./db.backup output for 42: 3.3A-->1.3A 712(amd-3) Si-CH3H...HO-Si two dimer closed (TSS for CH3...OH)
Status:
running
job.id 42
job.name {3.3A-->1.3A 712(amd-3) Si-CH3H...HO-Si two dimer closed (TSS for CH3...OH)}
job.description {
}
job.status pending
job.submitted {2024-09-28 23:25:10}
job.started {0000-00-00 00:00:00}
job.finished {0000-00-00 00:00:00}
job.queue 5
job.errormsg {}
job.pid 0
job.userid 1
job.priority 5
job.jobserverid 2
data.joboptions {_protocol_type_ JobControl _description_ {} passwd {} _name_ {} nproc 1 priority 5 _protocol_id_ 0 _protocol_pid_ 0 _version_ 1.1 context {} user user}
data.script set\ MedeADb\ \"C:/MD/Databases/MedeA.db\"\n#\n#\ Basic\ script\ for\ running\ TransitionStateSearch\ calculations\n#\n\npackage\ require\ database\npackage\ require\ MD.Results\npackage\ require\ TransitionStateSearch\npackage\ require\ Options\npackage\ require\ system\npackage\ require\ Simulation\n\n\nproc\ task\ \{args\}\ \{\}\nnamespace\ eval\ ::MD\ \{\}\n\nputs\ \"Opening\ the\ database\"\n\n#\n#\ Hmmm.\ An\ issue\ with\ SQL\ Server\ and\ MySql\ databases\ here\n#\ Need\ to\ try\ both!\n#\n\nopenMedeADb\ \$MedeADb\n\n#\ Drop\ the\ priority\n#\ if\ \{\[catch\ \{\n#\ \ \ \ \ package\ require\ WinUtil\n#\ \ \ \ \ ::WinUtil::priority\ low\n#\ \}\ msg\]\}\ \{\n#\ \ \ \ \ puts\ \"Unable\ to\ lower\ priority:\ \$msg\"\n#\ \}\n\nset\ tmp\ \[join\ \[lindex\ \[db\ \"SELECT\ value\ FROM\ data\ WHERE\ job\ =\ \$::job::id\ AND\ item\ =\ 'transitionstatesearchoptions'\"\]\ 0\]\]\n::TransitionStateSearch::Options\ transitionstatesearchoptions\neval\ transitionstatesearchoptions\ update\ \$tmp\n\nset\ tmp\ \[join\ \[lindex\ \[db\ \"SELECT\ value\ FROM\ data\ WHERE\ job\ =\ \$::job::id\ AND\ item\ =\ 'system'\"\]\ 0\]\]\nSystem\ system\ -data\ \$tmp\n\nset\ tmp\ \[join\ \[lindex\ \[db\ \"SELECT\ value\ FROM\ data\ WHERE\ job\ =\ \$::job::id\ AND\ item\ =\ 'finalsystem'\"\]\ 0\]\]\nif\ \{\$tmp\ !=\ \"\"\}\ \{\n\ \ \ \ System\ finalsystem\ -data\ \$tmp\n\}\n\nset\ tmp\ \[join\ \[lindex\ \[db\ \"SELECT\ value\ FROM\ data\ WHERE\ job\ =\ \$::job::id\ AND\ item\ =\ 'simulationoptions'\"\]\ 0\]\]\nSimulation::Options\ simulationoptions\neval\ simulationoptions\ update\ \$tmp\n\n\tset\ engine\ \[transitionstatesearchoptions\ get\ engine\]\n\tswitch\ \$engine\ \{\n\t\ \ \ \ VASP46\ \ \{\n\t\tpackage\ require\ VAMPBatch\n\t\tset\ tmp\ \[join\ \[lindex\ \[db\ \"SELECT\ value\ FROM\ data\ WHERE\ job\ =\ \$::job::id\ AND\ item\ =\ 'vaspoptions'\"\]\ 0\]\]\n\t\t::VAMP::Options\ vaspoptions\n\t\teval\ vaspoptions\ update\ \$tmp\n\n\t\t::MD::Results::Handler\ Results\ -file\ Job.xml\n\n\t\tnew\ VAMP::Batch\ VASP\ -options\ vaspoptions\ -system\ system\ -finalsystem\ finalsystem\ -simulationoptions\ \\\n\t\t\ \ \ \ simulationoptions\ -transitionstatesearchoptions\ transitionstatesearchoptions\ -results\ Results\n\t\t\$VASP\ TransitionStateSearch\n\n\t\tResults\ save\n\t\ \ \ \ \}\n\n\t\ \ \ \ VASP52\ \ \{\n\t\tpackage\ require\ VASP52Batch\n\t\tset\ tmp\ \[join\ \[lindex\ \[db\ \"SELECT\ value\ FROM\ data\ WHERE\ job\ =\ \$::job::id\ AND\ item\ =\ 'vaspoptions'\"\]\ 0\]\]\n\t\t::VASP52::Options\ vaspoptions\n\t\teval\ vaspoptions\ update\ \$tmp\n\t\tnew\ VASP52::Batch\ VASP\ -options\ vaspoptions\ -system\ system\ -finalsystem\ finalsystem\ -simulationoptions\ simulationoptions\ -transitionstatesearchoptions\ transitionstatesearchoptions\n\t\t\$VASP\ TransitionStateSearch\n\t\ \ \ \ \}\n\n\t\ \ \ \ VASP53\ \ \{\n\t\tpackage\ require\ VASP53Batch\n\t\tset\ tmp\ \[join\ \[lindex\ \[db\ \"SELECT\ value\ FROM\ data\ WHERE\ job\ =\ \$::job::id\ AND\ item\ =\ 'vaspoptions'\"\]\ 0\]\]\n\t\t::VASP53::Options\ vaspoptions\n\t\teval\ vaspoptions\ update\ \$tmp\n\t\tnew\ VASP53::Batch\ VASP\ -options\ vaspoptions\ -system\ system\ -finalsystem\ finalsystem\ -simulationoptions\ simulationoptions\ -transitionstatesearchoptions\ transitionstatesearchoptions\n\t\t\$VASP\ TransitionStateSearch\n\t\ \ \ \ \}\n\n\t\ \ \ \ VASP6\ \ \{\n\t\tpackage\ require\ VASP6Batch\n\t\tset\ tmp\ \[join\ \[lindex\ \[db\ \"SELECT\ value\ FROM\ data\ WHERE\ job\ =\ \$::job::id\ AND\ item\ =\ 'vaspoptions'\"\]\ 0\]\]\n\t\t::VASP6::Options\ vaspoptions\n\t\teval\ vaspoptions\ update\ \$tmp\n\t\tnew\ VASP6::Batch\ VASP\ -options\ vaspoptions\ -system\ system\ -finalsystem\ finalsystem\ -simulationoptions\ simulationoptions\ -transitionstatesearchoptions\ transitionstatesearchoptions\n\t\t\$VASP\ TransitionStateSearch\n\t\ \ \ \ \}\n\n\t\}\n
