├── .gitignore ├── AUTHORS ├── LICENSE ├── README.md ├── REVISION ├── bin ├── JADERC ├── jade.exe ├── main_overlap_slater.exe ├── sampling.x └── sampling2.x ├── doc ├── FEATURE ├── INSTALL ├── KEYWORDS ├── intro.pdf └── sampling-doc │ ├── KEYWORDS-NEW │ └── KEYWORDS-OLD └── src ├── Makefile ├── README ├── compiler.mk ├── database ├── elements.dat └── readme ├── dynamics ├── Makefile ├── README ├── include │ ├── param.def │ ├── var_n_atom.h │ └── var_n_mode.h ├── main_sh.f90 ├── mapping │ ├── Makefile │ ├── Readme │ ├── adia │ │ ├── Makefile │ │ ├── sub_calc_dV_eff_div_dx_nuc_adia.f90 │ │ ├── sub_calc_dV_eff_div_dx_nuc_adia.o │ │ ├── sub_calc_dV_eff_div_dx_nuc_adia_traj_adjusted.f90 │ │ ├── sub_calc_dV_eff_div_dx_nuc_adia_traj_adjusted.o │ │ ├── sub_calc_dp_nuc_kin__dij_term_adia.f90 │ │ ├── sub_calc_dp_nuc_kin__dij_term_adia.o │ │ ├── sub_elec_motion_2_aver_PES_1step_adia.f90 │ │ ├── sub_elec_motion_2_aver_PES_1step_adia.o │ │ ├── sub_elec_motion_2_aver_PES_1step_dx_div_dt_adia.f90 │ │ ├── sub_elec_motion_2_aver_PES_1step_dx_div_dt_adia.o │ │ ├── sub_elec_motion_2_aver_PES_adia.f90 │ │ ├── sub_elec_motion_2_aver_PES_adia.o │ │ ├── sub_motion_2_adia_aver_PES_1step.f90 │ │ ├── sub_motion_2_adia_aver_PES_1step.o │ │ ├── sub_nuc_get_dHmn_div_dX_adia.f90 │ │ ├── sub_nuc_get_dHmn_div_dX_adia.o │ │ ├── sub_nuc_motion_2_aver_PES_1step_dp_div_dt_adia.f90 │ │ ├── sub_nuc_motion_2_aver_PES_1step_dp_div_dt_adia.o │ │ ├── sub_nuc_motion_2_aver_PES_1step_dp_div_dt_adia_traj_adjusted.f90 │ │ ├── sub_nuc_motion_2_aver_PES_1step_dp_div_dt_adia_traj_adjusted.o │ │ ├── sub_nuc_motion_2_aver_PES_1step_dx_div_dt_adia.f90 │ │ ├── sub_nuc_motion_2_aver_PES_1step_dx_div_dt_adia.o │ │ ├── sub_nuc_motion_2_aver_PES_adia.f90 │ │ ├── sub_nuc_motion_2_aver_PES_adia.o │ │ ├── sub_p_kin_to_p.f90 │ │ ├── sub_p_kin_to_p.o │ │ ├── sub_p_to_p_kin.f90 │ │ ├── sub_p_to_p_kin.o │ │ ├── sub_write_trj_2_adia.f90 │ │ ├── sub_write_trj_2_adia.o │ │ ├── sub_write_trj_2_adia_traj_adjusted.f90 │ │ └── sub_write_trj_2_adia_traj_adjusted.o │ ├── bak │ │ ├── mod_main.f90 │ │ ├── sub_calc_dV_eff_div_dx_nuc_adia.f90 │ │ ├── sub_calc_dp_nuc_kin__dij_term_adia.f90 │ │ ├── sub_elec_motion_2_aver_PES_1step_adia.f90 │ │ ├── sub_elec_motion_2_aver_PES_1step_dx_div_dt_adia.f90 │ │ ├── sub_elec_motion_2_aver_PES_adia.f90 │ │ ├── sub_get_dia_grad.f90 │ │ ├── sub_mapping_ana_nac_tmp.f90 │ │ ├── sub_mapping_read_ini_trj_elec_2.f90 │ │ ├── sub_motion_2_adia_aver_PES_1step.f90 │ │ ├── sub_nuc_get_dHmn_div_dX_adia.f90 │ │ ├── sub_nuc_motion_2_aver_PES_1step_dp_div_dt_adia.f90 │ │ ├── sub_nuc_motion_2_aver_PES_adia.f90 │ │ ├── sub_p_kin_to_p.f90 │ │ ├── sub_p_to_p_kin.f90 │ │ └── sub_write_trj_2_adia.f90 │ ├── constant.f90 │ ├── ham4 │ │ ├── c_n.dat │ │ ├── dHmn_div_dX.dat │ │ ├── dyn.input │ │ ├── ene.input │ │ ├── freq.input │ │ ├── ham.dat │ │ ├── k_tun.input │ │ ├── lambda0_coupling.input │ │ ├── lambda1_coupling.input │ │ ├── pop_adia.dat │ │ ├── pop_dia.dat │ │ ├── reduced_mass_inv_tor.input │ │ ├── tor_pot_para.input │ │ ├── trj.dat │ │ ├── trj.input │ │ ├── trj_elec.dat │ │ ├── trj_elec.input │ │ ├── trj_elec_debug.dat │ │ ├── trj_elec_restart.input │ │ ├── trj_restart.input │ │ ├── x_p_debug.dat │ │ └── x_sq_add_p_sq.dat │ ├── mod_main.f90 │ ├── mod_main.mod │ ├── mod_main.o │ ├── on_the_fly │ │ ├── .ps_00000045f67bc10100000485 │ │ ├── Makefile │ │ ├── bak │ │ │ ├── sub_read_ini_trj_2_on_the_fly.f90 │ │ │ ├── sub_reshape_n_atom_to_n_mode_coor.f90 │ │ │ └── sub_reshape_n_mode_to_n_atom_coor.f90 │ │ ├── sub_evolution_mapping_2_on_the_fly.f90 │ │ ├── sub_evolution_mapping_2_on_the_fly.o │ │ ├── sub_evolution_mapping_2_on_the_fly_traj_adjusted.f90 │ │ ├── sub_evolution_mapping_2_on_the_fly_traj_adjusted.o │ │ ├── sub_many_ana_pes_mapping.f90 │ │ ├── sub_many_ana_pes_mapping.o │ │ ├── sub_nac_phase_mapping.f90 │ │ ├── sub_nac_phase_mapping.o │ │ ├── sub_read_current_geom_mapping.f90 │ │ ├── sub_read_current_geom_mapping.o │ │ ├── sub_read_parameter_on_the_fly.f90 │ │ ├── sub_read_parameter_on_the_fly.o │ │ ├── sub_reshape_n_atom_to_n_mode.f90 │ │ ├── sub_reshape_n_atom_to_n_mode.o │ │ ├── sub_reshape_n_mode_to_n_atom.f90 │ │ ├── sub_reshape_n_mode_to_n_atom.o │ │ ├── sub_test.f90 │ │ ├── sub_test.o │ │ ├── sub_write_current_geom_mapping.f90 │ │ ├── sub_write_current_geom_mapping.o │ │ ├── sub_write_geom.f90 │ │ ├── sub_write_geom.o │ │ ├── sub_write_geom_mapping.f90 │ │ ├── sub_write_geom_mapping.o │ │ ├── sub_write_geom_mapping_traj_adjusted.f90 │ │ └── sub_write_geom_mapping_traj_adjusted.o │ ├── sub_cal_gammas.f90 │ ├── sub_cal_gammas.o │ ├── sub_dia_to_adia.f90 │ ├── sub_dia_to_adia.o │ ├── sub_diag.f90 │ ├── sub_diag.o │ ├── sub_elec_get_dH_div_dx_or_dp.f90 │ ├── sub_elec_get_dH_div_dx_or_dp.o │ ├── sub_elec_get_dH_div_dx_or_dp_3.f90 │ ├── sub_elec_get_dH_div_dx_or_dp_3.o │ ├── sub_elec_get_dH_div_dx_or_dp_aver_PES.f90 │ ├── sub_elec_get_dH_div_dx_or_dp_aver_PES.o │ ├── sub_elec_motion_1.f90 │ ├── sub_elec_motion_1.o │ ├── sub_elec_motion_2.f90 │ ├── sub_elec_motion_2.o │ ├── sub_elec_motion_2_aver_PES.f90 │ ├── sub_elec_motion_2_aver_PES.o │ ├── sub_elec_motion_3.f90 │ ├── sub_elec_motion_3.o │ ├── sub_elec_motion_3_step1.f90 │ ├── sub_elec_motion_3_step1.o │ ├── sub_elec_motion_3_step1_2.f90 │ ├── sub_elec_motion_3_step1_2.o │ ├── sub_elec_motion_3_step2.f90 │ ├── sub_elec_motion_3_step2.o │ ├── sub_elec_motion_3_step2_2.f90 │ ├── sub_elec_motion_3_step2_2.o │ ├── sub_elec_motion_mapping_1_Ham_4.f90 │ ├── sub_elec_motion_mapping_1_Ham_4.o │ ├── sub_elec_motion_mapping_2_Ham_4_aver_PES.f90 │ ├── sub_elec_motion_mapping_2_Ham_4_aver_PES.o │ ├── sub_evolution_1.f90 │ ├── sub_evolution_1.o │ ├── sub_evolution_2.f90 │ ├── sub_evolution_2.o │ ├── sub_evolution_3.f90 │ ├── sub_evolution_3.o │ ├── sub_evolution_adia.f90 │ ├── sub_evolution_adia.o │ ├── sub_evolution_mapping_1_Ham_4.f90 │ ├── sub_evolution_mapping_1_Ham_4.o │ ├── sub_evolution_mapping_2_Ham_4.f90 │ ├── sub_evolution_mapping_2_Ham_4.o │ ├── sub_get_c_n_elec_1.f90 │ ├── sub_get_c_n_elec_1.o │ ├── sub_get_c_n_elec_2.f90 │ ├── sub_get_c_n_elec_2.o │ ├── sub_get_c_n_elec_2_traj_adjusted.f90 │ ├── sub_get_c_n_elec_2_traj_adjusted.o │ ├── sub_get_c_n_elec_3.f90 │ ├── sub_get_c_n_elec_3.o │ ├── sub_get_dia_Ham_elec.f90 │ ├── sub_get_dia_Ham_elec.o │ ├── sub_get_dia_Ham_elec_Ham_4.f90 │ ├── sub_get_dia_Ham_elec_Ham_4.o │ ├── sub_get_dia_Ham_elec_Ham_tor.f90 │ ├── sub_get_dia_Ham_elec_Ham_tor.o │ ├── sub_get_dia_V_elec.f90 │ ├── sub_mapping_ana_nac.f90 │ ├── sub_mapping_ana_nac.o │ ├── sub_move.f90 │ ├── sub_move.o │ ├── sub_nuc_get_dH_div_dP.f90 │ ├── sub_nuc_get_dH_div_dP.o │ ├── sub_nuc_get_dH_div_dP_aver_PES.f90 │ ├── sub_nuc_get_dH_div_dP_aver_PES.o │ ├── sub_nuc_get_dH_div_dX_or_dP.f90 │ ├── sub_nuc_get_dH_div_dX_or_dP.o │ ├── sub_nuc_get_dH_div_dX_or_dP_aver_PES.f90 │ ├── sub_nuc_get_dH_div_dX_or_dP_aver_PES.o │ ├── sub_nuc_get_dHmn_div_dP.f90 │ ├── sub_nuc_get_dHmn_div_dP.o │ ├── sub_nuc_get_dHmn_div_dX.f90 │ ├── sub_nuc_get_dHmn_div_dX.o │ ├── sub_nuc_get_dHmn_div_dX_Ham_tor.f90 │ ├── sub_nuc_get_dHmn_div_dX_Ham_tor.o │ ├── sub_nuc_motion.f90 │ ├── sub_nuc_motion.o │ ├── sub_nuc_motion_Ham_4.f90 │ ├── sub_nuc_motion_Ham_4.o │ ├── sub_nuc_motion_Ham_4_aver_PES.f90 │ ├── sub_nuc_motion_Ham_4_aver_PES.o │ ├── sub_nuc_motion_aver_PES.f90 │ ├── sub_nuc_motion_aver_PES.o │ ├── sub_read_control.f90 │ ├── sub_read_control.o │ ├── sub_read_ini_trj_1.f90 │ ├── sub_read_ini_trj_1.o │ ├── sub_read_ini_trj_2.f90 │ ├── sub_read_ini_trj_2.o │ ├── sub_read_ini_trj_2_on_the_fly.f90 │ ├── sub_read_parameter.f90 │ ├── sub_read_parameter.o │ ├── sub_read_parameter_Ham_4.f90 │ ├── sub_read_parameter_Ham_4.o │ ├── sub_sum_sq_sum_by4.f90 │ ├── sub_sum_sq_sum_by4.o │ ├── sub_write_trj_1.f90 │ ├── sub_write_trj_1.o │ ├── sub_write_trj_2.f90 │ ├── sub_write_trj_2.o │ ├── sub_write_trj_3.f90 │ └── sub_write_trj_3.o └── tsh │ ├── Makefile │ ├── check_random.f90 │ ├── constant.f90 │ ├── constant.mod │ ├── constant.o │ ├── langevin.f90 │ ├── langevin.mod │ ├── langevin.o │ ├── randomlib.mod │ ├── sub_bomd_excit.f90 │ ├── sub_decoherent_corr.f90 │ ├── sub_decoherent_corr.o │ ├── sub_get_mass.f90 │ ├── sub_get_mass.o │ ├── sub_lang_sh_num_nac.f90 │ ├── sub_lang_sh_num_nac.o │ ├── sub_many_ana_pes.f90 │ ├── sub_many_ana_pes.o │ ├── sub_many_pes_num_nac.f90 │ ├── sub_many_pes_num_nac.o │ ├── sub_nac_phase.f90 │ ├── sub_nac_phase.o │ ├── sub_newton_ang.f90 │ ├── sub_newton_angvel.f90 │ ├── sub_newton_coor.f90 │ ├── sub_newton_coor.o │ ├── sub_newton_vel.f90 │ ├── sub_newton_vel.o │ ├── sub_open_file.f90 │ ├── sub_random.f90 │ ├── sub_random.o │ ├── sub_random2.f90 │ ├── sub_random3.f90 │ ├── sub_random3.o │ ├── sub_read_coor.f90 │ ├── sub_read_coor.o │ ├── sub_read_current_geom.f90 │ ├── sub_read_current_geom.o │ ├── sub_read_ini_vel.f90 │ ├── sub_read_ini_vel.o │ ├── sub_read_restart.f90 │ ├── sub_read_restart.o │ ├── sub_restart.f90 │ ├── sub_save_energy.f90 │ ├── sub_save_energy.o │ ├── sub_save_grad.f90 │ ├── sub_save_grad.o │ ├── sub_save_gradient.f90 │ ├── sub_save_gradient.o │ ├── sub_save_hopping_ana_nac.f90 │ ├── sub_save_hopping_ana_nac.o │ ├── sub_save_hopping_num_nac.f90 │ ├── sub_save_hopping_num_nac.o │ ├── sub_save_pe.f90 │ ├── sub_save_pe.o │ ├── sub_save_restart.f90 │ ├── sub_save_restart.o │ ├── sub_save_traj.f90 │ ├── sub_save_traj.o │ ├── sub_sh_ana_nac.f90 │ ├── sub_sh_ana_nac.o │ ├── sub_sh_num_nac.f90 │ ├── sub_sh_num_nac.o │ ├── sub_sh_soc_dia.f90 │ ├── sub_sh_zn.f90 │ ├── sub_sh_zn.o │ ├── sub_string.f90 │ ├── sub_string.o │ ├── sub_tully_hopping_ana_nac.f90 │ ├── sub_tully_hopping_ana_nac.o │ ├── sub_tully_hopping_num_nac.f90 │ ├── sub_tully_hopping_num_nac.o │ ├── sub_velocity_scaling.f90 │ ├── sub_velocity_scaling.o │ ├── sub_write_current_geom.f90 │ ├── sub_write_current_geom.o │ ├── sub_zn_hopping.f90 │ └── sub_zn_hopping.o ├── electronic ├── Makefile ├── interface_bagel_qm │ ├── .gitignore │ ├── __init__.py │ ├── bagel.py │ ├── bagel_create.py │ ├── bagel_log_parser.py │ ├── bagel_parser.py │ ├── bagel_run.py │ ├── bagel_template.py │ └── config.in ├── interface_gamess_qm │ ├── __init__.py │ ├── config.in │ ├── details.txt │ ├── gamess.py │ ├── gms_ao_parser.py │ ├── gms_create.py │ ├── gms_log_parser.py │ ├── gms_log_parser2.py │ ├── gms_nac.py │ ├── gms_nonzero.py │ ├── gms_overlap.py │ ├── gms_parser.py │ ├── gms_run.py │ ├── gms_template.py │ ├── gms_zero.py │ ├── improve │ ├── readme │ └── scr │ │ ├── gamess.F10 │ │ └── gamess.dat ├── interface_gaussian_oniom │ ├── EXAM │ │ ├── gau.gjf │ │ ├── gau_template.gjf │ │ └── template.com │ ├── GAU_TMP │ │ └── interface.json │ ├── GAU_TMP_PREV │ │ └── interface.json │ ├── GauONIOM.py │ ├── ONIOM.doc │ ├── ONLYINPUT │ │ ├── high-model-check.gjf │ │ ├── layer.json │ │ ├── low-model-check.gjf │ │ ├── low-real-check.gjf │ │ ├── onlyinputfiles.gjf │ │ └── template.json │ ├── __init__.py │ ├── ao.gjf │ ├── ao_overlap.dat │ ├── calculator.py │ ├── check.xyz │ ├── ci.dat │ ├── ci_all.dat │ ├── ci_all_norm.dat │ ├── compare.json │ ├── config.in │ ├── cre_gau_input_tool.py │ ├── details.tex │ ├── dimension.json │ ├── dump.xyz │ ├── dyn.inp │ ├── excit_other.dat │ ├── frag │ │ ├── all.gjf │ │ ├── gaussian.gjf │ │ ├── highmodel.gjf │ │ ├── lowmodel.gjf │ │ └── lowreal.gjf │ ├── g09.lsf │ ├── gTrajParser.py │ ├── gau_ao_create.py │ ├── gau_create.py │ ├── gau_log2inp.py │ ├── gau_log_ao_parser.py │ ├── gau_log_eandg_parser.py │ ├── gau_log_parser.py │ ├── gau_log_wf_parser.py │ ├── gau_mo_modify.py │ ├── gau_model_create.py │ ├── gau_model_template.py │ ├── gau_nac.py │ ├── gau_nonzero.py │ ├── gau_onlyinp.py │ ├── gau_overlap.py │ ├── gau_parser.py │ ├── gau_run.py │ ├── gau_rwf_parser.py │ ├── gau_rwf_wf_parser.py │ ├── gau_template.py │ ├── gau_zero.py │ ├── high-model-check.gjf │ ├── high-model-energy.dat │ ├── high-model-gradient.dat │ ├── high-model-overlap.gjf │ ├── high-model.gjf │ ├── highao.gjf │ ├── highmodel.gjf │ ├── inp.json │ ├── interface.json │ ├── layer.json │ ├── lists.txt │ ├── low-model-check.gjf │ ├── low-model-energy.dat │ ├── low-model-gradient.dat │ ├── low-model.gjf │ ├── low-real-check.gjf │ ├── low-real-energy.dat │ ├── low-real-gradient.dat │ ├── low-real.gjf │ ├── lowmodel.gjf │ ├── mo.dat │ ├── model_energy.dat │ ├── model_other.dat │ ├── myoniom.py │ ├── oniom2 │ │ ├── 635R.dat │ │ ├── B2.gbs │ │ ├── PES.out │ │ ├── a.gjf │ │ ├── ao.gjf │ │ ├── b.gjf │ │ ├── b3lyp.gjf │ │ ├── embed.gjf │ │ ├── fort.7 │ │ ├── gaussian.gjf │ │ ├── h2o.gjf │ │ ├── hm.fchk │ │ ├── hm.gjf │ │ ├── inp.json │ │ ├── interface.json │ │ ├── mm.gjf │ │ ├── noembed.gjf │ │ ├── oniom.fchk │ │ ├── oniom.gjf │ │ ├── qm.fchk │ │ ├── qm.gjf │ │ ├── qm1.gjf │ │ ├── qm2.gjf │ │ ├── qm3.gjf │ │ ├── qmqm.gjf │ │ ├── readme │ │ ├── s2.gjf │ │ ├── t.gjf │ │ ├── template.json │ │ ├── test.gjf │ │ └── tt.gjf │ ├── oniom3 │ │ ├── h2o3.gjf │ │ ├── ok.gjf │ │ └── ok.pdb │ ├── oniom_other.dat │ ├── only.gjf │ ├── onlyinputfiles.gjf │ ├── overlap_all.dat │ ├── qm.dump │ ├── qm.gjf │ ├── qm_energy.dat │ ├── qm_gradient.dat │ ├── qm_gradient.dat.bak │ ├── qm_interface │ ├── qm_other.dat │ ├── qm_results.dat │ ├── readme │ ├── sh │ ├── task │ ├── tddft.txt │ ├── template.json │ ├── test │ │ ├── GAU_EXAM │ │ │ ├── gau.gjf │ │ │ ├── gau_template.gjf │ │ │ └── template.com │ │ ├── dyn.inp │ │ ├── model │ │ │ ├── CLA.xyz │ │ │ ├── admp │ │ │ │ ├── admp.gjf │ │ │ │ ├── mix.gjf │ │ │ │ └── t │ │ │ ├── amber │ │ │ │ ├── inp │ │ │ │ │ └── readme │ │ │ │ └── parms │ │ │ │ │ ├── ANTECHAMBER.ESP │ │ │ │ │ ├── ANTECHAMBER_AC.AC │ │ │ │ │ ├── ANTECHAMBER_AC.AC0 │ │ │ │ │ ├── ANTECHAMBER_BOND_TYPE.AC │ │ │ │ │ ├── ANTECHAMBER_BOND_TYPE.AC0 │ │ │ │ │ ├── ANTECHAMBER_RESP.AC │ │ │ │ │ ├── ANTECHAMBER_RESP1.IN │ │ │ │ │ ├── ANTECHAMBER_RESP1.OUT │ │ │ │ │ ├── ANTECHAMBER_RESP2.IN │ │ │ │ │ ├── ANTECHAMBER_RESP2.OUT │ │ │ │ │ ├── ATOMTYPE.INF │ │ │ │ │ ├── ch2nh2p.gjf │ │ │ │ │ ├── ch2nh2p.mol2 │ │ │ │ │ ├── esout │ │ │ │ │ ├── punch │ │ │ │ │ ├── readme │ │ │ │ │ └── solute.pdb │ │ │ ├── ch2nh2p.xyz │ │ │ ├── dye.doc │ │ │ ├── example │ │ │ │ ├── mixture.inp │ │ │ │ ├── mixture.pdb │ │ │ │ ├── urea.pdb │ │ │ │ └── water.pdb │ │ │ ├── h2o.xyz │ │ │ ├── mix.gjf │ │ │ ├── mix.pdb │ │ │ ├── mix.xyz │ │ │ ├── mix40.gjf │ │ │ ├── opt │ │ │ │ ├── ch2nh2p.gjf │ │ │ │ ├── ch2nh2p.xyz │ │ │ │ ├── h2o.gjf │ │ │ │ ├── h2o.xyz │ │ │ │ └── opted.gjf │ │ │ ├── solute.pdb │ │ │ ├── sphere.inp │ │ │ └── water.pdb │ │ └── opt │ │ │ ├── admp.gjf │ │ │ └── opt.gjf │ └── tutorial ├── interface_gaussian_qm │ ├── .gitignore │ ├── __init__.py │ ├── calculator.py │ ├── config.in │ ├── cre_gau_input_tool.py │ ├── details.tex │ ├── g09.lsf │ ├── gau_create.py │ ├── gau_log_parser.py │ ├── gau_nac.py │ ├── gau_nonzero.py │ ├── gau_overlap.py │ ├── gau_parser.py │ ├── gau_rwf_parser.py │ ├── gau_template.py │ ├── gau_zero.py │ ├── gaussian.py │ ├── readme │ ├── rwfdump.txt │ └── tddft.txt ├── interface_gaussian_spin │ ├── 0.gjf │ ├── 1.gjf │ ├── 2.gjf │ ├── CONSTANT.py │ ├── Collection.py │ ├── GAU_EXAM │ │ ├── gau_template.gjf │ │ └── template.com │ ├── GauSpin.py │ ├── PES.out │ ├── Package.py │ ├── Parser.py │ ├── Runner.py │ ├── Template.py │ ├── __init__.py │ ├── buildNAC.py │ ├── buildSOC.py │ ├── check.xyz │ ├── config.in │ ├── cre_gau_input_tool.py │ ├── createInp.py │ ├── dimension.json │ ├── ffRunner.py │ ├── filelist.dat │ ├── firstStep.py │ ├── gau_nonzero.py │ ├── gau_zero.py │ ├── gaussian.gjf │ ├── inp.json │ ├── interface.json │ ├── lists.txt │ ├── log_parser.py │ ├── nextStep.py │ ├── parseLog.py │ ├── qm.dump │ ├── qm_energy.dat │ ├── qm_gradient.dat │ ├── readme │ ├── setupEnv.py │ ├── soc.dat │ ├── tddft.txt │ └── template.json ├── interface_general_qm │ ├── README │ ├── __init__.py │ ├── general.py │ ├── gms_create.py │ ├── gms_nac.py │ ├── gms_nonzero.py │ ├── gms_parser.py │ ├── gms_run.py │ ├── gms_template.py │ ├── gms_zero.py │ └── overlap.py ├── interface_mndo_qm │ ├── .gitignore │ ├── __init__.py │ ├── config.in │ ├── mndo.py │ ├── mndo_create.py │ ├── mndo_log_parser.py │ ├── mndo_parser.py │ ├── mndo_run.py │ └── mndo_template.py ├── interface_molpro_qm │ ├── .gitignore │ ├── __init__.py │ ├── config.in │ ├── molpro.py │ ├── molpro_create.py │ ├── molpro_log_parser.py │ ├── molpro_parser.py │ ├── molpro_run.py │ ├── molpro_template.py │ └── usercmdlog ├── interface_qchem_qm │ ├── .gitignore │ ├── __init__.py │ ├── config.in │ ├── qchem.py │ ├── qchem_create.py │ ├── qchem_log_parser.py │ ├── qchem_parser.py │ ├── qchem_run.py │ └── qchem_template.py ├── interface_turbomole_qm │ ├── __init__.py │ ├── cre_tur_input_tool.py │ ├── cre_tur_input_tool_ricc.py │ ├── cre_tur_overlap_tool.py │ ├── cre_tur_overlap_tool.py_old │ ├── read_tur_overlap_tool.py │ ├── read_tur_tda.py │ ├── read_tur_tool.py │ ├── read_tur_tool_ricc.py │ ├── readme │ ├── tur_nac.py │ ├── tur_nac_tool.py │ ├── tur_nonzero.py │ ├── tur_nonzero_ricc.py │ ├── tur_overlap.py │ ├── tur_zero.py │ ├── tur_zero_ricc.py │ └── turbomole.py ├── main_overlap_slater.exe ├── overlap │ ├── Makefile │ ├── main_overlap_slater.a │ ├── main_overlap_slater.exe │ ├── main_overlap_slater.f90 │ ├── param.def │ ├── sub_csf_overlap.f90 │ ├── sub_determinant.f90 │ ├── sub_orbital_overlap.f90 │ ├── sub_read_all.f90 │ ├── sub_state_overlap.f90 │ └── sub_wf_overlap.f90 ├── quantum.py ├── readme └── tools │ ├── __init__.py │ ├── elements.dat │ ├── elements.py │ ├── gen.py │ ├── gen2.py │ ├── namelist.py │ ├── nma.inp │ ├── periodictable.py │ ├── test.py │ └── tools.py ├── krr ├── .gitignore ├── 0_prepare.py ├── 1_pre.py ├── 2_select_train_test_all_in_one.py ├── 3_kernel_regression_ini.py ├── 4_additional_test_all_in_one.py ├── 5_kkr_prediction_single_geom.py ├── 6_test_gradient.py ├── LICENSE ├── README.md ├── cal_gra_num.py ├── compare_gradient.py ├── instruction.txt ├── jade_kkr.py ├── molpro_log_gradient.py ├── split_grad_state.py ├── sub_collect_x_y.py ├── sub_compare_vectors.py ├── sub_coord_single.py ├── sub_copy_additional_test_data.py ├── sub_copy_data.py ├── sub_ener_state_cutoff.py ├── sub_energy_rescale.py ├── sub_inp_json.py ├── sub_kernel_regression_tool.py ├── sub_kkr_prediction_tool.py ├── sub_merge_traj_info.py ├── sub_plot_kkr.py ├── sub_select_sampling_rmsa_lixs.py ├── sub_select_train_test.py ├── sub_split_coord.py └── tools.py ├── potential ├── README ├── __init__.py ├── constraints │ ├── __init__.py │ ├── active-admp.gjf │ ├── active-oniom.gjf │ ├── activeset.py │ ├── admp.gjf │ ├── cons_atom_id │ ├── cons_energy.dat │ ├── cons_gradient.dat │ ├── constraints.py │ ├── curr_coord │ ├── oniom.gjf │ ├── partion.py │ ├── ref.xyz │ ├── ref_coord │ ├── ref_coord.json │ ├── region │ ├── sphere.pdb │ └── xyz └── potential.py ├── sampling ├── Makefile ├── atom_number_to_label.f90 ├── atom_number_to_label2.f90 ├── bin │ └── sampling.x ├── check_kinetic.f90 ├── check_random.f90 ├── check_random_2d.f90 ├── dimensionless_mode.f90 ├── displacement_hand.f90 ├── info_comm.itf ├── main.a ├── main.f90 ├── main_input ├── param.def ├── parser │ ├── __init__.py │ ├── elements.dat │ ├── elements.py │ ├── gaussian_parser.py │ ├── molden_parser.py │ ├── normal_mode_parser.py │ ├── readme │ └── turbomole_parser.py ├── prepare.py ├── random_gau.f90 ├── read_gaussian.f90 ├── read_mndo_molden.f90 ├── read_normal_mode.f90 ├── read_normal_mode2.f90 ├── read_tool.f ├── read_turbomole.f90 ├── readme ├── sampling.py ├── sampling.x ├── sub_get_mass.f90 ├── sub_string.f90 ├── usage ├── wigner.a └── wigner_1.f90 ├── sampling2 ├── DOC ├── Makefile ├── README ├── atom_number_to_label.f90 ├── atom_number_to_label2.f90 ├── check_kinetic.f90 ├── check_random.f90 ├── check_random_2d.f90 ├── dimensionless_mode.f90 ├── displacement_hand.f90 ├── info_comm.itf ├── label_to_mass.f90 ├── main_initial_sampling.a ├── main_initial_sampling.f90 ├── param.def ├── parser │ ├── __init__.py │ ├── gaussian_parser.py │ ├── molden_parser.py │ ├── normal_mode_parser.py │ ├── pd.py │ └── turbomole_parser.py ├── prepare.py ├── random_gau.f90 ├── random_gaussian_2d_tk.f90 ├── random_mu_st_1.f90 ├── random_mu_st_2.f90 ├── random_ts_3.f90 ├── read_gaussian.f90 ├── read_mndo_molden.f90 ├── read_normal_mode.f90 ├── read_normal_mode2.f90 ├── read_tool.f ├── read_turbomole.f90 ├── sampling.py ├── sampling.x ├── usercmdlog └── wigner_1.f90 └── sampling_xy ├── SQC ├── a.out ├── action_angle_gau │ ├── Makefile │ ├── ini_n_elec.inp │ ├── main_action_angle_elec_input │ ├── main_action_angle_gau.a │ ├── main_action_angle_gau.exe │ ├── main_action_angle_gau.f90 │ ├── param.def │ ├── random_gau_2d.dat │ └── sub_random_gau_1d.f90 ├── action_angle_uni │ ├── ini_n_elec.inp │ ├── main_action_angle_uni.exe │ ├── main_action_angle_uni.f90 │ ├── main_action_angle_uni_angular_triangle.f90 │ ├── main_action_angle_uni_inside.exe │ ├── main_action_angle_uni_inside.f90 │ ├── main_action_angle_uni_triangle.exe │ ├── main_action_angle_uni_triangle.f90 │ ├── main_action_angle_uni_triangle_many_state_miller.exe │ ├── main_action_angle_uni_triangle_many_state_miller.f90 │ ├── main_action_angle_x_y_p_x_p_y.exe │ ├── main_action_angle_x_y_p_x_p_y.f90 │ ├── main_action_angle_x_y_p_x_p_y_elec_input │ ├── main_action_angle_x_y_p_x_p_y_zpe.exe │ ├── main_action_angle_x_y_p_x_p_y_zpe.f90 │ ├── param.def │ ├── traj_1.inp │ └── traj_2.inp ├── cp.sh ├── ini_n_elec.inp ├── ini_n_nuc.inp ├── main_action_angle.exe ├── main_action_angle_elec_input ├── main_action_angle_nuc_input ├── main_gau_test.f90 ├── param.def ├── random_gau.agr ├── random_gau.dat ├── random_gau_2d.dat └── sub_random_gau.f90 ├── action_angle ├── cp.sh ├── ini_n_elec.inp ├── ini_n_nuc.inp ├── main_action_angle.exe ├── main_action_angle.f90 ├── main_action_angle_elec_input ├── main_action_angle_nuc_input ├── main_action_angle_x_y_p_x_p_y.exe ├── main_action_angle_x_y_p_x_p_y.f90 ├── main_action_angle_x_y_p_x_p_y_zpe.exe ├── main_action_angle_x_y_p_x_p_y_zpe.f90 ├── main_action_angle_x_y_p_x_p_y_zpe_input ├── param.def ├── traj_1.inp └── traj_2.inp └── sampling2_pjw ├── DOC ├── Makefile ├── README ├── atom_number_to_label.f90 ├── atom_number_to_label2.f90 ├── check_kinetic.f90 ├── check_random.f90 ├── check_random_2d.f90 ├── dimensionless_mode.f90 ├── displacement_hand.f90 ├── extra_ini_trj.py ├── info_comm.itf ├── label_to_mass.f90 ├── main_initial_sampling.a ├── main_initial_sampling.exe ├── main_initial_sampling.f90 ├── output.pdf ├── param.def ├── parser ├── __init__.py ├── gaussian_parser.py ├── main_input ├── molden_parser.py ├── normal_mode_parser.py ├── output.pdf ├── pd.py └── turbomole_parser.py ├── prepare.py ├── random_gau.f90 ├── random_gaussian_2d_tk.f90 ├── random_mu_st_1.f90 ├── random_mu_st_2.f90 ├── random_ts_3.f90 ├── read_gaussian.f90 ├── read_mndo_molden.f90 ├── read_normal_mode.f90 ├── read_normal_mode2.f90 ├── read_tool.f ├── read_turbomole.f90 ├── sampling.py ├── sampling.x └── wigner_1.f90 /AUTHORS: -------------------------------------------------------------------------------- 1 | ****************************************** 2 | 3 | the JADE Program 4 | 5 | an on-the-fly surface hopping code for poly-atomic systems by Prof. Zhenggang Lan and co-workers 6 | 7 | Copyright (c) 2014 8 | 9 | ****************************************** 10 | 11 | The JADE Program & related tools has been developed by 12 | 13 | Likai Du (dulk@qibebt.ac.cn), Zhenggang Lan* (lanzg@qibebt.ac.cn) 14 | e-mail - dulikai@gmail.com 15 | 16 | Contact info: 17 | Prof. Dr. Zhenggang Lan 18 | e-mail - lanzg@qibebt.ac.cn 19 | 20 | 21 | with contributions by 22 | 23 | Jun Wang (wang_jun@qibebt.ac.cn) 24 | Jing Huang (huangjing@qibebt.ac.cn) 25 | Deping Hu (hudp@qibebt.ac.cn) 26 | 27 | -------------------------------- 28 | -------------------------------------------------------------------------------- /REVISION: -------------------------------------------------------------------------------- 1 | ==== 2 | JADE PACKAGE 3 | VERSION 1.0 alpha 4 | ================= 5 | 6 | 2014.10 7 | version 1.0 alpha 8 | a few bug fixed 9 | some interface was re-written and tested. 