./db.backup output for 3: 3.3A-->1.3A 709 (amd-9) Si-H2N...HCH2-Si two dimer (TSS)
Status:
running
job.id 3
job.name {3.3A-->1.3A 709 (amd-9) Si-H2N...HCH2-Si two dimer (TSS)}
job.description {}
job.status running
job.submitted {2024-09-28 22:42:51}
job.started {2024-09-28 22:42:52}
job.finished {0000-00-00 00:00:00}
job.queue 2
job.errormsg {}
job.pid 6899
job.userid 1
job.priority 5
job.jobserverid 2
data.joboptions {_protocol_type_ JobControl _description_ {} passwd {} _name_ {} nproc 3 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 ::system18 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 {} initialimage9 {} 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 9 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 1 refineTS_RMMDIIS 1 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 709 Si-H2N...HCH2-Si two dimer (TSS)} 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 {} {0.199935282067 0.529643061979 0.301496033017} C1 1 1
14 {} {0.25387642255 0.492677954647 0.259645352183} Si1 2 1
14 {} {0.153229137346 0.538168250574 0.220526348456} Si2 3 1
8 {} {0.266500310909 0.525891935575 0.161906057349} O1 4 1
8 {} {0.293820223708 0.512945264722 0.330664787066} O2 5 1
6 {} {0.251900932138 0.399479738131 0.252635548661} C2 6 1
6 {} {0.121702555279 0.458440552998 0.20274510714} C3 7 1
8 {} {0.177732721821 0.563961049722 0.126222295208} O3 8 1
8 {} {0.117883895847 0.599336578956 0.24735475669} O4 9 1
14 {} {0.345319584713 0.541855334239 0.335711719858} Si3 10 1
7 {} {0.380065685767 0.478948368494 0.377347127063} N1 11 1
14 {} {0.43451423767 0.477423844949 0.336514733017} Si4 12 1
14 {} {0.359679931456 0.424761809943 0.46014645387} Si5 13 1
7 {} {0.330566781674 0.46259570576 0.545552847662} N2 14 1
7 {} {0.456486223022 0.557158174307 0.342700782296} N3 15 1
1 {} {0.188316563828 0.501050459929 0.360003593197} H1 16 1
1 {} {0.207748917585 0.580481916934 0.325698580336} H2 17 1
1 {} {0.240917559008 0.545878022823 0.13116490364} H3 18 1
1 {} {0.246745213527 0.376546309015 0.318523769794} H4 19 1
1 {} {0.283626780276 0.380508052673 0.225837707697} H5 20 1
1 {} {0.225124831861 0.382383813687 0.20792260537} H6 21 1
1 {} {0.0951802205141 0.464601459062 0.152696706706} H7 22 1
1 {} {0.106169686503 0.440675392028 0.264915796094} H8 23 1
1 {} {0.144110205567 0.41864196451 0.179118831444} H9 24 1
1 {} {0.159255175376 0.587072958121 0.0829812100745} H10 25 1
1 {} {0.0895068406496 0.586958759178 0.273463117199} H11 26 1
1 {} {0.361718152826 0.561843983686 0.245777087074} H12 27 1
1 {} {0.344188315795 0.6007414551 0.396802851255} H13 28 1
1 {} {0.4585242447 0.424994464063 0.389130899383} H14 29 1
1 {} {0.436614215954 0.460098292549 0.239695881251} H15 30 1
1 {} {0.328194519491 0.375592240849 0.419888043944} H16 31 1
1 {} {0.399147177279 0.390527553948 0.499463971856} H17 32 1
1 {} {0.29894370409 0.479055399258 0.534619387214} H18 33 1
1 {} {0.346590911863 0.492959955565 0.589585682867} H19 34 1
1 {} {0.479344612713 0.572072018171 0.296638981384} H20 35 1
1 {} {0.462302776795 0.579281643326 0.402663184502} H21 36 1
6 {} {0.660261528646 0.63616120598 0.511209916337} C4 37 1
14 {} {0.620769156363 0.572320023562 0.463274682657} Si6 38 1
14 {} {0.657893506115 0.722796978989 0.466341291827} Si7 39 1
8 {} {0.618503332646 0.580599045473 0.35362824836} O5 40 1
