From 9c9912d5aeddaf23176e6011c0e4c4c9bd7eb611 Mon Sep 17 00:00:00 2001 From: HeFuxiang94 <78629482+HeFuxiang94@users.noreply.github.com> Date: Wed, 22 Feb 2023 12:53:26 +0800 Subject: [PATCH 01/11] Add the dipole and spectrum post-processing script. (#1928) * Add the Dipole and post-processing script necessary to calculate the spectrum using TDDFT. * fix td_val test bug. --- source/module_io/write_dipole.cpp | 45 ++++++------- tools/ABACUS_dipole_plot.py | 102 ++++++++++++++++++++++++++++++ 2 files changed, 125 insertions(+), 22 deletions(-) create mode 100644 tools/ABACUS_dipole_plot.py diff --git a/source/module_io/write_dipole.cpp b/source/module_io/write_dipole.cpp index 2e34bc29fe..948ce85605 100644 --- a/source/module_io/write_dipole.cpp +++ b/source/module_io/write_dipole.cpp @@ -196,18 +196,18 @@ void ModuleIO::write_dipole(const double *rho_save, ofs << istep << " " << dipole_elec_x << " " << dipole_elec_y << " " << dipole_elec_z << std::endl; - /* + double dipole_ion_x = 0.0, dipole_ion_y = 0.0, dipole_ion_z = 0.0, dipole_sum = 0.0; if (GlobalC::ucell.ntype == 1) { for (int ia = 0; ia < GlobalC::ucell.atoms[0].na; ia++) { dipole_ion_x += GlobalC::ucell.atoms[0].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_01; + * INPUT.td_val_elec_01; dipole_ion_y += GlobalC::ucell.atoms[0].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_01; + * INPUT.td_val_elec_01; dipole_ion_z += GlobalC::ucell.atoms[0].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_01; + * INPUT.td_val_elec_01; } } else if (GlobalC::ucell.ntype == 2) @@ -215,20 +215,20 @@ void ModuleIO::write_dipole(const double *rho_save, for (int ia = 0; ia < GlobalC::ucell.atoms[0].na; ia++) { dipole_ion_x += GlobalC::ucell.atoms[0].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_01; + * INPUT.td_val_elec_01; dipole_ion_y += GlobalC::ucell.atoms[0].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_01; + * INPUT.td_val_elec_01; dipole_ion_z += GlobalC::ucell.atoms[0].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_01; + * INPUT.td_val_elec_01; } for (int ia = 0; ia < GlobalC::ucell.atoms[1].na; ia++) { dipole_ion_x += GlobalC::ucell.atoms[1].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_02; + * INPUT.td_val_elec_02; dipole_ion_y += GlobalC::ucell.atoms[1].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_02; + * INPUT.td_val_elec_02; dipole_ion_z += GlobalC::ucell.atoms[1].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_02; + * INPUT.td_val_elec_02; } } else if (GlobalC::ucell.ntype == 3) @@ -236,35 +236,36 @@ void ModuleIO::write_dipole(const double *rho_save, for (int ia = 0; ia < GlobalC::ucell.atoms[0].na; ia++) { dipole_ion_x += GlobalC::ucell.atoms[0].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_01; + * INPUT.td_val_elec_01; dipole_ion_y += GlobalC::ucell.atoms[0].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_01; + * INPUT.td_val_elec_01; dipole_ion_z += GlobalC::ucell.atoms[0].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_01; + * INPUT.td_val_elec_01; } for (int ia = 0; ia < GlobalC::ucell.atoms[1].na; ia++) { dipole_ion_x += GlobalC::ucell.atoms[1].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_02; + * INPUT.td_val_elec_02; dipole_ion_y += GlobalC::ucell.atoms[1].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_02; + * INPUT.td_val_elec_02; dipole_ion_z += GlobalC::ucell.atoms[1].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_02; + * INPUT.td_val_elec_02; } for (int ia = 0; ia < GlobalC::ucell.atoms[2].na; ia++) { dipole_ion_x += GlobalC::ucell.atoms[2].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_03; + * INPUT.td_val_elec_03; dipole_ion_y += GlobalC::ucell.atoms[2].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_03; + * INPUT.td_val_elec_03; dipole_ion_z += GlobalC::ucell.atoms[2].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * ELEC_evolve::td_val_elec_03; + * INPUT.td_val_elec_03; } } else { std::cout << "atom ntype is too large!" << std::endl; } +/* for(int it=1; it<(GlobalC::ucell.ntype); it++) { for(int ia=0; ia Date: Sat, 25 Feb 2023 18:07:17 +0800 Subject: [PATCH 02/11] Fix: bug in parsing strings mixed with " ", "\t" (#1951) * Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: bug in parsing strings mixed with " ", "\t" --------- Co-authored-by: jiyuang --- source/module_io/input_conv.cpp | 38 ++++++++++++++++++++++----------- 1 file changed, 25 insertions(+), 13 deletions(-) diff --git a/source/module_io/input_conv.cpp b/source/module_io/input_conv.cpp index b7b13928a6..08f9dc20dc 100644 --- a/source/module_io/input_conv.cpp +++ b/source/module_io/input_conv.cpp @@ -34,20 +34,32 @@ template void Input_Conv::parse_expression(const std::string &fn, s int count = 0; std::string pattern("([0-9]+\\*[0-9.]+|[0-9,.]+)"); std::vector str; - std::string::size_type pos1, pos2; - std::string c = " "; - pos2 = fn.find(c); - pos1 = 0; - while (std::string::npos != pos2) - { - str.push_back(fn.substr(pos1, pos2 - pos1)); - pos1 = pos2 + c.size(); - pos2 = fn.find(c, pos1); - } - if (pos1 != fn.length()) - { - str.push_back(fn.substr(pos1)); + std::stringstream ss(fn); + std::string section; + while (ss >> section) { + int index = 0; + if (str.empty()) { + while (index < section.size() && std::isspace(section[index])) { + index++; + } + } + section.erase(0, index); + str.push_back(section); } + // std::string::size_type pos1, pos2; + // std::string c = " "; + // pos2 = fn.find(c); + // pos1 = 0; + // while (std::string::npos != pos2) + // { + // str.push_back(fn.substr(pos1, pos2 - pos1)); + // pos1 = pos2 + c.size(); + // pos2 = fn.find(c, pos1); + // } + // if (pos1 != fn.length()) + // { + // str.push_back(fn.substr(pos1)); + // } regex_t reg; regcomp(®, pattern.c_str(), REG_EXTENDED); regmatch_t pmatch[1]; From 85708c8c286846dde711db8ca95863c11723100c Mon Sep 17 00:00:00 2001 From: lyb9812 <88070104+lyb9812@users.noreply.github.com> Date: Fri, 3 Mar 2023 17:21:48 +0800 Subject: [PATCH 03/11] solve conflicts --- .../potentials/H_TDDFT_pw.cpp | 79 ++++-- .../module_elecstate/potentials/H_TDDFT_pw.h | 2 + source/module_io/dipole_io.h | 13 +- source/module_io/write_dipole.cpp | 260 +++++------------- .../601_NO_TDDFT_H2_len_trape/result.ref | 10 +- 5 files changed, 144 insertions(+), 220 deletions(-) diff --git a/source/module_elecstate/potentials/H_TDDFT_pw.cpp b/source/module_elecstate/potentials/H_TDDFT_pw.cpp index a5ab2c513c..d11575f6d8 100644 --- a/source/module_elecstate/potentials/H_TDDFT_pw.cpp +++ b/source/module_elecstate/potentials/H_TDDFT_pw.cpp @@ -1,10 +1,12 @@ #include "H_TDDFT_pw.h" -#include "module_io/input.h" #include "module_base/constants.h" #include "module_base/timer.h" #include "module_hamilt_lcao/module_tddft/ELEC_evolve.h" +#include "module_io/input.h" #include "module_io/input_conv.h" +#include "module_hamilt_pw/hamilt_pwdft/global.h" + namespace elecstate { @@ -16,7 +18,7 @@ int H_TDDFT_pw::istep = -1; // fuxiang add in 2017-05 //========================================================== -void H_TDDFT_pw::cal_fixed_v(double* vl_pseudo) +void H_TDDFT_pw::cal_fixed_v(double *vl_pseudo) { ModuleBase::TITLE("H_TDDFT_pw", "cal_fixed_v"); @@ -39,18 +41,18 @@ void H_TDDFT_pw::cal_fixed_v(double* vl_pseudo) for (auto direc: ELEC_evolve::td_vext_dire_case) { std::vector vext_space(this->rho_basis_->nrxx, 0.0); - double vext_time = cal_v_time(ttype[count]); + double vext_time = cal_v_time(ttype[count]); if (ELEC_evolve::out_efield && GlobalV::MY_RANK == 0) { std::stringstream as; - as << GlobalV::global_out_dir << "efield_"<rho_basis_->nrxx; ++ir) vl_pseudo[ir] += vext_space[ir] * vext_time; count++; @@ -94,7 +96,7 @@ void H_TDDFT_pw::read_parameters(Input *in) gauss_count = 0; gauss_omega = set_parameters(in->td_gauss_freq, 2 * ModuleBase::PI * ModuleBase::AU_to_FS); // time(a.u.)^-1 gauss_phase = set_parameters(in->td_gauss_phase, 1.0); - gauss_sigma = set_parameters(in->td_gauss_sigma, 1/ModuleBase::AU_to_FS); + gauss_sigma = set_parameters(in->td_gauss_sigma, 1 / ModuleBase::AU_to_FS); gauss_t0 = set_parameters(in->td_gauss_t0, 1.0); gauss_amp = set_parameters(in->td_gauss_amp, ModuleBase::BOHR_TO_A / ModuleBase::Ry_to_eV); // Ry/bohr @@ -163,6 +165,12 @@ void H_TDDFT_pw::cal_v_space_length(std::vector &vext_space, int direc) ModuleBase::TITLE("H_TDDFT_pw", "cal_v_space_length"); ModuleBase::timer::tick("H_TDDFT_pw", "cal_v_space_length"); + double bmod[3]; + for (int i = 0; i < 3; i++) + { + bmod[i] = prepare(GlobalC::ucell, i); + } + for (int ir = 0; ir < this->rho_basis_->nrxx; ++ir) { int i = ir / (this->rho_basis_->ny * this->rho_basis_->nplane); @@ -175,15 +183,15 @@ void H_TDDFT_pw::cal_v_space_length(std::vector &vext_space, int direc) switch (direc) { case 1: - vext_space[ir] = cal_v_space_length_potential(x); + vext_space[ir] = cal_v_space_length_potential(x) / bmod[0]; break; case 2: - vext_space[ir] = cal_v_space_length_potential(y); + vext_space[ir] = cal_v_space_length_potential(y) / bmod[1]; break; case 3: - vext_space[ir] = cal_v_space_length_potential(z); + vext_space[ir] = cal_v_space_length_potential(z) / bmod[2]; break; default: @@ -198,10 +206,10 @@ void H_TDDFT_pw::cal_v_space_length(std::vector &vext_space, int direc) double H_TDDFT_pw::cal_v_space_length_potential(double i) { - double vext_space=0.0; - if (i < this->rho_basis_->nx * lcut1) + double vext_space = 0.0; + if (i < lcut1) { - vext_space = ((i / this->rho_basis_->nx - lcut1)*(lcut2-lcut1) / (lcut1 + 1.0 - lcut2) - lcut1) * this->ucell_->lat0; + vext_space = ((i - lcut1) * (lcut2 - lcut1) / (lcut1 + 1.0 - lcut2) - lcut1) * this->ucell_->lat0; } else if (i >= this->rho_basis_->nx * lcut1 && i < this->rho_basis_->nx * lcut2) { @@ -209,7 +217,7 @@ double H_TDDFT_pw::cal_v_space_length_potential(double i) } else if (i >= this->rho_basis_->nx * lcut2) { - vext_space = ((i / this->rho_basis_->nx - lcut2)*(lcut2-lcut1) / (lcut1 + 1.0 - lcut2) - lcut2) * this->ucell_->lat0; + vext_space = ((i - lcut2) * (lcut2 - lcut1) / (lcut1 + 1.0 - lcut2) - lcut2) * this->ucell_->lat0; } return vext_space; } @@ -229,6 +237,10 @@ double H_TDDFT_pw::cal_v_time(int t_type) vext_time = cal_v_time_Gauss(); break; + case 1: + vext_time = cal_v_time_trapezoid(); + break; + case 2: vext_time = cal_v_time_trigonometric(); break; @@ -237,9 +249,9 @@ double H_TDDFT_pw::cal_v_time(int t_type) vext_time = cal_v_time_heaviside(); break; - // case 4: - // vext_time = cal_v_time_HHG(); - // break; + // case 4: + // vext_time = cal_v_time_HHG(); + // break; default: std::cout << "time_domain_type of electric field is wrong" << endl; @@ -304,8 +316,7 @@ double H_TDDFT_pw::cal_v_time_trigonometric() const double timenow = istep * dt; - vext_time = amp * cos(omega1 * timenow + phase1) * sin(omega2 * timenow + phase2) - * sin(omega2 * timenow + phase2); + vext_time = amp * cos(omega1 * timenow + phase1) * sin(omega2 * timenow + phase2) * sin(omega2 * timenow + phase2); trigo_count++; return vext_time; @@ -345,4 +356,34 @@ double H_TDDFT_pw::cal_v_time_heaviside() // return vext_time; // } +double H_TDDFT_pw::prepare(const UnitCell &cell, int &dir) +{ + double bvec[3] = {0.0}; + double bmod = 0.0; + if (dir == 0) + { + bvec[0] = cell.G.e11; + bvec[1] = cell.G.e12; + bvec[2] = cell.G.e13; + } + else if (dir == 1) + { + bvec[0] = cell.G.e21; + bvec[1] = cell.G.e22; + bvec[2] = cell.G.e23; + } + else if (dir == 2) + { + bvec[0] = cell.G.e31; + bvec[1] = cell.G.e32; + bvec[2] = cell.G.e33; + } + else + { + ModuleBase::WARNING_QUIT("H_TDDFT_pw::prepare", "direction is wrong!"); + } + bmod = sqrt(pow(bvec[0], 2) + pow(bvec[1], 2) + pow(bvec[2], 2)); + return bmod; +} + } // namespace elecstate diff --git a/source/module_elecstate/potentials/H_TDDFT_pw.h b/source/module_elecstate/potentials/H_TDDFT_pw.h index df9ea2b3d3..e600219b24 100644 --- a/source/module_elecstate/potentials/H_TDDFT_pw.h +++ b/source/module_elecstate/potentials/H_TDDFT_pw.h @@ -109,6 +109,8 @@ class H_TDDFT_pw : public PotBase double cal_v_time_trigonometric(); double cal_v_time_heaviside(); // double cal_v_time_HHG(); + + double prepare(const UnitCell &cell, int &dir); }; } // namespace elecstate diff --git a/source/module_io/dipole_io.h b/source/module_io/dipole_io.h index fbd3d8f0a2..4817f0e3c1 