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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,159 @@ | ||
| #include "check_atomic_stru.h" | ||
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| #include "module_base/element_covalent_radius.h" | ||
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| void Check_Atomic_Stru::check_atomic_stru(UnitCell& ucell, double& factor) { | ||
| // First we calculate all bond length in the structure, | ||
| // and compare with the covalent_bond_length, | ||
| // if there has bond length is shorter than covalent_bond_length * factor, | ||
| // we think this structure is unreasonable. | ||
| const double warning_coef = 0.6; | ||
| assert(ucell.ntype > 0); | ||
| std::stringstream errorlog; | ||
| bool all_pass = true; | ||
| bool no_warning = true; | ||
| for (int it1 = 0; it1 < ucell.ntype; it1++) { | ||
| std::string symbol1 = ""; | ||
| for (char ch: ucell.atoms[it1].label) { | ||
| if (std::isalpha(ch)) { | ||
| symbol1.push_back(ch); | ||
| } | ||
| } | ||
| // std::string symbol1 = ucell.atoms[it1].label; | ||
| double symbol1_covalent_radius; | ||
| if (ModuleBase::CovalentRadius.find(symbol1) | ||
| != ModuleBase::CovalentRadius.end()) { | ||
| symbol1_covalent_radius = ModuleBase::CovalentRadius.at(symbol1); | ||
| } else { | ||
| std::stringstream mess; | ||
| mess << "Notice: symbol '" << symbol1 | ||
| << "' is not an element symbol!!!! "; | ||
| mess << "set the covalent radius to be 0." << std::endl; | ||
| GlobalV::ofs_running << mess.str(); | ||
| std::cout << mess.str(); | ||
| symbol1_covalent_radius = 0.0; | ||
| } | ||
|
|
||
| for (int ia1 = 0; ia1 < ucell.atoms[it1].na; ia1++) { | ||
| double x1 = ucell.atoms[it1].taud[ia1].x; | ||
| double y1 = ucell.atoms[it1].taud[ia1].y; | ||
| double z1 = ucell.atoms[it1].taud[ia1].z; | ||
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| for (int it2 = 0; it2 < ucell.ntype; it2++) { | ||
| std::string symbol2 = ucell.atoms[it2].label; | ||
| double symbol2_covalent_radius; | ||
| if (ModuleBase::CovalentRadius.find(symbol2) | ||
| != ModuleBase::CovalentRadius.end()) { | ||
| symbol2_covalent_radius | ||
| = ModuleBase::CovalentRadius.at(symbol2); | ||
| } else { | ||
| symbol2_covalent_radius = 0.0; | ||
| } | ||
|
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||
| double covalent_length | ||
| = (symbol1_covalent_radius + symbol2_covalent_radius) | ||
| / ModuleBase::BOHR_TO_A; | ||
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| for (int ia2 = 0; ia2 < ucell.atoms[it2].na; ia2++) { | ||
| for (int a = -1; a < 2; a++) { | ||
| for (int b = -1; b < 2; b++) { | ||
| for (int c = -1; c < 2; c++) { | ||
| if (it1 > it2) | ||
| continue; | ||
| else if (it1 == it2 && ia1 > ia2) | ||
| continue; | ||
| else if (it1 == it2 && ia1 == ia2 && a == 0 | ||
| && b == 0 && c == 0) | ||
| continue; | ||
|
|
||
| double x2 = ucell.atoms[it2].taud[ia2].x + a; | ||
| double y2 = ucell.atoms[it2].taud[ia2].y + b; | ||
| double z2 = ucell.atoms[it2].taud[ia2].z + c; | ||
|
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||
| double bond_length | ||
| = sqrt(pow((x2 - x1) * ucell.a1.x | ||
| + (y2 - y1) * ucell.a2.x | ||
| + (z2 - z1) * ucell.a3.x, | ||
| 2) | ||
| + pow((x2 - x1) * ucell.a1.y | ||
| + (y2 - y1) * ucell.a2.y | ||
| + (z2 - z1) * ucell.a3.y, | ||
| 2) | ||
| + pow((x2 - x1) * ucell.a1.z | ||
| + (y2 - y1) * ucell.a2.z | ||
| + (z2 - z1) * ucell.a3.z, | ||
| 2)) | ||
| * ucell.lat0; | ||
|
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||
| if (bond_length < covalent_length * factor | ||
| || bond_length | ||
| < covalent_length * warning_coef) { | ||
| errorlog.setf(std::ios_base::fixed, | ||
| std::ios_base::floatfield); | ||
| errorlog << std::setw(3) << ia1 + 1 | ||
| << "-th " << std::setw(3) | ||
| << ucell.atoms[it1].label << ", "; | ||
| errorlog << std::setw(3) << ia2 + 1 | ||
| << "-th " << std::setw(3) | ||
| << ucell.atoms[it2].label; | ||
| errorlog << " (cell:" << std::setw(2) << a | ||
| << " " << std::setw(2) << b << " " | ||
| << std::setw(2) << c << ")"; | ||
| errorlog << ", distance= " | ||
| << std::setprecision(3) | ||
| << bond_length << " Bohr ("; | ||
| errorlog | ||
| << bond_length * ModuleBase::BOHR_TO_A | ||
| << " Angstrom)" << std::endl; | ||
|
|
||
| if (bond_length | ||
| < covalent_length * factor) { | ||
| all_pass = false; | ||
| } else { | ||
| no_warning = false; | ||
| } | ||
| } | ||
| } // c | ||
| } // b | ||
| } // a | ||
| } // ia2 | ||
| } // it2 | ||
| } // ia1 | ||
| } // it1 | ||
|
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||
| if (!all_pass || !no_warning) { | ||
| std::stringstream mess; | ||
| mess << "\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%" | ||
| << std::endl; | ||
| mess << "%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%" | ||
| << std::endl; | ||
| mess << "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%" | ||
| << std::endl; | ||
| mess << "!!! WARNING: Some atoms are too close!!!" << std::endl; | ||
| mess << "!!! Please check the nearest-neighbor list in log file." | ||
| << std::endl; | ||
| mess << "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%" | ||
| << std::endl; | ||
| mess << "%%%%%% WARNING WARNING WARNING WARNING WARNING %%%%%%" | ||
| << std::endl; | ||
| mess << "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%" | ||
| << std::endl; | ||
|
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||
| GlobalV::ofs_running << mess.str() << mess.str() << mess.str() | ||
| << errorlog.str(); | ||
| std::cout << mess.str() << mess.str() << mess.str() << std::endl; | ||
|
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||
| if (!all_pass) { | ||
| mess.clear(); | ||
| mess.str(""); | ||
| mess << "If this structure is what you want, you can set " | ||
| "'min_dist_coef'" | ||
| << std::endl; | ||
| mess << "as a smaller value (the current value is " << factor | ||
| << ") in INPUT file." << std::endl; | ||
| GlobalV::ofs_running << mess.str(); | ||
| std::cout << mess.str(); | ||
| ModuleBase::WARNING_QUIT("Input", "The structure is unreasonable!"); | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| #ifndef CHECK_ATOMIC_STRU_H | ||
| #define CHECK_ATOMIC_STRU_H | ||
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| #include "unitcell.h" | ||
|
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| class Check_Atomic_Stru { | ||
| public: | ||
| static void check_atomic_stru(UnitCell& ucell, double& factor); | ||
| }; | ||
|
|
||
| #endif |
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