Merge branch 'master' into feature-cnt
This commit is contained in:
iafoss
190
src/atom.h
190
src/atom.h
@ -39,6 +39,8 @@ class Atom : protected Pointers {
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bigint ntris; // number of triangles
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bigint nbodies; // number of bodies
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// system properties
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bigint nbonds,nangles,ndihedrals,nimpropers;
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int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
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int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
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@ -49,74 +51,30 @@ class Atom : protected Pointers {
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int nfirst; // # of atoms in first group on this proc
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char *firstgroupname; // group-ID to store first, NULL if unset
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// per-atom arrays
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// customize by adding new array
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// --------------------------------------------------------------------
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// 1st customization section: customize by adding new per-atom variable
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// per-atom vectors and arrays
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tagint *tag;
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int *type,*mask;
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imageint *image;
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double **x,**v,**f;
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tagint *molecule;
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int *molindex,*molatom;
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// charged and dipolar particles
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double *rmass;
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double *q,**mu;
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// finite-size particles
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double *radius;
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double **omega,**angmom,**torque;
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double *radius,*rmass;
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int *ellipsoid,*line,*tri,*body;
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// SPIN package
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// molecular systems
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double **sp;
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double **fm;
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double **fm_long;
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// PERI package
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double *vfrac,*s0;
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double **x0;
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// USER-EFF and USER-AWPMD packages
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int *spin;
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double *eradius,*ervel,*erforce,*ervelforce;
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double *cs,*csforce,*vforce;
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int *etag;
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// USER-SPH package
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double *rho,*drho,*e,*de,*cv;
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double **vest;
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// USER-SMD package
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double *contact_radius;
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double **smd_data_9;
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double **smd_stress;
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double *eff_plastic_strain;
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double *eff_plastic_strain_rate;
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double *damage;
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// USER-DPD package
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double *uCond,*uMech,*uChem,*uCGnew,*uCG;
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double *duChem;
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double *dpdTheta;
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int nspecies_dpd;
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// USER-MESO package
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double **cc, **cc_flux; // cc = chemical concentration
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double *edpd_temp,*edpd_flux; // temperature and heat flux
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double *edpd_cv; // heat capacity
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int cc_species;
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// USER-MESONT package
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double *length;
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int *buckling;
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tagint **bond_nt;
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// molecular info
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tagint *molecule;
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int *molindex,*molatom;
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int **nspecial; // 0,1,2 = cumulative # of 1-2,1-3,1-4 neighs
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tagint **special; // IDs of 1-2,1-3,1-4 neighs of each atom
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@ -138,19 +96,66 @@ class Atom : protected Pointers {
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int **improper_type;
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tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
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// custom arrays used by fix property/atom
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// PERI package
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int **ivector;
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double **dvector;
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char **iname,**dname;
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int nivector,ndvector;
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double *vfrac,*s0;
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double **x0;
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// atom style and per-atom array existence flags
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// customize by adding new flag
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// SPIN package
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double **sp,**fm,**fm_long;
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// USER_EFF and USER-AWPMD packages
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int *spin;
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double *eradius,*ervel,*erforce;
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double *ervelforce;
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double **cs,**csforce,**vforce;
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int *etag;
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// USER-DPD package
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double *uCond,*uMech,*uChem,*uCGnew,*uCG;
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double *duChem;
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double *dpdTheta;
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int nspecies_dpd;
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// USER-MESO package
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double **cc,**cc_flux; // cc = chemical concentration
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double *edpd_temp,*edpd_flux; // temperature and heat flux
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double *vest_temp;
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double *edpd_cv; // heat capacity
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int cc_species;
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double *contact_radius;
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double **smd_data_9;
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double **smd_stress;
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double *eff_plastic_strain;
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double *eff_plastic_strain_rate;
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double *damage;
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// USER-MESONT package
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double *length;
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int *buckling;
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tagint **bond_nt;
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// USER-SPH package
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double *rho,*drho,*esph,*desph,*cv;
