Commit 17092d47 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2356 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 8f699198

tools/restart2data.cpp

+77 −14
Original line number Diff line number Diff line
@@ -74,7 +74,7 @@ class Data { 
  char *atom_style;

  int style_angle,style_atomic,style_bond,style_charge,style_dipole;

  int style_dpd,style_ellipsoid,style_full,style_granular;

  int style_hybrid,style_molecular;

  int style_hybrid,style_molecular,style_peri;



  int natoms,nbonds,nangles,ndihedrals,nimpropers;

  int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
@@ -176,10 +176,11 @@ class Data { 


  double *mass,*shape,*dipole;

  double *x,*y,*z,*vx,*vy,*vz;

  double *xphix,*xphiy,*xphiz,*omegax,*omegay,*omegaz;

  double *omegax,*omegay,*omegaz;

  int *tag,*type,*mask,*image;

  int *molecule;

  double *q,*mux,*muy,*muz,*radius,*density;

  double *q,*mux,*muy,*muz,*radius,*density,*vfrac,*rmass;

  double *s0,*x0x,*x0y,*x0z;

  double *quatw,*quati,*quatj,*quatk,*angmomx,*angmomy,*angmomz;

  int *bond_type,*angle_type,*dihedral_type,*improper_type;

  int *bond_atom1,*bond_atom2;
@@ -203,6 +204,7 @@ class Data { 
  void write_atom_full(FILE *, int, int, int, int);

  void write_atom_granular(FILE *, int, int, int, int);

  void write_atom_molecular(FILE *, int, int, int, int);

  void write_atom_peri(FILE *, int, int, int, int);



  void write_atom_angle_extra(FILE *, int);

  void write_atom_atomic_extra(FILE *, int);
@@ -214,6 +216,7 @@ class Data { 
  void write_atom_full_extra(FILE *, int);

  void write_atom_granular_extra(FILE *, int);

  void write_atom_molecular_extra(FILE *, int);

  void write_atom_peri_extra(FILE *, int);



  void write_vel_angle(FILE *, int);

  void write_vel_atomic(FILE *, int);
@@ -225,6 +228,7 @@ class Data { 
  void write_vel_full(FILE *, int);

  void write_vel_granular(FILE *, int);

  void write_vel_molecular(FILE *, int);

  void write_vel_peri(FILE *, int);



  void write_vel_angle_extra(FILE *, int);

  void write_vel_atomic_extra(FILE *, int);
@@ -236,6 +240,7 @@ class Data { 
  void write_vel_full_extra(FILE *, int);

  void write_vel_granular_extra(FILE *, int);

  void write_vel_molecular_extra(FILE *, int);

  void write_vel_peri_extra(FILE *, int);

};



// ---------------------------------------------------------------------
@@ -265,6 +270,7 @@ void allocate_ellipsoid(Data &data); 
void allocate_full(Data &data);

void allocate_granular(Data &data);

void allocate_molecular(Data &data);

void allocate_peri(Data &data);



int atom_angle(double *, Data &, int);

int atom_atomic(double *, Data &, int);
@@ -276,6 +282,7 @@ int atom_ellipsoid(double *, Data &, int); 
int atom_full(double *, Data &, int);

int atom_granular(double *, Data &, int);

int atom_molecular(double *, Data &, int);

int atom_peri(double *, Data &, int);



int read_int(FILE *fp);

double read_double(FILE *fp);
@@ -454,7 +461,7 @@ void header(FILE *fp, Data &data) 
      data.style_angle = data.style_atomic = data.style_bond = 

	data.style_charge = data.style_dipole =	data.style_dpd =

	data.style_ellipsoid = data.style_full = data.style_granular =

	data.style_hybrid = data.style_molecular = 0;

	data.style_hybrid = data.style_molecular = data.style_peri = 0;



      data.atom_style = read_char(fp);

      set_style(data.atom_style,data,1);
@@ -532,6 +539,7 @@ void set_style(char *name, Data &data, int flag) 
  else if (strcmp(name,"granular") == 0) data.style_granular = flag;

