[Fri Sep 15 22:36:36 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/529/pcff+.frc md5 sum: 271FB553B535FE0449E31A6F8A0898D3 MedeA version 3.6.0 #------------------------------------------------------------------------------- # This calculation has 2 stages #------------------------------------------------------------------------------- Stage 1: Variables tstep = 1 fs T = 298.2 K P = 1 atm Stage 2: This LAMMPS calculation has 6 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/529/pcff+.frc) Current system formula: K671Na2Li10Mg206S31Cl1033O2892H5536 (K671Na2Li10Mg206S31Cl1033O2892H5536) The nonbond terms are handled with a cutoff at 12 Angstrom. The long-range Coulomb interactions are handled with the pppm method to a precision of 0.00001. The long-range van der Waals interactions are included via tail corrections. Stage 2.2: Minimize using conjugate gradients and linesearch fast Relative energy convergence: 0.0 Force convergence: 1.0 Maximum atomic motion: 0.05 Maximum number of iterations: 1000 Maximum number of force evaluations: 10000 Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NVT integration for 2 ns with a timestep of 1 fs T is 298.2 K Stage 2.5: NVT integration for 5 ns with a timestep of 1 fs T is 298.2 K Stage 2.6: Surface tension calculation using NVT integration for 2 ns with a timestep of 1 fs, T is 298.2 K #------------------------------------------------------------------------------- # Running the calculation #------------------------------------------------------------------------------- Stage 1: Variables tstep = 1 fs T = 298.2 K P = 1 atm Stage 2: This LAMMPS calculation has 6 stages: ***** LAMMPS error in LAMMPS.out ***** ERROR: Atom count is inconsistent, cannot write restart file (../write_restart.cpp:228) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/529/pcff+.frc) Current system formula: K671Na2Li10Mg206S31Cl1033O2892H5536 (K671Na2Li10Mg206S31Cl1033O2892H5536) The nonbond terms are handled with a cutoff at 12 Angstrom. The long-range Coulomb interactions are handled with the pppm method to a precision of 0.00001. The long-range van der Waals interactions are included via tail corrections. Stage 2.2: Minimize using conjugate gradients and linesearch fast Relative energy convergence: 0.0 Force convergence: 1.0 Maximum atomic motion: 0.05 Maximum number of iterations: 1000 Maximum number of force evaluations: 10000 Note: 2.2_Minimization.out contains warning messages from LAMMPS - examine this file for additional information. The minimization finished after 35 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 35 Initial Fmax: 20673.8 kJ/mol/Ang Fmax: 31141.7 kJ/mol/Ang Initial Frms: 961.0 kJ/mol/Ang Frms: 577.0 kJ/mol/Ang P: 7956.8 atm V: 138883.6 Ang^3 rho: 1.4446 g/mL Sxx: -8931.7 atm Syy: -8273.0 atm Szz: -6665.7 atm Syz: -112.2 atm Sxz: 316.2 atm Sxy: -413.8 atm Initial Epot: -27843.4 kJ/mol Epot: -1012668.2 kJ/mol a: 35.8935 Ang b: 35.8935 Ang c: 107.8000 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: -0.1 kJ/mol/Ang sum_fy: 0.0 kJ/mol/Ang sum_fz: -17.3 kJ/mol/Ang Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NVT integration for 2 ns with a timestep of 1 fs T is 298.2 K An error occurred creating the resulting structure file 2.4.sci: Native TableSystem method set caught exception St13runtime_error set: the number of values 10378 must be the same as size of the array, 10381, or 1 Native TableSystem method set caught exception St13runtime_error set: the number of values 10378 must be the same as size of the array, 10381, or 1 while executing "$this workspace eval [concat $system $args]" (object "::nVT0" method "::MD::Stage::Base::system" body line 2) invoked from within "$this system asymmetricatoms set Fractional $fracs" (object "::nVT0" method "::MD::LAMMPS::Stage::Base::xyzToSci" body line 72) invoked from within "::nVT0 xyzToSci 2.4.xyz" ("eval" body line 1) invoked from within "eval ::nVT0 $args" (procedure "md-lammps-stage-6fd3d79f-7131-4ec3-867d-d261c5cd5808" line 1) invoked from within "$stage xyzToSci $sid.xyz" Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.24 +/- 0.18 K 0 0.0% P: 548 +/- 15 atm 0 0.0% V: 138884 +/- 0 Ang^3 0 0.0% rho: 1.44443 +/- 0 g/mL 0 0.0% Etotal: -1098620 +/- 230 kJ/mol 0 0.0% Epot: -1125030 +/- 220 kJ/mol 0 0.0% Ekin: 26409 +/- 16 kJ/mol 0 0.0% Evdw: 125894 +/- 37 kJ/mol 0 0.0% Ecoul: -1251460 +/- 200 kJ/mol 0 0.0% Sxx: -870 +/- 19 atm 0 0.0% Syy: -807 +/- 24 atm 0 0.0% Szz: 33 +/- 32 atm 0 0.0% Syz: 7 +/- 15 atm 0 0.0% Sxz: 10 +/- 14 atm 0 0.0% Sxy: -13 +/- 12 atm 0 0.0% Stage 2.5: NVT integration for 5 ns with a timestep of 1 fs T is 298.2 K Error in stage md-lammps-stage-481e3a21-e051-4b19-8344-e98825132864 analyze: Compute group/group output file does not exist - see LAMMPS.out for details Compute group/group output file does not exist - see LAMMPS.out for details while executing "error "Compute group/group output file does not exist - see LAMMPS.out for details"" (object "::groupInteractions0" method "::MD::Analysis::GroupInteractions::analyze" body line 34) invoked from within "$myObjects($id) analyze" (object "::analyses4" method "::MD::Analysis::Analyses::analyze" body line 3) invoked from within "$myAnalyses analyze" (object "::nVT1" method "::MD::LAMMPS::Stage::Base::analyze" body line 169) invoked from within "chain $system" (object "::nVT1" method "::MD::LAMMPS::Stage::NVT::analyze" body line 5) invoked from within "::nVT1 analyze {}" ("eval" body line 1) invoked from within "eval ::nVT1 $args" (procedure "md-lammps-stage-481e3a21-e051-4b19-8344-e98825132864" line 1) invoked from within "$stage analyze $sys" Entire job completed on Sat 16 September 2023 at 06:59:19 CST after 30155 s (8:22:35) and running 1 tasks.