data.transitionstatesearchoptions {MD_minimizer BFGS2 Solid-VTST_minimizer Quick-Min VTST_minimizer Global-LBFGS VTST_minimizer_dimer Global-LBFGS _description_ {} _name_ {} _protocol_id_ 0 _protocol_pid_ 0 _protocol_type_ TransitionStateSearch _version_ 1.0 calculation {Nudged Elastic Band} center_mass_motion 1 climbing_image 0 convergence 0.25 convergence_dimer 0.1 convergence_for_climbing 1.0 convergence_transitionstatesearch 0.1 damping_factor 1 debug_minimizer 0 description {} dimer_calculation {Dimer method (VASP)} dimer_frozen_mode {for the initial dimer orientation only} dimer_orientation {towards final configuration} dimer_refineTS_RMMDIIS 1 dimer_separation 0.01 double_nudging 0 dynamical_timestep 0.1 dynamical_timestep_dimer 0.1 ending_image 1.0 engine VASP6 finalsystem ::system30 findTS 1 finite_difference {forward finite difference} image_initialization {linear interpolation} include_boundary_translations 0 initial_dimer_shift 0.1 initial_invhessian 0.001 initialimages {initialimage7 {} initialimage3 {} initialimage8 {} initialimage4 {} initialimage5 {} initialimage1 {} initialimage6 {} initialimage2 {}} interpolation_range {full range} lower_finalarea_image 0.8 mapReactionPath 1 max_stepnumber 150 max_stepnumber_dimer 100 maximum_number_rotations 1 maximum_rotation_force 1.0 menu .transitionstatesearch minimum_rotation 0.01 minimum_rotation_force 0.01 number_of_images 8 number_of_images_transitionstatesearch 1 number_of_random_directions 1 number_of_refinements 0 optimize_transitionstate 1 quickmin_damping 0.4 quickmin_damping_dimer 0.4 refineTS 0 refineTS_RMMDIIS 0 refineTSmethod {Elastic Band Methods} refine_transitionstate {all identified saddle points} relaxalgo RMM-DIIS search_transitionstate {for the highest saddle point only} shift_dimer 0 spring_constant 0.1 starting_image 0.0 step_size 0.01 step_size_max 0.1 summary {3.3A-->1.3A 712(amd-3) Si-CH3H...HO-Si two dimer closed (TSS for CH3...OH)} tangent_estimation improved task {Map out the minimum energy path by elastic band methods} theOtherGUI 1 transitionstate_search_method {Elastic Band Methods} translation_criterion 0.5 upper_initialarea_image 0.2 use_wavecars 0}
data.vaspoptions {ACFDT-RPARmode 0 ACFDT-RPAmode 0 ActualKMesh {1 1 1} ActualKSpacings {0.209 0.314 0.419} BandStructure/_description_ {} BandStructure/_name_ {} BandStructure/_protocol_id_ 0 BandStructure/_protocol_pid_ 0 BandStructure/_protocol_type_ BandStructure BandStructure/_version_ 2.1 BandStructure/explicitpath 0 BandStructure/labels {} BandStructure/maxpoints 40 BandStructure/module VASP BandStructure/npertask 40 BandStructure/npoints {} BandStructure/symmetrypoints {} BandStructure/vertices {} DDH-DSH_decay 1.26 DDH-DSH_longrange 0.1 DimerVASP 0 Efield_direction x-axis ElPhonmode 0 FFTcharges 0 GWRcalc {quasiparticle shifts} GWRmode 0 GW_ismear Gaussian GW_metals 0 GW_mporder 1 GW_sigma 0.2 GW_sigmaGauss 0.05 GWalgorithm {eigenvalues for G (GW0)} GWcalc {quasiparticle shifts} GWmode 0 Gshift 1 HF_Gshift 1 HF_amix 0.2 HF_bstr_kmesh {as for non-local exchange} HF_kInputmode {set spacing between k-points} HF_kPointMode 0 HF_kSpacing 0.5 HF_nk1_base 1 HF_nk2_base 1 HF_nk3_base 1 HF_nkodd 0 HF_nkx 4 HF_nky 4 HF_nkz 4 HF_timestep 0.4 HF_timestep_initial 0.4 MLFF_Task_MD {Create forcefield by on-the-fly learning} ML_Gwidth_angular {} ML_Gwidth_radial 0.5 ML_Rcut_angular 5.0 ML_Rcut_radial 8.0 ML_atomicEnergy 0 ML_atomicenergy {} ML_energyscaling {average energy of training data} ML_handleOverflow 1 ML_heatFlux 0 ML_lmax 3 ML_nMLFFstepsmin {} ML_nbasisfunct_angular 8 ML_nbasisfunct_radial 12 ML_nconfigstemp 5 ML_nrefconfigsmax {} ML_nstructuremax {} ML_output_frequency 1 ML_pair-correlation 1 