Commit 43a6c13f authored by jrgissing's avatar jrgissing
Browse files

change 'groups' to 'fragments'

parent 73186e4d

doc/src/Errors_messages.rst

+1 −1
Original line number Diff line number Diff line
@@ -4801,7 +4801,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>` 
   Atom IDs must be positive integers and within range of defined

   atoms.



*Invalid atom ID in Groups section of molecule file*

*Invalid atom ID in Fragments section of molecule file*

   Self-explanatory.



*Invalid atom ID in Impropers section of data file*

doc/src/molecule.rst

+7 −6
Original line number Diff line number Diff line
@@ -64,6 +64,7 @@ templates include: 
* :doc:`fix rigid/small <fix_rigid>`

* :doc:`fix shake <fix_shake>`

* :doc:`fix gcmc <fix_gcmc>`

* :doc:`fix bond/react <fix_bond_react>`

* :doc:`create_atoms <create_atoms>`

* :doc:`atom_style template <atom_style>`
@@ -148,7 +149,7 @@ appear if the value(s) are different than the default. 
* Na *angles* = # of angles Na in molecule, default = 0

* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0

* Ni *impropers* = # of impropers Ni in molecule, default = 0

* Ng *groups* = # of groups in molecule, default = 0

* Nf *fragments* = # of fragments in molecule, default = 0

* Mtotal *mass* = total mass of molecule

* Xc Yc Zc *com* = coordinates of center-of-mass of molecule

* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
@@ -171,7 +172,7 @@ internally. 


These are the allowed section keywords for the body of the file.



* *Coords, Types, Molecules, Groups, Charges, Diameters, Masses* = atom-property sections

* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections

* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections

* *Special Bond Counts, Special Bonds* = special neighbor info

* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
@@ -244,13 +245,13 @@ listed in order from 1 to Nlines, but LAMMPS does not check for this. 
----------





*Groups* section:

*Fragments* section:



* one line per group

* one line per fragment

* line syntax: ID a b c d ...

* a,b,c,d,... = IDs of atoms in group

* a,b,c,d,... = IDs of atoms in fragment



The ID of a group can only contain alphanumeric characters and

The ID of a fragment can only contain alphanumeric characters and

underscores.  The atom IDs should be values from 1 to Natoms, where

Natoms = # of atoms in the molecule.

src/molecule.cpp

+28 −28
Original line number Diff line number Diff line
@@ -46,7 +46,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) : 
  improper_atom3(NULL), improper_atom4(NULL), nspecial(NULL), special(NULL),

  shake_flag(NULL), shake_atom(NULL), shake_type(NULL), avec_body(NULL), ibodyparams(NULL),

  dbodyparams(NULL), dx(NULL), dxcom(NULL), dxbody(NULL), quat_external(NULL),

  fp(NULL), count(NULL), groupmask(NULL)

  fp(NULL), count(NULL), fragmentmask(NULL)

{

  me = comm->me;
@@ -447,8 +447,8 @@ void Molecule::read(int flag) 
    } else if (strstr(line,"impropers")) {

      nmatch = sscanf(line,"%d",&nimpropers);

      nwant = 1;

    } else if (strstr(line,"groups")) {

      nmatch = sscanf(line,"%d",&ngroups);

    } else if (strstr(line,"fragments")) {

      nmatch = sscanf(line,"%d",&nfragments);

      nwant = 1;

    } else if (strstr(line,"mass")) {

      massflag = 1;
@@ -526,10 +526,10 @@ void Molecule::read(int flag) 
      moleculeflag = 1;

      if (flag) molecules(line);

      else skip_lines(natoms,line);

    } else if (strcmp(keyword,"Groups") == 0) {

      groupflag = 1;

      if (flag) groups(line);

      else skip_lines(ngroups,line);

    } else if (strcmp(keyword,"Fragments") == 0) {

      fragmentflag = 1;

      if (flag) fragments(line);

      else skip_lines(nfragments,line);

    } else if (strcmp(keyword,"Charges") == 0) {

      qflag = 1;

      if (flag) charges(line);
@@ -729,28 +729,28 @@ void Molecule::molecules(char *line) 
}



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

   read groups from file

   read fragments from file

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



void Molecule::groups(char *line)

void Molecule::fragments(char *line)

{

  int n,m,atomID,nwords;

  char **words = new char*[natoms+1];



  for (int i = 0; i < ngroups; i++) {

  for (int i = 0; i < nfragments; i++) {

    readline(line);

    nwords = parse(line,words,natoms+1);

    if (nwords > natoms+1)

      error->all(FLERR,"Invalid atom ID in Groups section of molecule file");

      error->all(FLERR,"Invalid atom ID in Fragments section of molecule file");

    n = strlen(words[0]) + 1;

    groupnames[i] = new char[n];

    strcpy(groupnames[i],words[0]);

    fragmentnames[i] = new char[n];

    strcpy(fragmentnames[i],words[0]);



    for (m = 1; m < nwords; m++) {

      atomID = atoi(words[m]);

      if (atomID <= 0 || atomID > natoms)

        error->all(FLERR,"Invalid atom ID in Groups section of molecule file");

      groupmask[i][atomID-1] = 1;

        error->all(FLERR,"Invalid atom ID in Fragments section of molecule file");

      fragmentmask[i][atomID-1] = 1;

