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Merge branch 'develop' of github.com:lammps/lammps into kk_3280

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This commit is contained in:
Stan Gerald Moore
2022-05-31 12:38:03 -06:00
parent 77835a4258 7c0c7ce93c
commit 3b4e698421
28 changed files with 1145 additions and 1214 deletions
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25
src/DIELECTRIC/pppm_dielectric.cpp
View File

@ -58,6 +58,9 @@ PPPMDielectric::PPPMDielectric(LAMMPS *_lmp) : PPPM(_lmp)
phi = nullptr;
potflag = 0;
// no warnings about non-neutral systems from qsum_qsq()
warn_nonneutral = 2;
avec = dynamic_cast<AtomVecDielectric *>( atom->style_match("dielectric"));
if (!avec) error->all(FLERR,"pppm/dielectric requires atom style dielectric");
}
@ -463,25 +466,3 @@ void PPPMDielectric::slabcorr()
efield[i][2] += ffact * eps[i]*(dipole_all - qsum*x[i][2]);
}
}
/* ----------------------------------------------------------------------
compute qsum,qsqsum,q2 and ignore error/warning if not charge neutral
called whenever charges are changed
------------------------------------------------------------------------- */
void PPPMDielectric::qsum_qsq()
{
const double * const q = atom->q;
const int nlocal = atom->nlocal;
double qsum_local(0.0), qsqsum_local(0.0);
for (int i = 0; i < nlocal; i++) {
qsum_local += q[i];
qsqsum_local += q[i]*q[i];
}
MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&qsqsum_local,&qsqsum,1,MPI_DOUBLE,MPI_SUM,world);
q2 = qsqsum * force->qqrd2e;
}

2
src/DIELECTRIC/pppm_dielectric.h
View File

@ -34,8 +34,6 @@ class PPPMDielectric : public PPPM {
double *phi;
int potflag; // 1/0 if per-atom electrostatic potential phi is needed
void qsum_qsq();
protected:
void slabcorr() override;

25
src/DIELECTRIC/pppm_disp_dielectric.cpp
View File

@ -65,6 +65,9 @@ PPPMDispDielectric::PPPMDispDielectric(LAMMPS *_lmp) : PPPMDisp(_lmp)
mu_flag = 0;
// no warnings about non-neutral systems from qsum_qsq()
warn_nonneutral = 2;
efield = nullptr;
phi = nullptr;
potflag = 0;
@ -837,25 +840,3 @@ double PPPMDispDielectric::memory_usage()
bytes += nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
compute qsum,qsqsum,q2 and give error/warning if not charge neutral
called initially, when particle count changes, when charges are changed
------------------------------------------------------------------------- */
void PPPMDispDielectric::qsum_qsq()
{
const double * const q = atom->q;
const int nlocal = atom->nlocal;
double qsum_local(0.0), qsqsum_local(0.0);
for (int i = 0; i < nlocal; i++) {
qsum_local += q[i];
qsqsum_local += q[i]*q[i];
}
MPI_Allreduce(&qsum_local,&qsum,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&qsqsum_local,&qsqsum,1,MPI_DOUBLE,MPI_SUM,world);
q2 = qsqsum * force->qqrd2e;
}

3
src/DIELECTRIC/pppm_disp_dielectric.h
View File

@ -30,8 +30,7 @@ class PPPMDispDielectric : public PPPMDisp {
~PPPMDispDielectric() override;
double memory_usage() override;
void compute(int, int) override;
void qsum_qsq();
void slabcorr(int);
void slabcorr(int) override;
double **efield;
double *phi;