ML_thresholdconfigfactor 0.6 ML_thresholdfactor {} ML_thresholdforceserror 0.002 ML_thresholdsparsification {} ML_thresholdupdate automatic ML_thresholdupdatefactor 1.0 ML_weight_energy 1.0 ML_weight_forces 1.0 ML_weight_radial 0.1 ML_weight_stress 1.0 MP2mode 0 NEBinVASP 0 TDHFmode 0 TimeEv_nbands_occ {} TimeEv_nbands_unocc {} TimeEvmode 0 TimeStep_definition {via complex shift} _description_ {} _name_ {} _protocol_id_ 0 _protocol_pid_ 0 _protocol_type_ VASP _version_ 2.4 acfdt-rpa_metals 0 addgrid 0 algo {Normal (blocked Davidson)} algoHF {Damped molecular dynamics} amix 0.2 apaco {} applyMLFF_ElPhon 0 applyMLFF_MT 0 applyMLFF_OPT 0 applyMLFF_SP 0 apply_localization immediately apply_solvation 0 backgroundCharge 0 bandstructure 0 cshift 0.1 cshiftGW {} cshiftTimeEv {} default_encut 400.000 delayeach 0 description {} displacement 0.015 displacement_number 1 dos 0 dos_Gshift 1 dos_ismear {Tetrahedron method} dos_kInputmode {set spacing between k-points} dos_kSpacing 0.25 dos_mporder 1 dos_nkodd 0 dos_nkx 9 dos_nkxmult 2 dos_nky 9 dos_nkymult 2 dos_nkz 9 dos_nkzmult 2 dos_projection {automatic choice} dos_sigma 0.2 dos_sigmaGauss 0.05 ediff 1.0e-05 ediffg -0.02 efield 0 efield_dir none elastic 0 elements_sites elements elphon_calculation {Single configuration (Zacharias-Giustino)} elphon_nstruct 100 elphon_temperature 0.0 emax {} emin {} enaug {} encut {} encutGW {} encut_nmr {} engine {for GPUs} explicitKPoints 0 extrainput {} file_return Normal fixcharg 0 functional {Density functional} gwr_nomega 16 gwr_sigma 0.1 gwr_tempmode {T = 0K (systems with band gap)} hybrid_functional HSE06 ibrion -1 icharg {Atomic charge densities} images 3 increase_encut 0 indepParticleApprox_TimeEv 0 initialDimerDir {} iniwav {Random numbers} involveMLFF_MD 0 isif {} ismear Methfessel-Paxton ispin 0 istart 0 isym {} iwave {from scratch} iwaveder 0 iwtmp 0 j_parameter {} kInputmode {set spacing between k-points} kSpacing 0.5 kblock {} kpoints {} lEoF 0 l_parameter {} laechg 0 lcharg 0 ldapu {Standard LDA or GGA} lefg 0 lelf 0 lepsilon 0 lhyperfine 0 lmaxHF {lmax = 4} lmaxaeGW {full shape up to lmax = 4} lmaxmp2 {up to lmax = 2} localization_ediff 1.0e-03 localization_steps 10 lpead 0 lreal {Real space} lscalapack 0 lsol 0 lspectral 1 ltmp2_nomega 6 lvhar 1 lvtot 0 lwave 0 lwaveder 0 magmom 1 magnetism {Defined by model} maxbandpoints 40 maxmem {} meta-GGA revTPSS modelBSE 0 modelBSE_AEXX {} modelBSE_HFSCREEN {} modelBSE_nbands_occ {} modelBSE_nbands_unocc {} mp2_calculation {Møller-Plesset perturbation theory (MP2)} mporder 1 nTimeSteps 100 napaco {} nbands {} nbandsGW {} nbands_GW {} nbands_TDHF {} nbands_TimeEv {} nbands_occ {} nbands_opt {} nbands_unocc {} nblk {} nblock 1 nedos 3000 nelm 200 nelmGW 4 nelmdl {} nelmin 2 nfree 2 ngx 0 ngy 0 ngz 0 nkodd 0 nkx 4 nkxmult 1 nky 4 nkymult 1 nkz 4 nkzmult 1 nmr 0 nmr_maxkpoints 10 nomega 50 nomega_acfdt 12 nomega_tdhf 50 nosymmetry 0 nsw 0 nuj {} nwrite 1 oddonlyGW 0 optical_matrix_elements 0 optics 0 phonons_ismear Methfessel-Paxton phonons_mporder 1 phonons_sigma 0.2 phonons_sigmaGauss 0.05 poscar_filename {} potentials {GGA-PBE PAW {8 O 14 Si 1 H 6 C 7 N}} potentials_version {Version 54} potim {} prec Normal precision Normal precisionHF Normal precsym 1.0E-05 pressure 0 protHF_MD {DFT Single Point + Non-local Molecular Dynamics} protHF_Opt {DFT Single Point + Non-local Structure Optimization} protHF_SP {DFT Single Point + Non-local Single Point} read_poscar 0 reducedFFTHF 0 refit_MLFF {for fast running applications} response 0 response_ismear {Tetrahedron with Bloechl corrections} response_kmesh {as for DOS and optics} response_mporder 1 response_sigma 0.2 response_sigmaGauss 0.05 restart_MLFF {} restart_MLFF_prefix {} restart_chg {} restart_chg_prefix {} restart_type {constant energy cutoff} restart_wave {} restart_wave_prefix {} restart_waveder {} restart_wtmp {} rpar_calculation {single point energy (all systems)} rpar_convergence 0.02 rpar_mintrjfrequency 1 rpar_nomega 12 rpar_nsteps 100 rpar_sigma 0.1 rpar_tempmode {T = 0K (systems with band gap)} scissors {} sigma 0.2 sigmaGauss 0.05 sltmp2_estop {} sltmp2_nstorb {} smass {} smass_real {} solvation_energy 0 solvent_dielectric 78.4 spinaxis_x {} spinaxis_y {} spinaxis_z {} spininterpol Vosko-Wilk-Nusair spring -5 summary {} tebeg {} teend {} thomasFermi 1.8 thomasFermi_choice {average valence density} thomasFermi_fromDensity 1.8 timestep 0.4 timestep_initial 0.4 totalmoment {} u-j_parameter {} u_parameter {} van_der_Waals None van_der_Waals_functional optB86b-vdW vibrations 0 voskown {} weights {} workfunction 0}
