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remove trailing whitespace

This commit is contained in:
Axel Kohlmeyer 2019-03-26 11:17:21 -04:00
parent 1266b866e0
commit fff28a8666
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GPG Key ID: D9B44E93BF0C375A
9 changed files with 126 additions and 126 deletions
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16
src/RIGID/fix_rigid_small.cpp
View File

@ -601,7 +601,7 @@ void FixRigidSmall::init()
// for atom types in rigid bodies - need a more careful test
double cutghost = MAX(neighbor->cutneighmax,comm->cutghostuser);
if (maxextent > cutghost)
if (maxextent > cutghost)
error->all(FLERR,"Rigid body extent > ghost cutoff - use comm_modify cutoff");
// error if npt,nph fix comes before rigid fix
@ -1549,7 +1549,7 @@ void FixRigidSmall::create_bodies(tagint *bodyID)
// allocate buffer for input to rendezvous comm
// ncount = # of my atoms in bodies
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -1559,7 +1559,7 @@ void FixRigidSmall::create_bodies(tagint *bodyID)
int *proclist;
memory->create(proclist,ncount,"rigid/small:proclist");
InRvous *inbuf = (InRvous *)
InRvous *inbuf = (InRvous *)
memory->smalloc(ncount*sizeof(InRvous),"rigid/small:inbuf");
// setup buf to pass to rendezvous comm
@ -1594,13 +1594,13 @@ void FixRigidSmall::create_bodies(tagint *bodyID)
rendezvous_body,0,buf,sizeof(OutRvous),
(void *) this);
OutRvous *outbuf = (OutRvous *) buf;
memory->destroy(proclist);
memory->sfree(inbuf);
// set bodytag of all owned atoms based on outbuf info for constituent atoms
for (i = 0; i < nlocal; i++)
for (i = 0; i < nlocal; i++)
if (!(mask[i] & groupbit)) bodytag[i] = 0;
for (m = 0; m < nreturn; m++)
@ -1650,7 +1650,7 @@ int FixRigidSmall::rendezvous_body(int n, char *inbuf,
InRvous *in = (InRvous *) inbuf;
std::map<tagint,int> hash;
tagint id;
int ncount = 0;
for (i = 0; i < n; i++) {
id = in[i].bodyID;
@ -1722,7 +1722,7 @@ int FixRigidSmall::rendezvous_body(int n, char *inbuf,
// compute rsqfar for all bodies I own
// set rsqfar back in caller
double rsqfar = 0.0;
for (int i = 0; i < n; i++) {
@ -1742,7 +1742,7 @@ int FixRigidSmall::rendezvous_body(int n, char *inbuf,
int nout = n;
memory->create(proclist,nout,"rigid/small:proclist");
OutRvous *out = (OutRvous *)
OutRvous *out = (OutRvous *)
memory->smalloc(nout*sizeof(OutRvous),"rigid/small:out");
for (int i = 0; i < nout; i++) {

