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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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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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320
src/atom_vec_hybrid.cpp
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@ -1,4 +1,3 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
@ -12,6 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "atom_vec_hybrid.h"
#include "atom.h"
@ -33,7 +33,7 @@ using namespace LAMMPS_NS;
AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
int i,m;
int i,k;
if (narg < 1) error->all("Illegal atom_style command");
@ -44,8 +44,8 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
keywords = new char*[nstyles];
for (i = 0; i < narg; i++) {
for (m = 0; m < i; m++)
if (strcmp(arg[i],keywords[m]) == 0)
for (k = 0; k < i; k++)
if (strcmp(arg[i],keywords[k]) == 0)
error->all("Atom style hybrid cannot use same atom style twice");
if (strcmp(arg[i],"hybrid") == 0)
error->all("Atom style hybrid cannot have hybrid as an argument");
@ -55,21 +55,31 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
}
// hybrid settings are MAX or MIN of sub-style settings
// size_border has +1 for hybrid[] value that is also communicated
// hybrid sizes are minimial values plus extra values for each sub-style
for (m = 0; m < nstyles; m++) {
molecular = MAX(molecular,styles[m]->molecular);
bonds_allow = MAX(bonds_allow,styles[m]->bonds_allow);
angles_allow = MAX(angles_allow,styles[m]->angles_allow);
dihedrals_allow = MAX(dihedrals_allow,styles[m]->dihedrals_allow);
impropers_allow = MAX(impropers_allow,styles[m]->impropers_allow);
mass_type = MAX(mass_type,styles[m]->mass_type);
dipole_type = MAX(dipole_type,styles[m]->dipole_type);
comm_x_only = MIN(comm_x_only,styles[m]->comm_x_only);
comm_f_only = MIN(comm_f_only,styles[m]->comm_f_only);
size_comm = MAX(size_comm,styles[m]->size_comm);
size_reverse = MAX(size_reverse,styles[m]->size_reverse);
size_border = MAX(size_border,styles[m]->size_border) + 1;
size_comm = 3;
size_reverse = 3;
size_border = 6;
size_data_atom = 5;
size_data_vel = 4;
xcol_data = 3;
for (k = 0; k < nstyles; k++) {
molecular = MAX(molecular,styles[k]->molecular);
bonds_allow = MAX(bonds_allow,styles[k]->bonds_allow);
angles_allow = MAX(angles_allow,styles[k]->angles_allow);
dihedrals_allow = MAX(dihedrals_allow,styles[k]->dihedrals_allow);
impropers_allow = MAX(impropers_allow,styles[k]->impropers_allow);
mass_type = MAX(mass_type,styles[k]->mass_type);
shape_type = MAX(shape_type,styles[k]->shape_type);
dipole_type = MAX(dipole_type,styles[k]->dipole_type);
comm_x_only = MIN(comm_x_only,styles[k]->comm_x_only);
comm_f_only = MIN(comm_f_only,styles[k]->comm_f_only);
size_comm += styles[k]->size_comm - 3;
size_reverse += styles[k]->size_reverse - 3;
size_border += styles[k]->size_border - 6;
size_data_atom += styles[k]->size_data_atom - 5;
size_data_vel += styles[k]->size_data_vel - 4;
}
}
@ -77,9 +87,9 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
AtomVecHybrid::~AtomVecHybrid()
{
for (int m = 0; m < nstyles; m++) delete styles[m];
for (int k = 0; k < nstyles; k++) delete styles[k];
delete [] styles;
for (int m = 0; m < nstyles; m++) delete [] keywords[m];
for (int k = 0; k < nstyles; k++) delete [] keywords[k];
delete [] keywords;
}
@ -97,7 +107,7 @@ void AtomVecHybrid::grow(int n)
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
for (int m = 0; m < nstyles; m++) styles[m]->grow(nmax);
for (int k = 0; k < nstyles; k++) styles[k]->grow(nmax);
atom->nextra_grow = tmp;
// pointers for arrays used directly by hybrid style
@ -110,9 +120,6 @@ void AtomVecHybrid::grow(int n)
v = atom->v;
f = atom->f;
hybrid = atom->hybrid = (int *)
memory->srealloc(atom->hybrid,nmax*sizeof(int),"atom:hybrid");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
@ -120,33 +127,25 @@ void AtomVecHybrid::grow(int n)
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::reset_ptrs()
void AtomVecHybrid::reset_special()
{
for (int m = 0; m < nstyles; m++) styles[m]->reset_ptrs();
tag = atom->tag;
type = atom->type;
mask = atom->mask;
image = atom->image;
x = atom->x;
v = atom->v;
f = atom->f;
hybrid = atom->hybrid;
for (int k = 0; k < nstyles; k++) styles[k]->reset_special();
}
/* ----------------------------------------------------------------------
copy array values based on hybrid style of atom i
zero auxiliary arrays for all other styles before copy
copy array values for all sub-styles
------------------------------------------------------------------------- */
void AtomVecHybrid::copy(int i, int j)
{
int ihybrid = hybrid[i];
for (int m = 0; m < nstyles; m++)
if (m != ihybrid) styles[m]->zero_owned(j);
styles[ihybrid]->copy(i,j);
hybrid[j] = ihybrid;
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
for (int k = 0; k < nstyles; k++) styles[k]->copy(i,j);
