ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

add read_buf method and fix bugs in inheritance

Browse Source
This commit is contained in:
nw13slx
2021-12-11 14:02:08 -05:00
parent b1e7333348
commit eff26ba0b3
3 changed files with 52 additions and 50 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
src/reader_native.h
View File

@ -42,11 +42,12 @@ class ReaderNative : public Reader {
std::map<std::string, int> labels);
void read_atoms(int, int, double **);
protected:
int *fieldindex; //
private:
char *line; // line read from dump file
int nwords; // # of per-atom columns in dump file
int *fieldindex; //
int nwords; // # of per-atom columns in dump file
int find_label(const std::string &label, const std::map<std::string, int> &labels);
void read_lines(int);

82
src/reader_native_bin.cpp
View File

@ -23,10 +23,6 @@
using namespace LAMMPS_NS;
#define MAXLINE 1024 // max line length in dump file
// also in read_dump.cpp
enum{ID,TYPE,X,Y,Z,VX,VY,VZ,Q,IX,IY,IZ,FX,FY,FZ};
enum{UNSET,NOSCALE_NOWRAP,NOSCALE_WRAP,SCALE_NOWRAP,SCALE_WRAP};
@ -34,7 +30,6 @@ enum{UNSET,NOSCALE_NOWRAP,NOSCALE_WRAP,SCALE_NOWRAP,SCALE_WRAP};
ReaderNativeBin::ReaderNativeBin(LAMMPS *lmp) : ReaderNative(lmp)
{
line = new char[MAXLINE];
fieldindex = nullptr;
}
@ -42,7 +37,6 @@ ReaderNativeBin::ReaderNativeBin(LAMMPS *lmp) : ReaderNative(lmp)
ReaderNativeBin::~ReaderNativeBin()
{
delete [] line;
memory->destroy(fieldindex);
}
@ -55,7 +49,7 @@ ReaderNativeBin::~ReaderNativeBin()
int ReaderNativeBin::read_time(bigint &ntimestep)
{
endian = 0x0001;
int endian = 0x0001;
revision = 0x0001;
magic_string = nullptr;
unit_style = nullptr;
@ -72,17 +66,17 @@ int ReaderNativeBin::read_time(bigint &ntimestep)
delete[] magic_string;
magic_string = new char[magic_string_len + 1];
fread(magic_string, sizeof(char), magic_string_len, fp);
read_buf(magic_string, sizeof(char), magic_string_len);
magic_string[magic_string_len] = '\0';
// read endian flag
fread(&endian, sizeof(int), 1, fp);
read_buf(&endian, sizeof(int), 1);
// read revision number
fread(&revision, sizeof(int), 1, fp);
read_buf(&revision, sizeof(int), 1);
// read the real ntimestep
fread(&ntimestep, sizeof(bigint), 1, fp);
read_buf(&ntimestep, sizeof(bigint), 1);
}
return 0;
@ -96,14 +90,17 @@ int ReaderNativeBin::read_time(bigint &ntimestep)
void ReaderNativeBin::skip()
{
int nchunk;
fread(&nchunk, sizeof(int), 1, fp);
read_buf(&nchunk, sizeof(int), 1);
if (feof(fp)) {
error->one(FLERR,"Unexpected end of dump file");
}
double *buf = new double[maxbuf];
for (int i = 0; i < nchunk; i++) {
int n;
fread(&n, sizeof(int), 1, fp);
read_buf(&n, sizeof(int), 1);
// extend buffer to fit chunk size
@ -113,12 +110,13 @@ void ReaderNativeBin::skip()
maxbuf = n;
}
// read chunk and write as size_one values per line
fread(buf, sizeof(double), n, fp);
read_buf(buf, sizeof(double), n);
if (feof(fp)) {
error->one(FLERR,"Unexpected end of dump file");
}
}
delete[] buf;
delete[] magic_string;
delete[] unit_style;
magic_string = nullptr;
@ -148,31 +146,31 @@ bigint ReaderNativeBin::read_header(double box[3][3], int &boxinfo, int &triclin
{
bigint natoms;
fread(&natoms, sizeof(bigint), 1, fp);
read_buf(&natoms, sizeof(bigint), 1);
boxinfo = 1;
triclinic = 0;
box[0][2] = box[1][2] = box[2][2] = 0.0;
int boundary[3][2];
fread(&triclinic, sizeof(int), 1, fp);
fread(&boundary[0][0], 6 * sizeof(int), 1, fp);
fread(&box[0][0], sizeof(double), 1, fp);
fread(&box[0][1], sizeof(double), 1, fp);
fread(&box[1][0], sizeof(double), 1, fp);
fread(&box[1][1], sizeof(double), 1, fp);
fread(&box[2][0], sizeof(double), 1, fp);
fread(&box[2][1], sizeof(double), 1, fp);
