Unverified Commit 4d4ae93e authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

add missing group names in fix widom. refactor group definition in fix widom and gcmc

parent 93ed07f4

examples/README

+1 −1
Original line number Original line Diff line number Diff line
@@ -75,7 +75,7 @@ eim: NaCl using the EIM potential 
ellipse:  ellipsoidal particles in spherical solvent, 2d system

ellipse:  ellipsoidal particles in spherical solvent, 2d system

flow:     Couette and Poiseuille flow in a 2d channel

flow:     Couette and Poiseuille flow in a 2d channel

friction: frictional contact of spherical asperities between 2d surfaces

friction: frictional contact of spherical asperities between 2d surfaces

gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command

gcmc:     Grand Canonical MC with fix gcmc, Widom insertion with fix widom

gjf:      use of fix langevin Gronbech-Jensen/Farago option

gjf:      use of fix langevin Gronbech-Jensen/Farago option

granregion: use of fix wall/region/gran as boundary on granular particles

granregion: use of fix wall/region/gran as boundary on granular particles

hugoniostat: Hugoniostat shock dynamics

hugoniostat: Hugoniostat shock dynamics

src/MC/fix_gcmc.cpp

+10 −29
Original line number Original line Diff line number Diff line
@@ -493,11 +493,7 @@ void FixGCMC::init() 
    }

    }

  }

  }





  if (full_flag) {

  if (full_flag) c_pe = modify->compute[modify->find_compute("thermo_pe")];

    char *id_pe = (char *) "thermo_pe";

    int ipe = modify->find_compute(id_pe);

    c_pe = modify->compute[ipe];

  }





  int *type = atom->type;

  int *type = atom->type;
@@ -580,18 +576,12 @@ void FixGCMC::init() 
  // skip if already exists from previous init()

  // skip if already exists from previous init()





  if (full_flag && !exclusion_group_bit) {

  if (full_flag && !exclusion_group_bit) {

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





    // create unique group name for atoms to be excluded

    // create unique group name for atoms to be excluded





    int len = strlen(id) + 30;

    auto group_id = std::string("FixGCMC:gcmc_exclusion_group:") + id;

    group_arg[0] = new char[len];

    group->assign(group_id + " subtract all all");

    sprintf(group_arg[0],"FixGCMC:gcmc_exclusion_group:%s",id);

    exclusion_group = group->find(group_id);

    group_arg[1] = (char *) "subtract";

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

    group_arg[3] = (char *) "all";

    group->assign(4,group_arg);

    exclusion_group = group->find(group_arg[0]);

    if (exclusion_group == -1)

    if (exclusion_group == -1)

      error->all(FLERR,"Could not find fix gcmc exclusion group ID");

      error->all(FLERR,"Could not find fix gcmc exclusion group ID");

    exclusion_group_bit = group->bitmask[exclusion_group];

    exclusion_group_bit = group->bitmask[exclusion_group];
@@ -603,34 +593,25 @@ void FixGCMC::init() 
    char **arg = new char*[narg];;

    char **arg = new char*[narg];;

    arg[0] = (char *) "exclude";

    arg[0] = (char *) "exclude";

    arg[1] = (char *) "group";

    arg[1] = (char *) "group";

    arg[2] = group_arg[0];

    arg[2] = (char *) group_id.c_str();

    arg[3] = (char *) "all";

    arg[3] = (char *) "all";

    neighbor->modify_params(narg,arg);

    neighbor->modify_params(narg,arg);

    delete [] group_arg[0];

    delete [] group_arg;

    delete [] arg;

    delete [] arg;

  }

  }





  // create a new group for temporary use with selected molecules

  // create a new group for temporary use with selected molecules





  if (exchmode == EXCHMOL || movemode == MOVEMOL) {

  if (exchmode == EXCHMOL || movemode == MOVEMOL) {

    char **group_arg = new char*[3];



    // create unique group name for atoms to be rotated

    // create unique group name for atoms to be rotated

    int len = strlen(id) + 30;



    group_arg[0] = new char[len];

    auto group_id = std::string("FixGCMC:rotation_gas_atoms:") + id;

    sprintf(group_arg[0],"FixGCMC:rotation_gas_atoms:%s",id);

    group->assign(group_id + " molecule -1");

    group_arg[1] = (char *) "molecule";

    molecule_group = group->find(group_id);

    char digits[12];

    sprintf(digits,"%d",-1);

    group_arg[2] = digits;

    group->assign(3,group_arg);

    molecule_group = group->find(group_arg[0]);

    if (molecule_group == -1)

    if (molecule_group == -1)

      error->all(FLERR,"Could not find fix gcmc rotation group ID");

      error->all(FLERR,"Could not find fix gcmc rotation group ID");

    molecule_group_bit = group->bitmask[molecule_group];

    molecule_group_bit = group->bitmask[molecule_group];

    molecule_group_inversebit = molecule_group_bit ^ ~0;

    molecule_group_inversebit = molecule_group_bit ^ ~0;

    delete [] group_arg[0];

    delete [] group_arg;