data.vaspDimeroptions {ACFDT-RPARmode 0 ACFDT-RPAmode 0 ActualKMesh {1 1 1} ActualKSpacings {0.209 0.314 0.419} BandStructure/_description_ {} BandStructure/_name_ {} BandStructure/_protocol_id_ 0 BandStructure/_protocol_pid_ 0 BandStructure/_protocol_type_ BandStructure BandStructure/_version_ 2.1 BandStructure/explicitpath 0 BandStructure/labels {} BandStructure/maxpoints 40 BandStructure/module VASP BandStructure/npertask 40 BandStructure/npoints {} BandStructure/symmetrypoints {} BandStructure/vertices {} DDH-DSH_decay 1.26 DDH-DSH_longrange 0.1 DimerVASP 0 Efield_direction x-axis ElPhonmode 0 FFTcharges 0 GWRcalc {quasiparticle shifts} GWRmode 0 GW_ismear Gaussian GW_metals 0 GW_mporder 1 GW_sigma 0.2 GW_sigmaGauss 0.05 GWalgorithm {eigenvalues for G (GW0)} GWcalc {quasiparticle shifts} GWmode 0 Gshift 1 HF_Gshift 1 HF_amix 0.2 HF_bstr_kmesh {as for non-local exchange} HF_kInputmode {set spacing between k-points} HF_kPointMode 0 HF_kSpacing 0.5 HF_nk1_base 1 HF_nk2_base 1 HF_nk3_base 1 HF_nkodd 0 HF_nkx 4 HF_nky 4 HF_nkz 4 HF_timestep 0.4 HF_timestep_initial 0.4 MLFF_Task_MD {Create forcefield by on-the-fly learning} ML_Gwidth_angular {} ML_Gwidth_radial 0.5 ML_Rcut_angular 5.0 ML_Rcut_radial 8.0 ML_atomicEnergy 0 ML_atomicenergy {} ML_energyscaling {average energy of training data} ML_handleOverflow 1 ML_heatFlux 0 ML_lmax 3 ML_nMLFFstepsmin {} ML_nbasisfunct_angular 8 ML_nbasisfunct_radial 12 ML_nconfigstemp 5 ML_nrefconfigsmax {} ML_nstructuremax {} ML_output_frequency 1 ML_pair-correlation 1 ML_thresholdconfigfactor 0.6 ML_thresholdfactor {} ML_thresholdforceserror 0.002 ML_thresholdsparsification {} ML_thresholdupdate automatic ML_thresholdupdatefactor 1.0 ML_weight_energy 1.0 ML_weight_forces 1.0 ML_weight_radial 0.1 ML_weight_stress 1.0 MP2mode 0 NEBinVASP 0 TDHFmode 0 TimeEv_nbands_occ {} TimeEv_nbands_unocc {} TimeEvmode 0 TimeStep_definition {via complex shift} _description_ {} _name_ {} _protocol_id_ 0 _protocol_pid_ 0 _protocol_type_ VASP _version_ 2.4 acfdt-rpa_metals 0 addgrid 0 algo {Normal (blocked Davidson)} algoHF {Damped molecular dynamics} amix 0.2 apaco {} applyMLFF_ElPhon 0 applyMLFF_MT 0 applyMLFF_OPT 0 applyMLFF_SP 0 apply_localization immediately apply_solvation 0 backgroundCharge 0 bandstructure 0 cshift 0.1 cshiftGW {} cshiftTimeEv {} default_encut 400.000 delayeach 0 description {} displacement 0.015 displacement_number 1 dos 0 dos_Gshift 1 dos_ismear {Tetrahedron method} dos_kInputmode {set spacing between k-points} dos_kSpacing 0.25 dos_mporder 1 dos_nkodd 0 dos_nkx 9 dos_nkxmult 2 dos_nky 9 dos_nkymult 2 dos_nkz 9 dos_nkzmult 2 dos_projection {automatic choice} dos_sigma 0.2 dos_sigmaGauss 0.05 ediff 1.0e-05 ediffg -0.02 efield 0 efield_dir none elastic 0 elements_sites elements elphon_calculation {Single configuration (Zacharias-Giustino)} elphon_nstruct 100 elphon_temperature 0.0 emax {} emin {} enaug {} encut {} encutGW {} encut_nmr {} engine standard explicitKPoints 0 extrainput {} file_return Normal fixcharg 0 functional {Density functional} gwr_nomega 16 gwr_sigma 0.1 gwr_tempmode {T = 0K (systems with band gap)} hybrid_functional HSE06 ibrion -1 icharg {Atomic charge densities} images 3 increase_encut 0 indepParticleApprox_TimeEv 0 initialDimerDir {} iniwav {Random numbers} involveMLFF_MD 0 isif {} ismear Methfessel-Paxton ispin 0 istart 0 isym {} iwave {from scratch} iwaveder 0 iwtmp 0 j_parameter {} kInputmode {set spacing between k-points} kSpacing 0.5 kblock {} kpoints {} lEoF 0 l_parameter {} laechg 0 lcharg 0 ldapu {Standard LDA or GGA} lefg 0 lelf 0 lepsilon 0 lhyperfine 0 lmaxHF {lmax = 4} lmaxaeGW {full shape up to lmax = 4} lmaxmp2 {up to lmax = 2} localization_ediff 1.0e-03 localization_steps 10 lpead 0 lreal {Real space} lscalapack 0 lsol 0 lspectral 1 ltmp2_nomega 6 lvhar 1 lvtot 0 lwave 0 lwaveder 0 magmom 1 magnetism {Defined by model} maxbandpoints 40 maxmem {} meta-GGA revTPSS modelBSE 0 modelBSE_AEXX {} modelBSE_HFSCREEN {} modelBSE_nbands_occ {} modelBSE_nbands_unocc {} mp2_calculation {Møller-Plesset perturbation theory (MP2)} mporder 1 nTimeSteps 100 napaco {} nbands {} nbandsGW {} nbands_GW {} nbands_TDHF {} nbands_TimeEv {} nbands_occ {} nbands_opt {} nbands_unocc {} nblk {} nblock 1 nedos 3000 nelm 60 nelmGW 4 nelmdl {} nelmin 2 nfree 2 ngx 0 ngy 0 ngz 0 nkodd 0 nkx 4 nkxmult 1 nky 4 nkymult 1 nkz 4 nkzmult 1 nmr 0 nmr_maxkpoints 10 nomega 50 nomega_acfdt 12 nomega_tdhf 50 nosymmetry 0 nsw 0 nuj {} nwrite 1 oddonlyGW 0 optical_matrix_elements 0 optics 0 phonons_ismear Methfessel-Paxton phonons_mporder 1 phonons_sigma 0.2 phonons_sigmaGauss 0.05 poscar_filename {} potentials {GGA-PBE PAW {8 O 14 Si 1 H 6 C 7 N}} potentials_version {Version 54} potim {} prec Normal precision Normal precisionHF Normal precsym 1.0E-05 pressure 0 protHF_MD {DFT Single Point + Non-local Molecular Dynamics} protHF_Opt {DFT Single Point + Non-local Structure Optimization} protHF_SP {DFT Single Point + Non-local Single Point} read_poscar 0 reducedFFTHF 0 refit_MLFF {for fast running applications} response 0 response_ismear {Tetrahedron with Bloechl corrections} response_kmesh {as for DOS and optics} response_mporder 1 response_sigma 0.2 response_sigmaGauss 0.05 restart_MLFF {} restart_MLFF_prefix {} restart_chg {} restart_chg_prefix {} restart_type {constant energy cutoff} restart_wave {} restart_wave_prefix {} restart_waveder {} restart_wtmp {} rpar_calculation {single point energy (all systems)} rpar_convergence 0.02 rpar_mintrjfrequency 1 rpar_nomega 12 rpar_nsteps 100 rpar_sigma 0.1 rpar_tempmode {T = 0K (systems with band gap)} scissors {} sigma 0.2 sigmaGauss 0.05 sltmp2_estop {} sltmp2_nstorb {} smass {} smass_real {} solvation_energy 0 solvent_dielectric 78.4 spinaxis_x {} spinaxis_y {} spinaxis_z {} spininterpol Vosko-Wilk-Nusair spring -5 summary {} tebeg {} teend {} thomasFermi 1.8 thomasFermi_choice {average valence density} thomasFermi_fromDensity 1.8 timestep 0.4 timestep_initial 0.4 totalmoment {} u-j_parameter {} u_parameter {} van_der_Waals None van_der_Waals_functional optB86b-vdW vibrations 0 voskown {} weights {} workfunction 0}
data.simulationoptions {_description_ {} _name_ {} _protocol_id_ 0 _protocol_pid_ 0 _protocol_type_ Simulation _version_ 2.0 a 1 alpha 1 andersen_prob 0.1 averagefrequency 40.0 b 1 beta 1 c 1 calculation {Single Point} convergence 0.02 eachstep 0 econvergence 1.0e-03 endtemperature {} ensemble {micro canonical (nVE)} gamma 1 mintrjfile trajectory.data mintrjfrequency 1 nosemass {} npt_alpha constrain npt_aparam none npt_beta constrain npt_bparam none npt_constraints isotropic npt_cparam none npt_gamma constrain npt_monitoralpha none npt_monitoraparam none npt_monitorbeta none npt_monitorbparam none npt_monitorcparam none npt_monitorgamma none npt_monitorvolume monitor npt_volume none nsteps 100 nve_thermostat Nosé-Hoover nvt_thermostat Nosé-Hoover paircorrdistance 16.0 paircorrslots 256 pmass {} relaxalgo {Conjugate Gradient} relaxatompos 1 relaxatoms 1 relaxcell 0 relaxvolume 0 restart_md {} restart_md_prefix {} strain 0.01 strains 0.005 temperature 298.0 time 120.0 timestep 4.0 trjfile trajectory.data trjfrequency 1 use_wavecars 0 version 6 yinatoms {} yinyang 0}