    }

  }
@@ -1423,13 +1423,13 @@ void Molecule::body(int flag, int pflag, char *line) 
}



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

   return group index if name matches existing group, -1 if no such group

   return fragment index if name matches existing fragment, -1 if no such fragment

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



int Molecule::findgroup(const char *name)

int Molecule::findfragment(const char *name)

{

  for (int igroup = 0; igroup < ngroups; igroup++)

    if (groupnames[igroup] && strcmp(name,groupnames[igroup]) == 0) return igroup;

  for (int i = 0; i < nfragments; i++)

    if (fragmentnames[i] && strcmp(name,fragmentnames[i]) == 0) return i;

  return -1;

}
@@ -1513,7 +1513,7 @@ void Molecule::initialize() 
  bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;

  maxspecial = 0;



  xflag = typeflag = moleculeflag = groupflag = qflag = radiusflag = rmassflag = 0;

  xflag = typeflag = moleculeflag = fragmentflag = qflag = radiusflag = rmassflag = 0;

  bondflag = angleflag = dihedralflag = improperflag = 0;

  nspecialflag = specialflag = 0;

  shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
@@ -1569,10 +1569,10 @@ void Molecule::allocate() 
  if (xflag) memory->create(x,natoms,3,"molecule:x");

  if (typeflag) memory->create(type,natoms,"molecule:type");

  if (moleculeflag) memory->create(molecule,natoms,"molecule:molecule");

  if (groupflag) groupnames = new char*[ngroups];

  if (groupflag) memory->create(groupmask,ngroups,natoms,"molecule:groupmask");

  for (int i = 0; i < ngroups; i++)

    for (int j = 0; j < natoms; j++) groupmask[i][j] = 0;

  if (fragmentflag) fragmentnames = new char*[nfragments];

  if (fragmentflag) memory->create(fragmentmask,nfragments,natoms,"molecule:fragmentmask");

  for (int i = 0; i < nfragments; i++)

    for (int j = 0; j < natoms; j++) fragmentmask[i][j] = 0;

  if (qflag) memory->create(q,natoms,"molecule:q");

  if (radiusflag) memory->create(radius,natoms,"molecule:radius");

  if (rmassflag) memory->create(rmass,natoms,"molecule:rmass");
@@ -1665,10 +1665,10 @@ void Molecule::deallocate() 
  memory->destroy(radius);

  memory->destroy(rmass);



  memory->destroy(groupmask);

  if (groupflag) {

    for (int i = 0; i < ngroups; i++) delete [] groupnames[i];

    delete [] groupnames;

  memory->destroy(fragmentmask);

  if (fragmentflag) {

    for (int i = 0; i < nfragments; i++) delete [] fragmentnames[i];

    delete [] fragmentnames;

  }



  memory->destroy(num_bond);

src/molecule.h

+8 −8
Original line number Diff line number Diff line
@@ -30,13 +30,13 @@ class Molecule : protected Pointers { 


  int natoms;

  int nbonds,nangles,ndihedrals,nimpropers;

  int ntypes,nmolecules,ngroups;

  int ntypes,nmolecules,nfragments;

  int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;

  int nibody,ndbody;



  // group info

  char **groupnames;

  int **groupmask; // ngroups by natoms

  // fragment info

  char **fragmentnames;

  int **fragmentmask; // nfragments by natoms



  // max bond,angle,etc per atom
@@ -45,7 +45,7 @@ class Molecule : protected Pointers { 


  // 1 if attribute defined in file, 0 if not



  int xflag,typeflag,moleculeflag,groupflag,qflag,radiusflag,rmassflag;

  int xflag,typeflag,moleculeflag,fragmentflag,qflag,radiusflag,rmassflag;

  int bondflag,angleflag,dihedralflag,improperflag;

  int nspecialflag,specialflag;

  int shakeflag,shakeflagflag,shakeatomflag,shaketypeflag;
@@ -123,7 +123,7 @@ class Molecule : protected Pointers { 
  void compute_mass();

  void compute_com();

  void compute_inertia();

  int findgroup(const char *);

  int findfragment(const char *);

  void check_attributes(int);



 private:
@@ -138,7 +138,7 @@ class Molecule : protected Pointers { 
  void coords(char *);

  void types(char *);

  void molecules(char *);

  void groups(char *);

  void fragments(char *);

  void charges(char *);

  void diameters(char *);

  void masses(char *);
@@ -379,7 +379,7 @@ E: Invalid Molecules section in molecule file 


Self-explanatory.



E: Invalid atom ID in Groups section of molecule file

E: Invalid atom ID in Fragments section of molecule file



Self-explanatory.

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