100644 --- a/source/module_io/dipole_io.h +++ b/source/module_io/dipole_io.h @@ -6,11 +6,14 @@ namespace ModuleIO { void write_dipole(const double *rho_save, - const int &is, - const int &istep, - const std::string &fn, - const int &precision = 11, - const bool for_plot = false); + const int &is, + const int &istep, + const std::string &fn, + const int &precision = 11, + const bool for_plot = false); + +double prepare(const UnitCell &cell, int &dir); + } // namespace ModuleIO #endif diff --git a/source/module_io/write_dipole.cpp b/source/module_io/write_dipole.cpp index 948ce85605..5acaa72c58 100644 --- a/source/module_io/write_dipole.cpp +++ b/source/module_io/write_dipole.cpp @@ -28,6 +28,12 @@ void ModuleIO::write_dipole(const double *rho_save, } } + double bmod[3]; + for (int i = 0; i < 3; i++) + { + bmod[i] = prepare(GlobalC::ucell, i); + } + #ifndef __MPI double dipole_elec_x = 0.0, dipole_elec_y = 0.0, dipole_elec_z = 0.0; for (int k = 0; k < GlobalC::rhopw->nz; k++) @@ -54,89 +60,6 @@ void ModuleIO::write_dipole(const double *rho_save, ofs << istep << " " << dipole_elec_x << " " << dipole_elec_y << dipole_elec_z; #else - double dipole_elec_x = 0.0, dipole_elec_y = 0.0, dipole_elec_z = 0.0; - - // only do in the first pool. - if (GlobalV::MY_POOL == 0) - { - // num_z: how many planes on processor 'ip' - int *num_z = new int[GlobalV::NPROC_IN_POOL]; - ModuleBase::GlobalFunc::ZEROS(num_z, GlobalV::NPROC_IN_POOL); - for (int iz = 0; iz < GlobalC::bigpw->nbz; iz++) - { - int ip = iz % GlobalV::NPROC_IN_POOL; - num_z[ip] += GlobalC::bigpw->bz; - } - - // start_z: start position of z in - // processor ip. - int *start_z = new int[GlobalV::NPROC_IN_POOL]; - ModuleBase::GlobalFunc::ZEROS(start_z, GlobalV::NPROC_IN_POOL); - for (int ip = 1; ip < GlobalV::NPROC_IN_POOL; ip++) - { - start_z[ip] = start_z[ip - 1] + num_z[ip - 1]; - } - - // which_ip: found iz belongs to which ip. - int *which_ip = new int[GlobalC::rhopw->nz]; - ModuleBase::GlobalFunc::ZEROS(which_ip, GlobalC::rhopw->nz); - for (int iz = 0; iz < GlobalC::rhopw->nz; iz++) - { - for (int ip = 0; ip < GlobalV::NPROC_IN_POOL; ip++) - { - if (iz >= start_z[GlobalV::NPROC_IN_POOL - 1]) - { - which_ip[iz] = GlobalV::NPROC_IN_POOL - 1; - break; - } - else if (iz >= start_z[ip] && iz < start_z[ip + 1]) - { - which_ip[iz] = ip; - break; - } - } - // GlobalV::ofs_running << "\n iz=" << iz << " ip=" << which_ip[iz]; - } - - // int count=0; - int nxy = GlobalC::rhopw->nx * GlobalC::rhopw->ny; - double *zpiece = new double[nxy]; - - // save the rho one z by one z. - for (int iz = 0; iz < GlobalC::rhopw->nz; iz++) - { - // std::cout << "\n iz=" << iz << std::endl; - // tag must be different for different iz. - ModuleBase::GlobalFunc::ZEROS(zpiece, nxy); - int tag = iz; - MPI_Status ierror; - - // case 1: the first part of rho in processor 0. - if (which_ip[iz] == 0 && GlobalV::RANK_IN_POOL == 0) - { - for (int ir = 0; ir < nxy; ir++) - { - // mohan change to rho_save on 2012-02-10 - // because this can make our next restart calculation lead - // to the same scf_thr as the one saved. - zpiece[ir] = rho_save[ir * GlobalC::rhopw->nplane + iz - GlobalC::rhopw->startz_current]; - // GlobalV::ofs_running << "\n get zpiece[" << ir << "]=" << zpiece[ir] << " - // ir*GlobalC::pw.nczp+iz=" << ir*GlobalC::pw.nczp+iz; - } - } - // case 2: > first part rho: send the rho to - // processor 0. - else if (which_ip[iz] == GlobalV::RANK_IN_POOL) - { - for (int ir = 0; ir < nxy; ir++) - { - // zpiece[ir] = rho[is][ir*num_z[GlobalV::RANK_IN_POOL]+iz]; - zpiece[ir] = rho_save[ir * GlobalC::rhopw->nplane + iz - GlobalC::rhopw->startz_current]; - // GlobalV::ofs_running << "\n get zpiece[" << ir << "]=" << zpiece[ir] << " - // ir*GlobalC::pw.nczp+iz=" << ir*GlobalC::pw.nczp+iz; - } - MPI_Send(zpiece, nxy, MPI_DOUBLE, 0, tag, POOL_WORLD); - } // case 2: > first part rho: processor 0 receive the rho // from other processors @@ -185,10 +108,13 @@ void ModuleIO::write_dipole(const double *rho_save, delete[] zpiece; - double nxyz = GlobalC::rhopw->nx * GlobalC::rhopw->ny * GlobalC::rhopw->nz; - dipole_elec_x *= GlobalC::ucell.omega / static_cast(nxyz); - dipole_elec_y *= GlobalC::ucell.omega / static_cast(nxyz); - dipole_elec_z *= GlobalC::ucell.omega / static_cast(nxyz); + Parallel_Reduce::reduce_double_pool(dipole_elec[0]); + Parallel_Reduce::reduce_double_pool(dipole_elec[1]); + Parallel_Reduce::reduce_double_pool(dipole_elec[2]); + for (int i = 0; i < 3; ++i) + { + dipole_elec[i] *= GlobalC::ucell.lat0 / bmod[i] * GlobalC::ucell.omega / GlobalC::rhopw->nxyz; + } std::cout << std::setprecision(8) << "dipole_elec_x: " << dipole_elec_x << std::endl; std::cout << std::setprecision(8) << "dipole_elec_y: " << dipole_elec_y << std::endl; @@ -196,117 +122,39 @@ void ModuleIO::write_dipole(const double *rho_save, ofs << istep << " " << dipole_elec_x << " " << dipole_elec_y << " " << dipole_elec_z << std::endl; - - double dipole_ion_x = 0.0, dipole_ion_y = 0.0, dipole_ion_z = 0.0, dipole_sum = 0.0; - if (GlobalC::ucell.ntype == 1) - { - for (int ia = 0; ia < GlobalC::ucell.atoms[0].na; ia++) - { - dipole_ion_x += GlobalC::ucell.atoms[0].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_01; - dipole_ion_y += GlobalC::ucell.atoms[0].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_01; - dipole_ion_z += GlobalC::ucell.atoms[0].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_01; - } - } - else if (GlobalC::ucell.ntype == 2) - { - for (int ia = 0; ia < GlobalC::ucell.atoms[0].na; ia++) - { - dipole_ion_x += GlobalC::ucell.atoms[0].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_01; - dipole_ion_y += GlobalC::ucell.atoms[0].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_01; - dipole_ion_z += GlobalC::ucell.atoms[0].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_01; - } - for (int ia = 0; ia < GlobalC::ucell.atoms[1].na; ia++) - { - dipole_ion_x += GlobalC::ucell.atoms[1].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_02; - dipole_ion_y += GlobalC::ucell.atoms[1].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_02; - dipole_ion_z += GlobalC::ucell.atoms[1].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_02; - } - } - else if (GlobalC::ucell.ntype == 3) + double dipole_ion[3] = {0.0}; + double dipole_sum = 0.0; + + for (int i = 0; i < 3; ++i) + { + for (int it = 0; it < GlobalC::ucell.ntype; ++it) { - for (int ia = 0; ia < GlobalC::ucell.atoms[0].na; ia++) + double sum = 0; + for (int ia = 0; ia < GlobalC::ucell.atoms[it].na; ++ia) { - dipole_ion_x += GlobalC::ucell.atoms[0].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_01; - dipole_ion_y += GlobalC::ucell.atoms[0].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_01; - dipole_ion_z += GlobalC::ucell.atoms[0].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_01; - } - for (int ia = 0; ia < GlobalC::ucell.atoms[1].na; ia++) - { - dipole_ion_x += GlobalC::ucell.atoms[1].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_02; - dipole_ion_y += GlobalC::ucell.atoms[1].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_02; - dipole_ion_z += GlobalC::ucell.atoms[1].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_02; - } - for (int ia = 0; ia < GlobalC::ucell.atoms[2].na; ia++) - { - dipole_ion_x += GlobalC::ucell.atoms[2].taud[ia].x * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_03; - dipole_ion_y += GlobalC::ucell.atoms[2].taud[ia].y * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_03; - dipole_ion_z += GlobalC::ucell.atoms[2].taud[ia].z * GlobalC::ucell.lat0 * 0.529177 - * INPUT.td_val_elec_03; + + sum += GlobalC::ucell.atoms[it].taud[ia][i]; } + dipole_ion[i] += sum * GlobalC::ucell.atoms[it].ncpp.zv; } - else - { - std::cout << "atom ntype is too large!" << std::endl; - } -/* - for(int it=1; it<(GlobalC::ucell.ntype); it++) - { - for(int ia=0; ia Date: Wed, 8 Mar 2023 11:31:35 +0800 Subject: [PATCH 04/11] solve conflicts --- tools/ABACUS_dipole_plot.py | 102 --------------- tools/plot-tools/README.md | 165 +++++++++++++++---------- tools/plot-tools/abacus_plot/dipole.py | 123 ++++++++++++++++++ tools/plot-tools/abacus_plot/utils.py | 9 +- 4 files changed, 227 insertions(+), 172 deletions(-) delete mode 100644 tools/ABACUS_dipole_plot.py create mode 100644 tools/plot-tools/abacus_plot/dipole.py diff --git a/tools/ABACUS_dipole_plot.py b/tools/ABACUS_dipole_plot.py deleted file mode 100644 index 72f9b1f9d4..0000000000 --- a/tools/ABACUS_dipole_plot.py +++ /dev/null @@ -1,102 +0,0 @@ -from re import split -import numpy as np -import matplotlib.pyplot as plt -from ase.units import Bohr -from math import pi -from scipy.constants import c -from os import listdir -from os import mkdir -from shutil import move -from shutil import copyfile -from os import path -def Sp_plot(t_name,out,file,move=0,N_t=-1,dt=0.0034,direction=-1): - Dipole=dipole_read(t_name,out,file,direction=direction) - if(N_t==-1): - N_t=Dipole.shape[1] - N_t-=move - shift_omega_step=1 - lambda_x=(c/np.linspace(shift_omega_step,N_t-1,N_t-shift_omega_step)*dt*N_t*1e-6) - fig,ax=plt.subplots() - if(direction==1 or direction==-1): - alpha_x=np.fft.fft(Dipole[0][move:N_t]) - S_x=np.abs(alpha_x.imag) - ax.plot(lambda_x,S_x[shift_omega_step:],label='X') - if(direction==2 or direction==-1): - alpha_y=np.fft.fft(Dipole[1][move:N_t]) - S_y=np.abs(alpha_y.imag) - ax.plot(lambda_x,S_y[shift_omega_step:],label='Y') - if(direction==3 or direction==-1): - alpha_z=np.fft.fft(Dipole[2][move:N_t]) - S_z=np.abs(alpha_z.imag) - ax.plot(lambda_x,S_x[shift_omega_step:],label='Z') - ax.set_ylabel('Strength') - ax.set_xlabel('frequency(eV)') - ax.set_title("Spectra") - ax.set_xlim(80,200) - plt.legend() - plt.savefig('./'+out+'/'+file+'spec.png') - -def Sp_field_plot(): - pass -def dipole_read(total_name,out,file,dt=0.0034,direction=-1): - #Initial - list_d=[[] for i in range(3)] - #N_t=nstep-move_step #step used in fft - #Read in cycle - m=0 #Dimension label - line=1 - with open(total_name,mode='r')as f1: - while(line!=''): - while(m<3): - line=f1.readline() - if(line==''):break - tmp=line.split() - if (m==0): - list_d[0].append(float(tmp[1])) - elif (m==1): - list_d[1].append(float(tmp[1])) - elif (m==2): - list_d[2].append(float(tmp[1])) - m+=1 - m=0 - #Plot part - Dipole=np.array(list_d) - N_t=Dipole.shape[1] - Ti=np.linspace(0,(N_t-1)*dt,N_t) - fig,ax=plt.subplots() - if(direction==1 or direction==-1): - ax.plot(Ti,Dipole[0],label='X') - if(direction==2 or direction==-1): - ax.plot(Ti,Dipole[1],label='Y') - if(direction==3 or direction==-1): - ax.plot(Ti,Dipole[2],label='Z') - ax.set_ylabel('Strength') - ax.set_xlabel('time(fs)') - ax.set_title('Dipole') - plt.legend() - plt.savefig('./'+out+'/'+file+'dipole.png') - return Dipole -#reading para -def autoanlysis(filename,dir,out): - list_dir=listdir("./"+dir+"/") - count=0 - print("total file: "+str(len(list_dir))) - #main cycle - for file in list_dir: - if(filename in file): - count+=1 - t_name="./"+dir+"/"+file - Sp_plot(t_name,out,file) - -#main part -filename='dipole.dat' -dir='dipole_nomove' -out='PIC' -file='C2H2_nomove_X_dipole.dat' -if(not path.exists('./'+out)): - mkdir(out) -#direction='X' -#autoanlysis(filename,dir,out) -#single plot -t_name="./"+dir+"/"+file -Sp_plot(t_name,out,file,direction=1) \ No newline at end of file diff --git a/tools/plot-tools/README.md b/tools/plot-tools/README.md index 3d573b3746..974ee37561 100644 --- a/tools/plot-tools/README.md +++ b/tools/plot-tools/README.md @@ -7,49 +7,62 @@ # Plotting tool for ABACUS +- Band Structure and Fat Bands +- DOS and PDOS +- Dipole and Absorption + ## Requirements -- [NumPy](https://numpy.org/) -- [Matplotlib](https://matplotlib.org/) -- [lxml](https://lxml.de/) -- [setuptools](https://setuptools.pypa.io/en/latest/index.html) + +- [NumPy](https://numpy.org/) +- [Matplotlib](https://matplotlib.org/) +- [lxml](https://lxml.de/) +- [setuptools](https://setuptools.pypa.io/en/latest/index.html) ## Installation + Use the following command to install this tool: + ```shell python setup.py install ``` ## Usage + There are two ways to use this tool: -1. Specify parameters in `band.py` or `dos.py` directly, and then `python band.py` or `python dos.py`. And you can also import module in your own script e.g. `from abacus_plot.band import Band`. (Recommend) + +1. Specify parameters in `band.py` (`dos.py`, `dipole.py`) directly, and then `python **.py`. And you can also import module in your own script e.g. `from abacus_plot.band import Band`. (Recommend) 2. Command-line tools are also supported in this tool. In this way, you need prepare an input file and execute some commands (see below). You can use `abacus-plot -h` to check command-line information ### Band Structure + First, prepare a file named 'config.json' in json format: + ```json { - "bandfile" : "BANDS_1.dat", - "efermi" : 6.585653952007503, - "energy_range" : [-1.5, 6], - "kptfile" : "KPT" + "bandfile": "BANDS_1.dat", + "efermi": 6.585653952007503, + "energy_range": [-1.5, 6], + "kptfile": "KPT" } ``` -| Property | Type | Note | -| :------------: | :-------------------------------------------------------------------------: | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | -| *bandfile* | `str` or `List[str]` | Bands data file output from ABACUS. 