78
src/RIGID/fix_shake.cpp
View File

@ -816,7 +816,7 @@ void FixShake::find_clusters()
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all(FLERR,"Did not find fix shake partner info");
// -----------------------------------------------------
// identify SHAKEable bonds
// set nshake[i] = # of SHAKE bonds attached to atom i
@ -873,7 +873,7 @@ void FixShake::find_clusters()
// -----------------------------------------------------
nshake_info(npartner,partner_tag,partner_nshake);
// -----------------------------------------------------
// error checks
// no atom with nshake > 3
@ -1052,7 +1052,7 @@ void FixShake::atom_owners()
int *proclist;
memory->create(proclist,nlocal,"shake:proclist");
IDRvous *idbuf = (IDRvous *)
IDRvous *idbuf = (IDRvous *)
memory->smalloc((bigint) nlocal*sizeof(IDRvous),"shake:idbuf");
// setup input buf to rendezvous comm
@ -1068,7 +1068,7 @@ void FixShake::atom_owners()
// perform rendezvous operation
// each proc assigned every 1/Pth atom
char *buf;
comm->rendezvous(RVOUS,nlocal,(char *) idbuf,sizeof(IDRvous),
0,proclist,
@ -1091,7 +1091,7 @@ void FixShake::partner_info(int *npartner, tagint **partner_tag,
// nsend = # of my datums to send
// one datum for every off-processor partner
int nsend = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
@ -1102,7 +1102,7 @@ void FixShake::partner_info(int *npartner, tagint **partner_tag,
int *proclist;
memory->create(proclist,nsend,"special:proclist");
PartnerInfo *inbuf = (PartnerInfo *)
PartnerInfo *inbuf = (PartnerInfo *)
memory->smalloc((bigint) nsend*sizeof(PartnerInfo),"special:inbuf");
// set values in 4 partner arrays for all partner atoms I own
@ -1117,9 +1117,9 @@ void FixShake::partner_info(int *npartner, tagint **partner_tag,
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
double massone;
nsend = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
@ -1129,7 +1129,7 @@ void FixShake::partner_info(int *npartner, tagint **partner_tag,
partner_bondtype[i][j] = 0;
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
partner_mask[i][j] = mask[m];
partner_type[i][j] = type[m];
@ -1182,13 +1182,13 @@ void FixShake::partner_info(int *npartner, tagint **partner_tag,
0,buf,sizeof(PartnerInfo),
(void *) this);
PartnerInfo *outbuf = (PartnerInfo *) buf;
memory->destroy(proclist);
memory->sfree(inbuf);
// set partner 4 values for un-onwed partners based on output info
// outbuf.atomID = my owned atom, outbuf.partnerID = partner the info is for
for (m = 0; m < nreturn; m++) {
i = atom->map(outbuf[m].atomID);
for (j = 0; j < npartner[i]; j++)
@ -1200,7 +1200,7 @@ void FixShake::partner_info(int *npartner, tagint **partner_tag,
// only set partner_bondtype if my atom did not set it
// when setting up rendezvous
// if this proc set it, then sender of this datum set outbuf.bondtype = 0
if (partner_bondtype[i][j] == 0)
partner_bondtype[i][j] = outbuf[m].bondtype;
}
@ -1220,7 +1220,7 @@ void FixShake::nshake_info(int *npartner, tagint **partner_tag,
// nsend = # of my datums to send
// one datum for every off-processor partner
int nsend = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
@ -1231,7 +1231,7 @@ void FixShake::nshake_info(int *npartner, tagint **partner_tag,
int *proclist;
memory->create(proclist,nsend,"special:proclist");
NShakeInfo *inbuf = (NShakeInfo *)
NShakeInfo *inbuf = (NShakeInfo *)
memory->smalloc((bigint) nsend*sizeof(NShakeInfo),"special:inbuf");
// set partner_nshake for all partner atoms I own
@ -1270,7 +1270,7 @@ void FixShake::nshake_info(int *npartner, tagint **partner_tag,
rendezvous_nshake,0,buf,sizeof(NShakeInfo),
(void *) this);
NShakeInfo *outbuf = (NShakeInfo *) buf;
memory->destroy(proclist);
memory->sfree(inbuf);
@ -1299,7 +1299,7 @@ void FixShake::shake_info(int *npartner, tagint **partner_tag,
// nsend = # of my datums to send
// one datum for every off-processor partner
int nsend = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
@ -1310,7 +1310,7 @@ void FixShake::shake_info(int *npartner, tagint **partner_tag,
int *proclist;
memory->create(proclist,nsend,"special:proclist");
