job.id 64 job.name {63-->62 AMIa + NH2, to AMIa Si-NH2 + OCH3* (TSS)} job.description { } job.status finished job.submitted {2024-10-03 21:54:28} job.started {2024-10-03 21:54:29} job.finished {2024-10-04 12:25:33} job.queue 2 job.errormsg {} job.pid 0 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 ::system77 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 0 refineTS_RMMDIIS 0 refineTSmethod {Elastic Band Methods} refine_transitionstate {the highest saddle point only} 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 {63-->62 AMIa + NH2, to AMIa Si-NH2 + OCH3* (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 {0.419 0.419 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 {0.419 0.419 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 {} 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 Spin double 0.0 WyckoffPosition int -1 @end @data 7 {} {0.598650641545 0.387987996995 0.452899799734} N 1 0.52800000000000002 1 1 {} {0.621422395398 0.396557509937 0.517805160622} H2 2 -0.0040000000000000001 1 1 {} {0.530233362852 0.37972130881 0.462291285365} H3 3 -0.0040000000000000001 1 6 {} {0.379695758503 0.544703983134 0.48085859062} C1 4 0.001 1 14 {} {0.311344166396 0.442195940379 0.459959254898} Si1 5 0.0 1 14 {} {0.32084690799 0.647089847401 0.520568022886} Si2 6 0.0 1 8 {} {0.30864249207 0.631750904879 0.629245274333} O1 7 0.0 1 6 {} {0.26916566717 0.695621456246 0.687621817861} C2 8 0.0 1 1 {} {0.302375484505 0.760962460482 0.682137332218} H4 9 0.0 1 1 {} {0.197387106294 0.703995823844 0.673670738174} H5 10 0.0 1 1 {} {0.27669993175 0.671171667164 0.756315489012} H6 11 0.0 1 8 {} {0.384967014559 0.737105704064 0.510553768219} O2 12 0.0 1 6 {} {0.395954797778 0.78951521268 0.432427639348} C3 13 0.0 1 1 {} {0.436460151157 0.754436528136 0.38187285588} H7 14 0.0 1 1 {} {0.331350907182 0.807714295194 0.402115459083} H8 15 0.0 1 1 {} {0.430989191961 0.851209016904 0.45101199062} H9 16 0.0 1 8 {} {0.230716464743 0.426615836426 0.533881825427} O3 17 0.0 1 6 {} {0.244929105154 0.411073386034 0.626895274947} C4 18 0.0 1 1 {} {0.180409242671 0.393277569354 0.656841118162} H10 19 0.0 1 1 {} {0.29191724988 0.355555194566 0.637954496448} H11 20 0.0 1 1 {} {0.270631590399 0.471482788669 0.659882131496} H12 21 0.0 1 8 {} {0.385172727473 0.35891690227 0.464406954739} O4 22 -0.002 1 6 {} {0.359862328992 0.267284626995 0.457157416215} C5 23 0.0 1 1 {} {0.359669937261 0.235781122088 0.523542965205} H13 24 0.0 1 1 {} {0.292987673801 0.259095265409 0.427670169739} H14 25 0.0 1 1 {} {0.408585873677 0.232498854807 0.414750412615} H15 26 0.0 1 6 {} {0.21141028743 0.667733802279 0.46378494635} C6 27 0.0 1 1 {} {0.180298341877 0.729844211973 0.487472843436} H16 28 0.0 1 1 {} {0.218856298264 0.673153588269 0.390933986081} H17 29 0.0 1 1 {} {0.165013413391 0.612524733311 0.477311747801} H18 30 0.0 1 6 {} {0.252951934402 