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Update value parsing in Molecule

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This commit is contained in:
Richard Berger
2020-06-09 12:12:52 -04:00
parent c1f6c004ca
commit c2b557233e
2 changed files with 419 additions and 252 deletions
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508
src/molecule.cpp
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@ -27,6 +27,7 @@
#include "error.h"
#include "utils.h"
#include "fmt/format.h"
#include "tokenizer.h"
using namespace LAMMPS_NS;
@ -47,7 +48,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
improper_type(NULL), improper_atom1(NULL), improper_atom2(NULL),
improper_atom3(NULL), improper_atom4(NULL), nspecial(NULL), special(NULL),
shake_flag(NULL), shake_atom(NULL), shake_type(NULL), avec_body(NULL), ibodyparams(NULL),
dbodyparams(NULL), fragmentmask(NULL), fragmentnames(NULL),
dbodyparams(NULL), fragmentmask(NULL),
dx(NULL), dxcom(NULL), dxbody(NULL), quat_external(NULL), fp(NULL), count(NULL)
{
me = comm->me;
@ -431,47 +432,54 @@ void Molecule::read(int flag)
if (strspn(line," \t\n\r") == strlen(line)) continue;
// search line for header keywords and set corresponding variable
try {
ValueTokenizer values(line);
int nmatch = 0;
int nmatch = values.count();
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,"fragments")) {
nmatch = sscanf(line,"%d",&nfragments);
nwant = 1;
} else if (strstr(line,"mass")) {
if (values.contains("atoms")) {
natoms = values.next_int();
nwant = 2;
} else if (values.contains("bonds")) {
nbonds = values.next_int();
nwant = 2;
} else if (values.contains("angles")) {
nangles = values.next_int();
nwant = 2;
} else if (values.contains("dihedrals")) {
ndihedrals = values.next_int();
nwant = 2;
} else if (values.contains("impropers")) {
nimpropers = values.next_int();
nwant = 2;
} else if (values.contains("fragments")) {
nfragments = values.next_int();
nwant = 2;
} else if (values.contains("mass")) {
massflag = 1;
nmatch = sscanf(line,"%lg",&masstotal);
nwant = 1;
masstotal = values.next_double();
nwant = 2;
masstotal *= sizescale*sizescale*sizescale;
} else if (strstr(line,"com")) {
} else if (values.contains("com")) {
comflag = 1;
nmatch = sscanf(line,"%lg %lg %lg",&com[0],&com[1],&com[2]);
nwant = 3;
com[0] = values.next_double();
com[1] = values.next_double();
com[2] = values.next_double();
nwant = 4;
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 (values.contains("inertia")) {
inertiaflag = 1;
nmatch = sscanf(line,"%lg %lg %lg %lg %lg %lg",
&itensor[0],&itensor[1],&itensor[2],
&itensor[3],&itensor[4],&itensor[5]);
nwant = 6;
itensor[0] = values.next_double();
itensor[1] = values.next_double();
itensor[2] = values.next_double();
itensor[3] = values.next_double();
itensor[4] = values.next_double();
itensor[5] = values.next_double();
nwant = 7;
const double scale5 = sizescale*sizescale*sizescale*sizescale*sizescale;
itensor[0] *= scale5;
itensor[1] *= scale5;
@ -479,17 +487,22 @@ void Molecule::read(int flag)
itensor[3] *= scale5;
itensor[4] *= scale5;
itensor[5] *= scale5;
} else if (strstr(line,"body")) {
} else if (values.contains("body")) {
bodyflag = 1;
avec_body = (AtomVecBody *) atom->style_match("body");
if (!avec_body)
error->all(FLERR,"Molecule file requires atom style body");
nmatch = sscanf(line,"%d %d",&nibody,&ndbody);
nwant = 2;
nibody = values.next_int();
ndbody = values.next_int();
nwant = 3;
} else break;
if (nmatch != nwant)
error->all(FLERR,"Invalid header in molecule file");
