_group);

  char **newarg;

  cmd = fmt::format("{} dynamic all property limit_tags",master_group);

  newarg = new char*[5];

  group->assign(cmd);

  newarg[0] = master_group;

  newarg[1] = (char *) "dynamic";

  newarg[2] = (char *) "all";

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

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

  group->assign(5,newarg);

  delete [] newarg;





  if (stabilization_flag == 1) {

  if (stabilization_flag == 1) {

    int igroup = group->find(exclude_group);

    int igroup = group->find(exclude_group);

    // create exclude_group if not already existing, or use as parent group if static

    // create exclude_group if not already existing, or use as parent group if static

    if (igroup == -1 || group->dynamic[igroup] == 0) {

    if (igroup == -1 || group->dynamic[igroup] == 0) {

      // create stabilization per-atom property

      // create stabilization per-atom property

      len = strlen("bond_react_stabilization_internal") + 1;

      cmd = std::string("bond_react_stabilization_internal");

      id_fix3 = new char[len];

      id_fix3 = new char[cmd.size()+1];

      strcpy(id_fix3,"bond_react_stabilization_internal");

      strcpy(id_fix3,cmd.c_str());





      ifix = modify->find_fix(id_fix3);

      ifix = modify->find_fix(id_fix3);

      if (ifix == -1) {

      if (ifix == -1) {

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

        cmd += std::string(" all property/atom i_statted_tags ghost yes");

        newarg[0] = (char *) id_fix3;

        modify->add_fix(cmd);

        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];

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

        delete [] newarg;

      }

      }





      len = strlen("statted_tags") + 1;

      len = strlen("statted_tags") + 1;
@@ -680,16 +655,11 @@ void FixBondReact::post_constructor() 
      strcat(exclude_group,"_REACT");

      strcat(exclude_group,"_REACT");





      group->find_or_create(exclude_group);

      group->find_or_create(exclude_group);

      char **newarg;

      if (igroup == -1)

      newarg = new char*[5];

        cmd = fmt::format("{} dynamic all property statted_tags",exclude_group);

      newarg[0] = exclude_group;

      else

      newarg[1] = (char *) "dynamic";

        cmd = fmt::format("{} dynamic {} property statted_tags",exclude_group,exclude_PARENT_group);

      if (igroup == -1) newarg[2] = (char *) "all";

      group->assign(cmd);

      else newarg[2] = (char *) exclude_PARENT_group;

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

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

      group->assign(5,newarg);

      delete [] newarg;

      delete [] exclude_PARENT_group;

      delete [] exclude_PARENT_group;





      // on to statted_tags (system-wide thermostat)

      // on to statted_tags (system-wide thermostat)
@@ -737,21 +707,16 @@ void FixBondReact::post_constructor() 








    // let's create a new nve/limit fix to limit newly reacted atoms

    // let's create a new nve/limit fix to limit newly reacted atoms

    len = strlen("bond_react_MASTER_nve_limit") + 1;

    cmd = std::string("bond_react_MASTER_nve_limit");

    id_fix1 = new char[len];

    id_fix1 = new char[cmd.size()+1];

    strcpy(id_fix1,"bond_react_MASTER_nve_limit");

    strcpy(id_fix1,cmd.c_str());





    ifix = modify->find_fix(id_fix1);

    ifix = modify->find_fix(id_fix1);





    if (ifix == -1) {

    if (ifix == -1) {

      char **newarg = new char*[4];

      cmd += fmt::format(" {} nve/limit  {}",master_group,nve_limit_xmax);

      newarg[0] = id_fix1;

      modify->add_fix(cmd);

      newarg[1] = master_group;

      newarg[2] = (char *) "nve/limit";

      newarg[3] = nve_limit_xmax;

      modify->add_fix(4,newarg);

      fix1 = modify->fix[modify->nfix-1];

      fix1 = modify->fix[modify->nfix-1];

      delete [] newarg;

    }

    }

  }

  }

}

}

src/group.cpp

+16 −0
Original line number Original line Diff line number Diff line
@@ -547,6 +547,22 @@ void Group::assign(int narg, char **arg) 
  }

  }

}

}





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

   convenience function to allow assigning to groups from a single string

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



void Group::assign(const std::string &groupcmd)

{

  std::vector<std::string> args = utils::split_words(groupcmd);

  char **newarg = new char*[args.size()];

  int i=0;

  for (const auto &arg : args) {

    newarg[i++] = (char *)arg.c_str();

  }

  assign(args.size(),newarg);

  delete[] newarg;

}



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

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

   add flagged atoms to a new or existing group

   add flagged atoms to a new or existing group

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

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

src/group.h

+2 −0
Original line number Original line Diff line number Diff line
@@ -16,6 +16,7 @@ 




#include "pointers.h"

#include "pointers.h"

#include <map>

#include <map>

#include <string>





namespace LAMMPS_NS {

namespace LAMMPS_NS {
@@ -30,6 +31,7 @@ class Group : protected Pointers { 
  Group(class LAMMPS *);

  Group(class LAMMPS *);

  ~Group();

  ~Group();

  void assign(int, char **);         // assign atoms to a group

  void assign(int, char **);         // assign atoms to a group

  void assign(const std::string &);  // convenience function

  void create(char *, int *);        // add flagged atoms to a group

  void create(char *, int *);        // add flagged atoms to a group

  int find(const char *);            // lookup name in list of groups

  int find(const char *);            // lookup name in list of groups

  int find_or_create(const char *);  // lookup name or create new group

  int find_or_create(const char *);  // lookup name or create new group

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