[Tue Sep 05 01:40:25 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir0/490/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/dir0/490/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 3 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/dir0/490/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 32 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 32 Initial Fmax: 413.1 kJ/mol/Ang Fmax: 193767.3 kJ/mol/Ang Initial Frms: 140.7 kJ/mol/Ang Frms: 3735.4 kJ/mol/Ang P: -4360.7 atm V: 195013.5 Ang^3 rho: 0.6225 g/mL Sxx: 3977.4 atm Syy: 4934.8 atm Szz: 4169.9 atm Syz: -456.0 atm Sxz: -11.4 atm Sxy: -120.6 atm Initial Epot: -660361.2 kJ/mol Epot: -711848.9 kJ/mol a: 45.2837 Ang b: 45.2837 Ang c: 95.1000 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 3 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 $args" (procedure "md-lammps-stage-1e7cca57-6d08-489d-b893-d29c5779d991" line 1) invoked from within "$stage xyzToSci $sid.xyz" Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 3000000.0 fs T: 298.162 +/- 0.076 K 0 0.0% P: -187.1 +/- 6.9 atm 0 0.0% V: 195014 +/- 0 Ang^3 0 0.0% rho: 0.622393 +/- 0 g/mL 0 0.0% Etotal: -648049 +/- 42 kJ/mol 1000 10.0% Epot: -671595 +/- 43 kJ/mol 1000 10.0% Ekin: 23546.1 +/- 6 kJ/mol 0 0.0% Evdw: 88376 +/- 33 kJ/mol 1000 10.0% Ecoul: -760448 +/- 56 kJ/mol 1000 10.0% Sxx: 242 +/- 14 atm 0 0.0% Syy: 243 +/- 11 atm 0 0.0% Szz: 75.8 +/- 5.9 atm 0 0.0% Syz: -0.8 +/- 2.2 atm 0 0.0% Sxz: 1.2 +/- 1.5 atm 0 0.0% Sxy: 3.2 +/- 4.9 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 Tue 05 September 2023 at 11:28:11 CST after 35260 s (9:47:40) with the following error: ERROR: Atom count is inconsistent, cannot write restart file (../write_restart.cpp:228) ********************************************* Entire job completed on Tue 05 September 2023 at 11:28:12 CST after 35261 s (9:47:41) and running 1 tasks.