error->one(FLERR,"Invalid header in molecule file");
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid header in molecule file\n"
"{}", e.what()));
}
}
// error checks
@ -666,16 +679,26 @@ void Molecule::read(int flag)
void Molecule::coords(char *line)
{
int tmp;
try {
for (int i = 0; i < natoms; i++) {
readline(line);
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");
ValueTokenizer values(line);
if (values.count() != 4) error->one(FLERR,"Invalid Coords section in molecule file");
values.next_int();
x[i][0] = values.next_double();
x[i][1] = values.next_double();
x[i][2] = values.next_double();
x[i][0] *= sizescale;
x[i][1] *= sizescale;
x[i][2] *= sizescale;
}
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Coords section in molecule file\n"
"{}", e.what()));
}
if (domain->dimension == 2) {
for (int i = 0; i < natoms; i++)
@ -691,13 +714,21 @@ void Molecule::coords(char *line)
void Molecule::types(char *line)
{
int tmp;
try {
for (int i = 0; i < natoms; i++) {
readline(line);
if (2 != sscanf(line,"%d %d",&tmp,&type[i]))
error->all(FLERR,"Invalid Types section in molecule file");
ValueTokenizer values(line);
if (values.count() != 2) error->one(FLERR,"Invalid Types section in molecule file");
values.next_int();
type[i] = values.next_int();
type[i] += toffset;
}
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Types section in molecule file\n"
"{}", e.what()));
}
for (int i = 0; i < natoms; i++)
if (type[i] <= 0 || type[i] > atom->ntypes)
@ -714,13 +745,20 @@ void Molecule::types(char *line)
void Molecule::molecules(char *line)
{
int tmp;
try {
for (int i = 0; i < natoms; i++) {
readline(line);
if (2 != sscanf(line,"%d %d",&tmp,&molecule[i]))
error->all(FLERR,"Invalid Molecules section in molecule file");
ValueTokenizer values(line);
if (values.count() != 2) error->one(FLERR,"Invalid Molecules section in molecule file");
values.next_int();
molecule[i] = values.next_int();
// molecule[i] += moffset; // placeholder for possible molecule offset
}
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Molecules section in molecule file\n"
"{}", e.what()));
}
for (int i = 0; i < natoms; i++)
if (molecule[i] <= 0)
@ -736,27 +774,28 @@ void Molecule::molecules(char *line)
void Molecule::fragments(char *line)
{
int n,m,atomID,nwords;
char **words = new char*[natoms+1];
try {
for (int i = 0; i < nfragments; i++) {
readline(line);
nwords = parse(line,words,natoms+1);
if (nwords > natoms+1)
error->all(FLERR,"Invalid atom ID in Fragments section of molecule file");
n = strlen(words[0]) + 1;
fragmentnames[i] = new char[n];
strcpy(fragmentnames[i],words[0]);
for (m = 1; m < nwords; m++) {
atomID = atoi(words[m]);
ValueTokenizer values(line);
if (values.count() > natoms+1)
error->one(FLERR,"Invalid atom ID in Fragments section of molecule file");
fragmentnames[i] = values.next_string();
while(values.has_next()) {
int atomID = values.next_int();
if (atomID <= 0 || atomID > natoms)
error->all(FLERR,"Invalid atom ID in Fragments section of molecule file");
error->one(FLERR,"Invalid atom ID in Fragments section of molecule file");
fragmentmask[i][atomID-1] = 1;
}
}
delete [] words;
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid atom ID in Fragments section of molecule file\n"
"{}", e.what()));
}
}
/* ----------------------------------------------------------------------
@ -765,11 +804,19 @@ void Molecule::fragments(char *line)
void Molecule::charges(char *line)
{
int tmp;
try {
for (int i = 0; i < natoms; i++) {
readline(line);
if (2 != sscanf(line,"%d %lg",&tmp,&q[i]))
