Unverified Commit aa1503b7 authored by Steve Plimpton's avatar Steve Plimpton Committed by GitHub
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Merge pull request #800 from athomps/fix_gcmc_segfault_fix 

Added warning to discourage use of group all and fixed some segfault …
parents d9d072df 1d403b2a

doc/src/fix_gcmc.txt

+8 −2
Original line number Diff line number Diff line
@@ -95,8 +95,8 @@ which will result in roughly one MC move per atom or molecule 
per MC cycle.



All inserted particles are always added to two groups: the default

group "all" and the fix group specified in the fix command (which can

also be "all"). In addition, particles are also added to any groups

group "all" and the fix group specified in the fix command.

In addition, particles are also added to any groups

specified by the {group} and {grouptype} keywords.  If inserted

particles are individual atoms, they are assigned the atom type given

by the type argument.  If they are molecules, the type argument has no
@@ -104,6 +104,12 @@ effect and must be set to zero. Instead, the type of each atom in the 
inserted molecule is specified in the file read by the

"molecule"_molecule.html command.



NOTE: Care should be taken to apply fix gcmc only to

a group that contains only those atoms and molecules

that you wish to manipulate using Monte Carlo.

Hence it is generally not a good idea to specify

the default group "all" in the fix command, although it is allowed.



This fix cannot be used to perform GCMC insertions of gas atoms or

molecules other than the exchanged type, but GCMC deletions,

and MC translations, and rotations can be performed on any atom/molecule in

examples/gcmc/in.gcmc.co2

+4 −4
Original line number Diff line number Diff line
@@ -58,21 +58,21 @@ timestep 1.0 


# rigid constraints with thermostat 



fix             myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol

fix             myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol

fix_modify	myrigidnvt dynamic/dof no



# gcmc



variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)

fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &

fix             mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &

                co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt



# atom counts



variable 	carbon atom "type==1"

variable        oxygen atom "type==2"

group 		carbon dynamic all var carbon

group 	        oxygen dynamic all var oxygen

group 		carbon dynamic co2 var carbon

group 	        oxygen dynamic co2 var oxygen

variable        nC equal count(carbon)

variable        nO equal count(oxygen)

examples/gcmc/in.gcmc.lj

+6 −2
Original line number Diff line number Diff line
@@ -29,14 +29,18 @@ create_box 1 box 
pair_coeff	* * 1.0 1.0

mass		* 1.0



# we recommend setting up a dedicated group for gcmc



group		gcmcgroup type 1



# gcmc



fix             mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}

fix             mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}



# atom count



variable 	type1 atom "type==1"

group 		type1 dynamic all var type1

group 		type1 dynamic gcmcgroup var type1

variable        n1 equal count(type1)



# averaging

src/MC/fix_gcmc.cpp

+37 −18
Original line number Diff line number Diff line
@@ -72,7 +72,8 @@ enum{MOVEATOM,MOVEMOL}; // movemode 
FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :

  Fix(lmp, narg, arg),

  idregion(NULL), full_flag(0), ngroups(0), groupstrings(NULL), ngrouptypes(0), grouptypestrings(NULL),

  grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), molcoords(NULL), random_equal(NULL), random_unequal(NULL),

  grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), molcoords(NULL), molq(NULL), molimage(NULL),

  random_equal(NULL), random_unequal(NULL),

  fixrigid(NULL), fixshake(NULL), idrigid(NULL), idshake(NULL)

{

  if (narg < 11) error->all(FLERR,"Illegal fix gcmc command");
@@ -199,8 +200,8 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) : 
  

  if (exchmode == EXCHATOM) natoms_per_molecule = 1;

  else natoms_per_molecule = onemols[imol]->natoms;

  nmaxmolcoords = natoms_per_molecule;

  memory->create(molcoords,nmaxmolcoords,3,"gcmc:molcoords");

  nmaxmolatoms = natoms_per_molecule;

  grow_molecule_arrays(nmaxmolatoms);



  // compute the number of MC cycles that occur nevery timesteps
@@ -513,7 +514,7 @@ void FixGCMC::init() 
       "Fix gcmc cannot exchange individual atoms belonging to a molecule");

  }



  // if molecules are exchanged are moves, check for unset mol IDs

  // if molecules are exchanged or moved, check for unset mol IDs



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

    tagint *molecule = atom->molecule;
@@ -683,6 +684,12 @@ void FixGCMC::init() 
  imagezero = ((imageint) IMGMAX << IMG2BITS) |

             ((imageint) IMGMAX << IMGBITS) | IMGMAX;



  // warning if group id is "all"



  if (groupbit & 1)

    error->warning(FLERR, "Fix gcmc is being applied "

                   "to the default group all");

    

  // construct group bitmask for all new atoms

  // aggregated over all group keywords
@@ -1153,10 +1160,8 @@ void FixGCMC::attempt_molecule_rotation() 
    }

  }



  if (nmolcoords > nmaxmolcoords) {

    nmaxmolcoords = nmolcoords;

    molcoords = memory->grow(molcoords,nmaxmolcoords,3,"gcmc:molcoords");