ShakeInfo *inbuf = (ShakeInfo *)
ShakeInfo *inbuf = (ShakeInfo *)
memory->smalloc((bigint) nsend*sizeof(ShakeInfo),"special:inbuf");
// set 3 shake arrays for all partner atoms I own
@ -1326,7 +1326,7 @@ void FixShake::shake_info(int *npartner, tagint **partner_tag,
for (j = 0; j < npartner[i]; j++) {
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
shake_flag[m] = shake_flag[i];
shake_atom[m][0] = shake_atom[i][0];
@ -1363,7 +1363,7 @@ void FixShake::shake_info(int *npartner, tagint **partner_tag,
rendezvous_shake,0,buf,sizeof(ShakeInfo),
(void *) this);
ShakeInfo *outbuf = (ShakeInfo *) buf;
memory->destroy(proclist);
memory->sfree(inbuf);
@ -1399,10 +1399,10 @@ int FixShake::rendezvous_ids(int n, char *inbuf,
tagint *atomIDs;
int *procowner;
memory->create(atomIDs,n,"special:atomIDs");
memory->create(procowner,n,"special:procowner");
IDRvous *in = (IDRvous *) inbuf;
for (int i = 0; i < n; i++) {
@ -1411,13 +1411,13 @@ int FixShake::rendezvous_ids(int n, char *inbuf,
}
// store rendezvous data in FixShake class
fsptr->nrvous = n;
fsptr->atomIDs = atomIDs;
fsptr->procowner = procowner;
// flag = 0: no second comm needed in rendezvous
flag = 0;
return 0;
}
@ -1433,7 +1433,7 @@ int FixShake::rendezvous_partners_info(int n, char *inbuf,
void *ptr)
{
int i,m;
FixShake *fsptr = (FixShake *) ptr;
Atom *atom = fsptr->atom;
Memory *memory = fsptr->memory;
@ -1444,7 +1444,7 @@ int FixShake::rendezvous_partners_info(int n, char *inbuf,
atom->map_clear();
// hash atom IDs stored in rendezvous decomposition
int nrvous = fsptr->nrvous;
tagint *atomIDs = fsptr->atomIDs;
@ -1453,7 +1453,7 @@ int FixShake::rendezvous_partners_info(int n, char *inbuf,
// proclist = owner of atomID in caller decomposition
// outbuf = info about owned atomID = 4 values
PartnerInfo *in = (PartnerInfo *) inbuf;
int *procowner = fsptr->procowner;
memory->create(proclist,n,"shake:proclist");
@ -1467,7 +1467,7 @@ int FixShake::rendezvous_partners_info(int n, char *inbuf,
}
outbuf = inbuf;
// re-create atom map
atom->map_init(0);
@ -1475,7 +1475,7 @@ int FixShake::rendezvous_partners_info(int n, char *inbuf,
atom->map_set();
// flag = 1: outbuf = inbuf
flag = 1;
return n;
}
@ -1491,7 +1491,7 @@ int FixShake::rendezvous_nshake(int n, char *inbuf,
void *ptr)
{
int i,j,m;
FixShake *fsptr = (FixShake *) ptr;
Atom *atom = fsptr->atom;
Memory *memory = fsptr->memory;
@ -1502,7 +1502,7 @@ int FixShake::rendezvous_nshake(int n, char *inbuf,
atom->map_clear();
// hash atom IDs stored in rendezvous decomposition
int nrvous = fsptr->nrvous;
tagint *atomIDs = fsptr->atomIDs;
@ -1511,18 +1511,18 @@ int FixShake::rendezvous_nshake(int n, char *inbuf,
// proclist = owner of atomID in caller decomposition
// outbuf = info about owned atomID
NShakeInfo *in = (NShakeInfo *) inbuf;
int *procowner = fsptr->procowner;
memory->create(proclist,n,"shake:proclist");
for (i = 0; i < n; i++) {
m = atom->map(in[i].atomID);
proclist[i] = procowner[m];
}
outbuf = inbuf;
// re-create atom map
atom->map_init(0);
@ -1530,7 +1530,7 @@ int FixShake::rendezvous_nshake(int n, char *inbuf,
atom->map_set();
// flag = 1: outbuf = inbuf
flag = 1;
return n;
}
@ -1545,7 +1545,7 @@ int FixShake::rendezvous_shake(int n, char *inbuf,
void *ptr)
{
int i,j,m;
FixShake *fsptr = (FixShake *) ptr;
Atom *atom = fsptr->atom;
Memory *memory = fsptr->memory;
@ -1556,7 +1556,7 @@ int FixShake::rendezvous_shake(int n, char *inbuf,
atom->map_clear();
// hash atom IDs stored in rendezvous decomposition
int nrvous = fsptr->nrvous;
tagint *atomIDs = fsptr->atomIDs;
@ -1565,7 +1565,7 @@ int FixShake::rendezvous_shake(int n, char *inbuf,
// proclist = owner of atomID in caller decomposition
// outbuf = info about owned atomID
ShakeInfo *in = (ShakeInfo *) inbuf;
int *procowner = fsptr->procowner;
memory->create(proclist,n,"shake:proclist");
@ -1576,7 +1576,7 @@ int FixShake::rendezvous_shake(int n, char *inbuf,
}
outbuf = inbuf;
// re-create atom map
atom->map_init(0);
@ -1584,7 +1584,7 @@ int FixShake::rendezvous_shake(int n, char *inbuf,
atom->map_set();
// flag = 1: outbuf = inbuf;
flag = 1;
return n;
}

