[Fri Sep 15 20:07:57 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/528/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 5 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/528/pcff+.frc) Current system formula: K31Na2Li10Mg206S31Cl393O2892H5536 (K31Na2Li10Mg206S31Cl393O2892H5536) 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 #------------------------------------------------------------------------------- # Running the calculation #------------------------------------------------------------------------------- Stage 1: Variables tstep = 1 fs T = 298.2 K P = 1 atm Stage 2: This LAMMPS calculation has 5 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/dir500/528/pcff+.frc) Current system formula: K31Na2Li10Mg206S31Cl393O2892H5536 (K31Na2Li10Mg206S31Cl393O2892H5536) 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 45 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 45 Initial Fmax: 23771.0 kJ/mol/Ang Fmax: 81103.5 kJ/mol/Ang Initial Frms: 1091.3 kJ/mol/Ang Frms: 1543.6 kJ/mol/Ang P: 12576.9 atm V: 92859.5 Ang^3 rho: 1.3074 g/mL Sxx: -14197.3 atm Syy: -13009.1 atm Szz: -10524.2 atm Syz: 166.9 atm Sxz: 516.5 atm Sxy: 979.1 atm Initial Epot: 410979.2 kJ/mol Epot: -596640.5 kJ/mol a: 35.8935 Ang b: 35.8935 Ang c: 72.0766 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: 0.0 kJ/mol/Ang sum_fy: -0.0 kJ/mol/Ang sum_fz: -0.0 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 9098 must be the same as size of the array, 9101, or 1 Native TableSystem method set caught exception St13runtime_error set: the number of values 9098 must be the same as size of the array, 9101, 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 $args" (procedure "md-lammps-stage-139aa711-709c-4990-b1e1-92c95cc20c72" line 1) invoked from within "$stage xyzToSci $sid.xyz" Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.19 +/- 0.18 K 0 0.0% P: 2700 +/- 23 atm 0 0.0% V: 92859.5 +/- 0 Ang^3 0 0.0% rho: 1.30708 +/- 0 g/mL 0 0.0% Etotal: -653260 +/- 190 kJ/mol 0 0.0% Epot: -676810 +/- 180 kJ/mol 0 0.0% Ekin: 23548 +/- 14 kJ/mol 0 0.0% Evdw: 93381 +/- 35 kJ/mol 0 0.0% Ecoul: -770680 +/- 170 kJ/mol 0 0.0% Sxx: -2704 +/- 28 atm 0 0.0% Syy: -2707 +/- 35 atm 0 0.0% Szz: -2690 +/- 25 atm 0 0.0% Syz: -8 +/- 19 atm 0 0.0% Sxz: -11 +/- 24 atm 0 0.0% Sxy: -3 +/- 20 atm 0 0.0% Stage 2.5: NVT integration for 5 ns with a timestep of 1 fs T is 298.2 K Error in stage md-lammps-stage-1ff957d3-c1aa-4a35-9ebd-9208a0f17139 analyze: Pair Correlation coordinates file does not exist - see LAMMPS.out for details Pair Correlation coordinates file does not exist - see LAMMPS.out for details while executing "error "Pair Correlation coordinates file does not exist - see LAMMPS.out for details"" (object "::pairCorrelations0" method "::MD::Analysis::PairCorrelations::analyze" body line 12) invoked from within "$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 $args" (procedure "md-lammps-stage-1ff957d3-c1aa-4a35-9ebd-9208a0f17139" line 1) invoked from within "$stage analyze $sys" Entire job completed on Sat 16 September 2023 at 02:59:20 CST after 24675 s (6:51:15) and running 1 tasks.