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This commit is contained in:
Axel Kohlmeyer
2023-08-04 12:11:59 -04:00
parent 8eb7f56491
commit a6767c85b0
9 changed files with 31 additions and 25 deletions
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2
src/fix_update_special_bonds.cpp
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@ -258,6 +258,6 @@ void FixUpdateSpecialBonds::write_restart(FILE *fp)
pre_exchange();
if (comm->me == 0) {
int size = 0;
fwrite(&size,sizeof(int),1,fp);
fwrite(&size, sizeof(int), 1, fp);
}
}

10
src/force.cpp
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@ -346,7 +346,7 @@ Bond *Force::new_bond(const std::string &style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->non_pair_suffix()) {
sflag = 1 + 2*lmp->pair_only_flag;
sflag = 1 + 2 * lmp->pair_only_flag;
std::string estyle = style + "/" + lmp->non_pair_suffix();
if (bond_map->find(estyle) != bond_map->end()) {
BondCreator &bond_creator = (*bond_map)[estyle];
@ -414,7 +414,7 @@ Angle *Force::new_angle(const std::string &style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->non_pair_suffix()) {
sflag = 1 + 2*lmp->pair_only_flag;
sflag = 1 + 2 * lmp->pair_only_flag;
std::string estyle = style + "/" + lmp->non_pair_suffix();
if (angle_map->find(estyle) != angle_map->end()) {
AngleCreator &angle_creator = (*angle_map)[estyle];
@ -482,7 +482,7 @@ Dihedral *Force::new_dihedral(const std::string &style, int trysuffix, int &sfla
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->non_pair_suffix()) {
sflag = 1 + 2*lmp->pair_only_flag;
sflag = 1 + 2 * lmp->pair_only_flag;
std::string estyle = style + "/" + lmp->non_pair_suffix();
if (dihedral_map->find(estyle) != dihedral_map->end()) {
DihedralCreator &dihedral_creator = (*dihedral_map)[estyle];
@ -550,7 +550,7 @@ Improper *Force::new_improper(const std::string &style, int trysuffix, int &sfla
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->non_pair_suffix()) {
sflag = 1 + 2*lmp->pair_only_flag;
sflag = 1 + 2 * lmp->pair_only_flag;
std::string estyle = style + "/" + lmp->non_pair_suffix();
if (improper_map->find(estyle) != improper_map->end()) {
ImproperCreator &improper_creator = (*improper_map)[estyle];
@ -618,7 +618,7 @@ KSpace *Force::new_kspace(const std::string &style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->non_pair_suffix()) {
sflag = 1 + 2*lmp->pair_only_flag;
sflag = 1 + 2 * lmp->pair_only_flag;
std::string estyle = style + "/" + lmp->non_pair_suffix();
if (kspace_map->find(estyle) != kspace_map->end()) {
KSpaceCreator &kspace_creator = (*kspace_map)[estyle];

6
src/pair_buck_coul_cut.cpp
View File

@ -477,8 +477,8 @@ double PairBuckCoulCut::single(int i, int j, int itype, int jtype, double rsq, d
/* ---------------------------------------------------------------------- */
void PairBuckCoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj, double &dupair,
double &du2pair)
double factor_coul, double factor_lj, double &dupair,
double &du2pair)
{
double rinv, r2inv, r3inv, r6inv, r7inv, r8inv, r, rexp;
double du_lj, du2_lj, du_coul, du2_coul;
@ -487,7 +487,7 @@ void PairBuckCoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq
double qqrd2e = force->qqrd2e;
r = sqrt(rsq);
rexp = exp(-r*rhoinv[itype][jtype]);
rexp = exp(-r * rhoinv[itype][jtype]);
r2inv = 1.0 / rsq;
rinv = sqrt(r2inv);

4
src/pair_coul_cut.cpp
View File

@ -331,8 +331,8 @@ double PairCoulCut::single(int i, int j, int /*itype*/, int /*jtype*/, double rs
/* ---------------------------------------------------------------------- */
void PairCoulCut::born_matrix(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
double factor_coul, double /*factor_lj*/, double &dupair,
double &du2pair)
double factor_coul, double /*factor_lj*/, double &dupair,
double &du2pair)
{
double rinv, r2inv, r3inv;
double du_coul, du2_coul;

4
src/pair_lj_cut_coul_cut.cpp
View File

@ -462,8 +462,8 @@ double PairLJCutCoulCut::single(int i, int j, int itype, int jtype, double rsq,
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj, double &dupair,
double &du2pair)
double factor_coul, double factor_lj, double &dupair,
double &du2pair)
{
double rinv, r2inv, r3inv, r6inv;
double du_lj, du2_lj, du_coul, du2_coul;

