job.id 5 job.name {753-->748: AMIa + NH2*, to AMIa-ONH2 + CH3* (TSS)} job.description { } job.status finished job.submitted {2024-09-29 22:09:57} job.started {2024-09-29 22:09:58} job.finished {2024-09-30 08:47:48} 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 ::system92 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 300 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 {753-->748: AMIa + NH2*, to AMIa-ONH2 + CH3* (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 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 Spin double 0.0 WyckoffPosition int -1 @end @data 7 {} {0.616490121384 0.409312223982 0.417791265595} N 1 0.53400000000000003 1 1 {} {0.557029775704 0.390787564918 0.448768006044} H2 2 -0.0040000000000000001 1 1 {} {0.657200637301 0.354280445885 0.428484483595} H3 3 -0.0040000000000000001 1 6 {} {0.393498794475 0.542798078612 0.497688184301} C1 4 0.0 1 14 {} {0.33923913821 0.432850854778 0.473883551705} Si1 5 0.0 1 14 {} {0.322027290644 0.640399625817 0.527357276488} Si2 6 0.0 1 8 {} {0.301040841601 0.629144419041 0.635111139799} O1 7 0.0 1 6 {} {0.254954401126 0.693916266074 0.687318627347} C2 8 0.0 1 1 {} {0.288250228574 0.759367531898 0.684049724552} H4 9 0.0 1 1 {} {0.185112254062 0.701573589726 0.665328189698} H5 10 0.0 1 1 {} {0.254921307649 0.670897390262 0.756928641659} H6 11 0.0 1 8 {} {0.378614407015 0.735556625691 0.518499595936} O2 12 0.0 1 6 {} {0.397968730487 0.780914191159 0.437647908593} C3 13 0.0 1 1 {} {0.44305772477 0.741609112741 0.39463127999} H7 14 0.0 1 1 {} {0.3368563026 0.796316326436 0.399529331922} H8 15 0.0 1 1 {} {0.431428387682 0.844021109134 0.454274860987} H9 16 0.0 1 8 {} {0.253902765087 0.409253216569 0.539743277753} O3 17 0.0 1 6 {} {0.258968934606 0.401153770039 0.634690916066} C4 18 0.0 1 1 {} {0.194501358348 0.37544251394 0.658334367881} H10 19 0.0 1 1 {} {0.311765522706 0.35410888761 0.655023438765} H11 20 0.0 1 1 {} {0.271555257084 0.466401750344 0.665991421454} H12 21 0.0 1 8 {} {0.421136956241 0.35847669029 0.489124482296} O4 22 -0.001 1 6 {} {0.405913159932 0.264697556662 0.481071611634} C5 23 0.0 1 1 {} {0.461068497277 0.229658335533 0.514307372486} H13 24 0.0 1 1 {} {0.342773309324 0.24450073965 0.512869077941} H14 25 0.0 1 1 {} {0.404350039506 0.244157969941 0.410470003395} H15 26 0.0 1 6 {} {0.216677674103 0.64907302641 0.460618462624} C6 27 0.0 1 1 {} {0.177627025594 0.707983111087 0.48046776731} H16 28 0.0 1 1 {} {0.230236308096 0.654849934067 0.388677071431} H17 29 0.0 1 1 {} {0.174896102423 0.589612545435 0.470753525067} H18 30 0.0 1 6 {} {0.293045115967 0.425277420655 0.358414147133} C7 31 0.0 1 1 {} {0.239654847031 0.474402838172 0.347807450111} H19 32 0.0 1 1 {} {0.34541889519 0.437310020145 0.30847790957} H20 33 0.0 1 1 {} {0.264570732343 0.358822040307 0.346078713115} H21 34 0.0 1 1 {} {0.434083216336 0.560052081527 0.438641149728} H22 35 0.0 1 1 {} {0.441377169521 0.534321905462 0.552938766029} 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 21 4 0 0 22 21 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 4 21 {0 0 0} 0 33 21 22 {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 {} {0.503849830907 0.370964242958 0.447415528453} N 1 0.0030000000000000001 1 1 {} {0.554114801403 0.375416497669 0.493932047735} H2 2 0.0 1 1 {} {0.51205009659 0.309270382158 0.418316721836} H3 3 0.0 1 6 {} {0.397029747169 0.552799600105 0.494597080304} C1 4 0.0 1 14 {} {0.348670617052 0.438910598895 0.474922618485} Si1 5 0.0 1 14 {} {0.320374625824 0.645693528215 0.526852339091} Si2 6 0.0 1 8 {} {0.304324032136 0.63260878724 0.635310082413} O1 7 0.0 1 6 {} {0.256102961582 0.693779400572 0.689818444417} C2 8 0.0 1 1 {} {0.28498394475 0.761256574684 0.686059536032} H4 9 0.0 1 1 {} {0.185162625847 0.697182278374 0.670413300109} H5 10 0.0 1 1 {} {0.260043088052 0.670185252888 0.759141457093} H6 11 0.0 1 8 {} {0.36906382016 0.744959066008 0.516692103131} O2 12 0.0 1 6 {} {0.381855127752 0.792512944109 0.435838138651} C3 13 0.0 1 1 {} {0.431595669671 0.759567060632 0.392625864767} H7 14 0.0 1 1 {} {0.319168957569 0.799884216572 0.397883189539} H8 15 0.0 1 1 {} {0.406664391002 0.85953336968 0.452379157094} H9 16 0.0 1 8 {} {0.262824792753 0.415601485034 0.539914565272} O3 17 0.0 1 6 {} {0.265500862171 0.406961905975 0.634837162798} C4 18 0.0 1 1 {} {0.197406766206 0.392219959041 0.657656355675} H10 19 0.0 1 1 {} {0.309598516028 0.351738032763 0.654895325404} H11 20 0.0 1 1 {} {0.288148248157 0.469249541498 0.666543433835} H12 21 0.0 1 8 {} {0.423676672884 0.358894958474 0.502001697389} O4 22 0.0 1 6 {} {0.424856821738 0.129024532822 0.440516000787} C5 23 0.39900000000000002 1 1 {} {0.464769699739 0.0833329110361 0.480319849688} H13 24 -0.0040000000000000001 1 1 {} {0.403558090736 0.192570496399 0.468480974169} H14 25 -0.0040000000000000001 1 1 {} {0.40358335107 0.109331496089 0.373987602664} H15 26 -0.0040000000000000001 1 6 {} {0.212383435729 0.646021285664 0.463802284396} C6 27 0.0 1 1 {} {0.168200985599 0.700063918706 0.486542989193} H16 28 0.0 1 1 {} {0.222897409724 0.655016623863 0.391680555364} H17 29 0.0 1 1 {} {0.177396725567 0.582246521044 0.473502351151} H18 30 0.0 1 6 {} {0.308796185676 0.425014833651 0.358004930477} C7 31 0.0 1 1 {} {0.260350836257 0.47706429694 0.340019180475} H19 32 0.0 1 1 {} {0.365103870364 0.429043147024 0.311157632424} H20 33 0.0 1 1 {} {0.276232514499 0.359839678107 0.349693843903} H21 34 0.0 1 1 {} {0.432731278045 0.571832715107 0.433064511148} H22 35 0.0 1 1 {} {0.448156069594 0.548923950002 0.54742091464} 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 21 4 0 0 21 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 4 21 {0 0 0} 0 33 0 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}