'BANDS_*.dat' for band structure and 'PBANDS_*' for projected band structure | -| *efermi* | `float` or `List[float]` | Fermi level in eV | -| *energy_range* | `list` | Range of energy in eV | -| *shift* | `bool` | If set `'true'`, it will evaluate band gap (only for semiconductors and insulators). Default: `'false'` | -| *index* | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PBANDS of each atom from 'PBANDS_*' file e.g. [index_0, index_1...] or {index_0:[l_0, l_1, ...], ...}, [index_0:{l_0:[m_0, m_1, ...], ...}, ...] | -| *atom_index* | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PBANDS of each atom with same atom_index from 'PBANDS_*' file e.g. [atom_index_0, atom_index_1...] or {atom_index_0:[l_0, l_1, ...], ...}, [atom_index_0:{l_0:[m_0, m_1, ...], ...}, ...] | -| *species* | `List[str]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PBANDS of each atom with same species from 'PBANDS_*' file e.g. [elem_0, elem_1...] or {elem_0:[l_0, l_1, ...], ...}, [elem_0:{l_0:[m_0, m_1, ...], ...}, ...] | -| *kptfile* | `str` | K-points file with `Line` mode in ABACUS format | -| *label* | `str` or `List[str]` | Label of band structure | -| *color* | `str` or `List[str]` | Color of band structure | - -If you want to plot band structure of `nspin=2` or compare two band structure on same k-path, you can set *bandfile*, *efermi*, *label*, *color* in `list` type. - -The *kptfile* should be as follows, and notes after `#` will be set as k-points label automatically. + +| Property | Type | Note | +| :------------: | :-------------------------------------------------------------------------: | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | +| _bandfile_ | `str` or `List[str]` | Bands data file output from ABACUS. 'BANDS*\*.dat' for band structure and 'PBANDS*\*' for projected band structure | +| _efermi_ | `float` or `List[float]` | Fermi level in eV | +| _energy_range_ | `list` | Range of energy in eV | +| _shift_ | `bool` | If set `'true'`, it will evaluate band gap (only for semiconductors and insulators). Default: `'false'` | +| _index_ | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PBANDS of each atom from 'PBANDS\_\*' file e.g. [index_0, index_1...] or {index_0:[l_0, l_1, ...], ...}, [index_0:{l_0:[m_0, m_1, ...], ...}, ...] | +| _atom_index_ | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PBANDS of each atom with same atom*index from 'PBANDS*\*' file e.g. [atom_index_0, atom_index_1...] or {atom_index_0:[l_0, l_1, ...], ...}, [atom_index_0:{l_0:[m_0, m_1, ...], ...}, ...] | +| _species_ | `List[str]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PBANDS of each atom with same species from 'PBANDS\_\*' file e.g. [elem_0, elem_1...] or {elem_0:[l_0, l_1, ...], ...}, [elem_0:{l_0:[m_0, m_1, ...], ...}, ...] | +| _kptfile_ | `str` | K-points file with `Line` mode in ABACUS format | +| _label_ | `str` or `List[str]` | Label of band structure | +| _color_ | `str` or `List[str]` | Color of band structure | + +If you want to plot band structure of `nspin=2` or compare two band structure on same k-path, you can set _bandfile_, _efermi_, _label_, _color_ in `list` type. + +The _kptfile_ should be as follows, and notes after `#` will be set as k-points label automatically. + ```shell K_POINTS 7 @@ -62,78 +75,96 @@ Line 0.375 0.375 0.75 20 #K 0.0 0.0 0.0 1 #G ``` + Then, use the following command to plot band structure: + ```shell -abacus-plot -b +abacus-plot -b ``` Then, the following command will plot projected band structure and figures output to directory `PBAND*_FIG` ($*=1$ for $nspin=1$, $*=2$ for $nspin=2$): + ```shell -abacus-plot -d -p +abacus-plot -d -p ``` Then, the following command will output parsed partial DOS to directory `PBAND*_FILE` ($*=1$ for $nspin=1$, $*=2$ for $nspin=2$): + ```shell abacus-plot -d -o ``` ### DOS + First, prepare a file named 'config.json' in json format: + ```json { - "pdosfile": "PDOS", - "efermi": 6.585653952007503, - "energy_range": [ - -5, - 7 - ], - "dos_range": [ - 0, - 5 - ], - "species": { - "C": { - "0": [ - 0 - ], - "1": [ - 0, - 1 - ] - }, - "Si": [ - 0, - 1 - ] - }, - "pdosfig": "pdos.png" + "pdosfile": "PDOS", + "efermi": 6.585653952007503, + "energy_range": [-5, 7], + "dos_range": [0, 5], + "species": { + "C": { + "0": [0], + "1": [0, 1] + }, + "Si": [0, 1] + }, + "pdosfig": "pdos.png" } ``` + If you only want to plot total DOS, you can modify `pdosfile` to `tdosfile` and do not set `species` and `pdosfig`. -| Property | Type | Note | +| Property | Type | Note | | :------------: | :-------------------------------------------------------------------------: | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------: | -| *tdosfile* | `str` | Total DOS data file output from ABACUS | -| *pdosfile* | `str` | Partial DOS data file output from ABACUS in xml format | -| *efermi* | `float` | Fermi level in eV | -| *energy_range* | `list` | Range of energy in eV | -| *shift* | `bool` | If set `'true'`, it will evaluate band gap. Default: `'false'` | -| *index* | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[str, List[int]]]]` | Extract PDOS of each atom e.g. [index_0, index_1...] or {index_0:[l_0, l_1, ...], ...}, [index_0:{l_0:[m_0, m_1, ...], ...}, ...] | -| *atom_index* | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[str, List[int]]]]` | Extract PDOS of each atom with same atom_index e.g. [atom_index_0, atom_index_1...] or {atom_index_0:[l_0, l_1, ...], ...}, [atom_index_0:{l_0:[m_0, m_1, ...], ...}, ...] | -| *species* | `List[str]` or `Dict[str, List[int]]` or `Dict[str, Dict[str, List[int]]]]` | Extract PDOS of each atom with same species e.g. [elem_0, elem_1...] or {elem_0:[l_0, l_1, ...], ...}, [elem_0:{l_0:[m_0, m_1, ...], ...}, ...] | -| *tdosfig* | `str` | Output picture of total DOS | -| *pdosfig* | `str` | Output picture of partial DOS | +| _tdosfile_ | `str` | Total DOS data file output from ABACUS | +| _pdosfile_ | `str` | Partial DOS data file output from ABACUS in xml format | +| _efermi_ | `float` | Fermi level in eV | +| _energy_range_ | `list` | Range of energy in eV | +| _shift_ | `bool` | If set `'true'`, it will evaluate band gap. Default: `'false'` | +| _index_ | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[str, List[int]]]]` | Extract PDOS of each atom e.g. [index_0, index_1...] or {index*0:[l_0, l_1, ...], ...}, [index_0:{l_0:[m_0, m_1, ...], ...}, ...] | +| \_atom_index* | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[str, List[int]]]]` | Extract PDOS of each atom with same atom*index e.g. [atom_index_0, atom_index_1...] or {atom_index_0:[l_0, l_1, ...], ...}, [atom_index_0:{l_0:[m_0, m_1, ...], ...}, ...] | +| \_species* | `List[str]` or `Dict[str, List[int]]` or `Dict[str, Dict[str, List[int]]]]` | Extract PDOS of each atom with same species e.g. [elem_0, elem_1...] or {elem*0:[l_0, l_1, ...], ...}, [elem_0:{l_0:[m_0, m_1, ...], ...}, ...] | +| \_tdosfig* | `str` | Output picture of total DOS | +| _pdosfig_ | `str` | Output picture of partial DOS | Then, the following command will plot total DOS: + ```shell -abacus-plot -d +abacus-plot -d ``` Then, the following command will plot partial DOS: + ```shell -abacus-plot -d -p +abacus-plot -d -p ``` Then, the following command will output parsed partial DOS to directory `PDOS_FILE`: + ```shell abacus-plot -d -o -``` \ No newline at end of file +``` + +### Dipole and Absorption + +```python + +from abacus_plot.dipole import Dipole +import matplotlib.pyplot as plt + +dipolefile = './SPIN1_DIPOLE' +dipole = Dipole(dipolefile, dt=0.0034) + +fig1, ax1 = plt.subplots() +fig1, ax1 = dipole.plot_dipole(fig1, ax1) +fig1.savefig('dipole.png') + +fig2, ax2 = plt.subplots() +unit = 'eV' # or 'nm' +x_range = [0, 25] +fig2, ax2 = dipole.plot_abs( + fig2, ax2, x_range=x_range, unit=unit) +fig2.savefig('abs.png') +``` diff --git a/tools/plot-tools/abacus_plot/dipole.py b/tools/plot-tools/abacus_plot/dipole.py new file mode 100644 index 0000000000..ea9e7609f9 --- /dev/null +++ b/tools/plot-tools/abacus_plot/dipole.py @@ -0,0 +1,123 @@ +import numpy as np +from os import PathLike +from matplotlib.figure import Figure +from matplotlib import axes +import scipy.constants as sc + +Freq2eV = sc.h/sc.eV*1e15 # 1/fs to eV + + +class Dipole: + """Parse Dipole Data""" + + def __init__(self, dipolefile: PathLike, dt: float) -> None: + self.dipolefile = dipolefile + self._indices, self.dipole_x, self.dipole_y, self.dipole_z = self.read( + self.dipolefile) + self.dt = dt # in fs + self.time = self._indices*dt + self.energies = Freq2eV*self._indices/dt/len(self._indices) + + @classmethod + def read(cls, filename: PathLike): + """Read dipole data file + + :params filename: string of dipole data file + """ + + data = np.loadtxt(filename, dtype=float) + indices = data[:, 0] + x = data[:, 1] + y = data[:, 2] + z = data[:, 3] + + return indices, x, y, z + + @property + def dipole_data(self): + return {0: self.dipole_x, 1: self.dipole_y, 2: self.dipole_z} + + def plot_dipole(self, fig: Figure, ax: axes.Axes, directions: list = [0, 1, 2], time_range: list = []): + """Plot dipole data in x,y,z directions + + :params fig: (matplotlib.figure.Figure) + :params ax: (matplotlib.axes.Axes) + :params directions: (list) 0->X, 1->Y, 2->Z + :params time_range: (list) range of time (in unit fs) to plot + """ + + labels = {0: 'X', 1: 'Y', 2: 'Z'} + + for direc in directions: + ax.plot(self.time, self.dipole_data[direc], label=labels[direc]) + + ax.set_xlabel('Times (fs)') + ax.set_ylabel('Dipole') + ax.legend() + if time_range: + ax.set_xlim(time_range) + + return fig, ax + + @property + def alpha_x(self): + return np.fft.fft(self.dipole_x) + + @property + def alpha_y(self): + return np.fft.fft(self.dipole_y) + + @property + def alpha_z(self): + return np.fft.fft(self.dipole_z) + + @property + def alpha_data(self): + return {0: self.alpha_x, 1: self.alpha_y, 2: self.alpha_z} + + def get_abs(self, direc: int): + S = np.abs(self.alpha_data[direc].imag) + return S + + def plot_abs(self, fig: Figure, ax: axes.Axes, directions: list = [0, 1, 2], x_range: list = [], unit: str = 'eV'): + """Plot Absportion Spectrum under Delta light field in x,y,z directions + + :params fig: (matplotlib.figure.Figure) + :params ax: (matplotlib.axes.Axes) + :params directions: (list) 0->X, 1->Y, 2->Z + :params x_range: (list) range of energies (in unit eV) to plot + :params unit: (str) + """ + + assert unit in ['eV', 'nm'] + labels = {0: 'X', 1: 'Y', 2: 'Z'} + x_data = self.energies if unit == 'eV' else sc.nu2lambda( + sc.eV/sc.h*self.energies)*1e9 + + for direc in directions: + ax.plot(x_data, self.get_abs(direc), label=labels[direc]) + + xlabel = 'Energy (eV)' if unit == 'eV' else 'Wave Length (nm)' + ax.set_xlabel(xlabel) + ax.set_ylabel('Absportion') + ax.legend() + if x_range: + ax.set_xlim(x_range) + + return fig, ax + + +if __name__ == "__main__": + dipolefile = './SPIN1_DIPOLE' + dipole = Dipole(dipolefile, dt=0.0034) + + import matplotlib.pyplot as plt + fig1, ax1 = plt.subplots() + fig1, ax1 = dipole.plot_dipole(fig1, ax1) + fig1.savefig('dipole.png') + + fig2, ax2 = plt.subplots() + x_range = [0, 400] + fig2, ax2 = dipole.plot_abs( + fig2, ax2, x_range=x_range, unit='nm') + fig2.savefig('abs.png') diff --git a/tools/plot-tools/abacus_plot/utils.py b/tools/plot-tools/abacus_plot/utils.py index 7fd3679f1c..55d6ec6804 100644 --- a/tools/plot-tools/abacus_plot/utils.py +++ b/tools/plot-tools/abacus_plot/utils.py @@ -22,6 +22,7 @@ def remove_empty(a: list) -> list: while [] in a: a.remove([]) + def handle_data(data): data.remove('') @@ -31,6 +32,7 @@ def handle_elem(elem): return elist return list(map(handle_elem, data)) + def skip_notes(line: str) -> str: """Delete comments lines with '#' or '//' @@ -332,9 +334,10 @@ def parse_projected_data(orbitals, species: Union[Sequence[Any], Dict[Any, List[ return data, totnum + def key2int(species): """Convert keys of dict in str type to int""" - + new_species = {} if isinstance(species, dict): elements = list(map(int, species.keys())) @@ -352,5 +355,5 @@ def key2int(species): new_species[elem] = [] for l_index in l[i]: new_species[elem].append(int(l_index)) - - return new_species \ No newline at end of file + + return new_species From 5d19ead34c72bd0f500238f2debd7165ab9cc16e Mon Sep 17 00:00:00 2001 From: lyb9812 <88070104+lyb9812@users.noreply.github.com> Date: Wed, 8 Mar 2023 14:23:26 +0800 Subject: [PATCH 05/11] solve conflicts --- docs/advanced/input_files/input-main.md | 21 ------------------- .../potentials/H_TDDFT_pw.cpp | 6 +++--- .../module_esolver/esolver_ks_lcao_tddft.cpp | 6 +++++- .../module_tddft/ELEC_evolve.cpp | 3 --- .../module_tddft/ELEC_evolve.h | 3 --- source/module_io/input.cpp | 18 ---------------- source/module_io/input.h | 3 --- source/module_io/input_conv.cpp | 3 --- source/module_io/test/input_test.cpp | 6 ------ source/module_io/write_input.cpp | 3 --- tests/integrate/601_NO_TDDFT_CO/result.ref | 8 +++---- .../integrate/601_NO_TDDFT_CO_occ/result.ref | 8 +++---- tests/integrate/601_NO_TDDFT_H2/result.ref | 4 ++-- .../601_NO_TDDFT_H2_kpoint/result.ref | 4 ++-- .../601_NO_TDDFT_H2_len_gauss/result.ref | 10 ++++----- .../601_NO_TDDFT_H2_len_gauss_dire/result.ref | 10 ++++----- .../601_NO_TDDFT_H2_len_heavi/result.ref | 10 ++++----- .../601_NO_TDDFT_H2_len_hhg/result.ref | 10 ++++----- .../601_NO_TDDFT_H2_len_trape/result.ref | 10 ++++----- .../601_NO_TDDFT_H2_len_trigo/result.ref | 8 +++---- .../601_NO_TDDFT_H2_oldedm/result.ref | 4 ++-- tests/integrate/601_NO_TDDFT_O3/result.ref | 6 +++--- .../601_NO_TDDFT_graphene_kpoint/result.ref | 4 ++-- 23 files changed, 56 insertions(+), 112 deletions(-) diff --git a/docs/advanced/input_files/input-main.md b/docs/advanced/input_files/input-main.md index 494cf83099..d0430de33c 100644 --- a/docs/advanced/input_files/input-main.md +++ b/docs/advanced/input_files/input-main.md @@ -312,9 +312,6 @@ - [out\_efield](#out_efield) - [ocp](#ocp) - [ocp\_set](#ocp_set) - - [td\_val\_elec\_01](#td_val_elec_01) - - [td\_val\_elec\_02](#td_val_elec_02) - - [td\_val\_elec\_03](#td_val_elec_03) - [Variables useful for debugging](#variables-useful-for-debugging) - [nurse](#nurse) - [t\_in\_h](#t_in_h) @@ -2588,24 +2585,6 @@ These variables are used to control berry phase and wannier90 interface paramete - **Description**: If ocp is true, the ocp_set is a string to set the number of occupancy, like 1 10 * 1 0 1 representing the 13 band occupancy, 12th band occupancy 0 and the rest 1, the code is parsing this string into an array through a regular expression. - **Default**: none -### td_val_elec_01 - -- **Type**: Integer -- **Description**: Only useful when calculating the dipole. Specifies the number of valence electron associated with the first element. -- **Default**: 1.0 - -### td_val_elec_02 - -- **Type**: Integer -- **Description**: Only useful when calculating the dipole. Specifies the number of valence electron associated with the second element. -- **Default**: 1.0 - -### td_val_elec_03 - -- **Type**: Integer -- **Description**: Only useful when calculating the dipole. Specifies the number of valence electron associated with the third element. -- **Default**: 1.0 - [back to top](#full-list-of-input-keywords) ## Variables useful for debugging diff --git a/source/module_elecstate/potentials/H_TDDFT_pw.cpp b/source/module_elecstate/potentials/H_TDDFT_pw.cpp index d11575f6d8..50e8bcc6eb 100644 --- a/source/module_elecstate/potentials/H_TDDFT_pw.cpp +++ b/source/module_elecstate/potentials/H_TDDFT_pw.cpp @@ -3,10 +3,9 @@ #include "module_base/constants.h" #include "module_base/timer.h" #include "module_hamilt_lcao/module_tddft/ELEC_evolve.h" +#include "module_hamilt_pw/hamilt_pwdft/global.h" #include "module_io/input.h" #include "module_io/input_conv.h" -#include "module_hamilt_pw/hamilt_pwdft/global.h" - namespace elecstate { @@ -48,7 +47,8 @@ void H_TDDFT_pw::cal_fixed_v(double *vl_pseudo) std::stringstream as; as << GlobalV::global_out_dir << "efield_" << count << ".dat"; std::ofstream ofs(as.str().c_str(), std::ofstream::app); - ofs << H_TDDFT_pw::istep * dt * ModuleBase::AU_to_FS << "\t" << vext_time << endl; + ofs << H_TDDFT_pw::istep * dt * ModuleBase::AU_to_FS << "\t" + << vext_time * ModuleBase::Ry_to_eV / ModuleBase::BOHR_TO_A << endl; ofs.close(); } diff --git a/source/module_esolver/esolver_ks_lcao_tddft.cpp b/source/module_esolver/esolver_ks_lcao_tddft.cpp index 8c7bc4a2c9..00edfc0d8b 100644 --- a/source/module_esolver/esolver_ks_lcao_tddft.cpp +++ b/source/module_esolver/esolver_ks_lcao_tddft.cpp @@ -369,7 +369,11 @@ void ESolver_KS_LCAO_TDDFT::updatepot(const int istep, const int iter) std::complex *p_psi_laststep = &psi_laststep[0](0,0,0); for (int index = 0; index < psi[0].size(); ++index) { - p_psi_laststep[index] = p_psi[index]; + this->psi->fix_k(ik); + this->psi_laststep->fix_k(ik); + int size0 = psi->get_nbands() * psi->get_nbasis(); + for (int index = 0; index < size0; ++index) + psi_laststep[0].get_pointer()[index] = psi[0].get_pointer()[index]; } if (istep > 1 && ELEC_evolve::td_edm == 0) this->cal_edm_tddft(); diff --git a/source/module_hamilt_lcao/module_tddft/ELEC_evolve.cpp b/source/module_hamilt_lcao/module_tddft/ELEC_evolve.cpp index ade328fce4..66a8fcb1a7 100644 --- a/source/module_hamilt_lcao/module_tddft/ELEC_evolve.cpp +++ b/source/module_hamilt_lcao/module_tddft/ELEC_evolve.cpp @@ -12,9 +12,6 @@ ELEC_evolve::ELEC_evolve(){}; ELEC_evolve::~ELEC_evolve(){}; double ELEC_evolve::td_force_dt; -int ELEC_evolve::td_val_elec_01; -int ELEC_evolve::td_val_elec_02; -int ELEC_evolve::td_val_elec_03; bool ELEC_evolve::td_vext; std::vector ELEC_evolve::td_vext_dire_case; bool ELEC_evolve::out_dipole; diff --git a/source/module_hamilt_lcao/module_tddft/ELEC_evolve.h b/source/module_hamilt_lcao/module_tddft/ELEC_evolve.h index 86277853c6..6571e72033 100644 --- a/source/module_hamilt_lcao/module_tddft/ELEC_evolve.h +++ b/source/module_hamilt_lcao/module_tddft/ELEC_evolve.h @@ -30,9 +30,6 @@ class ELEC_evolve // fuxiang add 2021-05-25 static double td_force_dt; - static int td_val_elec_01; - static int td_val_elec_02; - static int td_val_elec_03; static bool td_vext; static std::vector td_vext_dire_case; static bool out_dipole; diff --git a/source/module_io/input.cpp b/source/module_io/input.cpp index c1787a23a6..1f1eaac91c 100644 --- a/source/module_io/input.cpp +++ b/source/module_io/input.cpp @@ -405,9 +405,6 @@ void Input::Default(void) // tddft //---------------------------------------------------------- td_force_dt = 0.02; - td_val_elec_01 = 1; - td_val_elec_02 = 1; - td_val_elec_03 = 1; td_vext = false; td_vext_dire = "1"; @@ -1524,18 +1521,6 @@ bool Input::Read(const std::string &fn) { read_value(ifs, td_force_dt); } - else if (strcmp("td_val_elec_01", word) == 0) - { - read_value(ifs, td_val_elec_01); - } - else if (strcmp("td_val_elec_02", word) == 0) - { - read_value(ifs, td_val_elec_02); - } - else if (strcmp("td_val_elec_03", word) == 0) - { - read_value(ifs, td_val_elec_03); - } else if (strcmp("td_vext", word) == 0) { read_value(ifs, td_vext); @@ -2969,9 +2954,6 @@ void Input::Bcast() Parallel_Common::bcast_int(vdw_cutoff_period.y); Parallel_Common::bcast_int(vdw_cutoff_period.z); // Fuxiang He add 2016-10-26 - Parallel_Common::bcast_int(td_val_elec_01); - Parallel_Common::bcast_int(td_val_elec_02); - Parallel_Common::bcast_int(td_val_elec_03); Parallel_Common::bcast_double(td_force_dt); Parallel_Common::bcast_bool(td_vext); Parallel_Common::bcast_string(td_vext_dire); diff --git a/source/module_io/input.h b/source/module_io/input.h index 9678b31cce..f9002da4f6 100644 --- a/source/module_io/input.h +++ b/source/module_io/input.h @@ -372,9 +372,6 @@ class Input // Fuxiang He add 2016-10-26 //========================================================== double td_force_dt; //"fs" - int td_val_elec_01; // valence electron 01 - int td_val_elec_02; // valence electron 02 - int td_val_elec_03; // valence electron 03 bool td_vext; // add extern potential or not std::string td_vext_dire; // vext direction bool out_dipole; // output the dipole or not diff --git a/source/module_io/input_conv.cpp b/source/module_io/input_conv.cpp index 08f9dc20dc..88bc762a23 100644 --- a/source/module_io/input_conv.cpp +++ b/source/module_io/input_conv.cpp @@ -341,9 +341,6 @@ void Input_Conv::Convert(void) //---------------------------------------------------------- #ifdef __LCAO ELEC_evolve::td_force_dt = INPUT.td_force_dt; - ELEC_evolve::td_val_elec_01 = INPUT.td_val_elec_01; - ELEC_evolve::td_val_elec_02 = INPUT.td_val_elec_02; - ELEC_evolve::td_val_elec_03 = INPUT.td_val_elec_03; ELEC_evolve::td_vext = INPUT.td_vext; if (ELEC_evolve::td_vext) { diff --git a/source/module_io/test/input_test.cpp b/source/module_io/test/input_test.cpp index 1be1966969..b594b63e8d 100644 --- a/source/module_io/test/input_test.cpp +++ b/source/module_io/test/input_test.cpp @@ -250,9 +250,6 @@ TEST_F(InputTest, Default) EXPECT_DOUBLE_EQ(INPUT.soc_lambda,1.0); EXPECT_EQ(INPUT.input_error,0); EXPECT_DOUBLE_EQ(INPUT.td_force_dt,0.02); - EXPECT_EQ(INPUT.td_val_elec_01,1); - EXPECT_EQ(INPUT.td_val_elec_02,1); - EXPECT_EQ(INPUT.td_val_elec_03,1); EXPECT_FALSE(INPUT.td_vext); EXPECT_EQ(INPUT.td_vext_dire,"1"); EXPECT_EQ(INPUT.td_stype,0); @@ -585,9 +582,6 @@ TEST_F(InputTest, Read) EXPECT_DOUBLE_EQ(INPUT.soc_lambda,1.0); EXPECT_EQ(INPUT.input_error,0); EXPECT_DOUBLE_EQ(INPUT.td_force_dt,0.02); - EXPECT_EQ(INPUT.td_val_elec_01,1); - EXPECT_EQ(INPUT.td_val_elec_02,1); - EXPECT_EQ(INPUT.td_val_elec_03,1); EXPECT_EQ(INPUT.td_vext,0); // EXPECT_EQ(INPUT.td_vext_dire,"1"); EXPECT_EQ(INPUT.td_stype,0); diff --git a/source/module_io/write_input.cpp b/source/module_io/write_input.cpp index 19a3fadc7f..aa91fffd7e 100644 --- a/source/module_io/write_input.cpp +++ b/source/module_io/write_input.cpp @@ -362,9 +362,6 @@ ModuleBase::GlobalFunc::OUTP(ofs, "out_bandgap", out_bandgap, "if true, print ou ofs << "\n#Parameters (16.tddft)" << std::endl; ModuleBase::GlobalFunc::OUTP(ofs, "td_force_dt", td_force_dt, "time of force change"); - ModuleBase::GlobalFunc::OUTP(ofs, "td_val_elec_01", td_val_elec_01, "td_val_elec_01"); - ModuleBase::GlobalFunc::OUTP(ofs, "td_val_elec_02", td_val_elec_02, "td_val_elec_02"); - ModuleBase::GlobalFunc::OUTP(ofs, "td_val_elec_03", td_val_elec_03, "td_val_elec_03"); ModuleBase::GlobalFunc::OUTP(ofs, "td_vext", td_vext, "add extern potential or not"); ModuleBase::GlobalFunc::OUTP(ofs, "td_vext_dire", td_vext_dire, "extern potential direction"); ModuleBase::GlobalFunc::OUTP(ofs, "out_dipole", out_dipole, "output dipole or not"); diff --git a/tests/integrate/601_NO_TDDFT_CO/result.ref b/tests/integrate/601_NO_TDDFT_CO/result.ref index 9a3221dfc6..27a1c2fe89 100644 --- a/tests/integrate/601_NO_TDDFT_CO/result.ref +++ b/tests/integrate/601_NO_TDDFT_CO/result.ref @@ -1,5 +1,5 @@ -etotref -602.8643311620368 -etotperatomref -301.4321655810 +etotref -602.8643309993128 +etotperatomref -301.4321654997 totalforceref 16.350762 -totalstressref 30.184781 -totaltimeref +15.198 +totalstressref 30.184735 +totaltimeref +7.1335 diff --git a/tests/integrate/601_NO_TDDFT_CO_occ/result.ref b/tests/integrate/601_NO_TDDFT_CO_occ/result.ref index cdb8f9da08..271e8953a8 100644 --- a/tests/integrate/601_NO_TDDFT_CO_occ/result.ref +++ b/tests/integrate/601_NO_TDDFT_CO_occ/result.ref @@ -1,5 +1,5 @@ -etotref -602.8643311790730 -etotperatomref -301.4321655895 +etotref -602.8643311305311 +etotperatomref -301.4321655653 totalforceref 16.350762 -totalstressref 30.185059 -totaltimeref +14.507 +totalstressref 30.185015 +totaltimeref +7.0590 diff --git a/tests/integrate/601_NO_TDDFT_H2/result.ref b/tests/integrate/601_NO_TDDFT_H2/result.ref index 205ab74c78..9bffc30214 100644 --- a/tests/integrate/601_NO_TDDFT_H2/result.ref +++ b/tests/integrate/601_NO_TDDFT_H2/result.ref @@ -1,5 +1,5 @@ -etotref -18.05421597484686 +etotref -18.05421597483996 etotperatomref -9.0271079874 totalforceref 44.953238 totalstressref 79.612084 -totaltimeref +8.5400 +totaltimeref +3.7961 diff --git a/tests/integrate/601_NO_TDDFT_H2_kpoint/result.ref b/tests/integrate/601_NO_TDDFT_H2_kpoint/result.ref index 1bd279c204..40dca31f18 100644 --- a/tests/integrate/601_NO_TDDFT_H2_kpoint/result.ref +++ b/tests/integrate/601_NO_TDDFT_H2_kpoint/result.ref @@ -1,5 +1,5 @@ -etotref -18.05362763740970 +etotref -18.05362763740304 etotperatomref -9.0268138187 totalforceref 44.990644 totalstressref 79.754356 -totaltimeref +7.8584 +totaltimeref +3.8596 diff --git a/tests/integrate/601_NO_TDDFT_H2_len_gauss/result.ref b/tests/integrate/601_NO_TDDFT_H2_len_gauss/result.ref index 6e91bdc3dd..f7f4110f52 100644 --- a/tests/integrate/601_NO_TDDFT_H2_len_gauss/result.ref +++ b/tests/integrate/601_NO_TDDFT_H2_len_gauss/result.ref @@ -1,5 +1,5 @@ -etotref -31.32286584977389 -etotperatomref -15.6614329249 -totalforceref 0.578686 -totalstressref 5.022287 -totaltimeref +7.5452 +etotref -31.36567798859614 +etotperatomref -15.6828389943 +totalforceref 0.578604 +totalstressref 5.433996 +totaltimeref +3.9632 diff --git a/tests/integrate/601_NO_TDDFT_H2_len_gauss_dire/result.ref b/tests/integrate/601_NO_TDDFT_H2_len_gauss_dire/result.ref index 0847470c16..59c1620fa8 100644 --- a/tests/integrate/601_NO_TDDFT_H2_len_gauss_dire/result.ref +++ b/tests/integrate/601_NO_TDDFT_H2_len_gauss_dire/result.ref @@ -1,5 +1,5 @@ -etotref -31.32286467552767 -etotperatomref -15.6614323378 -totalforceref 0.578678 -totalstressref 5.022297 -totaltimeref +7.8011 +etotref -31.36554049797190 +etotperatomref -15.6827702490 +totalforceref 0.577232 +totalstressref 5.434161 +totaltimeref +4.0295 diff --git a/tests/integrate/601_NO_TDDFT_H2_len_heavi/result.ref b/tests/integrate/601_NO_TDDFT_H2_len_heavi/result.ref index 339c80b1db..3e52430584 100644 --- a/tests/integrate/601_NO_TDDFT_H2_len_heavi/result.ref +++ b/tests/integrate/601_NO_TDDFT_H2_len_heavi/result.ref @@ -1,5 +1,5 @@ -etotref -38.10208812355281 -etotperatomref -19.0510440618 -totalforceref 0.577890 -totalstressref 70.174712 -totaltimeref +7.6539 +etotref -38.85116666973314 +etotperatomref -19.4255833349 +totalforceref 0.568498 +totalstressref 77.448537 +totaltimeref +3.8784 diff --git a/tests/integrate/601_NO_TDDFT_H2_len_hhg/result.ref b/tests/integrate/601_NO_TDDFT_H2_len_hhg/result.ref index 1acb4ea54e..b6d67e9d5b 100644 --- a/tests/integrate/601_NO_TDDFT_H2_len_hhg/result.ref +++ b/tests/integrate/601_NO_TDDFT_H2_len_hhg/result.ref @@ -1,5 +1,5 @@ -etotref -77.57538889287757 -etotperatomref -38.7876944464 -totalforceref 0.554418 -totalstressref 449.531857 -totaltimeref +8.1812 +etotref -82.60904651293552 +etotperatomref -41.3045232565 +totalforceref 0.754930 +totalstressref 500.961654 +totaltimeref +4.0425 diff --git a/tests/integrate/601_NO_TDDFT_H2_len_trape/result.ref b/tests/integrate/601_NO_TDDFT_H2_len_trape/result.ref index 117f16dc78..4f21088bfc 100644 --- a/tests/integrate/601_NO_TDDFT_H2_len_trape/result.ref +++ b/tests/integrate/601_NO_TDDFT_H2_len_trape/result.ref @@ -1,5 +1,5 @@ -etotref -30.92097334578261 -etotperatomref -15.4604866729 -totalforceref 0.578804 -totalstressref 1.159829 -totaltimeref +4.0557 +etotref -30.92097257037962 +etotperatomref -15.4604862852 +totalforceref 0.578690 +totalstressref 1.159819 +totaltimeref +3.5993 diff --git a/tests/integrate/601_NO_TDDFT_H2_len_trigo/result.ref b/tests/integrate/601_NO_TDDFT_H2_len_trigo/result.ref index ba319834bc..542503a9f7 100644 --- a/tests/integrate/601_NO_TDDFT_H2_len_trigo/result.ref +++ b/tests/integrate/601_NO_TDDFT_H2_len_trigo/result.ref @@ -1,5 +1,5 @@ -etotref -30.91122825985007 -etotperatomref -15.4556141299 +etotref -30.91150616526584 +etotperatomref -15.4557530826 totalforceref 0.578692 -totalstressref 1.066168 -totaltimeref +7.3268 +totalstressref 1.068838 +totaltimeref +3.6067 diff --git a/tests/integrate/601_NO_TDDFT_H2_oldedm/result.ref b/tests/integrate/601_NO_TDDFT_H2_oldedm/result.ref index f8d641858d..ff03624d80 100644 --- a/tests/integrate/601_NO_TDDFT_H2_oldedm/result.ref +++ b/tests/integrate/601_NO_TDDFT_H2_oldedm/result.ref @@ -1,5 +1,5 @@ -etotref -18.05362763740969 +etotref -18.05362763740304 etotperatomref -9.0268138187 totalforceref 44.990644 totalstressref 79.754356 -totaltimeref +7.7911 +totaltimeref +3.8057 diff --git a/tests/integrate/601_NO_TDDFT_O3/result.ref b/tests/integrate/601_NO_TDDFT_O3/result.ref index f1a7b650d5..d9794538f9 100644 --- a/tests/integrate/601_NO_TDDFT_O3/result.ref +++ b/tests/integrate/601_NO_TDDFT_O3/result.ref @@ -1,5 +1,5 @@ -etotref -1335.872362260817 -etotperatomref -445.2907874203 +etotref -1335.872362260576 +etotperatomref -445.2907874202 totalforceref 13.319759 totalstressref 54.934057 -totaltimeref +36.788 +totaltimeref +23.556 diff --git a/tests/integrate/601_NO_TDDFT_graphene_kpoint/result.ref b/tests/integrate/601_NO_TDDFT_graphene_kpoint/result.ref index e5ec22be7a..2314206da8 100644 --- a/tests/integrate/601_NO_TDDFT_graphene_kpoint/result.ref +++ b/tests/integrate/601_NO_TDDFT_graphene_kpoint/result.ref @@ -1,5 +1,5 @@ -etotref -321.2175762984269 +etotref -321.2175762983792 etotperatomref -107.0725254328 totalforceref 13.778433 totalstressref 1806.432527 -totaltimeref +66.090 +totaltimeref +35.306 From 75d942e0d94ed004a61e0f879fb7bb7de7dbd261 Mon Sep 17 00:00:00 2001 From: lyb9812 <88070104+lyb9812@users.noreply.github.com> Date: Wed, 8 Mar 2023 14:23:26 +0800 Subject: [PATCH 06/11] solve conflicts --- source/module_io/test/support/witestfile | 3 --- 1 file changed, 3 deletions(-) diff --git a/source/module_io/test/support/witestfile b/source/module_io/test/support/witestfile index 0495a2b03f..0d03e30a17 100644 --- a/source/module_io/test/support/witestfile +++ b/source/module_io/test/support/witestfile @@ -276,9 +276,6 @@ exx_opt_orb_tolerence 0 # #Parameters (16.tddft) td_force_dt 0.02 #time of force change -td_val_elec_01 1 #td_val_elec_01 -td_val_elec_02 1 #td_val_elec_02 -td_val_elec_03 1 #td_val_elec_03 td_vext 0 #add extern potential or not td_vext_dire 1 #extern potential direction td_stype 0 #space domain type From 382fdebec3e98314157696128a97f0c96e84e797 Mon Sep 17 00:00:00 2001 From: lyb9812 <88070104+lyb9812@users.noreply.github.com> Date: Wed, 8 Mar 2023 14:23:26 +0800 Subject: [PATCH 07/11] solve conflicts --- source/module_io/test/support/witestfile | 706 +++++++++++------------ 1 file changed, 353 insertions(+), 353 deletions(-) diff --git a/source/module_io/test/support/witestfile b/source/module_io/test/support/witestfile index 0d03e30a17..67ce58da05 100644 --- a/source/module_io/test/support/witestfile +++ b/source/module_io/test/support/witestfile @@ -1,353 +1,353 @@ -INPUT_PARAMETERS -#Parameters (1.General) -suffix autotest #the name of main output directory -latname none #the name of lattice name -stru_file ./support/STRU #the filename of file containing atom positions -kpoint_file KPT #the name of file containing k points -pseudo_dir ../../PP_ORB/ #the directory containing pseudo files -orbital_dir ../../PP_ORB/ #the directory containing orbital files -pseudo_rcut 15 #cut-off radius for radial integration -pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE -lmaxmax 2 #maximum of l channels used -dft_functional hse #exchange correlation functional -xc_temperature 0 #temperature for finite temperature functionals -calculation scf #test; scf; relax; nscf; ienvelope; istate -esolver_type ksdft #the energy solver: ksdft, sdft, ofdft, tddft, lj, dp -ntype 1 #atom species number -nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin -kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file -min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms -nbands 8 #number of bands -nbands_sto 256 #number of stochastic bands -nbands_istate 5 #number of bands around Fermi level for istate calulation -symmetry 1 #the control of symmetry -init_vel False #read velocity from STRU or not -symmetry_prec 1e-05 #accuracy for symmetry -nelec 0 #input number of electrons -out_mul 0 # mulliken charge or not -noncolin 0 #using non-collinear-spin -lspinorb 0 #consider the spin-orbit interaction -kpar 1 #devide all processors into kpar groups and k points will be distributed among each group -bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group -out_freq_elec 0 #the frequency ( >= 0) of electronic iter to output charge density and wavefunction. 0: output only when converged -dft_plus_dmft 0 #true:DFT+DMFT; false: standard DFT calcullation(default) -rpa 0 #true:generate output files used in rpa calculation; false:(default) -printe 100 #Print out energy for each band for every printe steps -mem_saver 0 #Only for nscf calculations. if set to 1, then a memory saving technique will be used for many k point calculations. -diago_proc 4 #the number of procs used to do diagonalization -nbspline -1 #the order of B-spline basis -wannier_card none #input card for wannier functions -soc_lambda 1 #The fraction of averaged SOC pseudopotential is given by (1-soc_lambda) -cal_force 0 #if calculate the force at the end of the electronic iteration -out_freq_ion 0 #the frequency ( >= 0 ) of ionic step to output charge density and wavefunction. 0: output only when ion steps are finished -device cpu #the computing device for ABACUS - -#Parameters (2.PW) -ecutwfc 20 ##energy cutoff for wave functions -pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations -scf_thr 1e-08 #charge density error -init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' -init_chg atomic #start charge is from 'atomic' or file -chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA -out_chg FALSE #>0 output charge density for selected electron steps -out_pot 2 #output realspace potential -out_wfc_pw 0 #output wave functions -out_wfc_r 0 #output wave functions in realspace -out_dos 0 #output energy and dos -out_band false #output energy and band structure -out_proj_band FaLse #output projected band structure -restart_save f #print to disk every step for restart -restart_load F #restart from disk -read_file_dir auto #directory of files for reading -nx 0 #number of points along x axis for FFT grid -ny 0 #number of points along y axis for FFT grid -nz 0 #number of points along z axis for FFT grid -cell_factor 1.2 #used in the construction of the pseudopotential tables -pw_seed 1 #random seed for initializing wave functions - -#Parameters (3.Stochastic DFT) -method_sto 3 #1: slow and save memory, 2: fast and waste memory -npart_sto 1 #Reduce memory when calculating Stochastic DOS -nbands_sto 256 #number of stochstic orbitals -nche_sto 100 #Chebyshev expansion orders -emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator -emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator -seed_sto 0 #the random seed to generate stochastic orbitals -initsto_freq 0 #frequency to generate new stochastic orbitals when running md -cal_cond 0 #calculate electronic conductivities -cond_nche 20 #orders of Chebyshev expansions for conductivities -cond_dw 0.1 #frequency interval for conductivities -cond_wcut 10 #cutoff frequency (omega) for conductivities -cond_dt 0.07 #control the t interval -cond_dtbatch 2 #control dt batch -cond_fwhm 0.3 #FWHM for conductivities -cond_nonlocal 1 #Nonlocal effects for conductivities - -#Parameters (4.Relaxation) -ks_solver genelpa #cg; dav; lapack; genelpa; scalapack_gvx; cusolver -scf_nmax 50 ##number of electron iterations -relax_nmax 1 #number of ion iteration steps -out_stru 0 #output the structure files after each ion step -force_thr 0.001 #force threshold, unit: Ry/Bohr -force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom -force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom -relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom -stress_thr 0.01 #stress