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update list and order of include files from include-what-you-use analysis

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This commit is contained in:
Axel Kohlmeyer
2021-09-18 11:35:24 -04:00
parent db76edbade
commit bca99f684f
195 changed files with 587 additions and 787 deletions
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71
src/COMPRESS/dump_atom_zstd.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,6 +18,7 @@
#ifdef LAMMPS_ZSTD
#include "domain.h"
#include "dump_atom_zstd.h"
#include "error.h"
#include "file_writer.h"
@ -26,21 +26,16 @@
#include <cstring>
using namespace LAMMPS_NS;
DumpAtomZstd::DumpAtomZstd(LAMMPS *lmp, int narg, char **arg) :
DumpAtom(lmp, narg, arg)
DumpAtomZstd::DumpAtomZstd(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg)
{
if (!compressed)
error->all(FLERR,"Dump atom/zstd only writes compressed files");
if (!compressed) error->all(FLERR, "Dump atom/zstd only writes compressed files");
}
/* ---------------------------------------------------------------------- */
DumpAtomZstd::~DumpAtomZstd()
{
}
DumpAtomZstd::~DumpAtomZstd() {}
/* ----------------------------------------------------------------------
generic opening of a dump file
@ -63,16 +58,15 @@ void DumpAtomZstd::openfile()
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
char *ptr = strchr(filestar, '*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, update->ntimestep, ptr + 1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
char bif[8], pad[16];
strcpy(bif, BIGINT_FORMAT);
sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]);
sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1);
}
*ptr = '*';
if (maxfiles > 0) {
@ -102,7 +96,7 @@ void DumpAtomZstd::openfile()
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
if (multifile) delete[] filecurrent;
}
/* ---------------------------------------------------------------------- */
@ -114,12 +108,10 @@ void DumpAtomZstd::write_header(bigint ndump)
if ((multiproc) || (!multiproc && me == 0)) {
if (unit_flag && !unit_count) {
++unit_count;
header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
header = fmt::format("ITEM: UNITS\n{}\n", update->unit_style);
}
if (time_flag) {
header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
}
if (time_flag) { header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); }
header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
@ -153,14 +145,14 @@ void DumpAtomZstd::write_data(int n, double *mybuf)
for (int i = 0; i < n; i++) {
int written = 0;
if (image_flag == 1) {
written = snprintf(vbuffer, VBUFFER_SIZE, format,
static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
written = snprintf(vbuffer, VBUFFER_SIZE, format, static_cast<tagint>(mybuf[m]),
static_cast<int>(mybuf[m + 1]), mybuf[m + 2], mybuf[m + 3], mybuf[m + 4],
static_cast<int>(mybuf[m + 5]), static_cast<int>(mybuf[m + 6]),
static_cast<int>(mybuf[m + 7]));
} else {
written = snprintf(vbuffer, VBUFFER_SIZE, format,
static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
written =
snprintf(vbuffer, VBUFFER_SIZE, format, static_cast<tagint>(mybuf[m]),
static_cast<int>(mybuf[m + 1]), mybuf[m + 2], mybuf[m + 3], mybuf[m + 4]);
}
if (written > 0) {
writer.write(vbuffer, written);
@ -182,9 +174,7 @@ void DumpAtomZstd::write()
if (multifile) {
writer.close();
} else {
if (flush_flag && writer.isopen()) {
writer.flush();
}
if (flush_flag && writer.isopen()) { writer.flush(); }
}
}
}
@ -196,20 +186,23 @@ int DumpAtomZstd::modify_param(int narg, char **arg)
int consumed = DumpAtom::modify_param(narg, arg);
if (consumed == 0) {
try {
if (strcmp(arg[0],"checksum") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) writer.setChecksum(true);
else if (strcmp(arg[1],"no") == 0) writer.setChecksum(false);
else error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[0], "checksum") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
if (strcmp(arg[1], "yes") == 0)
writer.setChecksum(true);
else if (strcmp(arg[1], "no") == 0)
writer.setChecksum(false);
else
error->all(FLERR, "Illegal dump_modify command");
return 2;
} else if (strcmp(arg[0],"compression_level") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
} else if (strcmp(arg[0], "compression_level") == 0) {
if (narg < 2) error->all(FLERR, "Illegal dump_modify command");
int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
writer.setCompressionLevel(compression_level);
return 2;
}
} catch (FileWriterException &e) {
error->one(FLERR,"Illegal dump_modify command: {}", e.what());
error->one(FLERR, "Illegal dump_modify command: {}", e.what());
}
}
return consumed;