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Merge remote branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	doc/Manual.html
	doc/Manual.txt
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Axel Kohlmeyer
2014-04-11 12:22:52 +02:00
parent 9655351ef8 e579757de1
commit 00a141d5ce
22 changed files with 159 additions and 128 deletions
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4
doc/Manual.html
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@ -1,7 +1,7 @@
<HTML>
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="9 Apr 2014 version">
<META NAME="docnumber" CONTENT="11 Apr 2014 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -22,7 +22,7 @@
<CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER>
<CENTER><H4>9 Apr 2014 version
<CENTER><H4>11 Apr 2014 version
</H4></CENTER>
<H4>Version info:
</H4>

4
doc/Manual.txt
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@ -1,7 +1,7 @@
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="9 Apr 2014 version">
<META NAME="docnumber" CONTENT="11 Apr 2014 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -19,7 +19,7 @@
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
9 Apr 2014 version :c,h4
11 Apr 2014 version :c,h4
Version info: :h4

25
doc/fix_bond_swap.html
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@ -15,15 +15,17 @@
</P>
<PRE>fix ID group-ID bond/swap fraction cutoff seed
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>bond/swap = style name of this fix command
<LI>fraction = fraction of group atoms to consider for swapping
<LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
bond/swap = style name of this fix command
Nevery = attempt bond swapping every this many steps
<UL><LI>fraction = fraction of group atoms to consider for swapping
<LI>cutoff = distance at which swapping will be considered (distance units)
<LI>seed = random # seed (positive integer)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all bond/swap 0.5 1.3 598934
<PRE>fix 1 all bond/swap 50 0.5 1.3 598934
</PRE>
<P><B>Description:</B>
</P>
@ -55,13 +57,14 @@ undergone a dramatic conformational change. This reference provides
more details on how the algorithm works and its application:
<A HREF = "#Sides">(Sides)</A>.
</P>
<P>The bond swapping operation is invoked each time neighbor lists are
built during a simulation, since it potentially alters the list of
which neighbors are considered for pairwise interaction. At each
reneighboring step, each processor considers a random specified
<I>fraction</I> of its atoms as potential swapping monomers for this
timestep. Choosing a small <I>fraction</I> value can reduce the likelihood
of a reverse swap occurring soon after an initial swap.
<P>The bond swapping operation is invoked every <I>Nevery</I> timesteps. If
any bond is swapped, a re-build of the neighbor lists is triggered,
since a swap alters the list of which neighbors are considered for
pairwise interaction. At each invocation, each processor considers a
random specified <I>fraction</I> of its atoms as potential swapping
monomers for this timestep. Choosing a small <I>fraction</I> value can
reduce the likelihood of a reverse swap occurring soon after an
initial swap.
</P>
<P>For each monomer A1, its neighbors are examined to find a possible B1
monomer. Both A1 and B1 must be in the fix group, their separation

18
doc/fix_bond_swap.txt
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@ -14,13 +14,14 @@ fix ID group-ID bond/swap fraction cutoff seed :pre
ID, group-ID are documented in "fix"_fix.html command
bond/swap = style name of this fix command
Nevery = attempt bond swapping every this many steps :l
fraction = fraction of group atoms to consider for swapping
cutoff = distance at which swapping will be considered (distance units)
seed = random # seed (positive integer) :ul
[Examples:]
fix 1 all bond/swap 0.5 1.3 598934 :pre
fix 1 all bond/swap 50 0.5 1.3 598934 :pre
[Description:]
@ -52,13 +53,14 @@ undergone a dramatic conformational change. This reference provides
more details on how the algorithm works and its application:
"(Sides)"_#Sides.
The bond swapping operation is invoked each time neighbor lists are
built during a simulation, since it potentially alters the list of
which neighbors are considered for pairwise interaction. At each
reneighboring step, each processor considers a random specified
{fraction} of its atoms as potential swapping monomers for this
timestep. Choosing a small {fraction} value can reduce the likelihood
of a reverse swap occurring soon after an initial swap.
The bond swapping operation is invoked every {Nevery} timesteps. If
any bond is swapped, a re-build of the neighbor lists is triggered,
since a swap alters the list of which neighbors are considered for
pairwise interaction. At each invocation, each processor considers a
random specified {fraction} of its atoms as potential swapping
monomers for this timestep. Choosing a small {fraction} value can
reduce the likelihood of a reverse swap occurring soon after an
initial swap.
For each monomer A1, its neighbors are examined to find a possible B1
monomer. Both A1 and B1 must be in the fix group, their separation

