From 2a7d2dee3652a229ad7a2a02e77ef558d63ed0a5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 10 Aug 2017 14:49:51 -0400
Subject: [PATCH] add more strict checking of data when parsing molecule files
to detect format errors
---
src/molecule.cpp | 433 +++++++++++++++++++++++------------------------
1 file changed, 213 insertions(+), 220 deletions(-)
diff --git a/src/molecule.cpp b/src/molecule.cpp
index e0e9ec8aaf..b0fec4bcbc 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -427,47 +427,61 @@ void Molecule::read(int flag)
// search line for header keywords and set corresponding variable
- if (strstr(line,"atoms")) sscanf(line,"%d",&natoms);
- else if (strstr(line,"bonds")) sscanf(line,"%d",&nbonds);
- else if (strstr(line,"angles")) sscanf(line,"%d",&nangles);
- else if (strstr(line,"dihedrals")) sscanf(line,"%d",&ndihedrals);
- else if (strstr(line,"impropers")) sscanf(line,"%d",&nimpropers);
-
- else if (strstr(line,"mass")) {
+ int nmatch = 0;
+ int nwant = 0;
+ if (strstr(line,"atoms")) {
+ nmatch = sscanf(line,"%d",&natoms);
+ nwant = 1;
+ } else if (strstr(line,"bonds")) {
+ nmatch = sscanf(line,"%d",&nbonds);
+ nwant = 1;
+ } else if (strstr(line,"angles")) {
+ nmatch = sscanf(line,"%d",&nangles);
+ nwant = 1;
+ } else if (strstr(line,"dihedrals")) {
+ nmatch = sscanf(line,"%d",&ndihedrals);
+ nwant = 1;
+ } else if (strstr(line,"impropers")) {
+ nmatch = sscanf(line,"%d",&nimpropers);
+ nwant = 1;
+ } else if (strstr(line,"mass")) {
massflag = 1;
- sscanf(line,"%lg",&masstotal);
+ nmatch = sscanf(line,"%lg",&masstotal);
+ nwant = 1;
masstotal *= sizescale*sizescale*sizescale;
- }
- else if (strstr(line,"com")) {
+ } else if (strstr(line,"com")) {
comflag = 1;
- sscanf(line,"%lg %lg %lg",&com[0],&com[1],&com[2]);
+ nmatch = sscanf(line,"%lg %lg %lg",&com[0],&com[1],&com[2]);
+ nwant = 3;
com[0] *= sizescale;
com[1] *= sizescale;
com[2] *= sizescale;
if (domain->dimension == 2 && com[2] != 0.0)
error->all(FLERR,"Molecule file z center-of-mass must be 0.0 for 2d");
- }
- else if (strstr(line,"inertia")) {
+ } else if (strstr(line,"inertia")) {
inertiaflag = 1;
- sscanf(line,"%lg %lg %lg %lg %lg %lg",
- &itensor[0],&itensor[1],&itensor[2],
- &itensor[3],&itensor[4],&itensor[5]);
- itensor[0] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- itensor[1] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- itensor[2] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- itensor[3] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- itensor[4] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- itensor[5] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- }
- else if (strstr(line,"body")) {
+ nmatch = sscanf(line,"%lg %lg %lg %lg %lg %lg",
+ &itensor[0],&itensor[1],&itensor[2],
+ &itensor[3],&itensor[4],&itensor[5]);
+ nwant = 6;
+ const double scale5 = sizescale*sizescale*sizescale*sizescale*sizescale;
+ itensor[0] *= scale5;
+ itensor[1] *= scale5;
+ itensor[2] *= scale5;
+ itensor[3] *= scale5;
+ itensor[4] *= scale5;
+ itensor[5] *= scale5;
+ } else if (strstr(line,"body")) {
bodyflag = 1;
avec_body = (AtomVecBody *) atom->style_match("body");
if (!avec_body)
error->all(FLERR,"Molecule file requires atom style body");
- sscanf(line,"%d %d",&nibody,&ndbody);
- }
+ nmatch = sscanf(line,"%d %d",&nibody,&ndbody);
+ nwant = 2;
+ } else break;
- else break;
+ if (nmatch != nwant)
+ error->all(FLERR,"Invalid header in molecule file");