8 {} {0.640454393445 0.497560906217 0.487545335031} O6 41 1
6 {} {0.563669010097 0.578464734746 0.512302297222} C5 42 1
6 {} {0.610318997408 0.773248270105 0.511056753271} C6 43 1
8 {} {0.653573231261 0.712065157641 0.355890472163} O7 44 1
8 {} {0.705540479457 0.76415411746 0.482018371693} O8 45 1
14 {} {0.651081511585 0.419703611154 0.459654570887} Si8 46 1
7 {} {0.605745181596 0.367507058063 0.47776930403} N4 47 1
14 {} {0.586188549076 0.318312359198 0.389262280777} Si9 48 1
14 {} {0.581091898365 0.364215968177 0.584296491014} Si10 49 1
7 {} {0.616285193644 0.382965665438 0.671224794072} N5 50 1
7 {} {0.621239823032 0.255615666531 0.352001481369} N6 51 1
1 {} {0.65612185163 0.637701134977 0.584285228276} H22 52 1
1 {} {0.694322258879 0.617335786353 0.498749436156} H23 53 1
1 {} {0.630802565834 0.622961375433 0.331825746358} H24 54 1
1 {} {0.563849751286 0.568489409148 0.584449267959} H25 55 1
1 {} {0.541588272208 0.541518976175 0.480525845243} H26 56 1
1 {} {0.549248224375 0.628438497188 0.501485715452} H27 57 1
1 {} {0.609573122685 0.823687326997 0.481684948362} H28 58 1
1 {} {0.612383789591 0.778773034696 0.583987351943} H29 59 1
1 {} {0.578257338288 0.749080743132 0.495856166833} H30 60 1
1 {} {0.66162513468 0.749439965274 0.317937344335} H31 61 1
1 {} {0.70586937577 0.79920438269 0.526634604916} H32 62 1
1 {} {0.662627520639 0.414637118965 0.362923454859} H33 63 1
1 {} {0.690258468808 0.399317474287 0.514438468497} H34 64 1
1 {} {0.544419162201 0.286275828632 0.42215322939} H35 65 1
1 {} {0.578032715376 0.36116111551 0.309685430699} H36 66 1
1 {} {0.543902876888 0.413606189624 0.590455019144} H37 67 1
1 {} {0.563869099274 0.294814395077 0.595981656065} H38 68 1
1 {} {0.622871311294 0.431557048821 0.686188211123} H39 69 1
1 {} {0.643298938216 0.35385679557 0.68431462785} H40 70 1
1 {} {0.645859610444 0.266664726795 0.307754586159} H41 71 1
1 {} {0.630796124384 0.217837117856 0.393252755668} 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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69 50 71 {0 0 0} 0
@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}
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 {} {0.199935282067 0.529643061979 0.301496033017} C1 1 1
14 {} {0.25387642255 0.492677954647 0.259645352183} Si1 2 1
14 {} {0.153229137346 0.538168250574 0.220526348456} Si2 3 1
8 {} {0.266500310909 0.525891935575 0.161906057349} O1 4 1
8 {} {0.293820223708 0.512945264722 0.330664787066} O2 5 1
6 {} {0.251900932138 0.399479738131 0.252635548661} C2 6 1
6 {} {0.121702555279 0.458440552998 0.20274510714} C3 7 1
8 {} {0.177732721821 0.563961049722 0.126222295208} O3 8 1
8 {} {0.117883895847 0.599336578956 0.24735475669} O4 9 1
14 {} {0.345319584713 0.541855334239 0.335711719858} Si3 10 1
7 {} {0.380065685767 0.478948368494 0.377347127063} N1 11 1
14 {} {0.43451423767 0.477423844949 0.336514733017} Si4 12 1
14 {} {0.359679931456 0.424761809943 0.46014645387} Si5 13 1
7 {} {0.330566781674 0.46259570576 0.545552847662} N2 14 1
7 {} {0.456486223022 0.557158174307 0.342700782296} N3 15 1
1 {} {0.188316563828 0.501050459929 0.360003593197} H1 16 1
1 {} {0.207748917585 0.580481916934 0.325698580336} H2 17 1
1 {} {0.240917559008 0.545878022823 0.13116490364} H3 18 1
