[Fri Sep 15 13:22:01 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/526/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/dir500/526/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 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: Too many groups (../group.cpp:159) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/526/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 35 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 35 Initial Fmax: 14980.9 kJ/mol/Ang Fmax: 22355.9 kJ/mol/Ang Initial Frms: 1013.1 kJ/mol/Ang Frms: 386.3 kJ/mol/Ang P: 8866.6 atm V: 93962.5 Ang^3 rho: 1.2789 g/mL Sxx: -10468.3 atm Syy: -9357.7 atm Szz: -6773.7 atm Syz: 278.4 atm Sxz: 273.7 atm Sxy: -1095.6 atm Initial Epot: 467858.0 kJ/mol Epot: -501004.7 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 2 ns with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.18 +/- 0.19 K 0 0.0% P: 1994 +/- 31 atm 0 0.0% V: 93962.5 +/- 0 Ang^3 0 0.0% rho: 1.27891 +/- 0 g/mL 0 0.0% Etotal: -566330 +/- 170 kJ/mol 0 0.0% Epot: -590040 +/- 160 kJ/mol 0 0.0% Ekin: 23707 +/- 15 kJ/mol 0 0.0% Evdw: 81614 +/- 45 kJ/mol 0 0.0% Ecoul: -672130 +/- 140 kJ/mol 0 0.0% Sxx: -1988 +/- 36 atm 0 0.0% Syy: -2007 +/- 36 atm 0 0.0% Szz: -1986 +/- 31 atm 0 0.0% Syz: -7 +/- 10 atm 0 0.0% Sxz: 5 +/- 18 atm 0 0.0% Sxy: 2 +/- 16 atm 0 0.0% Stage 2.5: NVT integration for 5 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! Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_4.tab" u 2:1:3title "all Pair Correlation Li+ Li+" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_5.tab" u 2:1:3title "all Pair Correlation Li+ Na+" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_6.tab" u 2:1:3title "all Pair Correlation Li+ K+" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_7.tab" u 2:1:3title "all Pair Correlation Li+ mg+" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_8.tab" u 2:1:3title "all Pair Correlation Li+ Cl" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_9.tab" u 2:1:3title "all Pair Correlation Li+ s4o-" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_10.tab" u 2:1:3title "all Pair Correlation Li+ o*" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_11.tab" u 2:1:3title "all Pair Correlation Na+ Na+" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_12.tab" u 2:1:3title "all Pair Correlation Na+ K+" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_13.tab" u 2:1:3title "all Pair Correlation Na+ mg+" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_14.tab" u 2:1:3title "all Pair Correlation Na+ Cl" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_15.tab" u 2:1:3title "all Pair Correlation Na+ s4o-" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_16.tab" u 2:1:3title "all Pair Correlation Na+ o*" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_17.tab" u 2:1:3title "all Pair Correlation K+ K+" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_18.tab" u 2:1:3title "all Pair Correlation K+ mg+" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_19.tab" u 2:1:3title "all Pair Correlation K+ Cl" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_20.tab" u 2:1:3title "all Pair Correlation K+ s4o-" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_21.tab" u 2:1:3title "all Pair Correlation K+ o1S-" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_22.tab" u 2:1:3title "all Pair Correlation mg+ mg+" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Gnuplot error: line 0: warning: No usable data in this plot to auto-scale axis range gnuplot> splot "2.5_3DPairCorrelation_all_23.tab" u 2:1:3title "all Pair Correlation mg+ Cl" ^ line 0: All points x value undefined gnuplot> replot ^ line 0: no previous plot child process exited abnormally Error in stage md-lammps-stage-nvt-a557925f-9cc6-4c7b-a392-f69c7a0c80a1 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 "::pairCorrelations20" method "::MD::Analysis::PairCorrelations::analyze" body line 12) invoked from within "$myObjects($id) analyze" (object "::analyses1" 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 $args" (procedure "md-lammps-stage-nvt-a557925f-9cc6-4c7b-a392-f69c7a0c80a1" line 1) invoked from within "$stage analyze $sys" Entire job completed on Fri 15 September 2023 at 20:07:56 CST after 24349 s (6:45:49) and running 1 tasks.