2
src/GRANULAR/fix_pour.h
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@ -52,7 +52,7 @@ class FixPour : public Fix {
char *idrigid,*idshake;
class Molecule *onemol;
int natom;
int natom; // # of atoms per inserted particle
double **coords;
imageint *imageflags;
class Fix *fixrigid,*fixshake;

8
src/MANYBODY/fix_qeq_comb.cpp
View File

@ -133,12 +133,6 @@ void FixQEQComb::init()
ngroup = group->count(igroup);
if (ngroup == 0) error->all(FLERR,"Fix qeq/comb group has no atoms");
int irequest = neighbor->request(this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
/* ---------------------------------------------------------------------- */
@ -320,5 +314,3 @@ void FixQEQComb::unpack_comm(int n, int first, double *buf)
last = first + n ;
for (i = first; i < last; i++) atom->q[i] = buf[m++];
}
/* ---------------------------------------------------------------------- */

4
src/MC/fix_bond_create.cpp
View File

@ -200,11 +200,12 @@ void FixBondCreate::init()
"dihedrals, or impropers");
}
// need a half neighbor list, built when ever re-neighboring occurs
// need a half neighbor list, built every Nevery steps
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->occasional = 1;
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
@ -317,6 +318,7 @@ void FixBondCreate::post_integrate()
int *mask = atom->mask;
int *type = atom->type;
neighbor->build_one(list->index,1);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;

43
src/MC/fix_bond_swap.cpp
View File

@ -58,18 +58,23 @@ FixBondSwap::FixBondSwap(LAMMPS *lmp, int narg, char **arg) :
if (narg != 6) error->all(FLERR,"Illegal fix bond/swap command");
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix bond/swap command");
force_reneighbor = 1;
next_reneighbor = -1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 0;
fraction = force->numeric(FLERR,arg[3]);
double cutoff = force->numeric(FLERR,arg[4]);
fraction = force->numeric(FLERR,arg[4]);
double cutoff = force->numeric(FLERR,arg[5]);
cutsq = cutoff*cutoff;
// initialize Marsaglia RNG with processor-unique seed
int seed = force->inumeric(FLERR,arg[5]);
int seed = force->inumeric(FLERR,arg[6]);
random = new RanMars(lmp,seed + comm->me);
// error check
@ -120,7 +125,7 @@ FixBondSwap::~FixBondSwap()
int FixBondSwap::setmask()
{
int mask = 0;
mask |= PRE_NEIGHBOR;
mask |= POST_INTEGRATE;
return mask;
}
@ -159,11 +164,12 @@ void FixBondSwap::init()
force->special_lj[3] != 1.0)
error->all(FLERR,"Fix bond/swap requires special_bonds = 0,1,1");
// need a half neighbor list, built when ever re-neighboring occurs
// need a half neighbor list, built every Nevery steps
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->occasional = 1;
// zero out stats
@ -179,9 +185,16 @@ void FixBondSwap::init_list(int id, NeighList *ptr)
list = ptr;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
look for and perform swaps
NOTE: used to do this every pre_neighbor(), but think that is a bug
b/c was doing it after exchange() and before neighbor->build()
which is when neigh lists are actually out-of-date or even bogus,
now do it based on user-specified Nevery, and trigger reneigh
if any swaps performed, like fix bond/create
------------------------------------------------------------------------- */
void FixBondSwap::pre_neighbor()
void FixBondSwap::post_integrate()
{
int i,j,ii,jj,m,inum,jnum;
int inext,iprev,ilast,jnext,jprev,jlast,ibond,iangle,jbond,jangle;
@ -191,6 +204,8 @@ void FixBondSwap::pre_neighbor()
int *ilist,*jlist,*numneigh,**firstneigh;
double delta,factor;
if (update->ntimestep % nevery) return;
// compute current temp for Boltzmann factor test
double t_current = temperature->compute_scalar();
@ -216,6 +231,7 @@ void FixBondSwap::pre_neighbor()
type = atom->type;
x = atom->x;
neighbor->build_one(list->index,1);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@ -418,6 +434,13 @@ void FixBondSwap::pre_neighbor()
}
done:
// trigger immediate reneighboring if any swaps occurred
int accept_any;
MPI_Allreduce(&accept,&accept_any,1,MPI_INT,MPI_SUM,world);
if (accept_any) next_reneighbor = update->ntimestep;
if (!accept) return;
naccept++;
@ -629,11 +652,13 @@ int FixBondSwap::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID");
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,"Fix_modify temperature ID does not compute temperature");
error->all(FLERR,"Fix_modify temperature ID does not "
"compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;

