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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7003 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-09-23 18:06:55 +00:00
parent 2d99de131d
commit 19e8c92a90
468 changed files with 4628 additions and 5204 deletions
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85
src/neighbor.cpp
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@ -49,9 +49,6 @@ using namespace LAMMPS_NS;
#define BIG 1.0e20
#define CUT2BIN_RATIO 100
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
enum{NSQ,BIN,MULTI}; // also in neigh_list.cpp
//#define NEIGH_LIST_DEBUG 1
@ -196,10 +193,10 @@ void Neighbor::init()
// error check
if (delay > 0 && (delay % every) != 0)
error->all("Neighbor delay must be 0 or multiple of every setting");
error->all(FLERR,"Neighbor delay must be 0 or multiple of every setting");
if (pgsize < 10*oneatom)
error->all("Neighbor page size must be >= 10x the one atom setting");
error->all(FLERR,"Neighbor page size must be >= 10x the one atom setting");
// ------------------------------------------------------------------
// settings
@ -382,7 +379,7 @@ void Neighbor::init()
for (i = 0; i < nex_type; i++) {
if (ex1_type[i] <= 0 || ex1_type[i] > n ||
ex2_type[i] <= 0 || ex2_type[i] > n)
error->all("Invalid atom type in neighbor exclusion list");
error->all(FLERR,"Invalid atom type in neighbor exclusion list");
ex_type[ex1_type[i]][ex2_type[i]] = 1;
ex_type[ex2_type[i]][ex1_type[i]] = 1;
}
@ -857,16 +854,16 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
if (style == NSQ) {
if (rq->ghost == 0) pb = &Neighbor::full_nsq;
else if (includegroup)
error->all("Neighbor include group not allowed with ghost neighbors");
error->all(FLERR,"Neighbor include group not allowed with ghost neighbors");
else if (rq->ghost == 1) pb = &Neighbor::full_nsq_ghost;
} else if (style == BIN) {
if (rq->ghost == 0) pb = &Neighbor::full_bin;
else if (includegroup)
error->all("Neighbor include group not allowed with ghost neighbors");
error->all(FLERR,"Neighbor include group not allowed with ghost neighbors");
else if (rq->ghost == 1) pb = &Neighbor::full_bin_ghost;
} else if (style == MULTI) {
if (rq->ghost == 0) pb = &Neighbor::full_multi;
else error->all("Neighbor multi not yet enabled for ghost neighbors");
else error->all(FLERR,"Neighbor multi not yet enabled for ghost neighbors");
}
} else if (rq->gran) {
@ -878,7 +875,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else if (triclinic == 0) pb = &Neighbor::granular_bin_newton;
else if (triclinic == 1) pb = &Neighbor::granular_bin_newton_tri;
} else if (style == MULTI)
error->all("Neighbor multi not yet enabled for granular");
error->all(FLERR,"Neighbor multi not yet enabled for granular");
} else if (rq->respaouter) {
if (style == NSQ) {
@ -889,13 +886,13 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else if (triclinic == 0) pb = &Neighbor::respa_bin_newton;
else if (triclinic == 1) pb = &Neighbor::respa_bin_newton_tri;
} else if (style == MULTI)
error->all("Neighbor multi not yet enabled for rRESPA");
error->all(FLERR,"Neighbor multi not yet enabled for rRESPA");
}
// general error check
if (rq->ghost && !rq->full)
error->all("Neighbors of ghost atoms only allowed for full neighbor lists");
error->all(FLERR,"Neighbors of ghost atoms only allowed for full neighbor lists");
pair_build[index] = pb;
}
@ -1181,7 +1178,7 @@ void Neighbor::build()
// check that neighbor list with special bond flags will not overflow
if (atom->nlocal+atom->nghost > NEIGHMASK)
error->one("Too many local+ghost atoms for neighbor list");
error->one(FLERR,"Too many local+ghost atoms for neighbor list");
// invoke building of pair and molecular neighbor lists
// only for pairwise lists with buildflag set
@ -1224,7 +1221,7 @@ void Neighbor::build_one(int i)
// check that neighbor list with special bond flags will not overflow
if (atom->nlocal+atom->nghost > NEIGHMASK)
error->one("Too many local+ghost atoms for neighbor list");
error->one(FLERR,"Too many local+ghost atoms for neighbor list");
// when occasional list built, LAMMPS can crash if atoms have moved too far
// why is this?, give warning if this is the case
@ -1235,7 +1232,7 @@ void Neighbor::build_one(int i)
int flag = 0;
if (dist_check && update->whichflag) flag = check_distance();
if (flag && me == 0)
error->warning("Building an occasional neighobr list when "
error->warning(FLERR,"Building an occasional neighobr list when "
"atoms may have moved too far");
(this->*pair_build[i])(lists[i]);
@ -1313,7 +1310,7 @@ void Neighbor::setup_bins()
if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT ||
bbox[2]*binsizeinv > MAXSMALLINT)
error->all("Domain too large for neighbor bins");
error->all(FLERR,"Domain too large for neighbor bins");
// create actual bins
// always have one bin even if cutoff > bbox
@ -1345,7 +1342,7 @@ void Neighbor::setup_bins()
if (binsize_optimal*bininvx > CUT2BIN_RATIO ||
binsize_optimal*bininvy > CUT2BIN_RATIO ||
binsize_optimal*bininvz > CUT2BIN_RATIO)
error->all("Cannot use neighbor bins - box size << cutoff");
error->all(FLERR,"Cannot use neighbor bins - box size << cutoff");
// mbinlo/hi = lowest and highest global bins my ghost atoms could be in
