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Clean up the code
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@ttadano
ttadano committed Nov 20, 2017
1 parent bfe448a commit 567923f
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Showing 19 changed files with 169 additions and 144 deletions.
3 changes: 1 addition & 2 deletions alm/alamode.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ ALM::ALM(int narg, char **arg)

finalize();

std::cout << std::endl << " Job finished at "
std::cout << std::endl << " Job finished at "
<< timer->DateAndTime() << std::endl;
}

Expand Down Expand Up @@ -116,4 +116,3 @@ void ALM::finalize()
delete writes;
delete memory;
}

24 changes: 13 additions & 11 deletions alm/constraint.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,9 @@

using namespace ALM_NS;

Constraint::Constraint(ALM *alm) : Pointers(alm) {}
Constraint::Constraint(ALM *alm) : Pointers(alm)
{
}

Constraint::~Constraint()
{
Expand Down Expand Up @@ -559,7 +561,7 @@ void Constraint::constraint_from_symmetry(std::vector<ConstraintClass> *const_ou
double *arr_constraint;
bool has_constraint_from_symm = false;
std::set<FcProperty> list_found;
std::vector<std::vector<double> > const_mat;
std::vector<std::vector<double>> const_mat;

for (isym = 0; isym < symmetry->nsym; ++isym) {
if (symmetry->sym_available[isym]) continue;
Expand Down Expand Up @@ -616,7 +618,7 @@ void Constraint::constraint_from_symmetry(std::vector<ConstraintClass> *const_ou

std::set<FcProperty>::iterator iter_found;
std::vector<double> const_now_omp;
std::vector<std::vector<double> > const_omp;
std::vector<std::vector<double>> const_omp;

memory->allocate(ind, order + 2);
memory->allocate(atm_index, order + 2);
Expand Down Expand Up @@ -682,7 +684,7 @@ void Constraint::constraint_from_symmetry(std::vector<ConstraintClass> *const_ou
// Merge vectors
#pragma omp critical
{
for (std::vector<std::vector<double> >::iterator it = const_omp.begin();
for (std::vector<std::vector<double>>::iterator it = const_omp.begin();
it != const_omp.end(); ++it) {
const_mat.push_back(*it);
}
Expand All @@ -699,7 +701,7 @@ void Constraint::constraint_from_symmetry(std::vector<ConstraintClass> *const_ou
} // close openmp region

memory->allocate(arr_constraint, nparams);
for (std::vector<std::vector<double> >::reverse_iterator it = const_mat.rbegin();
for (std::vector<std::vector<double>>::reverse_iterator it = const_mat.rbegin();
it != const_mat.rend(); ++it) {
for (i = 0; i < (*it).size(); ++i) {
arr_constraint[i] = (*it)[i];
Expand Down Expand Up @@ -752,11 +754,11 @@ void Constraint::translational_invariance()
std::vector<int> intlist, data;
std::set<FcProperty> list_found;
std::set<FcProperty>::iterator iter_found;
std::vector<std::vector<int> > data_vec;
std::vector<std::vector<int>> data_vec;
std::vector<FcProperty> list_vec;
std::vector<FcProperty>::iterator iter_vec;
std::vector<int> const_now;
std::vector<std::vector<int> > const_mat;
std::vector<std::vector<int>> const_mat;

std::cout << " Generating constraints for translational invariance ..." << std::endl;

Expand Down Expand Up @@ -888,7 +890,7 @@ void Constraint::translational_invariance()
memory->allocate(intarr_omp, order + 2);
memory->allocate(intarr_copy_omp, order + 2);

std::vector<std::vector<int> > const_omp;
std::vector<std::vector<int>> const_omp;
std::vector<int> data_omp;
std::vector<int> const_now_omp;

Expand Down Expand Up @@ -953,7 +955,7 @@ void Constraint::translational_invariance()
// Merge vectors
#pragma omp critical
{
for (std::vector<std::vector<int> >::iterator it = const_omp.begin();
for (std::vector<std::vector<int>>::iterator it = const_omp.begin();
it != const_omp.end(); ++it) {
const_mat.push_back(*it);
}
Expand Down Expand Up @@ -983,7 +985,7 @@ void Constraint::translational_invariance()
// Copy to constraint class

const_translation[order].clear();
for (std::vector<std::vector<int> >::reverse_iterator it = const_mat.rbegin();
for (std::vector<std::vector<int>>::reverse_iterator it = const_mat.rbegin();
it != const_mat.rend(); ++it) {
for (i = 0; i < (*it).size(); ++i) {
arr_constraint[i] = static_cast<double>((*it)[i]);
Expand Down Expand Up @@ -1047,7 +1049,7 @@ void Constraint::rotational_invariance()
CombinationWithRepetition<int> g;

std::vector<int> atom_tmp;
std::vector<std::vector<int> > cell_dummy;
std::vector<std::vector<int>> cell_dummy;
std::set<MinimumDistanceCluster>::iterator iter_cluster;

setup_rotation_axis(valid_rotation_axis);
Expand Down
9 changes: 6 additions & 3 deletions alm/error.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,9 +15,13 @@

using namespace ALM_NS;