0.444478135724 0.349935699725} C7 31 0.0 1 1 {} {0.202458879983 0.497598694092 0.347926631741} H19 32 0.0 1 1 {} {0.300565811589 0.455911058642 0.295322476069} H20 33 0.0 1 1 {} {0.218510631811 0.38101960819 0.337018100081} H21 34 0.0 1 1 {} {0.415560569852 0.560251961488 0.41844000102} H22 35 0.0 1 1 {} {0.431521170242 0.529389053166 0.530815733831} H23 36 0.0 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} {15 15 15 90 90 90} {{1 0 0} {0 1 0} {0 0 1}} {{1 0 0} {0 1 0} {0 0 1}} P1 1 {{15 0 0} {0 15 0} {0 0 15}} {{0.0666666666667 0 0} {0 0.0666666666667 0} {0 0 0.0666666666667}} @end @Columns AsymmetricBond Atom1 reference AsymmetricAtom Atom2 reference AsymmetricAtom Key int 0 Order int 0 @end @data 1 0 0 0 2 0 0 0 5 3 0 0 6 5 0 0 7 6 0 0 8 7 0 0 9 7 0 0 10 7 0 0 11 5 0 0 12 11 0 0 13 12 0 0 14 12 0 0 15 12 0 0 16 4 0 0 17 16 0 0 18 17 0 0 19 17 0 0 20 17 0 0 23 22 0 0 24 22 0 0 25 22 0 0 26 5 0 0 27 26 0 0 28 26 0 0 29 26 0 0 30 4 0 0 31 30 0 0 32 30 0 0 33 30 0 0 34 3 0 0 35 3 0 0 4 3 0 0 22 21 0 0 21 4 0 0 @end @Columns Bond AsymmetricBond reference AsymmetricBond Atom1 reference Atom Atom2 reference Atom CellOffset2 int {{0 0 0}} Key int 0 @end @data 0 0 1 {0 0 0} 0 1 0 2 {0 0 0} 0 2 3 5 {0 0 0} 0 3 5 6 {0 0 0} 0 4 7 6 {0 0 0} 0 5 8 7 {0 0 0} 0 6 9 7 {0 0 0} 0 7 10 7 {0 0 0} 0 8 5 11 {0 0 0} 0 9 12 11 {0 0 0} 0 10 13 12 {0 0 0} 0 11 14 12 {0 0 0} 0 12 15 12 {0 0 0} 0 13 4 16 {0 0 0} 0 14 17 16 {0 0 0} 0 15 18 17 {0 0 0} 0 16 19 17 {0 0 0} 0 17 20 17 {0 0 0} 0 18 23 22 {0 0 0} 0 19 24 22 {0 0 0} 0 20 25 22 {0 0 0} 0 21 5 26 {0 0 0} 0 22 26 27 {0 0 0} 0 23 26 28 {0 0 0} 0 24 26 29 {0 0 0} 0 25 4 30 {0 0 0} 0 26 30 31 {0 0 0} 0 27 30 32 {0 0 0} 0 28 30 33 {0 0 0} 0 29 3 34 {0 0 0} 0 30 3 35 {0 0 0} 0 31 3 4 {0 0 0} 0 32 21 22 {0 0 0} 0 33 4 21 {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 Spin double 0.0 WyckoffPosition int -1 @end @data 7 {} {0.413814898662 0.36960739479 0.467594621597} N 1 0.084000000000000005 1 1 {} {0.46994982582 0.377547998452 0.504661788262} H2 2 0.0 1 1 {} {0.405622916487 0.305162564716 0.445715040578} H3 3 0.0 1 6 {} {0.389003916191 0.560280732915 0.484866090715} C1 4 0.002 1 14 {} {0.33164963935 0.450694942258 0.46276791691} Si1 5 0.0 1 14 {} {0.321144521471 0.656897934217 0.524611683597} Si2 6 0.001 1 8 {} {0.309425812655 0.64114078581 0.633243088306} O1 7 0.0 1 6 {} {0.264212791064 0.701544066198 0.69101189917} C2 8 0.0 1 1 {} {0.292924355992 0.769101578373 0.686878108091} H4 9 0.0 1 1 {} {0.192375882603 0.705128324347 0.675318478173} H5 10 0.0 1 1 {} {0.271655235386 0.677033344536 0.759709068258} H6 11 0.0 1 8 {} {0.377169309184 0.752564118594 0.515253448445} O2 12 0.001 1 6 {} {0.391526139971 0.799653540488 0.434453533873} C3 13 0.0 1 1 {} {0.434461995592 0.761836845653 0.387989737992} H7 14 0.0 1 1 {} {0.328285885028 0.815436526787 0.400117673674} H8 15 0.0 1 1 {} {0.425503921333 