mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2356 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
8f6991985a
commit
17092d4799
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@ -74,7 +74,7 @@ class Data {
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char *atom_style;
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int style_angle,style_atomic,style_bond,style_charge,style_dipole;
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int style_dpd,style_ellipsoid,style_full,style_granular;
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int style_hybrid,style_molecular;
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int style_hybrid,style_molecular,style_peri;
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int natoms,nbonds,nangles,ndihedrals,nimpropers;
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int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
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@ -176,10 +176,11 @@ class Data {
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double *mass,*shape,*dipole;
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double *x,*y,*z,*vx,*vy,*vz;
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double *xphix,*xphiy,*xphiz,*omegax,*omegay,*omegaz;
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double *omegax,*omegay,*omegaz;
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int *tag,*type,*mask,*image;
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int *molecule;
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double *q,*mux,*muy,*muz,*radius,*density;
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double *q,*mux,*muy,*muz,*radius,*density,*vfrac,*rmass;
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double *s0,*x0x,*x0y,*x0z;
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double *quatw,*quati,*quatj,*quatk,*angmomx,*angmomy,*angmomz;
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int *bond_type,*angle_type,*dihedral_type,*improper_type;
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int *bond_atom1,*bond_atom2;
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@ -203,6 +204,7 @@ class Data {
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void write_atom_full(FILE *, int, int, int, int);
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void write_atom_granular(FILE *, int, int, int, int);
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void write_atom_molecular(FILE *, int, int, int, int);
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void write_atom_peri(FILE *, int, int, int, int);
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void write_atom_angle_extra(FILE *, int);
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void write_atom_atomic_extra(FILE *, int);
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@ -214,6 +216,7 @@ class Data {
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void write_atom_full_extra(FILE *, int);
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void write_atom_granular_extra(FILE *, int);
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void write_atom_molecular_extra(FILE *, int);
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void write_atom_peri_extra(FILE *, int);
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void write_vel_angle(FILE *, int);
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void write_vel_atomic(FILE *, int);
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@ -225,6 +228,7 @@ class Data {
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void write_vel_full(FILE *, int);
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void write_vel_granular(FILE *, int);
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void write_vel_molecular(FILE *, int);
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void write_vel_peri(FILE *, int);
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void write_vel_angle_extra(FILE *, int);
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void write_vel_atomic_extra(FILE *, int);
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@ -236,6 +240,7 @@ class Data {
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void write_vel_full_extra(FILE *, int);
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void write_vel_granular_extra(FILE *, int);
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void write_vel_molecular_extra(FILE *, int);
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void write_vel_peri_extra(FILE *, int);
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};
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// ---------------------------------------------------------------------
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@ -265,6 +270,7 @@ void allocate_ellipsoid(Data &data);
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void allocate_full(Data &data);
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void allocate_granular(Data &data);
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void allocate_molecular(Data &data);
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void allocate_peri(Data &data);
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int atom_angle(double *, Data &, int);
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int atom_atomic(double *, Data &, int);
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@ -276,6 +282,7 @@ int atom_ellipsoid(double *, Data &, int);
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int atom_full(double *, Data &, int);
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int atom_granular(double *, Data &, int);
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int atom_molecular(double *, Data &, int);
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int atom_peri(double *, Data &, int);
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int read_int(FILE *fp);
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double read_double(FILE *fp);
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@ -454,7 +461,7 @@ void header(FILE *fp, Data &data)
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data.style_angle = data.style_atomic = data.style_bond =
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data.style_charge = data.style_dipole = data.style_dpd =
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data.style_ellipsoid = data.style_full = data.style_granular =
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data.style_hybrid = data.style_molecular = 0;
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data.style_hybrid = data.style_molecular = data.style_peri = 0;
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data.atom_style = read_char(fp);
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set_style(data.atom_style,data,1);
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@ -532,6 +539,7 @@ void set_style(char *name, Data &data, int flag)
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else if (strcmp(name,"granular") == 0) data.style_granular = flag;
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else if (strcmp(name,"hybrid") == 0) data.style_hybrid = flag;
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else if (strcmp(name,"molecular") == 0) data.style_molecular = flag;
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else if (strcmp(name,"peri") == 0) data.style_peri = flag;