  else if (strcmp(name,"hybrid") == 0) data.style_hybrid = flag;

  else if (strcmp(name,"molecular") == 0) data.style_molecular = flag;

  else if (strcmp(name,"peri") == 0) data.style_peri = flag;

  else {

    printf("ERROR: Unknown atom style %s\n",name);

    exit(1);
@@ -698,6 +706,7 @@ int atom(double *buf, Data &data) 
    if (data.style_full) allocate_full(data);

    if (data.style_granular) allocate_granular(data);

    if (data.style_molecular) allocate_molecular(data);

    if (data.style_peri) allocate_peri(data);

  }



  // read atom quantities from buf
@@ -720,6 +729,7 @@ int atom(double *buf, Data &data) 
    if (k == data.style_full) m += atom_full(&buf[m],data,iatoms);

    if (k == data.style_granular) m += atom_granular(&buf[m],data,iatoms);

    if (k == data.style_molecular) m += atom_molecular(&buf[m],data,iatoms);

    if (k == data.style_peri) m += atom_peri(&buf[m],data,iatoms);

  }



  data.iatoms++;
@@ -929,9 +939,6 @@ int atom_granular(double *buf, Data &data, int iatoms) 


  data.radius[iatoms] = buf[m++];

  data.density[iatoms] = buf[m++];

  data.xphix[iatoms] = buf[m++];

  data.xphiy[iatoms] = buf[m++];

  data.xphiz[iatoms] = buf[m++];

  data.omegax[iatoms] = buf[m++];

  data.omegay[iatoms] = buf[m++];

  data.omegaz[iatoms] = buf[m++];
@@ -1104,6 +1111,31 @@ int atom_molecular(double *buf, Data &data, int iatoms) 
  return m;

}



int atom_peri(double *buf, Data &data, int iatoms)

{

  int m = 1;

  data.x[iatoms] = buf[m++];

  data.y[iatoms] = buf[m++];

  data.z[iatoms] = buf[m++];

  data.tag[iatoms] = static_cast<int> (buf[m++]);

  data.type[iatoms] = static_cast<int> (buf[m++]);

  data.mask[iatoms] = static_cast<int> (buf[m++]);

  data.image[iatoms] = static_cast<int> (buf[m++]);

  data.vx[iatoms] = buf[m++];

  data.vy[iatoms] = buf[m++];

  data.vz[iatoms] = buf[m++];



  data.vfrac[iatoms] = buf[m++];

  data.density[iatoms] = buf[m++];

  data.rmass[iatoms] = buf[m++];

  data.s0[iatoms] = buf[m++];

  data.x0x[iatoms] = buf[m++];

  data.x0y[iatoms] = buf[m++];

  data.x0z[iatoms] = buf[m++];



  return m;

}



// ---------------------------------------------------------------------

// per-atom memory allocation routines

// one routine per atom style
@@ -1184,9 +1216,6 @@ void allocate_granular(Data &data) 
{

  data.radius = new double[data.natoms];

  data.density = new double[data.natoms];

  data.xphix = new double[data.natoms];

  data.xphiy = new double[data.natoms];

  data.xphiz = new double[data.natoms];

  data.omegax = new double[data.natoms];

  data.omegay = new double[data.natoms];

  data.omegaz = new double[data.natoms];
@@ -1214,6 +1243,17 @@ void allocate_molecular(Data &data) 
  data.improper_atom4 = new int[data.nimpropers];

}



void allocate_peri(Data &data)

{

  data.vfrac = new double[data.natoms];

  data.density = new double[data.natoms];

  data.rmass = new double[data.natoms];

  data.s0 = new double[data.natoms];

  data.x0x = new double[data.natoms];

  data.x0y = new double[data.natoms];

  data.x0z = new double[data.natoms];

}



// ---------------------------------------------------------------------

// pair coeffs

// one section for each pair style
@@ -1488,12 +1528,14 @@ void pair(FILE *fp, Data &data, char *style, int flag) 
      }

