diff --git a/src/atom.cpp b/src/atom.cpp index 323f88719a..6063398f40 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -161,7 +161,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) sp = fm = fm_long = nullptr; - // USER-EFF and USER-AWPMD packages + // EFF and AWPMD packages spin = nullptr; eradius = ervel = erforce = nullptr; @@ -169,27 +169,27 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) cs = csforce = vforce = nullptr; etag = nullptr; - // USER-CGDNA package + // CG-DNA package id5p = nullptr; - // USER-DPD package + // DPD-REACT package uCond = uMech = uChem = uCG = uCGnew = nullptr; duChem = dpdTheta = nullptr; - // USER-MESO package + // MESO package cc = cc_flux = nullptr; edpd_temp = edpd_flux = edpd_cv = nullptr; - // USER-MESONT package + // MESONT package length = nullptr; buckling = nullptr; bond_nt = nullptr; - // USER-SMD package + // MACHDYN package contact_radius = nullptr; smd_data_9 = nullptr; @@ -198,12 +198,12 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) eff_plastic_strain_rate = nullptr; damage = nullptr; - // USER-SPH package + // SPH package rho = drho = esph = desph = cv = nullptr; vest = nullptr; - // USER-DIELECTRIC package + // DIELECTRIC package area = ed = em = epsilon = curvature = q_unscaled = nullptr; @@ -461,14 +461,14 @@ void Atom::peratom_create() add_peratom("fm",&fm,DOUBLE,3,1); add_peratom("fm_long",&fm_long,DOUBLE,3,1); - // USER-EFF package + // EFF package add_peratom("spin",&spin,INT,0); add_peratom("eradius",&eradius,DOUBLE,0); add_peratom("ervel",&ervel,DOUBLE,0); add_peratom("erforce",&erforce,DOUBLE,0,1); // set per-thread flag - // USER-AWPMD package + // AWPMD package add_peratom("cs",&cs,DOUBLE,2); add_peratom("csforce",&csforce,DOUBLE,2); @@ -476,11 +476,11 @@ void Atom::peratom_create() add_peratom("ervelforce",&ervelforce,DOUBLE,0); add_peratom("etag",&etag,INT,0); - // USER-CGDNA package + // CG-DNA package add_peratom("id5p",&id5p,tagintsize,0); - // USER-DPD package + // DPD-REACT package add_peratom("dpdTheta",&dpdTheta,DOUBLE,0); add_peratom("uCond",&uCond,DOUBLE,0); @@ -490,7 +490,7 @@ void Atom::peratom_create() add_peratom("uCGnew",&uCGnew,DOUBLE,0); add_peratom("duChem",&duChem,DOUBLE,0); - // USER-MESO package + // MESO package add_peratom("edpd_cv",&edpd_cv,DOUBLE,0); add_peratom("edpd_temp",&edpd_temp,DOUBLE,0); @@ -499,13 +499,13 @@ void Atom::peratom_create() add_peratom("cc",&cc,DOUBLE,1); add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag - // USER-MESONT package + // MESONT package add_peratom("length",&length,DOUBLE,0); add_peratom("buckling",&buckling,INT,0); add_peratom("bond_nt",&bond_nt,tagintsize,2); - // USER-SPH package + // SPH package add_peratom("rho",&rho,DOUBLE,0); add_peratom("drho",&drho,DOUBLE,0,1); // set per-thread flag @@ -514,7 +514,7 @@ void Atom::peratom_create() add_peratom("vest",&vest,DOUBLE,3); add_peratom("cv",&cv,DOUBLE,0); - // USER-SMD package + // MACHDYN package add_peratom("contact_radius",&contact_radius,DOUBLE,0); add_peratom("smd_data_9",&smd_data_9,DOUBLE,1); @@ -523,7 +523,7 @@ void Atom::peratom_create() add_peratom("eff_plastic_strain_rate",&eff_plastic_strain_rate,DOUBLE,0); add_peratom("damage",&damage,DOUBLE,0); - // USER-DIELECTRIC package + // DIELECTRIC package add_peratom("area",&area,DOUBLE,0); add_peratom("ed",&ed,DOUBLE,0); @@ -1302,7 +1302,6 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, } } } - buf = next + 1; } } @@ -2657,7 +2656,7 @@ void *Atom::extract(const char *name) if (strcmp(name,"cv") == 0) return (void *) cv; if (strcmp(name,"vest") == 0) return (void *) vest; - // USER-MESONT package + // MESONT package if (strcmp(name,"length") == 0) return (void *) length; if (strcmp(name,"buckling") == 0) return (void *) buckling; if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt; @@ -2674,7 +2673,7 @@ void *Atom::extract(const char *name) if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta; if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp; - // USER-DIELECTRIC + // DIELECTRIC if (strcmp(name,"area") == 0) return (void *) area; if (strcmp(name,"ed") == 0) return (void *) ed; if (strcmp(name,"em") == 0) return (void *) em; @@ -2750,7 +2749,7 @@ int Atom::extract_datatype(const char *name) if (strcmp(name,"cv") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"vest") == 0) return LAMMPS_DOUBLE_2D; - // USER-MESONT package + // MESONT package if (strcmp(name,"length") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"buckling") == 0) return LAMMPS_INT; if (strcmp(name,"bond_nt") == 0) return LAMMPS_TAGINT_2D; @@ -2765,7 +2764,7 @@ int Atom::extract_datatype(const char *name) if (strcmp(name,"dpdTheta") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"edpd_temp") == 0) return LAMMPS_DOUBLE; - // USER-DIELECTRIC + // DIELECTRIC if (strcmp(name,"area") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"ed") == 0) return LAMMPS_DOUBLE; if (strcmp(name,"em") == 0) return LAMMPS_DOUBLE; diff --git a/src/atom.h b/src/atom.h index 22165fa053..daf2f04f8a 100644 --- a/src/atom.h +++ b/src/atom.h @@ -114,7 +114,7 @@ class Atom : protected Pointers { double **sp, **fm, **fm_long; - // USER_EFF and USER-AWPMD packages + // EFF and AWPMD packages int *spin; double *eradius, *ervel, *erforce; @@ -122,18 +122,18 @@ class Atom : protected Pointers { double **cs, **csforce, **vforce; int *etag; - // USER-CGDNA package + // CG-DNA package tagint *id5p; - // USER-DPD package + // DPD-REACT package double *uCond, *uMech, *uChem, *uCGnew, *uCG; double *duChem; double *dpdTheta; int nspecies_dpd; - // USER-MESO package + // MESO package double **cc, **cc_flux; // cc = chemical concentration double *edpd_temp, *edpd_flux; // temperature and heat flux @@ -141,13 +141,13 @@ class Atom : protected Pointers { double *edpd_cv; // heat capacity int cc_species; - // USER-MESONT package + // MESONT package double *length; int *buckling; tagint **bond_nt; - // USER-SMD package + // MACHDYN package double *contact_radius; double **smd_data_9; @@ -156,12 +156,12 @@ class Atom : protected Pointers { double *eff_plastic_strain_rate; double *damage; - // USER-SPH package + // SPH package double *rho, *drho, *esph, *desph, *cv; double **vest; - // USER-DIELECTRIC package + // DIELECTRIC package double *area,*ed,*em,*epsilon,*curvature,*q_unscaled; @@ -191,7 +191,7 @@ class Atom : protected Pointers { int sp_flag; - // USER-SMD package + // MACHDYN package int x0_flag; int smd_flag, damage_flag; diff --git a/src/read_data.cpp b/src/read_data.cpp index 183ef30648..12ad6c3b8c 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -71,7 +71,6 @@ ReadData::ReadData(LAMMPS *lmp) : Command(lmp) keyword = new char[MAXLINE]; style = new char[MAXLINE]; buffer = new char[CHUNK*MAXLINE]; - buffer_post = new char[CHUNK*MAXLINE]; ncoeffarg = maxcoeffarg = 0; coeffarg = nullptr; fp = nullptr; @@ -87,11 +86,6 @@ ReadData::ReadData(LAMMPS *lmp) : Command(lmp) avec_tri = (AtomVecTri *) atom->style_match("tri"); nbodies = 0; avec_body = (AtomVecBody *) atom->style_match("body"); - - if (atom->style_match("oxdna")) - avec = (AtomVec *) atom->style_match("oxdna"); - else - avec = atom->avec; } /* ---------------------------------------------------------------------- */ @@ -102,7 +96,6 @@ ReadData::~ReadData() delete [] keyword; delete [] style; delete [] buffer; - delete [] buffer_post; memory->sfree(coeffarg); for (int i = 0; i < nfix; i++) { @@ -1340,7 +1333,6 @@ void ReadData::bonds(int firstpass) nchunk = MIN(nbonds-nread,CHUNK); eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world); if (eof) error->all(FLERR,"Unexpected end of data file"); - strcpy(buffer_post,buffer); atom->data_bonds(nchunk,buffer,count,id_offset,boffset); nread += nchunk; } diff --git a/src/read_data.h b/src/read_data.h index 1f240a18bc..482c45e6e6 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -32,7 +32,7 @@ class ReadData : public Command { private: int me, compressed; - char *line, *keyword, *buffer, *buffer_post, *style; + char *line, *keyword, *buffer, *style; FILE *fp; char **coeffarg; int ncoeffarg, maxcoeffarg; @@ -54,7 +54,6 @@ class ReadData : public Command { class AtomVecTri *avec_tri; bigint nbodies; class AtomVecBody *avec_body; - class AtomVec *avec; // box info