}
// error checks
@@ -493,7 +507,7 @@ void Molecule::read(int flag)
// loop over sections of molecule file
- while (strlen(keyword)) {
+ while (strlen(keyword) > 0) {
if (strcmp(keyword,"Coords") == 0) {
xflag = 1;
if (flag) coords(line);
@@ -517,22 +531,22 @@ void Molecule::read(int flag)
} else if (strcmp(keyword,"Bonds") == 0) {
if (nbonds == 0)
- error->all(FLERR,"Molecule file has bonds but no nbonds setting");
+ error->all(FLERR,"Molecule file has bonds but no nbonds setting");
bondflag = tag_require = 1;
bonds(flag,line);
} else if (strcmp(keyword,"Angles") == 0) {
if (nangles == 0)
- error->all(FLERR,"Molecule file has angles but no nangles setting");
+ error->all(FLERR,"Molecule file has angles but no nangles setting");
angleflag = tag_require = 1;
angles(flag,line);
} else if (strcmp(keyword,"Dihedrals") == 0) {
if (ndihedrals == 0) error->all(FLERR,"Molecule file has dihedrals "
- "but no ndihedrals setting");
+ "but no ndihedrals setting");
dihedralflag = tag_require = 1;
dihedrals(flag,line);
} else if (strcmp(keyword,"Impropers") == 0) {
if (nimpropers == 0) error->all(FLERR,"Molecule file has impropers "
- "but no nimpropers setting");
+ "but no nimpropers setting");
improperflag = tag_require = 1;
impropers(flag,line);
@@ -552,26 +566,26 @@ void Molecule::read(int flag)
shakeatomflag = tag_require = 1;
if (shaketypeflag) shakeflag = 1;
if (!shakeflagflag)
- error->all(FLERR,"Molecule file shake flags not before shake atoms");
+ error->all(FLERR,"Molecule file shake flags not before shake atoms");
if (flag) shakeatom_read(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Shake Bond Types") == 0) {
shaketypeflag = 1;
if (shakeatomflag) shakeflag = 1;
if (!shakeflagflag)
- error->all(FLERR,"Molecule file shake flags not before shake bonds");
+ error->all(FLERR,"Molecule file shake flags not before shake bonds");
if (flag) shaketype_read(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Body Integers") == 0) {
if (bodyflag == 0 || nibody == 0)
- error->all(FLERR,"Molecule file has body params "
+ error->all(FLERR,"Molecule file has body params "
"but no setting for them");
ibodyflag = 1;
body(flag,0,line);
} else if (strcmp(keyword,"Body Doubles") == 0) {
if (bodyflag == 0 || ndbody == 0)
- error->all(FLERR,"Molecule file has body params "
+ error->all(FLERR,"Molecule file has body params "
"but no setting for them");
dbodyflag = 1;
body(flag,1,line);
@@ -618,7 +632,7 @@ void Molecule::read(int flag)
// body particle must have natom = 1
// set radius by having body class compute its own radius
-
+
if (bodyflag) {
radiusflag = 1;
if (natoms != 1)
@@ -641,12 +655,9 @@ void Molecule::coords(char *line)
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 4)
- error->all(FLERR,"Invalid Coords section in molecule file");
- }
- sscanf(line,"%d %lg %lg %lg",&tmp,&x[i][0],&x[i][1],&x[i][2]);
+ if (4 != sscanf(line,"%d %lg %lg %lg",&tmp,&x[i][0],&x[i][1],&x[i][2]))
+ error->all(FLERR,"Invalid Coords section in molecule file");
+
x[i][0] *= sizescale;
x[i][1] *= sizescale;
x[i][2] *= sizescale;
@@ -669,12 +680,8 @@ void Molecule::types(char *line)
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 2)
- error->all(FLERR,"Invalid Types section in molecule file");
- }
- sscanf(line,"%d %d",&tmp,&type[i]);
+ if (2 != sscanf(line,"%d %d",&tmp,&type[i]))
+ error->all(FLERR,"Invalid Types section in molecule file");
type[i] += toffset;
}