2
src/RIGID/fix_shake.h
View File

@ -124,7 +124,7 @@ class FixShake : public Fix {
void partner_info(int *, tagint **, int **, int **, int **, int **);
void nshake_info(int *, tagint **, int **);
void shake_info(int *, tagint **, int **);
int masscheck(double);
void unconstrained_update();
void unconstrained_update_respa(int);

46
src/comm.cpp
View File

@ -738,7 +738,7 @@ void Comm::ring(int n, int nper, void *inbuf, int messtag,
inbuf = vector of input datums
insize = byte size of each input datum
inorder = 0 for inbuf in random proc order, 1 for datums ordered by proc
procs: inorder 0 = proc to send each datum to, 1 = # of datums/proc,
procs: inorder 0 = proc to send each datum to, 1 = # of datums/proc,
callback = caller function to invoke in rendezvous decomposition
takes input datums, returns output datums
outorder = same as inorder, but for datums returned by callback()
@ -781,11 +781,11 @@ rendezvous(int which, int n, char *inbuf, int insize,
int Comm::
rendezvous_irregular(int n, char *inbuf, int insize, int inorder, int *procs,
int (*callback)(int, char *, int &, int *&, char *&, void *),
int outorder, char *&outbuf,
int outorder, char *&outbuf,
int outsize, void *ptr, int statflag)
{
// irregular comm of inbuf from caller decomp to rendezvous decomp
Irregular *irregular = new Irregular(lmp);
int nrvous;
@ -812,7 +812,7 @@ rendezvous_irregular(int n, char *inbuf, int insize, int inorder, int *procs,
if (flag != 1) memory->sfree(inbuf_rvous); // outbuf_rvous = inbuf_vous
if (flag == 0) {
if (statflag) rendezvous_stats(n,0,nrvous,nrvous_out,insize,outsize,
(bigint) nrvous_out*sizeof(int) +
(bigint) nrvous_out*sizeof(int) +
irregular1_bytes);
return 0; // all nout_rvous are 0, no 2nd comm stage
}
@ -821,9 +821,9 @@ rendezvous_irregular(int n, char *inbuf, int insize, int inorder, int *procs,
// caller will free outbuf
irregular = new Irregular(lmp);
int nout;
if (outorder)
if (outorder)
nout = irregular->create_data_grouped(nrvous_out,procs_rvous);
else nout = irregular->create_data(nrvous_out,procs_rvous);
@ -842,7 +842,7 @@ rendezvous_irregular(int n, char *inbuf, int insize, int inorder, int *procs,
// last arg to stats() = memory for procs_rvous + irregular comm
if (statflag) rendezvous_stats(n,nout,nrvous,nrvous_out,insize,outsize,
(bigint) nrvous_out*sizeof(int) +
(bigint) nrvous_out*sizeof(int) +
MAX(irregular1_bytes,irregular2_bytes));
return nout;
}
@ -863,7 +863,7 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
char *inbuf_a2a,*outbuf_a2a;
// create procs and inbuf for All2all if necesary
if (!inorder) {
memory->create(procs_a2a,nprocs,"rendezvous:procs");
inbuf_a2a = (char *) memory->smalloc((bigint) n*insize,
@ -894,10 +894,10 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
}
// create args for MPI_Alltoallv() on input data
memory->create(sendcount,nprocs,"rendezvous:sendcount");
memcpy(sendcount,procs_a2a,nprocs*sizeof(int));
memory->create(recvcount,nprocs,"rendezvous:recvcount");
MPI_Alltoall(sendcount,1,MPI_INT,recvcount,1,MPI_INT,world);
