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Remove strtok from reader_native.cpp

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This commit is contained in:
Richard Berger
2020-08-10 15:30:33 -04:00
parent b12f9d5150
commit 7d8dcb0fb0
2 changed files with 47 additions and 54 deletions
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95
src/reader_native.cpp
View File

@ -18,6 +18,7 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "tokenizer.h"
using namespace LAMMPS_NS;
@ -33,7 +34,6 @@ enum{UNSET,NOSCALE_NOWRAP,NOSCALE_WRAP,SCALE_NOWRAP,SCALE_WRAP};
ReaderNative::ReaderNative(LAMMPS *lmp) : Reader(lmp)
{
line = new char[MAXLINE];
words = NULL;
fieldindex = NULL;
}
@ -42,7 +42,6 @@ ReaderNative::ReaderNative(LAMMPS *lmp) : Reader(lmp)
ReaderNative::~ReaderNative()
{
delete [] line;
delete [] words;
memory->destroy(fieldindex);
}
@ -162,19 +161,16 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
char *labelline = &line[strlen("ITEM: ATOMS ")];
nwords = utils::trim_and_count_words(labelline);
char **labels = new char*[nwords];
labels[0] = strtok(labelline," \t\n\r\f");
if (labels[0] == NULL) {
delete[] labels;
return 1;
std::map<std::string, int> labels;
Tokenizer tokens(labelline);
nwords = 0;
while(tokens.has_next()) {
labels[tokens.next()] = nwords++;
}
for (int m = 1; m < nwords; m++) {
labels[m] = strtok(NULL," \t\n\r\f");
if (labels[m] == NULL) {
delete[] labels;
return 1;
}
if(nwords == 0) {
return 1;
}
// match each field with a column of per-atom data
@ -191,25 +187,25 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
for (int i = 0; i < nfield; i++) {
if (fieldlabel[i]) {
fieldindex[i] = find_label(fieldlabel[i],nwords,labels);
fieldindex[i] = find_label(fieldlabel[i], labels);
if (fieldtype[i] == X) xflag = 2*scaleflag + wrapflag + 1;
else if (fieldtype[i] == Y) yflag = 2*scaleflag + wrapflag + 1;
else if (fieldtype[i] == Z) zflag = 2*scaleflag + wrapflag + 1;
}
else if (fieldtype[i] == ID)
fieldindex[i] = find_label("id",nwords,labels);
fieldindex[i] = find_label("id", labels);
else if (fieldtype[i] == TYPE)
fieldindex[i] = find_label("type",nwords,labels);
fieldindex[i] = find_label("type", labels);
else if (fieldtype[i] == X) {
fieldindex[i] = find_label("x",nwords,labels);
fieldindex[i] = find_label("x", labels);
xflag = NOSCALE_WRAP;
if (fieldindex[i] < 0) {
fieldindex[i] = nwords;
s_index = find_label("xs",nwords,labels);
u_index = find_label("xu",nwords,labels);
su_index = find_label("xsu",nwords,labels);
s_index = find_label("xs", labels);
u_index = find_label("xu", labels);
su_index = find_label("xsu", labels);
if (s_index >= 0 && s_index < fieldindex[i]) {
fieldindex[i] = s_index;
xflag = SCALE_WRAP;
@ -226,13 +222,13 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
if (fieldindex[i] == nwords) fieldindex[i] = -1;
} else if (fieldtype[i] == Y) {
fieldindex[i] = find_label("y",nwords,labels);
fieldindex[i] = find_label("y", labels);
yflag = NOSCALE_WRAP;
if (fieldindex[i] < 0) {
fieldindex[i] = nwords;
s_index = find_label("ys",nwords,labels);
u_index = find_label("yu",nwords,labels);
su_index = find_label("ysu",nwords,labels);
s_index = find_label("ys", labels);
u_index = find_label("yu", labels);
su_index = find_label("ysu", labels);
if (s_index >= 0 && s_index < fieldindex[i]) {
fieldindex[i] = s_index;
yflag = SCALE_WRAP;
@ -249,13 +245,13 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
if (fieldindex[i] == nwords) fieldindex[i] = -1;
} else if (fieldtype[i] == Z) {
fieldindex[i] = find_label("z",nwords,labels);
fieldindex[i] = find_label("z", labels);
zflag = NOSCALE_WRAP;
if (fieldindex[i] < 0) {