threshold -press1 0 #target pressure, unit: KBar -press2 0 #target pressure, unit: KBar -press3 0 #target pressure, unit: KBar -relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs -relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs -relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr -relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr -relax_bfgs_init 0.5 #initial trust radius, unit: Bohr -cal_stress 0 #calculate the stress or not -fixed_axes None #which axes are fixed -fixed_ibrav 0 #whether to preseve lattice type during relaxation -fixed_atoms 0 #whether to preseve direct coordinates of atoms during relaxation -relax_method cg #bfgs; sd; cg; cg_bfgs; -relax_new TRUE #whether to use the new relaxation method -relax_scale_force 0.5 #controls the size of the first CG step if relax_new is true -out_level ie #ie(for electrons); i(for ions); -out_dm 0 #>0 output density matrix -deepks_out_labels 0 #>0 compute descriptor for deepks -deepks_scf 0 #>0 add V_delta to Hamiltonian -deepks_bandgap 0 #>0 for bandgap label -deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test -deepks_model #file dir of traced pytorch model: 'model.ptg - -#Parameters (5.LCAO) -basis_type lcao #PW; LCAO in pw; LCAO -nb2d 0 #2d distribution of atoms -gamma_only T #Only for localized orbitals set and gamma point. If set to 1, a fast algorithm is used -search_radius -1 #input search radius (Bohr) -search_pbc 1 #input periodic boundary condition -lcao_ecut 20 #energy cutoff for LCAO -lcao_dk 0.01 #delta k for 1D integration in LCAO -lcao_dr 0.01 #delta r for 1D integration in LCAO -lcao_rmax 30 #max R for 1D two-center integration table -out_mat_hs 0 #output H and S matrix -out_mat_hs2 0 #output H(R) and S(R) matrix -out_hs2_interval 1 #interval for printing H(R) and S(R) matrix during MD -out_element_info 0 #output (projected) wavefunction of each element -out_mat_r 0 #output r(R) matrix -out_wfc_lcao 0 #ouput LCAO wave functions -bx 2 #division of an element grid in FFT grid along x -by 2 #division of an element grid in FFT grid along y -bz 2 #division of an element grid in FFT grid along z - -bessel_nao_smooth 1 -bessel_nao_sigma 0.1 -bessel_nao_ecut default -bessel_nao_rcut 6.0 #-1.0 for forcing manual setting -bessel_nao_tolerence 1E-12 - -bessel_descriptor_lmax 2 # -1 for forcing manual setting -bessel_descriptor_smooth 1 -bessel_descriptor_sigma 0.1 -bessel_descriptor_ecut default -bessel_descriptor_rcut 6.0 #-1.0 for forcing manual setting -bessel_descriptor_tolerence 1E-12 - -#Parameters (6.Smearing) -smearing_method gauss #type of smearing_method: gauss; fd; fixed; mp; mp2; mv -smearing_sigma 0.002 #energy range for smearing - -#Parameters (7.Charge Mixing) -mixing_type pulay #plain; pulay; broyden -mixing_beta 0.7 #mixing parameter: 0 means no new charge -mixing_ndim 8 #mixing dimension in pulay -mixing_gg0 0 #mixing parameter in kerker - -#Parameters (8.DOS) -dos_emin_ev -15 #minimal range for dos -dos_emax_ev 15 #maximal range for dos -dos_edelta_ev 0.01 #delta energy for dos -dos_scale 0.01 #scale dos range by -dos_sigma 0.07 #gauss b coefficeinet(default=0.07) -dos_nche 100 #orders of Chebyshev expansions for dos - -#Parameters (9.Molecular dynamics) -md_type nvt #choose ensemble -md_thermostat nhc #choose thermostat -md_nstep 10 #md steps -md_dt 1 #time step -md_tchain 1 #number of Nose-Hoover chains -md_tfirst -1 #temperature first -md_tlast -1 #temperature last -md_dumpfreq 1 #The period to dump MD information -md_restartfreq 5 #The period to output MD restart information -md_seed -1 #random seed for MD -md_restart 0 #whether restart -lj_rcut 8.5 #cutoff radius of LJ potential -lj_epsilon 0.01032 #the value of epsilon for LJ potential -lj_sigma 3.405 #the value of sigma for LJ potential -pot_file graph.pb #the filename of potential files for CMD such as DP -msst_direction 2 #the direction of shock wave -msst_vel 0 #the velocity of shock wave -msst_vis 0 #artificial viscosity -msst_tscale 0.01 #reduction in initial temperature -msst_qmass -1 #mass of thermostat -md_tfreq 0 #oscillation frequency, used to determine qmass of NHC -md_damp 1 #damping parameter (time units) used to add force in Langevin method -md_nraise 1 #parameters used when md_type=nvt -md_tolerance 100 #tolerance for velocity rescaling (K) -md_pmode iso #NPT ensemble mode: iso, aniso, tri -md_pcouple none #whether couple different components: xyz, xy, yz, xz, none -md_pchain 1 #num of thermostats coupled with barostat -md_pfirst -1 #initial target pressure -md_plast -1 #final target pressure -md_pfreq 0 #oscillation frequency, used to determine qmass of thermostats coupled with barostat -dump_force 0 #output atomic forces into the file MD_dump or not. -dump_vel 0 #output atomic velocities into the file MD_dump or not -dump_virial 0 #output lattice virial into the file MD_dump or not - -#Parameters (10.Electric field and dipole correction) -efield_flag 0 #add electric field -dip_cor_flag 0 #dipole correction -efield_dir 2 #the direction of the electric field or dipole correction -efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir -efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases -efield_amp 0 #amplitude of the electric field - -#Parameters (11.Gate field) -gate_flag 0 #compensating charge or not -zgate 0.5 #position of charged plate -relax 0 #allow relaxation along the specific direction -block 0 #add a block potential or not -block_down 0.45 #low bound of the block -block_up 0.55 #high bound of the block -block_height 0.1 #height of the block - -#Parameters (12.Test) -out_alllog F #output information for each processor, when parallel -nurse 0 #for coders -colour 0 #for coders, make their live colourful -t_in_h 1 #calculate the kinetic energy or not -vl_in_h 1 #calculate the local potential or not -vnl_in_h 1 #calculate the nonlocal potential or not -vh_in_h 1 #calculate the hartree potential or not -vion_in_h 1 #calculate the local ionic potential or not -test_force 0 #test the force -test_stress 0 #test the force -test_skip_ewald 0 #skip ewald energy - -#Parameters (13.vdW Correction) -vdw_method d2 #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj -vdw_s6 default #scale parameter of d2/d3_0/d3_bj -vdw_s8 default #scale parameter of d3_0/d3_bj -vdw_a1 default #damping parameter of d3_0/d3_bj -vdw_a2 default #damping parameter of d3_bj -vdw_d 20 #damping parameter of d2 -vdw_abc 0 #third-order term? -vdw_C6_file default #filename of C6 -vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 -vdw_R0_file default #filename of R0 -vdw_R0_unit A #unit of R0, A or Bohr -vdw_cutoff_type radius #expression model of periodic structure, radius or period -vdw_cutoff_radius default #radius cutoff for periodic structure -vdw_radius_unit Bohr #unit of radius cutoff for periodic structure -vdw_cn_thr 40 #radius cutoff for cn -vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom -vdw_cutoff_period 3 3 3 #periods of periodic structure - -#Parameters (14.exx) -exx_hybrid_alpha default # -exx_hse_omega 0.11 # -exx_separate_loop 1 #0 or 1 -exx_hybrid_step 100 # -exx_lambda 0.3 # -exx_real_number default #0 or 1 -exx_pca_threshold 0 # -exx_c_threshold 0 # -exx_v_threshold 0 # -exx_dm_threshold 0 # -exx_schwarz_threshold 0 # -exx_cauchy_threshold 0 # -exx_c_grad_threshold 0 # -exx_v_grad_threshold 0 # -exx_cauchy_grad_threshold 0 # -exx_ccp_threshold 1e-08 # -exx_ccp_rmesh_times default # -exx_distribute_type htime #htime or kmeans1 or kmeans2 -exx_opt_orb_lmax 0 # -exx_opt_orb_ecut 0 # -exx_opt_orb_tolerence 0 # - -#Parameters (16.tddft) -td_force_dt 0.02 #time of force change -td_vext 0 #add extern potential or not -td_vext_dire 1 #extern potential direction -td_stype 0 #space domain type -td_ttype 0 #time domain type -td_tstart 1 #the start step of electric field -td_tend 1000 #the start step of electric field -td_lcut1 0.05 # separator in length gauge -td_lcut2 0.95 # separator in length gauge -# parameters of Gauss electric field -td_gauss_freq 22.13 # fs^-1 -td_gauss_phase 0.0 -td_gauss_sigma 30.0 # fs -td_gauss_t0 100.0 -td_gauss_amp 0.25 # V/A -# parameters of Trapezoid electric field -td_trape_freq 1.60 # fs^-1 -td_trape_phase 0.0 -td_trape_t1 1875 -td_trape_t2 5625 -td_trape_t3 7500 -td_trape_amp 2.74 # V/A -#parameters of Trigonometric electric field -td_trigo_freq1 1.164656 # fs^-1 -td_trigo_freq2 0.029116 # fs^-1 -td_trigo_phase1 0.0 -td_trigo_phase2 0.0 -td_trigo_amp 2.74 # V/A -#parameters of Heaviside electric field -td_heavi_t0 100 -td_heavi_amp 1.0 # V/A -td_print_eij -1.0 # threshold to output Eij elements -td_edm 0 # 0: new edm method 1: old edm method -out_dipole 0 #output dipole or not -out_efield 0 #output efield or not -ocp 0 #change occupation or not -ocp_set none #set occupation - -#Parameters (17.berry_wannier) -berry_phase 0 #calculate berry phase or not -gdir 3 #calculate the polarization in the direction of the lattice vector -towannier90 0 #use wannier90 code interface or not -nnkpfile seedname.nnkp #the wannier90 code nnkp file name -wannier_spin up #calculate spin in wannier90 code interface - -#Parameters (18.implicit_solvation) -imp_sol 0 #calculate implicit solvation correction or not -eb_k 80 #the relative permittivity of the bulk solvent -tau 1.0798e-05 #the effective surface tension parameter -sigma_k 0.6 # the width of the diffuse cavity -nc_k 0.00037 # the cut-off charge density - -#Parameters (19.orbital free density functional theory) -of_kinetic vw #kinetic energy functional, such as tf, vw, wt -of_method tn #optimization method used in OFDFT, including cg1, cg2, tn (default) -of_conv energy #the convergence criterion, potential, energy (default), or both -of_tole 1e-06 #tolerance of the energy change (in Ry) for determining the convergence, default=2e-6 Ry -of_tolp 1e-05 #tolerance of potential for determining the convergence, default=1e-5 in a.u. -of_tf_weight 1 #weight of TF KEDF -of_vw_weight 1 #weight of vW KEDF -of_wt_alpha 0.833333 #parameter alpha of WT KEDF -of_wt_beta 0.833333 #parameter beta of WT KEDF -of_wt_rho0 1 #the average density of system, used in WT KEDF, in Bohr^-3 -of_hold_rho0 0 #If set to 1, the rho0 will be fixed even if the volume of system has changed, it will be set to 1 automaticly if of_wt_rho0 is not zero -of_full_pw 0 #If set to 1, ecut will be ignored when collect planewaves, so that all planewaves will be used -of_full_pw_dim 0 #If of_full_pw = true, dimention of FFT is testricted to be (0) either odd or even; (1) odd only; (2) even only -of_read_kernel 0 #If set to 1, the kernel of WT KEDF will be filled from file of_kernel_file, not from formula. Only usable for WT KEDF -of_kernel_file WTkernel.txt #The name of WT kernel file. - -#Parameters (19.dft+u) -dft_plus_u 0 #true:DFT+U correction; false: standard DFT calcullation(default) -yukawa_lambda -1 #default:0.0 -yukawa_potential 0 #default: false -omc 0 #the mode of occupation matrix control -hubbard_u 0 #Hubbard Coulomb interaction parameter U(ev) -orbital_corr -1 #which correlated orbitals need corrected ; d:2 ,f:3, do not need correction:-1 +INPUT_PARAMETERS +#Parameters (1.General) +suffix autotest #the name of main output directory +latname none #the name of lattice name +stru_file ./support/STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir ../../PP_ORB/ #the directory containing pseudo files +orbital_dir ../../PP_ORB/ #the directory containing orbital files +pseudo_rcut 15 #cut-off radius for radial integration +pseudo_mesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional hse #exchange correlation functional +xc_temperature 0 #temperature for finite temperature functionals +calculation scf #test; scf; relax; nscf; ienvelope; istate +esolver_type ksdft #the energy solver: ksdft, sdft, ofdft, tddft, lj, dp +ntype 1 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +kspacing 0 #unit in 1/bohr, should be > 0, default is 0 which means read KPT file +min_dist_coef 0.2 #factor related to the allowed minimum distance between two atoms +nbands 8 #number of bands +nbands_sto 256 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +symmetry 1 #the control of symmetry +init_vel False #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +out_mul 0 # mulliken charge or not +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction +kpar 1 #devide all processors into kpar groups and k points will be distributed among each group +bndpar 1 #devide all processors into bndpar groups and bands will be distributed among each group +out_freq_elec 0 #the frequency ( >= 0) of electronic iter to output charge density and wavefunction. 