@ -912,14 +912,14 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
// test for overflow of input data due to imbalance or insize
// means that individual sdispls or rdispls values overflow
int overflow = 0;
if ((bigint) n*insize > MAXSMALLINT) overflow = 1;
if ((bigint) nrvous*insize > MAXSMALLINT) overflow = 1;
int overflowall;
MPI_Allreduce(&overflow,&overflowall,1,MPI_INT,MPI_MAX,world);
if (overflowall) error->all(FLERR,"Overflow input size in rendezvous_a2a");
for (int i = 0; i < nprocs; i++) {
sendcount[i] *= insize;
sdispls[i] *= insize;
@ -958,7 +958,7 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
memory->destroy(sdispls);
memory->destroy(rdispls);
if (statflag) rendezvous_stats(n,0,nrvous,nrvous_out,insize,outsize,
(bigint) nrvous_out*sizeof(int) +
(bigint) nrvous_out*sizeof(int) +
4*nprocs*sizeof(int) + all2all1_bytes);
return 0; // all nout_rvous are 0, no 2nd irregular
}
@ -969,7 +969,7 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
// create procs and outbuf for All2all if necesary
if (!outorder) {
memory->create(procs_a2a,nprocs,"rendezvous_a2a:procs");
@ -991,8 +991,8 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
offsets[iproc] += outsize;
offset += outsize;
}
all2all2_bytes = nprocs*sizeof(int) + nprocs*sizeof(bigint) +
all2all2_bytes = nprocs*sizeof(int) + nprocs*sizeof(bigint) +
nrvous_out*outsize;
} else {
@ -1004,9 +1004,9 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
// comm outbuf from rendezvous decomposition back to caller
memcpy(sendcount,procs_a2a,nprocs*sizeof(int));
MPI_Alltoall(sendcount,1,MPI_INT,recvcount,1,MPI_INT,world);
sdispls[0] = rdispls[0] = 0;
for (int i = 1; i < nprocs; i++) {
sdispls[i] = sdispls[i-1] + sendcount[i-1];
@ -1016,13 +1016,13 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
// test for overflow of outbuf due to imbalance or outsize
// means that individual sdispls or rdispls values overflow
overflow = 0;
if ((bigint) nrvous*outsize > MAXSMALLINT) overflow = 1;
if ((bigint) nout*outsize > MAXSMALLINT) overflow = 1;
MPI_Allreduce(&overflow,&overflowall,1,MPI_INT,MPI_MAX,world);
if (overflowall) error->all(FLERR,"Overflow output in rendezvous_a2a");
for (int i = 0; i < nprocs; i++) {
sendcount[i] *= outsize;
sdispls[i] *= outsize;
@ -1058,8 +1058,8 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
// last arg to stats() = mem for procs_rvous + per-proc vecs + reordering ops
if (statflag) rendezvous_stats(n,nout,nrvous,nrvous_out,insize,outsize,
(bigint) nrvous_out*sizeof(int) +
4*nprocs*sizeof(int) +
(bigint) nrvous_out*sizeof(int) +
4*nprocs*sizeof(int) +
MAX(all2all1_bytes,all2all2_bytes));
return nout;
}
@ -1120,7 +1120,7 @@ void Comm::rendezvous_stats(int n, int nout, int nrvous, int nrvous_out,
BIGINT_FORMAT " %g " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
size_out_all/outsize,1.0*size_out_all/nprocs/outsize,
size_out_max/outsize,size_out_min/outsize);
else
else
fprintf(screen," output datum count: "
BIGINT_FORMAT " %g " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
0,0.0,0,0);