Error::Error(ALM *alm): Pointers(alm) {}
Error::Error(ALM *alm): Pointers(alm)
{
}

Error::~Error() {}
Error::~Error()
{
}

void Error::warn(const char *file, const char *message)
{
Expand All @@ -41,4 +45,3 @@ void Error::exit(const char *file, const char *message, const char *info)
std::cout << " ERROR in " << file << " MESSAGE: " << message << info << std::endl;
std::exit(EXIT_FAILURE);
}

8 changes: 6 additions & 2 deletions alm/fcs.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -26,9 +26,13 @@

using namespace ALM_NS;

Fcs::Fcs(ALM *alm) : Pointers(alm) {};
Fcs::Fcs(ALM *alm) : Pointers(alm)
{
};

Fcs::~Fcs() {};
Fcs::~Fcs()
{
};

void Fcs::init()
{
Expand Down
4 changes: 3 additions & 1 deletion alm/files.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,9 @@

using namespace ALM_NS;

Files::Files(ALM *alm): Pointers(alm) {}
Files::Files(ALM *alm): Pointers(alm)
{
}

Files::~Files()
{
Expand Down
4 changes: 2 additions & 2 deletions alm/fitting.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -641,7 +641,7 @@ void Fitting::fit_algebraic_constraints(int N,
memory->allocate(S, LMIN);

// transpose matrix A
// memory->allocate(amat_mod, M * N);
// memory->allocate(amat_mod, M * N);
memory->allocate(fsum2, LMAX);

//k = 0;
Expand Down Expand Up @@ -717,7 +717,7 @@ void Fitting::fit_algebraic_constraints(int N,
memory->deallocate(WORK);
memory->deallocate(S);
memory->deallocate(fsum2);
// memory->deallocate(amat_mod);
// memory->deallocate(amat_mod);
}


Expand Down
12 changes: 8 additions & 4 deletions alm/input.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -29,9 +29,13 @@

using namespace ALM_NS;

Input::Input(ALM *alm, int narg, char **arg): Pointers(alm) {}
Input::Input(ALM *alm, int narg, char **arg): Pointers(alm)
{
}

Input::~Input() {}
Input::~Input()
{
}

void Input::parse_input(int narg, char **arg)
{
Expand Down Expand Up @@ -879,7 +883,7 @@ void Input::parse_atomic_positions()
}

boost::trim_if(line_wo_comment, boost::is_any_of("\t\n\r "));
// boost::trim_left(line_wo_comment);
// boost::trim_left(line_wo_comment);
if (line_wo_comment.empty()) continue;
if (is_endof_entry(line_wo_comment)) break;

Expand All @@ -899,7 +903,7 @@ void Input::parse_atomic_positions()
}

boost::trim_if(line_wo_comment, boost::is_any_of("\t\n\r "));
// boost::trim_left(line_wo_comment);
// boost::trim_left(line_wo_comment);
if (line_wo_comment.empty()) continue;
if (is_endof_entry(line_wo_comment)) break;

Expand Down
16 changes: 9 additions & 7 deletions alm/interaction.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,9 @@ or http://opensource.org/licenses/mit-license.php for information.

using namespace ALM_NS;

Interaction::Interaction(ALM *alm) : Pointers(alm) {}
Interaction::Interaction(ALM *alm) : Pointers(alm)
{
}

Interaction::~Interaction()
{
Expand Down Expand Up @@ -724,15 +726,15 @@ void Interaction::calc_mindist_clusters(std::vector<int> **interaction_pair_in,
std::vector<int> intlist;
std::vector<int> cell_vector;
std::vector<double> dist_vector;
std::vector<std::vector<int> > pairs_icell, comb_cell, comb_cell_min;
std::vector<std::vector<int> > comb_cell_atom_center;
std::vector<std::vector<int>> pairs_icell, comb_cell, comb_cell_min;
std::vector<std::vector<int>> comb_cell_atom_center;
std::vector<int> accum_tmp;
std::vector<int> atom_tmp, cell_tmp;
std::vector<int> intpair_uniq, cellpair;
std::vector<int> group_atom;
std::vector<int> data_now;
std::vector<MinDistList> distance_list;
std::vector<std::vector<int> > data_vec;
std::vector<std::vector<int>> data_vec;

for (order = 0; order < maxorder; ++order) {
for (i = 0; i < symmetry->natmin; ++i) {
Expand Down Expand Up @@ -986,7 +988,7 @@ void Interaction::calc_mindist_clusters2(std::vector<int> **interaction_pair_in,

std::vector<int> cell_vector;
std::vector<double> dist_vector;
std::vector<std::vector<int> > pairs_icell, comb_cell, comb_cell_min;
std::vector<std::vector<int>> pairs_icell, comb_cell, comb_cell_min;
std::vector<int> accum_tmp;
std::vector<int> atom_tmp, cell_tmp;
std::vector<int> intpair_uniq, cellpair;
Expand Down Expand Up @@ -1178,10 +1180,10 @@ void Interaction::calc_mindist_clusters2(std::vector<int> **interaction_pair_in,
}