0: output only when converged +dft_plus_dmft 0 #true:DFT+DMFT; false: standard DFT calcullation(default) +rpa 0 #true:generate output files used in rpa calculation; false:(default) +printe 100 #Print out energy for each band for every printe steps +mem_saver 0 #Only for nscf calculations. if set to 1, then a memory saving technique will be used for many k point calculations. +diago_proc 4 #the number of procs used to do diagonalization +nbspline -1 #the order of B-spline basis +wannier_card none #input card for wannier functions +soc_lambda 1 #The fraction of averaged SOC pseudopotential is given by (1-soc_lambda) +cal_force 0 #if calculate the force at the end of the electronic iteration +out_freq_ion 0 #the frequency ( >= 0 ) of ionic step to output charge density and wavefunction. 0: output only when ion steps are finished +device cpu #the computing device for ABACUS + +#Parameters (2.PW) +ecutwfc 20 ##energy cutoff for wave functions +pw_diag_thr 0.01 #threshold for eigenvalues is cg electron iterations +scf_thr 1e-08 #charge density error +init_wfc atomic #start wave functions are from 'atomic', 'atomic+random', 'random' or 'file' +init_chg atomic #start charge is from 'atomic' or file +chg_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_chg FALSE #>0 output charge density for selected electron steps +out_pot 2 #output realspace potential +out_wfc_pw 0 #output wave functions +out_wfc_r 0 #output wave functions in realspace +out_dos 0 #output energy and dos +out_band false #output energy and band structure +out_proj_band FaLse #output projected band structure +restart_save f #print to disk every step for restart +restart_load F #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables +pw_seed 1 #random seed for initializing wave functions + +#Parameters (3.Stochastic DFT) +method_sto 3 #1: slow and save memory, 2: fast and waste memory +npart_sto 1 #Reduce memory when calculating Stochastic DOS +nbands_sto 256 #number of stochstic orbitals +nche_sto 100 #Chebyshev expansion orders +emin_sto 0 #trial energy to guess the lower bound of eigen energies of the Hamitonian operator +emax_sto 0 #trial energy to guess the upper bound of eigen energies of the Hamitonian operator +seed_sto 0 #the random seed to generate stochastic orbitals +initsto_freq 0 #frequency to generate new stochastic orbitals when running md +cal_cond 0 #calculate electronic conductivities +cond_nche 20 #orders of Chebyshev expansions for conductivities +cond_dw 0.1 #frequency interval for conductivities +cond_wcut 10 #cutoff frequency (omega) for conductivities +cond_dt 0.07 #control the t interval +cond_dtbatch 2 #control dt batch +cond_fwhm 0.3 #FWHM for conductivities +cond_nonlocal 1 #Nonlocal effects for conductivities + +#Parameters (4.Relaxation) +ks_solver genelpa #cg; dav; lapack; genelpa; scalapack_gvx; cusolver +scf_nmax 50 ##number of electron iterations +relax_nmax 1 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.001 #force threshold, unit: Ry/Bohr +force_thr_ev 0.0257112 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +relax_cg_thr 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +relax_bfgs_w1 0.01 #wolfe condition 1 for bfgs +relax_bfgs_w2 0.5 #wolfe condition 2 for bfgs +relax_bfgs_rmax 0.8 #maximal trust radius, unit: Bohr +relax_bfgs_rmin 1e-05 #minimal trust radius, unit: Bohr +relax_bfgs_init 0.5 #initial trust radius, unit: Bohr +cal_stress 0 #calculate the stress or not +fixed_axes None #which axes are fixed +fixed_ibrav 0 #whether to preseve lattice type during relaxation +fixed_atoms 0 #whether to preseve direct coordinates of atoms during relaxation +relax_method cg #bfgs; sd; cg; cg_bfgs; +relax_new TRUE #whether to use the new relaxation method +relax_scale_force 0.5 #controls the size of the first CG step if relax_new is true +out_level ie #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +deepks_out_labels 0 #>0 compute descriptor for deepks +deepks_scf 0 #>0 add V_delta to Hamiltonian +deepks_bandgap 0 #>0 for bandgap label +deepks_out_unittest 0 #if set 1, prints intermediate quantities that shall be used for making unit test +deepks_model #file dir of traced pytorch model: 'model.ptg + +#Parameters (5.LCAO) +basis_type lcao #PW; LCAO in pw; LCAO +nb2d 0 #2d distribution of atoms +gamma_only T #Only for localized orbitals set and gamma point. If set to 1, a fast algorithm is used +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 20 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_mat_hs 0 #output H and S matrix +out_mat_hs2 0 #output H(R) and S(R) matrix +out_hs2_interval 1 #interval for printing H(R) and S(R) matrix during MD +out_element_info 0 #output (projected) wavefunction of each element +out_mat_r 0 #output r(R) matrix +out_wfc_lcao 0 #ouput LCAO wave functions +bx 2 #division of an element grid in FFT grid along x +by 2 #division of an element grid in FFT grid along y +bz 2 #division of an element grid in FFT grid along z + +bessel_nao_smooth 1 +bessel_nao_sigma 0.1 +bessel_nao_ecut default +bessel_nao_rcut 6.0 #-1.0 for forcing manual setting +bessel_nao_tolerence 1E-12 + +bessel_descriptor_lmax 2 # -1 for forcing manual setting +bessel_descriptor_smooth 1 +bessel_descriptor_sigma 0.1 +bessel_descriptor_ecut default +bessel_descriptor_rcut 6.0 #-1.0 for forcing manual setting +bessel_descriptor_tolerence 1E-12 + +#Parameters (6.Smearing) +smearing_method gauss #type of smearing_method: gauss; fd; fixed; mp; mp2; mv +smearing_sigma 0.002 #energy range for smearing + +#Parameters (7.Charge Mixing) +mixing_type pulay #plain; pulay; broyden +mixing_beta 0.7 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (8.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) +dos_nche 100 #orders of Chebyshev expansions for dos + +#Parameters (9.Molecular dynamics) +md_type nvt #choose ensemble +md_thermostat nhc #choose thermostat +md_nstep 10 #md steps +md_dt 1 #time step +md_tchain 1 #number of Nose-Hoover chains +md_tfirst -1 #temperature first +md_tlast -1 #temperature last +md_dumpfreq 1 #The period to dump MD information +md_restartfreq 5 #The period to output MD restart information +md_seed -1 #random seed for MD +md_restart 0 #whether restart +lj_rcut 8.5 #cutoff radius of LJ potential +lj_epsilon 0.01032 #the value of epsilon for LJ potential +lj_sigma 3.405 #the value of sigma for LJ potential +pot_file graph.pb #the filename of potential files for CMD such as DP +msst_direction 2 #the direction of shock wave +msst_vel 0 #the velocity of shock wave +msst_vis 0 #artificial viscosity +msst_tscale 0.01 #reduction in initial temperature +msst_qmass -1 #mass of thermostat +md_tfreq 0 #oscillation frequency, used to determine qmass of NHC +md_damp 1 #damping parameter (time units) used to add force in Langevin method +md_nraise 1 #parameters used when md_type=nvt +md_tolerance 100 #tolerance for velocity rescaling (K) +md_pmode iso #NPT ensemble mode: iso, aniso, tri +md_pcouple none #whether couple different components: xyz, xy, yz, xz, none +md_pchain 1 #num of thermostats coupled with barostat +md_pfirst -1 #initial target pressure +md_plast -1 #final target pressure +md_pfreq 0 #oscillation frequency, used to determine qmass of thermostats coupled with barostat +dump_force 0 #output atomic forces into the file MD_dump or not. +dump_vel 0 #output atomic velocities into the file MD_dump or not +dump_virial 0 #output lattice virial into the file MD_dump or not + +#Parameters (10.Electric field and dipole correction) +efield_flag 0 #add electric field +dip_cor_flag 0 #dipole correction +efield_dir 2 #the direction of the electric field or dipole correction +efield_pos_max 0.5 #position of the maximum of the saw-like potential along crystal axis efield_dir +efield_pos_dec 0.1 #zone in the unit cell where the saw-like potential decreases +efield_amp 0 #amplitude of the electric field + +#Parameters (11.Gate field) +gate_flag 0 #compensating charge or not +zgate 0.5 #position of charged plate +relax 0 #allow relaxation along the specific direction +block 0 #add a block potential or not +block_down 0.45 #low bound of the block +block_up 0.55 #high bound of the block +block_height 0.1 #height of the block + +#Parameters (12.Test) +out_alllog F #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force +test_skip_ewald 0 #skip ewald energy + +#Parameters (13.vdW Correction) +vdw_method d2 #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_cutoff_type radius #expression model of periodic structure, radius or period +vdw_cutoff_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_cutoff_period 3 3 3 #periods of periodic structure + +#Parameters (14.exx) +exx_hybrid_alpha default # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_real_number default #0 or 1 +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold 0 # +exx_cauchy_threshold 0 # +exx_c_grad_threshold 0 # +exx_v_grad_threshold 0 # +exx_cauchy_grad_threshold 0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times default # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence 0 # + +#Parameters (16.tddft) +td_force_dt 0.02 #time of force change +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_stype 0 #space domain type +td_ttype 0 #time domain type +td_tstart 1 #the start step of electric field +td_tend 1000 #the start step of electric field +td_lcut1 0.05 # separator in length gauge +td_lcut2 0.95 # separator in length gauge +# parameters of Gauss electric field +td_gauss_freq 22.13 # fs^-1 +td_gauss_phase 0.0 +td_gauss_sigma 30.0 # fs +td_gauss_t0 100.0 +td_gauss_amp 0.25 # V/A +# parameters of Trapezoid electric field +td_trape_freq 1.60 # fs^-1 +td_trape_phase 0.0 +td_trape_t1 1875 +td_trape_t2 5625 +td_trape_t3 7500 +td_trape_amp 2.74 # V/A +#parameters of Trigonometric electric field +td_trigo_freq1 1.164656 # fs^-1 +td_trigo_freq2 0.029116 # fs^-1 +td_trigo_phase1 0.0 +td_trigo_phase2 0.0 +td_trigo_amp 2.74 # V/A +#parameters of Heaviside electric field +td_heavi_t0 100 +td_heavi_amp 1.0 # V/A +td_print_eij -1.0 # threshold to output Eij elements +td_edm 0 # 0: new edm method 1: old edm method +out_dipole 0 #output dipole or not +out_efield 0 #output efield or not +ocp 0 #change occupation or not +ocp_set none #set occupation + +#Parameters (17.