[Sat Sep 16 11:59:10 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/532/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/dir500/532/pcff+.frc) Current system formula: K40Na56Li7Mg151S31Cl343O2936H5624 (K40Na56Li7Mg151S31Cl343O2936H5624) 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 1 ns with a timestep of 1 fs T is 298.2 K Stage 2.5: NVT integration for 1 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/dir500/532/pcff+.frc) Current system formula: K40Na56Li7Mg151S31Cl343O2936H5624 (K40Na56Li7Mg151S31Cl343O2936H5624) 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 39 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 39 Initial Fmax: 36123.8 kJ/mol/Ang Fmax: 107474.0 kJ/mol/Ang Initial Frms: 1496.2 kJ/mol/Ang Frms: 1623.3 kJ/mol/Ang P: 8794.8 atm V: 93962.5 Ang^3 rho: 1.2789 g/mL Sxx: -7112.0 atm Syy: -10810.0 atm Szz: -8462.4 atm Syz: -109.9 atm Sxz: -1280.3 atm Sxy: -9.1 atm Initial Epot: 430230.1 kJ/mol Epot: -506648.6 kJ/mol a: 32.7352 Ang b: 32.7352 Ang c: 87.6849 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 1 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 9185 must be the same as size of the array, 9188, or 1 Native TableSystem method set caught exception St13runtime_error set: the number of values 9185 must be the same as size of the array, 9188, 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 $args" (procedure "md-lammps-stage-1508a80e-28eb-4e2c-b876-808dee28f984" line 1) invoked from within "$stage xyzToSci $sid.xyz" Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 1000000.0 fs T: 298.35 +/- 0.31 K 0 0.0% P: 1977 +/- 37 atm 0 0.0% V: 93962.5 +/- 0 Ang^3 0 0.0% rho: 1.27859 +/- 0 g/mL 0 0.0% Etotal: -566140 +/- 260 kJ/mol 0 0.0% Epot: -589860 +/- 240 kJ/mol 0 0.0% Ekin: 23721 +/- 25 kJ/mol 0 0.0% Evdw: 81393 +/- 68 kJ/mol 0 0.0% Ecoul: -671820 +/- 190 kJ/mol 0 0.0% Sxx: -1980 +/- 45 atm 0 0.0% Syy: -1965 +/- 46 atm 0 0.0% Szz: -1987 +/- 30 atm 0 0.0% Syz: -6 +/- 14 atm 0 0.0% Sxz: 2 +/- 11 atm 0 0.0% Sxy: -6 +/- 17 atm 0 0.0% Stage 2.5: NVT integration for 1 ns with a timestep of 1 fs T is 298.2 K Error in stage md-lammps-stage-55487455-ed43-4c47-9b3c-a8b9ba29d8d5 analyze: Pair Correlation coordinates file does not exist - see LAMMPS.out for details Pair Correlation coordinates file does not exist - see LAMMPS.out for details while executing "error "Pair Correlation coordinates file does not exist - see LAMMPS.out for details"" (object "::pairCorrelations0" method "::MD::Analysis::PairCorrelations::analyze" body line 12) invoked from within "$myObjects($id) analyze" (object "::analyses5" method "::MD::Analysis::Analyses::analyze" body line 3) invoked from within "$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 $args" (procedure "md-lammps-stage-55487455-ed43-4c47-9b3c-a8b9ba29d8d5" line 1) invoked from within "$stage analyze $sys" Entire job completed on Sat 16 September 2023 at 14:07:47 CST after 7710 s (2:08:30) and running 1 tasks.