2
src/MC/fix_bond_swap.h
View File

@ -32,7 +32,7 @@ class FixBondSwap : public Fix {
int setmask();
void init();
void init_list(int, class NeighList *);
void pre_neighbor();
void post_integrate();
int modify_param(int, char **);
double compute_vector(int);
double memory_usage();

2
src/PERI/fix_peri_neigh.cpp
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@ -177,7 +177,7 @@ void FixPeriNeigh::setup(int vflag)
if (!first) return;
first = 0;
// invoke full neighbor list (will copy or build if necessary)
// build full neighbor list, will copy or build as necessary
neighbor->build_one(list->index);

5
src/USER-REAXC/fix_qeq_reax.cpp
View File

@ -322,13 +322,14 @@ void FixQEqReax::init()
error->all(FLERR,"Must use pair_style reax/c with fix qeq/reax");
// need a half neighbor list w/ Newton off and ghost neighbors
// built whenever re-neighboring occurs
// make it occasional if QeQ not performed every timestep
int irequest = neighbor->request(this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->newton = 2;
neighbor->requests[irequest]->ghost = 1;
if (nevery) neighbor->requests[irequest]->occasional = 1;
init_shielding();
init_taper();
@ -523,12 +524,14 @@ void FixQEqReax::compute_H()
tagint *tag = atom->tag;
x = atom->x;
if (nevery > 1) neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// fill in the H matrix
m_fill = 0;
r_sqr = 0;
for( ii = 0; ii < inum; ii++ ) {

6
src/delete_atoms.cpp
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@ -266,8 +266,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
error->all(FLERR,"Delete_atoms cutoff > neighbor cutoff");
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor list based on earlier request
// acquire ghosts and build standard neighbor lists
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
@ -277,6 +276,9 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
// build neighbor list this command needs based on earlier request
NeighList *list = neighbor->lists[irequest];
neighbor->build_one(irequest);

10
src/modify.cpp
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@ -535,7 +535,7 @@ double Modify::min_energy(double *fextra)
}
/* ----------------------------------------------------------------------
store current state of extra dof, only for relevant fixes
store current state of extra minimizer dof, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_store()
@ -545,7 +545,7 @@ void Modify::min_store()
}
/* ----------------------------------------------------------------------
mange state of extra dof on a stack, only for relevant fixes
manage state of extra minimizer dof on a stack, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_clearstore()
@ -567,7 +567,7 @@ void Modify::min_popstore()
}
/* ----------------------------------------------------------------------
displace extra dof along vector hextra, only for relevant fixes
displace extra minimizer dof along vector hextra, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_step(double alpha, double *hextra)
@ -602,7 +602,7 @@ double Modify::max_alpha(double *hextra)
}
/* ----------------------------------------------------------------------
extract extra dof for minimization, only for relevant fixes
extract extra minimizer dof, only for relevant fixes
------------------------------------------------------------------------- */
int Modify::min_dof()
@ -614,7 +614,7 @@ int Modify::min_dof()
}
/* ----------------------------------------------------------------------
reset reference state of fix, only for relevant fixes
reset minimizer reference state of fix, only for relevant fixes
------------------------------------------------------------------------- */
int Modify::min_reset_ref()

6
src/neigh_full.cpp
View File

@ -247,7 +247,7 @@ void Neighbor::full_bin(NeighList *list)
// bin owned & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -355,7 +355,7 @@ void Neighbor::full_bin_ghost(NeighList *list)
// bin owned & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -491,7 +491,7 @@ void Neighbor::full_multi(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;

8
src/neigh_half_bin.cpp
View File

@ -38,7 +38,7 @@ void Neighbor::half_bin_no_newton(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -151,7 +151,7 @@ void Neighbor::half_bin_no_newton_ghost(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -291,7 +291,7 @@ void Neighbor::half_bin_newton(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -433,7 +433,7 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;

6
src/neigh_half_multi.cpp
View File

@ -40,7 +40,7 @@ void Neighbor::half_multi_no_newton(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -156,7 +156,7 @@ void Neighbor::half_multi_newton(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -306,7 +306,7 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;

2
src/neigh_list.cpp
View File

@ -42,6 +42,8 @@ NeighList::NeighList(LAMMPS *lmp) :
dnum = 0;
last_build = -1;
iskip = NULL;
ijskip = NULL;