data.simulationDimeroptions {_description_ {} _name_ {} _protocol_id_ 0 _protocol_pid_ 0 _protocol_type_ Simulation _version_ 2.0 a 1 alpha 1 andersen_prob 0.1 averagefrequency 40.0 b 1 beta 1 c 1 calculation {Single Point} convergence 0.02 eachstep 0 econvergence 1.0e-03 endtemperature {} ensemble {micro canonical (nVE)} gamma 1 mintrjfile trajectory.data mintrjfrequency 1 nosemass {} npt_alpha constrain npt_aparam none npt_beta constrain npt_bparam none npt_constraints isotropic npt_cparam none npt_gamma constrain npt_monitoralpha none npt_monitoraparam none npt_monitorbeta none npt_monitorbparam none npt_monitorcparam none npt_monitorgamma none npt_monitorvolume monitor npt_volume none nsteps 100 nve_thermostat Nosé-Hoover nvt_thermostat Nosé-Hoover paircorrdistance 16.0 paircorrslots 256 pmass {} relaxalgo {Conjugate Gradient} relaxatompos 1 relaxatoms 1 relaxcell 0 relaxvolume 0 restart_md {} restart_md_prefix {} strain 0.01 strains 0.005 temperature 298.0 time 120.0 timestep 4.0 trjfile trajectory.data trjfrequency 1 use_wavecars 0 version 6 yinatoms {} yinyang 0}
data.system {@Title Untitled
@Columns AsymmetricAtom
AtomicNumber int 0
Connections string {{}}
Fractional double {{0.0 0.0 0.0}}
Name string {{}}
Site int 1
WyckoffPosition int -1
@end
@data
6 {} {0.356215080463 0.541933749908 0.414455307153} C1 1 1
14 {} {0.332928714747 0.515282169489 0.525145864441} Si1 2 1
14 {} {0.417862368236 0.552746870246 0.410038596796} Si2 3 1
8 {} {0.346074968831 0.572028645655 0.601153234939} O1 4 1
8 {} {0.277930721356 0.513397802895 0.518206060394} O2 5 1
6 {} {0.3518680401 0.430068776367 0.559824456645} C2 6 1
6 {} {0.449108755003 0.472560804886 0.395363288594} C3 7 1
8 {} {0.430806398159 0.587755553059 0.508897744911} O3 8 1
8 {} {0.430898935087 0.604105921033 0.326926819366} O4 9 1
14 {} {0.227546853328 0.518014207252 0.55942475283} Si3 10 1
7 {} {0.207834510043 0.439919262605 0.593572375731} N1 11 1
14 {} {0.185381329295 0.431635163583 0.701026380003} Si4 12 1
14 {} {0.20839883029 0.372221127301 0.518540127934} Si5 13 1
7 {} {0.202339517141 0.393646575144 0.408196113354} N2 14 1
7 {} {0.134954880603 0.470683935895 0.721095828919} N3 15 1
1 {} {0.346200161106 0.5061854174 0.362133910999} H1 16 1
1 {} {0.3405833936 0.590287850424 0.397440837538} H2 17 1
1 {} {0.375943952764 0.590461740171 0.591529842512} H3 18 1
1 {} {0.343150302466 0.391498288915 0.510501790517} H4 19 1
1 {} {0.336162951772 0.416279347872 0.623544984719} H5 20 1
1 {} {0.388209097822 0.428863692452 0.569807553211} H6 21 1
1 {} {0.48519722294 0.482153824543 0.392200341503} H7 22 1
1 {} {0.43951999204 0.448271231048 0.332355632691} H8 23 1
1 {} {0.442987894528 0.436978834653 0.449851889947} H9 24 1
1 {} {0.461554207215 0.602365306885 0.515128502113} H10 25 1
1 {} {0.462871415256 0.606962149172 0.315574507495} H11 26 1
1 {} {0.225798074646 0.562228614989 0.63968236598} H12 27 1
1 {} {0.19866588078 0.546164604082 0.48776992211} H13 28 1
1 {} {0.178665608681 0.358555829269 0.715304437073} H14 29 1
1 {} {0.216921652342 0.460836607183 0.76705211782} H15 30 1
1 {} {0.251709722617 0.335733580122 0.524353222433} H16 31 1
1 {} {0.170825572075 0.327537480895 0.545104779017} H17 32 1
1 {} {0.229332073358 0.408076555703 0.372018421526} H18 33 1
1 {} {0.174300274697 0.416809910693 0.385880731214} H19 34 1
1 {} {0.134174753388 0.520270753847 0.73619648444} H20 35 1
1 {} {0.106905990969 0.456942844306 0.687611323297} H21 36 1
6 {} {0.634602736181 0.650748723499 0.348553131508} C4 37 1
14 {} {0.591516862624 0.588229490889 0.385948831447} Si6 38 1
14 {} {0.628959910199 0.739223090451 0.385025971615} Si7 39 1
8 {} {0.541236423643 0.623866889841 0.380536525523} O5 40 1
8 {} {0.592285253308 0.523743585237 0.318852324535} O6 41 1
6 {} {0.602565464447 0.556272684366 0.50084257017} C5 42 1
6 {} {0.647108937057 0.756286539792 0.50224919052} C6 43 1
8 {} {0.574106832973 0.754061959827 0.373485711429} O7 44 1
8 {} {0.656817040304 0.788531636195 0.315218391959} O8 45 1
14 {} {0.585884276713 0.463341837554 0.245944890121} Si8 46 1
7 {} {0.598379000641 0.385281606861 0.288932139478} N4 47 1
14 {} {0.55476457748 0.328942676596 0.312356877795} Si9 48 1
14 {} {0.65292418881 0.359931718283 0.314160677183} Si10 49 1
7 {} {0.694029758117 0.40602810252 0.263073786556} N5 50 1
7 {} {0.530742742304 0.285769367452 0.225547935705} N6 51 1
1 {} {0.668019452106 0.632405226952 0.367333130894} H22 52 1
1 {} {0.633868425032 0.651537698982 0.2748771218} H23 53 1
1 {} {0.54347749338 0.672917928184 0.375591593424} H24 54 1
1 {} {0.634684993451 0.529702236514 0.503517950998} H25 55 1
