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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5932 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-04-13 21:40:14 +00:00
parent e45fbd89d1
commit 819524ebd6
71 changed files with 1167 additions and 2718 deletions
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237
src/atom.cpp
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@ -70,8 +70,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
molecule = NULL;
q = NULL;
mu = NULL;
quat = omega = angmom = torque = NULL;
radius = density = rmass = NULL;
quat = omega = angmom = torque = shape = NULL;
radius = rmass = NULL;
vfrac = s0 = NULL;
x0 = NULL;
@ -96,23 +96,20 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
improper_type = improper_atom1 = improper_atom2 = NULL;
improper_atom3 = improper_atom4 = NULL;
// initialize atom array existence flags
// initialize atom style and array existence flags
// customize by adding new flag
molecule_flag = 0;
q_flag = mu_flag = 0;
quat_flag = omega_flag = angmom_flag = torque_flag = 0;
radius_flag = density_flag = rmass_flag = vfrac_flag = 0;
spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
sphere_flag = ellipsoid_flag = peri_flag = dipole_flag = electron_flag = 0;
molecule_flag = q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = 0;
quat_flag = shape_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
// ntype-length arrays
mass = NULL;
mass_setflag = NULL;
shape = NULL;
shape_setflag = NULL;
dipole = NULL;
dipole_setflag = NULL;
// callback lists & extra restart info
@ -171,12 +168,12 @@ Atom::~Atom()
memory->destroy(q);
memory->destroy(mu);
memory->destroy(quat);
memory->destroy(shape);
memory->destroy(omega);
memory->destroy(angmom);
memory->destroy(torque);
memory->destroy(radius);
memory->destroy(density);
memory->destroy(rmass);
memory->destroy(vfrac);
memory->destroy(s0);
@ -220,10 +217,6 @@ Atom::~Atom()
delete [] mass;
delete [] mass_setflag;
memory->destroy(shape);
delete [] shape_setflag;
delete [] dipole;
delete [] dipole_setflag;
// delete extra arrays
@ -256,14 +249,16 @@ void Atom::create_avec(const char *style, int narg, char **arg)
delete [] atom_style;
if (avec) delete avec;
// unset atom array existence flags that may have been set by old avec
// unset atom style and array existence flags
// may have been set by old avec
// customize by adding new flag
molecule_flag = 0;
q_flag = mu_flag = 0;
quat_flag = omega_flag = angmom_flag = torque_flag = 0;
radius_flag = density_flag = rmass_flag = vfrac_flag = 0;
spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
sphere_flag = ellipsoid_flag = peri_flag = dipole_flag = electron_flag = 0;
molecule_flag = q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = 0;
quat_flag = shape_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
avec = new_avec(style,narg,arg);
int n = strlen(style) + 1;
@ -309,8 +304,6 @@ void Atom::init()
// check arrays that are atom type in length
check_mass();
check_shape();
check_dipole();
// setup of firstgroup
@ -1066,16 +1059,6 @@ 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) {
memory->create(shape,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];
for (int itype = 1; itype <= ntypes; itype++) dipole_setflag[itype] = 0;
}
}
/* ----------------------------------------------------------------------
@ -1161,161 +1144,61 @@ void Atom::check_mass()
}
/* ----------------------------------------------------------------------
set particle shape and flag it as set
called from reading of data file
check that radii of all particles of itype are the same
return 1 if true, else return 0
also return the radius value for that type
------------------------------------------------------------------------- */
void Atom::set_shape(const char *str)
int Atom::radius_consistency(int itype, double &rad)
{
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;
if (shape[itype][0] < 0.0 || shape[itype][1] < 0.0 ||
shape[itype][2] < 0.0)
error->all("Invalid shape value");
if (shape[itype][0] > 0.0 || shape[itype][1] > 0.0 ||
shape[itype][2] > 0.0) {
if (shape[itype][0] == 0.0 || shape[itype][1] == 0.0 ||
shape[itype][2] == 0.0)
error->all("Invalid shape value");
double value = -1.0;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (type[i] != itype) continue;
if (value < 0.0) value = radius[i];
else if (value != radius[i]) flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) return 0;
MPI_Allreduce(&value,&rad,1,MPI_DOUBLE,MPI_MAX,world);
return 1;
}
/* ----------------------------------------------------------------------
set one or more particle shapes and flag them as set
called from reading of input script
check that shape of all particles of itype are the same
return 1 if true, else return 0
also return the radius value for that type
------------------------------------------------------------------------- */
void Atom::set_shape(int narg, char **arg)
int Atom::shape_consistency(int itype,
double &shapex, double &shapey, double &shapez)
{
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;
if (shape[itype][0] < 0.0 || shape[itype][1] < 0.0 ||
shape[itype][2] < 0.0)
error->all("Invalid shape value");
if (shape[itype][0] > 0.0 || shape[itype][1] > 0.0 ||
shape[itype][2] > 0.0) {
if (shape[itype][0] == 0.0 || shape[itype][1] == 0.0 ||
shape[itype][2] == 0.0)
error->all("Invalid shape value");
}
double one[3];
one[0] = one[1] = one[2] = -1.0;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (type[i] != itype) continue;
if (one[0] < 0.0) {
one[0] = shape[i][0];
one[1] = shape[i][1];
one[2] = shape[i][2];
} else if (one[0] != shape[i][0] || one[1] != shape[i][1] ||
one[2] != shape[i][2]) flag = 1;
}
}
/* ----------------------------------------------------------------------
set all particle shapes as read in from restart file
------------------------------------------------------------------------- */
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) return 0;
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
------------------------------------------------------------------------- */
void Atom::set_dipole(const char *str)
{
if (dipole == NULL) error->all("Cannot set dipole for this atom style");
int itype;
double dipole_one;
int n = sscanf(str,"%d %lg",&itype,&dipole_one);
if (n != 2) error->all("Invalid dipole line in data file");
dipole[itype] = dipole_one;
dipole_setflag[itype] = 1;
if (dipole[itype] < 0.0) error->all("Invalid dipole value");
}
/* ----------------------------------------------------------------------
set one or more dipole moments and flag them as set
called from reading of input script
------------------------------------------------------------------------- */
void Atom::set_dipole(int narg, char **arg)
{
if (dipole == NULL) error->all("Cannot set dipole for this atom style");
int lo,hi;
force->bounds(arg[0],ntypes,lo,hi);
if (lo < 1 || hi > ntypes) error->all("Invalid type for dipole set");
for (int itype = lo; itype <= hi; itype++) {
dipole[itype] = atof(arg[1]);
dipole_setflag[itype] = 1;
if (dipole[itype] < 0.0) error->all("Invalid dipole value");
}
}
/* ----------------------------------------------------------------------
set all dipole moments as read in from restart file
------------------------------------------------------------------------- */
void Atom::set_dipole(double *values)
{
for (int itype = 1; itype <= ntypes; itype++) {
dipole[itype] = values[itype];
dipole_setflag[itype] = 1;
}
}
/* ----------------------------------------------------------------------
check that all dipole moments have been set
------------------------------------------------------------------------- */
void Atom::check_dipole()
{
if (dipole == NULL) return;
for (int itype = 1; itype <= ntypes; itype++)
if (dipole_setflag[itype] == 0)
error->all("All dipole moments are not set");
double oneall[3];
MPI_Allreduce(one,oneall,3,MPI_DOUBLE,MPI_MAX,world);
shapex = oneall[0];
shapey = oneall[1];
shapez = oneall[2];
return 1;
}
/* ----------------------------------------------------------------------