@@ -695,12 +702,8 @@ void Molecule::charges(char *line)
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 2)
- error->all(FLERR,"Invalid Charges section in molecule file");
- }
- sscanf(line,"%d %lg",&tmp,&q[i]);
+ if (2 != sscanf(line,"%d %lg",&tmp,&q[i]))
+ error->all(FLERR,"Invalid Charges section in molecule file");
}
}
@@ -714,12 +717,8 @@ void Molecule::diameters(char *line)
maxradius = 0.0;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 2)
- error->all(FLERR,"Invalid Diameters section in molecule file");
- }
- sscanf(line,"%d %lg",&tmp,&radius[i]);
+ if (2 != sscanf(line,"%d %lg",&tmp,&radius[i]))
+ error->all(FLERR,"Invalid Diameters section in molecule file");
radius[i] *= sizescale;
radius[i] *= 0.5;
maxradius = MAX(maxradius,radius[i]);
@@ -739,12 +738,8 @@ void Molecule::masses(char *line)
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 2)
- error->all(FLERR,"Invalid Masses section in molecule file");
- }
- sscanf(line,"%d %lg",&tmp,&rmass[i]);
+ if (2 != sscanf(line,"%d %lg",&tmp,&rmass[i]))
+ error->all(FLERR,"Invalid Masses section in molecule file");
rmass[i] *= sizescale*sizescale*sizescale;
}
@@ -773,17 +768,13 @@ void Molecule::bonds(int flag, char *line)
for (int i = 0; i < nbonds; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 4)
- error->all(FLERR,"Invalid Bonds section in molecule file");
- }
- sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&itype,&atom1,&atom2);
+ if (4 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&itype,&atom1,&atom2))
+ error->all(FLERR,"Invalid Bonds section in molecule file");
itype += boffset;
if (atom1 <= 0 || atom1 > natoms ||
- atom2 <= 0 || atom2 > natoms)
+ atom2 <= 0 || atom2 > natoms)
error->one(FLERR,"Invalid atom ID in Bonds section of molecule file");
if (itype <= 0)
error->one(FLERR,"Invalid bond type in Bonds section of molecule file");
@@ -795,10 +786,10 @@ void Molecule::bonds(int flag, char *line)
bond_atom[m][num_bond[m]] = atom2;
num_bond[m]++;
if (newton_bond == 0) {
- m = atom2-1;
- bond_type[m][num_bond[m]] = itype;
- bond_atom[m][num_bond[m]] = atom1;
- num_bond[m]++;
+ m = atom2-1;
+ bond_type[m][num_bond[m]] = itype;
+ bond_atom[m][num_bond[m]] = atom1;
+ num_bond[m]++;
}
} else {
count[atom1-1]++;
@@ -835,13 +826,9 @@ void Molecule::angles(int flag, char *line)
for (int i = 0; i < nangles; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 5)
- error->all(FLERR,"Invalid Angles section in molecule file");
- }
- sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&itype,&atom1,&atom2,&atom3);
+ if (5 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&itype,&atom1,&atom2,&atom3))
+ error->all(FLERR,"Invalid Angles section in molecule file");
itype += aoffset;
if (atom1 <= 0 || atom1 > natoms ||
@@ -860,24 +847,24 @@ void Molecule::angles(int flag, char *line)
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
if (newton_bond == 0) {
- m = atom1-1;
- angle_type[m][num_angle[m]] = itype;
- angle_atom1[m][num_angle[m]] = atom1;
- angle_atom2[m][num_angle[m]] = atom2;
- angle_atom3[m][num_angle[m]] = atom3;
- num_angle[m]++;
- m = atom3-1;
- angle_type[m][num_angle[m]] = itype;
- angle_atom1[m][num_angle[m]] = atom1;
- angle_atom2[m][num_angle[m]] = atom2;
- angle_atom3[m][num_angle[m]] = atom3;
- num_angle[m]++;
+ m = atom1-1;
+ angle_type[m][num_angle[m]] = itype;
+ angle_atom1[m][num_angle[m]] = atom1;
+ angle_atom2[m][num_angle[m]] = atom2;
