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more parsing updates

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This commit is contained in:
Axel Kohlmeyer
2022-03-30 07:38:33 -04:00
parent 999c880dfd
commit 9aad583c7d
1 changed files with 24 additions and 25 deletions
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49
src/reader_native.cpp
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@ -138,14 +138,12 @@ void ReaderNative::skip()
} else {
read_lines(2);
// parse natoms value so we error out on incorrectly formatted dumps
utils::bnumeric(FLERR, utils::trim(line), true, lmp);
bigint nremain = utils::bnumeric(FLERR, utils::trim(line), true, lmp);
read_lines(5);
// invoke read_lines() in chunks no larger than MAXSMALLINT
int nchunk;
bigint nremain = natoms;
while (nremain) {
nchunk = MIN(nremain,MAXSMALLINT);
read_lines(nchunk);
@ -226,16 +224,13 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
return natoms;
}
if (is_known_magic_str() && revision > 0x0001) {
// newer format includes units string, columns string
// and time
read_buf(&len, sizeof(int), 1);
if (len > 0) {
// has units
unit_style = read_binary_str(len);
}
// has units
if (len > 0) unit_style = read_binary_str(len);
char flag = 0;
read_buf(&flag, sizeof(char), 1);
@ -255,12 +250,9 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
ichunk = 0;
iatom_chunk = 0;
} else {
int rv;
read_lines(2);
rv = sscanf(line,BIGINT_FORMAT,&natoms);
if (rv != 1)
error->one(FLERR,"Dump file is incorrectly formatted");
natoms = utils::bnumeric(FLERR, utils::trim(line), true, lmp);
boxinfo = 1;
triclinic = 0;
@ -268,20 +260,27 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
read_lines(1);
if (line[strlen("ITEM: BOX BOUNDS ")] == 'x') triclinic = 1;
read_lines(1);
if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[0][0],&box[0][1]);
else rv = 3 - sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]);
if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
try {
read_lines(1);
ValueTokenizer values(line);
box[0][0] = values.next_double();
box[0][1] = values.next_double();
if (triclinic) box[0][2] = values.next_double();
read_lines(1);
if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[1][0],&box[1][1]);
else rv = 3 - sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]);
if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
read_lines(1);
values = ValueTokenizer(line);
box[1][0] = values.next_double();
box[1][1] = values.next_double();
if (triclinic) box[1][2] = values.next_double();
read_lines(1);
if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[2][0],&box[2][1]);
else rv = 3 - sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]);
if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
read_lines(1);
values = ValueTokenizer(line);
box[2][0] = values.next_double();
box[2][1] = values.next_double();
if (triclinic) box[2][2] = values.next_double();
} catch (std::exception &e) {
error->one(FLERR, "Dump file is incorrectly formatted: {}", e.what());
}
read_lines(1);
@ -291,7 +290,7 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
// extract column labels and match to requested fields
labelline = &line[strlen("ITEM: ATOMS ")];
labelline = line + strlen("ITEM: ATOMS ");
}
Tokenizer tokens(labelline);