10 | 11 | 2014.4 12 | version 0.3 13 | GAMESS(US) interface 14 | Langevin Dynamics 15 | 16 | 2013.12 17 | version 0.2 18 | Gaussian interface 19 | TDDFT/TDA etc 20 | 21 | 2012.1 22 | version 0.1 23 | interface to turbomole 24 | surface hopping 25 | TDDFT ADC(2) etc. 26 | 27 | 28 | ------------------ 29 | 30 | @ Group of Prof. Dr. Zhenggang Lan 31 | Qingdao Institute of Bioenergy and Bioprocess Technology, 32 | Chinese Academy of Sciences, 33 | Qingdao, Shandong, China 34 | 35 | ------------------ 36 | 37 | 38 | -------------------------------------------------------------------------------- /bin/JADERC: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env bash 2 | # suppose the JADE_HOME env. is exported 3 | # 4 | # i.e. 5 | export JADE_HOME=/data/home/hudp/program/jade_mapping 6 | 7 | # binary 8 | export PATH=$JADE_HOME/bin:$PATH 9 | 10 | # # interface 11 | export JADE_HOME_INTERFACE=$JADE_HOME/src/electronic 12 | export PATH=$JADE_HOME_INTERFACE:$PATH 13 | ## kkr 14 | export JADE_HOME_INTERFACE=$JADE_HOME/src/krr 15 | export PATH=$JADE_HOME_INTERFACE:$PATH 16 | # # sampling 17 | export JADE_HOME_SAMPLE=$JADE_HOME/src/sampling2 18 | export PATH=$JADE_HOME_SAMPLE:$PATH 19 | # # pop 20 | export JADE_POPULATION=$JADE_HOME/contrib/population_ana 21 | export PATH=$JADE_POPULATION:$PATH 22 | # # contrib : analysis tools 23 | export JADE_CONTRIB=$JADE_HOME/contrib 24 | export PATH=$JADE_CONTRIB:$PATH 25 | # 26 | -------------------------------------------------------------------------------- /bin/jade.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/bin/jade.exe -------------------------------------------------------------------------------- /bin/main_overlap_slater.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/bin/main_overlap_slater.exe -------------------------------------------------------------------------------- /bin/sampling.x: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/bin/sampling.x -------------------------------------------------------------------------------- /bin/sampling2.x: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/bin/sampling2.x -------------------------------------------------------------------------------- /doc/FEATURE: -------------------------------------------------------------------------------- 1 | Dynamics 2 | -On-the-fly dynamics surface hopping dynamics 3 | -the velocity-Verlet algorithm; 4 | -fewest switches algorithms 5 | -Langevin thermostat 6 | Interfaces 7 | -TURBOMOLE (CIS, TD-DFT, RI-CC2, ADC(2)) 8 | -GAUSSIAN (CIS, TD-DFT) 9 | -GAMESS (US) (CIS TD-DFT) 10 | -Q-CHEM (in progress) 11 | -Molpro (in progress) 12 | Initial conditions 13 | -Wigner distribution 14 | -ground state dynamics 15 | enviroment effects 16 | -Langevin dynamics 17 | -effective fragment potential (interface with Gamess-US & Q-CHEM) in process 18 | Output and analysis 19 | -Statistical analysis of results 20 | -transition density analysis tools 21 | -------------------------------------------------------------------------------- /doc/intro.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/doc/intro.pdf -------------------------------------------------------------------------------- /doc/sampling-doc/KEYWORDS-NEW: -------------------------------------------------------------------------------- 1 | [wigner] 2 | n_atom = 6 3 | n_mode = 12 4 | label_random = 1 5 | nr = 5000 6 | nbin = 50 ! used to check random 7 | label_read_vib = 1 8 | label_es_output = 3 9 | filename_es_output = freq.log 10 | label_displacement = 1 11 | label_dis_wigner = 1 12 | n_geom = 1000 13 | label_frozen = 0 14 | number_frozen = 2 15 | list_frozen = 1, 2 16 | 17 | -------------------------------------------------------------------------------- /src/Makefile: -------------------------------------------------------------------------------- 1 | # 2 | 3 | JADE = 4 | 5 | OUTPUT := ../bin 6 | 7 | DIRS = dynamics electronic sampling sampling2 8 | 9 | .PHONY: all clean distclean install $(DIRS) 10 | 11 | all: $(DIRS) 12 | install: $(DIRS) 13 | clean: $(DIRS) 14 | 15 | $(DIRS): 16 | $(MAKE) -j2 -C $@ $(MAKECMDGOALS) 17 | 18 | -------------------------------------------------------------------------------- /src/README: -------------------------------------------------------------------------------- 1 | JADE SOURCE CODE 2 | version 1.0 alpha 3 | ---- 4 | 5 | contains most of the important of Fortran and python scripts 6 | 7 | -------------------------------------------------------------------------------- /src/compiler.mk: -------------------------------------------------------------------------------- 1 | LIB = -L/share/intel/composerxe/mkl/lib/intel64 -lmkl_lapack95_lp64 -lmkl_blas95_lp64 -lmkl_core -lmkl_sequential -lmkl_intel_lp64 2 | 3 | 4 | -------------------------------------------------------------------------------- /src/database/readme: -------------------------------------------------------------------------------- 1 | constants 2 | 3 | i.e. elements periodic table 4 | 5 | may be later 6 | force field 7 | 8 | -------------------------------------------------------------------------------- /src/dynamics/README: -------------------------------------------------------------------------------- 1 | the dynamics module 2 | this is the core routine to execute the surface-hopping dynamics 3 | 4 | 2015-6-20 5 | dump the gradient along the trajectory 6 | add sub_save_grad.f90 7 | modify sub_sh_num_nac.f90 and sub_lang_sh_num_nac.f90 8 | also modify sub_save_save_hopping_num_nac.f90 which can dump a fort.902 9 | containing the gradient info. 10 | note: 11 | sub_sh_ana_nac is not modified now 12 | however, it can also dump fort.902, which contain the gradient info. 13 | 14 | 15 | -------------------------------------------------------------------------------- /src/dynamics/include/var_n_mode.h: -------------------------------------------------------------------------------- 1 | 2 | real(kind=8) x_nuc_cur(n_mode) 3 | real(kind=8) p_nuc_cur(n_mode) 4 | real(kind=8) x_nuc_pre(n_mode) 5 | real(kind=8) p_nuc_pre(n_mode) 6 | real(kind=8) p_nuc_kin_cur(n_mode) 7 | real(kind=8) p_nuc_kin_pre(n_mode) 8 | real(kind=8) x_elec(n_state) 9 | real(kind=8) p_elec(n_state) 10 | real(kind=8) gammas(n_state) 11 | real(kind=8) grad(n_state, n_mode) 12 | real(kind=8) dij_cur(n_state, n_state, n_mode) 13 | real(kind=8) dij_pre(n_state, n_state, n_mode) 14 | real(kind=8) ene_adia_cur(n_state) 15 | real(kind=8) mass(n_mode) 16 | 17 | 18 | 19 | -------------------------------------------------------------------------------- /src/dynamics/mapping/Readme: -------------------------------------------------------------------------------- 1 | elec: vv 2 | 3 | average PES done 4 | 5 | model 2: torsional potential: 0.5 * I_inverse * P_i **2 + 0.5 * V_i_n * ( 1 - cos(A) ) * c_n 6 | 7 | model 1: torsional potential: 0.5 * I_inverse * P_i **2 + 0.5 * V_i_n * ( 1 - cos(A) ) * c_n 8 | 9 | -------------------------------------------------------------------------------- /src/dynamics/mapping/adia/sub_calc_dV_eff_div_dx_nuc_adia.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/adia/sub_calc_dV_eff_div_dx_nuc_adia.o 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https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/adia/sub_elec_motion_2_aver_PES_adia.o -------------------------------------------------------------------------------- /src/dynamics/mapping/adia/sub_motion_2_adia_aver_PES_1step.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/adia/sub_motion_2_adia_aver_PES_1step.o -------------------------------------------------------------------------------- /src/dynamics/mapping/adia/sub_nuc_get_dHmn_div_dX_adia.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_nuc_get_dHmn_div_dX_adia(dHmn_div_dX, & 2 | mat_U, & 3 | dHmn_div_dX_adia) 4 | use mod_main 5 | implicit none 6 | include "param.def" 7 | real(kind=8), dimension(n_state, n_state) :: mat_U, & 8 | delta_v_tmp1 9 | real(kind=8), dimension(n_mode, n_state, n_state) :: dHmn_div_dX_adia, & 10 | dHmn_div_dX 11 | integer :: k 12 | 13 | 14 | !adiabatic gradient 15 | do k = 1, n_mode 16 | delta_v_tmp1 = dHmn_div_dX(k, :, :) 17 | delta_v_tmp1 = matmul(transpose(mat_U), delta_v_tmp1) 18 | delta_v_tmp1 = matmul(delta_v_tmp1, mat_U) 19 | dHmn_div_dX_adia(k, :, :) = delta_v_tmp1 20 | enddo 21 | 22 | return 23 | end 24 | -------------------------------------------------------------------------------- /src/dynamics/mapping/adia/sub_nuc_get_dHmn_div_dX_adia.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/adia/sub_nuc_get_dHmn_div_dX_adia.o -------------------------------------------------------------------------------- /src/dynamics/mapping/adia/sub_nuc_motion_2_aver_PES_1step_dp_div_dt_adia.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_nuc_motion_2_aver_PES_1step_dp_div_dt_adia(dp_div_dt, & 2 | grad, & 3 | x_elec, p_elec, & 4 | ene, & 5 | dij) 6 | use mod_main 7 | implicit none 8 | ! --- arguments --- 9 | real(kind=8), dimension(n_mode) :: dp_div_dt 10 | real(kind=8), dimension(n_state, n_mode) :: grad 11 | real(kind=8), dimension(n_state) :: x_elec, p_elec 12 | real(kind=8), dimension(n_state) :: ene 13 | real(kind=8), dimension(n_state, n_state, n_mode) :: dij 14 | 15 | ! --- local variables --- 16 | real(kind=8), dimension(n_mode) :: dV_eff_div_dx_nuc 17 | real(kind=8), dimension(n_mode) :: dp_nuc_kin__dij_term 18 | 19 | 20 | call sub_calc_dV_eff_div_dx_nuc_adia(dV_eff_div_dx_nuc, & 21 | x_elec, p_elec, & 22 | grad) 23 | 24 | call sub_calc_dp_nuc_kin__dij_term_adia(dp_nuc_kin__dij_term, & 25 | x_elec, p_elec, & 26 | ene, & 27 | dij) 28 | 29 | dp_div_dt = - dV_eff_div_dx_nuc - dp_nuc_kin__dij_term 30 | 31 | return 32 | end 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-------------------------------------------------------------------------------- 1 | subroutine sub_nuc_motion_2_aver_PES_1step_dx_div_dt_adia( & 2 | vel_nuc_kin_cur, & 3 | p_nuc_kin_cur, & 4 | x_elec, p_elec, & 5 | mass) 6 | use mod_main 7 | implicit none 8 | 9 | real(kind=8), dimension(n_mode) :: vel_nuc_kin_cur 10 | real(kind=8), dimension(n_mode) :: p_nuc_kin_cur 11 | real(kind=8), dimension(n_mode) :: mass 12 | real(kind=8), dimension(n_state) :: x_elec, p_elec 13 | 14 | 15 | 16 | vel_nuc_kin_cur = p_nuc_kin_cur / mass 17 | return 18 | end 19 | -------------------------------------------------------------------------------- /src/dynamics/mapping/adia/sub_nuc_motion_2_aver_PES_1step_dx_div_dt_adia.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/adia/sub_nuc_motion_2_aver_PES_1step_dx_div_dt_adia.o 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-------------------------------------------------------------------------------- 1 | module mod_main 2 | integer :: n_state, & 3 | n_mode, & 4 | n_save_trj, & 5 | label_restart, & 6 | n_ele_dt, & 7 | label_aver_PES 8 | integer label_debug 9 | double precision :: nuc_dt 10 | double precision :: ggamma 11 | 12 | end 13 | -------------------------------------------------------------------------------- /src/dynamics/mapping/bak/sub_get_dia_grad.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_get_dia_grad(x_mode, & 2 | freq,k_tun, & 3 | grad) 4 | use mod_main 5 | implicit none 6 | 7 | ! --- arguments --- 8 | real(kind=8), dimension(n_state, n_state) :: Ham 9 | real(kind=8), dimension(n_mode_HO, n_state, n_state) :: lambda0, lambda1 10 | real(kind=8), dimension(n_mode_HO) :: x_mode, & 11 | p_mode 12 | real(kind=8) k_tun(n_state,n_mode_HO) 13 | real(kind=8) freq(n_state,n_mode_HO) 14 | real(kind=8) grad(n_state,n_mode_HO) 15 | 16 | ! -- local variables --- 17 | integer i, j, k 18 | real(kind=8) tmp, x_tmp, p_tmp, freq_tmp 19 | 20 | Ham = 0.d0 21 | 22 | do i = 1, n_state 23 | do j = 1, n_mode_HO 24 | x_tmp = x_mode(j) 25 | freq_tmp = freq(i,j) 26 | grad(i,j) = 0.5d0 * freq_tmp * x_tmp & 27 | + k_tun(i,j) 28 | enddo 29 | enddo 30 | 31 | 32 | return 33 | end 34 | -------------------------------------------------------------------------------- /src/dynamics/mapping/bak/sub_mapping_read_ini_trj_elec_2.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_mapping_read_ini_trj_elec_2(x_elec, p_elec) 2 | use mod_main 3 | implicit none 4 | 5 | include "param.def" 6 | 7 | integer :: i_mode, & 8 | file_ini_input, & 9 | file_restart_input 10 | 11 | !double precision :: q 12 | real(kind=8), dimension(n_state) :: x_elec, p_elec 13 | 14 | integer i_state 15 | 16 | 17 | 18 | 19 | !call RANDOM_NUMBER(q) 20 | 21 | !q=q*PI 22 | 23 | !ele_coe(1)=cmplx(0.d0,0.d0) 24 | !ele_coe(2)=cmplx(cos(q),sin(q)) 25 | ! ele_coe(3)=(0.d0,0.d0) 26 | 27 | if (label_restart .eq. 0 ) then 28 | 29 | 30 | open(21, file="trj_elec.input") 31 | do i_state = 1, n_state 32 | read(21, *) x_elec(i_state), p_elec(i_state) 33 | enddo 34 | close(21) 35 | 36 | endif 37 | 38 | 39 | if (label_restart .eq. 1 ) then 40 | 41 | open(21, file="trj_elec_restart.input") 42 | do i_state = 1, n_state 43 | read(21, *) x_elec(i_state), p_elec(i_state) 44 | enddo 45 | close(21) 46 | 47 | endif 48 | 49 | end 50 | -------------------------------------------------------------------------------- /src/dynamics/mapping/bak/sub_nuc_get_dHmn_div_dX_adia.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_nuc_get_dHmn_div_dX_adia(dHmn_div_dX, & 2 | mat_U, & 3 | dHmn_div_dX_adia) 4 | use mod_main 5 | implicit none 6 | include "param.def" 7 | real(kind=8), dimension(n_state, n_state) :: mat_U, & 8 | delta_v_tmp1 9 | real(kind=8), dimension(n_mode, n_state, n_state) :: dHmn_div_dX_adia, & 10 | dHmn_div_dX 11 | integer :: k 12 | 13 | 14 | !adiabatic gradient 15 | do k = 1, n_mode 16 | delta_v_tmp1 = dHmn_div_dX(k, :, :) 17 | delta_v_tmp1 = matmul(transpose(mat_U), delta_v_tmp1) 18 | delta_v_tmp1 = matmul(delta_v_tmp1, mat_U) 19 | dHmn_div_dX_adia(k, :, :) = delta_v_tmp1 20 | enddo 21 | 22 | return 23 | end 24 | -------------------------------------------------------------------------------- /src/dynamics/mapping/bak/sub_nuc_motion_2_aver_PES_1step_dp_div_dt_adia.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_nuc_motion_2_aver_PES_1step_dp_div_dt_adia(dp_div_dt, & 2 | grad, & 3 | x_elec, p_elec, & 4 | ene, & 5 | dij) 6 | use mod_main 7 | implicit none 8 | ! --- arguments --- 9 | real(kind=8), dimension(n_mode) :: dp_div_dt 10 | real(kind=8), dimension(n_state, n_mode) :: grad 11 | real(kind=8), dimension(n_state) :: x_elec, p_elec 12 | real(kind=8), dimension(n_state) :: ene 13 | real(kind=8), dimension(n_state, n_state, n_mode) :: dij 14 | 15 | ! --- local variables --- 16 | real(kind=8), dimension(n_mode) :: dV_eff_div_dx_nuc 17 | real(kind=8), dimension(n_mode) :: dp_nuc_kin__dij_term 18 | 19 | 20 | call sub_calc_dV_eff_div_dx_nuc_adia(dV_eff_div_dx_nuc, & 21 | x_elec, p_elec, & 22 | grad) 23 | 24 | call sub_calc_dp_nuc_kin__dij_term_adia(dp_nuc_kin__dij_term, & 25 | x_elec, p_elec, & 26 | ene, & 27 | dij) 28 | 29 | dp_div_dt = - dV_eff_div_dx_nuc - dp_nuc_kin__dij_term 30 | 31 | return 32 | end -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/dyn.input: -------------------------------------------------------------------------------- 1 | &dyn_control 2 | n_state = 2 3 | n_mode = 201 4 | n_mode_HO = 200 5 | n_mode_tor = 1 6 | ggamma = 0 7 | n_step = 1 8 | nuc_dt = 0.01 9 | n_ele_dt = 10 10 | n_save_trj = 25 11 | label_restart = 0 12 | label_diabatic = 1 13 | label_debug = 1 14 | hamilton_type = 4 15 | mapping_model = 1 16 | label_aver_PES = 1 17 | / 18 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/ene.input: -------------------------------------------------------------------------------- 1 | 0.0124 2 | 0.0 3 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/ham.dat: -------------------------------------------------------------------------------- 1 | 0 0.8236054439 0.0004556914 2 | 0 0.0004556914 0.4933582745 3 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/pop_adia.dat: -------------------------------------------------------------------------------- 1 | 0 -0.0000000000 0.0000000000 2 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/pop_dia.dat: -------------------------------------------------------------------------------- 1 | 0 0.0000000000 0.0000000000 2 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/reduced_mass_inv_tor.input: -------------------------------------------------------------------------------- 1 | 0.00111 0.00111 2 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/tor_pot_para.input: -------------------------------------------------------------------------------- 1 | 4.5 -4.5 2 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/trj_elec.dat: -------------------------------------------------------------------------------- 1 | 0 1.0000000000 0.0000000000 0.0000000000 0.0000000000 2 | 0 0.0000000000 0.0000000000 0.0000000000 0.0000000000 3 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/trj_elec.input: -------------------------------------------------------------------------------- 1 | 1 0 0 0 2 | 0 0 0 0 3 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/trj_elec_debug.dat: -------------------------------------------------------------------------------- 1 | 0 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 2 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/trj_elec_restart.input: -------------------------------------------------------------------------------- 1 | 1.0000000000 0.0000000000 0.0000000000 0.0000000000 2 | 0.0000000000 0.0000000000 0.0000000000 0.0000000000 3 | -------------------------------------------------------------------------------- /src/dynamics/mapping/ham4/x_p_debug.dat: -------------------------------------------------------------------------------- 1 | -7.0831674736355280E-002 -0.24534001750426648 2 | -------------------------------------------------------------------------------- /src/dynamics/mapping/mod_main.f90: -------------------------------------------------------------------------------- 1 | module mod_main 2 | integer :: n_state, & 3 | n_atom, & 4 | n_mode, & 5 | n_mode_HO, & 6 | n_mode_tor, & 7 | n_step, & 8 | n_save_trj, & 9 | label_restart, & 10 | label_diabatic, & 11 | n_ele_dt, & 12 | qm_method, & 13 | label_aver_PES 14 | integer label_debug 15 | integer label_nac_phase 16 | integer hamilton_type 17 | integer mapping_model 18 | double precision :: nuc_dt 19 | double precision :: ggamma 20 | 21 | end 22 | -------------------------------------------------------------------------------- /src/dynamics/mapping/mod_main.mod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/mod_main.mod 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coor_x, coor_y, coor_z) 3 | use mod_main 4 | implicit none 5 | real(kind=8) x_nuc_cur(n_mode) 6 | double precision, dimension(n_atom) :: & 7 | coor_x, & 8 | coor_y, & 9 | coor_z 10 | integer i_atom 11 | 12 | do i_atom = 1, n_atom 13 | x_nuc_cur(3 * (i_atom - 1) + 1) = coor_x(i_atom) 14 | x_nuc_cur(3 * (i_atom - 1) + 2) = coor_y(i_atom) 15 | x_nuc_cur(3 * (i_atom - 1) + 3) = coor_z(i_atom) 16 | enddo 17 | 18 | return 19 | end 20 | -------------------------------------------------------------------------------- /src/dynamics/mapping/on_the_fly/bak/sub_reshape_n_mode_to_n_atom_coor.