[Thu Jul 27 09:56:33 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir0/379/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/dir0/379/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 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 constrained isotropically 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/dir0/379/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 53 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 53 Initial Fmax: 17881.6 kJ/mol/Ang Fmax: 32454.2 kJ/mol/Ang Initial Frms: 1306.1 kJ/mol/Ang Frms: 868.7 kJ/mol/Ang P: 4860.4 atm V: 65360.0 Ang^3 rho: 1.3291 g/mL Sxx: -4915.3 atm Syy: -4594.0 atm Szz: -5072.0 atm Syz: -908.3 atm Sxz: 1245.6 atm Sxy: -1666.4 atm Initial Epot: 320588.4 kJ/mol Epot: -493809.7 kJ/mol a: 40.2814 Ang b: 40.2814 Ang c: 40.2814 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 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 $args" (procedure "md-lammps-stage-deb5e2c8-47a5-415e-9956-f62efc6ac1db" line 1) invoked from within "$stage xyzToSci $sid.xyz" Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.23 +/- 0.11 K 0 0.0% P: 3338 +/- 36 atm 0 0.0% V: 65360 +/- 0 Ang^3 0 0.0% rho: 1.32865 +/- 0 g/mL 0 0.0% Etotal: -510390 +/- 160 kJ/mol 0 0.0% Epot: -526970 +/- 150 kJ/mol 0 0.0% Ekin: 16581.2 +/- 6.2 kJ/mol 0 0.0% Evdw: 72588 +/- 42 kJ/mol 0 0.0% Ecoul: -599930 +/- 150 kJ/mol 0 0.0% Sxx: -3321 +/- 48 atm 0 0.0% Syy: -3390 +/- 53 atm 0 0.0% Szz: -3304 +/- 55 atm 0 0.0% Syz: 13 +/- 25 atm 0 0.0% Sxz: 16 +/- 22 atm 0 0.0% Sxy: 3 +/- 23 atm 0 0.0% Stage 2.5: NPT integration for 2 ns with a timestep of 1 fs P is 1 atm with cell constrained isotropically T is 298.2 K ********************************************* WARNING: this LAMMPS stage completed on Thu 27 July 2023 at 12:12:42 CST after 8163 s (2:16:03) with the following error: ERROR: Atom count is inconsistent, cannot write restart file (../write_restart.cpp:228) ********************************************* Entire job completed on Thu 27 July 2023 at 12:12:42 CST after 8163 s (2:16:03) and running 1 tasks.