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Handle mass better

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This commit is contained in:
Francois-Xavier Coudert
2025-03-27 20:14:29 +01:00
parent dcb844b01b
commit 032c1c39b0
1 changed files with 29 additions and 24 deletions
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53
src/EXTRA-DUMP/dump_extxyz.cpp
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@ -145,6 +145,7 @@ void DumpExtXYZ::pack(tagint *ids)
double **v = atom->v; double **v = atom->v;
double **f = atom->f; double **f = atom->f;
double *mass = atom->mass; double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
m = n = 0; m = n = 0;
@ -166,7 +167,11 @@ void DumpExtXYZ::pack(tagint *ids)
buf[m++] = f[i][2]; buf[m++] = f[i][2];
} }
if (with_mass) { if (with_mass) {
buf[m++] = mass[type[i]]; if (rmass) {
buf[m++] = rmass[i];
} else {
buf[m++] = mass[type[i]];
}
} }
if (ids) ids[n++] = tag[i]; if (ids) ids[n++] = tag[i];
@ -191,31 +196,31 @@ int DumpExtXYZ::convert_string(int n, double *mybuf)
if (size_one == 5) { if (size_one == 5) {
offset += offset +=
snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])], snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])],
mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]); mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]);
} else if (size_one == 6) { } else if (size_one == 6) {
offset += offset +=
snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])], snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])],
mybuf[m + 2], mybuf[m + 3], mybuf[m + 4], mybuf[m + 5]); mybuf[m + 2], mybuf[m + 3], mybuf[m + 4], mybuf[m + 5]);
} else if (size_one == 8) { } else if (size_one == 8) {
offset += offset +=
snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])], snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])],
mybuf[m + 2], mybuf[m + 3], mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7]); mybuf[m + 2], mybuf[m + 3], mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7]);
} else if (size_one == 9) { } else if (size_one == 9) {
offset += offset +=
snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])], snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])],
mybuf[m + 2], mybuf[m + 3], mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 2], mybuf[m + 3], mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7],
mybuf[m + 8]); mybuf[m + 8]);
} else if (size_one == 11) { } else if (size_one == 11) {
offset += offset +=
snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])], snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])],
mybuf[m + 2], mybuf[m + 3], mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 2], mybuf[m + 3], mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7],
mybuf[m + 8], mybuf[m + 9], mybuf[m + 10]); mybuf[m + 8], mybuf[m + 9], mybuf[m + 10]);
} else if (size_one == 12) { } else if (size_one == 12) {
offset += offset +=
snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])], snprintf(&sbuf[offset], maxsbuf - offset, format, typenames[static_cast<int>(mybuf[m + 1])],
mybuf[m + 2], mybuf[m + 3], mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 2], mybuf[m + 3], mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7],
mybuf[m + 8], mybuf[m + 9], mybuf[m + 10], mybuf[m + 11]); mybuf[m + 8], mybuf[m + 9], mybuf[m + 10], mybuf[m + 11]);
} else { } else {
error->all(FLERR,"Invalid value of size_one for dump extxyz format."); error->all(FLERR,"Invalid value of size_one for dump extxyz format.");
} }
@ -233,24 +238,24 @@ void DumpExtXYZ::write_lines(int n, double *mybuf)
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
if (size_one == 5) { if (size_one == 5) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3], fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4]); mybuf[m + 4]);
} else if (size_one == 6) { } else if (size_one == 6) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3], fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5]); mybuf[m + 4], mybuf[m + 5]);
} else if (size_one == 8) { } else if (size_one == 8) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3], fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7]); mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7]);
} else if (size_one == 9) { } else if (size_one == 9) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3], fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8]); mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8]);
} else if (size_one == 11) { } else if (size_one == 11) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3], fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8], mybuf[m + 9], mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8], mybuf[m + 9],
mybuf[m + 10]); mybuf[m + 10]);
} else if (size_one == 12) { } else if (size_one == 12) {
fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3], fprintf(fp, format, typenames[static_cast<int>(mybuf[m + 1])], mybuf[m + 2], mybuf[m + 3],
mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8], mybuf[m + 9], mybuf[m + 4], mybuf[m + 5], mybuf[m + 6], mybuf[m + 7], mybuf[m + 8], mybuf[m + 9],
mybuf[m + 10], mybuf[m + 11]); mybuf[m + 10], mybuf[m + 11]);
} else { } else {
error->all(FLERR,"Invalid value of size_one for dump extxyz format."); error->all(FLERR,"Invalid value of size_one for dump extxyz format.");
} }