[Sun Sep 17 15:48:02 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/541/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/dir500/541/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: NVT integration for 200 ps with a timestep of 1 fs T is 298.2 K Stage 2.5: NVT integration for 200 ps 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/dir500/541/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 33 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 33 Initial Fmax: 15135.7 kJ/mol/Ang Fmax: 24161.6 kJ/mol/Ang Initial Frms: 950.9 kJ/mol/Ang Frms: 407.6 kJ/mol/Ang P: 11300.1 atm V: 129127.0 Ang^3 rho: 1.4116 g/mL Sxx: -12850.0 atm Syy: -11301.2 atm Szz: -9749.0 atm Syz: 279.7 atm Sxz: 31.0 atm Sxy: -654.2 atm Initial Epot: 24343.7 kJ/mol Epot: -944734.0 kJ/mol a: 32.7352 Ang b: 32.7352 Ang c: 120.5000 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: -0.1 kJ/mol/Ang sum_fy: 0.2 kJ/mol/Ang sum_fz: 59.5 kJ/mol/Ang Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NVT integration for 200 ps with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 200000 fs T: 299.2 +/- 2.3 K 0 0.0% P: 598 +/- 62 atm 0 0.0% V: 129127 +/- 0 Ang^3 0 0.0% rho: 1.41163 +/- 0 g/mL 0 0.0% Etotal: -1049200 +/- 1100 kJ/mol 0 0.0% Epot: -1075890 +/- 930 kJ/mol 0 0.0% Ekin: 26650 +/- 210 kJ/mol 0 0.0% Evdw: 123760 +/- 130 kJ/mol 0 0.0% Ecoul: -1200200 +/- 1000 kJ/mol 0 0.0% Sxx: -809 +/- 59 atm 0 0.0% Syy: -809 +/- 64 atm 0 0.0% Szz: -178 +/- 77 atm 0 0.0% Syz: -4 +/- 24 atm 0 0.0% Sxz: -5 +/- 23 atm 0 0.0% Sxy: -11 +/- 30 atm 0 0.0% Stage 2.5: NVT integration for 200 ps 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_2.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_3.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_4.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_6.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_7.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_8.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_9.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_10.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_11.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_12.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_13.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_14.tab" u 2:1:3title "all Pair Correlation K+ 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_15.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_16.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 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 mg+ 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_18.tab" u 2:1:3title "all Pair Correlation mg+ 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_19.tab" u 2:1:3title "all Pair Correlation Cl 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 Cl o*" ^ 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-2ba15d91-1ac1-4b69-a4ed-60ece1518fe9 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 "::pairCorrelations18" 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 $args" (procedure "md-lammps-stage-nvt-2ba15d91-1ac1-4b69-a4ed-60ece1518fe9" line 1) invoked from within "$stage analyze $sys" Entire job completed on Sun 17 September 2023 at 16:39:17 CST after 3067 s (0:51:07) and running 1 tasks.