  }

  if (nmolcoords > nmaxmolatoms)

    grow_molecule_arrays(nmolcoords);

  

  double com[3];

  com[0] = com[1] = com[2] = 0.0;
@@ -1816,10 +1821,8 @@ void FixGCMC::attempt_molecule_rotation_full() 
    }

  }



  if (nmolcoords > nmaxmolcoords) {

    nmaxmolcoords = nmolcoords;

    molcoords = memory->grow(molcoords,nmaxmolcoords,3,"gcmc:molcoords");

  }

  if (nmolcoords > nmaxmolatoms)

    grow_molecule_arrays(nmolcoords);

  

  double com[3];

  com[0] = com[1] = com[2] = 0.0;
@@ -1844,14 +1847,14 @@ void FixGCMC::attempt_molecule_rotation_full() 


  double **x = atom->x;

  imageint *image = atom->image;

  imageint image_orig[natoms_per_molecule];

  

  int n = 0;

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

    if (mask[i] & molecule_group_bit) {

      molcoords[n][0] = x[i][0];

      molcoords[n][1] = x[i][1];

      molcoords[n][2] = x[i][2];

      image_orig[n] = image[i];

      molimage[n] = image[i];

      double xtmp[3];

      domain->unmap(x[i],image[i],xtmp);

      xtmp[0] -= com[0];
@@ -1884,7 +1887,7 @@ void FixGCMC::attempt_molecule_rotation_full() 
        x[i][0] = molcoords[n][0];

        x[i][1] = molcoords[n][1];

        x[i][2] = molcoords[n][2];

        image[i] = image_orig[n];

        image[i] = molimage[n];

        n++;

      }

    }
@@ -1906,8 +1909,17 @@ void FixGCMC::attempt_molecule_deletion_full() 


  double energy_before = energy_stored;



  // check nmolq, grow arrays if necessary



  int nmolq = 0;

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

    if (atom->molecule[i] == deletion_molecule)

      if (atom->q_flag) nmolq++;

  

  if (nmolq > nmaxmolatoms)

    grow_molecule_arrays(nmolq);

  

  int m = 0;

  double q_tmp[natoms_per_molecule];

  int tmpmask[atom->nlocal];

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

    if (atom->molecule[i] == deletion_molecule) {
@@ -1915,7 +1927,7 @@ void FixGCMC::attempt_molecule_deletion_full() 
      atom->mask[i] = exclusion_group_bit;

      toggle_intramolecular(i);

      if (atom->q_flag) {

        q_tmp[m] = atom->q[i];

        molq[m] = atom->q[i];

        m++;

        atom->q[i] = 0.0;

      }
@@ -1948,7 +1960,7 @@ void FixGCMC::attempt_molecule_deletion_full() 
        atom->mask[i] = tmpmask[i];

        toggle_intramolecular(i);

        if (atom->q_flag) {

          atom->q[i] = q_tmp[m];

          atom->q[i] = molq[m];

          m++;

        }

      }
@@ -2521,3 +2533,10 @@ void FixGCMC::restart(char *buf) 


  next_reneighbor = static_cast<int> (list[n++]);

}



void FixGCMC::grow_molecule_arrays(int nmolatoms) {

    nmaxmolatoms = nmolatoms;

    molcoords = memory->grow(molcoords,nmaxmolatoms,3,"gcmc:molcoords");

    molq = memory->grow(molq,nmaxmolatoms,"gcmc:molq");

    molimage = memory->grow(molimage,nmaxmolatoms,"gcmc:molimage");

}

src/MC/fix_gcmc.h

+11 −2
Original line number Diff line number Diff line
@@ -57,6 +57,7 @@ class FixGCMC : public Fix { 
  double memory_usage();

  void write_restart(FILE *);

  void restart(char *);

  void grow_molecule_arrays(int);

  

 private:

  int molecule_group,molecule_group_bit;
@@ -78,7 +79,7 @@ class FixGCMC : public Fix { 
  bool full_flag;           // true if doing full system energy calculations



  int natoms_per_molecule;  // number of atoms in each inserted molecule

  int nmaxmolcoords;        // number of atoms allocated for molcoords

  int nmaxmolatoms;         // number of atoms allocated for molecule arrays



  int groupbitall;          // group bitmask for inserted atoms

  int ngroups;              // number of group-ids for inserted atoms
@@ -114,6 +115,8 @@ class FixGCMC : public Fix { 
  int *local_gas_list;

  double **cutsq;

  double **molcoords;

  double *molq;

  imageint *molimage;

  imageint imagezero;

  double overlap_cutoffsq; // square distance cutoff for overlap 

  int overlap_flag;
@@ -224,6 +227,12 @@ W: Energy of old configuration in fix gcmc is > MAXENERGYTEST. 
This probably means that a pair of atoms are closer than the 

overlap cutoff distance for keyword overlap_cutoff.



W: Fix gcmc is being applied to the default group all



This is allowed, but it will result in Monte Carlo moves

being performed on all the atoms in the system, which is

often not what is intended.



E: Invalid atom type in fix gcmc command



The atom type specified in the gcmc command does not exist.

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