12
src/comm.h
View File

@ -109,8 +109,8 @@ class Comm : protected Pointers {
void ring(int, int, void *, int, void (*)(int, char *, void *),
void *, void *, int self = 1);
int rendezvous(int, int, char *, int, int, int *,
int (*)(int, char *, int &, int *&, char *&, void *),
int rendezvous(int, int, char *, int, int, int *,
int (*)(int, char *, int &, int *&, char *&, void *),
int, char *&, int, void *, int statflag=0);
int read_lines_from_file(FILE *, int, int, char *);
@ -147,11 +147,11 @@ class Comm : protected Pointers {
int coregrid[3]; // 3d grid of cores within a node
int user_coregrid[3]; // user request for cores in each dim
int rendezvous_irregular(int, char *, int, int, int *,
int (*)(int, char *, int &, int *&, char *&, void *),
int rendezvous_irregular(int, char *, int, int, int *,
int (*)(int, char *, int &, int *&, char *&, void *),
int, char *&, int, void *, int);
int rendezvous_all2all(int, char *, int, int, int *,
int (*)(int, char *, int &, int *&, char *&, void *),
int rendezvous_all2all(int, char *, int, int, int *,
int (*)(int, char *, int &, int *&, char *&, void *),
int, char *&, int, void *, int);
void rendezvous_stats(int, int, int, int, int, int, bigint);

12
src/hashlittle.cpp
View File

@ -43,7 +43,7 @@ This was tested for:
the output delta to a Gray code (a^(a>>1)) so a string of 1's (as
is commonly produced by subtraction) look like a single 1-bit
difference.
* the base values were pseudorandom, all zero but one bit set, or
* the base values were pseudorandom, all zero but one bit set, or
all zero plus a counter that starts at zero.
Some k values for my "a-=c; a^=rot(c,k); c+=b;" arrangement that
@ -53,7 +53,7 @@ satisfy this are
14 9 3 7 17 3
Well, "9 15 3 18 27 15" didn't quite get 32 bits diffing
for "differ" defined as + with a one-bit base and a two-bit delta. I
used http://burtleburtle.net/bob/hash/avalanche.html to choose
used http://burtleburtle.net/bob/hash/avalanche.html to choose
the operations, constants, and arrangements of the variables.
This does not achieve avalanche. There are input bits of (a,b,c)
@ -92,7 +92,7 @@ produce values of c that look totally different. This was tested for
the output delta to a Gray code (a^(a>>1)) so a string of 1's (as
is commonly produced by subtraction) look like a single 1-bit
difference.
* the base values were pseudorandom, all zero but one bit set, or
* the base values were pseudorandom, all zero but one bit set, or
all zero plus a counter that starts at zero.
These constants passed:
@ -169,7 +169,7 @@ uint32_t hashlittle( const void *key, size_t length, uint32_t initval)
}
/*----------------------------- handle the last (probably partial) block */
/*
/*
* "k[2]&0xffffff" actually reads beyond the end of the string, but
* then masks off the part it's not allowed to read. Because the
* string is aligned, the masked-off tail is in the same word as the
@ -314,9 +314,9 @@ uint32_t hashlittle( const void *key, size_t length, uint32_t initval)
#else /* PURIFY_HATES_HASHLITTLE */
/* I don't know what it is about Jenkins' hashlittle function, but
* it drives purify insane, even with VALGRIND defined. It makes
* it drives purify insane, even with VALGRIND defined. It makes
* purify unusable!! The code execution doesn't even make sense.
* Below is a (probably) weaker hash function that at least allows
* Below is a (probably) weaker hash function that at least allows
* testing with purify.
*/
#define MAXINT_DIV_PHI 11400714819323198485U

2
src/irregular.cpp
View File

@ -761,7 +761,7 @@ int Irregular::create_data_grouped(int n, int *procs, int sortflag)
#ifdef LAMMPS_RS_ALLREDUCE_INPLACE
MPI_Allreduce(MPI_IN_PLACE,work1,nprocs,MPI_INT,MPI_SUM,world);
nrecv_proc = work1[me];
#else
#else
#ifdef LAMMPS_RS_ALLREDUCE
MPI_Allreduce(work1,work2,nprocs,MPI_INT,MPI_SUM,world);
nrecv_proc = work2[me];