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_reshape_n_atom_to_n_mode_coor(x_nuc_cur, & 2 | coor_x, coor_y, coor_z) 3 | use mod_main 4 | implicit none 5 | real(kind=8) x_nuc_cur(n_mode) 6 | double precision, dimension(n_atom) :: & 7 | coor_x, & 8 | coor_y, & 9 | coor_z 10 | integer i_atom 11 | 12 | do i_atom = 1, n_atom 13 | coor_x(i_atom) = x_nuc_cur(3 * (i_atom - 1) + 1) 14 | coor_y(i_atom) = x_nuc_cur(3 * (i_atom - 1) + 2) 15 | coor_z(i_atom) = x_nuc_cur(3 * (i_atom - 1) + 3) 16 | enddo 17 | 18 | return 19 | end 20 | -------------------------------------------------------------------------------- /src/dynamics/mapping/on_the_fly/sub_evolution_mapping_2_on_the_fly.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/on_the_fly/sub_evolution_mapping_2_on_the_fly.o -------------------------------------------------------------------------------- /src/dynamics/mapping/on_the_fly/sub_evolution_mapping_2_on_the_fly_traj_adjusted.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/on_the_fly/sub_evolution_mapping_2_on_the_fly_traj_adjusted.o 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https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/on_the_fly/sub_test.o -------------------------------------------------------------------------------- /src/dynamics/mapping/on_the_fly/sub_write_current_geom_mapping.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_write_current_geom_mapping(x_nuc_cur, & 2 | p_nuc_cur, & 3 | atom_label, & 4 | x_elec, p_elec, & 5 | i_step) 6 | use mod_main 7 | implicit none 8 | include 'var_n_atom.h' 9 | include 'var_n_mode.h' 10 | integer index_state !useless 11 | integer i_step 12 | integer i_state 13 | 14 | 15 | call sub_reshape_n_mode_to_n_atom(x_nuc_cur, & 16 | p_nuc_cur, & 17 | grad, & 18 | dij_cur, & 19 | coor_x, coor_y, coor_z, & 20 | vel_x, vel_y, vel_z, & 21 | gra_all_x, gra_all_y, gra_all_z, & 22 | nac_x, nac_y, nac_z) 23 | !write(*,*) atom_label(1) 24 | call sub_write_current_geom (n_atom, & 25 | coor_x, coor_y, coor_z, & 26 | vel_x, vel_y, vel_z, & 27 | atom_label, & 28 | n_state, & 29 | rho, & 30 | index_state, & 31 | i_step, time ) 32 | 33 | return 34 | end 35 | -------------------------------------------------------------------------------- /src/dynamics/mapping/on_the_fly/sub_write_current_geom_mapping.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/on_the_fly/sub_write_current_geom_mapping.o -------------------------------------------------------------------------------- /src/dynamics/mapping/on_the_fly/sub_write_geom.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/on_the_fly/sub_write_geom.o -------------------------------------------------------------------------------- /src/dynamics/mapping/on_the_fly/sub_write_geom_mapping.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/on_the_fly/sub_write_geom_mapping.o -------------------------------------------------------------------------------- /src/dynamics/mapping/on_the_fly/sub_write_geom_mapping_traj_adjusted.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/on_the_fly/sub_write_geom_mapping_traj_adjusted.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_cal_gammas.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_cal_gammas(x_elec, p_elec, & 2 | gammas) 3 | use mod_main 4 | implicit none 5 | ! --- arguments --- 6 | integer i_step 7 | real(kind=8), dimension(n_state) :: x_elec, p_elec, gammas 8 | 9 | ! --- lacal variables --- 10 | integer i, j, i_state 11 | real(kind=8) tmp 12 | 13 | ! Here, the defination of gamma is different from Miller's. 14 | ! 0.5 * ( x**2 + p**2 - gamma) 15 | do i_state = 1, n_state 16 | tmp = x_elec(i_state) ** 2 + p_elec(i_state) ** 2 17 | if ( tmp >= 2.d0 ) then 18 | write(*,*) "gammas > 2.0, gammas = gammas - 2.0" 19 | gammas(i_state) = tmp - 2.d0 20 | else 21 | gammas(i_state) = tmp 22 | endif 23 | enddo 24 | 25 | return 26 | end 27 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_cal_gammas.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_cal_gammas.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_dia_to_adia.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_dia_to_adia.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_diag.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_diag(n, mat_nondiag, mat_U, eig) 2 | implicit none 3 | ! --- arguments --- 4 | integer n 5 | real(kind=8), dimension(n,n) :: mat_nondiag, mat_U 6 | real(kind=8), dimension(n) :: eig 7 | !complex(kind=8), dimension(n, n) :: mat_U 8 | 9 | ! --- local variables --- 10 | real(kind=8), allocatable, dimension(:) :: work 11 | !complex(kind=8), allocatable, dimension(:,:) :: rwork 12 | integer lwork, info 13 | 14 | !lwork= n*(n+1) 15 | lwork= 3*n 16 | allocate (work(lwork)) 17 | !allocate (rwork(3*n-2,3*n-2)) 18 | 19 | mat_U = mat_nondiag 20 | 21 | !call ZHEEV('V','U', n, mat_U, n, & 22 | ! E_adia, work, lwork, rwork, info) 23 | call DSYEV('V','U', n, mat_U, n, & 24 | eig, work, lwork, info) 25 | 26 | 27 | 9998 format(10(f20.10, 1x)) 28 | 9999 format(i8,1x,999(f20.10, 1x)) 29 | return 30 | end 31 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_diag.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_diag.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_get_dH_div_dx_or_dp.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_elec_get_dH_div_dx_or_dp(n_state, Ham, x_elec, dH_div_dx) 2 | implicit none 3 | ! --- arguments --- 4 | integer n_state 5 | real(kind=8) Ham(n_state, n_state) 6 | real(kind=8), dimension(n_state) :: x_elec 7 | real(kind=8), dimension(n_state) :: dH_div_dx 8 | 9 | ! --- local variables --- 10 | integer i,j 11 | 12 | dH_div_dx = 0.d0 13 | do i = 1, n_state 14 | do j = 1, n_state 15 | dH_div_dx(i) = dH_div_dx(i) + Ham(i,j) * x_elec(j) 16 | enddo 17 | enddo 18 | 19 | return 20 | end 21 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_get_dH_div_dx_or_dp.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_elec_get_dH_div_dx_or_dp.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_get_dH_div_dx_or_dp_3.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_elec_get_dH_div_dx_or_dp_3(n_state, Ham, x_elec, dH_div_dx) 2 | implicit none 3 | ! --- arguments --- 4 | integer n_state 5 | real(kind=8) Ham(n_state, n_state) 6 | real(kind=8), dimension(n_state) :: x_elec 7 | real(kind=8), dimension(n_state) :: dH_div_dx 8 | 9 | ! --- local variables --- 10 | integer i,j 11 | 12 | dH_div_dx = 0.d0 13 | do i = 1, n_state 14 | do j = 1, n_state 15 | if (i==j) then 16 | dH_div_dx(i) = dH_div_dx(i) + 0.5 * Ham(i,j) * x_elec(j) 17 | else 18 | dH_div_dx(i) = dH_div_dx(i) + Ham(i,j) * x_elec(j) 19 | endif 20 | enddo 21 | enddo 22 | 23 | return 24 | end 25 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_get_dH_div_dx_or_dp_3.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_elec_get_dH_div_dx_or_dp_3.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_get_dH_div_dx_or_dp_aver_PES.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_elec_get_dH_div_dx_or_dp_aver_PES(n_state, Ham, x_elec, dH_div_dx) 2 | implicit none 3 | ! --- arguments --- 4 | integer n_state 5 | real(kind=8) Ham(n_state, n_state) 6 | real(kind=8), dimension(n_state) :: x_elec 7 | real(kind=8), dimension(n_state) :: dH_div_dx 8 | 9 | ! --- local variables --- 10 | integer i,j 11 | real(kind=8) H_diag_aver 12 | 13 | H_diag_aver = 0.d0 14 | do i = 1, n_state 15 | H_diag_aver = H_diag_aver + Ham(i,i) 16 | enddo 17 | H_diag_aver = H_diag_aver / dble(n_state) 18 | 19 | dH_div_dx = 0.d0 20 | do i = 1, n_state 21 | do j = 1, n_state 22 | dH_div_dx(i) = dH_div_dx(i) + Ham(i,j) * x_elec(j) 23 | enddo 24 | dH_div_dx(i) = dH_div_dx(i) - H_diag_aver * x_elec(i) 25 | enddo 26 | 27 | return 28 | end 29 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_get_dH_div_dx_or_dp_aver_PES.o: 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-------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_motion_3_step1_2.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_elec_motion_3_step1_2(n_state, Ham, x_elec, y_elec, ele_dt) 2 | implicit none 3 | ! --- arguments --- 4 | integer n_state 5 | real(kind=8) Ham(n_state, n_state) 6 | real(kind=8), dimension(n_state) :: x_elec 7 | real(kind=8), dimension(n_state) :: y_elec 8 | real(kind=8) ele_dt 9 | 10 | ! --- local variables --- 11 | integer i,j 12 | real(kind=8), dimension(n_state) :: dH_div_dx 13 | real(kind=8) delt(n_state) 14 | 15 | call sub_elec_get_dH_div_dx_or_dp_3(n_state, Ham, y_elec, dH_div_dx) 16 | !write(*,*) 'dH_div_d', dH_div_dx 17 | delt = - dH_div_dx !!! 18 | !write(*,*) 'delt', delt 19 | call sub_move(n_state, x_elec, delt, ele_dt) 20 | 21 | return 22 | end 23 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_motion_3_step1_2.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_elec_motion_3_step1_2.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_motion_3_step2.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_elec_motion_3_step2.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_motion_3_step2_2.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_elec_motion_3_step2_2(n_state, Ham, x_elec, y_elec, ele_dt) 2 | implicit none 3 | ! --- arguments --- 4 | integer n_state 5 | real(kind=8) Ham(n_state, n_state) 6 | real(kind=8), dimension(n_state) :: x_elec 7 | real(kind=8), dimension(n_state) :: y_elec 8 | real(kind=8) ele_dt 9 | 10 | ! --- local variables --- 11 | integer i,j 12 | real(kind=8), dimension(n_state) :: dH_div_dx 13 | real(kind=8) delt(n_state) 14 | 15 | call sub_elec_get_dH_div_dx_or_dp_3(n_state, Ham, y_elec, dH_div_dx) 16 | delt = dH_div_dx !!! 17 | call sub_move(n_state, x_elec, delt, ele_dt) 18 | 19 | return 20 | end 21 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_motion_3_step2_2.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_elec_motion_3_step2_2.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_elec_motion_mapping_1_Ham_4.o: 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-------------------------------------------------------------------------------- 1 | subroutine sub_get_c_n_elec_1(x, y, p_x, p_y, c_n) 2 | use mod_main, only : label_debug, n_state, ggamma 3 | implicit none 4 | 5 | ! --- arguments --- 6 | real(kind=8) x(n_state) 7 | real(kind=8) y(n_state) 8 | real(kind=8) p_x(n_state) 9 | real(kind=8) p_y(n_state) 10 | real(kind=8) c_n(n_state, n_state) 11 | 12 | ! --- local variables --- 13 | integer i, j 14 | 15 | do i = 1, n_state 16 | do j = 1, n_state 17 | if(i==j) then 18 | c_n(i,j) = x(i) * p_y(j) - y(i) * p_x(j) - ggamma 19 | else 20 | c_n(i,j) = x(i) * p_y(j) - y(i) * p_x(j) 21 | endif 22 | enddo 23 | enddo 24 | 25 | if (label_debug >= 2)then 26 | open(10, file='c_n.dat', access='append') 27 | do i = 1, n_state 28 | write(10, *) c_n(i,:) 29 | enddo 30 | close(10) 31 | endif 32 | 33 | return 34 | end 35 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_get_c_n_elec_1.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_get_c_n_elec_1.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_get_c_n_elec_2.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_get_c_n_elec_2(x, p, c_n) 2 | use mod_main, only : label_debug, n_state, ggamma 3 | implicit none 4 | 5 | ! --- arguments --- 6 | real(kind=8) x(n_state) 7 | real(kind=8) p(n_state) 8 | real(kind=8) c_n(n_state, n_state) 9 | 10 | ! --- local variables --- 11 | integer i, j 12 | 13 | 14 | do i = 1, n_state 15 | c_n(i,i) = 0.5 * (x(i)**2 + p(i)**2 - ggamma) 16 | enddo 17 | 18 | do i = 1, n_state-1 19 | do j = i+1, n_state 20 | c_n(i,j) = 0.5 * ( x(i) * x(j) + p(i) * p(j) ) 21 | c_n(j,i) = c_n(i,j) 22 | enddo 23 | enddo 24 | 25 | open(10, file='c_n.dat', access='append') 26 | do i = 1, n_state 27 | write(10, 9999, advance='no') c_n(i,:) 28 | enddo 29 | write(10, *) 30 | close(10) 31 | 32 | 9999 format(10(f20.10, 1x)) 33 | 34 | return 35 | end 36 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_get_c_n_elec_2.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_get_c_n_elec_2.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_get_c_n_elec_2_traj_adjusted.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_get_c_n_elec_2_traj_adjusted(x, p, gammas, c_n) 2 | use mod_main, only : label_debug, n_state, ggamma 3 | implicit none 4 | 5 | ! --- arguments --- 6 | real(kind=8) x(n_state) 7 | real(kind=8) p(n_state) 8 | real(kind=8) gammas(n_state) 9 | real(kind=8) c_n(n_state, n_state) 10 | 11 | ! --- local variables --- 12 | integer i, j 13 | 14 | 15 | do i = 1, n_state 16 | c_n(i,i) = 0.5 * (x(i)**2 + p(i)**2 - gammas(i) ) 17 | enddo 18 | 19 | do i = 1, n_state-1 20 | do j = i+1, n_state 21 | c_n(i,j) = 0.5 * ( x(i) * x(j) + p(i) * p(j) ) 22 | c_n(j,i) = c_n(i,j) 23 | enddo 24 | enddo 25 | 26 | open(10, file='c_n.dat', access='append') 27 | do i = 1, n_state 28 | write(10, 9999, advance='no') c_n(i,:) 29 | enddo 30 | write(10, *) 31 | close(10) 32 | 33 | 9999 format(10(f20.10, 1x)) 34 | 35 | return 36 | end 37 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_get_c_n_elec_2_traj_adjusted.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_get_c_n_elec_2_traj_adjusted.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_get_c_n_elec_3.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_get_c_n_elec_3(x, y, p_x, p_y, c_n) 2 | use mod_main, only : label_debug, n_state, ggamma 3 | implicit none 4 | 5 | ! --- arguments --- 6 | real(kind=8) x(n_state) 7 | real(kind=8) y(n_state) 8 | real(kind=8) p_x(n_state) 9 | real(kind=8) p_y(n_state) 10 | real(kind=8) c_n(n_state, n_state) 11 | 12 | ! --- local variables --- 13 | integer i, j 14 | 15 | do i = 1, n_state 16 | call sub_sum_sq_sum_by4(x(i), & 17 | p_y(i), & 18 | y(i), & 19 | p_x(i), & 20 | c_n(i,i)) 21 | do j = 1, n_state 22 | if (i .ne. j) c_n(i,j) = x(i) * p_y(j) - y(i) * p_x(j) 23 | enddo 24 | enddo 25 | 26 | if (label_debug >= 2)then 27 | open(10, file='c_n.dat', access='append') 28 | do i = 1, n_state 29 | write(10, *) c_n(i,:) 30 | enddo 31 | close(10) 32 | endif 33 | 34 | return 35 | end 36 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-------------------------------------------------------------------------------- 1 | subroutine sub_move(n, X, delt_X, dt) 2 | implicit none 3 | ! --- arguments --- 4 | integer n 5 | real(kind=8), dimension(n) :: X, delt_X 6 | real(kind=8) dt 7 | 8 | X = X + delt_X * dt 9 | 10 | return 11 | end 12 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_move.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_move.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_nuc_get_dH_div_dP.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_nuc_get_dH_div_dP(n_mode, n_state, & 2 | x_mode, p_mode, & 3 | freq, & 4 | dH_div_dP) 5 | implicit none 6 | ! --- arguments --- 7 | integer n_state 8 | integer n_mode 9 | real(kind=8) nuc_dt 10 | !real(kind=8) k_tun(n_state, n_mode) 11 | !real(kind=8) lambda(n_mode, n_state, n_state) 12 | real(kind=8), dimension(n_mode) :: x_mode, p_mode 13 | real(kind=8), dimension(n_state, n_mode) :: freq 14 | real(kind=8), dimension(n_mode) :: dH_div_dP 15 | 16 | ! --- local variables --- 17 | integer i_mode, i_state, j_state 18 | 19 | !write(*,*) freq(1,n_mode) 20 | 21 | do i_mode = 1, n_mode 22 | do i_state = 1, n_state 23 | ! do j_state = 1, n_state 24 | ! if ( freq(i_state, i_mode) /= freq(j_state, i_mode) ) then 25 | ! write(*,*) "freq of mode", i_mode, "of state ", i_state, "is different from that of state", j_state 26 | ! write(*,*) "Now this program is only designed for the same-frequency cases!" 27 | ! stop 28 | ! endif 29 | ! enddo 30 | dH_div_dP(i_mode) & 31 | = freq(i_state, i_mode) * p_mode(i_mode) 32 | enddo 33 | enddo 34 | 35 | 36 | return 37 | end 38 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_nuc_get_dH_div_dP.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_nuc_get_dH_div_dP.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_nuc_get_dH_div_dP_aver_PES.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_nuc_get_dH_div_dP_aver_PES(n_mode, n_state, & 2 | x_mode, p_mode, & 3 | freq, & 4 | dH_div_dP) 5 | implicit none 6 | ! --- arguments --- 7 | integer n_state 8 | integer n_mode 9 | real(kind=8) nuc_dt 10 | !real(kind=8) k_tun(n_state, n_mode) 11 | !real(kind=8) lambda(n_mode, n_state, n_state) 12 | real(kind=8), dimension(n_mode) :: x_mode, p_mode 13 | real(kind=8), dimension(n_state, n_mode) :: freq 14 | real(kind=8), dimension(n_mode) :: dH_div_dP 15 | 16 | ! --- local variables --- 17 | integer i_mode, i_state, j_state 18 | 19 | !write(*,*) freq(1,n_mode) 20 | 21 | do i_mode = 1, n_mode 22 | do i_state = 1, n_state 23 | ! do j_state = 1, n_state 24 | ! if ( freq(i_state, i_mode) /= freq(j_state, i_mode) ) then 25 | ! write(*,*) "freq of mode", i_mode, "of state ", i_state, "is different from that of state", j_state 26 | ! write(*,*) "Now this program is only designed for the same-frequency cases!" 27 | ! stop 28 | ! endif 29 | ! enddo 30 | dH_div_dP(i_mode) & 31 | = freq(i_state, i_mode) * p_mode(i_mode) 32 | enddo 33 | enddo 34 | 35 | 36 | return 37 | end 38 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_nuc_get_dH_div_dP_aver_PES.o: -------------------------------------------------------------------------------- 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= 1, n_state 25 | !if(i_mode == 1)then 26 | !write(*,*) i_mode, i_state, j_state 27 | !write(*,*) dHmn_div_dX(i_mode, i_state, j_state) 28 | !endif 29 | dH_div_dX(i_mode) & 30 | = dH_div_dX(i_mode) + & 31 | c_n(i_state, j_state) * & 32 | dHmn_div_dX(i_mode, i_state, j_state) 33 | 34 | enddo 35 | enddo 36 | enddo 37 | 38 | 39 | return 40 | end 41 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_nuc_get_dH_div_dX_or_dP.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_nuc_get_dH_div_dX_or_dP.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_nuc_get_dH_div_dX_or_dP_aver_PES.o: -------------------------------------------------------------------------------- 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do j_state = 1, n_state 24 | if (i_state == j_state) then 25 | 26 | dHmn_div_dP(i_mode, i_state, j_state) & 27 | = freq(i_state, i_mode) * p_mode(i_mode) 28 | 29 | else 30 | 31 | dHmn_div_dP(i_mode, i_state, j_state) & 32 | = 0.d0 33 | 34 | endif 35 | enddo 36 | enddo 37 | enddo 38 | 39 | return 40 | end 41 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_nuc_get_dHmn_div_dP.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_nuc_get_dHmn_div_dP.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_nuc_get_dHmn_div_dX.o: -------------------------------------------------------------------------------- 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x_mode(i_mode) ) 22 | enddo 23 | enddo 24 | 25 | 26 | 27 | !open(10, file= 'dHmn_div_dX.dat', access='append') 28 | !do i_mode = 1, n_mode 29 | ! write(10,*) i_mode 30 | ! do i_state = 1, n_state 31 | ! write(10,*) dHmn_div_dX(i_mode, i_state, :) 32 | ! enddo 33 | !enddo 34 | !close(10) 35 | 36 | return 37 | end 38 | -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_nuc_get_dHmn_div_dX_Ham_tor.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/mapping/sub_nuc_get_dHmn_div_dX_Ham_tor.o -------------------------------------------------------------------------------- /src/dynamics/mapping/sub_nuc_motion.o: -------------------------------------------------------------------------------- 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random_seed(put=seed) 19 | 20 | deallocate(seed) 21 | end subroutine init_random_seed 22 | 23 | 24 | 25 | subroutine get_random_number(num) 26 | implicit none 27 | double precision :: num 28 | 29 | call random_number(num) 30 | 31 | end subroutine get_random_number 32 | 33 | 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /src/dynamics/tsh/sub_random.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/tsh/sub_random.o -------------------------------------------------------------------------------- /src/dynamics/tsh/sub_random3.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/tsh/sub_random3.o 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Local variables 20 | 21 | write (file_save_pe, 9999) it, time*TOFS, & 22 | pes_all(:), & 23 | pes_all(index_state) 24 | 25 | 26 | 27 | 28 | 9999 format(i10, 1x, 20(f20.10, 1x)) 29 | 30 | return 31 | 32 | end subroutine sub_save_pe 33 | -------------------------------------------------------------------------------- /src/dynamics/tsh/sub_save_pe.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/tsh/sub_save_pe.o -------------------------------------------------------------------------------- /src/dynamics/tsh/sub_save_restart.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/dynamics/tsh/sub_save_restart.o -------------------------------------------------------------------------------- /src/dynamics/tsh/sub_save_traj.o: 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-------------------------------------------------------------------------------- 1 | 2 | clean: 3 | cd overlap; make clean 4 | all: 5 | cd overlap; make 6 | install: 7 | cd overlap; make install 8 | cp ./overlap/main_overlap_slater.exe ../../bin/main_overlap_slater.exe 9 | cp ./overlap/main_overlap_slater.exe . 10 | 11 | 12 | -------------------------------------------------------------------------------- /src/electronic/interface_bagel_qm/.gitignore: -------------------------------------------------------------------------------- 1 | # 2 | test 3 | -------------------------------------------------------------------------------- /src/electronic/interface_bagel_qm/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from bagel_create import * 4 | from bagel_parser import * 5 | from bagel_run import * 6 | from bagel_template import * 7 | 8 | __all__ = ["bagel_template", "bagel_create", "bagel_parser", "bagel_run"] 9 | 10 | __revision__ = "$Revision: 0 $" 11 | -------------------------------------------------------------------------------- /src/electronic/interface_bagel_qm/bagel_parser.