1 {} {0.576476423668 0.520721166916 0.521169138562} H26 56 1
1 {} {0.603488543921 0.596784678401 0.550445960331} H27 57 1
1 {} {0.641850150886 0.809059342476 0.520426461958} H28 58 1
1 {} {0.682702339071 0.744890435576 0.511627318156} H29 59 1
1 {} {0.628132595818 0.725732345279 0.550008338923} H30 60 1
1 {} {0.563678949968 0.799925775509 0.37063795427} H31 61 1
1 {} {0.67464286226 0.824298818214 0.340320008866} H32 62 1
1 {} {0.538229953459 0.461458050839 0.217208322338} H33 63 1
1 {} {0.615090352254 0.479428831015 0.168424460562} H34 64 1
1 {} {0.574723882763 0.278275938946 0.373626484554} H35 65 1
1 {} {0.518021023629 0.366947376304 0.35567826935} H36 66 1
1 {} {0.662221571294 0.365983400686 0.411670926819} H37 67 1
1 {} {0.656709367807 0.288503566325 0.286105740965} H38 68 1
1 {} {0.707204751604 0.446921991684 0.293354192493} H39 69 1
1 {} {0.696974791147 0.409096742695 0.195700641627} H40 70 1
1 {} {0.508687968084 0.309189270202 0.184549609436} H41 71 1
1 {} {0.548282331251 0.250430490213 0.191638490186} H42 72 1
@end
@Columns Cell
Constraints string {a b c A B G}
Origin int {{0 0 0}}
Parameters double {{10.0 10.0 10.0 90.0 90.0 90.0}}
PrimitiveData double {{{1.0 0.0 0.0} {0.0 1.0 0.0} {0.0 0.0 1.0}}}
RotationMatrix double {{{1.0 0.0 0.0} {0.0 1.0 0.0} {0.0 0.0 1.0}}}
SpaceGroup string P1
SpaceGroupNumber int 1
ToCartesians double {{{10.0 0.0 0.0} {0.0 10.0 0.0} {0.0 0.0 10.0}}}
ToFractionals double {{{0.10000000000000001 0.0 0.0} {0.0 0.10000000000000001 0.0} {0.0 0.0 0.10000000000000001}}}
@end
@data
{a b c A B G} {0 0 0} {30 20 15 90 90 90} {{1 0 0} {0 1 0} {0 0 1}} {{1 0 0} {0 1 0} {0 0 1}} P1 1 {{30 0 0} {0 20 0} {0 0 15}} {{0.0333333333333 0 0} {0 0.05 0} {0 0 0.0666666666667}}
@end
@Columns AsymmetricBond
Atom1 reference AsymmetricAtom
Atom2 reference AsymmetricAtom
Key int 0
Order int 0
@end
@data
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@end
@Columns Bond
AsymmetricBond reference AsymmetricBond
Atom1 reference Atom
Atom2 reference Atom
CellOffset2 int {{0 0 0}}
Key int 0
@end
@data
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@Columns Subset
Color string {{#65d9f0}}
Criteria string {{}}
DisplayLine int 0
IeqJ int 1
IgtJ int 0
IltJ int 0
Length int 1
Name string {{}}
Table string {{}}
Type string atom
UseColor int 0
@end
@data
@end}
data.finalsystem {@Title Untitled
@Columns AsymmetricAtom
AtomicNumber int 0
Connections string {{}}
Fractional double {{0.0 0.0 0.0}}
Name string {{}}
Site int 1
WyckoffPosition int -1
@end
@data
6 {} {0.356215080463 0.541933749908 0.414455307153} C1 1 1
14 {} {0.332928714747 0.515282169489 0.525145864441} Si1 2 1
14 {} {0.417862368236 0.552746870246 0.410038596796} Si2 3 1
8 {} {0.346074968831 0.572028645655 0.601153234939} O1 4 1
8 {} {0.277930721356 0.513397802895 0.518206060394} O2 5 1
6 {} {0.3518680401 0.430068776367 0.559824456645} C2 6 1
6 {} {0.449108755003 0.472560804886 0.395363288594} C3 7 1
8 {} {0.430806398159 0.587755553059 0.508897744911} O3 8 1
8 {} {0.430898935087 0.604105921033 0.326926819366} O4 9 1
14 {} {0.227546853328 0.518014207252 0.55942475283} Si3 10 1
7 {} {0.207834510043 0.439919262605 0.593572375731} N1 11 1
14 {} {0.185381329295 0.431635163583 0.701026380003} Si4 12 1
14 {} {0.20839883029 0.372221127301 0.518540127934} Si5 13 1
7 {} {0.202339517141 0.393646575144 0.408196113354} N2 14 1
7 {} {0.134954880603 0.470683935895 0.721095828919} N3 15 1
1 {} {0.346200161106 0.5061854174 0.362133910999} H1 16 1
1 {} {0.3405833936 0.590287850424 0.397440837538} H2 17 1
1 {} {0.375943952764 0.590461740171 0.591529842512} H3 18 1
1 {} {0.343150302466 0.391498288915 0.510501790517} H4 19 1
1 {} {0.336162951772 0.416279347872 0.623544984719} H5 20 1
1 {} {0.388209097822 0.428863692452 0.569807553211} H6 21 1
1 {} {0.48519722294 0.482153824543 0.392200341503} H7 22 1
1 {} {0.43951999204 0.448271231048 0.332355632691} H8 23 1
1 {} {0.442987894528 0.436978834653 0.449851889947} H9 24 1
1 {} {0.461554207215 0.602365306885 0.515128502113} H10 25 1
1 {} {0.462871415256 0.606962149172 0.315574507495} H11 26 1
1 {} {0.225798074646 0.562228614989 0.63968236598} H12 27 1