82
src/special.cpp
View File

@ -171,7 +171,7 @@ void Special::atom_owners()
int *proclist;
memory->create(proclist,nlocal,"special:proclist");
IDRvous *idbuf = (IDRvous *)
IDRvous *idbuf = (IDRvous *)
memory->smalloc((bigint) nlocal*sizeof(IDRvous),"special:idbuf");
// setup input buf for rendezvous comm
@ -185,7 +185,7 @@ void Special::atom_owners()
}
// perform rendezvous operation
char *buf;
comm->rendezvous(RVOUS,nlocal,(char *) idbuf,sizeof(IDRvous),0,proclist,
rendezvous_ids,0,buf,0,(void *) this);
@ -210,7 +210,7 @@ void Special::onetwo_build_newton()
int nlocal = atom->nlocal;
// nsend = # of my datums to send
int nsend = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < num_bond[i]; j++) {
@ -221,7 +221,7 @@ void Special::onetwo_build_newton()
int *proclist;
memory->create(proclist,nsend,"special:proclist");
PairRvous *inbuf = (PairRvous *)
PairRvous *inbuf = (PairRvous *)
memory->smalloc((bigint) nsend*sizeof(PairRvous),"special:inbuf");
// setup input buf to rendezvous comm
@ -239,7 +239,7 @@ void Special::onetwo_build_newton()
nsend++;
}
}
// perform rendezvous operation
char *buf;
@ -248,7 +248,7 @@ void Special::onetwo_build_newton()
rendezvous_pairs,0,buf,sizeof(PairRvous),
(void *) this);
PairRvous *outbuf = (PairRvous *) buf;
memory->destroy(proclist);
memory->sfree(inbuf);
@ -268,14 +268,14 @@ void Special::onetwo_build_newton()
i = atom->map(outbuf[m].atomID);
nspecial[i][0]++;
}
int max = 0;
for (i = 0; i < nlocal; i++)
max = MAX(max,nspecial[i][0]);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
memory->create(onetwo,nlocal,maxall,"special:onetwo");
for (i = 0; i < nlocal; i++) nspecial[i][0] = 0;
for (i = 0; i < nlocal; i++) {
@ -290,7 +290,7 @@ void Special::onetwo_build_newton()
i = atom->map(outbuf[m].atomID);
onetwo[i][nspecial[i][0]++] = outbuf[m].partnerID;
}
memory->sfree(outbuf);
}
@ -311,13 +311,13 @@ void Special::onetwo_build_newton_off()
int max = 0;
for (i = 0; i < nlocal; i++)
max = MAX(max,num_bond[i]);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
memory->create(onetwo,nlocal,maxall,"special:onetwo");
// nsend = # of my datums to send
// include nlocal datums with owner of each atom
for (i = 0; i < nlocal; i++) {
nspecial[i][0] = num_bond[i];
for (j = 0; j < num_bond[i]; j++)
@ -350,7 +350,7 @@ void Special::onethree_build()
int *proclist;
memory->create(proclist,nsend,"special:proclist");
PairRvous *inbuf = (PairRvous *)
PairRvous *inbuf = (PairRvous *)
memory->smalloc((bigint) nsend*sizeof(PairRvous),"special:inbuf");
// setup input buf to rendezvous comm
@ -402,11 +402,11 @@ void Special::onethree_build()
i = atom->map(outbuf[m].atomID);
nspecial[i][1]++;
}
int max = 0;
for (i = 0; i < nlocal; i++)
max = MAX(max,nspecial[i][1]);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
memory->create(onethree,nlocal,maxall,"special:onethree");
@ -456,7 +456,7 @@ void Special::onefour_build()
int *proclist;
memory->create(proclist,nsend,"special:proclist");
PairRvous *inbuf = (PairRvous *)
PairRvous *inbuf = (PairRvous *)
memory->smalloc((bigint) nsend*sizeof(PairRvous),"special:inbuf");
// setup input buf to rendezvous comm
@ -507,11 +507,11 @@ void Special::onefour_build()
i = atom->map(outbuf[m].atomID);
nspecial[i][2]++;
}
int max = 0;
for (i = 0; i < nlocal; i++)
max = MAX(max,nspecial[i][2]);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
memory->create(onefour,nlocal,maxall,"special:onefour");
@ -843,7 +843,7 @@ void Special::angle_trim()
int *proclist;
memory->create(proclist,nsend,"special:proclist");
PairRvous *inbuf = (PairRvous *)
PairRvous *inbuf = (PairRvous *)
memory->smalloc((bigint) nsend*sizeof(PairRvous),"special:inbuf");