1 {} {0.246745213527 0.376546309015 0.318523769794} H4 19 1
1 {} {0.283626780276 0.380508052673 0.225837707697} H5 20 1
1 {} {0.225124831861 0.382383813687 0.20792260537} H6 21 1
1 {} {0.0951802205141 0.464601459062 0.152696706706} H7 22 1
1 {} {0.106169686503 0.440675392028 0.264915796094} H8 23 1
1 {} {0.144110205567 0.41864196451 0.179118831444} H9 24 1
1 {} {0.159255175376 0.587072958121 0.0829812100745} H10 25 1
1 {} {0.0895068406496 0.586958759178 0.273463117199} H11 26 1
1 {} {0.361718152826 0.561843983686 0.245777087074} H12 27 1
1 {} {0.344188315795 0.6007414551 0.396802851255} H13 28 1
1 {} {0.4585242447 0.424994464063 0.389130899383} H14 29 1
1 {} {0.436614215954 0.460098292549 0.239695881251} H15 30 1
1 {} {0.328194519491 0.375592240849 0.419888043944} H16 31 1
1 {} {0.399147177279 0.390527553948 0.499463971856} H17 32 1
1 {} {0.29894370409 0.479055399258 0.534619387214} H18 33 1
1 {} {0.346590911863 0.492959955565 0.589585682867} H19 34 1
1 {} {0.479344612713 0.572072018171 0.296638981384} H20 35 1
1 {} {0.462302776795 0.579281643326 0.402663184502} H21 36 1
6 {} {0.608684529139 0.645639507878 0.427679575157} C4 37 1
14 {} {0.569192156856 0.58179832546 0.379744341477} Si6 38 1
14 {} {0.606316506608 0.732275280887 0.382810950647} Si7 39 1
8 {} {0.566926333139 0.590077347371 0.27009790718} O5 40 1
8 {} {0.588877393938 0.507039208115 0.404014993851} O6 41 1
6 {} {0.51209201059 0.587943036644 0.428771956042} C5 42 1
6 {} {0.558741997901 0.782726572003 0.427526412091} C6 43 1
8 {} {0.601996231754 0.721543459539 0.272360130983} O7 44 1
8 {} {0.65396347995 0.773632419358 0.398488030513} O8 45 1
14 {} {0.599504512078 0.429181913052 0.376124229707} Si8 46 1
7 {} {0.554168182089 0.376985359961 0.39423896285} N4 47 1
14 {} {0.534611549569 0.327790661096 0.305731939597} Si9 48 1
14 {} {0.529514898858 0.373694270075 0.500766149834} Si10 49 1
7 {} {0.564708194137 0.392443967336 0.587694452892} N5 50 1
7 {} {0.569662823525 0.265093968429 0.268471140189} N6 51 1
1 {} {0.604544852123 0.647179436875 0.500754887096} H22 52 1
1 {} {0.642745259372 0.626814088251 0.415219094976} H23 53 1
1 {} {0.579225566327 0.632439677331 0.248295405178} H24 54 1
1 {} {0.512272751779 0.577967711046 0.500918926779} H25 55 1
1 {} {0.490011272701 0.550997278073 0.396995504063} H26 56 1
1 {} {0.497671224868 0.637916799086 0.417955374272} H27 57 1
1 {} {0.557996123178 0.833165628895 0.398154607182} H28 58 1
1 {} {0.560806790084 0.788251336594 0.500457010763} H29 59 1
1 {} {0.526680338781 0.75855904503 0.412325825653} H30 60 1
1 {} {0.610048135173 0.758918267172 0.234407003155} H31 61 1
1 {} {0.654292376263 0.808682684588 0.443104263736} H32 62 1
1 {} {0.611050521132 0.424115420863 0.279393113679} H33 63 1
1 {} {0.638681469301 0.408795776185 0.430908127317} H34 64 1
1 {} {0.492842162694 0.29575413053 0.33862288821} H35 65 1
1 {} {0.526455715869 0.370639417408 0.226155089519} H36 66 1
1 {} {0.492325877381 0.423084491522 0.506924677964} H37 67 1
1 {} {0.512292099767 0.304292696975 0.512451314885} H38 68 1
1 {} {0.571294311787 0.441035350719 0.602657869943} H39 69 1
1 {} {0.591721938709 0.363335097468 0.60078428667} H40 70 1
1 {} {0.594282610937 0.276143028693 0.224224244979} H41 71 1
1 {} {0.579219124877 0.227315419754 0.309722414488} 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}