Use latest versions in master branch
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Oliver Henrich
43
src/atom.cpp
43
src/atom.cpp
@ -161,7 +161,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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sp = fm = fm_long = nullptr;
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// USER-EFF and USER-AWPMD packages
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// EFF and AWPMD packages
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spin = nullptr;
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eradius = ervel = erforce = nullptr;
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@ -169,27 +169,27 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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cs = csforce = vforce = nullptr;
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etag = nullptr;
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// USER-CGDNA package
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// CG-DNA package
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id5p = nullptr;
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// USER-DPD package
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// DPD-REACT package
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uCond = uMech = uChem = uCG = uCGnew = nullptr;
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duChem = dpdTheta = nullptr;
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// USER-MESO package
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// MESO package
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cc = cc_flux = nullptr;
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edpd_temp = edpd_flux = edpd_cv = nullptr;
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// USER-MESONT package
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// MESONT package
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length = nullptr;
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buckling = nullptr;
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bond_nt = nullptr;
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// USER-SMD package
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// MACHDYN package
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contact_radius = nullptr;
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smd_data_9 = nullptr;
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@ -198,12 +198,12 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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eff_plastic_strain_rate = nullptr;
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damage = nullptr;
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// USER-SPH package
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// SPH package
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rho = drho = esph = desph = cv = nullptr;
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vest = nullptr;
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// USER-DIELECTRIC package
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// DIELECTRIC package
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area = ed = em = epsilon = curvature = q_unscaled = nullptr;
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@ -461,14 +461,14 @@ void Atom::peratom_create()
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add_peratom("fm",&fm,DOUBLE,3,1);
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add_peratom("fm_long",&fm_long,DOUBLE,3,1);
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// USER-EFF package
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// EFF package
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add_peratom("spin",&spin,INT,0);
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add_peratom("eradius",&eradius,DOUBLE,0);
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add_peratom("ervel",&ervel,DOUBLE,0);
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add_peratom("erforce",&erforce,DOUBLE,0,1); // set per-thread flag
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// USER-AWPMD package
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// AWPMD package
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add_peratom("cs",&cs,DOUBLE,2);
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add_peratom("csforce",&csforce,DOUBLE,2);
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@ -476,11 +476,11 @@ void Atom::peratom_create()
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add_peratom("ervelforce",&ervelforce,DOUBLE,0);
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add_peratom("etag",&etag,INT,0);
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// USER-CGDNA package
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// CG-DNA package
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add_peratom("id5p",&id5p,tagintsize,0);
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// USER-DPD package
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// DPD-REACT package
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add_peratom("dpdTheta",&dpdTheta,DOUBLE,0);
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add_peratom("uCond",&uCond,DOUBLE,0);
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@ -490,7 +490,7 @@ void Atom::peratom_create()
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add_peratom("uCGnew",&uCGnew,DOUBLE,0);
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add_peratom("duChem",&duChem,DOUBLE,0);
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// USER-MESO package
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// MESO package
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add_peratom("edpd_cv",&edpd_cv,DOUBLE,0);
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add_peratom("edpd_temp",&edpd_temp,DOUBLE,0);
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@ -499,13 +499,13 @@ void Atom::peratom_create()
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add_peratom("cc",&cc,DOUBLE,1);
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add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag
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// USER-MESONT package
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// MESONT package
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add_peratom("length",&length,DOUBLE,0);
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add_peratom("buckling",&buckling,INT,0);
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add_peratom("bond_nt",&bond_nt,tagintsize,2);
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// USER-SPH package
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// SPH package
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add_peratom("rho",&rho,DOUBLE,0);
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add_peratom("drho",&drho,DOUBLE,0,1); // set per-thread flag
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@ -514,7 +514,7 @@ void Atom::peratom_create()
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add_peratom("vest",&vest,DOUBLE,3);
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add_peratom("cv",&cv,DOUBLE,0);
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// USER-SMD package
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// MACHDYN package
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add_peratom("contact_radius",&contact_radius,DOUBLE,0);
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add_peratom("smd_data_9",&smd_data_9,DOUBLE,1);
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@ -523,7 +523,7 @@ void Atom::peratom_create()
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add_peratom("eff_plastic_strain_rate",&eff_plastic_strain_rate,DOUBLE,0);
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add_peratom("damage",&damage,DOUBLE,0);
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// USER-DIELECTRIC package
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// DIELECTRIC package
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add_peratom("area",&area,DOUBLE,0);
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add_peratom("ed",&ed,DOUBLE,0);
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@ -1302,7 +1302,6 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
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}
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}
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}
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buf = next + 1;
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}
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}
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@ -2657,7 +2656,7 @@ void *Atom::extract(const char *name)
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if (strcmp(name,"cv") == 0) return (void *) cv;
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if (strcmp(name,"vest") == 0) return (void *) vest;
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// USER-MESONT package
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// MESONT package
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if (strcmp(name,"length") == 0) return (void *) length;
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if (strcmp(name,"buckling") == 0) return (void *) buckling;
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if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