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from bagel_log_parser import * 4 | 5 | # mndo parser 6 | 7 | 8 | class bagel_parser(): 9 | def __init__(self, config={}): 10 | """ 11 | parser mndo log or fort files to extract relevant data. 12 | """ 13 | self.config = config 14 | 15 | return 16 | 17 | def get_log_dat(self): 18 | """ 19 | parse one tddft calculation result. 20 | """ 21 | log = bagel_log_parser(self.config) 22 | 23 | # forces 24 | log.get_energy() 25 | log.get_gradient() 26 | log.get_nac() 27 | log.collect_qm() 28 | 29 | return 30 | -------------------------------------------------------------------------------- /src/electronic/interface_bagel_qm/config.in: -------------------------------------------------------------------------------- 1 | { 2 | "root": "./", 3 | "dirs": { 4 | "home": "QC_TMP", 5 | "work": "BAGEL_TMP", 6 | "template": "BAGEL_EXAM" 7 | }, 8 | "files": { 9 | "dyn": "inp.json", 10 | "interface": "interface.json", 11 | "template": "template.json", 12 | "bagel_template": "bagel_template.json", 13 | "bagel_log": "bagel.log", 14 | "bagel_wfu": "wfu.archive", 15 | "bagel_input": "bagel.json" 16 | }, 17 | "command": { 18 | "bagel": "BAGEL" 19 | } 20 | 21 | } 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gamess_qm/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from gms_template import * 4 | from gms_create import * 5 | from gms_parser import * 6 | from gms_zero import * 7 | from gms_nonzero import * 8 | from gms_overlap import * 9 | from gms_nac import * 10 | from gamess import * 11 | 12 | __all__ = ["gamess", "gms_template", "gms_create", "gms_parser", "gms_zero", "gms_nonzero", "gms_overlap", "gms_nac"] 13 | 14 | 15 | __revision__ = "$Revision: 0 $" 16 | 17 | 18 | 19 | -------------------------------------------------------------------------------- /src/electronic/interface_gamess_qm/config.in: -------------------------------------------------------------------------------- 1 | { 2 | "root": "./", 3 | "dirs": { 4 | "home": "QC_TMP", 5 | "work": "GMS_TMP", 6 | "work_prev": "GMS_TMP_PREV", 7 | "overlap": "OVERLAP", 8 | "template": "GMS_EXAM", 9 | "nac": "NAC", 10 | "userscr": "scr" 11 | }, 12 | "files": { 13 | "dyn": "inp.json", 14 | "interface": "interface.json", 15 | "template": "template.json", 16 | "gms_template": "gms_template.inp", 17 | "job_log": "gamess.log", 18 | "job_log2": "gamess2.log", 19 | "job_dat": "gamess.dat", 20 | "job_dat2": "gamess2.dat", 21 | "job_inp": "gamess.inp", 22 | "job_inp2": "gamess2.inp", 23 | "dimension": "dimension.json" 24 | }, 25 | "command": { 26 | "exec": "rungms", 27 | "GMS_VERSION_NO": "06", 28 | "GMS_N_CPU": "2" 29 | }, 30 | "constant": { 31 | "BOHR2ANGSTROM": "0.529177249" 32 | } 33 | 34 | 35 | 36 | } 37 | 38 | 39 | -------------------------------------------------------------------------------- /src/electronic/interface_gamess_qm/improve: -------------------------------------------------------------------------------- 1 | 1. create template run parser is variable 2 | 2. other is constant 3 | 3. config => vars : define rules for clarity 4 | -------------------------------------------------------------------------------- /src/electronic/interface_gamess_qm/readme: -------------------------------------------------------------------------------- 1 | export variables: 2 | 3 | if 'GMS_VERSION_NO' in os.environ: 4 | verno = os.environ.get('GMS_VERSION_NO') 5 | print "use gamess value: version-no: ", verno 6 | else: 7 | verno = "06" 8 | print "GMS_VERSION_NO cannot be found ???" 9 | print "use default value: version-no: 06" 10 | self.vars['verno'] = verno 11 | 12 | if 'GMS_N_CPU' in os.environ: 13 | n_cpu = os.environ.get('GMS_VERSION_NO') 14 | print "use cpu value: n_cpu: ", n_cpu 15 | else: 16 | n_cpu = 2 17 | print "GMS_N_CPU cannot be found ???" 18 | print "use default value: n_cpu: 2" 19 | self.vars['n_cpu'] = n_cpu 20 | 21 | 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gamess_qm/scr/gamess.F10: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/interface_gamess_qm/scr/gamess.F10 -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/EXAM/gau.gjf: -------------------------------------------------------------------------------- 1 | %chk=gaussian.chk 2 | %mem=1GB 3 | %nproc=2 4 | # force td(singlet, root=2, nstates=3) b3lyp/6-31G** scf=(tight,maxcycle=10000) iop(9/40=20) nosymm 5 | 6 | [0] [0] 7 | 8 | 1 1 9 | c -5.5338175 0.7125130 0.4057093 10 | n -1.4757217 0.1805686 0.1102563 11 | h -6.1187275 1.6438646 2.2895698 12 | h -6.6370856 -0.4341665 -1.0859286 13 | h -0.8548232 -0.9878324 -1.3343232 14 | h -0.4005556 0.8548868 1.6017769 15 | 16 | 17 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/EXAM/gau_template.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %nproc=2 3 | %mem=1GB 4 | #p force ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):pm6)=(EmbedCharge,inputfiles) 5 | nosymm geom=connectivity pop=full 6 | 7 | ch2nh2 iop(9/40=20) 8 | 9 | 0 1 0 1 0 1 10 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 12 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 13 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 15 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 16 | 17 | 1 2 1.0 3 1.0 18 | 2 19 | 3 20 | 4 5 1.0 6 1.0 21 | 5 22 | 6 23 | 24 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/EXAM/template.com: -------------------------------------------------------------------------------- 1 | #n B3LYP/6-31G(d) nosymm iop(2/12=3,3/33=1) guess=only pop=full 2 | 3 | ch2nh2 4 | 5 | 1 1 6 | N -4.42461 2.03755 0.00000 7 | C -2.46682 0.54857 0.00000 8 | H -4.67735 2.26769 -0.96102 9 | H -4.22139 2.88810 0.52504 10 | H -2.69299 -0.33883 -0.55341 11 | H -1.64286 1.05092 -0.46220 12 | 13 | 14 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/ONIOM.doc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/interface_gaussian_oniom/ONIOM.doc -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/ONLYINPUT/high-model-check.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) B3LYP/6-31G(D,P) TD(SINGLET,NSTATES=3,ROOT=1) 2 | 3 | ch2nh2 iop(9/40=20) 4 | Point 2 -- high level on model system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-#6--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-#6-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-#6-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/ONLYINPUT/low-model-check.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) PM6 2 | 3 | ch2nh2 iop(9/40=20) 4 | Point 1 -- low level on model system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-#6--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-#6-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-#6-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/ONLYINPUT/low-real-check.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) PM6 2 | 3 | ch2nh2 iop(9/40=20) 4 | Point 3 -- low level on real system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-O_3--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-H_-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-H_-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/ONLYINPUT/onlyinputfiles.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %nproc=2 3 | %mem=1GB 4 | #p force ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):pm6)=(EmbedCharge,inputfiles) 5 | nosymm geom=connectivity pop=full 6 | 7 | ch2nh2 iop(9/40=20) 8 | 9 | 0 1 0 1 0 1 10 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 12 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 13 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 15 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 16 | 17 | 1 2 1.0 3 1.0 18 | 2 19 | 3 20 | 4 5 1.0 6 1.0 21 | 5 22 | 6 23 | 24 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from gau_template import * 4 | from gau_create import * 5 | from gau_parser import * 6 | from gau_zero import * 7 | from gau_nonzero import * 8 | from gau_overlap import * 9 | from gau_nac import * 10 | 11 | __all__ = ["gau_template", "gau_create", "gau_parser", "gau_zero", "gau_nonzero", "gau_overlap", "gau_nac"] 12 | 13 | 14 | 15 | __revision__ = "$Revision: 0 $" 16 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/ao.gjf: -------------------------------------------------------------------------------- 1 | %chk=ao.chk 2 | %mem=1GB 3 | %nproc=2 4 | %nproclinda=1 5 | #p oniom(b3lyp/6-31g(d,p):uff)=(embed,inputfiles) nosymm iop(2/12=3,3/33=1) guess=only pop=full 6 | 7 | ch2nh2 8 | 9 | 0 1 0 1 0 1 10 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 12 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 13 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 15 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 16 | 17 | 1 2 1.0 3 1.0 18 | 2 19 | 3 20 | 4 5 1.0 6 1.0 21 | 5 22 | 6 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/config.in: -------------------------------------------------------------------------------- 1 | { 2 | "root": "./", 3 | "dirs": { 4 | "home": "QC_TMP", 5 | "work": "GAU_TMP", 6 | "work_prev": "GAU_TMP_PREV", 7 | "overlap": "OVERLAP", 8 | "template": "GAU_EXAM", 9 | "onlyinput": "ONLYINPUT", 10 | "nac": "NAC" 11 | }, 12 | "files": { 13 | "dyn": "inp.json", 14 | "interface": "interface.json", 15 | "template": "template.json", 16 | "layer": "layer.json", 17 | "onlyinput": "onlyinputfiles", 18 | "gau_template": "gau_template.gjf", 19 | "high-model-inp": "high-model.gjf", 20 | "high-model-chk": "high-model.chk", 21 | "high-model-log": "high-model.log", 22 | "ao-overlap-inp": "high-model-overlap.gjf", 23 | "ao-overlap-log": "high-model-overlap.log", 24 | "dimension": "dimension.json" 25 | }, 26 | "command": { 27 | "exec": "g09" 28 | } 29 | 30 | } 31 | 32 | 33 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/details.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/interface_gaussian_oniom/details.tex -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/dimension.json: -------------------------------------------------------------------------------- 1 | { 2 | "n_col": 5, 3 | "n_active": 6, 4 | "n_atom": 42 5 | } -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/dyn.inp: -------------------------------------------------------------------------------- 1 | &control 2 | dyn_method = 2, 3 | ntime = 200, 4 | dtime = 0.2, 5 | ntime_ele = 100, 6 | n_sav_stat = 1, 7 | n_sav_traj = 1, 8 | qm_method = 11, 9 | n_state = 4, 10 | md_state_list = "1, 2, 3", 11 | i_state = 2, 12 | seed_random = -1, 13 | cor_dec = 0.1, 14 | label_nac_phase = 1, 15 | label_reject_hops = 1, 16 | hop_e = 10, 17 | label_read_velocity = 0, 18 | label_restart = 0, 19 | / 20 | 21 | &quantum 22 | qm_method = 21, 23 | label_external = 1 24 | qm_package = 102, 25 | ci_td_use_file_type = "rwf", 26 | ci_assign_problem = "X+Y", 27 | is_do_cis_casida = "no", 28 | / 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/frag/all.gjf: -------------------------------------------------------------------------------- 1 | %chk=only.chk 2 | %mem=1GB 3 | #p force ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):pm6)=(EmbedCharge,inputfiles) 4 | nosymm geom=connectivity 5 | 6 | ch2nh2 iop(9/40=20) 7 | 8 | 0 1 0 1 0 1 9 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 10 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 12 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 13 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 15 | 16 | 1 2 1.0 3 1.0 17 | 2 18 | 3 19 | 4 5 1.0 6 1.0 20 | 5 21 | 6 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/frag/gaussian.gjf: -------------------------------------------------------------------------------- 1 | %chk=gaussian.chk 2 | %mem=1GB 3 | %nproc=2 4 | %nproclinda=1 5 | # b3lyp/6-31g* scf=(tight,maxcycle=10000) iop(9/40=20) nosymm pop=full 6 | 7 | 8 | [0] [0] 9 | 10 | 1 1 11 | c -2.3968646 0.3831220 0.1112106 12 | n -1.2430054 0.2067258 0.1604477 13 | h -2.8445472 0.1433187 1.1013360 14 | h -2.4035079 -0.0993059 -0.8237197 15 | h -0.3621920 0.3638379 -0.6948661 16 | h -1.0178066 0.9613559 0.8665966 17 | 18 | --LINK1-- 19 | %chk=gaussian.chk 20 | %mem=1GB 21 | %nproc=2 22 | %nproclinda=1 23 | # force b3lyp/ChkBasis scf=(tight,maxcycle=10000) iop(9/40=20) nosymm p 24 | op=full geom=AllCheck Guess=Read 25 | 26 | --LINK1-- 27 | %chk=gaussian.chk 28 | %mem=1GB 29 | %nproc=2 30 | %nproclinda=1 31 | # td(singlet, root=0, nstates=2) b3lyp/ChkBasis scf=(tight,maxcycle=10 32 | 000) iop(9/40=20) nosymm pop=full geom=AllCheck Guess=Read 33 | 34 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/frag/highmodel.gjf: -------------------------------------------------------------------------------- 1 | #P force Test IOp(2/15=1,5/32=2,5/38=1) B3LYP/6-31G(D,P) TD(SINGLET,NSTATES=3,ROOT=1) 2 | 3 | ch2nh2 iop(9/40=20) 4 | Point 2 -- high level on model system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-#6--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-#6-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-#6-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/frag/lowmodel.gjf: -------------------------------------------------------------------------------- 1 | #P force Test IOp(2/15=1,5/32=2,5/38=1) PM6 2 | 3 | ch2nh2 iop(9/40=20) 4 | Point 1 -- low level on model system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-#6--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-#6-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-#6-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/frag/lowreal.gjf: -------------------------------------------------------------------------------- 1 | #P force Test IOp(2/15=1,5/32=2,5/38=1) PM6 2 | 3 | ch2nh2 iop(9/40=20) 4 | Point 3 -- low level on real system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-O_3--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-H_-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-H_-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/high-model-check.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) B3LYP/6-31G(D,P) TD(SINGLET,NSTATES=3,ROOT=1) 2 | 3 | ch2nh2 4 | Point 2 -- high level on model system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-#6--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-#6-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-#6-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/high-model-energy.dat: -------------------------------------------------------------------------------- 1 | S0 -75.5442755925 2 | S1 -64.0748755925 3 | S2 -62.4200755925 4 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/high-model-gradient.dat: -------------------------------------------------------------------------------- 1 | 2.096463665 2.961805252 -0.0 2 | -3.179796024 0.030329958 -0.0 3 | 1.092988088 -2.968139863 -0.0 4 | -0.028665686 0.050407714 -0.0 5 | 0.019294193 -0.068254379 -0.0 6 | -0.000284236 -0.006148681 -0.0 7 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/high-model-overlap.gjf: -------------------------------------------------------------------------------- 1 | %mem=1GB 2 | %nproc=2 3 | %nproclinda=1 4 | # HF/6-31G(D,P) nosymm iop(2/12=3,3/33=1) guess=only pop=full 5 | 6 | ch2nh2 iop(9/40=20) 7 | Point 2 -- high level on model system. 8 | 9 | 0 1 10 | o -2.39686552 0.12698128 0.11121069 11 | h -1.24300588 0.20672591 0.16044778 12 | h -2.84454833 0.14331878 1.10133648 13 | o -2.39686552 0.38312217 0.11121069 14 | h -1.24300588 0.20672591 0.16044778 15 | h -2.84454833 0.14331878 1.10133648 16 | 17 | 18 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/high-model.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %mem=1GB 3 | %nproc=2 4 | %nproclinda=1 5 | #P IOp(2/15=1,5/32=2,5/38=1) B3LYP/6-31G(D,P) pop=full 6 | 7 | ch2nh2 iop(9/40=20) 8 | Point 2 -- high level on model system. 9 | 10 | 0 1 11 | O-O_3--0.834000 -0.19511030 -1.16114422 0.00000000 12 | H-H_-0.417000 0.31289982 -1.16114422 0.00000000 13 | H-H_-0.417000 -0.36468756 -0.68227280 0.00000000 14 | O-#6--0.834000 -1.24204361 0.18083393 0.00000000 15 | H-#6-0.417000 -0.73403349 0.18083393 0.00000000 16 | H-#6-0.417000 -1.41162088 0.65970535 0.00000000 17 | 18 | 1 2 1.000 3 1.000 19 | 2 1 1.000 20 | 3 1 1.000 21 | 4 5 1.000 6 1.000 22 | 5 4 1.000 23 | 6 4 1.000 24 | 25 | --LINK1-- 26 | %chk=oniom.chk 27 | %mem=1GB 28 | %nproc=2 29 | %nproclinda=1 30 | #P force B3LYP/6-31G(D,P) TD(SINGLET,nstates=2,root=1) IOp(2/15=1,5/32=2,5/38=1) geom=AllCheck Guess=Read iop(9/40=20) pop=full 31 | 32 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/highao.gjf: -------------------------------------------------------------------------------- 1 | #P B3LYP/6-31G(D,P) nosymm iop(2/12=3,3/33=1) guess=only pop=full 2 | 3 | ch2nh2 4 | Point 2 -- high level on model system. 5 | 6 | 0,1 7 | O -0.368705030000 -2.194244570000 0.000000000000 8 | H 0.591294970000 -2.194244570000 0.000000000000 9 | H -0.689159620000 -1.289308740000 0.000000000000 10 | O -2.347122270000 0.341726610000 0.000000000000 11 | H -1.387122270000 0.341726610000 0.000000000000 12 | H -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 15 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/highmodel.gjf: -------------------------------------------------------------------------------- 1 | #P force Test IOp(2/15=1,5/32=2,5/38=1) B3LYP/6-31G(D,P) TD(SINGLET,NSTATES=3,ROOT=1) iop(9/40=20) 2 | 3 | ch2nh2 4 | Point 2 -- high level on model system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-#6--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-#6-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-#6-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/inp.json: -------------------------------------------------------------------------------- 1 | { 2 | "control": { 3 | "n_sav_stat": "1", 4 | "hop_e": "10", 5 | "label_nac_phase": "1", 6 | "label_reject_hops": "1", 7 | "dtime": "0.2", 8 | "i_state": "2", 9 | "cor_dec": "0.1", 10 | "md_state_list": "1 2 3", 11 | "label_restart": "0", 12 | "dyn_method": "2", 13 | "n_state": "4", 14 | "seed_random": "-1", 15 | "ntime_ele": "100", 16 | "label_read_velocity": "0", 17 | "qm_method": "11", 18 | "ntime": "200", 19 | "n_sav_traj": "1" 20 | }, 21 | "quantum": { 22 | "ci_td_use_file_type": "rwf", 23 | "ci_assign_problem": "X+Y", 24 | "ci_assign_factor": "0.0 0.0", 25 | "is_do_ci_assignment": "no", 26 | "qm_method": "11", 27 | "qm_package": "102" 28 | } 29 | } 30 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/lists.txt: -------------------------------------------------------------------------------- 1 | gau_template 2 | gau_create 3 | gau_log_parser 4 | 5 | gau_zero 6 | gau_nonzero 7 | gau_overlap 8 | 9 | gau_nac 10 | 11 | gaussian 12 | 13 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/low-model-check.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) UFF 2 | 3 | ch2nh2 4 | Point 1 -- low level on model system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-#6--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-#6-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-#6-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/low-model-energy.dat: -------------------------------------------------------------------------------- 1 | 13.369728500000 2 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/low-model-gradient.dat: -------------------------------------------------------------------------------- 1 | 71.947537604 -11.06683408 2.802707357 2 | -71.937272176 11.040368807 -3.008205819 3 | 0.012856403 -0.01472892 0.093078796 4 | -0.023663581 0.069719392 0.106942645 5 | -0.007885257 -0.004583781 0.017491169 6 | 0.008427009 -0.02394142 -0.012014147 7 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/low-model.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %mem=1GB 3 | %nproc=2 4 | %nproclinda=1 5 | #P force IOp(2/15=1,5/32=2,5/38=1) PM6 6 | 7 | ch2nh2 iop(9/40=20) 8 | Point 1 -- low level on model system. 9 | 10 | 0 1 11 | O-O_3--0.834000 -2.39686552 0.38312217 0.11121069 12 | H-H_-0.417000 -1.24300588 0.20672591 0.16044778 13 | H-H_-0.417000 -2.84454833 0.14331878 1.10133648 14 | O-#6--0.834000 -2.40350883 -0.09930598 -0.82372000 15 | H-#6-0.417000 -0.36219210 0.36383800 -0.69486638 16 | H-#6-0.417000 -1.01780703 0.96135626 0.86659694 17 | 18 | 1 2 1.000 3 1.000 19 | 2 1 1.000 20 | 3 1 1.000 21 | 4 5 1.000 6 1.000 22 | 5 4 1.000 23 | 6 4 1.000 24 | 25 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/low-real-check.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) UFF 2 | 3 | ch2nh2 4 | Point 3 -- low level on real system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-O_3--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-H_-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-H_-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/low-real-energy.dat: -------------------------------------------------------------------------------- 1 | 27.481108000000 2 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/low-real-gradient.dat: -------------------------------------------------------------------------------- 1 | 72.427757601 -10.958651047 3.119230963 2 | -51.495556017 62.850288096 37.192683589 3 | 0.063402619 0.056544038 0.098611001 4 | 1.365895139 0.474961235 1.204749155 5 | -6.634073116 -1.150203421 6.47403199 6 | -15.727426226 -51.272938901 -48.089306697 7 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/low-real.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %mem=1GB 3 | %nproc=2 4 | %nproclinda=1 5 | #P force IOp(2/15=1,5/32=2,5/38=1) PM6 6 | 7 | ch2nh2 iop(9/40=20) 8 | Point 3 -- low level on real system. 9 | 10 | 0 1 11 | O-O_3--0.834000 -2.39686552 0.38312217 0.11121069 12 | H-H_-0.417000 -1.24300588 0.20672591 0.16044778 13 | H-H_-0.417000 -2.84454833 0.14331878 1.10133648 14 | O-O_3--0.834000 -2.40350883 -0.09930598 -0.82372000 15 | H-H_-0.417000 -0.36219210 0.36383800 -0.69486638 16 | H-H_-0.417000 -1.01780703 0.96135626 0.86659694 17 | 18 | 1 2 1.000 3 1.000 19 | 2 1 1.000 20 | 3 1 1.000 21 | 4 5 1.000 6 1.000 22 | 5 4 1.000 23 | 6 4 1.000 24 | 25 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/lowmodel.