fieldindex[i] = nwords;
s_index = find_label("zs",nwords,labels);
u_index = find_label("zu",nwords,labels);
su_index = find_label("zsu",nwords,labels);
s_index = find_label("zs", labels);
u_index = find_label("zu", labels);
su_index = find_label("zsu", labels);
if (s_index >= 0 && s_index < fieldindex[i]) {
fieldindex[i] = s_index;
zflag = SCALE_WRAP;
@ -272,42 +268,36 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
if (fieldindex[i] == nwords) fieldindex[i] = -1;
} else if (fieldtype[i] == VX)
fieldindex[i] = find_label("vx",nwords,labels);
fieldindex[i] = find_label("vx", labels);
else if (fieldtype[i] == VY)
fieldindex[i] = find_label("vy",nwords,labels);
fieldindex[i] = find_label("vy", labels);
else if (fieldtype[i] == VZ)
fieldindex[i] = find_label("vz",nwords,labels);
fieldindex[i] = find_label("vz", labels);
else if (fieldtype[i] == FX)
fieldindex[i] = find_label("fx",nwords,labels);
fieldindex[i] = find_label("fx", labels);
else if (fieldtype[i] == FY)
fieldindex[i] = find_label("fy",nwords,labels);
fieldindex[i] = find_label("fy", labels);
else if (fieldtype[i] == FZ)
fieldindex[i] = find_label("fz",nwords,labels);
fieldindex[i] = find_label("fz", labels);
else if (fieldtype[i] == Q)
fieldindex[i] = find_label("q",nwords,labels);
fieldindex[i] = find_label("q", labels);
else if (fieldtype[i] == IX)
fieldindex[i] = find_label("ix",nwords,labels);
fieldindex[i] = find_label("ix", labels);
else if (fieldtype[i] == IY)
fieldindex[i] = find_label("iy",nwords,labels);
fieldindex[i] = find_label("iy", labels);
else if (fieldtype[i] == IZ)
fieldindex[i] = find_label("iz",nwords,labels);
fieldindex[i] = find_label("iz", labels);
}
delete [] labels;
// set fieldflag = -1 if any unfound fields
fieldflag = 0;
for (int i = 0; i < nfield; i++)
if (fieldindex[i] < 0) fieldflag = -1;
// create internal vector of word ptrs for future parsing of per-atom lines
words = new char*[nwords];
return natoms;
}
@ -328,15 +318,14 @@ void ReaderNative::read_atoms(int n, int nfield, double **fields)
if (eof == NULL) error->one(FLERR,"Unexpected end of dump file");
// tokenize the line
std::vector<std::string> words = Tokenizer(line).as_vector();
words[0] = strtok(line," \t\n\r\f");
for (m = 1; m < nwords; m++)
words[m] = strtok(NULL," \t\n\r\f");
if (words.size() < nwords) error->one(FLERR,"Insufficient columns in dump file");
// convert selected fields to floats
for (m = 0; m < nfield; m++)
fields[i][m] = atof(words[fieldindex[m]]);
fields[i][m] = atof(words[fieldindex[m]].c_str());
}
}
@ -345,10 +334,12 @@ void ReaderNative::read_atoms(int n, int nfield, double **fields)
return index of match or -1 if no match
------------------------------------------------------------------------- */
int ReaderNative::find_label(const char *label, int n, char **labels)
int ReaderNative::find_label(const std::string & label, const std::map<std::string, int> & labels)
{
for (int i = 0; i < n; i++)
if (strcmp(label,labels[i]) == 0) return i;
auto it = labels.find(label);
if (it != labels.end()) {
return it->second;
}
return -1;
}

6
src/reader_native.h
View File

@ -23,6 +23,9 @@ ReaderStyle(native,ReaderNative)
#define LMP_READER_NATIVE_H
#include "reader.h"
#include <string>
#include <map>
#include <vector>
namespace LAMMPS_NS {
@ -41,10 +44,9 @@ private:
char *line; // line read from dump file
int nwords; // # of per-atom columns in dump file
char **words; // ptrs to values in parsed per-atom line
int *fieldindex; //
int find_label(const char *, int, char **);
int find_label(const std::string & label, const std::map<std::string, int> & labels);
void read_lines(int);
};