atom->nextra_grow = tmp;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
@ -154,7 +153,7 @@ void AtomVecHybrid::copy(int i, int j)
int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
int i,j,k,m;
double dx,dy,dz;
m = 0;
@ -164,7 +163,8 @@ int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
m += styles[hybrid[j]]->pack_comm_one(j,&buf[m]);
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_one(j,&buf[m]);
}
} else {
if (domain->triclinic == 0) {
@ -181,7 +181,8 @@ int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
m += styles[hybrid[j]]->pack_comm_one(j,&buf[m]);
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_one(j,&buf[m]);
}
}
return m;
@ -191,15 +192,16 @@ int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
void AtomVecHybrid::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
int i,k,last;
m = 0;
int m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
m += styles[hybrid[i]]->unpack_comm_one(i,&buf[m]);
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_comm_one(i,&buf[m]);
}
}
@ -207,15 +209,16 @@ void AtomVecHybrid::unpack_comm(int n, int first, double *buf)
int AtomVecHybrid::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
int i,k,last;
m = 0;
int m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
m += styles[hybrid[i]]->pack_reverse_one(i,&buf[m]);
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_reverse_one(i,&buf[m]);
}
return m;
}
@ -224,7 +227,7 @@ int AtomVecHybrid::pack_reverse(int n, int first, double *buf)
void AtomVecHybrid::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
int i,j,k,m;
m = 0;
for (i = 0; i < n; i++) {
@ -232,7 +235,8 @@ void AtomVecHybrid::unpack_reverse(int n, int *list, double *buf)
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
m += styles[hybrid[j]]->unpack_reverse_one(j,&buf[m]);
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_reverse_one(j,&buf[m]);
}
}
@ -241,7 +245,7 @@ void AtomVecHybrid::unpack_reverse(int n, int *list, double *buf)
int AtomVecHybrid::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
int i,j,k,m;
double dx,dy,dz;
m = 0;
@ -254,8 +258,8 @@ int AtomVecHybrid::pack_border(int n, int *list, double *buf,
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = hybrid[j];
m += styles[hybrid[j]]->pack_border_one(j,&buf[m]);
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_one(j,&buf[m]);
}
} else {
if (domain->triclinic == 0) {
@ -275,24 +279,18 @@ int AtomVecHybrid::pack_border(int n, int *list, double *buf,
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = hybrid[j];
m += styles[hybrid[j]]->pack_border_one(j,&buf[m]);
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_one(j,&buf[m]);
}
}
return m;
}
/* ----------------------------------------------------------------------
unpack border ghost atom data
zero auxiliary ghost arrays for all styles before unpack
grow() is called in zero_ghost() and here (in case zero_ghost is no-op)
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_border(int n, int first, double *buf)
{
int i,m,last;
for (m = 0; m < nstyles; m++) styles[m]->zero_ghost(n,first);
int i,k,m,last;
m = 0;
last = first + n;
@ -304,30 +302,40 @@ void AtomVecHybrid::unpack_border(int n, int first, double *buf)
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
hybrid[i] = static_cast<int> (buf[m++]);
m += styles[hybrid[i]]->unpack_border_one(i,&buf[m]);
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_border_one(i,&buf[m]);
}
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
sub-style does packing
append hybrid[i] and increment count stored in buf[0]
pack each sub-style one after the other
------------------------------------------------------------------------- */
int AtomVecHybrid::pack_exchange(int i, double *buf)
{
int m = styles[hybrid[i]]->pack_exchange(i,buf);
buf[m++] = hybrid[i];
buf[0] = m;
int k;
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
int m = 0;
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_exchange(i,&buf[m]);
atom->nextra_grow = tmp;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
return m;
}
/* ----------------------------------------------------------------------
unpack data for single atom received from another proc
sub-style does unpacking
grow() must occur here so arrays for all sub-styles are grown
extract hybrid[nlocal] from end of buf
unpack each sub-style one after the other
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
int AtomVecHybrid::unpack_exchange(double *buf)
@ -335,9 +343,23 @@ int AtomVecHybrid::unpack_exchange(double *buf)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = static_cast<int> (buf[0]);
hybrid[nlocal] = static_cast<int> (buf[m-1]);
int tmp = styles[hybrid[nlocal]]->unpack_exchange(buf);
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
int m = 0;
for (int k = 0; k < nstyles; k++) {
m += styles[k]->unpack_exchange(buf);
atom->nlocal--;
}
atom->nextra_grow = tmp;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