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) UFF 2 | 3 | ch2nh2 4 | Point 3 -- low level on real system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-O_3--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-H_-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-H_-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/model_energy.dat: -------------------------------------------------------------------------------- 1 | S0 -76.7397877961 2 | S1 -76.449817244 3 | S2 -76.3738086143 4 | S3 -76.3674399562 5 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/B2.gbs: -------------------------------------------------------------------------------- 1 | 2 | 3 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/a.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %mem=1GB 3 | #p ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):uff)=(embed,inputfiles) nosymm geom=connectivity pop=full iop(9/40=20) 4 | 5 | ch2nh2 6 | 7 | 0 1 0 1 0 1 8 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 9 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 10 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 11 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 12 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 13 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 14 | 15 | 1 2 1.0 3 1.0 16 | 2 17 | 3 18 | 4 5 1.0 6 1.0 19 | 5 20 | 6 21 | 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/ao.gjf: -------------------------------------------------------------------------------- 1 | %chk=ao.chk 2 | %mem=1GB 3 | %nproc=2 4 | %nproclinda=1 5 | #p oniom(b3lyp/6-31g(d,p):uff)=embed nosymm iop(2/12=3,3/33=1) guess=only pop=full 6 | 7 | ch2nh2 8 | 9 | 0 1 0 1 0 1 10 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 12 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 13 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 15 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 16 | 17 | 1 2 1.0 3 1.0 18 | 2 19 | 3 20 | 4 5 1.0 6 1.0 21 | 5 22 | 6 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/b.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %mem=1GB 3 | #p td(singlet,nstates=3,root=1) oniom(b3lyp/6-31g(d,p):uff)=(embed,inputfiles) nosymm geom=connectivity pop=full iop(9/40=20) 4 | 5 | ch2nh2 6 | 7 | 0 1 0 1 0 1 8 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 9 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 10 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 11 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 12 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 13 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 14 | 15 | 1 2 1.0 3 1.0 16 | 2 17 | 3 18 | 4 5 1.0 6 1.0 19 | 5 20 | 6 21 | 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/b3lyp.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) B3LYP/6-31G(D,P) TD(SINGLET,NSTATES=3,ROOT=1) 2 | 3 | ch2nh2 iop(9/40=20) 4 | Point 2 -- high level on model system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | O-#6--0.834000 -2.347122270000 0.341726610000 0.000000000000 11 | H-#6-0.417000 -1.387122270000 0.341726610000 0.000000000000 12 | H-#6-0.417000 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/embed.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %mem=1GB 3 | #p force ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):uff)=(EmbedCharge,inputfiles) 4 | nosymm geom=connectivity pop=full 5 | 6 | ch2nh2 iop(9/40=20) 7 | 8 | 0 1 0 1 0 1 9 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 10 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 12 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 13 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 15 | 16 | 1 2 1.0 3 1.0 17 | 2 18 | 3 19 | 4 5 1.0 6 1.0 20 | 5 21 | 6 22 | 23 | 24 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/gaussian.gjf: -------------------------------------------------------------------------------- 1 | %chk=force.chk 2 | %mem=1GB 3 | #p force ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):uff)=(embed,inputfiles) nosymm geom=connectivity pop=full iop(9/40=20) 4 | 5 | ch2nh2 6 | 7 | 0 1 0 1 0 1 8 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 9 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 10 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 11 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 12 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 13 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 14 | 15 | 1 2 1.0 3 1.0 16 | 2 17 | 3 18 | 4 5 1.0 6 1.0 19 | 5 20 | 6 21 | 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/h2o.gjf: -------------------------------------------------------------------------------- 1 | %chk=h2o.chk 2 | # force td(singlet,nstates=3,root=1) oniom(b3lyp/6-31g(d):uff)=embed geom=connectivity 3 | 4 | Title Card Required 5 | 6 | 1 2 1 2 0 1 7 | O-O_3--0.834000 0 1.95331702 1.80589678 0.00000000 H 8 | H-H_-0.417000 0 2.91331702 1.80589678 0.00000000 H 9 | H-H_-0.417000 0 1.63286243 2.71083261 0.00000000 H 10 | O-O_3--0.834000 0 -0.82934594 1.68460960 -0.85549805 L 11 | H-H_-0.417000 0 0.13065406 1.68460960 -0.85549805 L 12 | H-H_-0.417000 0 -1.14980053 2.58954543 -0.85549805 L 13 | 14 | 1 2 1.0 3 1.0 15 | 2 16 | 3 17 | 4 5 1.0 6 1.0 18 | 5 19 | 6 20 | 21 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/hm.gjf: -------------------------------------------------------------------------------- 1 | %chk=hm.chk 2 | #P Test IOp(2/15=1,5/32=2,5/38=1) B3LYP/6-31G(D,P) TD(SINGLET,NSTATES=3,ROOT=1) 3 | 4 | ch2nh2 5 | Point 2 -- high level on model system. 6 | 7 | 0,1 8 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 10 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 11 | O-#6--0.834000 -2.347122270000 0.341726610000 0.000000000000 12 | H-#6-0.417000 -1.387122270000 0.341726610000 0.000000000000 13 | H-#6-0.417000 -2.667576860000 1.246662440000 0.000000000000 14 | 15 | 1 2 1.000 3 1.000 16 | 2 1 1.000 17 | 3 1 1.000 18 | 4 5 1.000 6 1.000 19 | 5 4 1.000 20 | 6 4 1.000 21 | 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/inp.json: -------------------------------------------------------------------------------- 1 | { 2 | "control": { 3 | "n_sav_stat": "1", 4 | "hop_e": "10", 5 | "label_nac_phase": "1", 6 | "label_reject_hops": "1", 7 | "dtime": "0.2", 8 | "i_state": "3", 9 | "cor_dec": "0.1", 10 | "md_state_list": "1 2 3", 11 | "label_restart": "0", 12 | "dyn_method": "2", 13 | "n_state": "3", 14 | "seed_random": "-1", 15 | "ntime_ele": "100", 16 | "label_read_velocity": "0", 17 | "qm_method": "11", 18 | "ntime": "200", 19 | "n_sav_traj": "1" 20 | }, 21 | "quantum": { 22 | "ci_td_use_file_type": "log", 23 | "ci_assign_problem": "X", 24 | "is_do_cis_casida": "no", 25 | "qm_method": "11", 26 | "qm_package": "102" 27 | } 28 | } 29 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/mm.gjf: -------------------------------------------------------------------------------- 1 | #P Test UFF 2 | 3 | ch2nh2 4 | Point 1 -- low level on model system. 5 | 6 | 0,1 7 | O-O_3--0.834000 -0.368705030000 -2.194244570000 0.000000000000 8 | H-H_-0.417000 0.591294970000 -2.194244570000 0.000000000000 9 | H-H_-0.417000 -0.689159620000 -1.289308740000 0.000000000000 10 | 11 | 1 2 1.000 3 1.000 12 | 2 1 1.000 13 | 3 1 1.000 14 | 15 | 16 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/noembed.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %mem=1GB 3 | #p force ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):uff)=(noEmbedCharge,inputfiles) 4 | nosymm geom=connectivity pop=full 5 | 6 | ch2nh2 iop(9/40=20) 7 | 8 | 0 1 0 1 0 1 9 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 10 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 12 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 13 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 15 | 16 | 1 2 1.0 3 1.0 17 | 2 18 | 3 19 | 4 5 1.0 6 1.0 20 | 5 21 | 6 22 | 23 | 24 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/oniom.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %mem=1GB 3 | #p force ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):pm6)=(EmbedCharge,inputfiles) 4 | nosymm geom=connectivity pop=full 5 | 6 | ch2nh2 iop(9/40=20) 7 | 8 | 0 1 0 1 0 1 9 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 10 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 12 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 13 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 15 | 16 | 1 2 1.0 3 1.0 17 | 2 18 | 3 19 | 4 5 1.0 6 1.0 20 | 5 21 | 6 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/qm.gjf: -------------------------------------------------------------------------------- 1 | %chk=qm.chk 2 | %mem=1GB 3 | # force td=(nstates=3,root=1,singlet) nosymm geom=connectivity 4 | 5 | ch2nh2 6 | 7 | 1 1 8 | N-N_2 -3.91983642 1.74252582 -0.19144495 9 | C-C_2 -2.80887592 1.08729284 -0.29062899 10 | H-H_ -4.78505229 1.29768271 -0.42278042 11 | H-H_ -3.91343348 2.69388816 0.11656269 12 | H-H_ -2.81572695 0.06933552 -0.62019835 13 | H-H_ -1.88309494 1.56327495 -0.04309998 14 | 15 | 1 3 1.0 4 1.0 2 2.0 16 | 2 5 1.0 6 1.0 17 | 3 18 | 4 19 | 5 20 | 6 21 | 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/qm1.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) B3LYP/6-31G* 2 | 3 | ch2nh2 iop(9/40=20) 4 | Point 3 -- low level on real system. 5 | 6 | 0,1 7 | O -0.368705030000 -2.194244570000 0.000000000000 8 | H 0.591294970000 -2.194244570000 0.000000000000 9 | H -0.689159620000 -1.289308740000 0.000000000000 10 | O -2.347122270000 0.341726610000 0.000000000000 11 | H -1.387122270000 0.341726610000 0.000000000000 12 | H -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/qm2.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) B3LYP/6-31G(D,P) TD(SINGLET,NSTATES=3,ROOT=1) 2 | 3 | ch2nh2 iop(9/40=20) 4 | Point 2 -- high level on model system. 5 | 6 | 0,1 7 | O -0.368705030000 -2.194244570000 0.000000000000 8 | H 0.591294970000 -2.194244570000 0.000000000000 9 | H -0.689159620000 -1.289308740000 0.000000000000 10 | O-#6 -2.347122270000 0.341726610000 0.000000000000 11 | H-#6 -1.387122270000 0.341726610000 0.000000000000 12 | H-#6 -2.667576860000 1.246662440000 0.000000000000 13 | 14 | 1 2 1.000 3 1.000 15 | 2 1 1.000 16 | 3 1 1.000 17 | 4 5 1.000 6 1.000 18 | 5 4 1.000 19 | 6 4 1.000 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/qm3.gjf: -------------------------------------------------------------------------------- 1 | #P Test IOp(2/15=1,5/32=2,5/38=1) B3LYP/6-31G* 2 | 3 | ch2nh2 iop(9/40=20) 4 | Point 1 -- low level on model system. 5 | 6 | 0,1 7 | O -0.368705030000 -2.194244570000 0.000000000000 8 | H 0.591294970000 -2.194244570000 0.000000000000 9 | H -0.689159620000 -1.289308740000 0.000000000000 10 | 11 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/qmqm.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %mem=1GB 3 | #p force ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):b3lyp/6-31G*)=(EmbedCharge,inputfiles) 4 | nosymm geom=connectivity pop=full 5 | 6 | ch2nh2 iop(9/40=20) 7 | 8 | 0 1 0 1 0 1 9 | O 0 -0.36870503 -2.19424457 0.00000000 H 10 | H 0 0.59129497 -2.19424457 0.00000000 H 11 | H 0 -0.68915962 -1.28930874 0.00000000 H 12 | O 0 -2.34712227 0.34172661 0.00000000 M 13 | H 0 -1.38712227 0.34172661 0.00000000 M 14 | H 0 -2.66757686 1.24666244 0.00000000 M 15 | 16 | 1 2 1.0 3 1.0 17 | 2 18 | 3 19 | 4 5 1.0 6 1.0 20 | 5 21 | 6 22 | 23 | 24 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/readme: -------------------------------------------------------------------------------- 1 | overlap is the same, but onlyinputfiles is prefer 2 | scheme 1. use log 3 | overlap 4 | iop 5 | scheme 2. use chk 6 | generate onlyinputfiles 7 | extract to inputfile 8 | dump data 9 | further data 10 | 11 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/s2.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %mem=1GB 3 | #p force ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=2):uff)=(EmbedCharge,inputfiles) 4 | nosymm geom=connectivity pop=full 5 | 6 | ch2nh2 iop(9/40=20) 7 | 8 | 0 1 0 1 0 1 9 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 10 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 12 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 13 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 15 | 16 | 1 2 1.0 3 1.0 17 | 2 18 | 3 19 | 4 5 1.0 6 1.0 20 | 5 21 | 6 22 | 23 | 24 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/t.gjf: -------------------------------------------------------------------------------- 1 | %chk=t.chk 2 | %mem=1GB 3 | %nproc=2 4 | %nproclinda=1 5 | #p hf/6-31G** iop(2/12=3,3/33=1) guess=only pop=full 6 | 7 | ch2nh2 8 | 9 | 0 1 10 | O -0.36870503 -2.19424457 0.00000000 11 | H 0.59129497 -2.19424457 0.00000000 12 | H -0.68915962 -1.28930874 0.00000000 13 | 14 | 15 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom2/tt.gjf: -------------------------------------------------------------------------------- 1 | %mem=1GB 2 | #p force ONIOM(b3lyp/6-31g(d,p):uff)=(EmbedCharge,inputfiles) 3 | nosymm geom=connectivity pop=full 4 | 5 | ch2nh2 iop(9/40=20) 6 | 7 | 0 1 0 1 0 1 8 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 9 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 10 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 11 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 12 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 13 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 14 | 15 | 1 2 1.0 3 1.0 16 | 2 17 | 3 18 | 4 5 1.0 6 1.0 19 | 5 20 | 6 21 | 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom3/h2o3.gjf: -------------------------------------------------------------------------------- 1 | %chk=h2o3.chk 2 | # oniom(td/b3lyp/6-31g(d):pm6:uff)=(embed,onlyinputfiles) geom=connectivity 3 | 4 | Title Card Required 5 | 6 | 0 1 0 1 0 1 0 1 0 1 0 1 7 | O-O_3--0.834000 0 -2.86580727 1.39267837 0.00000000 H 8 | H-H_-0.417000 0 -1.90580730 1.39291947 0.00000000 H 9 | H-H_-0.417000 0 -3.18603457 2.29769465 0.00000000 H 10 | O-O_3--0.834000 0 -2.02356595 3.11642139 2.10449108 M 11 | H-H_-0.417000 0 -1.06356598 3.11666249 2.10449108 M 12 | H-H_-0.417000 0 -2.34379325 4.02143767 2.10449108 M 13 | O-O_3--0.834000 0 -3.12199382 4.08526776 0.24124313 L 14 | H-H_-0.417000 0 -2.16199385 4.08550887 0.24124313 L 15 | H-H_-0.417000 0 -3.44222112 4.99028405 0.24124313 L 16 | 17 | 1 2 1.0 3 1.0 18 | 2 19 | 3 20 | 4 5 1.0 6 1.0 21 | 5 22 | 6 23 | 7 8 1.0 9 1.0 24 | 8 25 | 9 26 | 27 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom3/ok.gjf: -------------------------------------------------------------------------------- 1 | %chk=ok.chk 2 | # oniom(B3LYP/6-31g**:uff)=(embed,onlyinputfiles) geom=connectivity 3 | 4 | Title Card Required 5 | 6 | 0 2 0 1 0 1 7 | C-C_3(PDBName=C,ResName=A,ResNum=0) 0 1.98800000 0.08700000 -0.87400000 H 8 | H-H_(PDBName=H,ResName=A,ResNum=0) 0 2.34300000 0.59100000 0.00100000 H 9 | H-H_(PDBName=H,ResName=A,ResNum=0) 0 2.34600000 0.59200000 -1.74600000 H 10 | H-H_(PDBName=H,ResName=A,ResNum=0) 0 0.91800000 0.08700000 -0.87600000 H 11 | H-H_(PDBName=H,ResName=A,ResNum=0) 0 2.34500000 -0.92200000 -0.87400000 L H-H_ 1 12 | C-C_3(PDBName=C,ResName=A,ResNum=0) 0 2.70100000 -1.93100000 -0.87400000 L 13 | H-H_(PDBName=H,ResName=A,ResNum=0) 0 3.77100000 -1.93100000 -0.87400000 L 14 | H-H_(PDBName=H,ResName=A,ResNum=0) 0 2.34500000 -2.43500000 -1.74700000 L 15 | H-H_(PDBName=H,ResName=A,ResNum=0) 0 2.34500000 -2.43500000 0.00000000 L 16 | 17 | 1 2 1.0 3 1.0 4 1.0 5 1.0 18 | 2 19 | 3 20 | 4 21 | 5 6 1.0 22 | 6 7 1.0 8 1.0 9 1.0 23 | 7 24 | 8 25 | 9 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom3/ok.pdb: -------------------------------------------------------------------------------- 1 | REMARK 1 File created by GaussView 5.0.9 2 | HETATM 1 C 0 1.988 0.087 -0.874 C 3 | HETATM 2 H 0 2.343 0.591 0.001 H 4 | HETATM 3 H 0 2.346 0.592 -1.746 H 5 | HETATM 4 H 0 0.918 0.087 -0.876 H 6 | HETATM 5 H 0 2.345 -0.922 -0.874 H 7 | HETATM 6 C 0 2.701 -1.931 -0.874 C 8 | HETATM 7 H 0 3.771 -1.931 -0.874 H 9 | HETATM 8 H 0 2.345 -2.435 -1.747 H 10 | HETATM 9 H 0 2.345 -2.435 -0.000 H 11 | END 12 | CONECT 1 2 3 4 5 13 | CONECT 2 1 14 | CONECT 3 1 15 | CONECT 4 1 16 | CONECT 5 6 1 17 | CONECT 6 7 5 8 9 18 | CONECT 7 6 19 | CONECT 8 6 20 | CONECT 9 6 21 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/oniom_other.dat: -------------------------------------------------------------------------------- 1 | Nuclear repulsion from inactive atom pairs= -0.6136354905 Hartrees. 2 | Nuclear repulsion from inactive atom pairs= -0.6136354905 Hartrees. 3 | --------------------------------------------- 4 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/only.gjf: -------------------------------------------------------------------------------- 1 | %chk=only.chk 2 | %nproc=2 3 | %mem=1GB 4 | #p ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):pm6)=(EmbedCharge,onlyinputfiles) 5 | nosymm geom=connectivity 6 | 7 | ch2nh2 iop(9/40=20) 8 | 9 | 0 1 0 1 0 1 10 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 12 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 13 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 15 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 16 | 17 | 1 2 1.0 3 1.0 18 | 2 19 | 3 20 | 4 5 1.0 6 1.0 21 | 5 22 | 6 23 | 24 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/onlyinputfiles.gjf: -------------------------------------------------------------------------------- 1 | %chk=onlyinputfiles.chk 2 | %nproc=2 3 | %mem=1GB 4 | #p ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):uff)=(EmbedCharge,onlyinputfiles) iop(9/40=20) 5 | nosymm iop(9/40=20) pop=full 6 | 7 | ch2nh2 8 | 9 | 0 1 0 1 0 1 10 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 12 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 13 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 15 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 16 | 17 | 1 2 1.0 3 1.0 18 | 2 19 | 3 20 | 4 5 1.0 6 1.0 21 | 5 22 | 6 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/qm.dump: -------------------------------------------------------------------------------- 1 | Noting done now. 2 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/qm.gjf: -------------------------------------------------------------------------------- 1 | #P B3LYP/6-31G(D,P) TD(SINGLET,NSTATES=3,ROOT=1) 2 | 3 | ch2nh2 4 | Point 2 -- high level on model system. 5 | 6 | 0,1 7 | O -0.368705030000 -2.194244570000 0.000000000000 8 | H 0.591294970000 -2.194244570000 0.000000000000 9 | H -0.689159620000 -1.289308740000 0.000000000000 10 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/qm_energy.dat: -------------------------------------------------------------------------------- 1 | S0 -61.432896092500 2 | S1 -49.963496092500 3 | S2 -48.308696092500 4 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/qm_gradient.dat: -------------------------------------------------------------------------------- 1 | 2.576683662000 3.069988285000 0.316523606000 2 | 17.261920135000 51.840249247000 40.200889408000 3 | 1.143534304000 -2.896866905000 0.005532205000 4 | 1.360893034000 0.455649557000 1.097806510000 5 | -6.606893666000 -1.213874019000 6.456540821000 6 | -15.736137471000 -51.255146162000 -48.077292550000 7 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/qm_gradient.dat.bak: -------------------------------------------------------------------------------- 1 | 2.576683662000 3.069988285000 0.316523606000 2 | 17.261920135000 51.840249247000 40.200889408000 3 | 1.143534304000 -2.896866905000 0.005532205000 4 | 1.360893034000 0.455649557000 1.097806510000 5 | -6.606893666000 -1.213874019000 6.456540821000 6 | -15.736137471000 -51.255146162000 -48.077292550000 7 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/qm_interface: -------------------------------------------------------------------------------- 1 | The interface between Fortran and Python 2 | Quan-Chem package: 11 1000 3 | ----------------------------------- 4 | Current Geometry 5 | 6 6 | UNIT(au) 7 | O -0.368705030000 -2.194244570000 0.000000000000 8 | H 0.591294970000 -2.194244570000 0.000000000000 9 | H -0.689159620000 -1.289308740000 0.000000000000 10 | O -2.347122270000 0.341726610000 0.000000000000 11 | H -1.387122270000 0.341726610000 0.000000000000 12 | H -2.667576860000 1.246662440000 0.000000000000 13 | ----------------------------------- 14 | Number of atom: 6 15 | Number of states involved in the dynamics: 3 16 | Current state: 1 17 | ~ 18 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/sh: -------------------------------------------------------------------------------- 1 | rwfdump td.chk 635R.dat 635R 2 | rwfdump td.chk 770R.dat 770R 3 | rwfdump td.chk 522R.dat 522R 4 | rwfdump td.chk 524R.dat 524R 5 | 6 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/task: -------------------------------------------------------------------------------- 1 | install numpy in any directory 2 | python setup.py install --prefix=/home/bao/installtest 3 | and 4 | export it in PYTHONPATH env. 5 | 6 | energy to real 7 | 8 | gau_create 9 | gau_overlap 10 | gau_nac 11 | 12 | & 13 | mix 14 | 15 | finally 16 | X+y OR X OR F OR XF 17 | 18 | 19 | how to fix outer layer atoms 20 | 21 | sbmd 22 | lang 23 | frozen.. 