[Thu Sep 14 19:07:39 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/519/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 7 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/519/pcff+.frc) Current system formula: K40Na696Li7Mg151S31Cl983O2936H5624 (K40Na696Li7Mg151S31Cl983O2936H5624) 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: NPT integration for 2 ns with a timestep of 1 fs P is 1 atm with cell dimensions 'a' 'b' 'alpha' 'beta' 'gamma' fixed, others relaxed T is 298.2 K Stage 2.5: NVT integration for 3 ns with a timestep of 1 fs T is 298.2 K Stage 2.6: NVT integration for 1 ns with a timestep of 1 fs T is 298.2 K Stage 2.7: Surface tension calculation using 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 7 stages: ***** LAMMPS error in LAMMPS.out ***** ERROR: Compute chunk/atom for triclinic boxes requires units reduced (../compute_chunk_atom.cpp:358) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/519/pcff+.frc) Current system formula: K40Na696Li7Mg151S31Cl983O2936H5624 (K40Na696Li7Mg151S31Cl983O2936H5624) 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 1000 steps ending because the max iterations Property Value Units ------------------ ---------- ----------- nSteps: 1000 Initial Fmax: 541.5 kJ/mol/Ang Fmax: 5.3 kJ/mol/Ang Initial Frms: 127.8 kJ/mol/Ang Frms: 0.3 kJ/mol/Ang P: -6899.3 atm V: 131377.3 Ang^3 rho: 1.3874 g/mL Sxx: 7026.7 atm Syy: 6888.4 atm Szz: 6782.7 atm Syz: -176.4 atm Sxz: 133.4 atm Sxy: 26.2 atm Initial Epot: -1071266.2 kJ/mol Epot: -1119990.2 kJ/mol a: 32.7352 Ang b: 32.7352 Ang c: 122.6000 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: NPT integration for 2 ns with a timestep of 1 fs P is 1 atm with cell dimensions 'a' 'b' 'alpha' 'beta' 'gamma' fixed, others relaxed T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.166 +/- 0.067 K 0 0.0% P: 877 +/- 10 atm 0 0.0% V: 129703 +/- 79 Ang^3 0 0.0% rho: 1.40537 +/- 0.00085 g/mL 0 0.0% Etotal: -1045793 +/- 54 kJ/mol 0 0.0% a: 32.7352 +/- 0 Ang 0 0.0% b: 32.7352 +/- 0 Ang 0 0.0% c: 121.038 +/- 0.074 Ang 0 0.0% alpha: 90.00022 +/- 0 degree 0 0.0% beta: 90.00022 +/- 0 degree 0 0.0% gamma: 90.00022 +/- 0 degree 0 0.0% Epot: -1074260 +/- 53 kJ/mol 0 0.0% Ekin: 28466.2 +/- 6.4 kJ/mol 0 0.0% Evdw: 124133 +/- 42 kJ/mol 0 0.0% Ecoul: -1198848 +/- 83 kJ/mol 0 0.0% Sxx: -1316 +/- 16 atm 0 0.0% Syy: -1315 +/- 17 atm 0 0.0% Szz: -1 +/- 8 atm 0 0.0% Syz: -3 +/- 15 atm 0 0.0% Sxz: -1 +/- 15 atm 0 0.0% Sxy: -4 +/- 8.6 atm 0 0.0% Stage 2.5: NVT integration for 3 ns with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: fs Error with T: The run is not long enough to analyze. Sorry! Error with P: The run is not long enough to analyze. Sorry! Error with V: The run is not long enough to analyze. Sorry! Error with rho: The run is not long enough to analyze. Sorry! Error with Etotal: The run is not long enough to analyze. Sorry! Error with Epot: The run is not long enough to analyze. Sorry! Error with Ekin: The run is not long enough to analyze. Sorry! Error with Evdw: The run is not long enough to analyze. Sorry! Error with Ecoul: The run is not long enough to analyze. Sorry! Error with Sxx: The run is not long enough to analyze. Sorry! Error with Syy: The run is not long enough to analyze. Sorry! Error with Szz: The run is not long enough to analyze. Sorry! Error with Syz: The run is not long enough to analyze. Sorry! Error with Sxz: The run is not long enough to analyze. Sorry! Error with Sxy: The run is not long enough to analyze. Sorry! Error in stage md-lammps-stage-b552a832-e983-4f7b-a965-43447f255ca5 analyze: domain error: argument not in valid range domain error: argument not in valid range while executing "expr {$s_eab/$nvals}" (object "::groupInteractions0" method "::MD::Analysis::GroupInteractions::analyze" body line 65) invoked from within "$myObjects($id) analyze" (object "::analyses4" method "::MD::Analysis::Analyses::analyze" body line 3) invoked from within "$myAnalyses analyze" (object "::nVT0" method "::MD::LAMMPS::Stage::Base::analyze" body line 169) invoked from within "chain $system" (object "::nVT0" method "::MD::LAMMPS::Stage::NVT::analyze" body line 5) invoked from within "::nVT0 analyze {}" ("eval" body line 1) invoked from within "eval ::nVT0 $args" (procedure "md-lammps-stage-b552a832-e983-4f7b-a965-43447f255ca5" line 1) invoked from within "$stage analyze $sys" Entire job completed on Fri 15 September 2023 at 00:49:37 CST after 20511 s (5:41:51) and running 1 tasks.