+ angle_atom3[m][num_angle[m]] = atom3;
+ num_angle[m]++;
+ m = atom3-1;
+ angle_type[m][num_angle[m]] = itype;
+ angle_atom1[m][num_angle[m]] = atom1;
+ angle_atom2[m][num_angle[m]] = atom2;
+ angle_atom3[m][num_angle[m]] = atom3;
+ num_angle[m]++;
}
} else {
count[atom2-1]++;
if (newton_bond == 0) {
- count[atom1-1]++;
- count[atom3-1]++;
+ count[atom1-1]++;
+ count[atom3-1]++;
}
}
}
@@ -911,14 +898,10 @@ void Molecule::dihedrals(int flag, char *line)
for (int i = 0; i < ndihedrals; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 6)
- error->all(FLERR,"Invalid Dihedrals section in molecule file");
- }
- sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ if (6 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
- &tmp,&itype,&atom1,&atom2,&atom3,&atom4);
+ &tmp,&itype,&atom1,&atom2,&atom3,&atom4))
+ error->all(FLERR,"Invalid Dihedrals section in molecule file");
itype += doffset;
if (atom1 <= 0 || atom1 > natoms ||
@@ -926,10 +909,10 @@ void Molecule::dihedrals(int flag, char *line)
atom3 <= 0 || atom3 > natoms ||
atom4 <= 0 || atom4 > natoms)
error->one(FLERR,
- "Invalid atom ID in dihedrals section of molecule file");
+ "Invalid atom ID in dihedrals section of molecule file");
if (itype <= 0)
error->one(FLERR,
- "Invalid dihedral type in dihedrals section of molecule file");
+ "Invalid dihedral type in dihedrals section of molecule file");
if (flag) {
m = atom2-1;
@@ -941,34 +924,34 @@ void Molecule::dihedrals(int flag, char *line)
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
if (newton_bond == 0) {
- m = atom1-1;
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
- m = atom3-1;
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
- m = atom4-1;
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
+ m = atom1-1;
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
+ m = atom3-1;
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
+ m = atom4-1;
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
}
} else {
count[atom2-1]++;
if (newton_bond == 0) {
- count[atom1-1]++;
- count[atom3-1]++;
- count[atom4-1]++;
+ count[atom1-1]++;
+ count[atom3-1]++;
+ count[atom4-1]++;
}
}
}
@@ -1002,14 +985,10 @@ void Molecule::impropers(int flag, char *line)
for (int i = 0; i < nimpropers; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 6)
- error->all(FLERR,"Invalid Impropers section in molecule file");
- }
- sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ if (6 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
- &tmp,&itype,&atom1,&atom2,&atom3,&atom4);
+ &tmp,&itype,&atom1,&atom2,&atom3,&atom4))
+ error->all(FLERR,"Invalid Impropers section in molecule file");
itype += ioffset;
if (atom1 <= 0 || atom1 > natoms ||
@@ -1017,10 +996,10 @@ void Molecule::impropers(int flag, char *line)
atom3 <= 0 || atom3 > natoms ||
atom4 <= 0 || atom4 > natoms)
error->one(FLERR,
- "Invalid atom ID in impropers section of molecule file");
+ "Invalid atom ID in impropers section of molecule file");
if (itype <= 0)
error->one(FLERR,
- "Invalid improper type in impropers section of molecule file");
+ "Invalid improper type in impropers section of molecule file");
if (flag) {
m = atom2-1;
@@ -1032,34 +1011,34 @@ void Molecule::impropers(int flag, char *line)
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
if (newton_bond == 0) {
- m = atom1-1;
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
- m = atom3-1;
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
