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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5947 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-04-15 22:25:19 +00:00
parent 74c219743e
commit 8ff0659bae
62 changed files with 1016 additions and 822 deletions
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113
src/atom.cpp
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@ -19,6 +19,7 @@
#include "atom.h"
#include "style_atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "neighbor.h"
#include "force.h"
@ -70,11 +71,11 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
molecule = NULL;
q = NULL;
mu = NULL;
quat = omega = angmom = torque = shape = NULL;
omega = angmom = torque = NULL;
radius = rmass = NULL;
vfrac = s0 = NULL;
x0 = NULL;
ellipsoid = NULL;
spin = NULL;
eradius = ervel = erforce = NULL;
@ -102,8 +103,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
sphere_flag = ellipsoid_flag = peri_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;
rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
// ntype-length arrays
@ -167,18 +167,15 @@ 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(rmass);
memory->destroy(vfrac);
memory->destroy(s0);
memory->destroy(x0);
memory->destroy(ellipsoid);
memory->destroy(spin);
memory->destroy(eradius);
memory->destroy(ervel);
@ -256,8 +253,7 @@ void Atom::create_avec(const char *style, int narg, char **arg)
sphere_flag = ellipsoid_flag = peri_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;
rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
avec = new_avec(style,narg,arg);
@ -329,19 +325,20 @@ void Atom::setup()
}
/* ----------------------------------------------------------------------
return 1 if style matches atom style or hybrid sub-style
else return 0
return ptr to AtomVec class if matches style or to matching hybrid sub-class
return NULL if no match
------------------------------------------------------------------------- */
int Atom::style_match(const char *style)
AtomVec *Atom::style_match(const char *style)
{
if (strcmp(atom_style,style) == 0) return 1;
if (strcmp(atom_style,style) == 0) return avec;
else if (strcmp(atom_style,"hybrid") == 0) {
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) avec;
for (int i = 0; i < avec_hybrid->nstyles; i++)
if (strcmp(avec_hybrid->keywords[i],style) == 0) return 1;
if (strcmp(avec_hybrid->keywords[i],style) == 0)
return avec_hybrid->styles[i];
}
return 0;
return NULL;
}
/* ----------------------------------------------------------------------
@ -847,6 +844,53 @@ void Atom::data_vels(int n, char *buf)
delete [] values;
}
/* ----------------------------------------------------------------------
unpack n lines from atom-style specific section of data file
check that atom IDs are > 0 and <= map_tag_max
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
{
int j,m,tagdata;
char *next;
next = strchr(buf,'\n');
*next = '\0';
int nwords = count_words(buf);
*next = '\n';
if (nwords != avec_bonus->size_data_bonus)
error->all("Incorrect bonus data format in data file");
char **values = new char*[nwords];
// loop over lines of bonus atom data
// tokenize the line into values
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
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 Bonus section of data file");
// ok to call child's data_atom_bonus() method thru parent avec_bonus,
// since data_bonus() was called with child ptr, and method is virtual
if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,&values[1]);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
@ -1170,23 +1214,32 @@ int Atom::radius_consistency(int itype, double &rad)
/* ----------------------------------------------------------------------
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
also return the 3 shape params for itype
------------------------------------------------------------------------- */
int Atom::shape_consistency(int itype,
double &shapex, double &shapey, double &shapez)
{
double one[3];
one[0] = one[1] = one[2] = -1.0;
double zero[3] = {0.0, 0.0, 0.0};
double one[3] = {-1.0, -1.0, -1.0};
double *shape;
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (type[i] != itype) continue;
if (ellipsoid[i] < 0) shape = zero;
else shape = bonus[ellipsoid[i]].shape;
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;
one[0] = shape[0];
one[1] = shape[1];
one[2] = shape[2];
} else if (one[0] != shape[0] || one[1] != shape[1] || one[2] != shape[2])
flag = 1;
}
int flagall;
@ -1223,9 +1276,9 @@ void Atom::first_reorder()
for (int i = 0; i < nlocal; i++) {
if (mask[i] & bitmask && i > nfirst) {
avec->copy(i,nlocal);
avec->copy(nfirst,i);
avec->copy(nlocal,nfirst);
avec->copy(i,nlocal,0);
avec->copy(nfirst,i,0);
avec->copy(nlocal,nfirst,0);
while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;
}
}
@ -1310,13 +1363,13 @@ void Atom::sort()
for (i = 0; i < nlocal; i++) {
if (current[i] == permute[i]) continue;
avec->copy(i,nlocal);
avec->copy(i,nlocal,0);
empty = i;
while (permute[empty] != i) {
avec->copy(permute[empty],empty);
avec->copy(permute[empty],empty,0);
empty = current[empty] = permute[empty];
}
avec->copy(nlocal,empty);
avec->copy(nlocal,empty,0);
current[empty] = permute[empty];
}