error->all(FLERR,"Invalid Charges section in molecule file");
ValueTokenizer values(line);
if (values.count() != 2) error->one(FLERR,"Invalid Charges section in molecule file");
values.next_int();
q[i] = values.next_double();
}
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Charges section in molecule file\n"
"{}", e.what()));
}
}
@ -779,16 +826,24 @@ void Molecule::charges(char *line)
void Molecule::diameters(char *line)
{
int tmp;
try {
maxradius = 0.0;
for (int i = 0; i < natoms; i++) {
readline(line);
if (2 != sscanf(line,"%d %lg",&tmp,&radius[i]))
error->all(FLERR,"Invalid Diameters section in molecule file");
ValueTokenizer values(line);
if (values.count() != 2) error->one(FLERR,"Invalid Diameters section in molecule file");
values.next_int();
radius[i] = values.next_double();
radius[i] *= sizescale;
radius[i] *= 0.5;
maxradius = MAX(maxradius,radius[i]);
}
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Diameters section in molecule file\n"
"{}", e.what()));
}
for (int i = 0; i < natoms; i++)
if (radius[i] < 0.0)
@ -801,13 +856,21 @@ void Molecule::diameters(char *line)
void Molecule::masses(char *line)
{
int tmp;
try {
for (int i = 0; i < natoms; i++) {
readline(line);
if (2 != sscanf(line,"%d %lg",&tmp,&rmass[i]))
error->all(FLERR,"Invalid Masses section in molecule file");
ValueTokenizer values(line);
if (values.count() != 2) error->one(FLERR,"Invalid Masses section in molecule file");
values.next_int();
rmass[i] = values.next_double();
rmass[i] *= sizescale*sizescale*sizescale;
}
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Masses section in molecule file\n"
"{}", e.what()));
}
for (int i = 0; i < natoms; i++)
if (rmass[i] <= 0.0) error->all(FLERR,"Invalid atom mass in molecule file");
@ -834,9 +897,19 @@ void Molecule::bonds(int flag, char *line)
for (int i = 0; i < nbonds; i++) {
readline(line);
if (4 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2))
error->all(FLERR,"Invalid Bonds section in molecule file");
try {
ValueTokenizer values(line);
if (values.count() != 4) error->one(FLERR,"Invalid Bonds section in molecule file");
values.next_int();
itype = values.next_int();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Bonds section in molecule file\n"
"{}", e.what()));
}
itype += boffset;
if ((atom1 <= 0) || (atom1 > natoms) ||
@ -892,9 +965,20 @@ void Molecule::angles(int flag, char *line)
for (int i = 0; i < nangles; i++) {
readline(line);
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");
try {
ValueTokenizer values(line);
if (values.count() != 5) error->one(FLERR,"Invalid Angles section in molecule file");
values.next_int();
itype = values.next_int();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Angles section in molecule file\n"
"{}", e.what()));
}
itype += aoffset;
if ((atom1 <= 0) || (atom1 > natoms) ||
@ -965,10 +1049,21 @@ void Molecule::dihedrals(int flag, char *line)
for (int i = 0; i < ndihedrals; i++) {
readline(line);
if (6 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
&tmp,&itype,&atom1,&atom2,&atom3,&atom4))
error->all(FLERR,"Invalid Dihedrals section in molecule file");
try {
ValueTokenizer values(line);
if (values.count() != 6) error->one(FLERR,"Invalid Dihedrals section in molecule file");
values.next_int();
itype = values.next_int();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Dihedrals section in molecule file\n"
"{}", e.what()));
}
itype += doffset;
if ((atom1 <= 0) || (atom1 > natoms) ||
@ -1054,10 +1149,21 @@ void Molecule::impropers(int flag, char *line)
for (int i = 0; i < nimpropers; i++) {