- m = atom4-1;
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
+ m = atom1-1;
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
+ m = atom3-1;
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
+ m = atom4-1;
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
}
} else {
count[atom2-1]++;
if (newton_bond == 0) {
- count[atom1-1]++;
- count[atom3-1]++;
- count[atom4-1]++;
+ count[atom1-1]++;
+ count[atom3-1]++;
+ count[atom4-1]++;
}
}
}
@@ -1087,13 +1066,9 @@ void Molecule::nspecial_read(int flag, char *line)
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 4)
- error->all(FLERR,"Invalid Special Bond Counts section in "
- "molecule file");
- }
- sscanf(line,"%d %d %d %d",&tmp,&c1,&c2,&c3);
+ if (4 != sscanf(line,"%d %d %d %d",&tmp,&c1,&c2,&c3))
+ error->all(FLERR,"Invalid Special Bond Counts section in "
+ "molecule file");
if (flag) {
nspecial[i][0] = c1;
@@ -1117,13 +1092,13 @@ void Molecule::special_read(char *line)
nwords = parse(line,words,maxspecial+1);
if (nwords != nspecial[i][2]+1)
error->all(FLERR,"Molecule file special list "
- "does not match special count");
+ "does not match special count");
for (m = 1; m < nwords; m++) {
special[i][m-1] = ATOTAGINT(words[m]);
if (special[i][m-1] <= 0 || special[i][m-1] > natoms ||
- special[i][m-1] == i+1)
- error->all(FLERR,"Invalid special atom index in molecule file");
+ special[i][m-1] == i+1)
+ error->all(FLERR,"Invalid special atom index in molecule file");
}
}
@@ -1229,7 +1204,8 @@ void Molecule::shakeflag_read(char *line)
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
- sscanf(line,"%d %d",&tmp,&shake_flag[i]);
+ if (2 != sscanf(line,"%d %d",&tmp,&shake_flag[i]))
+ error->all(FLERR,"Invalid Shake Flags section in molecule file");
}
for (int i = 0; i < natoms; i++)
@@ -1243,23 +1219,32 @@ void Molecule::shakeflag_read(char *line)
void Molecule::shakeatom_read(char *line)
{
- int tmp;
+ int tmp, nmatch, nwant;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (shake_flag[i] == 1)
- sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
- else if (shake_flag[i] == 2)
- sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&shake_atom[i][0],&shake_atom[i][1]);
- else if (shake_flag[i] == 3)
- sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
- else if (shake_flag[i] == 4)
- sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&shake_atom[i][0],&shake_atom[i][1],
- &shake_atom[i][2],&shake_atom[i][3]);
+ if (shake_flag[i] == 1) {
+ nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT
+ " " TAGINT_FORMAT,&tmp,&shake_atom[i][0],
+ &shake_atom[i][1],&shake_atom[i][2]);
+ nwant = 4;
+ } else if (shake_flag[i] == 2) {
+ nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&shake_atom[i][0],&shake_atom[i][1]);
+ nwant = 3;
+ } else if (shake_flag[i] == 3) {
+ nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT
+ " " TAGINT_FORMAT,&tmp,&shake_atom[i][0],
+ &shake_atom[i][1],&shake_atom[i][2]);
+ nwant = 4;
+ } else if (shake_flag[i] == 4) {
+ nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&shake_atom[i][0],&shake_atom[i][1],
+ &shake_atom[i][2],&shake_atom[i][3]);
+ nwant = 5;
+ }
+ if (nmatch != nwant)
+ error->all(FLERR,"Invalid shake atom in molecule file");
}
for (int i = 0; i < natoms; i++) {
@@ -1277,19 +1262,27 @@ void Molecule::shakeatom_read(char *line)
void Molecule::shaketype_read(char *line)
{
- int tmp;
