[Thu Jul 27 21:57:02 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir0/383/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/dir0/383/pcff+.frc) Current system formula: K5Li10Mg171S20Cl317O2008H3856 (K5Li10Mg171S20Cl317O2008H3856) The nonbond terms are handled with a cutoff at 9.5 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 5 ns with a timestep of 1 fs T is 298.2 K Stage 2.5: Surface tension calculation using NVT integration for 3 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/dir0/383/pcff+.frc) Current system formula: K5Li10Mg171S20Cl317O2008H3856 (K5Li10Mg171S20Cl317O2008H3856) The nonbond terms are handled with a cutoff at 9.5 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 67 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 67 Initial Fmax: 22152.7 kJ/mol/Ang Fmax: 55275.1 kJ/mol/Ang Initial Frms: 767.7 kJ/mol/Ang Frms: 1628.2 kJ/mol/Ang P: -3198.3 atm V: 136142.8 Ang^3 rho: 0.6381 g/mL Sxx: 3660.7 atm Syy: 3051.1 atm Szz: 2883.2 atm Syz: -29.1 atm Sxz: 310.8 atm Sxy: 2.4 atm Initial Epot: -394397.9 kJ/mol Epot: -545371.7 kJ/mol a: 40.9978 Ang b: 40.9978 Ang c: 80.9978 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 5 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 6384 must be the same as size of the array, 6387, or 1 Native TableSystem method set caught exception St13runtime_error set: the number of values 6384 must be the same as size of the array, 6387, 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 $args" (procedure "md-lammps-stage-2d88584b-e86c-4c99-9f37-3ff85bfe0ab6" line 1) invoked from within "$stage xyzToSci $sid.xyz" Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 5000000.0 fs T: 298.214 +/- 0.08 K 0 0.0% P: -273.6 +/- 7.3 atm 0 0.0% V: 136143 +/- 0 Ang^3 0 0.0% rho: 0.637863 +/- 0 g/mL 0 0.0% Etotal: -505782 +/- 74 kJ/mol 0 0.0% Epot: -522363 +/- 71 kJ/mol 0 0.0% Ekin: 16580.3 +/- 4.4 kJ/mol 0 0.0% Evdw: 67906 +/- 27 kJ/mol 0 0.0% Ecoul: -590565 +/- 73 kJ/mol 0 0.0% Sxx: 329 +/- 16 atm 0 0.0% Syy: 340 +/- 10 atm 0 0.0% Szz: 151.5 +/- 3.6 atm 0 0.0% Syz: 2.3 +/- 2.8 atm 0 0.0% Sxz: -2.3 +/- 3.8 atm 0 0.0% Sxy: -4 +/- 12 atm 0 0.0% Stage 2.5: Surface tension calculation using NVT integration for 3 ns with a timestep of 1 fs, T is 298.2 K ********************************************* WARNING: this LAMMPS stage completed on Fri 28 July 2023 at 05:55:26 CST after 28699 s (7:58:19) with the following error: ERROR: Atom count is inconsistent, cannot write restart file (../write_restart.cpp:228) ********************************************* Entire job completed on Fri 28 July 2023 at 05:55:26 CST after 28699 s (7:58:19) and running 1 tasks.