readline(line);
if (6 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
&tmp,&itype,&atom1,&atom2,&atom3,&atom4))
error->all(FLERR,"Invalid Impropers section in molecule file");
try {
ValueTokenizer values(line);
if (values.count() != 6) error->one(FLERR,"Invalid Impropers section in molecule file");
values.next_int();
itype = values.next_int();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Impropers section in molecule file\n"
"{}", e.what()));
}
itype += ioffset;
if ((atom1 <= 0) || (atom1 > natoms) ||
@ -1131,15 +1237,24 @@ void Molecule::impropers(int flag, char *line)
void Molecule::nspecial_read(int flag, char *line)
{
int tmp,c1,c2,c3;
if (flag == 0) maxspecial = 0;
for (int i = 0; i < natoms; i++) {
readline(line);
if (4 != sscanf(line,"%d %d %d %d",&tmp,&c1,&c2,&c3))
error->all(FLERR,"Invalid Special Bond Counts section in "
"molecule file");
int c1, c2, c3;
try {
ValueTokenizer values(line);
if (values.count() != 4) error->one(FLERR,"Invalid Special Bond Counts section in molecule file");
values.next_int();
c1 = values.next_tagint();
c2 = values.next_tagint();
c3 = values.next_tagint();
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Special Bond Counts section in molecule file\n"
"{}", e.what()));
}
if (flag) {
nspecial[i][0] = c1;
@ -1155,25 +1270,30 @@ void Molecule::nspecial_read(int flag, char *line)
void Molecule::special_read(char *line)
{
int m,nwords;
char **words = new char*[maxspecial+1];
try {
for (int i = 0; i < natoms; i++) {
readline(line);
nwords = parse(line,words,maxspecial+1);
ValueTokenizer values(line);
int nwords = values.count();
if (nwords != nspecial[i][2]+1)
error->all(FLERR,"Molecule file special list "
error->one(FLERR,"Molecule file special list "
"does not match special count");
for (m = 1; m < nwords; m++) {
special[i][m-1] = ATOTAGINT(words[m]);
values.next_int(); // ignore
for (int m = 1; m < nwords; m++) {
special[i][m-1] = values.next_tagint();
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");
error->one(FLERR,"Invalid special atom index in molecule file");
}
}
delete [] words;
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Molecule file special list\n"
"{}", e.what()));
}
}
/* ----------------------------------------------------------------------
@ -1290,16 +1410,26 @@ void Molecule::special_generate()
void Molecule::shakeflag_read(char *line)
{
int tmp;
try {
for (int i = 0; i < natoms; i++) {
readline(line);
if (2 != sscanf(line,"%d %d",&tmp,&shake_flag[i]))
error->all(FLERR,"Invalid Shake Flags section in molecule file");
ValueTokenizer values(line);
if (values.count() != 2)
error->one(FLERR,"Invalid Shake Flags section in molecule file");
values.next_int();
shake_flag[i] = values.next_int();
}
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid Shake Flags section in molecule file\n"
"{}", e.what()));
}
for (int i = 0; i < natoms; i++)
if (shake_flag[i] < 0 || shake_flag[i] > 4)
error->all(FLERR,"Invalid shake flag in molecule file");
error->one(FLERR,"Invalid shake flag in molecule file");
}
/* ----------------------------------------------------------------------
@ -1308,32 +1438,58 @@ void Molecule::shakeflag_read(char *line)
void Molecule::shakeatom_read(char *line)
{
int tmp, nmatch=0, nwant=0;
int nmatch=0, nwant=0;
try {
for (int i = 0; i < natoms; i++) {
readline(line);
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]);
ValueTokenizer values(line);
nmatch = values.count();
switch (shake_flag[i]) {
case 1:
values.next_int();
shake_atom[i][0] = values.next_tagint();