@ -348,19 +370,19 @@ int AtomVecHybrid::unpack_exchange(double *buf)
int AtomVecHybrid::size_restart()
{
int i;
int nlocal = atom->nlocal;
// nlocal is added for per-atom hybrid value appended by pack_restart()
int tmp = atom->nextra_restart;
atom->nextra_restart = 0;
int n = 0;
for (i = 0; i < nlocal; i++)
n += styles[hybrid[i]]->size_restart_one(i);
n += nlocal;
for (int k = 0; k < nstyles; k++)
n += styles[k]->size_restart();
atom->nextra_restart = tmp;
int nlocal = atom->nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
for (int i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
@ -368,24 +390,33 @@ int AtomVecHybrid::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
sub-style does packing
append hybrid[i] and increment count stored in buf[0]
xyz must be 1st 3 values, so that read_restart can test on them
pack each sub-style one after the other
------------------------------------------------------------------------- */
int AtomVecHybrid::pack_restart(int i, double *buf)
{
int m = styles[hybrid[i]]->pack_restart(i,buf);
buf[m++] = hybrid[i];
int tmp = atom->nextra_restart;
atom->nextra_restart = 0;
int m = 0;
for (int k = 0; k < nstyles; k++)
m += styles[k]->pack_restart(i,&buf[m]);
atom->nextra_restart = tmp;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
sub-style does unpacking
grow() must occur here so arrays for all sub-styles are grown
zero auxiliary arrays for all other styles before unpack
extract hybrid[nlocal] from end of buf
unpack each sub-style one after the other
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
int AtomVecHybrid::unpack_restart(double *buf)
@ -399,74 +430,93 @@ int AtomVecHybrid::unpack_restart(double *buf)
"atom:extra");
}
int m = static_cast<int> (buf[0]);
int ihybrid = static_cast<int> (buf[m-1]);
for (int m = 0; m < nstyles; m++)
if (m != ihybrid) styles[m]->zero_owned(nlocal);
hybrid[nlocal] = ihybrid;
int tmp = atom->nextra_store;
atom->nextra_store = 0;
// size of extra unpack in sub-style includes end-of-buf entry of hybrid
// avoid this by resetting buf[0] to one less
int m = 0;
for (int k = 0; k < nstyles; k++) {
m += styles[k]->unpack_restart(&buf[m]);
atom->nlocal--;
}
atom->nextra_store = tmp;
buf[0] = m-1;
int tmp = styles[ihybrid]->unpack_restart(buf);
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord for ihybrid style
sub-style does create
grow() must occur here so arrays for all sub-styles are grown
zero auxiliary arrays for all other styles before create
create one atom of itype at coord
create each sub-style one after the other
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
void AtomVecHybrid::create_atom(int itype, double *coord, int ihybrid)
void AtomVecHybrid::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
for (int m = 0; m < nstyles; m++)
if (m != ihybrid) styles[m]->zero_owned(nlocal);
hybrid[nlocal] = ihybrid;
styles[ihybrid]->create_atom(itype,coord,0);
for (int k = 0; k < nstyles; k++) {
styles[k]->create_atom(itype,coord);
atom->nlocal--;
}
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
zero auxiliary arrays for all other styles before unpack
sub-style will increment nlocal
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
void AtomVecHybrid::data_atom(double *coord, int imagetmp, char **values,
int ihybrid)
void AtomVecHybrid::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
for (int m = 0; m < nstyles; m++)
if (m != ihybrid) styles[m]->zero_owned(nlocal);
hybrid[nlocal] = ihybrid;
styles[ihybrid]->data_atom(coord,imagetmp,values,0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
// each sub-style parses sub-style specific values
int m = 5;
for (int k = 0; k < nstyles; k++)
m += styles[k]->data_atom_hybrid(nlocal,&values[m]);
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecHybrid::data_vel(int m, char *line, int ihybrid)
void AtomVecHybrid::data_vel(int m, char **values)
{
styles[ihybrid]->data_vel(m,line,0);
}
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
/* ----------------------------------------------------------------------
set data file parameters for ihybrid sub-style
------------------------------------------------------------------------- */
// each sub-style parses sub-style specific values
void AtomVecHybrid::data_params(int ihybrid)
{
size_data_atom = styles[ihybrid]->size_data_atom;
size_data_vel = styles[ihybrid]->size_data_vel;
xcol_data = styles[ihybrid]->xcol_data;
int n = 3;
for (int k = 0; k < nstyles; k++)
n += styles[k]->data_vel_hybrid(m,&values[n]);
}
/* ----------------------------------------------------------------------
@ -476,8 +526,6 @@ void AtomVecHybrid::data_params(int ihybrid)
int AtomVecHybrid::memory_usage()
{
int bytes = 0;
for (int m = 0; m < nstyles; m++)
bytes += styles[m]->memory_usage();
if (atom->memcheck("hybrid")) bytes += nmax * sizeof(int);
for (int k = 0; k < nstyles; k++) bytes += styles[k]->memory_usage();
return bytes;
}