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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@622 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-06-20 13:17:59 +00:00
parent bde732bced
commit aaed6ebc33
131 changed files with 4277 additions and 2222 deletions
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140
src/atom.cpp
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@ -61,7 +61,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
molecule = NULL;
q = NULL;
mu = NULL;
xphi = omega = torque = NULL;
xphi = quat = omega = angmom = torque = NULL;
radius = density = rmass = vfrac = NULL;
maxspecial = 1;
@ -82,12 +82,12 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
improper_type = improper_atom1 = improper_atom2 = NULL;
improper_atom3 = improper_atom4 = NULL;
hybrid = NULL;
// ntype-length arrays
mass = NULL;
mass_setflag = NULL;
shape = NULL;
shape_setflag = NULL;
dipole = NULL;
dipole_setflag = NULL;
@ -143,8 +143,11 @@ Atom::~Atom()
memory->sfree(q);
memory->destroy_2d_double_array(mu);
memory->destroy_2d_double_array(xphi);
memory->destroy_2d_double_array(quat);
memory->destroy_2d_double_array(omega);
memory->destroy_2d_double_array(angmom);
memory->destroy_2d_double_array(torque);
memory->sfree(radius);
memory->sfree(density);
memory->sfree(rmass);
@ -179,12 +182,12 @@ Atom::~Atom()
memory->destroy_2d_int_array(improper_atom3);
memory->destroy_2d_int_array(improper_atom4);
memory->sfree(hybrid);
// delete per-type arrays
delete [] mass;
delete [] mass_setflag;
memory->destroy_2d_double_array(shape);
delete [] shape_setflag;
delete [] dipole;
delete [] dipole_setflag;
@ -250,6 +253,7 @@ void Atom::init()
// check arrays that are atom type in length
check_mass();
check_shape();
check_dipole();
// init sub-style
@ -258,11 +262,11 @@ void Atom::init()
}
/* ----------------------------------------------------------------------
check if atom style matches style
if hybrid, any sub-style can be a match
return 1 if style matches atom style hybrid sub-style
else return 0
------------------------------------------------------------------------- */
int Atom::check_style(char *style)
int Atom::style_match(char *style)
{
if (strcmp(atom_style,style) == 0) return 1;
else if (strcmp(atom_style,"hybrid") == 0) {
@ -612,10 +616,10 @@ int Atom::count_words(char *line)
/* ----------------------------------------------------------------------
unpack n lines from Atom section of data file
set all atom values and defaults
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_atoms(int n, char *buf, int ihybrid)
void Atom::data_atoms(int n, char *buf)
{
int m,imagedata,xptr,iptr;
double xdata[3],lamda[3],sublo[3],subhi[3];
@ -627,7 +631,6 @@ void Atom::data_atoms(int n, char *buf, int ihybrid)
int nwords = count_words(buf);
*next = '\n';
avec->data_params(ihybrid);
if (nwords != avec->size_data_atom && nwords != avec->size_data_atom + 3)
error->all("Incorrect atom format in data file");
@ -671,7 +674,8 @@ void Atom::data_atoms(int n, char *buf, int ihybrid)
// loop over lines of atom data
// tokenize the line into values
// extract xyz coords and image flags, remap them
// extract xyz coords and image flags
// remap atom into simulation box
// if atom is in my sub-domain, unpack its values
for (int i = 0; i < n; i++) {
@ -699,7 +703,7 @@ void Atom::data_atoms(int n, char *buf, int ihybrid)
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2])
avec->data_atom(xdata,imagedata,values,ihybrid);
avec->data_atom(xdata,imagedata,values);
buf = next + 1;
}
@ -713,9 +717,9 @@ void Atom::data_atoms(int n, char *buf, int ihybrid)
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_vels(int n, char *buf, int ihybrid)
void Atom::data_vels(int n, char *buf)
{
int m,tagtmp;
int j,m,tagdata;
char *next;
next = strchr(buf,'\n');
@ -723,19 +727,31 @@ void Atom::data_vels(int n, char *buf, int ihybrid)
int nwords = count_words(buf);
*next = '\n';
avec->data_params(ihybrid);
if (nwords != avec->size_data_vel)
error->all("Incorrect velocity format in data file");