2
src/neigh_list.h
View File

@ -45,6 +45,8 @@ class NeighList : protected Pointers {
MyPage<int> *ipage; // pages of neighbor indices
MyPage<double> *dpage; // pages of neighbor doubles, if dnum > 0
bigint last_build; // timestep of last build for occasional lists
// atom types to skip when building list
// iskip,ijskip are just ptrs to corresponding request

6
src/neigh_respa.cpp
View File

@ -378,7 +378,7 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -548,7 +548,7 @@ void Neighbor::respa_bin_newton(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;
@ -765,7 +765,7 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
// bin local & ghost atoms
bin_atoms();
if (binatomflag) bin_atoms();
double **x = atom->x;
int *type = atom->type;

117
src/neighbor.cpp
View File

@ -83,6 +83,7 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
binsizeflag = 0;
build_once = 0;
cluster_check = 0;
binatomflag = 1;
cutneighsq = NULL;
cutneighghostsq = NULL;
@ -508,27 +509,6 @@ void Neighbor::init()
// detect lists that are connected to other lists
// if-then-else sequence and processed flag is important
// since don't want to re-process skip or copy lists further down
// skip list needs to have granhistory or respa info added
// copy: point this list at request->otherlist, could be a skip list
// skip: point this list at request->otherlist, copy skip info from request
// also set granular and respa info if applicable
// half_from_full: point this list at preceeding full list
// granhistory: set preceeding list's listgranhistory to this list
// also set preceeding list's ptr to FixShearHistory
// respaouter: point this list at preceeding 1/2 inner/middle lists
// pair and half: if there is a full non-occasional non-skip list
// change this list to half_from_full and point at the full list
// parent could be copy list or pair or fix
// fix/compute requests:
// whether request is occasional or not doesn't matter
// if request = half and non-skip pair half/respaouter exists,
// become copy of that list if cudable flag matches
// if request = full and non-skip pair full exists,
// become copy of that list if cudable flag matches
// if request = half and non-skip pair full exists,
// become half_from_full of that list if cudable flag matches
// if no matches, do nothing, fix/compute list will be built directly
// ok if parent is copy list
int processed;
@ -536,20 +516,32 @@ void Neighbor::init()
if (!lists[i]) continue;
processed = 0;
// copy: point this list at request->otherlist, could be a skip list
if (requests[i]->copy) {
lists[i]->listcopy = lists[requests[i]->otherlist];
processed = 1;
// skip: point this list at request->otherlist,
// copy skip info from request
// skip list still needs to have granhistory or respa info added below
} else if (requests[i]->skip) {
lists[i]->listskip = lists[requests[i]->otherlist];
lists[i]->copy_skip_info(requests[i]->iskip,requests[i]->ijskip);
processed = 1;
// half_from_full: point this list at full list that comes right before
// will only be case if pair style requested one after other
} else if (requests[i]->half_from_full) {
lists[i]->listfull = lists[i-1];
processed = 1;
}
// granhistory: set preceeding list's listgranhistory to this list
// also set preceeding list's ptr to FixShearHistory
if (requests[i]->granhistory) {
lists[i-1]->listgranhistory = lists[i];
for (int ifix = 0; ifix < modify->nfix; ifix++)
@ -557,6 +549,8 @@ void Neighbor::init()
lists[i-1]->fix_history = (FixShearHistory *) modify->fix[ifix];
processed = 1;
// respaouter: point this list at preceeding 1/2 inner/middle lists
} else if (requests[i]->respaouter) {
if (requests[i-1]->respainner) {
lists[i]->respamiddle = 0;
@ -571,6 +565,10 @@ void Neighbor::init()
if (processed) continue;
// pair and half: if there is a full non-occasional non-skip list
// change this list to half_from_full and point at the full list
// parent could be copy list or pair or fix
if (requests[i]->pair && requests[i]->half) {
for (j = 0; j < nrequest; j++) {
if (!lists[j]) continue;
@ -583,6 +581,18 @@ void Neighbor::init()
lists[i]->listfull = lists[j];
}
// fix/compute requests:
// whether request is occasional or not doesn't matter
// if request = half and non-skip pair half/respaouter exists,
// become copy of that list if cudable flag matches
// if request = full and non-skip pair full exists,
// become copy of that list if cudable flag matches
// if request = half and non-skip pair full exists,
// become half_from_full of that list if cudable flag matches
// if no matches, do nothing
// fix/compute list will be built independently as needed
// ok if parent is itself a copy list
} else if (requests[i]->fix || requests[i]->compute) {
