[API] Add function for parsing hubbard.dat style files #933
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -10,5 +10,4 @@ Hubbard::Hubbard(Simulation_context& ctx__) | |
| return; | ||
| } | ||
| } | ||
| } // namespace sirius | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,215 @@ | ||
| #include <cstdio> | ||
| #include <cstdlib> | ||
| #include <string> | ||
| #include <vector> | ||
| #include <tuple> | ||
| #include "context/simulation_context.hpp" | ||
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| namespace sirius { | ||
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| static std::vector<std::string> | ||
| split(std::string str, std::string token) | ||
|
There was a problem hiding this comment. Check if this function can help There was a problem hiding this comment. yes it will. I will use it. |
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| { | ||
| std::vector<std::string> result; | ||
| while (str.size()) { | ||
| int index = str.find(token); | ||
| if (index != std::string::npos) { | ||
| result.push_back(str.substr(0, index)); | ||
| str = str.substr(index + token.size()); | ||
| if (str.size() == 0) | ||
| result.push_back(str); | ||
| } else { | ||
| result.push_back(str); | ||
| str = ""; | ||
| } | ||
| } | ||
| return result; | ||
| } | ||
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| static auto | ||
| parse_atom_string(std::string& at_str__) -> std::tuple<std::string, int, int> | ||
| { | ||
| std::vector<std::string> split_str_ = split(at_str__, "_"); | ||
| int n_ = -1; | ||
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There was a problem hiding this comment. why underscore in local variables? it is not needed |
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| int l_ = -1; | ||
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| // a bit pedantic.... | ||
| n_ = std::stoi(split_str_[1]); | ||
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| switch (split_str_[1][1]) { | ||
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There was a problem hiding this comment. there is a code repetition with https://github.com/electronic-structure/SIRIUS/blob/develop/src/unit_cell/atom_type.cpp#L412 better solution: introduce a pure function that returns l by charachter label. It can be defined for example in |
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| case 's': | ||
| case 'S': | ||
| l_ = 0; | ||
| break; | ||
| case 'p': | ||
| case 'P': | ||
| l_ = 1; | ||
| break; | ||
| case 'd': | ||
| case 'D': | ||
| l_ = 2; | ||
| break; | ||
| case 'f': | ||
| case 'F': | ||
| l_ = 3; | ||
| break; | ||
| case 'g': | ||
| case 'G': | ||
| l_ = 4; | ||
| break; | ||
| case 'h': | ||
| case 'H': | ||
| l_ = 5; | ||
| break; | ||
| case 'I': | ||
| case 'i': | ||
| l_ = 6; | ||
| break; | ||
| } | ||
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| return std::make_tuple(std::string{split_str_[0]}, n_, l_); | ||
| } | ||
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| void | ||
| add_hubbard_atom_pair(Simulation_context& ctx__, int* const atom_pair__, int* const translation__, int* const n__, | ||
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| int* const l__, const double coupling__) | ||
| { | ||
| json elem; | ||
| std::vector<int> atom_pair(atom_pair__, atom_pair__ + 2); | ||
| /* Fortran indices start from 1 */ | ||
| atom_pair[0] -= 1; | ||
| atom_pair[1] -= 1; | ||
| std::vector<int> n(n__, n__ + 2); | ||
| std::vector<int> l(l__, l__ + 2); | ||
| std::vector<int> translation(translation__, translation__ + 3); | ||
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| elem["atom_pair"] = atom_pair; | ||
| elem["T"] = translation; | ||
| elem["n"] = n; | ||
| elem["l"] = l; | ||
| elem["V"] = coupling__; | ||
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| bool test{false}; | ||
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| for (int idx = 0; idx < ctx__.cfg().hubbard().nonlocal().size(); idx++) { | ||
| auto v = ctx__.cfg().hubbard().nonlocal(idx); | ||
| auto at_pr = v.atom_pair(); | ||
| /* search if the pair is already present */ | ||
| if ((at_pr[0] == atom_pair[0]) && (at_pr[1] == atom_pair[1])) { | ||
| auto tr = v.T(); | ||
| if ((tr[0] == translation[0]) && (tr[1] == translation[1]) && (tr[2] == translation[2])) { | ||
| auto lvl = v.n(); | ||
| if ((lvl[0] == n[0]) && (lvl[0] == n[1])) { | ||
| auto li = v.l(); | ||
| if ((li[0] == l[0]) && (li[1] == l[1])) { | ||
| test = true; | ||
| break; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| if (!test) { | ||
| ctx__.cfg().hubbard().nonlocal().append(elem); | ||
| } else { | ||
| RTE_THROW("Atom pair for hubbard correction is already present"); | ||
| } | ||
| } | ||
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| void | ||
| parse_hubbard_file(Simulation_context& ctx__, const std::string& data_file__) | ||
|
There was a problem hiding this comment. our convention is |