void Interaction::cell_combination(std::vector<std::vector<int> > array,
void Interaction::cell_combination(std::vector<std::vector<int>> array,
int i,
std::vector<int> accum,
std::vector<std::vector<int> > &comb)
std::vector<std::vector<int>> &comb)
{
if (i == array.size()) {
comb.push_back(accum);
Expand Down
1 change: 0 additions & 1 deletion alm/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -22,4 +22,3 @@ int main(int argc, char **argv)

return EXIT_SUCCESS;
}

9 changes: 6 additions & 3 deletions alm/memory.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,10 @@

using namespace ALM_NS;

Memory::Memory(ALM *alm) : Pointers(alm) {}

Memory::~Memory() {};
Memory::Memory(ALM *alm) : Pointers(alm)
{
}

Memory::~Memory()
{
};
27 changes: 14 additions & 13 deletions alm/patterndisp.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,9 @@ or http://opensource.org/licenses/mit-license.php for information.

using namespace ALM_NS;

Displace::Displace(ALM *alm) : Pointers(alm) {}
Displace::Displace(ALM *alm) : Pointers(alm)
{
}

Displace::~Displace()
{
Expand Down Expand Up @@ -142,7 +144,7 @@ void Displace::generate_pattern_all(const int N,

std::vector<int> atoms, vec_tmp, nums;
std::vector<double> directions, directions_copy;
std::vector<std::vector<int> > *sign_prod, sign_reduced;
std::vector<std::vector<int>> *sign_prod, sign_reduced;


memory->allocate(sign_prod, N);
Expand All @@ -156,8 +158,8 @@ void Displace::generate_pattern_all(const int N,

pattern[order].clear();

for (std::set<DispAtomSet>::iterator it = dispset_in[order].begin();
it != dispset_in[order].end(); ++it) {
for (std::set<DispAtomSet>::iterator it = dispset_in[order].begin();
it != dispset_in[order].end(); ++it) {

atoms.clear();
directions.clear();
Expand Down Expand Up @@ -194,7 +196,7 @@ void Displace::generate_pattern_all(const int N,
std::copy(directions.begin(), directions.end(),
std::back_inserter(directions_copy));

for (std::vector<std::vector<int> >::const_iterator it2 = sign_reduced.begin();
for (std::vector<std::vector<int>>::const_iterator it2 = sign_reduced.begin();
it2 != sign_reduced.end(); ++it2) {
directions.clear();

Expand Down Expand Up @@ -225,7 +227,7 @@ void Displace::generate_pattern_all(const int N,
}

void Displace::generate_signvecs(const int N,
std::vector<std::vector<int> > &sign,
std::vector<std::vector<int>> &sign,
std::vector<int> vec)
{
// returns the product of signs ('+','-')
Expand All @@ -250,9 +252,9 @@ void Displace::generate_signvecs(const int N,
}

void Displace::find_unique_sign_pairs(const int N,
std::vector<std::vector<int> > sign_in,
std::vector<std::vector<int>> sign_in,
std::vector<int> pair_in,
std::vector<std::vector<int> > &sign_out)
std::vector<std::vector<int>> &sign_out)
{
int isym, i, j, k;
int mapped_atom;
Expand All @@ -267,7 +269,7 @@ void Displace::find_unique_sign_pairs(const int N,
std::vector<int> symnum_vec;
std::vector<int>::iterator loc;
std::vector<int> atom_tmp, pair_tmp;
std::vector<std::vector<int> > sign_found;
std::vector<std::vector<int>> sign_found;
std::vector<int> sign_tmp;
std::vector<int> list_disp_atom;
std::vector<IndexWithSign> index_for_sort;
Expand Down Expand Up @@ -333,7 +335,7 @@ void Displace::find_unique_sign_pairs(const int N,
for (j = 0; j < 3; ++j) {
disp_sym[mapped_atom][j] = 0.0;
for (k = 0; k < 3; ++k) {
disp_sym[mapped_atom][j]
disp_sym[mapped_atom][j]
+= symmetry->symrel[isym][j][k] * disp[list_disp_atom[i]][k];
}

Expand All @@ -356,8 +358,8 @@ void Displace::find_unique_sign_pairs(const int N,

sign_found.clear();

for (std::vector<std::vector<int> >::const_iterator it = sign_in.begin();
it != sign_in.end(); ++it) {
for (std::vector<std::vector<int>>::const_iterator it = sign_in.begin();
it != sign_in.end(); ++it) {

// if the sign has already been found before, cycle the loop.
// else, add the current sign pairs to the return variable.
Expand Down Expand Up @@ -422,4 +424,3 @@ void Displace::find_unique_sign_pairs(const int N,
memory->deallocate(disp);
memory->deallocate(disp_sym);
}

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