2
src/read_data.cpp
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@ -2021,7 +2021,7 @@ void ReadData::pairIJcoeffs()
if (eof) error->all(FLERR, "Unexpected end of data file");
if (tlabelflag && !lmap->is_complete(Atom::ATOM))
error->all(FLERR,"Label map is incomplete: all types must be assigned a unique type label");
error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label");
char *original = buf;
for (i = 0; i < ntypes; i++)

3
src/reset_atoms_id.cpp
View File

@ -43,7 +43,8 @@ static int compare_coords(const int, const int, void *);
/* ---------------------------------------------------------------------- */
ResetAtomsID::ResetAtomsID(LAMMPS *lmp) : Command(lmp) {
ResetAtomsID::ResetAtomsID(LAMMPS *lmp) : Command(lmp)
{
binlo = binhi = -1;
}

21
src/thermo.cpp
View File

@ -691,11 +691,12 @@ void Thermo::modify_params(int narg, char **arg)
utils::bounds(FLERR, arg[iarg + 1], 1, nfield_initial, nlo, nhi, error);
int icol = -1;
for (int i = nlo - 1; i < nhi; i++) {
if (i < 0) icol = nfield_initial + i + 1; // doesn't happen currently
else icol = i;
if (i < 0)
icol = nfield_initial + i + 1; // doesn't happen currently
else
icol = i;
if (icol < 0 || (icol >= nfield_initial))
error->all(FLERR, "Invalid thermo_modify format argument: {}",
arg[iarg + 1]);
error->all(FLERR, "Invalid thermo_modify format argument: {}", arg[iarg + 1]);
format_column_user[icol] = arg[iarg + 2];
}
} else {
@ -1135,7 +1136,8 @@ void Thermo::check_temp(const std::string &keyword)
error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init temperature",
keyword);
if (!temperature->is_initialized())
error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
error->all(FLERR, "Thermo keyword {} cannot be invoked before initialization by a run",
keyword);
if (!(temperature->invoked_flag & Compute::INVOKED_SCALAR)) {
temperature->compute_scalar();
temperature->invoked_flag |= Compute::INVOKED_SCALAR;
@ -1154,7 +1156,8 @@ void Thermo::check_pe(const std::string &keyword)
error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init potential energy",
keyword);
if (!pe->is_initialized())
error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
error->all(FLERR, "Thermo keyword {} cannot be invoked before initialization by a run",
keyword);
if (!(pe->invoked_flag & Compute::INVOKED_SCALAR)) {
pe->compute_scalar();
pe->invoked_flag |= Compute::INVOKED_SCALAR;
@ -1170,7 +1173,8 @@ void Thermo::check_press_scalar(const std::string &keyword)
if (!pressure)
error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init press", keyword);
if (!pressure->is_initialized())
error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
error->all(FLERR, "Thermo keyword {} cannot be invoked before initialization by a run",
keyword);
if (!(pressure->invoked_flag & Compute::INVOKED_SCALAR)) {
pressure->compute_scalar();
pressure->invoked_flag |= Compute::INVOKED_SCALAR;
@ -1186,7 +1190,8 @@ void Thermo::check_press_vector(const std::string &keyword)
if (!pressure)
error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init press", keyword);
if (!pressure->is_initialized())
error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
error->all(FLERR, "Thermo keyword {} cannot be invoked before initialization by a run",
keyword);
if (!(pressure->invoked_flag & Compute::INVOKED_VECTOR)) {
pressure->compute_vector();
pressure->invoked_flag |= Compute::INVOKED_VECTOR;

4
src/update.cpp
View File

@ -362,7 +362,7 @@ void Update::new_integrate(char *style, int narg, char **arg, int trysuffix, int
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->non_pair_suffix()) {
sflag = 1 + 2*lmp->pair_only_flag;
sflag = 1 + 2 * lmp->pair_only_flag;
std::string estyle = style + std::string("/") + lmp->non_pair_suffix();
if (integrate_map->find(estyle) != integrate_map->end()) {
IntegrateCreator &integrate_creator = (*integrate_map)[estyle];
@ -428,7 +428,7 @@ void Update::new_minimize(char *style, int /* narg */, char ** /* arg */, int tr
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->non_pair_suffix()) {
sflag = 1 + 2*lmp->pair_only_flag;
sflag = 1 + 2 * lmp->pair_only_flag;
std::string estyle = style + std::string("/") + lmp->non_pair_suffix();
if (minimize_map->find(estyle) != minimize_map->end()) {
MinimizeCreator &minimize_creator = (*minimize_map)[estyle];