shake_atom[i][1] = values.next_tagint();
shake_atom[i][2] = values.next_tagint();
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]);
break;
case 2:
values.next_int();
shake_atom[i][0] = values.next_tagint();
shake_atom[i][1] = values.next_tagint();
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]);
break;
case 3:
values.next_int();
shake_atom[i][0] = values.next_tagint();
shake_atom[i][1] = values.next_tagint();
shake_atom[i][2] = values.next_tagint();
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]);
break;
case 4:
values.next_int();
shake_atom[i][0] = values.next_tagint();
shake_atom[i][1] = values.next_tagint();
shake_atom[i][2] = values.next_tagint();
shake_atom[i][3] = values.next_tagint();
nwant = 5;
break;
default:
error->one(FLERR,"Invalid shake atom in molecule file");
}
if (nmatch != nwant)
error->all(FLERR,"Invalid shake atom in molecule file");
error->one(FLERR,"Invalid shake atom in molecule file");
}
} catch (TokenizerException & e) {
error->one(FLERR,fmt::format("Invalid shake atom in molecule file\n"
"{}", e.what()));
}
for (int i = 0; i < natoms; i++) {
@ -1341,7 +1497,7 @@ void Molecule::shakeatom_read(char *line)
if (m == 1) m = 3;
for (int j = 0; j < m; j++)
if (shake_atom[i][j] <= 0 || shake_atom[i][j] > natoms)
error->all(FLERR,"Invalid shake atom in molecule file");
error->one(FLERR,"Invalid shake atom in molecule file");
}
}
@ -1351,27 +1507,54 @@ void Molecule::shakeatom_read(char *line)
void Molecule::shaketype_read(char *line)
{
int tmp, nmatch=0, nwant=0;
try {
int nmatch=0, nwant=0;
for (int i = 0; i < natoms; i++) {
readline(line);
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]);
ValueTokenizer values(line);
nmatch = values.count();
switch (shake_flag[i]) {
case 1:
values.next_int();
shake_type[i][0] = values.next_int();
shake_type[i][1] = values.next_int();
shake_type[i][2] = values.next_int();
nwant = 4;
} else if (shake_flag[i] == 2) {
nmatch = sscanf(line,"%d %d",&tmp,&shake_type[i][0]);
break;
case 2:
values.next_int();
shake_type[i][0] = values.next_int();
nwant = 2;
} else if (shake_flag[i] == 3) {
nmatch = sscanf(line,"%d %d %d",&tmp,&shake_type[i][0],
&shake_type[i][1]);
break;
case 3:
values.next_int();
shake_type[i][0] = values.next_int();
shake_type[i][1] = values.next_int();
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]);
break;
case 4:
values.next_int();
shake_type[i][0] = values.next_int();
shake_type[i][1] = values.next_int();
shake_type[i][2] = values.next_int();
nwant = 4;
break;
default:
error->one(FLERR,"Invalid shake type data in molecule file");
}
if (nmatch != nwant)
error->all(FLERR,"Invalid shake type data in molecule file");
error->one(FLERR,"Invalid shake type data in molecule file");
}
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid shake type data in molecule file\n",
"{}", e.what()));
}
for (int i = 0; i < natoms; i++) {
@ -1379,10 +1562,10 @@ void Molecule::shaketype_read(char *line)
if (m == 1) m = 3;
for (int j = 0; j < m-1; j++)
if (shake_type[i][j] <= 0)
error->all(FLERR,"Invalid shake bond type in molecule file");
error->one(FLERR,"Invalid shake bond type in molecule file");
if (shake_flag[i] == 1)
if (shake_type[i][2] <= 0)
error->all(FLERR,"Invalid shake angle type in molecule file");
error->one(FLERR,"Invalid shake angle type in molecule file");
}
}
@ -1393,35 +1576,39 @@ void Molecule::shaketype_read(char *line)
void Molecule::body(int flag, int pflag, char *line)
{
int i,ncount;
int nparam = nibody;
if (pflag) nparam = ndbody;
int nword = 0;
try {
while (nword < nparam) {