read_buf(&triclinic, sizeof(int), 1);
read_buf(&boundary[0][0], 6 * sizeof(int), 1);
read_buf(&box[0][0], sizeof(double), 1);
read_buf(&box[0][1], sizeof(double), 1);
read_buf(&box[1][0], sizeof(double), 1);
read_buf(&box[1][1], sizeof(double), 1);
read_buf(&box[2][0], sizeof(double), 1);
read_buf(&box[2][1], sizeof(double), 1);
if (triclinic) {
fread(&box[0][2], sizeof(double), 1, fp);
fread(&box[1][2], sizeof(double), 1, fp);
fread(&box[2][2], sizeof(double), 1, fp);
read_buf(&box[0][2], sizeof(double), 1);
read_buf(&box[1][2], sizeof(double), 1);
read_buf(&box[2][2], sizeof(double), 1);
}
if (!fieldinfo) return natoms;
// exatract column labels and match to requested fields
fread(&size_one, sizeof(int), 1, fp);
read_buf(&size_one, sizeof(int), 1);
int len = 0;
char *labelline;
@ -180,33 +178,33 @@ bigint ReaderNativeBin::read_header(double box[3][3], int &boxinfo, int &triclin
if (magic_string && revision > 0x0001) {
// newer format includes units string, columns string
// and time
fread(&len, sizeof(int), 1, fp);
read_buf(&len, sizeof(int), 1);
labelline = new char[len + 1];
if (len > 0) {
// has units
delete[] unit_style;
unit_style = new char[len + 1];
fread(unit_style, sizeof(char), len, fp);
read_buf(unit_style, sizeof(char), len);
unit_style[len] = '\0';
}
char flag = 0;
fread(&flag, sizeof(char), 1, fp);
read_buf(&flag, sizeof(char), 1);
if (flag) {
double time;
fread(&time, sizeof(double), 1, fp);
read_buf(&time, sizeof(double), 1);
}
fread(&len, sizeof(int), 1, fp);
fread(labelline, sizeof(char), len, fp);
read_buf(&len, sizeof(int), 1);
read_buf(labelline, sizeof(char), len);
labelline[len] = '\0';
}
std::map<std::string, int> labels;
Tokenizer tokens(labelline);
nwords = 0;
int nwords = 0;
while (tokens.has_next()) {
labels[tokens.next()] = nwords++;
@ -234,12 +232,13 @@ void ReaderNativeBin::read_atoms(int n, int nfield, double **fields)
error->one(FLERR,"Unexpected end of dump file");
}
double *buf = new double[maxbuf];
int i_atom = 0;
int nchunk;
fread(&nchunk, sizeof(int), 1, fp);
read_buf(&nchunk, sizeof(int), 1);
for (int i = 0; i < nchunk; i++) {
fread(&n, sizeof(int), 1, fp);
read_buf(&n, sizeof(int), 1);
// extend buffer to fit chunk size
@ -251,7 +250,7 @@ void ReaderNativeBin::read_atoms(int n, int nfield, double **fields)
// read chunk and write as size_one values per line
fread(buf, sizeof(double), n, fp);
read_buf(buf, sizeof(double), n);
n /= size_one;
int m = 0;
for (int j = 0; j < n; j++)
@ -264,8 +263,17 @@ void ReaderNativeBin::read_atoms(int n, int nfield, double **fields)
}
}
delete[] buf;
delete[] magic_string;
delete[] unit_style;
magic_string = nullptr;
unit_style = nullptr;
}
void ReaderNativeBin::read_buf(void * ptr, size_t size, size_t count)
{
fread(ptr, size, count, fp);
// detect end-of-file
if (feof(fp)) error->one(FLERR,"Unexpected end of dump file");
}

15
src/reader_native_bin.h
View File

@ -15,7 +15,7 @@
#ifdef READER_CLASS
// clang-format off
ReaderStyle(native_bin,ReaderNative);
ReaderStyle(native_bin,ReaderNativeBin);
// clang-format on
#else
@ -40,21 +40,14 @@ class ReaderNativeBin : public ReaderNative {
void read_atoms(int, int, double **);
private:
char *line; // line read from dump file
int nwords; // # of per-atom columns in dump file
int *fieldindex; //
int endian;
int revision;
char *magic_string;
char *unit_style;
int size_one;
int maxbuf = 0;
double *buf = nullptr;
int maxbuf = 1;
double *buf;
int find_label(const std::string &label, const std::map<std::string, int> &labels);
void read_lines(int);
void read_buf(void *, size_t, size_t);
};
} // namespace LAMMPS_NS