24 | etc. 25 | 26 | other task 27 | include 28 | how to qm/mm or oniom 29 | 30 | and so on 31 | 32 | 33 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/GAU_EXAM/gau.gjf: -------------------------------------------------------------------------------- 1 | %chk=gaussian.chk 2 | %mem=1GB 3 | %nproc=2 4 | # force td(singlet, root=2, nstates=3) b3lyp/6-31G** scf=(tight,maxcycle=10000) iop(9/40=20) nosymm 5 | 6 | [0] [0] 7 | 8 | 1 1 9 | c -5.5338175 0.7125130 0.4057093 10 | n -1.4757217 0.1805686 0.1102563 11 | h -6.1187275 1.6438646 2.2895698 12 | h -6.6370856 -0.4341665 -1.0859286 13 | h -0.8548232 -0.9878324 -1.3343232 14 | h -0.4005556 0.8548868 1.6017769 15 | 16 | 17 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/GAU_EXAM/gau_template.gjf: -------------------------------------------------------------------------------- 1 | %chk=oniom.chk 2 | %nproc=2 3 | %mem=1GB 4 | #p force ONIOM(b3lyp/6-31g(d,p) td(singlet,nstates=3,root=1):pm6)=(EmbedCharge,inputfiles) 5 | nosymm geom=connectivity pop=full 6 | 7 | ch2nh2 iop(9/40=20) 8 | 9 | 0 1 0 1 0 1 10 | O-O_3--0.834000 0 -0.36870503 -2.19424457 0.00000000 H 11 | H-H_-0.417000 0 0.59129497 -2.19424457 0.00000000 H 12 | H-H_-0.417000 0 -0.68915962 -1.28930874 0.00000000 H 13 | O-O_3--0.834000 0 -2.34712227 0.34172661 0.00000000 M 14 | H-H_-0.417000 0 -1.38712227 0.34172661 0.00000000 M 15 | H-H_-0.417000 0 -2.66757686 1.24666244 0.00000000 M 16 | 17 | 1 2 1.0 3 1.0 18 | 2 19 | 3 20 | 4 5 1.0 6 1.0 21 | 5 22 | 6 23 | 24 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/GAU_EXAM/template.com: -------------------------------------------------------------------------------- 1 | #n B3LYP/6-31G(d) nosymm iop(2/12=3,3/33=1) guess=only pop=full 2 | 3 | ch2nh2 4 | 5 | 1 1 6 | N -4.42461 2.03755 0.00000 7 | C -2.46682 0.54857 0.00000 8 | H -4.67735 2.26769 -0.96102 9 | H -4.22139 2.88810 0.52504 10 | H -2.69299 -0.33883 -0.55341 11 | H -1.64286 1.05092 -0.46220 12 | 13 | 14 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/dyn.inp: -------------------------------------------------------------------------------- 1 | &control 2 | dyn_method = 2, 3 | ntime = 200, 4 | dtime = 0.2, 5 | ntime_ele = 100, 6 | n_sav_stat = 1, 7 | n_sav_traj = 1, 8 | qm_method = 11, 9 | n_state = 4, 10 | md_state_list = "1, 2, 3", 11 | i_state = 2, 12 | seed_random = -1, 13 | cor_dec = 0.1, 14 | label_nac_phase = 1, 15 | label_reject_hops = 1, 16 | hop_e = 10, 17 | label_read_velocity = 0, 18 | label_restart = 0, 19 | / 20 | 21 | &quantum 22 | qm_method = 11, 23 | qm_package = 1021, 24 | ci_td_use_file_type = "rwf", 25 | ci_assign_problem = "X+Y", 26 | is_do_ci_assignment = "no", 27 | ci_assign_factor = "0.0, 0.0", 28 | / 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/CLA.xyz: -------------------------------------------------------------------------------- 1 | 1 2 | 3 | CL 0.0 -0.0 -0.0 4 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/inp/readme: -------------------------------------------------------------------------------- 1 | build the solvent model 2 | 3 | ch2nh2+ and water 4 | 5 | in a 50 angstrom water box 6 | 7 | 8 | the tutorial of amber 9 | 10 | 11 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/ANTECHAMBER_AC.AC: -------------------------------------------------------------------------------- 1 | CHARGE 1.00 ( 1 ) 2 | Formula: H4 C1 N1 3 | ATOM 1 C1 MOL 1 0.000 0.000 -0.675 0.000000 c2 4 | ATOM 2 H1 MOL 1 0.000 0.944 -1.214 0.000000 h4 5 | ATOM 3 H2 MOL 1 0.000 -0.944 -1.214 0.000000 h4 6 | ATOM 4 N1 MOL 1 0.000 0.000 0.600 0.000000 nh 7 | ATOM 5 H3 MOL 1 0.000 0.867 1.140 0.000000 hn 8 | ATOM 6 H4 MOL 1 0.000 -0.867 1.140 0.000000 hn 9 | BOND 1 1 2 1 C1 H1 10 | BOND 2 1 3 1 C1 H2 11 | BOND 3 1 4 2 C1 N1 12 | BOND 4 4 5 1 N1 H3 13 | BOND 5 4 6 1 N1 H4 14 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/ANTECHAMBER_AC.AC0: -------------------------------------------------------------------------------- 1 | CHARGE 1.00 ( 1 ) 2 | Formula: H4 C1 N1 3 | ATOM 1 C1 MOL 1 0.000 0.000 -0.675 0.000000 C1 4 | ATOM 2 H1 MOL 1 0.000 0.944 -1.214 0.000000 H1 5 | ATOM 3 H2 MOL 1 0.000 -0.944 -1.214 0.000000 H2 6 | ATOM 4 N1 MOL 1 0.000 0.000 0.600 0.000000 N1 7 | ATOM 5 H3 MOL 1 0.000 0.867 1.140 0.000000 H3 8 | ATOM 6 H4 MOL 1 0.000 -0.867 1.140 0.000000 H4 9 | BOND 1 1 2 1 C1 H1 10 | BOND 2 1 3 1 C1 H2 11 | BOND 3 1 4 2 C1 N1 12 | BOND 4 4 5 1 N1 H3 13 | BOND 5 4 6 1 N1 H4 14 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/ANTECHAMBER_BOND_TYPE.AC: -------------------------------------------------------------------------------- 1 | CHARGE 1.00 ( 1 ) 2 | Formula: H4 C1 N1 3 | ATOM 1 C1 MOL 1 0.000 0.000 -0.675 0.000000 C1 4 | ATOM 2 H1 MOL 1 0.000 0.944 -1.214 0.000000 H1 5 | ATOM 3 H2 MOL 1 0.000 -0.944 -1.214 0.000000 H2 6 | ATOM 4 N1 MOL 1 0.000 0.000 0.600 0.000000 N1 7 | ATOM 5 H3 MOL 1 0.000 0.867 1.140 0.000000 H3 8 | ATOM 6 H4 MOL 1 0.000 -0.867 1.140 0.000000 H4 9 | BOND 1 1 2 1 C1 H1 10 | BOND 2 1 3 1 C1 H2 11 | BOND 3 1 4 2 C1 N1 12 | BOND 4 4 5 1 N1 H3 13 | BOND 5 4 6 1 N1 H4 14 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/ANTECHAMBER_BOND_TYPE.AC0: -------------------------------------------------------------------------------- 1 | CHARGE 1.00 ( 1 ) 2 | Formula: H4 C1 N1 3 | ATOM 1 C1 MOL 1 0.000 0.000 -0.675 0.000000 C1 4 | ATOM 2 H1 MOL 1 0.000 0.944 -1.214 0.000000 H1 5 | ATOM 3 H2 MOL 1 0.000 -0.944 -1.214 0.000000 H2 6 | ATOM 4 N1 MOL 1 0.000 0.000 0.600 0.000000 N1 7 | ATOM 5 H3 MOL 1 0.000 0.867 1.140 0.000000 H3 8 | ATOM 6 H4 MOL 1 0.000 -0.867 1.140 0.000000 H4 9 | BOND 1 1 2 0 C1 H1 10 | BOND 2 1 3 0 C1 H2 11 | BOND 3 1 4 0 C1 N1 12 | BOND 4 4 5 0 N1 H3 13 | BOND 5 4 6 0 N1 H4 14 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/ANTECHAMBER_RESP.AC: -------------------------------------------------------------------------------- 1 | CHARGE 1.00 ( 1 ) 2 | Formula: H4 C1 N1 3 | ATOM 1 C1 MOL 1 0.000 0.000 -0.675 0.000000 c2 4 | ATOM 2 H1 MOL 1 0.000 0.944 -1.214 0.000000 h4 5 | ATOM 3 H2 MOL 1 0.000 -0.944 -1.214 0.000000 h4 6 | ATOM 4 N1 MOL 1 0.000 0.000 0.600 0.000000 nh 7 | ATOM 5 H3 MOL 1 0.000 0.867 1.140 0.000000 hn 8 | ATOM 6 H4 MOL 1 0.000 -0.867 1.140 0.000000 hn 9 | BOND 1 1 2 1 C1 H1 10 | BOND 2 1 3 1 C1 H2 11 | BOND 3 1 4 2 C1 N1 12 | BOND 4 4 5 1 N1 H3 13 | BOND 5 4 6 1 N1 H4 14 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/ANTECHAMBER_RESP1.IN: -------------------------------------------------------------------------------- 1 | Resp charges for organic molecule 2 | 3 | &cntrl 4 | 5 | nmol = 1, 6 | ihfree = 1, 7 | ioutopt = 1, 8 | qwt = 0.00050, 9 | 10 | &end 11 | 1.0 12 | Resp charges for organic molecule 13 | 1 6 14 | 6 0 15 | 1 0 16 | 1 0 17 | 7 0 18 | 1 0 19 | 1 5 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/ANTECHAMBER_RESP2.IN: -------------------------------------------------------------------------------- 1 | Resp charges for organic molecule 2 | 3 | &cntrl 4 | 5 | nmol = 1, 6 | ihfree = 1, 7 | ioutopt = 1, 8 | iqopt = 2, 9 | qwt = 0.00100, 10 | 11 | &end 12 | 1.0 13 | Resp charges for organic molecule 14 | 1 6 15 | 6 0 16 | 1 0 17 | 1 2 18 | 7 -99 19 | 1 -99 20 | 1 -99 21 | 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/ch2nh2p.gjf: -------------------------------------------------------------------------------- 1 | %chk=ch2nh2p.chk 2 | # hf/6-31g* SCF=tight Test Pop=MK iop(6/33=2,6/42=6) 3 | 4 | title 5 | 6 | 1 1 7 | C 0.00000000 0.00000000 -0.67488700 8 | H 0.00000000 0.94447800 -1.21366500 9 | H 0.00000000 -0.94447800 -1.21366500 10 | N 0.00000000 0.00000000 0.59963600 11 | H 0.00000000 0.86746400 1.13960000 12 | H 0.00000000 -0.86746400 1.13960000 13 | 14 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/ch2nh2p.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MOL 3 | 6 5 1 0 0 4 | SMALL 5 | resp 6 | 7 | 8 | @ATOM 9 | 1 C1 0.0000 0.0000 -0.6750 c2 1 MOL 0.265141 10 | 2 H1 0.0000 0.9440 -1.2140 h4 1 MOL 0.199609 11 | 3 H2 0.0000 -0.9440 -1.2140 h4 1 MOL 0.199609 12 | 4 N1 0.0000 0.0000 0.6000 nh 1 MOL -0.542005 13 | 5 H3 0.0000 0.8670 1.1400 hn 1 MOL 0.438823 14 | 6 H4 0.0000 -0.8670 1.1400 hn 1 MOL 0.438823 15 | @BOND 16 | 1 1 2 1 17 | 2 1 3 1 18 | 3 1 4 2 19 | 4 4 5 1 20 | 5 4 6 1 21 | @SUBSTRUCTURE 22 | 1 MOL 1 TEMP 0 **** **** 0 ROOT 23 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/punch: -------------------------------------------------------------------------------- 1 | 2 | Resp charges for organic molecule 3 | 4 | iqopt irstrnt ihfree qwt 5 | 2 1 1 0.001000 6 | 7 | rel.rms dipole mom Qxx Qyy Qzz 8 | 0.00696 0.05621 -12.82585 1.82222 11.00363 9 | 10 | Point charges before & after optimization 11 | NO At.No. q0 q(opt) IVARY d(rstr)/dq 12 | 1 6 0.265605 0.265141 0 0.003529 13 | 2 1 0.199377 0.199609 0 0.000000 14 | 3 1 0.199377 0.199609 2 0.000000 15 | 4 7 -0.542005 -0.542005 -99 0.001814 16 | 5 1 0.438823 0.438823 -99 0.000000 17 | 6 1 0.438823 0.438823 -99 0.000000 18 | 19 | Statistics of the fitting: 20 | The initial sum of squares (ssvpot) 82.048 21 | The residual sum of squares (chipot) 0.004 22 | The std err of estimate (sqrt(chipot/N)) 0.00121 23 | ESP relative RMS (SQRT(chipot/ssvpot)) 0.00696 24 | 25 | Dipole Moment (Debye)= 0.05621 26 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/readme: -------------------------------------------------------------------------------- 1 | 2 | ESP input for gaussian 3 | 4 | # hf/6-31g* SCF=tight Test Pop=MK iop(6/33=2,6/42=6) 5 | 6 | ----------------- 7 | 8 | use gaussian 09 9 | antechamber -i ch2nh2p.log -fi gout -o ch2nh2p.mol2 -fo mol2 -c resp 10 | 11 | ---------------- 12 | 13 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/amber/parms/solute.pdb: -------------------------------------------------------------------------------- 1 | HEADER 2 | HETATM 1 C 2 2 0.000 0.000 -0.675 3 | HETATM 2 H 2 2 0.000 0.944 -1.214 4 | HETATM 3 H 2 2 0.000 -0.944 -1.214 5 | HETATM 4 N 2 2 0.000 0.000 0.600 6 | HETATM 5 H 2 2 0.000 0.867 1.140 7 | HETATM 6 H 2 2 0.000 -0.867 1.140 8 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/ch2nh2p.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | 3 | C 0.00000000 0.00000000 -0.67488700 4 | H 0.00000000 0.94447800 -1.21366500 5 | H 0.00000000 -0.94447800 -1.21366500 6 | N 0.00000000 0.00000000 0.59963600 7 | H 0.00000000 0.86746400 1.13960000 8 | H 0.00000000 -0.86746400 1.13960000 9 | 10 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/dye.doc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/interface_gaussian_oniom/test/model/dye.doc -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/example/mixture.inp: -------------------------------------------------------------------------------- 1 | # 2 | # A mixture of water and urea 3 | # 4 | 5 | tolerance 2.0 6 | filetype pdb 7 | output mixture.pdb 8 | 9 | structure water.pdb 10 | number 1000 11 | inside box 0. 0. 0. 40. 40. 40. 12 | end structure 13 | 14 | structure urea.pdb 15 | number 400 16 | inside box 0. 0. 0. 40. 40. 40. 17 | end structure 18 | 19 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/example/urea.pdb: -------------------------------------------------------------------------------- 1 | HEADER 2 | HETATM 1 C 2 2 0.000 0.000 1.400 3 | HETATM 2 N 2 2 -1.256 0.000 2.125 4 | HETATM 3 O 2 2 0.000 0.000 0.000 5 | HETATM 4 N 2 2 1.256 0.000 2.125 6 | HETATM 5 H 2 2 1.072 0.000 3.116 7 | HETATM 6 H 2 2 2.252 0.000 1.968 8 | HETATM 7 H 2 2 -1.072 0.000 3.116 9 | HETATM 8 H 2 2 -2.252 0.000 1.968 10 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/example/water.pdb: -------------------------------------------------------------------------------- 1 | HEADER water 2 | COMPND 3 | SOURCE 4 | HETATM 1 H HOH 1 9.626 6.787 12.673 5 | HETATM 2 H HOH 1 9.626 8.420 12.673 6 | HETATM 3 O HOH 1 10.203 7.604 12.673 7 | CONECT 1 3 8 | CONECT 2 3 9 | CONECT 3 1 2 10 | END 11 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/h2o.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | 3 | O -0.08715895 -0.24618189 -0.03121262 4 | H 0.87284105 -0.24618189 -0.03121262 5 | H -0.40761354 0.65875394 -0.03121262 6 | 7 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/opt/ch2nh2p.gjf: -------------------------------------------------------------------------------- 1 | %chk=gau.chk 2 | # opt cam-b3lyp/6-31g(d) geom=connectivity 3 | 4 | Title Card Required 5 | 6 | 1 1 7 | C 0.25939641 0.27083596 0.00000000 8 | H 0.79536859 -0.65524925 0.00000000 9 | H -0.81060300 0.26971305 0.00000000 10 | N 0.90502036 1.39180460 0.00000000 11 | H 1.90501981 1.39285405 0.00000000 12 | H 0.40411179 2.25730480 0.00000000 13 | 14 | 1 2 1.0 3 1.0 4 2.0 15 | 2 16 | 3 17 | 4 5 1.0 6 1.0 18 | 5 19 | 6 20 | 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/opt/ch2nh2p.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | 3 | C 0.00000000 0.00000000 -0.67488700 4 | H 0.00000000 0.94447800 -1.21366500 5 | H 0.00000000 -0.94447800 -1.21366500 6 | N 0.00000000 0.00000000 0.59963600 7 | H 0.00000000 0.86746400 1.13960000 8 | H 0.00000000 -0.86746400 1.13960000 9 | 10 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/opt/h2o.gjf: -------------------------------------------------------------------------------- 1 | %chk=G:\tree\Gitlib\jade\src\ci_overlap\interface_gaussian_oniom\test\model\opt\h2o.chk 2 | # hf/3-21g geom=connectivity 3 | 4 | Title Card Required 5 | 6 | 0 1 7 | O -0.08715895 -0.24618189 -0.03121262 8 | H 0.87284105 -0.24618189 -0.03121262 9 | H -0.40761354 0.65875394 -0.03121262 10 | 11 | 1 2 1.0 3 1.0 12 | 2 13 | 3 14 | 15 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/opt/h2o.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | 3 | O -0.08715895 -0.24618189 -0.03121262 4 | H 0.87284105 -0.24618189 -0.03121262 5 | H -0.40761354 0.65875394 -0.03121262 6 | 7 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/opt/opted.gjf: -------------------------------------------------------------------------------- 1 | %chk=G:\tree\Gitlib\jade\src\ci_overlap\interface_gaussian_oniom\test\model\opt\gau.chk 2 | # opt cam-b3lyp/6-31g(d) geom=connectivity 3 | 4 | Title Card Required 5 | 6 | 1 1 7 | C 0.00000000 0.00000000 -0.67488700 8 | H 0.00000000 0.94447800 -1.21366500 9 | H 0.00000000 -0.94447800 -1.21366500 10 | N 0.00000000 0.00000000 0.59963600 11 | H 0.00000000 0.86746400 1.13960000 12 | H 0.00000000 -0.86746400 1.13960000 13 | 14 | 1 2 1.0 3 1.0 4 2.0 15 | 2 16 | 3 17 | 4 5 1.0 6 1.0 18 | 5 19 | 6 20 | 21 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/solute.pdb: -------------------------------------------------------------------------------- 1 | HEADER 2 | HETATM 1 C 2 2 0.000 0.000 -0.675 3 | HETATM 2 H 2 2 0.000 0.944 -1.214 4 | HETATM 3 H 2 2 0.000 -0.944 -1.214 5 | HETATM 4 N 2 2 0.000 0.000 0.600 6 | HETATM 5 H 2 2 0.000 0.867 1.140 7 | HETATM 6 H 2 2 0.000 -0.867 1.140 8 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/sphere.inp: -------------------------------------------------------------------------------- 1 | # 2 | # Protein solvated by water and ions 3 | # 4 | 5 | tolerance 2.5 6 | 7 | filetype pdb 8 | 9 | structure solute.pdb 10 | number 1 11 | fixed 0. 0. 0. 0. 0. 0. 12 | centerofmass 13 | end structure 14 | 15 | structure water.pdb 16 | number 4000 17 | inside sphere 0. 0. 0. 35. 18 | end structure 19 | 20 | 21 | output mix.pdb 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/test/model/water.pdb: -------------------------------------------------------------------------------- 1 | HEADER 2 | HETATM 1 O 2 2 -0.087 -0.246 -0.031 3 | HETATM 2 H 2 2 0.873 -0.246 -0.031 4 | HETATM 3 H 2 2 -0.408 0.659 -0.031 5 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_oniom/tutorial: -------------------------------------------------------------------------------- 1 | model builder 2 | 3 | 1. use vmd or packmol to generate the model of the system. 4 | I suggested to use packmol for solvent model 5 | 6 | in chinese 7 | http://simulation.haotui.com/viewthread.php?tid=34723 8 | 9 | see 10 | http://www.ime.unicamp.br/~martinez/packmol/ 11 | 12 | input-file: 13 | ------------------------------------- 14 | tolerance 2.0 15 | 16 | filetype pdb 17 | 18 | structure solute.pdb 19 | number 1 20 | fixed 0. 0. 0. 0. 0. 0. 21 | centerofmass 22 | end structure 23 | 24 | structure water.pdb 25 | number 16000 26 | inside sphere 0. 0. 0. 50. 27 | end structure 28 | 29 | 30 | output mix.pdb 31 | 32 | ------------------------------------- 33 | rho = m/v = M*NA*n / v 34 | v = (4/3) * pi * R^3 35 | mix.pdb 36 | 37 | ==================================== 38 | 39 | 40 | HOW TO DEAL WITH ONIOM MODEL 41 | 42 | 1. MODEL BUILDER 43 | PACKMOL IS OK 44 | 45 | 2. PARAMETER SETS 46 | HOW? SCRIPTS? TAO? 47 | 48 | 3. HOW TO FIX ATOMS 49 | 50 | 51 | 4. HOW TO RUN ADMP 52 | 53 | 5. HOW TO ANALYZE MD RESULTS 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_qm/.gitignore: -------------------------------------------------------------------------------- 1 | # 2 | test 3 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_qm/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from gau_template import * 4 | from gau_create import * 5 | from gau_parser import * 6 | from gau_zero import * 7 | from gau_nonzero import * 8 | from gau_overlap import * 9 | from gau_nac import * 10 | 11 | __all__ = ["gau_template", "gau_create", "gau_parser", "gau_zero", "gau_nonzero", "gau_overlap", "gau_nac"] 12 | 13 | 14 | 15 | __revision__ = "$Revision: 0 $" 16 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_qm/config.in: -------------------------------------------------------------------------------- 1 | { 2 | "root": "./", 3 | "dirs": { 4 | "home": "QC_TMP", 5 | "work": "GAU_TMP", 6 | "work_prev": "GAU_TMP_PREV", 7 | "overlap": "OVERLAP", 8 | "template": "GAU_EXAM", 9 | "nac": "NAC" 10 | }, 11 | "files": { 12 | "dyn": "inp.json", 13 | "interface": "interface.json", 14 | "template": "template.json", 15 | "gau_template": "gau_template.gjf", 16 | "gau_log": "gaussian.log", 17 | "gau_chk": "gaussian.chk", 18 | "gau_input": "gaussian.gjf", 19 | "dimension": "dimension.json" 20 | }, 21 | "command": { 22 | "gaussian": "g16" 23 | } 24 | 25 | } 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_qm/details.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/interface_gaussian_qm/details.tex -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_qm/rwfdump.txt: -------------------------------------------------------------------------------- 1 | rwfdump td.chk 635R.dat 635R 2 | rwfdump td.chk 770R.dat 770R 3 | rwfdump td.chk 522R.dat 522R 4 | rwfdump td.chk 524R.dat 524R 5 | 6 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/0.gjf: -------------------------------------------------------------------------------- 1 | %chk=gaussian.chk 2 | %mem=1GB 3 | %nproc=2 4 | # b3lyp/ChkBasis scf=(tight,maxcycle=10000) iop(9/40=20) nosymm geom=AllCheck Guess=Read 5 | 6 | [0] [0] 7 | 8 | 1 1 9 | n -2.3414018 1.0782246 0.0000000 10 | c -1.3053844 0.2902906 0.0000000 11 | h -2.4751460 1.2000094 -0.5085497 12 | h -2.2338625 1.5283161 0.2778391 13 | h -1.4250684 -0.1793010 -0.2928518 14 | h -0.8693637 0.5561227 -0.2445856 15 | 16 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/1.gjf: -------------------------------------------------------------------------------- 1 | %chk=gaussian.chk 2 | %mem=1GB 3 | %nproc=2 4 | # b3lyp/ChkBasis scf=(tight,maxcycle=10000) iop(9/40=20) nosymm geom=AllCheck Guess=Read 5 | 6 | [0] [0] 7 | 8 | 1 3 9 | n -2.3414018 1.0782246 0.0000000 10 | c -1.3053844 0.2902906 0.0000000 11 | h -2.4751460 1.2000094 -0.5085497 12 | h -2.2338625 1.5283161 0.2778391 13 | h -1.4250684 -0.1793010 -0.2928518 14 | h -0.8693637 0.5561227 -0.2445856 15 | 16 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/2.gjf: -------------------------------------------------------------------------------- 1 | %chk=gaussian.chk 2 | %mem=1GB 3 | %nproc=2 4 | # b3lyp/6-31G** scf=(tight,maxcycle=10000) iop(9/40=20) nosymm force geom=AllCheck Guess=Read 5 | 6 | [0] [0] 7 | 8 | 1 5 9 | n -2.3414018 1.0782246 0.0000000 10 | c -1.3053844 0.2902906 0.0000000 11 | h -2.4751460 1.2000094 -0.5085497 12 | h -2.2338625 1.5283161 0.2778391 13 | h -1.4250684 -0.1793010 -0.2928518 14 | h -0.8693637 0.5561227 -0.2445856 15 | 16 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/CONSTANT.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | 3 | 4 | AU2ANGSTROM = 0.529177 -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/GAU_EXAM/gau_template.gjf: -------------------------------------------------------------------------------- 1 | %chk=gaussian.chk 2 | %mem=1GB 3 | %nproc=2 4 | # force b3lyp/6-31G** scf=(tight,maxcycle=10000) iop(9/40=20) nosymm 5 | 6 | [0] [0] 7 | 8 | 1 1 9 | c -5.5338175 0.7125130 0.4057093 10 | n -1.4757217 0.1805686 0.1102563 11 | h -6.1187275 1.6438646 2.2895698 12 | h -6.6370856 -0.4341665 -1.0859286 13 | h -0.8548232 -0.9878324 -1.3343232 14 | h -0.4005556 0.8548868 1.6017769 15 | 16 | 17 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/GAU_EXAM/template.com: -------------------------------------------------------------------------------- 1 | #n B3LYP/6-31G(d) nosymm iop(2/12=3,3/33=1) guess=only pop=full 2 | 3 | ch2nh2 4 | 5 | 1 1 6 | N -4.42461 2.03755 0.00000 7 | C -2.46682 0.54857 0.00000 8 | H -4.67735 2.26769 -0.96102 9 | H -4.22139 2.88810 0.52504 10 | H -2.69299 -0.33883 -0.55341 11 | H -1.64286 1.05092 -0.46220 12 | 13 | 14 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/Parser.