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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3674 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2010-01-13 20:55:06 +00:00
parent 363e6c371f
commit 1dbad849b7
7 changed files with 39 additions and 29 deletions
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35
src/atom.cpp
View File

@ -52,6 +52,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
extra_bond_per_atom = 0;
firstgroupname = NULL;
sortfreq = 0;
maxbin = maxnext = 0;
binhead = NULL;
next = permute = NULL;
// initialize atom arrays
// customize by adding new array
@ -110,13 +114,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
nextra_store = 0;
extra = NULL;
// sorting
sortflag = 0;
maxbin = maxnext = 0;
binhead = NULL;
next = permute = NULL;
// default mapping values and hash table primes
tag_enable = 1;
@ -146,7 +143,11 @@ Atom::~Atom()
{
delete [] atom_style;
delete avec;
delete [] firstgroupname;
memory->sfree(binhead);
memory->sfree(next);
memory->sfree(permute);
// delete atom arrays
// customize by adding new array
@ -211,12 +212,6 @@ Atom::~Atom()
delete [] dipole;
delete [] dipole_setflag;
// delete sorting arrays
memory->sfree(binhead);
memory->sfree(next);
memory->sfree(permute);
// delete extra arrays
memory->sfree(extra_grow);
@ -315,7 +310,7 @@ void Atom::setup()
// setup for sorting
// binsize = user setting or 1/2 of neighbor cutoff
if (sortflag) {
if (sortfreq > 0) {
double binsize;
if (userbinsize > 0.0) binsize = userbinsize;
else binsize = 0.5 * neighbor->cutneighmax;
@ -341,6 +336,8 @@ int Atom::style_match(const char *style)
/* ----------------------------------------------------------------------
modify parameters of the atom style
some options can only be invoked before simulation box is defined
first and sort options cannot be used together
------------------------------------------------------------------------- */
void Atom::modify_params(int narg, char **arg)
@ -354,6 +351,8 @@ void Atom::modify_params(int narg, char **arg)
if (strcmp(arg[iarg+1],"array") == 0) map_style = 1;
else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
else error->all("Illegal atom_modify command");
if (domain->box_exist)
error->all("Atom_modify map command after simulation box is defined");
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all("Illegal atom_modify command");
@ -363,6 +362,7 @@ void Atom::modify_params(int narg, char **arg)
firstgroupname = new char[n];
strcpy(firstgroupname,arg[iarg+1]);
}
sortfreq = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+3 > narg) error->all("Illegal atom_modify command");
@ -370,8 +370,9 @@ void Atom::modify_params(int narg, char **arg)
userbinsize = atof(arg[iarg+2]);
if (sortfreq < 0 || userbinsize < 0.0)
error->all("Illegal atom_modify command");
if (sortfreq == 0) sortflag = 0;
else sortflag = 1;
if (sortfreq >= 0 && firstgroupname)
error->all("Atom_modify sort and first options "
"cannot be used together");
iarg += 3;
} else error->all("Illegal atom_modify command");
}
@ -1370,7 +1371,7 @@ void Atom::sort()
permute = (int *) memory->smalloc(maxnext*sizeof(int),"atom:permute");
}
// insure one extra location at end of atom arrays
// insure there is one extra atom location at end of arrays for swaps
if (nlocal == nmax) avec->grow(0);

3
src/atom.h
View File

@ -102,7 +102,7 @@ class Atom : protected Pointers {
// spatial sorting of atoms
int sortflag; // 0 = off, 1 = on
int sortfreq; // sort atoms every this many steps, 0 = off
int nextsort; // next timestep to sort on
// functions
@ -203,7 +203,6 @@ class Atom : protected Pointers {
int *permute; // permutation vector
double userbinsize; // sorting bin size
double bininv;
int sortfreq;
int memlength; // allocated size of memstr
char *memstr; // string of array names already counted

4
src/compute_pressure.cpp
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@ -172,7 +172,7 @@ double ComputePressure::compute_scalar()
double t;
if (keflag) {
if (temperature->invoked_scalar == update->ntimestep)
if (temperature->invoked_scalar != update->ntimestep)
t = temperature->compute_scalar();
else t = temperature->scalar;
}
@ -209,7 +209,7 @@ void ComputePressure::compute_vector()
if (update->vflag_global != invoked_vector)
error->all("Virial was not tallied on needed timestep");
// invoke temperature it it hasn't been already
// invoke temperature if it hasn't been already
double *ke_tensor;
if (keflag) {

2
src/input.cpp
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@ -691,8 +691,6 @@ void Input::angle_style()
void Input::atom_modify()
{
if (domain->box_exist)
error->all("Atom_modify command after simulation box is defined");
atom->modify_params(narg,arg);
}

10
src/modify.cpp
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@ -192,12 +192,20 @@ void Modify::init()
list_init_compute();
// init each compute
// set invoked_scalar,vector,etc to -1 to force new run to re-compute them
// add initial timestep to all computes that store invocation times
// since any of them may be invoked by initial thermo
// do not clear out invocation times stored within a compute,
// b/c some may be holdovers from previous run, like for ave fixes
for (i = 0; i < ncompute; i++) compute[i]->init();
for (i = 0; i < ncompute; i++) {
compute[i]->init();
compute[i]->invoked_scalar = -1;
compute[i]->invoked_vector = -1;
compute[i]->invoked_array = -1;
compute[i]->invoked_peratom = -1;
compute[i]->invoked_local = -1;
}
addstep_compute_all(update->ntimestep);
// warn if any particle is time integrated more than once

4
src/update.cpp
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@ -222,7 +222,8 @@ void Update::create_minimize(int narg, char **arg)
do not allow any timestep-dependent fixes to be defined
do not allow any dynamic regions to be defined
reset eflag/vflag global so nothing will think eng/virial are current
reset invoked flags of computes, so nothing will think they are current
reset invoked flags of computes,
so nothing will think they are current between runs
clear timestep list of computes that store future invocation times
------------------------------------------------------------------------- */
@ -249,6 +250,7 @@ void Update::reset_timestep(int narg, char **arg)
for (int i = 0; i < modify->ncompute; i++) {
modify->compute[i]->invoked_scalar = -1;
modify->compute[i]->invoked_vector = -1;
modify->compute[i]->invoked_array = -1;
modify->compute[i]->invoked_peratom = -1;
modify->compute[i]->invoked_local = -1;
}

10
src/verlet.cpp
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@ -92,7 +92,7 @@ void Verlet::setup()
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atom->sortflag) atom->sort();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
@ -178,7 +178,7 @@ void Verlet::setup_minimal(int flag)
void Verlet::run(int n)
{
int nflag,ntimestep;
int nflag,ntimestep,sortflag;
int n_post_integrate = modify->n_post_integrate;
int n_pre_exchange = modify->n_pre_exchange;
@ -186,7 +186,9 @@ void Verlet::run(int n)
int n_pre_force = modify->n_pre_force;
int n_post_force = modify->n_post_force;
int n_end_of_step = modify->n_end_of_step;
int sortflag = atom->sortflag;
if (atom->sortfreq > 0) sortflag = 1;
else sortflag = 0;
for (int i = 0; i < n; i++) {
@ -217,7 +219,7 @@ void Verlet::run(int n)
}
timer->stamp();
comm->exchange();
if (sortflag && ntimestep > atom->nextsort) atom->sort();
if (sortflag && ntimestep >= atom->nextsort) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(TIME_COMM);