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Merge branch 'develop' into BPM

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This commit is contained in:
jtclemm
2022-01-12 10:52:11 -07:00
committed by GitHub
parent 744e615dbb 878557dd48
commit 19abc5d329
884 changed files with 39864 additions and 18216 deletions
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235
src/atom.cpp
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@ -29,6 +29,7 @@
#include "modify.h"
#include "molecule.h"
#include "neighbor.h"
#include "tokenizer.h"
#include "update.h"
#include "variable.h"
@ -889,10 +890,10 @@ void Atom::tag_check()
MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (minall < 0) error->all(FLERR,"One or more Atom IDs is negative");
if (maxall >= MAXTAGINT) error->all(FLERR,"One or more atom IDs is too big");
if (minall < 0) error->all(FLERR,"One or more Atom IDs are negative");
if (maxall >= MAXTAGINT) error->all(FLERR,"One or more atom IDs are too big");
if (maxall > 0 && minall == 0)
error->all(FLERR,"One or more atom IDs is zero");
error->all(FLERR,"One or more atom IDs are zero");
if (maxall > 0 && tag_enable == 0)
error->all(FLERR,"Non-zero atom IDs with atom_modify id = no");
if (maxall == 0 && natoms && tag_enable)
@ -1061,6 +1062,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
double *coord;
char *next;
// use the first line to detect and validate the number of words/tokens per line
next = strchr(buf,'\n');
*next = '\0';
int nwords = utils::trim_and_count_words(buf);
@ -1069,8 +1071,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
if (nwords != avec->size_data_atom && nwords != avec->size_data_atom + 3)
error->all(FLERR,"Incorrect atom format in data file");
char **values = new char*[nwords];
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// insures all data atoms will be owned even with round-off
@ -1141,15 +1141,10 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
for (m = 0; m < nwords; m++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
if (strlen(buf) == 0)
error->all(FLERR,"Incorrect atom format in data file");
values[m] = buf;
buf += strlen(buf)+1;
}
*next = '\0';
auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
if (values.size() != nwords)
error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
int imx = 0, imy = 0, imz = 0;
if (imageflag) {
@ -1196,7 +1191,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
@ -1208,7 +1202,6 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
void Atom::data_vels(int n, char *buf, tagint id_offset)
{
int j,m;
tagint tagdata;
char *next;
next = strchr(buf,'\n');
@ -1219,31 +1212,24 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
if (nwords != avec->size_data_vel)
error->all(FLERR,"Incorrect velocity format in data file");
char **values = new char*[nwords];
// loop over lines of atom velocities
// tokenize the line into values
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
if (values.size() != nwords)
error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
for (j = 0; j < nwords; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
values[j] = buf;
buf += strlen(buf)+1;
}
tagdata = ATOTAGINT(values[0]) + id_offset;
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Velocities section of data file");
if ((m = map(tagdata)) >= 0) avec->data_vel(m,&values[1]);
if ((m = map(tagdata)) >= 0) avec->data_vel(m,values);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
@ -1256,18 +1242,25 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype,rv;
int m,itype;
tagint atom1,atom2;
char *next;
int newton_bond = force->newton_bond;
auto location = "Bonds section of data file";
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2);
if (rv != 4)
error->one(FLERR,"Incorrect format of Bonds section in data file");
try {
ValueTokenizer values(utils::trim_comment(buf));
values.next_int();
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,"{} in {}: {}", e.what(), location, utils::trim(buf));
}
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
@ -1276,9 +1269,9 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(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 {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nbondtypes)
error->one(FLERR,"Invalid bond type in Bonds section of data file");
error->one(FLERR,"Invalid bond type in {}: {}", location, utils::trim(buf));
if ((m = map(atom1)) >= 0) {
if (count) count[m]++;
else {
@ -1313,18 +1306,26 @@ 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,
int type_offset)
{
int m,tmp,itype,rv;
int m,itype;
tagint atom1,atom2,atom3;
char *next;
int newton_bond = force->newton_bond;
auto location = "Angles section of data file";
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3);
if (rv != 5)
error->one(FLERR,"Incorrect format of Angles section in data file");
try {
ValueTokenizer values(utils::trim_comment(buf));
values.next_int();
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,"{} in {}: {}", e.what(), location, utils::trim(buf));
}
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
@ -1336,9 +1337,9 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
(atom2 <= 0) || (atom2 > map_tag_max) ||
(atom3 <= 0) || (atom3 > map_tag_max) ||
(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 {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nangletypes)
error->one(FLERR,"Invalid angle type in Angles section of data file");
error->one(FLERR,"Invalid angle type in {}: {}", location, utils::trim(buf));
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
@ -1385,19 +1386,27 @@ 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,
int type_offset)
{
int m,tmp,itype,rv;
int m,itype;
tagint atom1,atom2,atom3,atom4;
char *next;
int newton_bond = force->newton_bond;
auto location = "Dihedrals section of data file";
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT
" " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (rv != 6)
error->one(FLERR,"Incorrect format of Dihedrals section in data file");
try {
ValueTokenizer values(utils::trim_comment(buf));
values.next_int();
itype = values.next_int();
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,"{} in {}: {}", e.what(), location, utils::trim(buf));
}
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
@ -1412,10 +1421,9 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