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| { | ||
| std::ifstream infile(data_file__); | ||
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| if (!infile.is_open()) { | ||
| std::stringstream s; | ||
| s << "The file " << data_file__ << " is unreadable."; | ||
| RTE_THROW(s); | ||
| } | ||
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| std::string processed_str; | ||
| // std::vector<std::tuple<int, int, int, int>> construct_neighbors_(ctx__.unit_cell().num_atoms() * 27); | ||
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| // for (int atom_id_ = 0 ; atom_id_ < ctx__.unit_cell().num_atoms(); atom_id_++) { | ||
| // construct_neighbors_[atom_id_] = std::make_tuple<int, int, int, int>(0, 0, 0, atom_id_); | ||
| // } | ||
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| // index_ = ctx__.unit_cell().num_atoms(); | ||
| // we only need this list to initialize the input dictionary | ||
| // we can get the reverse from the index with this | ||
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| // for (int nx = -1; nx < 2; nx++) { | ||
| // for (int ny = -1; ny < 2; ny++) { | ||
| // for (int nz = -1; nz < 2; nz++) { | ||
| // for (int at = 0; at < ctx__.unit_cell().num_atoms(); at++) { | ||
| // construct_neighbors_[index_] = std::make_tuple<int, int, int, int>(nz, | ||
| // ny, | ||
| // nx, | ||
| // ((3 * (nx + 1) + (ny + 1)) * 3 + nz + | ||
| // 1) * ctx__.unit_cell().num_atoms() + | ||
| // at); | ||
| // index_++; | ||
| // } | ||
| // } | ||
| // } | ||
| // } | ||
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| while (std::getline(infile, processed_str)) { | ||
| std::vector<std::string> split_string = split(processed_str, std::string(" ")); | ||
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| if ((split_string.size() != 3) || (split_string.size() != 6) || (split_string[0] != "#")) { | ||
| std::stringstream s; | ||
| s << "The file " << data_file__ | ||
| << " seems to be corrupted.\nEach line should either be\nU atom_type-orbital real\n or \nV atom_type_1 " | ||
| "atom_type_2 int int real\n"; | ||
| RTE_THROW(s); | ||
| } | ||
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| if ((split_string[0] == "U") || (split_string[0] == "u")) { | ||
| const double U_ = std::stod(split_string[2]); | ||
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There was a problem hiding this comment. local variables should not have underscore |
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| std::string atom_type_; | ||
| int n_; | ||
| int l_; | ||
| std::tie(atom_type_, n_, l_) = parse_atom_string(split_string[1]); | ||
| json elem; | ||
| elem["atom_type"] = atom_type_; | ||
| elem["n"] = n_; | ||
| elem["l"] = l_; | ||
| elem["total_initial_occupancy"] = 0; | ||
| elem["U"] = U_; | ||
| ctx__.cfg().hubbard().local().append(elem); | ||
| } | ||
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| if (((split_string[0] == "V") || (split_string[0] == "v"))) { | ||
| std::string atom_type1_; | ||
| std::string atom_type2_; | ||
| int n_pair_[2]; | ||
| int l_pair_[2]; | ||
| std::tie(atom_type1_, n_pair_[0], l_pair_[0]) = parse_atom_string(split_string[1]); | ||
| std::tie(atom_type2_, n_pair_[1], l_pair_[1]) = parse_atom_string(split_string[2]); | ||
| const int atom_index1_ = std::stoi(split_string[3]); | ||
| const int atom_index2_ = std::stoi(split_string[4]); | ||
| const double V_ = std::stoi(split_string[5]); | ||
| int translation1[3] = {0, 0, 0}; | ||
| int atom_pair_[2]; | ||
| int translation2[3] = {0, 0, 0}; | ||
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There was a problem hiding this comment. this should be r3::vector T; |
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| atom_pair_[0] = atom_index1_ % ctx__.unit_cell().num_atoms(); | ||
| translation1[0] = (atom_index1_ / ctx__.unit_cell().num_atoms()) % 3 - 1; | ||
| translation1[1] = (atom_index1_ / 3 * ctx__.unit_cell().num_atoms()) % 3 - 1; | ||
| translation1[2] = (atom_index1_ / 9 * ctx__.unit_cell().num_atoms()) % 3 - 1; | ||
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| atom_pair_[1] = atom_index1_ % ctx__.unit_cell().num_atoms(); | ||
| translation2[0] = (atom_index2_ / ctx__.unit_cell().num_atoms()) % 3 - 1; | ||
| translation2[1] = (atom_index2_ / 3 * ctx__.unit_cell().num_atoms()) % 3 - 1; | ||
| translation2[2] = (atom_index2_ / 9 * ctx__.unit_cell().num_atoms()) % 3 - 1; | ||
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| translation2[0] -= translation1[0]; | ||
| translation2[1] -= translation1[1]; | ||
| translation2[2] -= translation1[2]; | ||
| add_hubbard_atom_pair(ctx__, atom_pair_, translation2, n_pair_, l_pair_, V_); | ||
| } | ||
| } | ||
| // ignore all the other lines | ||
| } | ||
| } // namespace sirius | ||
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this are normal functions on the c++ side. No raw pointers as arguments