73
src/MANYBODY/pair_bop.cpp
View File

@ -95,6 +95,7 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
pairParameters = nullptr;
tripletParameters = nullptr;
bop_elements = nullptr;
bop_masses = nullptr;
bop_types = 0;
pairlist1 = nullptr;
@ -183,6 +184,7 @@ PairBOP::~PairBOP()
if (bop_elements)
for (int i = 0; i < bop_types; i++) delete[] bop_elements[i];
delete[] bop_elements;
delete[] bop_masses;
}
/* ---------------------------------------------------------------------- */
@ -198,6 +200,7 @@ void PairBOP::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
int nlocal = atom->nlocal;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
tagint *tag = atom->tag;
@ -221,7 +224,15 @@ void PairBOP::compute(int eflag, int vflag)
temp_ij = BOP_index[i] + jj;
j = ilist[neigh_index[temp_ij]];
j_tag = tag[j];
if (j_tag <= i_tag) continue;
if (i_tag > j_tag) {
if ((i_tag+j_tag) % 2 == 0) continue;
} else if (i_tag < j_tag) {
if ((i_tag+j_tag) % 2 == 1) continue;
} else {
if (x[j][2] < x[i][2]) continue;
if (x[j][2] == x[i][2] && x[j][1] < x[i][1]) continue;
if (x[j][2] == x[i][2] && x[j][1] == x[i][1] && x[j][0] < x[i][0]) continue;
}
jtype = map[type[j]];
int param_ij = elem2param[itype][jtype];
sigB_0 = SigmaBo(ii,jj);
@ -251,7 +262,15 @@ void PairBOP::compute(int eflag, int vflag)
temp_ij = BOP_index2[i] + jj;
j = ilist[neigh_index2[temp_ij]];
j_tag = tag[j];
if (j_tag <= i_tag) continue;
if (i_tag > j_tag) {
if ((i_tag+j_tag) % 2 == 0) continue;
} else if (i_tag < j_tag) {
if ((i_tag+j_tag) % 2 == 1) continue;
} else {
if (x[j][2] < x[i][2]) continue;
if (x[j][2] == x[i][2] && x[j][1] < x[i][1]) continue;
if (x[j][2] == x[i][2] && x[j][1] == x[i][1] && x[j][0] < x[i][0]) continue;
}
PairList2 & p2_ij = pairlist2[temp_ij];
dpr2 = -p2_ij.dRep / p2_ij.r;
ftmp1 = dpr2 * p2_ij.dis[0];
@ -344,16 +363,16 @@ void PairBOP::settings(int narg, char **arg)
void PairBOP::coeff(int narg, char **arg)
{
const int n = atom->ntypes;
delete [] map;
map = new int[n+1];
const int np1 = atom->ntypes+1;
delete[] map;
map = new int[np1];
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cutghost);
memory->create(setflag,n+1,n+1,"BOP:setflag");
memory->create(cutsq,n+1,n+1,"BOP:cutsq");
memory->create(cutghost,n+1,n+1,"BOP:cutghost");
bytes = (n+1)*(n+1) * (sizeof (int) + 2.0*sizeof (double));
memory->create(setflag,np1,np1,"BOP:setflag");
memory->create(cutsq,np1,np1,"BOP:cutsq");
memory->create(cutghost,np1,np1,"BOP:cutghost");
bytes = np1*np1*(sizeof (int) + 2.0*sizeof (double));
map_element2type(narg-3, arg+3);
@ -365,22 +384,23 @@ void PairBOP::coeff(int narg, char **arg)
// and check for missing elements
if (comm->me == 0) {
for (int i = 1; i <= n; i++) {
for (int i = 1; i < np1; i++) {
int j;
if (map[i] >= 0) {
for (j = 0; j < bop_types; j++) {
if (strcmp(elements[map[i]],bop_elements[j]) == 0) {
if (strcmp(elements[map[i]], bop_elements[j]) == 0) {
map[i] = j;
atom->set_mass(FLERR, i, bop_masses[j]);
break;
}
}
if (j == bop_types)
error->one(FLERR,"Element {} not found in bop potential file {}",
elements[map[i]],arg[2]);
elements[map[i]], arg[2]);
}
}
}
MPI_Bcast(map,atom->ntypes+1,MPI_INT,0,world);
MPI_Bcast(map,np1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
@ -1844,9 +1864,10 @@ void PairBOP::read_table(char *filename)
PotentialFileReader *reader = nullptr;
if (bop_elements) {
for (int i = 0; i < bop_types; i++) delete [] bop_elements[i];
delete [] bop_elements;
for (int i = 0; i < bop_types; i++) delete[] bop_elements[i];
delete[] bop_elements;
}
delete[] bop_masses;
if (comm->me == 0) {
try {
@ -1857,10 +1878,11 @@ void PairBOP::read_table(char *filename)
"elements",bop_types));
bop_elements = new char*[bop_types];
bop_masses = new double[bop_types];
for (int i=0; i < bop_types; ++i) {
ValueTokenizer values = reader->next_values(3);
values.next_int(); // element number in PTE (ignored)
values.next_double(); // element mass (ignored)
values.next_int(); // element number (ignored)
bop_masses[i] = values.next_double(); // element mass
bop_elements[i] = utils::strdup(values.next_string());
}
} catch (TokenizerException &e) {
@ -1873,8 +1895,12 @@ void PairBOP::read_table(char *filename)
allocate();
memory->create(rcut,npairs,"BOP:rcut");
// copy element labels to all MPI ranks for use with write_tables()
if (comm->me != 0) bop_elements = new char*[bop_types];
// copy element labels and masses to all MPI ranks for use with
// write_tables() and to set the per-type masses
if (comm->me != 0) {
bop_elements = new char*[bop_types];
bop_masses = new double[bop_types];
}
for (int i = 0; i < bop_types; ++i) {
int n=0;
if (comm->me == 0) n = strlen(bop_elements[i])+1;
@ -1882,6 +1908,7 @@ void PairBOP::read_table(char *filename)
if (comm->me != 0) bop_elements[i] = new char[n];
MPI_Bcast(bop_elements[i],n,MPI_CHAR,0,world);
}
MPI_Bcast(bop_masses, bop_types, MPI_DOUBLE, 0, world);
if (comm->me == 0) {
try {
@ -2010,7 +2037,7 @@ void PairBOP::read_table(char *filename)
}
}
}
delete [] singletable;
delete[] singletable;
singletable = new double[nr];
for (int i = 0; i < npairs; i++) {
@ -2038,7 +2065,7 @@ void PairBOP::read_table(char *filename)
p.betaP = new TabularFunction();
(p.betaP)->set_values(nr, 0.0, rcut[i], singletable);
}
delete [] singletable;
delete[] singletable;
singletable = new double[nBOt];
for (int i = 0; i < npairs; i++) {
@ -2048,7 +2075,7 @@ void PairBOP::read_table(char *filename)
p.bo = new TabularFunction();
(p.bo)->set_values(nBOt, 0.0, 1.0, singletable);
}
delete [] singletable;
delete[] singletable;
nbuf = 0;
for (int i = 0; i < bop_types; i++) {
@ -2102,7 +2129,7 @@ void PairBOP::read_table(char *filename)
(p.cphi)->set_values(nr, 0.0, rcut[i], singletable);
}
}
delete [] singletable;
delete[] singletable;
}
memory->destroy(rcut);