readline(line);
ncount = utils::trim_and_count_words(line);
ValueTokenizer values(line);
int ncount = values.count();
if (ncount == 0)
error->one(FLERR,"Too few values in body section of molecule file");
if (nword+ncount > nparam)
error->all(FLERR,"Too many values in body section of molecule file");
error->one(FLERR,"Too many values in body section of molecule file");
if (flag) {
if (pflag == 0) {
ibodyparams[nword++] = force->inumeric(FLERR,strtok(line," \t\n\r\f"));
for (i = 1; i < ncount; i++)
ibodyparams[nword++] =
force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
while(values.has_next()) {
ibodyparams[nword++] = values.next_int();
}
} else {
dbodyparams[nword++] = force->numeric(FLERR,strtok(line," \t\n\r\f"));
for (i = 1; i < ncount; i++)
dbodyparams[nword++] =
force->numeric(FLERR,strtok(NULL," \t\n\r\f"));
while(values.has_next()) {
dbodyparams[nword++] = values.next_double();
}
}
} else nword += ncount;
}
} catch (TokenizerException & e) {
error->one(FLERR, fmt::format("Invalid body params in molecule file\n",
"{}", e.what()));
}
}
/* ----------------------------------------------------------------------
@ -1431,7 +1618,7 @@ void Molecule::body(int flag, int pflag, char *line)
int Molecule::findfragment(const char *name)
{
for (int i = 0; i < nfragments; i++)
if (fragmentnames[i] && strcmp(name,fragmentnames[i]) == 0) return i;
if (fragmentnames[i] == name) return i;
return -1;
}
@ -1572,7 +1759,7 @@ void Molecule::allocate()
if (typeflag) memory->create(type,natoms,"molecule:type");
if (moleculeflag) memory->create(molecule,natoms,"molecule:molecule");
if (fragmentflag) {
fragmentnames = new char*[nfragments];
fragmentnames.resize(nfragments);
memory->create(fragmentmask,nfragments,natoms,"molecule:fragmentmask");
for (int i = 0; i < nfragments; i++)
for (int j = 0; j < natoms; j++) fragmentmask[i][j] = 0;
@ -1671,9 +1858,9 @@ void Molecule::deallocate()
memory->destroy(molecule);
memory->destroy(fragmentmask);
if (fragmentflag) {
for (int i = 0; i < nfragments; i++) delete [] fragmentnames[i];
delete [] fragmentnames;
fragmentnames.clear();
}
memory->destroy(num_bond);
@ -1800,27 +1987,6 @@ void Molecule::skip_lines(int n, char *line)
for (int i = 0; i < n; i++) readline(line);
}
/* ----------------------------------------------------------------------
parse line into words separated by whitespace
return # of words
max = max pointers storable in words
------------------------------------------------------------------------- */
int Molecule::parse(char *line, char **words, int max)
{
char *ptr;
int nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((ptr = strtok(NULL," \t\n\r\f"))) {
if (nwords < max) words[nwords] = ptr;
nwords++;
}
return nwords;
}
/* ----------------------------------------------------------------------
proc 0 prints molecule params
------------------------------------------------------------------------- */

5
src/molecule.h
View File

@ -15,6 +15,8 @@
#define LMP_ONE_MOLECULE_H
#include "pointers.h"
#include <string>
#include <vector>
namespace LAMMPS_NS {
@ -94,7 +96,7 @@ class Molecule : protected Pointers {
// fragment info
int **fragmentmask; // nfragments by natoms
char **fragmentnames;
std::vector<std::string> fragmentnames;
double center[3]; // geometric center of molecule
double masstotal; // total mass of molecule
@ -163,7 +165,6 @@ class Molecule : protected Pointers {
void readline(char *);
void parse_keyword(int, char *, char *);
void skip_lines(int, char *);
int parse(char *, char **, int);
// void print();
};