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Merge pull request #1406 from akohlmey/fix-some-64-bit-integer-issues 

Fix some 64 bit integer issues
This commit is contained in:
Axel Kohlmeyer 2019-04-04 12:47:34 -04:00 committed by GitHub
parent 968ac3d8d7 50427ce05d
commit 605524ab66
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 134 additions and 118 deletions
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8
src/USER-MISC/fix_pimd.cpp
View File

@ -637,14 +637,14 @@ void FixPIMD::comm_exec(double **ptr)
if(nsend > max_nsend)
{
max_nsend = nsend+200;
tag_send = (int*) memory->srealloc(tag_send, sizeof(int)*max_nsend, "FixPIMD:tag_send");
tag_send = (tagint*) memory->srealloc(tag_send, sizeof(tagint)*max_nsend, "FixPIMD:tag_send");
buf_send = (double*) memory->srealloc(buf_send, sizeof(double)*max_nsend*3, "FixPIMD:x_send");
}
// send tags
MPI_Sendrecv( atom->tag, nlocal, MPI_INT, plan_send[iplan], 0,
tag_send, nsend, MPI_INT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE);
MPI_Sendrecv( atom->tag, nlocal, MPI_LMP_TAGINT, plan_send[iplan], 0,
tag_send, nsend, MPI_LMP_TAGINT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE);
// wrap positions
@ -661,7 +661,7 @@ void FixPIMD::comm_exec(double **ptr)
sprintf(error_line, "Atom " TAGINT_FORMAT " is missing at world [%d] "
"rank [%d] required by rank [%d] (" TAGINT_FORMAT ", "
TAGINT_FORMAT ", " TAGINT_FORMAT ").\n",tag_send[i],
TAGINT_FORMAT ", " TAGINT_FORMAT ").\n", tag_send[i],
universe->iworld, comm->me, plan_recv[iplan],
atom->tag[0], atom->tag[1], atom->tag[2]);

2
src/USER-MISC/fix_pimd.h
View File

@ -68,7 +68,7 @@ class FixPIMD : public Fix {
/* inter-partition communication */
int max_nsend;
int* tag_send;
tagint* tag_send;
double *buf_send;
int max_nlocal;

32
src/hashlittle.cpp
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@ -23,6 +23,16 @@
# endif
#endif
// declaration to indicate intended fallthrough cases in switch statements
// and thus silence the warnings produced by g++ -Wextra
#if defined(__GNUC__)
#define _fallthrough __attribute__ ((fallthrough))
#else
#define _fallthrough
#endif
#define rot(x,k) (((x)<<(k)) | ((x)>>(32-(k))))
/*
@ -291,17 +301,17 @@ uint32_t hashlittle( const void *key, size_t length, uint32_t initval)
/*-------------------------------- last block: affect all 32 bits of (c) */
switch(length) /* all the case statements fall through */
{
case 12: c+=((uint32_t)k[11])<<24;
case 11: c+=((uint32_t)k[10])<<16;
case 10: c+=((uint32_t)k[9])<<8;
case 9 : c+=k[8];
case 8 : b+=((uint32_t)k[7])<<24;
case 7 : b+=((uint32_t)k[6])<<16;
case 6 : b+=((uint32_t)k[5])<<8;
case 5 : b+=k[4];
case 4 : a+=((uint32_t)k[3])<<24;
case 3 : a+=((uint32_t)k[2])<<16;
case 2 : a+=((uint32_t)k[1])<<8;
case 12: c+=((uint32_t)k[11])<<24; _fallthrough;
case 11: c+=((uint32_t)k[10])<<16; _fallthrough;
case 10: c+=((uint32_t)k[9])<<8; _fallthrough;
case 9 : c+=k[8]; _fallthrough;
case 8 : b+=((uint32_t)k[7])<<24; _fallthrough;
case 7 : b+=((uint32_t)k[6])<<16; _fallthrough;
case 6 : b+=((uint32_t)k[5])<<8; _fallthrough;
case 5 : b+=k[4]; _fallthrough;
case 4 : a+=((uint32_t)k[3])<<24; _fallthrough;
case 3 : a+=((uint32_t)k[2])<<16; _fallthrough;
case 2 : a+=((uint32_t)k[1])<<8; _fallthrough;
case 1 : a+=k[0];
break;
case 0 : return c;

9
src/irregular.cpp
View File

@ -921,7 +921,7 @@ void Irregular::exchange_data(char *sendbuf, int nbytes, char *recvbuf)
// post all receives, starting after self copies
bigint offset = num_self*nbytes;
bigint offset = num_self*(bigint)nbytes;
for (int irecv = 0; irecv < nrecv_proc; irecv++) {
MPI_Irecv(&recvbuf[offset],num_recv[irecv]*nbytes,MPI_CHAR,
proc_recv[irecv],0,world,&request[irecv]);
@ -964,13 +964,6 @@ void Irregular::exchange_data(char *sendbuf, int nbytes, char *recvbuf)
// wait on all incoming messages
if (nrecv_proc) MPI_Waitall(nrecv_proc,request,status);
// approximate memory tally
// DEBUG lines
//bigint irregular_bytes = 2*nprocs*sizeof(int);
//irregular_bytes += maxindex*sizeof(int);
//irregular_bytes += maxbuf;
}
/* ----------------------------------------------------------------------