  }

  }





  // get all of the needed molecule data if exchanging

  // get all of the needed molecule data if exchanging

src/MC/fix_widom.cpp

+11 −37
Original line number Original line Diff line number Diff line
@@ -298,13 +298,7 @@ void FixWidom::init() 
    }

    }

  }

  }





  if (full_flag) {

  if (full_flag) c_pe = modify->compute[modify->find_compute("thermo_pe")];

    char *id_pe = (char *) "thermo_pe";

    int ipe = modify->find_compute(id_pe);

    c_pe = modify->compute[ipe];

  }



  int *type = atom->type;





  if (exchmode == EXCHATOM) {

  if (exchmode == EXCHATOM) {

    if (nwidom_type <= 0 || nwidom_type > atom->ntypes)

    if (nwidom_type <= 0 || nwidom_type > atom->ntypes)
@@ -340,19 +334,14 @@ void FixWidom::init() 
  // skip if already exists from previous init()

  // skip if already exists from previous init()





  if (full_flag && !exclusion_group_bit) {

  if (full_flag && !exclusion_group_bit) {

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





    // create unique group name for atoms to be excluded

    // create unique group name for atoms to be excluded





    int len = strlen(id) + 30;

    auto group_id = std::string("FixWidom:widom_exclusion_group:") + id;

    group_arg[0] = new char[len];

    group->assign(group_id + " subtract all all");

    group_arg[1] = (char *) "subtract";

    exclusion_group = group->find(group_id);

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

    group_arg[3] = (char *) "all";

    group->assign(4,group_arg);

    exclusion_group = group->find(group_arg[0]);

    if (exclusion_group == -1)

    if (exclusion_group == -1)

      error->all(FLERR,"Could not find fix Widom exclusion group ID");

      error->all(FLERR,"Could not find fix widom exclusion group ID");

    exclusion_group_bit = group->bitmask[exclusion_group];

    exclusion_group_bit = group->bitmask[exclusion_group];





    // neighbor list exclusion setup

    // neighbor list exclusion setup
@@ -362,33 +351,23 @@ void FixWidom::init() 
    char **arg = new char*[narg];;

    char **arg = new char*[narg];;

    arg[0] = (char *) "exclude";

    arg[0] = (char *) "exclude";

    arg[1] = (char *) "group";

    arg[1] = (char *) "group";

    arg[2] = group_arg[0];

    arg[2] = (char *) group_id.c_str();

    arg[3] = (char *) "all";

    arg[3] = (char *) "all";

    neighbor->modify_params(narg,arg);

    neighbor->modify_params(narg,arg);

    delete [] group_arg[0];

    delete [] group_arg;

    delete [] arg;

    delete [] arg;

  }

  }





  // create a new group for temporary use with selected molecules

  // create a new group for temporary use with selected molecules





  if (exchmode == EXCHMOL) {

  if (exchmode == EXCHMOL) {

    char **group_arg = new char*[3];



    // create unique group name for atoms to be rotated

    auto group_id = std::string("FixWidom:rotation_gas_atoms:") + id;

    int len = strlen(id) + 30;

    group->assign(group_id + " molecule -1");

    group_arg[0] = new char[len];

    molecule_group = group->find(group_id);

    group_arg[1] = (char *) "molecule";

    char digits[12];

    sprintf(digits,"%d",-1);

    group_arg[2] = digits;

    group->assign(3,group_arg);

    molecule_group = group->find(group_arg[0]);

    if (molecule_group == -1)

    if (molecule_group == -1)

      error->all(FLERR,"Could not find fix Widom rotation group ID");

      error->all(FLERR,"Could not find fix widom rotation group ID");

    molecule_group_bit = group->bitmask[molecule_group];

    molecule_group_bit = group->bitmask[molecule_group];

    molecule_group_inversebit = molecule_group_bit ^ ~0;

    molecule_group_inversebit = molecule_group_bit ^ ~0;

    delete [] group_arg[0];

    delete [] group_arg;

  }

  }





  // get all of the needed molecule data if exchanging

  // get all of the needed molecule data if exchanging
@@ -836,9 +815,6 @@ void FixWidom::attempt_molecule_insertion_full() 
  MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);

  MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);





  for (int imove = 0; imove < ninsertions; imove++) {

  for (int imove = 0; imove < ninsertions; imove++) {



    int nlocalprev = atom->nlocal;



    double com_coord[3];

    double com_coord[3];

    if (regionflag) {

    if (regionflag) {

      int region_attempt = 0;

      int region_attempt = 0;
@@ -1051,8 +1027,6 @@ double FixWidom::molecule_energy(tagint gas_molecule_id) 




double FixWidom::energy_full()

double FixWidom::energy_full()

{

{

  int imolecule;



  if (triclinic) domain->x2lamda(atom->nlocal);

  if (triclinic) domain->x2lamda(atom->nlocal);

  domain->pbc();

  domain->pbc();

  comm->exchange();

  comm->exchange();

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