[Thu Sep 07 18:23:03 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/505/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/dir500/505/pcff+.frc) Current system formula: K6Li14Mg240S27Cl446O2807H5398 (K6Li14Mg240S27Cl446O2807H5398) 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/dir500/505/pcff+.frc) Current system formula: K6Li14Mg240S27Cl446O2807H5398 (K6Li14Mg240S27Cl446O2807H5398) 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 62 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 62 Initial Fmax: 30519.0 kJ/mol/Ang Fmax: 71983.3 kJ/mol/Ang Initial Frms: 1319.2 kJ/mol/Ang Frms: 1633.4 kJ/mol/Ang P: 6294.2 atm V: 91446.3 Ang^3 rho: 1.3291 g/mL Sxx: -6227.3 atm Syy: -6864.9 atm Szz: -5790.3 atm Syz: 528.4 atm Sxz: 830.2 atm Sxy: 233.6 atm Initial Epot: 415166.6 kJ/mol Epot: -694151.6 kJ/mol a: 28.0207 Ang b: 49.0945 Ang c: 66.4743 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 8935 must be the same as size of the array, 8938, or 1 Native TableSystem method set caught exception St13runtime_error set: the number of values 8935 must be the same as size of the array, 8938, 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 $args" (procedure "md-lammps-stage-fe16fd98-b91c-4386-b2a8-bc6d965a8cf7" line 1) invoked from within "$stage xyzToSci $sid.xyz" Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.22 +/- 0.14 K 0 0.0% P: 3367 +/- 31 atm 0 0.0% V: 91446.3 +/- 1.7e-09 Ang^3 0 0.0% rho: 1.32878 +/- 0 g/mL 0 0.0% Etotal: -714290 +/- 220 kJ/mol 0 0.0% Epot: -737490 +/- 210 kJ/mol 0 0.0% Ekin: 23201 +/- 11 kJ/mol 0 0.0% Evdw: 101508 +/- 44 kJ/mol 0 0.0% Ecoul: -839490 +/- 180 kJ/mol 0 0.0% Sxx: -3387 +/- 42 atm 0 0.0% Syy: -3366 +/- 48 atm 0 0.0% Szz: -3347 +/- 40 atm 0 0.0% Syz: 4 +/- 27 atm 0 0.0% Sxz: -20 +/- 17 atm 0 0.0% Sxy: 22 +/- 22 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 Thu 07 September 2023 at 22:33:33 CST after 15024 s (4:10:24) with the following error: ERROR: Atom count is inconsistent, cannot write restart file (../write_restart.cpp:228) ********************************************* Entire job completed on Thu 07 September 2023 at 22:33:33 CST after 15024 s (4:10:24) and running 1 tasks.