201
src/special.cpp
View File

@ -821,21 +821,26 @@ void Special::angle_trim()
int nsend = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
m = atom->map(angle_atom1[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(angle_atom3[i][j]);
if (m < 0 || m >= nlocal) nsend++;
if (num_angle) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
m = atom->map(angle_atom1[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(angle_atom3[i][j]);
if (m < 0 || m >= nlocal) nsend++;
}
}
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
m = atom->map(dihedral_atom1[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(dihedral_atom3[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(dihedral_atom4[i][j]);
if (m < 0 || m >= nlocal) nsend++;
if (num_dihedral) {
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
m = atom->map(dihedral_atom1[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(dihedral_atom3[i][j]);
if (m < 0 || m >= nlocal) nsend++;
m = atom->map(dihedral_atom4[i][j]);
if (m < 0 || m >= nlocal) nsend++;
}
}
}
@ -852,51 +857,55 @@ void Special::angle_trim()
nsend = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
if (num_angle) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
m = atom->map(angle_atom1[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = angle_atom1[i][j] % nprocs;
inbuf[nsend].atomID = angle_atom1[i][j];
inbuf[nsend].partnerID = angle_atom3[i][j];
nsend++;
}
m = atom->map(angle_atom1[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = angle_atom1[i][j] % nprocs;
inbuf[nsend].atomID = angle_atom1[i][j];
inbuf[nsend].partnerID = angle_atom3[i][j];
nsend++;
}
m = atom->map(angle_atom3[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = angle_atom3[i][j] % nprocs;
inbuf[nsend].atomID = angle_atom3[i][j];
inbuf[nsend].partnerID = angle_atom1[i][j];
nsend++;
m = atom->map(angle_atom3[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = angle_atom3[i][j] % nprocs;
inbuf[nsend].atomID = angle_atom3[i][j];
inbuf[nsend].partnerID = angle_atom1[i][j];
nsend++;
}
}
}
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
if (num_dihedral) {
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
m = atom->map(dihedral_atom1[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom1[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom1[i][j];
inbuf[nsend].partnerID = dihedral_atom3[i][j];
nsend++;
}
m = atom->map(dihedral_atom1[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom1[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom1[i][j];
inbuf[nsend].partnerID = dihedral_atom3[i][j];
nsend++;
}
m = atom->map(dihedral_atom3[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom3[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom3[i][j];
inbuf[nsend].partnerID = dihedral_atom1[i][j];
nsend++;
}
m = atom->map(dihedral_atom3[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom3[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom3[i][j];
inbuf[nsend].partnerID = dihedral_atom1[i][j];
nsend++;
}
m = atom->map(dihedral_atom4[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom4[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom4[i][j];
inbuf[nsend].partnerID = dihedral_atom2[i][j];
nsend++;
m = atom->map(dihedral_atom4[i][j]);
if (m < 0 || m >= nlocal) {
proclist[nsend] = dihedral_atom4[i][j] % nprocs;
inbuf[nsend].atomID = dihedral_atom4[i][j];
inbuf[nsend].partnerID = dihedral_atom2[i][j];
nsend++;
}
}
}
}
@ -932,56 +941,60 @@ void Special::angle_trim()
// 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;
if (num_angle) {
for (j = 0; j < num_angle[i]; j++) {
if (tag[i] != angle_atom2[i][j]) continue;
m = atom->map(angle_atom1[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == angle_atom3[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(angle_atom1[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == angle_atom3[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(angle_atom3[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == angle_atom1[i][j]) {
flag[m][k] = 1;
break;
}
m = atom->map(angle_atom3[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == angle_atom1[i][j]) {
flag[m][k] = 1;
break;
}
}
}
}
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
if (num_dihedral) {
for (j = 0; j < num_dihedral[i]; j++) {
if (tag[i] != dihedral_atom2[i][j]) continue;
m = atom->map(dihedral_atom1[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom3[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(dihedral_atom1[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom3[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(dihedral_atom3[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom1[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(dihedral_atom3[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom1[i][j]) {
flag[m][k] = 1;
break;
}
}
m = atom->map(dihedral_atom4[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom2[i][j]) {
flag[m][k] = 1;
break;
}
m = atom->map(dihedral_atom4[i][j]);
if (m >= 0 && m < nlocal) {
for (k = 0; k < nspecial[m][1]; k++)
if (onethree[m][k] == dihedral_atom2[i][j]) {
flag[m][k] = 1;
break;
}
}
}
}
}
@ -1012,7 +1025,7 @@ void Special::angle_trim()
memory->destroy(flag);
// if no angles or dihedrals are defined, delete all 1-3 neighs
// if no angles or dihedrals are defined, delete all 1-3 neighs
} else {
for (i = 0; i < nlocal; i++) nspecial[i][1] = 0;