0.862728097057 0.450377559063} H9 16 0.0 1 8 {} {0.24876112232 0.433165856938 0.534540782039} O3 17 0.012 1 6 {} {0.259948405146 0.413806910399 0.626890780651} C4 18 0.0 1 1 {} {0.19413410834 0.396953315184 0.654546306076} H10 19 0.0 1 1 {} {0.304528768407 0.356072469843 0.636841596109} H11 20 0.0 1 1 {} {0.286634103342 0.471886723685 0.66329939758} H12 21 0.0 1 8 {} {0.365586067357 0.187727106225 0.428783497319} O4 22 0.49399999999999999 1 6 {} {0.390588642629 0.105837962899 0.459700625379} C5 23 0.0030000000000000001 1 1 {} {0.418099800588 0.112494468385 0.528590223882} H13 24 0.014999999999999999 1 1 {} {0.336782695882 0.0552308276268 0.460199914723} H14 25 -0.001 1 1 {} {0.449279491895 0.0806414404175 0.421417841559} H15 26 0.012 1 6 {} {0.210710680349 0.668849761636 0.467247963116} C6 27 0.0 1 1 {} {0.174182932808 0.727750784065 0.491471002987} H16 28 0.0 1 1 {} {0.218384612948 0.676040676279 0.394591065911} H17 29 0.0 1 1 {} {0.169358642853 0.609485565744 0.479448837436} H18 30 0.0 1 6 {} {0.27619568708 0.446076679128 0.351433243927} C7 31 0.001 1 1 {} {0.218782199448 0.491538178383 0.347936029097} H19 32 0.0 1 1 {} {0.32316367843 0.46376770029 0.297961729873} H20 33 0.0 1 1 {} {0.25176072208 0.378108944982 0.338487542794} H21 34 0.0 1 1 {} {0.423667759615 0.579691486154 0.422824549455} H22 35 0.0 1 1 {} {0.441726281695 0.550927466544 0.535457103384} H23 36 0.0 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} {15 15 15 90 90 90} {{1 0 0} {0 1 0} {0 0 1}} {{1 0 0} {0 1 0} {0 0 1}} P1 1 {{15 0 0} {0 15 0} {0 0 15}} {{0.0666666666667 0 0} {0 0.0666666666667 0} {0 0 0.0666666666667}} @end @Columns AsymmetricBond Atom1 reference AsymmetricAtom Atom2 reference AsymmetricAtom Key int 0 Order int 0 @end @data 1 0 0 0 2 0 0 0 5 3 0 0 6 5 0 0 7 6 0 0 8 7 0 0 9 7 0 0 10 7 0 0 11 5 0 0 12 11 0 0 13 12 0 0 14 12 0 0 15 12 0 0 16 4 0 0 17 16 0 0 18 17 0 0 19 17 0 0 20 17 0 0 23 22 0 0 24 22 0 0 25 22 0 0 26 5 0 0 27 26 0 0 28 26 0 0 29 26 0 0 30 4 0 0 31 30 0 0 32 30 0 0 33 30 0 0 34 3 0 0 35 3 0 0 4 3 0 0 22 21 0 0 4 0 0 0 @end @Columns Bond AsymmetricBond reference AsymmetricBond Atom1 reference Atom Atom2 reference Atom CellOffset2 int {{0 0 0}} Key int 0 @end @data 0 0 1 {0 0 0} 0 1 0 2 {0 0 0} 0 2 3 5 {0 0 0} 0 3 5 6 {0 0 0} 0 4 7 6 {0 0 0} 0 5 8 7 {0 0 0} 0 6 9 7 {0 0 0} 0 7 10 7 {0 0 0} 0 8 5 11 {0 0 0} 0 9 12 11 {0 0 0} 0 10 13 12 {0 0 0} 0 11 14 12 {0 0 0} 0 12 15 12 {0 0 0} 0 13 4 16 {0 0 0} 0 14 17 16 {0 0 0} 0 15 18 17 {0 0 0} 0 16 19 17 {0 0 0} 0 17 20 17 {0 0 0} 0 18 23 22 {0 0 0} 0 19 24 22 {0 0 0} 0 20 25 22 {0 0 0} 0 21 5 26 {0 0 0} 0 22 26 27 {0 0 0} 0 23 26 28 {0 0 0} 0 24 26 29 {0 0 0} 0 25 4 30 {0 0 0} 0 26 30 31 {0 0 0} 0 27 30 32 {0 0 0} 0 28 30 33 {0 0 0} 0 29 3 34 {0 0 0} 0 30 3 35 {0 0 0} 0 31 3 4 {0 0 0} 0 32 21 22 {0 0 0} 0 33 0 4 {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}