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from logParser import * 4 | 5 | # gaussian parser 6 | 7 | class Parser(): 8 | def __init__(self, config = {}): 9 | """ 10 | parser gaussian log or chk or rwf files to extract relevant data. 11 | """ 12 | self.config = config 13 | 14 | self.file_type = "log" 15 | 16 | return 17 | 18 | def get(self): 19 | """ parser gaussian output """ 20 | log = logParser(self.config) 21 | log.check_calc() 22 | log.get_dim_info() 23 | log.get_energy() 24 | log.get_gradient() 25 | log.get_geom() 26 | log.get_other() 27 | return 28 | 29 | # main program 30 | if __name__ == "__main__": 31 | par = Parser() 32 | par.get() 33 | 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from Template import * 4 | from createInp import * 5 | from setupEnv import * 6 | from ffRunner import * 7 | from Parser import * 8 | from goStep import * 9 | from Gaussian import * 10 | 11 | __all__ = ["Template", "createInp", "setupEnv", "ffRunner", "Parser", "goStep", "Gaussian"] 12 | 13 | 14 | 15 | __revision__ = "$Revision: 0.1 $" 16 | 17 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/check.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | 3 | C -5.53381800 0.71251300 0.40570900 4 | N -1.47572200 0.18056900 0.11025600 5 | H -6.11872800 1.64386500 2.28957000 6 | H -6.63708600 -0.43416700 -1.08592900 7 | H -0.85482300 -0.98783200 -1.33432300 8 | H -0.40055600 0.85488700 1.60177700 9 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/config.in: -------------------------------------------------------------------------------- 1 | { 2 | "root": "./", 3 | "dirs": { 4 | "home": "QC_TMP", 5 | "work": "GAU_TMP", 6 | "work_prev": "GAU_TMP_PREV", 7 | "overlap": "OVERLAP", 8 | "template": "GAU_EXAM", 9 | "nac": "NAC" 10 | }, 11 | "files": { 12 | "dyn": "inp.json", 13 | "interface": "interface.json", 14 | "template": "template.json", 15 | "inp_template": "gau_template.gjf", 16 | "log": "gaussian.log", 17 | "chk": "gaussian.chk", 18 | "inp": "gaussian.gjf", 19 | "dimension": "dimension.json" 20 | }, 21 | "command": { 22 | "gaussian": "g09" 23 | } 24 | 25 | } 26 | 27 | 28 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/dimension.json: -------------------------------------------------------------------------------- 1 | { 2 | "n_col": 5, 3 | "n_active": 6, 4 | "n_atom": 6 5 | } -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/filelist.dat: -------------------------------------------------------------------------------- 1 | [ 2 | "2.gjf", 3 | "1.gjf", 4 | "0.gjf" 5 | ] -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/gaussian.gjf: -------------------------------------------------------------------------------- 1 | %chk=gaussian.chk 2 | %mem=1GB 3 | %nproc=2 4 | # b3lyp/6-31G** scf=(tight,maxcycle=10000) iop(9/40=20) nosymm 5 | 6 | [0] [0] 7 | 8 | 1 3 9 | n -2.3414018 1.0782246 0.0000000 10 | c -1.3053844 0.2902906 0.0000000 11 | h -2.4751460 1.2000094 -0.5085497 12 | h -2.2338625 1.5283161 0.2778391 13 | h -1.4250684 -0.1793010 -0.2928518 14 | h -0.8693637 0.5561227 -0.2445856 15 | 16 | --LINK1-- 17 | %chk=gaussian.chk 18 | %mem=1GB 19 | %nproc=2 20 | # force b3lyp/6-31G** scf=(tight,maxcycle=10000) iop(9/40=20) nosymm geom=AllCheck Guess=Read 21 | 22 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/inp.json: -------------------------------------------------------------------------------- 1 | { 2 | "control": { 3 | "n_sav_stat": "1", 4 | "hop_e": "10", 5 | "label_nac_phase": "1", 6 | "label_reject_hops": "1", 7 | "dtime": "0.2", 8 | "i_state": "3", 9 | "cor_dec": "0.1", 10 | "md_state_list": "1 2 3", 11 | "label_restart": "0", 12 | "dyn_method": "2", 13 | "n_state": "3", 14 | "seed_random": "-1", 15 | "ntime_ele": "100", 16 | "label_read_velocity": "0", 17 | "qm_method": "11", 18 | "ntime": "200", 19 | "n_sav_traj": "1" 20 | }, 21 | "quantum": { 22 | "ci_td_use_file_type": "log", 23 | "ci_assign_problem": "X", 24 | "is_do_cis_casida": "no", 25 | "qm_method": "11", 26 | "qm_package": "102" 27 | } 28 | } 29 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/lists.txt: -------------------------------------------------------------------------------- 1 | gau_template 2 | gau_create 3 | gau_log_parser 4 | 5 | gau_zero 6 | gau_nonzero 7 | gau_overlap 8 | 9 | gau_nac 10 | 11 | gaussian 12 | 13 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/qm.dump: -------------------------------------------------------------------------------- 1 | Noting done now. 2 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/qm_energy.dat: -------------------------------------------------------------------------------- 1 | # energy (a.u.) 2 | -94.070865795500 3 | -94.070865795500 4 | -94.070865795500 5 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/readme: -------------------------------------------------------------------------------- 1 | dir in base 2 | cp file in Gau 3 | 4 | nocc nvir nbf should dumped 5 | 6 | read rwf for data. 7 | %rwf=td.rwf 8 | # force 9 | 10 | read punch for data. fort.7 11 | force punch=(Coord, Derivatives, MO, Archive) 12 | 13 | read PES.out 14 | op(7/32=3,9/40=20) 15 | 16 | gaussian gradient: 17 | only force is give in log file, use -force to get gradient. 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /src/electronic/interface_gaussian_spin/soc.dat: -------------------------------------------------------------------------------- 1 | 0.000000000000e+00 4.556337025517e-04 4.556337025517e-04 2 | 4.556337025517e-04 0.000000000000e+00 4.556337025517e-04 3 | 4.556337025517e-04 4.556337025517e-04 0.000000000000e+00 4 | -------------------------------------------------------------------------------- /src/electronic/interface_general_qm/README: -------------------------------------------------------------------------------- 1 | turbomole interface 2 | 3 | -------------------------------------------------------------------------------- /src/electronic/interface_general_qm/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/interface_general_qm/__init__.py -------------------------------------------------------------------------------- /src/electronic/interface_general_qm/general.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/interface_general_qm/general.py -------------------------------------------------------------------------------- /src/electronic/interface_mndo_qm/.gitignore: -------------------------------------------------------------------------------- 1 | # 2 | test 3 | -------------------------------------------------------------------------------- /src/electronic/interface_mndo_qm/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from mndo_template import * 4 | from mndo_create import * 5 | from mndo_parser import * 6 | from mndo_run import * 7 | 8 | __all__ = ["mndo_template", "mndo_create", "mndo_parser", "mndo_run"] 9 | 10 | __revision__ = "$Revision: 0 $" 11 | -------------------------------------------------------------------------------- /src/electronic/interface_mndo_qm/config.in: -------------------------------------------------------------------------------- 1 | { 2 | "root": "./", 3 | "dirs": { 4 | "home": "QC_TMP", 5 | "work": "MNDO_TMP", 6 | "template": "MNDO_EXAM" 7 | }, 8 | "files": { 9 | "dyn": "inp.json", 10 | "interface": "interface.json", 11 | "template": "template.json", 12 | "map": "imomap.dat", 13 | "mndo_template": "mndo_template.inp", 14 | "mndo_log": "mndo.log", 15 | "mndo_fort": "fort.15", 16 | "mndo_input": "mndo.inp" 17 | }, 18 | "command": { 19 | "mndo": "mndo99" 20 | } 21 | 22 | } 23 | 24 | -------------------------------------------------------------------------------- /src/electronic/interface_mndo_qm/mndo_parser.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from mndo_log_parser import * 4 | 5 | # mndo parser 6 | 7 | 8 | class mndo_parser(): 9 | def __init__(self, config={}): 10 | """ 11 | parser mndo log or fort files to extract relevant data. 12 | """ 13 | self.config = config 14 | 15 | return 16 | 17 | def get_log_dat(self): 18 | """ 19 | parse one tddft calculation result. 20 | """ 21 | log = mndo_log_parser(self.config) 22 | 23 | # forces 24 | log.get_energy() 25 | log.get_gradient() 26 | log.get_nac() 27 | log.collect_qm() 28 | 29 | return 30 | -------------------------------------------------------------------------------- /src/electronic/interface_molpro_qm/.gitignore: -------------------------------------------------------------------------------- 1 | # 2 | test 3 | -------------------------------------------------------------------------------- /src/electronic/interface_molpro_qm/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from molpro_create import * 4 | from molpro_parser import * 5 | from molpro_run import * 6 | from molpro_template import * 7 | 8 | __all__ = ["molpro_template", "molpro_create", "molpro_parser", "molpro_run"] 9 | 10 | __revision__ = "$Revision: 0 $" 11 | -------------------------------------------------------------------------------- /src/electronic/interface_molpro_qm/config.in: -------------------------------------------------------------------------------- 1 | { 2 | "root": "./", 3 | "dirs": { 4 | "home": "QC_TMP", 5 | "work": "MOLPRO_TMP", 6 | "template": "MOLPRO_EXAM" 7 | }, 8 | "files": { 9 | "dyn": "inp.json", 10 | "interface": "interface.json", 11 | "template": "template.json", 12 | "molpro_template": "molpro_template.inp", 13 | "molpro_log": "molpro.log", 14 | "molpro_wfu": "wfu", 15 | "molpro_input": "molpro.inp" 16 | }, 17 | "command": { 18 | "molpro": "molpro" 19 | } 20 | 21 | } 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_molpro_qm/molpro_parser.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from molpro_log_parser import * 4 | 5 | # mndo parser 6 | 7 | 8 | class molpro_parser(): 9 | def __init__(self, config={}): 10 | """ 11 | parser mndo log or fort files to extract relevant data. 12 | """ 13 | self.config = config 14 | 15 | return 16 | 17 | def get_log_dat(self): 18 | """ 19 | parse one tddft calculation result. 20 | """ 21 | log = molpro_log_parser(self.config) 22 | 23 | # forces 24 | log.get_energy() 25 | log.get_gradient() 26 | log.get_nac() 27 | log.collect_qm() 28 | 29 | return 30 | -------------------------------------------------------------------------------- /src/electronic/interface_qchem_qm/.gitignore: -------------------------------------------------------------------------------- 1 | # 2 | test 3 | -------------------------------------------------------------------------------- /src/electronic/interface_qchem_qm/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python2 2 | 3 | from qchem_create import * 4 | from qchem_parser import * 5 | from qchem_run import * 6 | from qchem_template import * 7 | 8 | __all__ = ["qchem_template", "qchem_create", "qchem_parser", "qchem_run"] 9 | 10 | __revision__ = "$Revision: 0 $" 11 | -------------------------------------------------------------------------------- /src/electronic/interface_qchem_qm/config.in: -------------------------------------------------------------------------------- 1 | { 2 | "root": "./", 3 | "dirs": { 4 | "home": "QC_TMP", 5 | "work": "QCHEM_TMP", 6 | "template": "QCHEM_EXAM" 7 | }, 8 | "files": { 9 | "dyn": "inp.json", 10 | "interface": "interface.json", 11 | "template": "template.json", 12 | "qchem_template": "qchem_template.inp", 13 | "qchem_log": "qchem.log", 14 | "qchem_wfu": "save", 15 | "qchem_input": "qchem.inp" 16 | }, 17 | "command": { 18 | "qchem": "qchem" 19 | } 20 | 21 | } 22 | 23 | -------------------------------------------------------------------------------- /src/electronic/interface_qchem_qm/qchem_parser.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | from qchem_log_parser import * 4 | 5 | # mndo parser 6 | 7 | 8 | class qchem_parser(): 9 | def __init__(self, config={}): 10 | """ 11 | parser mndo log or fort files to extract relevant data. 12 | """ 13 | self.config = config 14 | 15 | return 16 | 17 | def get_log_dat(self): 18 | """ 19 | parse one tddft calculation result. 20 | """ 21 | log = qchem_log_parser(self.config) 22 | 23 | # forces 24 | log.get_energy() 25 | log.get_gradient() 26 | log.get_nac() 27 | log.collect_qm() 28 | log.get_other() 29 | 30 | return 31 | -------------------------------------------------------------------------------- /src/electronic/interface_turbomole_qm/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | import turbomole 4 | 5 | __all__ = ['turbomole'] 6 | 7 | -------------------------------------------------------------------------------- /src/electronic/interface_turbomole_qm/readme: -------------------------------------------------------------------------------- 1 | 2 | call worker 3 | tur_zero.py 4 | tur_nonzero.py 5 | 6 | ci_hyb use x+y 7 | other use x 8 | without casida assignment 9 | -------------------------------------------------------------------------------- /src/electronic/main_overlap_slater.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/main_overlap_slater.exe -------------------------------------------------------------------------------- /src/electronic/overlap/main_overlap_slater.a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/overlap/main_overlap_slater.a -------------------------------------------------------------------------------- /src/electronic/overlap/main_overlap_slater.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/overlap/main_overlap_slater.exe -------------------------------------------------------------------------------- /src/electronic/readme: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/electronic/readme -------------------------------------------------------------------------------- /src/electronic/tools/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | from namelist import * 3 | from tools import * 4 | from periodictable import * 5 | 6 | __all__ = ["namelist", "tools", "periodictable"] 7 | -------------------------------------------------------------------------------- /src/electronic/tools/nma.inp: -------------------------------------------------------------------------------- 1 | &control 2 | n_sav_stat = 1, 3 | hop_e = 10, 4 | label_nac_phase = 1, 5 | label_reject_hops = 1, 6 | dtime = 0.2, 7 | i_state = 3, 8 | cor_dec = 0.1, 9 | md_state_list = 1, 2, 3 , 10 | label_restart = 0, 11 | dyn_method = 2, 12 | n_state = 3, 13 | seed_random = -1, 14 | ntime_ele = 100, 15 | label_read_velocity = 0, 16 | qm_method = 11, 17 | ntime = 200, 18 | n_sav_traj = 1, 19 | / 20 | &quantum 21 | ci_td_use_file_type = log , 22 | ci_assign_problem = X+Y , 23 | is_do_cis_casida = yes , 24 | qm_method = 11, 25 | qm_package = 102, 26 | / 27 | -------------------------------------------------------------------------------- /src/electronic/tools/test.py: -------------------------------------------------------------------------------- 1 | 2 | fp = open("elements.dat", "r") 3 | line = fp.readline() 4 | line = fp.readline() 5 | n_line = int(line) 6 | line = fp.readline() 7 | 8 | for i in xrange(n_line): 9 | line = fp.readline() 10 | rec = line.split() 11 | atom_name = rec[0] 12 | atom_mass = rec[4] 13 | print "'"+atom_name.upper()+"'"+": ", atom_mass, ",", 14 | if i % 3 == 2: 15 | print "\n ", 16 | 17 | fp.close() 18 | 19 | 20 | -------------------------------------------------------------------------------- /src/krr/0_prepare.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | 4 | import os 5 | 6 | import sub_inp_json 7 | 8 | filename = 'fitting.input' 9 | xxx = sub_inp_json.read_dat_with_label(filename) 10 | sub_inp_json.dump_json('input_initial.json', xxx) 11 | 12 | os.system('cp input_initial.json ../input_initial.json') 13 | -------------------------------------------------------------------------------- /src/krr/README.md: -------------------------------------------------------------------------------- 1 | # TSH-ML 2 | trajectory surface hopping with machine learning 3 | 4 | Main Contributors at the current stage 5 | Deping Hu (hudp@qibebt.ac.cn) Zhenggang Lan* (lanzg@qibebt.ac.cn) Yu Xie (xieyu@qibebt.ac.cn) Xusong Li (lixs@qibebt.ac.cn) 6 | 7 | 8 | TSH-ML package reference: 9 | 10 | Deping Hu, Yu Xie, Xusong Li, Lingyue Li, Zhenggang Lan*, Inclusion of Machine Learning Kernel Ridge Regression Potential Energy Surfaces in On-the-Fly Nonadiabatic Molecular Dynamics Simulation, Journal of Physical Chemistry Letters, 2018, 9, 2725−2732 11 | -------------------------------------------------------------------------------- /src/krr/molpro_log_gradient.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import re 4 | 5 | n_state = 3 6 | 7 | logfile = "cas.out" 8 | file_in = open(logfile, "r") 9 | 10 | pattern = re.compile("SA-MC GRADIENT FOR STATE") 11 | 12 | 13 | line = "NOT EMPTY LINE" 14 | for i_state in range(n_state): 15 | file_out = open("qm_gradient.dat_S" + str(i_state), "w") 16 | while line != "": 17 | line = file_in.readline() 18 | m = pattern.search(line) 19 | if m is not None: 20 | break 21 | 22 | line = file_in.readline() 23 | line = file_in.readline() 24 | line = file_in.readline() 25 | 26 | while line != "": 27 | line = file_in.readline() 28 | if line.strip() == "": 29 | break 30 | 31 | record = line.split() 32 | 33 | grad_x = float(record[1]) 34 | grad_y = float(record[2]) 35 | grad_z = float(record[3]) 36 | 37 | file_out.write('' + str(grad_x) + ' ' + \ 38 | str(grad_y) + ' ' + str(grad_z) + ' \n') 39 | file_out.close() 40 | file_in.close() 41 | -------------------------------------------------------------------------------- /src/krr/sub_copy_additional_test_data.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | 5 | 6 | def copy_geom_energy(n_traj): 7 | for i in range(1, n_traj + 1): 8 | tmp_dir = str(i) 9 | if os.path.exists(tmp_dir): 10 | command1 = 'rm -r ' + str(i) 11 | os.system(command1) 12 | command2 = 'mkdir ' + str(i) 13 | os.system(command2) 14 | command3 = "cp ../data_prescreening/" + str(i) + '/pe_time_aferselect_afterscale.out ./' + str(i) 15 | os.system(command3) 16 | command4 = "cp ../data_prescreening/" + str(i) + '/sample.xyz* ./' + str(i) 17 | os.system(command4) 18 | 19 | 20 | def data_copy(): 21 | n_traj = 100 22 | copy_geom_energy(n_traj) 23 | 24 | 25 | if __name__ == "__main__": 26 | data_copy() 27 | -------------------------------------------------------------------------------- /src/krr/sub_energy_rescale.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import numpy as np 4 | import os 5 | 6 | 7 | def scale_energy(file_energy_input, energy_zero, scaling_factor, file_energy_output, n_y_dim): 8 | en = np.loadtxt(file_energy_input) 9 | n_dim = en.ndim 10 | if n_dim == 1: 11 | if n_dim != n_y_dim: 12 | # print "A" 13 | print("Check the dimension of y: n_y_dim and energy") 14 | raise IOError 15 | else: 16 | # print "B" 17 | n_points = en.shape[0] 18 | n_state = n_dim 19 | else: 20 | n_points = en.shape[0] 21 | n_state = en.shape[1] 22 | en = en.reshape(n_points, n_state) 23 | en_new = (en - energy_zero) * scaling_factor 24 | np.savetxt(file_energy_output, en_new) 25 | 26 | 27 | def scale_energy_many(n_traj, energy_zero, scaling_factor, n_y_dim): 28 | curr_dir = os.getcwd() 29 | for i_traj in range(1, n_traj + 1): 30 | os.chdir(str(i_traj)) 31 | file_energy_input = "pe_time_aferselect.out" 32 | file_energy_output = "pe_time_aferselect_afterscale.out" 33 | scale_energy(file_energy_input, energy_zero, scaling_factor, file_energy_output, n_y_dim) 34 | os.chdir(curr_dir) 35 | -------------------------------------------------------------------------------- /src/potential/README: -------------------------------------------------------------------------------- 1 | mainly about analytical potential function 2 | 3 | 4 | -------------------------------------------------------------------------------- /src/potential/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | 3 | 4 | 5 | -------------------------------------------------------------------------------- /src/potential/constraints/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | ## from gau_template import * 4 | 5 | 6 | __all__ = ["gau_template", "gau_create", "gau_parser", "gau_zero", "gau_nonzero", "gau_overlap", "gau_nac"] 7 | 8 | 9 | 10 | __revision__ = "$Revision: 0 $" 11 | 12 | 13 | -------------------------------------------------------------------------------- /src/potential/constraints/cons_atom_id: -------------------------------------------------------------------------------- 1 | 3 4 5 2 | -------------------------------------------------------------------------------- /src/potential/constraints/cons_energy.dat: -------------------------------------------------------------------------------- 1 | 180.000000000000 2 | -------------------------------------------------------------------------------- /src/potential/constraints/cons_gradient.dat: -------------------------------------------------------------------------------- 1 | 600.000000000000 0.000000000000 0.000000000000 2 | 600.000000000000 0.000000000000 0.000000000000 3 | 0.000000000000 0.000000000000 0.000000000000 4 | 0.000000000000 0.000000000000 0.000000000000 5 | 0.000000000000 0.000000000000 0.000000000000 6 | 0.000000000000 0.000000000000 0.000000000000 7 | -------------------------------------------------------------------------------- /src/potential/constraints/curr_coord: -------------------------------------------------------------------------------- 1 | 6 2 | 3 | c -5.2338175 0.7125130 0.4057093 -1 -1 -1 4 | n -1.1757217 0.1805686 0.1102563 -1 -1 -1 5 | h -6.1187275 1.6438646 2.2895698 0 0 0 6 | h -6.6370856 -0.4341665 -1.0859286 0 0 0 7 | h -0.8548232 -0.9878324 -1.3343232 0 0 0 8 | h -0.4005556 0.8548868 1.6017769 0 0 0 9 | 10 | -------------------------------------------------------------------------------- /src/potential/constraints/ref.