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begin refactor of parsing of sections

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This commit is contained in:
Axel Kohlmeyer
2021-03-02 11:06:24 -05:00
parent e941d0fd4a
commit 371ee63c2c
2 changed files with 40 additions and 35 deletions
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71
src/molecule.cpp
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@ -393,8 +393,8 @@ void Molecule::compute_inertia()
void Molecule::read(int flag) void Molecule::read(int flag)
{ {
char line[MAXLINE],keyword[MAXLINE]; char line[MAXLINE];
char *eof,*ptr; char *eof;
// skip 1st line of file // skip 1st line of file
@ -493,7 +493,7 @@ void Molecule::read(int flag)
// error checks // error checks
if (natoms < 1) if (natoms < 1)
error->all(FLERR,"No count or invalid atom count in molecule file"); error->all(FLERR,"No or invalid atom count in molecule file");
if (nbonds < 0) error->all(FLERR,"Invalid bond count in molecule file"); if (nbonds < 0) error->all(FLERR,"Invalid bond count in molecule file");
if (nangles < 0) error->all(FLERR,"Invalid angle count in molecule file"); if (nangles < 0) error->all(FLERR,"Invalid angle count in molecule file");
if (ndihedrals < 0) if (ndihedrals < 0)
@ -673,11 +673,14 @@ void Molecule::coords(char *line)
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 4) error->one(FLERR,"Invalid Coords section in molecule file"); if (values.count() != 4)
error->one(FLERR,fmt::format("Invalid line in Coords section of "
"molecule file: {}",line));
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
if (iatom < 0 || iatom >= natoms) error->one(FLERR,"Invalid Coords section in molecule file"); if (iatom < 0 || iatom >= natoms)
error->one(FLERR,"Invalid Coords section in molecule file");
count[iatom]++; count[iatom]++;
x[iatom][0] = values.next_double(); x[iatom][0] = values.next_double();
x[iatom][1] = values.next_double(); x[iatom][1] = values.next_double();
@ -688,8 +691,8 @@ void Molecule::coords(char *line)
x[iatom][2] *= sizescale; x[iatom][2] *= sizescale;
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->one(FLERR, fmt::format("Invalid Coords section in molecule file\n" error->one(FLERR,fmt::format("Invalid line in Coords section of "
"{}", e.what())); "molecule file: {}. {}",e.what(),line));
} }
for (int i = 0; i < natoms; i++) for (int i = 0; i < natoms; i++)
@ -714,29 +717,31 @@ void Molecule::types(char *line)
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if (values.count() != 2) error->one(FLERR,"Invalid Types section in molecule file"); error->one(FLERR,fmt::format("Invalid line in Types section of "
"molecule file: {}",line));
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
if (iatom < 0 || iatom >= natoms) error->one(FLERR,"Invalid Types section in molecule file"); if (iatom < 0 || iatom >= natoms)
error->one(FLERR,"Invalid Types section in molecule file");
count[iatom]++; count[iatom]++;
type[iatom] = values.next_int(); type[iatom] = values.next_int();
type[iatom] += toffset; type[iatom] += toffset;
} }
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->one(FLERR, fmt::format("Invalid Types section in molecule file\n" error->one(FLERR, fmt::format("Invalid line in Types section of "
"{}", e.what())); "molecule file: {}. {}", e.what(),line));
} }
for (int i = 0; i < natoms; i++) for (int i = 0; i < natoms; i++) {
if (count[i] == 0) error->all(FLERR,"Invalid Types section in molecule file"); if (count[i] == 0) error->all(FLERR,fmt::format("Atom {} missing in Types "
"section of molecule file",i));
for (int i = 0; i < natoms; i++)
if ((type[i] <= 0) || (domain->box_exist && (type[i] > atom->ntypes))) if ((type[i] <= 0) || (domain->box_exist && (type[i] > atom->ntypes)))
error->all(FLERR,"Invalid atom type in molecule file"); error->all(FLERR,fmt::format("Invalid atom type {} in molecule file",type[i]));
for (int i = 0; i < natoms; i++)
ntypes = MAX(ntypes,type[i]); ntypes = MAX(ntypes,type[i]);
}
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -750,7 +755,7 @@ void Molecule::molecules(char *line)
try { try {
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if (values.count() != 2) error->one(FLERR,"Invalid Molecules section in molecule file"); if (values.count() != 2) error->one(FLERR,"Invalid Molecules section in molecule file");
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
@ -785,7 +790,7 @@ void Molecule::fragments(char *line)
for (int i = 0; i < nfragments; i++) { for (int i = 0; i < nfragments; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if ((int)values.count() > natoms+1) if ((int)values.count() > natoms+1)
error->one(FLERR,"Invalid atom ID in Fragments section of molecule file"); error->one(FLERR,"Invalid atom ID in Fragments section of molecule file");
@ -816,7 +821,7 @@ void Molecule::charges(char *line)
