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modernize parsing of Bonds/Angles/Dihedrals/Impropers section of data files

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This commit is contained in:
Axel Kohlmeyer
2021-12-29 19:18:42 -05:00
parent b39d1993bb
commit 78df5c2258
1 changed files with 62 additions and 32 deletions
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94
src/atom.cpp
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@ -29,6 +29,7 @@
#include "modify.h" #include "modify.h"
#include "molecule.h" #include "molecule.h"
#include "neighbor.h" #include "neighbor.h"
#include "tokenizer.h"
#include "update.h" #include "update.h"
#include "variable.h" #include "variable.h"
@ -1252,18 +1253,25 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset)
{ {
int m,tmp,itype,rv; int m,itype;
tagint atom1,atom2; tagint atom1,atom2;
char *next; char *next;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
const std::string errtxt = "Bonds section of data file: ";
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT, try {
&tmp,&itype,&atom1,&atom2); ValueTokenizer values(utils::trim_comment(buf));
if (rv != 4) values.next_int();
error->one(FLERR,"Incorrect format of Bonds section in data file"); itype = values.next_int();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,e.what() + std::string(" in ") + errtxt + utils::trim(buf));
}
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
@ -1272,9 +1280,9 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
if ((atom1 <= 0) || (atom1 > map_tag_max) || if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) || (atom1 == atom2)) (atom2 <= 0) || (atom2 > map_tag_max) || (atom1 == atom2))
error->one(FLERR,"Invalid atom ID in Bonds section of data file"); error->one(FLERR,"Invalid atom ID in " + errtxt + utils::trim(buf));
if (itype <= 0 || itype > nbondtypes) if (itype <= 0 || itype > nbondtypes)
error->one(FLERR,"Invalid bond type in Bonds section of data file"); error->one(FLERR,"Invalid bond type in " + errtxt + utils::trim(buf));
if ((m = map(atom1)) >= 0) { if ((m = map(atom1)) >= 0) {
if (count) count[m]++; if (count) count[m]++;
else { else {
@ -1309,18 +1317,26 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset, void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset)
{ {
int m,tmp,itype,rv; int m,itype;
tagint atom1,atom2,atom3; tagint atom1,atom2,atom3;
char *next; char *next;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
const std::string errtxt = "Angles section of data file: ";
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT, try {
&tmp,&itype,&atom1,&atom2,&atom3); ValueTokenizer values(utils::trim_comment(buf));
if (rv != 5) values.next_int();
error->one(FLERR,"Incorrect format of Angles section in data file"); itype = values.next_int();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,e.what() + std::string(" in ") + errtxt + utils::trim(buf));
}
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
@ -1332,9 +1348,9 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
(atom2 <= 0) || (atom2 > map_tag_max) || (atom2 <= 0) || (atom2 > map_tag_max) ||
(atom3 <= 0) || (atom3 > map_tag_max) || (atom3 <= 0) || (atom3 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3)) (atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
error->one(FLERR,"Invalid atom ID in Angles section of data file"); error->one(FLERR,"Invalid atom ID in " + errtxt + utils::trim(buf));
if (itype <= 0 || itype > nangletypes) if (itype <= 0 || itype > nangletypes)
error->one(FLERR,"Invalid angle type in Angles section of data file"); error->one(FLERR,"Invalid angle type in " + errtxt + utils::trim(buf));
if ((m = map(atom2)) >= 0) { if ((m = map(atom2)) >= 0) {
if (count) count[m]++; if (count) count[m]++;
else { else {
@ -1381,19 +1397,27 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset, void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset)
{ {
int m,tmp,itype,rv; int m,itype;
tagint atom1,atom2,atom3,atom4; tagint atom1,atom2,atom3,atom4;
char *next; char *next;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
const std::string errtxt = "Dihedrals section of data file: ";
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT try {
" " TAGINT_FORMAT " " TAGINT_FORMAT, ValueTokenizer values(utils::trim_comment(buf));
&tmp,&itype,&atom1,&atom2,&atom3,&atom4); values.next_int();
if (rv != 6) itype = values.next_int();
error->one(FLERR,"Incorrect format of Dihedrals section in data file"); atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,e.what() + std::string(" in ") + errtxt + utils::trim(buf));
}
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
@ -1408,10 +1432,9 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
(atom4 <= 0) || (atom4 > map_tag_max) || (atom4 <= 0) || (atom4 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) || (atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4)) (atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR,"Invalid atom ID in Dihedrals section of data file"); error->one(FLERR, "Invalid atom ID in " + errtxt + utils::trim(buf));
if (itype <= 0 || itype > ndihedraltypes) if (itype <= 0 || itype > ndihedraltypes)
error->one(FLERR, error->one(FLERR, "Invalid dihedral type in " + errtxt + utils::trim(buf));
"Invalid dihedral type in Dihedrals section of data file");
if ((m = map(atom2)) >= 0) { if ((m = map(atom2)) >= 0) {
if (count) count[m]++; if (count) count[m]++;
else { else {
@ -1472,19 +1495,27 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset, void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset)
{ {
int m,tmp,itype,rv; int m,itype;
tagint atom1,atom2,atom3,atom4; tagint atom1,atom2,atom3,atom4;
char *next; char *next;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
const std::string errtxt = "Impropers section of data file: ";
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
*next = '\0'; *next = '\0';
rv = sscanf(buf,"%d %d " try {
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT, ValueTokenizer values(utils::trim_comment(buf));
&tmp,&itype,&atom1,&atom2,&atom3,&atom4); values.next_int();
if (rv != 6) itype = values.next_int();
error->one(FLERR,"Incorrect format of Impropers section in data file"); atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,e.what() + std::string(" in ") + errtxt + utils::trim(buf));
}
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
@ -1499,10 +1530,9 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
(atom4 <= 0) || (atom4 > map_tag_max) || (atom4 <= 0) || (atom4 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) || (atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4)) (atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR,"Invalid atom ID in Impropers section of data file"); error->one(FLERR, "Invalid atom ID in " + errtxt + utils::trim(buf));
if (itype <= 0 || itype > nimpropertypes) if (itype <= 0 || itype > nimpropertypes)
error->one(FLERR, error->one(FLERR, "Invalid improper type in " + errtxt + utils::trim(buf));
"Invalid improper type in Impropers section of data file");
if ((m = map(atom2)) >= 0) { if ((m = map(atom2)) >= 0) {
if (count) count[m]++; if (count) count[m]++;
else { else {