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | 3 | c -5.53381750 0.71251300 0.40570930 -1 -1 -1 4 | n -1.47572170 0.18056860 0.11025630 -1 -1 -1 5 | h -6.11872750 1.64386460 2.28956980 -1 -1 -1 6 | h -6.63708560 -0.43416650 -1.08592860 -1 -1 -1 7 | h -0.85482320 -0.98783240 -1.33432320 -1 -1 -1 8 | h -0.40055560 0.85488680 1.60177690 -1 -1 -1 9 | -------------------------------------------------------------------------------- /src/potential/constraints/ref_coord: -------------------------------------------------------------------------------- 1 | 6 2 | 3 | c -5.5338175 0.7125130 0.4057093 -1 4 | n -1.4757217 0.1805686 0.1102563 -1 -1 -1 5 | h -6.1187275 1.6438646 2.2895698 0 0 0 6 | h -6.6370856 -0.4341665 -1.0859286 0 0 0 7 | h -0.8548232 -0.9878324 -1.3343232 0 0 0 8 | h -0.4005556 0.8548868 1.6017769 0 0 0 9 | 10 | -------------------------------------------------------------------------------- /src/potential/constraints/xyz: -------------------------------------------------------------------------------- 1 | 6 2 | 3 | c -5.5338175 0.7125130 0.4057093 4 | n -1.4757217 0.1805686 0.1102563 5 | h -6.1187275 1.6438646 2.2895698 6 | h -6.6370856 -0.4341665 -1.0859286 7 | h -0.8548232 -0.9878324 -1.3343232 8 | h -0.4005556 0.8548868 1.6017769 9 | 10 | -------------------------------------------------------------------------------- /src/potential/potential.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | 3 | # external force or something else 4 | 5 | 6 | -------------------------------------------------------------------------------- /src/sampling/bin/sampling.x: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling/bin/sampling.x -------------------------------------------------------------------------------- /src/sampling/info_comm.itf: -------------------------------------------------------------------------------- 1 | ! 2 | ! ----- Variables in common for the program ----- 3 | ! 4 | integer :: nr, nbin 5 | integer :: n_atom, n_mode 6 | 7 | 8 | common /random/ nr, nbin 9 | common /normal/ n_atom, n_mode 10 | 11 | -------------------------------------------------------------------------------- /src/sampling/main.a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling/main.a -------------------------------------------------------------------------------- /src/sampling/main_input: -------------------------------------------------------------------------------- 1 | 6 read (*,*) n_atom 2 | 12 read (*,*) n_mode 3 | read (*,*) 4 | 1 read (*,*) label_random 5 | 5000 read (*,*) nr 6 | 50 read (*,*) nbin 7 | read (*,*) 8 | 1 read (*,*) label_read_vib 9 | 3 read (*,*) label_es_output 10 | freq.log read (*,*) filename_es_output 11 | read (*,*) 12 | 1 read (*,*) label_displacement 13 | read (*,*) 14 | 1 read (*,*) label_dis_wigner 15 | 1000 read (*,*) n_geom 16 | 1 read (*,*) label_method 17 | read (*,*) 18 | 0 read (*,*) label_frozen 19 | 2 read (*,*) number_frozen 20 | 1 3 read (*,*) list_frozen 21 | 22 | -------------------------------------------------------------------------------- /src/sampling/parser/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python2 2 | 3 | import normal_mode_parser 4 | 5 | __all__ = ['normal_model_parser'] 6 | -------------------------------------------------------------------------------- /src/sampling/parser/readme: -------------------------------------------------------------------------------- 1 | 2014.7.1 2 | add full elements periodic table database 3 | 2014.5.9 4 | add new parser to deal with jujar output gaussian format 5 | 6 | -------------------------------------------------------------------------------- /src/sampling/prepare.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python2 2 | 3 | from parser.normal_mode_parser import * 4 | 5 | 6 | if __name__ == "__main__": 7 | g = normal_mode_parser() 8 | g.done() 9 | 10 | 11 | 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /src/sampling/readme: -------------------------------------------------------------------------------- 1 | initial condition sampling.. 2 | 3 | mainly wigner sampling method 4 | 5 | -------------------------------------------------------------------------------- /src/sampling/sampling.x: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling/sampling.x -------------------------------------------------------------------------------- /src/sampling/sub_string.f90: -------------------------------------------------------------------------------- 1 | subroutine lower_case(word) 2 | ! convert a word to lower case 3 | character (len=*) , intent(in out) :: word 4 | integer :: i,ic,nlen 5 | nlen = len(word) 6 | do i=1,nlen 7 | ic = ichar(word(i:i)) 8 | if (ic >= 65 .and. ic < 90) word(i:i) = char(ic+32) 9 | end do 10 | end subroutine lower_case 11 | 12 | 13 | -------------------------------------------------------------------------------- /src/sampling/usage: -------------------------------------------------------------------------------- 1 | use 2 | prepare.py 3 | to extract 'freq' related data. 4 | 5 | then 6 | generate main_input & run sampling.x 7 | 8 | later, i want to integrate prepare.py & sampliing.x & gen_input.py 9 | -------------------------------------------------------------------------------- /src/sampling/wigner.a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling/wigner.a -------------------------------------------------------------------------------- /src/sampling2/README: -------------------------------------------------------------------------------- 1 | initial condition sampling method 2 | 3 | ===== 4 | 5 | more sampling method is provided. 6 | 7 | 8 | use 9 | prepare.py 10 | to extract 'freq' related data. 11 | 12 | then 13 | generate main_input & run sampling.x 14 | 15 | later, i want to integrate prepare.py & sampliing.x & gen_input.py 16 | -------------------------------------------------------------------------------- /src/sampling2/info_comm.itf: -------------------------------------------------------------------------------- 1 | ! 2 | ! ----- Variables in common for the program ----- 3 | ! 4 | integer :: nr, nbin 5 | integer :: n_atom, n_mode 6 | 7 | 8 | common /random/ nr, nbin 9 | common /normal/ n_atom, n_mode 10 | 11 | -------------------------------------------------------------------------------- /src/sampling2/main_initial_sampling.a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling2/main_initial_sampling.a -------------------------------------------------------------------------------- /src/sampling2/parser/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python2 2 | 3 | import normal_mode_parser 4 | 5 | __all__ = ['normal_model_parser'] 6 | -------------------------------------------------------------------------------- /src/sampling2/parser/pd.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python2 2 | 3 | def periodictable(self): 4 | """ read in periodic table """ 5 | fp = open("elements.dat", "r") 6 | line = fp.readline() 7 | line = fp.readline() 8 | n_atom = int(line.split()[0]) 9 | self.table['number'] = n_atom 10 | self.table['elements'] = [] 11 | # read in p table 12 | line = fp.readline() 13 | for i in xrange(n_atom): 14 | line = fp.readline() 15 | #atom-label; atom-std-type; atom-eng-type; charge; mass(a.u.) 16 | record = line.split() 17 | atom_label = record[0] 18 | atom_type = record[1] 19 | atom_eng_type = record[2] 20 | charge = float(record[3]) 21 | mass = float(record[4]) 22 | element = {'atom_label': atom_label, 'atom_type': atom_type, \ 23 | 'atom_eng_type': atom_eng_type, 'atom_number': charge, \ 24 | 'mass': mass} 25 | self.table['elements'].append(element) 26 | return 27 | -------------------------------------------------------------------------------- /src/sampling2/prepare.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python2 2 | 3 | from parser.normal_mode_parser import * 4 | 5 | 6 | if __name__ == "__main__": 7 | g = normal_mode_parser() 8 | g.done() 9 | 10 | -------------------------------------------------------------------------------- /src/sampling2/sampling.x: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling2/sampling.x -------------------------------------------------------------------------------- /src/sampling2/usercmdlog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling2/usercmdlog -------------------------------------------------------------------------------- /src/sampling_xy/SQC/a.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/SQC/a.out -------------------------------------------------------------------------------- /src/sampling_xy/SQC/action_angle_gau/ini_n_elec.inp: -------------------------------------------------------------------------------- 1 | 1 2 | 1 3 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/action_angle_gau/main_action_angle_elec_input: -------------------------------------------------------------------------------- 1 | 2 # n_mode 2 | 2000 # n_traj 3 | ini_n_elec.inp # filename of initial n(occupation) 4 | 1 # gamma 5 | 0.5 # sigma 6 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/action_angle_gau/main_action_angle_gau.a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/SQC/action_angle_gau/main_action_angle_gau.a -------------------------------------------------------------------------------- /src/sampling_xy/SQC/action_angle_gau/main_action_angle_gau.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/SQC/action_angle_gau/main_action_angle_gau.exe -------------------------------------------------------------------------------- /src/sampling_xy/SQC/action_angle_gau/sub_random_gau_1d.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_random_gau_1d(n,random_gau) 2 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 3 | ! https://en.wikipedia.org/wiki/Box%E2%80%93Muller_transform 4 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 5 | implicit none 6 | 7 | include 'param.def' 8 | 9 | ! --- arguments --- 10 | integer n 11 | !real(kind=8) mu, sigma 12 | real(kind=8) random_gau(n) 13 | 14 | ! --- local variabes --- 15 | integer seed 16 | integer i 17 | real(kind=8) random_1(n) 18 | real(kind=8) random_2(n) 19 | integer, parameter :: two_PI = 2.d0 * PI 20 | 21 | CALL RANDOM_SEED() 22 | CALL RANDOM_NUMBER(random_1) 23 | 24 | seed = random_1(n/2)*6965896 25 | 26 | CALL RANDOM_SEED(seed) 27 | CALL RANDOM_NUMBER(random_2) 28 | 29 | do i = 1, n 30 | random_gau(i) = sqrt( - log(random_1(i)) / log(2.718281828) ) & 31 | * cos(two_PI * random_2(i)) 32 | enddo 33 | 34 | 35 | !do i = 1, n 36 | ! random_gau(i) = random_gau(i)*sigma + mu 37 | !enddo 38 | 39 | return 40 | end 41 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/action_angle_uni/ini_n_elec.inp: -------------------------------------------------------------------------------- 1 | 1 2 | 0 3 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /src/sampling_xy/SQC/action_angle_uni/main_action_angle_x_y_p_x_p_y_elec_input: -------------------------------------------------------------------------------- 1 | 2 # n_state 2 | 2 # n_traj 3 | ini_n_elec.inp # filename of initial n(occupation) 4 | 1 5 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/action_angle_uni/main_action_angle_x_y_p_x_p_y_zpe.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/SQC/action_angle_uni/main_action_angle_x_y_p_x_p_y_zpe.exe -------------------------------------------------------------------------------- /src/sampling_xy/SQC/action_angle_uni/traj_1.inp: -------------------------------------------------------------------------------- 1 | 0.82676158356027 0.01267803755662 -0.01267803755662 0.82676158356027 2 | 0.18764722981965 0.04081236280841 -0.04081236280841 0.18764722981965 3 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/action_angle_uni/traj_2.inp: -------------------------------------------------------------------------------- 1 | -0.78568265569232 0.35074380097392 -0.35074380097392 -0.78568265569232 2 | -0.00067374094856 0.05174128633884 -0.05174128633884 -0.00067374094856 3 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/cp.sh: -------------------------------------------------------------------------------- 1 | 2 | 3 | for((i=1;i<=2000;i++)) 4 | do 5 | mkdir -p trajs/$i 6 | cp elec/traj_${i}.inp trajs/$i/trj_elec.input 7 | cp nuc/traj_${i}.inp trajs/$i/trj.input 8 | done 9 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/ini_n_elec.inp: -------------------------------------------------------------------------------- 1 | 0 2 | 1 3 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/ini_n_nuc.inp: -------------------------------------------------------------------------------- 1 | 0 2 | 0 3 | 0 4 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/main_action_angle.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/SQC/main_action_angle.exe -------------------------------------------------------------------------------- /src/sampling_xy/SQC/main_action_angle_elec_input: -------------------------------------------------------------------------------- 1 | 2 # n_mode 2 | 2000 # n_traj 3 | ini_n_elec.inp # filename of initial n(occupation) 4 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/main_action_angle_nuc_input: -------------------------------------------------------------------------------- 1 | 3 # n_mode 2 | 2000 # n_traj 3 | ini_n_nuc.inp # filename of initial n(occupation) 4 | -------------------------------------------------------------------------------- /src/sampling_xy/SQC/sub_random_gau.f90: -------------------------------------------------------------------------------- 1 | subroutine sub_random_gau_1d(n, mu, sigma, random_gau) 2 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 3 | ! https://en.wikipedia.org/wiki/Box%E2%80%93Muller_transform 4 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 5 | implicit none 6 | 7 | include 'param.def' 8 | 9 | ! --- arguments --- 10 | integer n 11 | real(kind=8) mu, sigma 12 | real(kind=8) random_gau(n) 13 | 14 | ! --- local variabes --- 15 | integer seed 16 | integer i 17 | real(kind=8) random_1(n) 18 | real(kind=8) random_2(n) 19 | integer, parameter :: two_PI = 2.d0 * PI 20 | 21 | CALL RANDOM_SEED() 22 | CALL RANDOM_NUMBER(random_1) 23 | 24 | seed = random_1(nr/2)*6965896 25 | 26 | CALL RANDOM_SEED(seed) 27 | CALL RANDOM_NUMBER(random_2) 28 | 29 | do i = 1, n 30 | random_gau(i) = sqrt( - log(random_1(i)) / log(2.718281828) ) & 31 | * cos(two_PI * random_2(i)) 32 | enddo 33 | 34 | 35 | do i = 1, n 36 | random_gau(i) = random_gau(i)*sigma + mu 37 | enddo 38 | 39 | return 40 | end 41 | -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/cp.sh: -------------------------------------------------------------------------------- 1 | 2 | 3 | for((i=1;i<=2000;i++)) 4 | do 5 | mkdir -p trajs/$i 6 | cp elec/traj_${i}.inp trajs/$i/trj_elec.input 7 | cp nuc/traj_${i}.inp trajs/$i/trj.input 8 | done 9 | -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/ini_n_elec.inp: -------------------------------------------------------------------------------- 1 | 0 2 | 1 3 | -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/ini_n_nuc.inp: -------------------------------------------------------------------------------- 1 | 0 2 | 0 3 | 0 4 | -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/main_action_angle.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/action_angle/main_action_angle.exe -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/main_action_angle_elec_input: -------------------------------------------------------------------------------- 1 | 2 # n_mode 2 | 2 # n_traj 3 | ini_n_elec.inp # filename of initial n(occupation) 4 | 0 5 | -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/main_action_angle_nuc_input: -------------------------------------------------------------------------------- 1 | 3 # n_mode 2 | 2000 # n_traj 3 | ini_n_nuc.inp # filename of initial n(occupation) 4 | -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/main_action_angle_x_y_p_x_p_y.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/action_angle/main_action_angle_x_y_p_x_p_y.exe -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/main_action_angle_x_y_p_x_p_y_zpe.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/action_angle/main_action_angle_x_y_p_x_p_y_zpe.exe -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/main_action_angle_x_y_p_x_p_y_zpe_input: -------------------------------------------------------------------------------- 1 | 2 # n_mode 2 | 2 # n_traj 3 | ini_n_elec.inp # filename of initial n(occupation) 4 | 0.4 5 | -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/traj_1.inp: -------------------------------------------------------------------------------- 1 | 0.63238118444179 0.00969729673690 -0.00969729673690 0.63238118444179 2 | 1.15618573680305 0.25146479279052 -0.25146479279052 1.15618573680305 3 | -------------------------------------------------------------------------------- /src/sampling_xy/action_angle/traj_2.inp: -------------------------------------------------------------------------------- 1 | -0.57752112580317 0.25781650306185 -0.25781650306185 -0.57752112580317 2 | -0.01540575279081 1.18311565908873 -1.18311565908873 -0.01540575279081 3 | -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/README: -------------------------------------------------------------------------------- 1 | initial condition sampling method 2 | 3 | ===== 4 | 5 | more sampling method is provided. 6 | 7 | 8 | use 9 | prepare.py 10 | to extract 'freq' related data. 11 | 12 | then 13 | generate main_input & run sampling.x 14 | 15 | later, i want to integrate prepare.py & sampliing.x & gen_input.py 16 | -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/extra_ini_trj.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | import os 3 | import math 4 | from os import system 5 | from sys import exit 6 | 7 | 8 | 9 | n_traj = input('n_traj:\n') 10 | n_mode = input('n_mode:\n') 11 | n_line = int(n_traj * n_mode) 12 | 13 | trj = [] 14 | pop1= [] 15 | pop2= [] 16 | 17 | for i_line in range(n_line): 18 | trj.append([]) 19 | for i_x in range(2): 20 | trj[i_line].append(0.0) 21 | 22 | 23 | line_text =[] 24 | for i_line in range(n_line): 25 | line_text.append(0.0) 26 | 27 | filein1=open('random_gau.dat','r') 28 | line_all=filein1.read() 29 | filein1.close() 30 | 31 | line_text=line_all.split('\n') 32 | for i_line in range(n_line): 33 | trj[i_line][0] = float(line_text[i_line].split()[0]) 34 | trj[i_line][1] = float(line_text[i_line].split()[1]) 35 | 36 | for i_trj in range(n_traj): 37 | filein2=open('traj_' + str(i_trj+1) + '.inp','w') 38 | for i_mode in range(n_mode): 39 | filein2.write( str(trj[int(n_mode*i_trj + i_mode)][0]) + ' ' + str(trj[int(n_mode*i_trj + i_mode)][1]) + '\n' ) 40 | filein2.close() 41 | 42 | -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/info_comm.itf: -------------------------------------------------------------------------------- 1 | ! 2 | ! ----- Variables in common for the program ----- 3 | ! 4 | integer :: nr, nbin 5 | integer :: n_atom, n_mode 6 | 7 | 8 | common /random/ nr, nbin 9 | common /normal/ n_atom, n_mode 10 | 11 | -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/main_initial_sampling.a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/sampling2_pjw/main_initial_sampling.a -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/main_initial_sampling.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/sampling2_pjw/main_initial_sampling.exe -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/output.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/sampling2_pjw/output.pdf -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/parser/__init__.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/python 2 | 3 | import normal_mode_parser 4 | 5 | __all__ = ['normal_model_parser'] 6 | -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/parser/main_input: -------------------------------------------------------------------------------- 1 | 6 read (*,*) n_atom 2 | 12 read (*,*) n_mode 3 | read (*,*) 4 | 1 read (*,*) label_random 5 | 5000 read (*,*) nr 6 | 50 read (*,*) nbin 7 | read (*,*) 8 | 1 read (*,*) label_read_vib 9 | 3 read (*,*) label_es_output 10 | freq.log read (*,*) filename_es_output 11 | read (*,*) 12 | 1 read (*,*) label_displacement 13 | read (*,*) 14 | 1 read (*,*) label_dis_wigner 15 | 1000 read (*,*) n_geom 16 | 1 read (*,*) label_method 17 | read (*,*) 18 | 0 read (*,*) label_frozen 19 | 2 read (*,*) number_frozen 20 | 1 2 read (*,*) list_frozen 21 | -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/parser/output.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/sampling2_pjw/parser/output.pdf -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/parser/pd.py: -------------------------------------------------------------------------------- 1 | def periodictable(self): 2 | """ read in periodic table """ 3 | fp = open("elements.dat", "r") 4 | line = fp.readline() 5 | line = fp.readline() 6 | n_atom = int(line.split()[0]) 7 | self.table['number'] = n_atom 8 | self.table['elements'] = [] 9 | # read in p table 10 | line = fp.readline() 11 | for i in xrange(n_atom): 12 | line = fp.readline() 13 | #atom-label; atom-std-type; atom-eng-type; charge; mass(a.u.) 14 | record = line.split() 15 | atom_label = record[0] 16 | atom_type = record[1] 17 | atom_eng_type = record[2] 18 | charge = float(record[3]) 19 | mass = float(record[4]) 20 | element = {'atom_label': atom_label, 'atom_type': atom_type, \ 21 | 'atom_eng_type': atom_eng_type, 'atom_number': charge, \ 22 | 'mass': mass} 23 | self.table['elements'].append(element) 24 | return 25 | -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/prepare.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | 3 | from parser.normal_mode_parser import * 4 | 5 | 6 | if __name__ == "__main__": 7 | g = normal_mode_parser() 8 | g.done() 9 | 10 | 11 | 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /src/sampling_xy/sampling2_pjw/sampling.x: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zglan/JADE-NAMD/e61fb3fec0745286dd526530a0489ae8583f3e48/src/sampling_xy/sampling2_pjw/sampling.x --------------------------------------------------------------------------------