[Wed Sep 13 18:01:32 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/516/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/dir500/516/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: 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 #------------------------------------------------------------------------------- # 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/dir500/516/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 43 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 43 Initial Fmax: 21058.7 kJ/mol/Ang Fmax: 28993.4 kJ/mol/Ang Initial Frms: 1432.1 kJ/mol/Ang Frms: 430.3 kJ/mol/Ang P: 12833.0 atm V: 92859.5 Ang^3 rho: 1.3074 g/mL Sxx: -12138.1 atm Syy: -14153.8 atm Szz: -12207.1 atm Syz: 275.5 atm Sxz: 58.1 atm Sxy: -1130.3 atm Initial Epot: 434823.3 kJ/mol Epot: -579541.2 kJ/mol a: 32.7352 Ang b: 32.7352 Ang c: 86.6555 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 $args" (procedure "md-lammps-stage-bc06e214-d432-43c2-bc51-e6ee885fb89a" line 1) invoked from within "$stage xyzToSci $sid.xyz" Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.28 +/- 0.17 K 0 0.0% P: 2759 +/- 26 atm 0 0.0% V: 92859.5 +/- 0 Ang^3 0 0.0% rho: 1.30708 +/- 0 g/mL 0 0.0% Etotal: -653830 +/- 200 kJ/mol 0 0.0% Epot: -677380 +/- 180 kJ/mol 0 0.0% Ekin: 23555 +/- 14 kJ/mol 0 0.0% Evdw: 93532 +/- 37 kJ/mol 0 0.0% Ecoul: -771380 +/- 150 kJ/mol 0 0.0% Sxx: -2761 +/- 38 atm 0 0.0% Syy: -2759 +/- 45 atm 0 0.0% Szz: -2758 +/- 24 atm 0 0.0% Syz: -2 +/- 16 atm 0 0.0% Sxz: 11 +/- 13 atm 0 0.0% Sxy: 15 +/- 20 atm 0 0.0% Stage 2.5: 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 ********************************************* WARNING: this LAMMPS stage completed on Wed 13 September 2023 at 22:12:52 CST after 15068 s (4:11:08) with the following error: ERROR: Atom count is inconsistent, cannot write restart file (../write_restart.cpp:228) ********************************************* Entire job completed on Wed 13 September 2023 at 22:12:52 CST after 15068 s (4:11:08) and running 1 tasks.