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@ -2674,7 +2673,7 @@ void *Atom::extract(const char *name)
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if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
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if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp;
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// USER-DIELECTRIC
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// DIELECTRIC
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if (strcmp(name,"area") == 0) return (void *) area;
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if (strcmp(name,"ed") == 0) return (void *) ed;
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if (strcmp(name,"em") == 0) return (void *) em;
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@ -2750,7 +2749,7 @@ int Atom::extract_datatype(const char *name)
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if (strcmp(name,"cv") == 0) return LAMMPS_DOUBLE;
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if (strcmp(name,"vest") == 0) return LAMMPS_DOUBLE_2D;
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// USER-MESONT package
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// MESONT package
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if (strcmp(name,"length") == 0) return LAMMPS_DOUBLE;
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if (strcmp(name,"buckling") == 0) return LAMMPS_INT;
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if (strcmp(name,"bond_nt") == 0) return LAMMPS_TAGINT_2D;
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@ -2765,7 +2764,7 @@ int Atom::extract_datatype(const char *name)
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if (strcmp(name,"dpdTheta") == 0) return LAMMPS_DOUBLE;
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if (strcmp(name,"edpd_temp") == 0) return LAMMPS_DOUBLE;
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// USER-DIELECTRIC
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// DIELECTRIC
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if (strcmp(name,"area") == 0) return LAMMPS_DOUBLE;
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if (strcmp(name,"ed") == 0) return LAMMPS_DOUBLE;
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if (strcmp(name,"em") == 0) return LAMMPS_DOUBLE;
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18
src/atom.h
18
src/atom.h
@ -114,7 +114,7 @@ class Atom : protected Pointers {
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double **sp, **fm, **fm_long;
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// USER_EFF and USER-AWPMD packages
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// EFF and AWPMD packages
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int *spin;
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double *eradius, *ervel, *erforce;
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@ -122,18 +122,18 @@ class Atom : protected Pointers {
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double **cs, **csforce, **vforce;
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int *etag;
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// USER-CGDNA package
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// CG-DNA package
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tagint *id5p;
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// USER-DPD package
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// DPD-REACT 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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// 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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@ -141,13 +141,13 @@ class Atom : protected Pointers {
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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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// 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-SMD package
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// MACHDYN package
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double *contact_radius;
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double **smd_data_9;
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@ -156,12 +156,12 @@ class Atom : protected Pointers {
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double *eff_plastic_strain_rate;
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double *damage;
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// USER-SPH package
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// SPH package
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double *rho, *drho, *esph, *desph, *cv;
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double **vest;
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// USER-DIELECTRIC package
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// DIELECTRIC package
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double *area,*ed,*em,*epsilon,*curvature,*q_unscaled;
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@ -191,7 +191,7 @@ class Atom : protected Pointers {
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int sp_flag;
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// USER-SMD package
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// MACHDYN package
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int x0_flag;
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int smd_flag, damage_flag;
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@ -71,7 +71,6 @@ ReadData::ReadData(LAMMPS *lmp) : Command(lmp)
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keyword = new char[MAXLINE];
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style = new char[MAXLINE];
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buffer = new char[CHUNK*MAXLINE];
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buffer_post = new char[CHUNK*MAXLINE];
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ncoeffarg = maxcoeffarg = 0;
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coeffarg = nullptr;
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fp = nullptr;
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@ -87,11 +86,6 @@ ReadData::ReadData(LAMMPS *lmp) : Command(lmp)
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avec_tri = (AtomVecTri *) atom->style_match("tri");
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nbodies = 0;
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avec_body = (AtomVecBody *) atom->style_match("body");
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if (atom->style_match("oxdna"))
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avec = (AtomVec *) atom->style_match("oxdna");
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else
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avec = atom->avec;
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}
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/* ---------------------------------------------------------------------- */
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@ -102,7 +96,6 @@ ReadData::~ReadData()
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delete [] keyword;
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delete [] style;
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delete [] buffer;
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delete [] buffer_post;
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memory->sfree(coeffarg);
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for (int i = 0; i < nfix; i++) {
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@ -1340,7 +1333,6 @@ void ReadData::bonds(int firstpass)
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nchunk = MIN(nbonds-nread,CHUNK);
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eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
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if (eof) error->all(FLERR,"Unexpected end of data file");
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strcpy(buffer_post,buffer);
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atom->data_bonds(nchunk,buffer,count,id_offset,boffset);
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nread += nchunk;
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}
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@ -32,7 +32,7 @@ class ReadData : public Command {
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private:
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int me, compressed;
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char *line, *keyword, *buffer, *buffer_post, *style;
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char *line, *keyword, *buffer, *style;
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FILE *fp;
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char **coeffarg;
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int ncoeffarg, maxcoeffarg;
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@ -54,7 +54,6 @@ class ReadData : public Command {
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class AtomVecTri *avec_tri;
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bigint nbodies;
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class AtomVecBody *avec_body;
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class AtomVec *avec;
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// box info
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