// coord = lowest and highest values of coords for my ghost atoms
@ -1395,7 +1392,7 @@ void Neighbor::setup_bins()
// memory for bin ptrs
bigint bbin = mbinx*mbiny*mbinz;
if (bbin > MAXSMALLINT) error->one("Too many neighbor bins");
if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins");
mbins = bbin;
if (mbins > maxhead) {
maxhead = mbins;
@ -1455,15 +1452,15 @@ double Neighbor::bin_distance(int i, int j, int k)
void Neighbor::set(int narg, char **arg)
{
if (narg != 2) error->all("Illegal neighbor command");
if (narg != 2) error->all(FLERR,"Illegal neighbor command");
skin = atof(arg[0]);
if (skin < 0.0) error->all("Illegal neighbor command");
if (skin < 0.0) error->all(FLERR,"Illegal neighbor command");
if (strcmp(arg[1],"nsq") == 0) style = NSQ;
else if (strcmp(arg[1],"bin") == 0) style = BIN;
else if (strcmp(arg[1],"multi") == 0) style = MULTI;
else error->all("Illegal neighbor command");
else error->all(FLERR,"Illegal neighbor command");
}
/* ----------------------------------------------------------------------
@ -1475,55 +1472,55 @@ void Neighbor::modify_params(int narg, char **arg)
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
every = atoi(arg[iarg+1]);
if (every <= 0) error->all("Illegal neigh_modify command");
if (every <= 0) error->all(FLERR,"Illegal neigh_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"delay") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
delay = atoi(arg[iarg+1]);
if (delay < 0) error->all("Illegal neigh_modify command");
if (delay < 0) error->all(FLERR,"Illegal neigh_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"check") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) dist_check = 1;
else if (strcmp(arg[iarg+1],"no") == 0) dist_check = 0;
else error->all("Illegal neigh_modify command");
else error->all(FLERR,"Illegal neigh_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"once") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) build_once = 1;
else if (strcmp(arg[iarg+1],"no") == 0) build_once = 0;
else error->all("Illegal neigh_modify command");
else error->all(FLERR,"Illegal neigh_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"page") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
pgsize = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"one") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
oneatom = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"binsize") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
binsize_user = atof(arg[iarg+1]);
if (binsize_user <= 0.0) binsizeflag = 0;
else binsizeflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"include") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
includegroup = group->find(arg[iarg+1]);
if (includegroup < 0)
error->all("Invalid group ID in neigh_modify command");
error->all(FLERR,"Invalid group ID in neigh_modify command");
if (includegroup && (atom->firstgroupname == NULL ||
strcmp(arg[iarg+1],atom->firstgroupname) != 0))
error->all("Neigh_modify include group != atom_modify first group");
error->all(FLERR,"Neigh_modify include group != atom_modify first group");
iarg += 2;
} else if (strcmp(arg[iarg],"exclude") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (iarg+2 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (strcmp(arg[iarg+1],"type") == 0) {
if (iarg+4 > narg) error->all("Illegal neigh_modify command");
if (iarg+4 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (nex_type == maxex_type) {
maxex_type += EXDELTA;
memory->grow(ex1_type,maxex_type,"neigh:ex1_type");
@ -1535,7 +1532,7 @@ void Neighbor::modify_params(int narg, char **arg)
iarg += 4;
} else if (strcmp(arg[iarg+1],"group") == 0) {
if (iarg+4 > narg) error->all("Illegal neigh_modify command");
if (iarg+4 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (nex_group == maxex_group) {
maxex_group += EXDELTA;
memory->grow(ex1_group,maxex_group,"neigh:ex1_group");
@ -1544,16 +1541,16 @@ void Neighbor::modify_params(int narg, char **arg)
ex1_group[nex_group] = group->find(arg[iarg+2]);
ex2_group[nex_group] = group->find(arg[iarg+3]);
if (ex1_group[nex_group] == -1 || ex2_group[nex_group] == -1)
error->all("Invalid group ID in neigh_modify command");
error->all(FLERR,"Invalid group ID in neigh_modify command");
nex_group++;
iarg += 4;
} else if (strcmp(arg[iarg+1],"molecule") == 0) {
if (iarg+3 > narg) error->all("Illegal neigh_modify command");
if (iarg+3 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (atom->molecule_flag == 0) {
char *str = (char *)
"Neigh_modify exclude molecule requires atom attribute molecule";
error->all(str);
error->all(FLERR,str);
}
if (nex_mol == maxex_mol) {
maxex_mol += EXDELTA;
@ -1561,16 +1558,16 @@ void Neighbor::modify_params(int narg, char **arg)
}
ex_mol_group[nex_mol] = group->find(arg[iarg+2]);
if (ex_mol_group[nex_mol] == -1)
error->all("Invalid group ID in neigh_modify command");
error->all(FLERR,"Invalid group ID in neigh_modify command");
nex_mol++;
iarg += 3;
} else if (strcmp(arg[iarg+1],"none") == 0) {
nex_type = nex_group = nex_mol = 0;
iarg += 2;
} else error->all("Illegal neigh_modify command");
} else error->all(FLERR,"Illegal neigh_modify command");
} else error->all("Illegal neigh_modify command");
} else error->all(FLERR,"Illegal neigh_modify command");
}
}