char **values = new char*[nwords];
// loop over lines of atom velocities
// tokenize the line into values
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d",&tagtmp);
if (tagtmp <= 0 || tagtmp > map_tag_max)
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
tagdata = atoi(values[0]);
if (tagdata <= 0 || tagdata > map_tag_max)
error->one("Invalid atom ID in Velocities section of data file");
if ((m = map(tagtmp)) >= 0) avec->data_vel(m,buf,ihybrid);
if ((m = map(tagdata)) >= 0) avec->data_vel(m,&values[1]);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
@ -950,6 +966,11 @@ void Atom::allocate_type_arrays()
mass_setflag = new int[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) mass_setflag[itype] = 0;
}
if (avec->shape_type) {
shape = memory->create_2d_double_array(ntypes+1,3,"atom:shape");
shape_setflag = new int[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) shape_setflag[itype] = 0;
}
if (avec->dipole_type) {
dipole = new double[ntypes+1];
dipole_setflag = new int[ntypes+1];
@ -968,7 +989,8 @@ void Atom::set_mass(char *str)
int itype;
double mass_one;
sscanf(str,"%d %lg",&itype,&mass_one);
int n = sscanf(str,"%d %lg",&itype,&mass_one);
if (n != 2) error->all("Invalid mass line in data file");
if (itype < 1 || itype > ntypes) error->all("Invalid type for mass set");
@ -1032,6 +1054,79 @@ void Atom::check_mass()
if (mass_setflag[itype] == 0) error->all("All masses are not set");
}
/* ----------------------------------------------------------------------
set particle shape and flag it as set
called from reading of data file
------------------------------------------------------------------------- */
void Atom::set_shape(char *str)
{
if (shape == NULL) error->all("Cannot set shape for this atom style");
int itype;
double a,b,c;
int n = sscanf(str,"%d %lg %lg %lg",&itype,&a,&b,&c);
if (n != 4) error->all("Invalid shape line in data file");
if (itype < 1 || itype > ntypes) error->all("Invalid type for shape set");
// store shape as radius, though specified as diameter
shape[itype][0] = 0.5*a;
shape[itype][1] = 0.5*b;
shape[itype][2] = 0.5*c;
shape_setflag[itype] = 1;
}
/* ----------------------------------------------------------------------
set one or more particle shapes and flag them as set
called from reading of input script
------------------------------------------------------------------------- */
void Atom::set_shape(int narg, char **arg)
{
if (shape == NULL) error->all("Cannot set shape for this atom style");
int lo,hi;
force->bounds(arg[0],ntypes,lo,hi);
if (lo < 1 || hi > ntypes)
error->all("Invalid type for shape set");
// store shape as radius, though specified as diameter
for (int itype = lo; itype <= hi; itype++) {
shape[itype][0] = 0.5*atof(arg[1]);
shape[itype][1] = 0.5*atof(arg[2]);
shape[itype][2] = 0.5*atof(arg[3]);
shape_setflag[itype] = 1;
}
}
/* ----------------------------------------------------------------------
set all particle shapes as read in from restart file
------------------------------------------------------------------------- */
void Atom::set_shape(double **values)
{
for (int itype = 1; itype <= ntypes; itype++) {
shape[itype][0] = values[itype][0];
shape[itype][1] = values[itype][1];
shape[itype][2] = values[itype][2];
shape_setflag[itype] = 1;
}
}
/* ----------------------------------------------------------------------
check that all particle shapes have been set
------------------------------------------------------------------------- */
void Atom::check_shape()
{
if (shape == NULL) return;
for (int itype = 1; itype <= ntypes; itype++)
if (shape_setflag[itype] == 0) error->all("All shapes are not set");
}
/* ----------------------------------------------------------------------
set a dipole moment and flag it as set
called from reading of data file
@ -1043,7 +1138,8 @@ void Atom::set_dipole(char *str)
int i;
double dipole_one;
sscanf(str,"%d %lg",&i,&dipole_one);
int n = sscanf(str,"%d %lg",&i,&dipole_one);
if (n != 2) error->all("Invalid shape line in data file");
dipole[i] = dipole_one;
dipole_setflag[i] = 1;