for (j = 0; j < nrequest; j++) {
if (!lists[j]) continue;
@ -1349,8 +1359,8 @@ int Neighbor::check_distance()
}
/* ----------------------------------------------------------------------
build all perpetual neighbor lists every few timesteps
pairwise & topology lists are created as needed
build perpetuals neighbor lists
called at setup and every few timesteps during run or minimization
topology lists only built if topoflag = 1, USER-CUDA calls with topoflag = 0
------------------------------------------------------------------------- */
@ -1419,12 +1429,12 @@ void Neighbor::build(int topoflag)
memory->create(bins,maxbin,"bins");
}
// check that neighbor list with special bond flags will not overflow
// check that using special bond flags will not overflow neigh lists
if (atom->nlocal+atom->nghost > NEIGHMASK)
error->one(FLERR,"Too many local+ghost atoms for neighbor list");
// invoke building of pair and molecular neighbor lists
// invoke building of pair and molecular topology neighbor lists
// only for pairwise lists with buildflag set
// blist is for standard neigh lists, otherwise is a Kokkos list
@ -1455,9 +1465,22 @@ void Neighbor::build_topology()
called by other classes
------------------------------------------------------------------------- */
void Neighbor::build_one(int i)
void Neighbor::build_one(int i, int preflag)
{
// update stencils and grow atom arrays and bins as needed
// no need to build if already built since last re-neighbor
// preflag is set by fix bond/create and fix bond/swap
// b/c they invoke build_one() on same step neigh list is re-built,
// but before re-build, so need to use ">" instead of ">="
if (preflag) {
if (lists[i]->last_build > lastcall) return;
} else {
if (lists[i]->last_build >= lastcall) return;
}
lists[i]->last_build = update->ntimestep;
// update stencils and grow atom arrays as needed
// only for relevant settings of stencilflag and growflag
// grow atom array for this list to current size of perpetual lists
@ -1468,42 +1491,14 @@ void Neighbor::build_one(int i)
if (lists[i]->growflag) lists[i]->grow(maxatom);
// extend atom bin list if necessary
if (style != NSQ && atom->nmax > maxbin) {
maxbin = atom->nmax;
memory->destroy(bins);
memory->create(bins,maxbin,"bins");
}
// check that neighbor list with special bond flags will not overflow
if (atom->nlocal+atom->nghost > NEIGHMASK)
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? maybe b/c this list is derived from some now out-of-date list?
// give warning if this is the case
// no easy workaround b/c all neighbor lists really need to be rebuilt
// solution is for input script to check more often for rebuild
// only check_distance if running a simulation, not between simulations
// comment out for now
// is sometimes giving warning when there is no issue
// e.g. when a variable uses a fix with an occasional neigh list
// at the beginning of a timestep (e.g. fix move) where
// all neigh lists are about to be re-built anyway
/*
int flag = 0;
if (dist_check && update->whichflag) flag = check_distance();
if (flag && me == 0) {
printf("BUILD ONE ERROR: %ld\n",update->ntimestep);
error->warning(FLERR,"Building an occasional neighbor list when "
"atoms may have moved too far");
}
*/
// build list I, turning off atom binning
// binning results from last re-neighbor should be used instead
// if re-bin now, atoms may have moved outside of proc domain & bin extent,
// leading to errors or even a crash
binatomflag = 0;
(this->*pair_build[i])(lists[i]);
binatomflag = 1;
}
/* ----------------------------------------------------------------------

5
src/neighbor.h
View File

@ -75,7 +75,7 @@ class Neighbor : protected Pointers {
void setup_bins(); // setup bins based on box and cutoff
virtual void build(int topoflag=1); // create all neighbor lists (pair,bond)
virtual void build_topology(); // create all topology neighbor lists
void build_one(int); // create a single neighbor list
void build_one(int, int preflag=0); // create a single neighbor list
void set(int, char **); // set neighbor style and skin distance
void modify_params(int, char**); // modify parameters that control builds
bigint memory_usage();
@ -107,6 +107,9 @@ class Neighbor : protected Pointers {
double boxlo_hold[3],boxhi_hold[3]; // box size at last neighbor build
double corners_hold[8][3]; // box corners at last neighbor build
int binatomflag; // bin atoms or not when build neigh list
// turned off by build_one()
int nbinx,nbiny,nbinz; // # of global bins
int *bins; // ptr to next atom in each bin
int maxbin; // size of bins array

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "9 Apr 2014"
#define LAMMPS_VERSION "11 Apr 2014"