    }



  } else if ((strcmp(style,"gran/history") == 0) ||

	   (strcmp(style,"gran/no_history") == 0) ||

	   (strcmp(style,"gran/hertzian") == 0)) {

  } else if ((strcmp(style,"gran/hooke") == 0) ||

	   (strcmp(style,"gran/hooke/history") == 0) ||

	   (strcmp(style,"gran/hertz/history") == 0)) {



    double xkk = read_double(fp);

    double kn = read_double(fp);

    double kt = read_double(fp);

    double gamman = read_double(fp);

    double gammat = read_double(fp);

    double xmu = read_double(fp);

    int dampflag = read_int(fp);
@@ -2980,6 +3022,7 @@ void Data::write(FILE *fp, FILE *fp2) 
	if (style_full) write_atom_full(fp,i,ix,iy,iz);

	if (style_granular) write_atom_granular(fp,i,ix,iy,iz);

	if (style_molecular) write_atom_molecular(fp,i,ix,iy,iz);

	if (style_peri) write_atom_peri(fp,i,ix,iy,iz);

	fprintf(fp,"\n");



      } else {
@@ -2996,6 +3039,7 @@ void Data::write(FILE *fp, FILE *fp2) 
	  if (k == style_full) write_atom_full_extra(fp,i);

	  if (k == style_granular) write_atom_granular_extra(fp,i);

	  if (k == style_molecular) write_atom_molecular_extra(fp,i);

	  if (k == style_peri) write_atom_peri_extra(fp,i);

	}

	fprintf(fp," %d %d %d\n",ix,iy,iz);

      }
@@ -3017,6 +3061,7 @@ void Data::write(FILE *fp, FILE *fp2) 
	if (style_full) write_vel_full(fp,i);

	if (style_granular) write_vel_granular(fp,i);

	if (style_molecular) write_vel_molecular(fp,i);

	if (style_peri) write_vel_peri(fp,i);

	fprintf(fp,"\n");



      } else {
@@ -3032,6 +3077,7 @@ void Data::write(FILE *fp, FILE *fp2) 
	  if (k == style_full) write_vel_full_extra(fp,i);

	  if (k == style_granular) write_vel_granular_extra(fp,i);

	  if (k == style_molecular) write_vel_molecular_extra(fp,i);

	  if (k == style_peri) write_vel_peri_extra(fp,i);

	}

	fprintf(fp,"\n");

      }
@@ -3134,6 +3180,12 @@ void Data::write_atom_molecular(FILE *fp, int i, int ix, int iy, int iz) 
	  tag[i],molecule[i],type[i],x[i],y[i],z[i],ix,iy,iz);

}



void Data::write_atom_peri(FILE *fp, int i, int ix, int iy, int iz)

{

  fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",

	  tag[i],type[i],vfrac[i],density[i],rmass[i],x[i],y[i],z[i],ix,iy,iz);

}



// ---------------------------------------------------------------------

// per-atom write routines of extra quantities unique to style

// one routine per atom style
@@ -3183,6 +3235,11 @@ void Data::write_atom_molecular_extra(FILE *fp, int i) 
  fprintf(fp," %d",molecule[i]);

}



void Data::write_atom_peri_extra(FILE *fp, int i)

{

  fprintf(fp," %-1.16e %-1.16e %-1.16e",vfrac[i],density[i],rmass[i]);

}



// ---------------------------------------------------------------------

// per-atom velocity write routines

// one routine per atom style
@@ -3240,6 +3297,11 @@ void Data::write_vel_molecular(FILE *fp, int i) 
  fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);

}



void Data::write_vel_peri(FILE *fp, int i)

{

  fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);

}



// ---------------------------------------------------------------------

// per-atom velocity write routines of extra quantities unique to style

// one routine per atom style
@@ -3265,6 +3327,7 @@ void Data::write_vel_granular_extra(FILE *fp, int i) 
}



void Data::write_vel_molecular_extra(FILE *fp, int i) {}

void Data::write_vel_peri_extra(FILE *fp, int i) {}



// ---------------------------------------------------------------------

// binary reads from restart file

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