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double **vest;
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// end of customization section
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// --------------------------------------------------------------------
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// --------------------------------------------------------------------
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// 2nd customization section: customize by adding new flags
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// identical list as Atom::set_atomflag_defaults()
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// most are existence flags for per-atom vectors and arrays
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// 1 if variable is used, 0 if not
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int sphere_flag,ellipsoid_flag,line_flag,tri_flag,body_flag;
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int peri_flag,electron_flag;
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int ecp_flag;
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int wavepacket_flag,sph_flag;
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int molecule_flag,molindex_flag,molatom_flag;
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@ -158,29 +163,51 @@ class Atom : protected Pointers {
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int rmass_flag,radius_flag,omega_flag,torque_flag,angmom_flag;
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int vfrac_flag,spin_flag,eradius_flag,ervel_flag,erforce_flag;
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int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
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int rho_flag,e_flag,cv_flag,vest_flag;
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int rho_flag,esph_flag,cv_flag,vest_flag;
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int dpd_flag,edpd_flag,tdpd_flag;
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int mesont_flag;
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//USER-SPIN package
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// SPIN package
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int sp_flag;
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// USER-SMD package
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int smd_flag;
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int contact_radius_flag;
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int smd_data_9_flag;
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int smd_stress_flag;
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int x0_flag;
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int eff_plastic_strain_flag;
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int eff_plastic_strain_rate_flag;
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int damage_flag;
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int smd_flag,damage_flag;
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int contact_radius_flag,smd_data_9_flag,smd_stress_flag;
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int eff_plastic_strain_flag,eff_plastic_strain_rate_flag;
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// Peridynamics scale factor, used by dump cfg
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double pdscale;
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// end of customization section
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// --------------------------------------------------------------------
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// per-atom data struct describing all per-atom vectors/arrays
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struct PerAtom {
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char *name;
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void *address;
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void *address_length;
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int *address_maxcols;
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int datatype;
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int cols;
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int collength;
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int threadflag;
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};
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PerAtom *peratom;
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int nperatom,maxperatom;
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// custom arrays used by fix property/atom
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int **ivector;
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double **dvector;
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char **iname,**dname;
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int nivector,ndvector;
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// molecule templates
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// each template can be a set of consecutive molecules
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// each with same ID (stored in molecules)
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@ -227,14 +254,21 @@ class Atom : protected Pointers {
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typedef std::map<std::string,AtomVecCreator> AtomVecCreatorMap;
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AtomVecCreatorMap *avec_map;
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// --------------------------------------------------------------------
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// functions
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Atom(class LAMMPS *);
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~Atom();
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void settings(class Atom *);
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void peratom_create();
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void add_peratom(const char *, void *, int, int, int threadflag=0);
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void add_peratom_change_columns(const char *, int);
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void add_peratom_vary(const char *, void *, int, int *,
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void *, int collength=0);
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void create_avec(const char *, int, char **, int);
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virtual class AtomVec *new_avec(const char *, int, int &);
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void init();
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void setup();
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@ -259,7 +293,7 @@ class Atom : protected Pointers {
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void data_dihedrals(int, char *, int *, tagint, int);
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void data_impropers(int, char *, int *, tagint, int);
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void data_bonus(int, char *, class AtomVec *, tagint);
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void data_bodies(int, char *, class AtomVecBody *, tagint);
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void data_bodies(int, char *, class AtomVec *, tagint);
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void data_fix_compute_variable(int, int);
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virtual void allocate_type_arrays();
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@ -296,8 +330,10 @@ class Atom : protected Pointers {
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inline int get_max_same() {return max_same;};
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inline int get_map_maxarray() {return map_maxarray+1;};
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// NOTE: placeholder method until KOKKOS/AtomVec is refactored
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int memcheck(const char *) {return 1;}
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bigint memory_usage();
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int memcheck(const char *);
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// functions for global to local ID mapping
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// map lookup function inlined for efficiency
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@ -350,9 +386,7 @@ class Atom : protected Pointers {
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double bininvx,bininvy,bininvz; // inverse actual bin sizes
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double bboxlo[3],bboxhi[3]; // bounding box of my sub-domain
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int memlength; // allocated size of memstr
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char *memstr; // string of array names already counted
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void set_atomflag_defaults();
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void setup_sort_bins();
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int next_prime(int);
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