(atom4 <= 0) || (atom4 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == 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 {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > ndihedraltypes)
error->one(FLERR,
"Invalid dihedral type in Dihedrals section of data file");
error->one(FLERR, "Invalid dihedral type in {}: {}", location, utils::trim(buf));
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
@ -1476,19 +1484,27 @@ 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,
int type_offset)
{
int m,tmp,itype,rv;
int m,itype;
tagint atom1,atom2,atom3,atom4;
char *next;
int newton_bond = force->newton_bond;
auto location = "Impropers section of data file";
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
rv = sscanf(buf,"%d %d "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (rv != 6)
error->one(FLERR,"Incorrect format of Impropers section in data file");
try {
ValueTokenizer values(utils::trim_comment(buf));
values.next_int();
itype = values.next_int();
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,"{} in {}: {}", e.what(), location, utils::trim(buf));
}
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
@ -1503,10 +1519,9 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
(atom4 <= 0) || (atom4 > map_tag_max) ||
(atom1 == atom2) || (atom1 == atom3) || (atom1 == 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 {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nimpropertypes)
error->one(FLERR,
"Invalid improper type in Impropers section of data file");
error->one(FLERR, "Invalid improper type in {}: {}", location, utils::trim(buf));
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
@ -1565,7 +1580,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
{
int j,m,tagdata;
int j,m;
char *next;
next = strchr(buf,'\n');
@ -1576,35 +1591,28 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
if (nwords != avec_bonus->size_data_bonus)
error->all(FLERR,"Incorrect bonus data format in data file");
char **values = new char*[nwords];
// loop over lines of bonus atom data
// tokenize the line into values
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
if (values.size() != nwords)
error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
for (j = 0; j < nwords; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
values[j] = buf;
buf += strlen(buf)+1;
}
tagdata = ATOTAGINT(values[0]) + id_offset;
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bonus section of data file");
// ok to call child's data_atom_bonus() method thru parent avec_bonus,
// since data_bonus() was called with child ptr, and method is virtual
if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,&values[1]);
if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,values);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
@ -1616,12 +1624,8 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
{
int j,m,nvalues,tagdata,ninteger,ndouble;
int maxint = 0;
int maxdouble = 0;
int *ivalues = nullptr;
double *dvalues = nullptr;
std::vector<int> ivalues;
std::vector<double> dvalues;
if (!unique_tags) unique_tags = new std::set<tagint>;
@ -1630,69 +1634,51 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
// else skip values
for (int i = 0; i < n; i++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
tagdata = utils::tnumeric(FLERR,buf,false,lmp) + id_offset;
buf += strlen(buf)+1;
char *next = strchr(buf,'\n');
*next = '\0';
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bodies section of data file");
auto values = Tokenizer(utils::trim_comment(buf)).as_vector();
tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset;
int ninteger = utils::inumeric(FLERR,values[1],false,lmp);
int ndouble = utils::inumeric(FLERR,values[2],false,lmp);
if (unique_tags->find(tagdata) == unique_tags->end())
unique_tags->insert(tagdata);
else
error->one(FLERR,"Duplicate atom ID in Bodies section of data file");
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ninteger = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
buf = next + 1;
int m = map(tagdata);
if (m >= 0) {
ivalues.resize(ninteger);
dvalues.resize(ndouble);
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ndouble = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
if ((m = map(tagdata)) >= 0) {
if (ninteger > maxint) {
delete [] ivalues;
maxint = ninteger;
ivalues = new int[maxint];
}
if (ndouble > maxdouble) {
delete [] dvalues;
maxdouble = ndouble;
dvalues = new double[maxdouble];
}
for (j = 0; j < ninteger; j++) {
for (int j = 0; j < ninteger; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ivalues[j] = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
}
for (j = 0; j < ndouble; j++) {
for (int j = 0; j < ndouble; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
dvalues[j] = utils::numeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
}
avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
avec_body->data_body(m,ninteger,ndouble,ivalues.data(),dvalues.data());
} else {
nvalues = ninteger + ndouble; // number of values to skip
for (j = 0; j < nvalues; j++) {
int nvalues = ninteger + ndouble; // number of values to skip
for (int j = 0; j < nvalues; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
buf += strlen(buf)+1;
}
}
buf += strspn(buf," \t\n\r\f");
}
delete [] ivalues;
delete [] dvalues;
}
/* ----------------------------------------------------------------------
@ -1747,17 +1733,20 @@ void Atom::set_mass(const char *file, int line, const char *str, int type_offset
int itype;
double mass_one;
int n = sscanf(str,"%d %lg",&itype,&mass_one);
if (n != 2) error->all(file,line,"Invalid mass line in data file");
itype += type_offset;
try {
ValueTokenizer values(utils::trim_comment(str));
itype = values.next_int() + type_offset;
mass_one = values.next_double();
if (values.has_next()) throw TokenizerException("Too many tokens", "");
if (itype < 1 || itype > ntypes)
error->all(file,line,"Invalid type for mass set");
if (itype < 1 || itype > ntypes) throw TokenizerException("Invalid atom type", "");
if (mass_one <= 0.0) throw TokenizerException("Invalid mass value", "");
} catch (TokenizerException &e) {
error->all(file,line,"{} in Masses section of data file: {}", e.what(), utils::trim(str));
}
mass[itype] = mass_one;
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all(file,line,"Invalid mass value");
}
/* ----------------------------------------------------------------------