1
src/MANYBODY/pair_bop.h
View File

@ -109,6 +109,7 @@ class PairBOP : public Pair {
int npairs; // number of element pairs
int ntriples; // number of all triples
char **bop_elements; // names of elements in potential file
double *bop_masses; // masses of elements in potential file
double bytes;
int otfly; // = 1 faster, more memory, = 0 slower, less memory

14
src/MOLECULE/angle_table.cpp
View File

@ -402,26 +402,20 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword)
// read a,e,f table values from file
int cerror = 0;
reader.skip_line();
for (int i = 0; i < tb->ninput; i++) {
line = reader.next_line(4);
line = reader.next_line();
try {
ValueTokenizer values(line);
values.next_int();
tb->afile[i] = values.next_double();
tb->efile[i] = values.next_double();
tb->ffile[i] = values.next_double();
} catch (TokenizerException &) {
++cerror;
} catch (TokenizerException &e) {
error->one(FLERR, "Error parsing angle table '{}' line {} of {}. {}\nLine was: {}", keyword,
i + 1, tb->ninput, e.what(), line);
}
}
// warn if data was read incompletely, e.g. columns were missing
if (cerror)
error->warning(FLERR, "{} of {} lines in table incomplete or could not be parsed", cerror,
tb->ninput);
}
/* ----------------------------------------------------------------------