1 {} {0.19866588078 0.546164604082 0.48776992211} H13 28 1
1 {} {0.178665608681 0.358555829269 0.715304437073} H14 29 1
1 {} {0.216921652342 0.460836607183 0.76705211782} H15 30 1
1 {} {0.251709722617 0.335733580122 0.524353222433} H16 31 1
1 {} {0.170825572075 0.327537480895 0.545104779017} H17 32 1
1 {} {0.229332073358 0.408076555703 0.372018421526} H18 33 1
1 {} {0.174300274697 0.416809910693 0.385880731214} H19 34 1
1 {} {0.134174753388 0.520270753847 0.73619648444} H20 35 1
1 {} {0.106905990969 0.456942844306 0.687611323297} H21 36 1
6 {} {0.60063958424 0.564862017258 0.35562211089} C4 37 1
14 {} {0.557553710683 0.502342784648 0.393017810829} Si6 38 1
14 {} {0.594996758258 0.65333638421 0.392094950997} Si7 39 1
8 {} {0.507273271702 0.5379801836 0.387605504905} O5 40 1
8 {} {0.558322101367 0.437856878996 0.325921303917} O6 41 1
6 {} {0.568602312506 0.470385978125 0.507911549552} C5 42 1
6 {} {0.613145785116 0.670399833551 0.509318169902} C6 43 1
8 {} {0.540143681032 0.668175253586 0.380554690811} O7 44 1
8 {} {0.622853888363 0.702644929954 0.322287371341} O8 45 1
14 {} {0.551921124772 0.377455131313 0.253013869503} Si8 46 1
7 {} {0.5644158487 0.29939490062 0.29600111886} N4 47 1
14 {} {0.520801425539 0.243055970355 0.319425857177} Si9 48 1
14 {} {0.618961036869 0.274045012042 0.321229656565} Si10 49 1
7 {} {0.660066606176 0.320141396279 0.270142765938} N5 50 1
7 {} {0.496779590363 0.199882661211 0.232616915087} N6 51 1
1 {} {0.634056300165 0.546518520711 0.374402110276} H22 52 1
1 {} {0.599905273091 0.565650992741 0.281946101182} H23 53 1
1 {} {0.509514341439 0.587031221943 0.382660572806} H24 54 1
1 {} {0.60072184151 0.443815530273 0.51058693038} H25 55 1
1 {} {0.542513271727 0.434834460675 0.528238117944} H26 56 1
1 {} {0.56952539198 0.51089797216 0.557514939713} H27 57 1
1 {} {0.607886998945 0.723172636235 0.52749544134} H28 58 1
1 {} {0.64873918713 0.659003729335 0.518696297538} H29 59 1
1 {} {0.594169443877 0.639845639038 0.557077318305} H30 60 1
1 {} {0.529715798027 0.714039069268 0.377706933652} H31 61 1
1 {} {0.640679710319 0.738412111973 0.347388988248} H32 62 1
1 {} {0.504266801518 0.375571344598 0.22427730172} H33 63 1
1 {} {0.581127200313 0.393542124774 0.175493439944} H34 64 1
1 {} {0.540760730822 0.192389232705 0.380695463936} H35 65 1
1 {} {0.484057871688 0.281060670063 0.362747248732} H36 66 1
1 {} {0.628258419353 0.280096694445 0.418739906201} H37 67 1
1 {} {0.622746215866 0.202616860084 0.293174720347} H38 68 1
1 {} {0.673241599663 0.361035285443 0.300423171875} H39 69 1
1 {} {0.663011639206 0.323210036454 0.202769621009} H40 70 1
1 {} {0.474724816143 0.223302563961 0.191618588818} H41 71 1
1 {} {0.51431917931 0.164543783972 0.198707469568} H42 72 1
@end
@Columns Cell
Constraints string {a b c A B G}
Origin int {{0 0 0}}
Parameters double {{10.0 10.0 10.0 90.0 90.0 90.0}}
PrimitiveData double {{{1.0 0.0 0.0} {0.0 1.0 0.0} {0.0 0.0 1.0}}}
RotationMatrix double {{{1.0 0.0 0.0} {0.0 1.0 0.0} {0.0 0.0 1.0}}}
SpaceGroup string P1
SpaceGroupNumber int 1
ToCartesians double {{{10.0 0.0 0.0} {0.0 10.0 0.0} {0.0 0.0 10.0}}}
ToFractionals double {{{0.10000000000000001 0.0 0.0} {0.0 0.10000000000000001 0.0} {0.0 0.0 0.10000000000000001}}}
@end
@data
{a b c A B G} {0 0 0} {30 20 15 90 90 90} {{1 0 0} {0 1 0} {0 0 1}} {{1 0 0} {0 1 0} {0 0 1}} P1 1 {{30 0 0} {0 20 0} {0 0 15}} {{0.0333333333333 0 0} {0 0.05 0} {0 0 0.0666666666667}}
@end
@Columns AsymmetricBond
Atom1 reference AsymmetricAtom
Atom2 reference AsymmetricAtom
Key int 0
Order int 0
@end
@data
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@end
@Columns Bond
AsymmetricBond reference AsymmetricBond
Atom1 reference Atom
Atom2 reference Atom
CellOffset2 int {{0 0 0}}
Key int 0
@end
@data
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@end
@Columns Subset
Color string {{#65d9f0}}
Criteria string {{}}
DisplayLine int 0
IeqJ int 1
IgtJ int 0
IltJ int 0
Length int 1
Name string {{}}
Table string {{}}
Type string atom
UseColor int 0
@end
@data
@end}
job.status running
job.started {2024-09-28 23:25:10}
job.pid 12249