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else {
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printf("ERROR: Unknown atom style %s\n",name);
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exit(1);
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@ -698,6 +706,7 @@ int atom(double *buf, Data &data)
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if (data.style_full) allocate_full(data);
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if (data.style_granular) allocate_granular(data);
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if (data.style_molecular) allocate_molecular(data);
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if (data.style_peri) allocate_peri(data);
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}
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// read atom quantities from buf
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@ -720,6 +729,7 @@ int atom(double *buf, Data &data)
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if (k == data.style_full) m += atom_full(&buf[m],data,iatoms);
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if (k == data.style_granular) m += atom_granular(&buf[m],data,iatoms);
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if (k == data.style_molecular) m += atom_molecular(&buf[m],data,iatoms);
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if (k == data.style_peri) m += atom_peri(&buf[m],data,iatoms);
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}
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data.iatoms++;
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@ -929,9 +939,6 @@ int atom_granular(double *buf, Data &data, int iatoms)
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data.radius[iatoms] = buf[m++];
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data.density[iatoms] = buf[m++];
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data.xphix[iatoms] = buf[m++];
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data.xphiy[iatoms] = buf[m++];
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data.xphiz[iatoms] = buf[m++];
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data.omegax[iatoms] = buf[m++];
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data.omegay[iatoms] = buf[m++];
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data.omegaz[iatoms] = buf[m++];
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@ -1104,6 +1111,31 @@ int atom_molecular(double *buf, Data &data, int iatoms)
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return m;
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}
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int atom_peri(double *buf, Data &data, int iatoms)
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{
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int m = 1;
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data.x[iatoms] = buf[m++];
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data.y[iatoms] = buf[m++];
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data.z[iatoms] = buf[m++];
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data.tag[iatoms] = static_cast<int> (buf[m++]);
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data.type[iatoms] = static_cast<int> (buf[m++]);
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data.mask[iatoms] = static_cast<int> (buf[m++]);
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data.image[iatoms] = static_cast<int> (buf[m++]);
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data.vx[iatoms] = buf[m++];
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data.vy[iatoms] = buf[m++];
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data.vz[iatoms] = buf[m++];
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data.vfrac[iatoms] = buf[m++];
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data.density[iatoms] = buf[m++];
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data.rmass[iatoms] = buf[m++];
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data.s0[iatoms] = buf[m++];
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data.x0x[iatoms] = buf[m++];
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data.x0y[iatoms] = buf[m++];
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data.x0z[iatoms] = buf[m++];
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return m;
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}
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// ---------------------------------------------------------------------
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// per-atom memory allocation routines
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// one routine per atom style
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@ -1184,9 +1216,6 @@ void allocate_granular(Data &data)
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{
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data.radius = new double[data.natoms];
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data.density = new double[data.natoms];
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data.xphix = new double[data.natoms];
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data.xphiy = new double[data.natoms];
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data.xphiz = new double[data.natoms];
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data.omegax = new double[data.natoms];
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data.omegay = new double[data.natoms];
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data.omegaz = new double[data.natoms];
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@ -1214,6 +1243,17 @@ void allocate_molecular(Data &data)
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data.improper_atom4 = new int[data.nimpropers];
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}
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void allocate_peri(Data &data)
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{
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data.vfrac = new double[data.natoms];
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data.density = new double[data.natoms];
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data.rmass = new double[data.natoms];
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data.s0 = new double[data.natoms];
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data.x0x = new double[data.natoms];
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data.x0y = new double[data.natoms];
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data.x0z = new double[data.natoms];
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}
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// ---------------------------------------------------------------------
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// pair coeffs
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// one section for each pair style
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@ -1488,12 +1528,14 @@ void pair(FILE *fp, Data &data, char *style, int flag)
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}
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}
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} else if ((strcmp(style,"gran/history") == 0) ||
