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fix issues with changes in fix STORE/PERATOM

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This commit is contained in:
Axel Kohlmeyer
2023-03-13 19:43:08 -04:00
parent 3815c0ef76
commit c369c0252f
2 changed files with 32 additions and 36 deletions
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2
src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp
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@ -179,7 +179,7 @@ void BondHarmonicRestrain::init_style()
if (!initial) {
initial = dynamic_cast<FixStorePeratom *>(
modify->add_fix("BOND_RESTRAIN_X0 all STORE/PERATOM 3 0 1 1"));
modify->add_fix("BOND_RESTRAIN_X0 all STORE/PERATOM 3 0 1 1"));
if (!initial) error->all(FLERR, "Failure to create internal per-atom storage");
}
}

66
src/fix_store_peratom.cpp
View File

@ -23,7 +23,7 @@ using namespace LAMMPS_NS;
using namespace FixConst;
// INTERNAL fix for storing/communicating per-atom values
// syntax: id group style n1 n2 gflag rflag
// syntax: id group style n1 n2 gflag rflag
// N1 = 1, N2 = 0 is per-atom vector, single value per atom
// N1 > 1, N2 = 0 is per-atom array, N1 values per atom
// N1 > 0, N2 > 0 is per-atom tensor, N1xN2 array per atom
@ -35,34 +35,36 @@ using namespace FixConst;
FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), vstore(nullptr), astore(nullptr)
{
if (narg != 8)
error->all(FLERR, "Illegal fix STORE/PERATOM command: number of args");
if (narg != 7) error->all(FLERR, "Illegal fix STORE/PERATOM command: number of args");
disable = 0;
n1 = utils::inumeric(FLERR, arg[4], false, lmp);
n2 = utils::inumeric(FLERR, arg[5], false, lmp);
ghostflag = utils::inumeric(FLERR, arg[6], false, lmp);
restartflag = utils::inumeric(FLERR, arg[7], false, lmp);
n1 = utils::inumeric(FLERR, arg[3], false, lmp);
n2 = utils::inumeric(FLERR, arg[4], false, lmp);
ghostflag = utils::logical(FLERR, arg[5], false, lmp);
restartflag = utils::logical(FLERR, arg[6], false, lmp);
vecflag = arrayflag = tensorflag = 0;
if (n1 == 1 && n2 == 0) vecflag = 1;
else if (n1 > 1 && n2 == 0) arrayflag = 1;
else if (n1 > 0 && n2 > 0) tensorflag = 1;
else error->all(FLERR, "Illegal fix STORE/PERATOM dimension args: {} {}", n1, n2);
if (restartflag < 0 || restartflag > 1)
error->all(FLERR, "Illegal fix STORE/PERATOM restart flag: {}", restartflag);
if (ghostflag < 0 || ghostflag > 1)
error->all(FLERR, "Illegal fix STORE/PERATOM ghost flag: {}", ghostflag);
if (n1 == 1 && n2 == 0)
vecflag = 1;
else if (n1 > 1 && n2 == 0)
arrayflag = 1;
else if (n1 > 0 && n2 > 0)
tensorflag = 1;
else
error->all(FLERR, "Illegal fix STORE/PERATOM dimension args: {} {}", n1, n2);
if (vecflag || arrayflag) nvalues = n1;
else nvalues = n1 * n2;
if (vecflag || arrayflag)
nvalues = n1;
else
nvalues = n1 * n2;
nbytes = nvalues * sizeof(double);
if (ghostflag) comm_border = nvalues;
maxexchange = nvalues;
if (restartflag) restart_peratom = 1;
// allocate data structs and register with Atom class
vstore = nullptr;
@ -149,7 +151,7 @@ void FixStorePeratom::copy_arrays(int i, int j, int /*delflag*/)
int FixStorePeratom::pack_border(int n, int *list, double *buf)
{
int i, j, k, ncol;
int i, j, k;
int m = 0;
if (vecflag) {
@ -160,8 +162,7 @@ int FixStorePeratom::pack_border(int n, int *list, double *buf)
} else if (arrayflag) {
for (i = 0; i < n; i++) {
j = list[i];
for (k = 0; k < nvalues; k++)
buf[m++] = astore[j][k];
for (k = 0; k < nvalues; k++) buf[m++] = astore[j][k];
}
} else if (tensorflag) {
for (i = 0; i < n; i++) {
@ -180,23 +181,22 @@ int FixStorePeratom::pack_border(int n, int *list, double *buf)
int FixStorePeratom::unpack_border(int n, int first, double *buf)
{
int i, k, last, ncol;
int i, k, last;
int m = 0;
last = first + n;
if (vecflag) {
for (i = first; i < last; i++)
vstore[i] = buf[m++];
for (i = first; i < last; i++) vstore[i] = buf[m++];
} else if (arrayflag) {
for (i = first; i < last; i++)
for (k = 0; k < nvalues; k++)
astore[i][k] = buf[m++];
for (k = 0; k < nvalues; k++) astore[i][k] = buf[m++];
} else if (tensorflag) {
for (i = first; i < last; i++) {
memcpy(&tstore[i][0][0], &buf[m], nbytes);
m += nvalues;
}
}
return m;
}
/* ----------------------------------------------------------------------
@ -210,8 +210,7 @@ int FixStorePeratom::pack_exchange(int i, double *buf)
if (vecflag) {
buf[0] = vstore[i];
} else if (arrayflag) {
for (int m = 0; m < nvalues; m++)
buf[m] = astore[i][m];
for (int m = 0; m < nvalues; m++) buf[m] = astore[i][m];
} else if (tensorflag) {
memcpy(buf, &tstore[i][0][0], nbytes);
}
@ -230,8 +229,7 @@ int FixStorePeratom::unpack_exchange(int nlocal, double *buf)
if (vecflag) {
vstore[nlocal] = buf[0];
} else if (arrayflag) {
for (int m = 0; m < nvalues; m++)
astore[nlocal][m] = buf[m];
for (int m = 0; m < nvalues; m++) astore[nlocal][m] = buf[m];
} else if (tensorflag) {
memcpy(&tstore[nlocal][0][0], buf, nbytes);
}
@ -256,8 +254,7 @@ int FixStorePeratom::pack_restart(int i, double *buf)
if (vecflag) {
buf[1] = vstore[i];
} else if (arrayflag) {
for (int m = 0; m < nvalues; m++)
buf[m + 1] = astore[i][m];
for (int m = 0; m < nvalues; m++) buf[m + 1] = astore[i][m];
} else if (tensorflag) {
memcpy(&buf[1], &tstore[i][0][0], nbytes);
}
@ -285,8 +282,7 @@ void FixStorePeratom::unpack_restart(int nlocal, int nth)
if (vecflag) {
vstore[nlocal] = extra[nlocal][m];
} else if (arrayflag) {
for (int i = 0; i < nvalues; i++)
astore[nlocal][i] = extra[nlocal][m++];
for (int i = 0; i < nvalues; i++) astore[nlocal][i] = extra[nlocal][m++];
} else if (tensorflag) {
memcpy(&tstore[nlocal][0][0], &extra[nlocal][m], nbytes);
}