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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14418 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-01-11 22:00:04 +00:00
parent 7ae65d4dcf
commit f5946c73f7
1 changed files with 12 additions and 1 deletions
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13
src/molecule.h
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@ -26,11 +26,13 @@ class Molecule : protected Pointers {
int last; // 1 if last molecule in set, else 0
// number of atoms,bonds,etc in molecule
// nibody,ndbody = # of integer/double fields in body
int natoms;
int nbonds,nangles,ndihedrals,nimpropers;
int ntypes;
int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
int nibody,ndbody;
// max bond,angle,etc per atom
@ -43,6 +45,7 @@ class Molecule : protected Pointers {
int bondflag,angleflag,dihedralflag,improperflag;
int nspecialflag,specialflag;
int shakeflag,shakeflagflag,shakeatomflag,shaketypeflag;
int bodyflag,ibodyflag,dbodyflag;
// 1 if attribute defined or computed, 0 if not
@ -83,6 +86,10 @@ class Molecule : protected Pointers {
tagint **shake_atom;
int **shake_type;
class AtomVecBody *avec_body;
int *ibodyparams; // integer and double body params
double *dbodyparams;
double center[3]; // geometric center of molecule
double masstotal; // total mass of molecule
double com[3]; // center of mass of molecule
@ -102,6 +109,9 @@ class Molecule : protected Pointers {
double **dxbody; // displacement of each atom relative to COM
// in body frame (diagonalized interia tensor)
double *quat_external; // orientation imposed by external class
// e.g. FixPour or CreateAtoms
Molecule(class LAMMPS *, int, char **, int &);
~Molecule();
void compute_center();
@ -117,7 +127,7 @@ class Molecule : protected Pointers {
int toffset,boffset,aoffset,doffset,ioffset;
int autospecial;
double sizescale;
void read(int);
void coords(char *);
void types(char *);
@ -134,6 +144,7 @@ class Molecule : protected Pointers {
void shakeflag_read(char *);
void shakeatom_read(char *);
void shaketype_read(char *);
void body(int, int, char *);
void initialize();
void allocate();