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(strcmp(style,"gran/no_history") == 0) ||
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(strcmp(style,"gran/hertzian") == 0)) {
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} else if ((strcmp(style,"gran/hooke") == 0) ||
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(strcmp(style,"gran/hooke/history") == 0) ||
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(strcmp(style,"gran/hertz/history") == 0)) {
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double xkk = read_double(fp);
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double kn = read_double(fp);
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double kt = read_double(fp);
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double gamman = read_double(fp);
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double gammat = read_double(fp);
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double xmu = read_double(fp);
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int dampflag = read_int(fp);
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@ -2980,6 +3022,7 @@ void Data::write(FILE *fp, FILE *fp2)
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if (style_full) write_atom_full(fp,i,ix,iy,iz);
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if (style_granular) write_atom_granular(fp,i,ix,iy,iz);
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if (style_molecular) write_atom_molecular(fp,i,ix,iy,iz);
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if (style_peri) write_atom_peri(fp,i,ix,iy,iz);
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fprintf(fp,"\n");
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} else {
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@ -2996,6 +3039,7 @@ void Data::write(FILE *fp, FILE *fp2)
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if (k == style_full) write_atom_full_extra(fp,i);
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if (k == style_granular) write_atom_granular_extra(fp,i);
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if (k == style_molecular) write_atom_molecular_extra(fp,i);
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if (k == style_peri) write_atom_peri_extra(fp,i);
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}
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fprintf(fp," %d %d %d\n",ix,iy,iz);
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}
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@ -3017,6 +3061,7 @@ void Data::write(FILE *fp, FILE *fp2)
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if (style_full) write_vel_full(fp,i);
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if (style_granular) write_vel_granular(fp,i);
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if (style_molecular) write_vel_molecular(fp,i);
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if (style_peri) write_vel_peri(fp,i);
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fprintf(fp,"\n");
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} else {
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@ -3032,6 +3077,7 @@ void Data::write(FILE *fp, FILE *fp2)
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if (k == style_full) write_vel_full_extra(fp,i);
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if (k == style_granular) write_vel_granular_extra(fp,i);
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if (k == style_molecular) write_vel_molecular_extra(fp,i);
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if (k == style_peri) write_vel_peri_extra(fp,i);
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}
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fprintf(fp,"\n");
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}
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@ -3134,6 +3180,12 @@ void Data::write_atom_molecular(FILE *fp, int i, int ix, int iy, int iz)
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tag[i],molecule[i],type[i],x[i],y[i],z[i],ix,iy,iz);
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}
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void Data::write_atom_peri(FILE *fp, int i, int ix, int iy, int iz)
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{
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fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
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tag[i],type[i],vfrac[i],density[i],rmass[i],x[i],y[i],z[i],ix,iy,iz);
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}
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// ---------------------------------------------------------------------
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// per-atom write routines of extra quantities unique to style
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// one routine per atom style
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@ -3183,6 +3235,11 @@ void Data::write_atom_molecular_extra(FILE *fp, int i)
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fprintf(fp," %d",molecule[i]);
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}
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void Data::write_atom_peri_extra(FILE *fp, int i)
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{
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fprintf(fp," %-1.16e %-1.16e %-1.16e",vfrac[i],density[i],rmass[i]);
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}
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// ---------------------------------------------------------------------
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// per-atom velocity write routines
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// one routine per atom style
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@ -3240,6 +3297,11 @@ void Data::write_vel_molecular(FILE *fp, int i)
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fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
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}
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void Data::write_vel_peri(FILE *fp, int i)
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{
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fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
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}
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// ---------------------------------------------------------------------
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// per-atom velocity write routines of extra quantities unique to style
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// one routine per atom style
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@ -3265,6 +3327,7 @@ void Data::write_vel_granular_extra(FILE *fp, int i)
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}
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void Data::write_vel_molecular_extra(FILE *fp, int i) {}
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void Data::write_vel_peri_extra(FILE *fp, int i) {}
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// ---------------------------------------------------------------------
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// binary reads from restart file
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