+ int tmp,nmatch,nwant;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (shake_flag[i] == 1)
- sscanf(line,"%d %d %d %d",&tmp,
- &shake_type[i][0],&shake_type[i][1],&shake_type[i][2]);
- else if (shake_flag[i] == 2)
- sscanf(line,"%d %d",&tmp,&shake_type[i][0]);
- else if (shake_flag[i] == 3)
- sscanf(line,"%d %d %d",&tmp,&shake_type[i][0],&shake_type[i][1]);
- else if (shake_flag[i] == 4)
- sscanf(line,"%d %d %d %d",&tmp,
- &shake_type[i][0],&shake_type[i][1],&shake_type[i][2]);
+ if (shake_flag[i] == 1) {
+ nmatch = sscanf(line,"%d %d %d %d",&tmp,&shake_type[i][0],
+ &shake_type[i][1],&shake_type[i][2]);
+ nwant = 4;
+ } else if (shake_flag[i] == 2) {
+ nmatch = sscanf(line,"%d %d",&tmp,&shake_type[i][0]);
+ nwant = 2;
+ } else if (shake_flag[i] == 3) {
+ nmatch = sscanf(line,"%d %d %d",&tmp,&shake_type[i][0],
+ &shake_type[i][1]);
+ nwant = 3;
+ } else if (shake_flag[i] == 4) {
+ nmatch = sscanf(line,"%d %d %d %d",&tmp,&shake_type[i][0],
+ &shake_type[i][1],&shake_type[i][2]);
+ nwant = 4;
+ }
+ if (nmatch != nwant)
+ error->all(FLERR,"Invalid shake type data in molecule file");
}
for (int i = 0; i < natoms; i++) {
@@ -1501,46 +1494,46 @@ void Molecule::allocate()
if (bondflag) {
memory->create(bond_type,natoms,bond_per_atom,
- "molecule:bond_type");
+ "molecule:bond_type");
memory->create(bond_atom,natoms,bond_per_atom,
- "molecule:bond_atom");
+ "molecule:bond_atom");
}
if (angleflag) {
memory->create(angle_type,natoms,angle_per_atom,
- "molecule:angle_type");
+ "molecule:angle_type");
memory->create(angle_atom1,natoms,angle_per_atom,
- "molecule:angle_atom1");
+ "molecule:angle_atom1");
memory->create(angle_atom2,natoms,angle_per_atom,
- "molecule:angle_atom2");
+ "molecule:angle_atom2");
memory->create(angle_atom3,natoms,angle_per_atom,
- "molecule:angle_atom3");
+ "molecule:angle_atom3");
}
if (dihedralflag) {
memory->create(dihedral_type,natoms,dihedral_per_atom,
- "molecule:dihedral_type");
+ "molecule:dihedral_type");
memory->create(dihedral_atom1,natoms,dihedral_per_atom,
- "molecule:dihedral_atom1");
+ "molecule:dihedral_atom1");
memory->create(dihedral_atom2,natoms,dihedral_per_atom,
- "molecule:dihedral_atom2");
+ "molecule:dihedral_atom2");
memory->create(dihedral_atom3,natoms,dihedral_per_atom,
- "molecule:dihedral_atom3");
+ "molecule:dihedral_atom3");
memory->create(dihedral_atom4,natoms,dihedral_per_atom,
- "molecule:dihedral_atom4");
+ "molecule:dihedral_atom4");
}
if (improperflag) {
memory->create(improper_type,natoms,improper_per_atom,
- "molecule:improper_type");
+ "molecule:improper_type");
memory->create(improper_atom1,natoms,improper_per_atom,
- "molecule:improper_atom1");
+ "molecule:improper_atom1");
memory->create(improper_atom2,natoms,improper_per_atom,
- "molecule:improper_atom2");
+ "molecule:improper_atom2");
memory->create(improper_atom3,natoms,improper_per_atom,
- "molecule:improper_atom3");
+ "molecule:improper_atom3");
memory->create(improper_atom4,natoms,improper_per_atom,
- "molecule:improper_atom4");
+ "molecule:improper_atom4");
}
if (shakeflag) {
@@ -1653,7 +1646,7 @@ void Molecule::parse_keyword(int flag, char *line, char *keyword)
if (me == 0) {
if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) {
- if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
+ if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
}
if (fgets(keyword,MAXLINE,fp) == NULL) eof = 1;
}
--
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