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface + +#Parameters (18.implicit_solvation) +imp_sol 0 #calculate implicit solvation correction or not +eb_k 80 #the relative permittivity of the bulk solvent +tau 1.0798e-05 #the effective surface tension parameter +sigma_k 0.6 # the width of the diffuse cavity +nc_k 0.00037 # the cut-off charge density + +#Parameters (19.orbital free density functional theory) +of_kinetic vw #kinetic energy functional, such as tf, vw, wt +of_method tn #optimization method used in OFDFT, including cg1, cg2, tn (default) +of_conv energy #the convergence criterion, potential, energy (default), or both +of_tole 1e-06 #tolerance of the energy change (in Ry) for determining the convergence, default=2e-6 Ry +of_tolp 1e-05 #tolerance of potential for determining the convergence, default=1e-5 in a.u. +of_tf_weight 1 #weight of TF KEDF +of_vw_weight 1 #weight of vW KEDF +of_wt_alpha 0.833333 #parameter alpha of WT KEDF +of_wt_beta 0.833333 #parameter beta of WT KEDF +of_wt_rho0 1 #the average density of system, used in WT KEDF, in Bohr^-3 +of_hold_rho0 0 #If set to 1, the rho0 will be fixed even if the volume of system has changed, it will be set to 1 automaticly if of_wt_rho0 is not zero +of_full_pw 0 #If set to 1, ecut will be ignored when collect planewaves, so that all planewaves will be used +of_full_pw_dim 0 #If of_full_pw = true, dimention of FFT is testricted to be (0) either odd or even; (1) odd only; (2) even only +of_read_kernel 0 #If set to 1, the kernel of WT KEDF will be filled from file of_kernel_file, not from formula. Only usable for WT KEDF +of_kernel_file WTkernel.txt #The name of WT kernel file. + +#Parameters (19.dft+u) +dft_plus_u 0 #true:DFT+U correction; false: standard DFT calcullation(default) +yukawa_lambda -1 #default:0.0 +yukawa_potential 0 #default: false +omc 0 #the mode of occupation matrix control +hubbard_u 0 #Hubbard Coulomb interaction parameter U(ev) +orbital_corr -1 #which correlated orbitals need corrected ; d:2 ,f:3, do not need correction:-1 From 99bb07f1208f95779ae12370ef63d88d2c528974 Mon Sep 17 00:00:00 2001 From: lyb9812 <88070104+lyb9812@users.noreply.github.com> Date: Wed, 8 Mar 2023 14:23:26 +0800 Subject: [PATCH 08/11] Fix : bug of multi-kpoint for tddft (#2023) * fix bug of electric field in tddft * fix bug of dipole and electric field * fix bug of multi-kpoint for tddft * unit conversion of out_efield * delete useless paramters for tddft (td_val_elec*) * delete useless parameters for tddft From 98b96b874fdf0e7e8e90afb86e5d3812a317b103 Mon Sep 17 00:00:00 2001 From: lyb9812 Date: Sun, 16 Apr 2023 23:50:42 +0800 Subject: [PATCH 09/11] pack all changes in tddft --- .../parallel_reduce_test.sh~merged | 21 ++++++ .../potentials/H_TDDFT_pw.cpp | 6 +- .../module_esolver/esolver_ks_lcao_tddft.cpp | 5 +- source/module_io/write_dipole.cpp | 69 +++++-------------- 4 files changed, 45 insertions(+), 56 deletions(-) create mode 100755 source/module_base/test_parallel/parallel_reduce_test.sh~merged diff --git a/source/module_base/test_parallel/parallel_reduce_test.sh~merged b/source/module_base/test_parallel/parallel_reduce_test.sh~merged new file mode 100755 index 0000000000..6e8ae40e48 --- /dev/null +++ b/source/module_base/test_parallel/parallel_reduce_test.sh~merged @@ -0,0 +1,21 @@ +#!/bin/bash -e + +np=`cat /proc/cpuinfo | grep "cpu cores" | uniq| awk '{print $NF}'` +echo "nprocs in this machine is $np" + +for i in 4;do + if [[ $i -gt $np ]];then + continue + fi + echo "TEST in parallel, nprocs=$i" +<<<<<<< HEAD + mpirun -np $i ./base_ParaReduce +======= +<<<<<<< HEAD:source/module_base/test_parallel/parallel_global_test.sh + mpirun -np $i ./base_ParaGlobal +======= + mpirun -np $i ./base_ParaReduce +>>>>>>> 48501f02... Fix : bug of electric field in tddft (#1938):source/module_base/test_parallel/parallel_reduce_test.sh +>>>>>>> 48501f02... Fix : bug of electric field in tddft (#1938) + break +done diff --git a/source/module_elecstate/potentials/H_TDDFT_pw.cpp b/source/module_elecstate/potentials/H_TDDFT_pw.cpp index 50e8bcc6eb..a915af5b7b 100644 --- a/source/module_elecstate/potentials/H_TDDFT_pw.cpp +++ b/source/module_elecstate/potentials/H_TDDFT_pw.cpp @@ -211,11 +211,11 @@ double H_TDDFT_pw::cal_v_space_length_potential(double i) { vext_space = ((i - lcut1) * (lcut2 - lcut1) / (lcut1 + 1.0 - lcut2) - lcut1) * this->ucell_->lat0; } - else if (i >= this->rho_basis_->nx * lcut1 && i < this->rho_basis_->nx * lcut2) + else if (i >= lcut1 && i < lcut2) { - vext_space = -i / this->rho_basis_->nx * this->ucell_->lat0; + vext_space = -i * this->ucell_->lat0; } - else if (i >= this->rho_basis_->nx * lcut2) + else if (i >= lcut2) { vext_space = ((i - lcut2) * (lcut2 - lcut1) / (lcut1 + 1.0 - lcut2) - lcut2) * this->ucell_->lat0; } diff --git a/source/module_esolver/esolver_ks_lcao_tddft.cpp b/source/module_esolver/esolver_ks_lcao_tddft.cpp index 00edfc0d8b..1899cb9dfd 100644 --- a/source/module_esolver/esolver_ks_lcao_tddft.cpp +++ b/source/module_esolver/esolver_ks_lcao_tddft.cpp @@ -365,9 +365,7 @@ void ESolver_KS_LCAO_TDDFT::updatepot(const int istep, const int iter) = new psi::Psi>(GlobalC::kv.nks, GlobalV::NBANDS, GlobalV::NLOCAL, nullptr); #endif - std::complex *p_psi = &psi[0](0,0,0); - std::complex *p_psi_laststep = &psi_laststep[0](0,0,0); - for (int index = 0; index < psi[0].size(); ++index) + for (int ik = 0; ik < GlobalC::kv.nks; ++ik) { this->psi->fix_k(ik); this->psi_laststep->fix_k(ik); @@ -375,6 +373,7 @@ void ESolver_KS_LCAO_TDDFT::updatepot(const int istep, const int iter) for (int index = 0; index < size0; ++index) psi_laststep[0].get_pointer()[index] = psi[0].get_pointer()[index]; } + if (istep > 1 && ELEC_evolve::td_edm == 0) this->cal_edm_tddft(); } diff --git a/source/module_io/write_dipole.cpp b/source/module_io/write_dipole.cpp index 5acaa72c58..1b9dc884af 100644 --- a/source/module_io/write_dipole.cpp +++ b/source/module_io/write_dipole.cpp @@ -61,52 +61,21 @@ void ModuleIO::write_dipole(const double *rho_save, ofs << istep << " " << dipole_elec_x << " " << dipole_elec_y << dipole_elec_z; #else - // case 2: > first part rho: processor 0 receive the rho - // from other processors - else if (GlobalV::RANK_IN_POOL == 0) - { - MPI_Recv(zpiece, nxy, MPI_DOUBLE, which_ip[iz], tag, POOL_WORLD, &ierror); - // GlobalV::ofs_running << "\n Receieve First number = " << zpiece[0]; - } + double dipole_elec[3] = {0.0, 0.0, 0.0}; - // write data - if (GlobalV::MY_RANK == 0) - { - // ofs << "\niz=" << iz; - // mohan update 2011-03-30 - for (int iy = 0; iy < GlobalC::rhopw->ny; iy++) - { - for (int ix = 0; ix < GlobalC::rhopw->nx; ix++) - { - /* - if(ixny + iy] * ix * GlobalC::ucell.lat0 * 0.529177 - / GlobalC::rhopw->nx; - dipole_elec_y += zpiece[ix * GlobalC::rhopw->ny + iy] * iy * GlobalC::ucell.lat0 * 0.529177 - / GlobalC::rhopw->ny; - dipole_elec_z += zpiece[ix * GlobalC::rhopw->ny + iy] * iz * GlobalC::ucell.lat0 * 0.529177 - / GlobalC::rhopw->nz; - } - } - } - } // end iz - - delete[] zpiece; + for (int ir = 0; ir < GlobalC::rhopw->nrxx; ++ir) + { + int i = ir / (GlobalC::rhopw->ny * GlobalC::rhopw->nplane); + int j = ir / GlobalC::rhopw->nplane - i * GlobalC::rhopw->ny; + int k = ir % GlobalC::rhopw->nplane + GlobalC::rhopw->startz_current; + double x = (double)i / GlobalC::rhopw->nx; + double y = (double)j / GlobalC::rhopw->ny; + double z = (double)k / GlobalC::rhopw->nz; + + dipole_elec[0] += rho_save[ir] * x; + dipole_elec[1] += rho_save[ir] * y; + dipole_elec[2] += rho_save[ir] * z; + } Parallel_Reduce::reduce_double_pool(dipole_elec[0]); Parallel_Reduce::reduce_double_pool(dipole_elec[1]); @@ -116,11 +85,12 @@ void ModuleIO::write_dipole(const double *rho_save, dipole_elec[i] *= GlobalC::ucell.lat0 / bmod[i] * GlobalC::ucell.omega / GlobalC::rhopw->nxyz; } - std::cout << std::setprecision(8) << "dipole_elec_x: " << dipole_elec_x << std::endl; - std::cout << std::setprecision(8) << "dipole_elec_y: " << dipole_elec_y << std::endl; - std::cout << std::setprecision(8) << "dipole_elec_z: " << dipole_elec_z << std::endl; + std::cout << std::setprecision(8) << "dipole_elec_x: " << dipole_elec[0] << std::endl; + std::cout << std::setprecision(8) << "dipole_elec_y: " << dipole_elec[1] << std::endl; + std::cout << std::setprecision(8) << "dipole_elec_z: " << dipole_elec[2] << std::endl; - ofs << istep << " " << dipole_elec_x << " " << dipole_elec_y << " " << dipole_elec_z << std::endl; + ofs << std::setprecision(8) << istep << " " << dipole_elec[0] << " " << dipole_elec[1] << " " << dipole_elec[2] + << std::endl; double dipole_ion[3] = {0.0}; double dipole_sum = 0.0; @@ -157,7 +127,6 @@ void ModuleIO::write_dipole(const double *rho_save, #endif - // calculate ion dipole; if (GlobalV::MY_RANK == 0) { end = time(NULL); From 8b16fe70f6aa78371994000a8fa182c6928ce2d0 Mon Sep 17 00:00:00 2001 From: lyb9812 Date: Mon, 17 Apr 2023 00:00:21 +0800 Subject: [PATCH 10/11] solve conflicts --- .../parallel_reduce_test.sh~merged | 21 ------------------- 1 file changed, 21 deletions(-) delete mode 100755 source/module_base/test_parallel/parallel_reduce_test.sh~merged diff --git a/source/module_base/test_parallel/parallel_reduce_test.sh~merged b/source/module_base/test_parallel/parallel_reduce_test.sh~merged deleted file mode 100755 index 6e8ae40e48..0000000000 --- a/source/module_base/test_parallel/parallel_reduce_test.sh~merged +++ /dev/null @@ -1,21 +0,0 @@ -#!/bin/bash -e - -np=`cat /proc/cpuinfo | grep "cpu cores" | uniq| awk '{print $NF}'` -echo "nprocs in this machine is $np" - -for i in 4;do - if [[ $i -gt $np ]];then - continue - fi - echo "TEST in parallel, nprocs=$i" -<<<<<<< HEAD - mpirun -np $i ./base_ParaReduce -======= -<<<<<<< HEAD:source/module_base/test_parallel/parallel_global_test.sh - mpirun -np $i ./base_ParaGlobal -======= - mpirun -np $i ./base_ParaReduce ->>>>>>> 48501f02... Fix : bug of electric field in tddft (#1938):source/module_base/test_parallel/parallel_reduce_test.sh ->>>>>>> 48501f02... Fix : bug of electric field in tddft (#1938) - break -done From adec5accb0457aaf336faf309089096f805cbeec Mon Sep 17 00:00:00 2001 From: lyb9812 Date: Mon, 17 Apr 2023 00:18:01 +0800 Subject: [PATCH 11/11] delete td_val --- source/module_io/test/for_testing_input_conv.h | 3 --- source/module_io/test/input_conv_test.cpp | 3 --- source/module_io/test/input_test_para.cpp | 3 --- source/module_io/test/support/INPUT | 3 --- source/module_io/test/write_input_test.cpp | 3 --- 5 files changed, 15 deletions(-) diff --git a/source/module_io/test/for_testing_input_conv.h b/source/module_io/test/for_testing_input_conv.h index 5e5a5f0a08..1d0a17bb92 100644 --- a/source/module_io/test/for_testing_input_conv.h +++ b/source/module_io/test/for_testing_input_conv.h @@ -35,9 +35,6 @@ int hsolver::HSolverLCAO::out_mat_dh = 0; int Local_Orbital_Charge::out_dm = 0; int Local_Orbital_Charge::out_dm1 = 0; double ELEC_evolve::td_force_dt; -int ELEC_evolve::td_val_elec_01; -int ELEC_evolve::td_val_elec_02; -int ELEC_evolve::td_val_elec_03; bool ELEC_evolve::td_vext; std::vector ELEC_evolve::td_vext_dire_case; bool ELEC_evolve::out_dipole; diff --git a/source/module_io/test/input_conv_test.cpp b/source/module_io/test/input_conv_test.cpp index cadf9022d6..fd5f7a07ed 100644 --- a/source/module_io/test/input_conv_test.cpp +++ b/source/module_io/test/input_conv_test.cpp @@ -125,9 +125,6 @@ TEST_F(InputConvTest, Conv) EXPECT_DOUBLE_EQ(elecstate::Gatefield::block_height,0.1); EXPECT_EQ(ELEC_evolve::td_force_dt,0.02); - EXPECT_EQ(ELEC_evolve::td_val_elec_01,1); - EXPECT_EQ(ELEC_evolve::td_val_elec_02,1); - EXPECT_EQ(ELEC_evolve::td_val_elec_03,1); EXPECT_EQ(ELEC_evolve::td_vext,false); EXPECT_EQ(ELEC_evolve::out_dipole,false); EXPECT_EQ(ELEC_evolve::out_efield,false); diff --git a/source/module_io/test/input_test_para.cpp b/source/module_io/test/input_test_para.cpp index 85aae50512..b4b3afbcba 100644 --- a/source/module_io/test/input_test_para.cpp +++ b/source/module_io/test/input_test_para.cpp @@ -256,9 +256,6 @@ TEST_F(InputParaTest,Bcast) EXPECT_DOUBLE_EQ(INPUT.soc_lambda,1.0); EXPECT_EQ(INPUT.input_error,0); EXPECT_DOUBLE_EQ(INPUT.td_force_dt,0.02); - EXPECT_EQ(INPUT.td_val_elec_01,1); - EXPECT_EQ(INPUT.td_val_elec_02,1); - EXPECT_EQ(INPUT.td_val_elec_03,1); EXPECT_FALSE(INPUT.td_vext); EXPECT_EQ(INPUT.td_vext_dire,"1"); EXPECT_EQ(INPUT.td_stype,0); diff --git a/source/module_io/test/support/INPUT b/source/module_io/test/support/INPUT index 7565ad8493..91b4fc9de4 100644 --- a/source/module_io/test/support/INPUT +++ b/source/module_io/test/support/INPUT @@ -282,9 +282,6 @@ exx_opt_orb_tolerence 0 # #Parameters (16.tddft) td_force_dt 0.02 #time of force change -td_val_elec_01 1 #td_val_elec_01 -td_val_elec_02 1 #td_val_elec_02 -td_val_elec_03 1 #td_val_elec_03 td_vext 0 #add extern potential or not td_vext_dire 1 #extern potential direction td_stype 0 #space domain type diff --git a/source/module_io/test/write_input_test.cpp b/source/module_io/test/write_input_test.cpp index 67a71efce1..f7e9114a92 100644 --- a/source/module_io/test/write_input_test.cpp +++ b/source/module_io/test/write_input_test.cpp @@ -293,9 +293,6 @@ TEST_F(write_input,print) EXPECT_THAT(output,testing::HasSubstr("")); EXPECT_THAT(output,testing::HasSubstr("#Parameters (16.tddft)")); EXPECT_THAT(output,testing::HasSubstr("td_force_dt 0.02 #time of force change")); - EXPECT_THAT(output,testing::HasSubstr("td_val_elec_01 1 #td_val_elec_01")); - EXPECT_THAT(output,testing::HasSubstr("td_val_elec_02 1 #td_val_elec_02")); - EXPECT_THAT(output,testing::HasSubstr("td_val_elec_03 1 #td_val_elec_03")); EXPECT_THAT(output,testing::HasSubstr("td_vext 0 #add extern potential or not")); EXPECT_THAT(output,testing::HasSubstr("td_vext_dire 1 #extern potential direction")); EXPECT_THAT(output,testing::HasSubstr("out_dipole 0 #output dipole or not"));