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if ((int)values.count() != 2) error->one(FLERR,"Invalid Charges section in molecule file"); if ((int)values.count() != 2) error->one(FLERR,"Invalid Charges section in molecule file");
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
@ -845,7 +850,7 @@ void Molecule::diameters(char *line)
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if (values.count() != 2) error->one(FLERR,"Invalid Diameters section in molecule file"); if (values.count() != 2) error->one(FLERR,"Invalid Diameters section in molecule file");
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
@ -880,7 +885,7 @@ void Molecule::masses(char *line)
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if (values.count() != 2) error->one(FLERR,"Invalid Masses section in molecule file"); if (values.count() != 2) error->one(FLERR,"Invalid Masses section in molecule file");
int iatom = values.next_int() - 1; int iatom = values.next_int() - 1;
@ -924,7 +929,7 @@ void Molecule::bonds(int flag, char *line)
readline(line); readline(line);
try { try {
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if (values.count() != 4) error->one(FLERR,"Invalid Bonds section in molecule file"); if (values.count() != 4) error->one(FLERR,"Invalid Bonds section in molecule file");
values.next_int(); values.next_int();
itype = values.next_int(); itype = values.next_int();
@ -992,7 +997,7 @@ void Molecule::angles(int flag, char *line)
readline(line); readline(line);
try { try {
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if (values.count() != 5) error->one(FLERR,"Invalid Angles section in molecule file"); if (values.count() != 5) error->one(FLERR,"Invalid Angles section in molecule file");
values.next_int(); values.next_int();
itype = values.next_int(); itype = values.next_int();
@ -1076,7 +1081,7 @@ void Molecule::dihedrals(int flag, char *line)
readline(line); readline(line);
try { try {
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if (values.count() != 6) error->one(FLERR,"Invalid Dihedrals section in molecule file"); if (values.count() != 6) error->one(FLERR,"Invalid Dihedrals section in molecule file");
values.next_int(); values.next_int();
itype = values.next_int(); itype = values.next_int();
@ -1175,7 +1180,7 @@ void Molecule::impropers(int flag, char *line)
readline(line); readline(line);
try { try {
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if (values.count() != 6) error->one(FLERR,"Invalid Impropers section in molecule file"); if (values.count() != 6) error->one(FLERR,"Invalid Impropers section in molecule file");
values.next_int(); values.next_int();
itype = values.next_int(); itype = values.next_int();
@ -1268,7 +1273,7 @@ void Molecule::nspecial_read(int flag, char *line)
int c1, c2, c3; int c1, c2, c3;
try { try {
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if (values.count() != 4) error->one(FLERR,"Invalid Special Bond Counts section in molecule file"); if (values.count() != 4) error->one(FLERR,"Invalid Special Bond Counts section in molecule file");
values.next_int(); values.next_int();
c1 = values.next_tagint(); c1 = values.next_tagint();
@ -1297,7 +1302,7 @@ void Molecule::special_read(char *line)
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
int nwords = values.count(); int nwords = values.count();
if (nwords != nspecial[i][2]+1) if (nwords != nspecial[i][2]+1)
@ -1435,7 +1440,7 @@ void Molecule::shakeflag_read(char *line)
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
if (values.count() != 2) if (values.count() != 2)
error->one(FLERR,"Invalid Shake Flags section in molecule file"); error->one(FLERR,"Invalid Shake Flags section in molecule file");
@ -1464,7 +1469,7 @@ void Molecule::shakeatom_read(char *line)
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
nmatch = values.count(); nmatch = values.count();
switch (shake_flag[i]) { switch (shake_flag[i]) {
@ -1538,7 +1543,7 @@ void Molecule::shaketype_read(char *line)
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
nmatch = values.count(); nmatch = values.count();
switch (shake_flag[i]) { switch (shake_flag[i]) {
@ -1616,7 +1621,7 @@ void Molecule::body(int flag, int pflag, char *line)
while (nword < nparam) { while (nword < nparam) {
readline(line); readline(line);
ValueTokenizer values(line); ValueTokenizer values(utils::trim(utils::trim_comment(line)));
int ncount = values.count(); int ncount = values.count();
if (ncount == 0) if (ncount == 0)

4
src/molecule.h
View File

@ -163,8 +163,8 @@ class Molecule : protected Pointers {
void open(char *); void open(char *);
void readline(char *); void readline(char *);
void parse_keyword(int, char *, char *); std::string parse_keyword(int, char *);
void skip_lines(int, char *); void skip_lines(int, char *, const std::string &);
// void print(); // void print();
}; };