// setup input buf to rendezvous comm
@ -904,7 +904,7 @@ void Special::angle_trim()
}
// perform rendezvous operation
char *buf;
int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous),
0,proclist,
@ -921,18 +921,18 @@ void Special::angle_trim()
for (i = 0; i < nlocal; i++)
max = MAX(max,nspecial[i][1]);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
int **flag;
memory->create(flag,nlocal,maxall,"special:flag");
for (i = 0; i < nlocal; i++)
for (j = 0; j < nspecial[i][1]; j++)
flag[i][j] = 0;
// reset nspecial[1] and onethree for all owned atoms based on output info
// based on owned info plus rendezvous output info
// output datums = pairs of atoms that are 1-3 neighbors
for (i = 0; i < nlocal; i++) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
@ -1011,7 +1011,7 @@ void Special::angle_trim()
} else j++;
}
}
memory->destroy(flag);
// if no angles or dihedrals are defined, delete all 1-3 neighs
@ -1089,9 +1089,9 @@ void Special::dihedral_trim()
int *proclist;
memory->create(proclist,nsend,"special:proclist");
PairRvous *inbuf = (PairRvous *)
PairRvous *inbuf = (PairRvous *)
memory->smalloc((bigint) nsend*sizeof(PairRvous),"special:inbuf");
// setup input buf to rendezvous comm
// datums = pairs of onefour atom IDs in a dihedral defined for my atoms
// only dihedrals where I own atom2 (in case newton_bond off)
@ -1123,7 +1123,7 @@ void Special::dihedral_trim()
}
// perform rendezvous operation
char *buf;
int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous),
0,proclist,
@ -1140,14 +1140,14 @@ void Special::dihedral_trim()
for (i = 0; i < nlocal; i++)
max = MAX(max,nspecial[i][2]);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
int **flag;
memory->create(flag,nlocal,maxall,"special:flag");
for (i = 0; i < nlocal; i++)
for (j = 0; j < nspecial[i][2]; j++)
flag[i][j] = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
@ -1195,9 +1195,9 @@ void Special::dihedral_trim()
} else j++;
}
}
memory->destroy(flag);
// if no dihedrals are defined, delete all 1-4 neighs
} else {
@ -1235,10 +1235,10 @@ int Special::rendezvous_ids(int n, char *inbuf,
int *procowner;
tagint *atomIDs;
memory->create(procowner,n,"special:procowner");
memory->create(atomIDs,n,"special:atomIDs");
IDRvous *in = (IDRvous *) inbuf;
for (int i = 0; i < n; i++) {
@ -1247,17 +1247,17 @@ int Special::rendezvous_ids(int n, char *inbuf,
}
// store rendezvous data in Special class
sptr->nrvous = n;
sptr->procowner = procowner;
sptr->atomIDs = atomIDs;
// flag = 0: no second comm needed in rendezvous
flag = 0;
return 0;
}
/* ----------------------------------------------------------------------
process data for atoms assigned to me in rendezvous decomposition
@ -1279,7 +1279,7 @@ int Special::rendezvous_pairs(int n, char *inbuf,
atom->map_clear();
// hash atom IDs stored in rendezvous decomposition
int nrvous = sptr->nrvous;
tagint *atomIDs = sptr->atomIDs;
@ -1287,7 +1287,7 @@ int Special::rendezvous_pairs(int n, char *inbuf,
atom->map_one(atomIDs[i],i);
// proclist = owner of atomID in caller decomposition
PairRvous *in = (PairRvous *) inbuf;
int *procowner = sptr->procowner;
memory->create(proclist,n,"special:proclist");
@ -1299,7 +1299,7 @@ int Special::rendezvous_pairs(int n, char *inbuf,
}
outbuf = inbuf;
// re-create atom map
atom->map_init(0);
@ -1307,7 +1307,7 @@ int Special::rendezvous_pairs(int n, char *inbuf,
atom->map_set();
// flag = 1: outbuf = inbuf
flag = 1;
return n;
}

2
src/special.h
View File

@ -45,7 +45,7 @@ class Special : protected Pointers {
};
// private methods
void atom_owners();
void onetwo_build_newton();
void onetwo_build_newton_off();