20
src/MOLECULE/bond_table.cpp
View File

@ -325,20 +325,20 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
// read r,e,f table values from file
int cerror = 0;
int r0idx = -1;
reader.skip_line();
for (int i = 0; i < tb->ninput; i++) {
line = reader.next_line(4);
line = reader.next_line();
try {
ValueTokenizer values(line);
values.next_int();
tb->rfile[i] = values.next_double();
tb->efile[i] = values.next_double();
tb->ffile[i] = values.next_double();
} catch (TokenizerException &) {
++cerror;
} catch (TokenizerException &e) {
error->one(FLERR, "Error parsing bond table '{}' line {} of {}. {}\nLine was: {}", keyword,
i + 1, tb->ninput, e.what(), line);
}
if (tb->efile[i] < emin) {
@ -373,21 +373,11 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
if (f > fleft && f > fright) ferror++;
}
if (ferror) {
if (ferror)
error->warning(FLERR,
"{} of {} force values in table are inconsistent with -dE/dr.\n"
"WARNING: Should only be flagged at inflection points",
ferror, tb->ninput);
}
// warn if data was read incompletely, e.g. columns were missing
if (cerror) {
error->warning(FLERR,
"{} of {} lines in table were incomplete or could not be"
" parsed completely",
cerror, tb->ninput);
}
}
/* ----------------------------------------------------------------------

9
src/MOLECULE/dihedral_table.cpp
View File

@ -1020,23 +1020,24 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword)
// read a,e,f table values from file
for (int i = 0; i < tb->ninput; i++) {
line = reader.next_line();
try {
ValueTokenizer values(line);
if (tb->f_unspecified) {
ValueTokenizer values = reader.next_values(3);
values.next_int();
tb->phifile[i] = values.next_double();
tb->efile[i] = values.next_double();
} else {
ValueTokenizer values = reader.next_values(4);
values.next_int();
tb->phifile[i] = values.next_double();
tb->efile[i] = values.next_double();
tb->ffile[i] = values.next_double();
}
} catch (TokenizerException &e) {
error->one(FLERR, e.what());
error->one(FLERR, "Error parsing dihedral table '{}' line {} of {}. {}\nLine was: {}",
keyword, i + 1, tb->ninput, e.what(), line);
}
} //for (int i = 0; (i < tb->ninput) && fp; i++) {
}
}
/* ----------------------------------------------------------------------

18
src/pair_table.cpp
View File

@ -395,20 +395,18 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
union_int_float_t rsq_lookup;
int rerror = 0;
int cerror = 0;
reader.skip_line();
for (int i = 0; i < tb->ninput; i++) {
line = reader.next_line(4);
line = reader.next_line();
try {
ValueTokenizer values(line);
values.next_int();
rfile = values.next_double();
tb->efile[i] = conversion_factor * values.next_double();
tb->ffile[i] = conversion_factor * values.next_double();
} catch (TokenizerException &) {
++cerror;
} catch (TokenizerException &e) {
error->one(FLERR, "Error parsing pair table '{}' line {} of {}. {}\nLine was: {}", keyword,
i + 1, tb->ninput, e.what(), line);
}
rnew = rfile;
@ -474,14 +472,6 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
"{} of {} distance values in table {} with relative error\n"
"WARNING: over {} to re-computed values",
rerror, tb->ninput, EPSILONR, keyword);
// warn if data was read incompletely, e.g. columns were missing
if (cerror)
error->warning(FLERR,
"{} of {} lines in table {} were incomplete\n"
"WARNING: or could not be parsed completely",
cerror, tb->ninput, keyword);
}
/* ----------------------------------------------------------------------

6
src/platform.cpp
View File

@ -195,6 +195,8 @@ std::string platform::os_info()
if (build == "6002") {
buf = "Windows Vista";
} else if (build == "6003") {
buf = "Windows Server 2008";
} else if (build == "7601") {
buf = "Windows 7";
} else if (build == "9200") {
@ -227,8 +229,12 @@ std::string platform::os_info()
buf = "Windows 10 21H1";
} else if (build == "19044") {
buf = "Windows 10 21H2";
} else if (build == "20348") {
buf = "Windows Server 2022";
} else if (build == "22000") {
buf = "Windows 11 21H2";
} else if (build == "22621") {
buf = "Windows 11 22H2";
} else {
const char *entry = "ProductName";
RegGetValue(HKEY_LOCAL_MACHINE, subkey, entry, RRF_RT_REG_SZ, nullptr, &value,