[Mon Oct 09 08:41:00 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/634/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 bar 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/dir500/634/pcff+.frc) Current system formula: K40Na56Li7Mg151S31Cl343O2936H5624 (K40Na56Li7Mg151S31Cl343O2936H5624) 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: 3000 Maximum number of force evaluations: 10000 Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs P is 1 bar with cell dimensions 'a' 'b' 'alpha' 'beta' 'gamma' fixed, others relaxed T is 298.2 K Stage 2.5: Custom code -- Custom code reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo 100 fix 1 all nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 all adf 200 4 7 7 0 2.7 0 2.7 fix ad1 all ave/time 1 3000000 3000000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF2 all adf 200 6 7 7 0 3.3 0 3.3 fix ad2 all ave/time 1 3000000 3000000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 all adf 200 3 7 7 0 3.5 0 3.5 fix ad3 all ave/time 1 3000000 3000000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 all adf 200 5 7 7 0 3.0 0 3.0 fix ad4 all ave/time 1 3000000 3000000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 all adf 200 1 7 7 0 3.9 0 3.9 fix ad5 all ave/time 1 3000000 3000000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 all adf 200 9 7 7 0 4.8 0 4.8 fix ad6 all ave/time 1 3000000 3000000 c_myADF6\[*\] file tmp6.adf mode vector timestep 0.5 run 3000000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 #------------------------------------------------------------------------------- # Running the calculation #------------------------------------------------------------------------------- Stage 1: Variables tstep = 1 fs T = 298.2 K P = 1 bar Stage 2: This LAMMPS calculation has 5 stages: ***** LAMMPS error in LAMMPS.out ***** ERROR on proc 26: Angle atoms 9137 9135 9136 missing on proc 26 at step 2097861 (../ntopo_angle_all.cpp:64) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/634/pcff+.frc) Current system formula: K40Na56Li7Mg151S31Cl343O2936H5624 (K40Na56Li7Mg151S31Cl343O2936H5624) 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: 3000 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 46 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 46 Initial Fmax: 36105.9 kJ/mol/Ang Fmax: 4862.6 kJ/mol/Ang Initial Frms: 1871.8 kJ/mol/Ang Frms: 88.9 kJ/mol/Ang P: 2997.6 atm V: 93962.5 Ang^3 rho: 1.2789 g/mL Sxx: -2712.6 atm Syy: -3331.9 atm Szz: -2948.5 atm Syz: 984.6 atm Sxz: 44.6 atm Sxy: 707.5 atm Initial Epot: 480088.0 kJ/mol Epot: -539580.4 kJ/mol a: 36.8271 Ang b: 36.8271 Ang c: 69.2819 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: NPT integration for 2 ns with a timestep of 1 fs P is 1 bar with cell dimensions 'a' 'b' 'alpha' 'beta' 'gamma' fixed, others relaxed T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.25 +/- 0.082 K 0 0.0% P: 0 +/- 10 atm 0 0.0% V: 97867 +/- 57 Ang^3 0 0.0% rho: 1.2279 +/- 0.00071 g/mL 0 0.0% Etotal: -565010 +/- 130 kJ/mol 0 0.0% a: 36.8271 +/- 0 Ang 0 0.0% b: 36.8271 +/- 0 Ang 0 0.0% c: 72.161 +/- 0.042 Ang 0 0.0% alpha: 90.00022 +/- 0 degree 0 0.0% beta: 90.00022 +/- 0 degree 0 0.0% gamma: 90.00022 +/- 0 degree 0 0.0% Epot: -588720 +/- 130 kJ/mol 0 0.0% Ekin: 23713 +/- 6.5 kJ/mol 0 0.0% Evdw: 78427 +/- 40 kJ/mol 0 0.0% Ecoul: -667705 +/- 80 kJ/mol 0 0.0% Sxx: 0 +/- 22 atm 0 0.0% Syy: 5 +/- 13 atm 0 0.0% Szz: -4 +/- 11 atm 0 0.0% Syz: -2.9 +/- 7.8 atm 0 0.0% Sxz: -3 +/- 11 atm 0 0.0% Sxy: -3 +/- 16 atm 0 0.0% Stage 2.5: Custom code -- Custom code reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo 100 fix 1 all nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 all adf 200 4 7 7 0 2.7 0 2.7 fix ad1 all ave/time 1 3000000 3000000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF2 all adf 200 6 7 7 0 3.3 0 3.3 fix ad2 all ave/time 1 3000000 3000000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 all adf 200 3 7 7 0 3.5 0 3.5 fix ad3 all ave/time 1 3000000 3000000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 all adf 200 5 7 7 0 3.0 0 3.0 fix ad4 all ave/time 1 3000000 3000000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 all adf 200 1 7 7 0 3.9 0 3.9 fix ad5 all ave/time 1 3000000 3000000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 all adf 200 9 7 7 0 4.8 0 4.8 fix ad6 all ave/time 1 3000000 3000000 c_myADF6\[*\] file tmp6.adf mode vector timestep 0.5 run 3000000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 ********************************************* WARNING: this LAMMPS stage completed on Mon 09 October 2023 at 13:21:33 CST after 16827 s (4:40:27) with the following error: ERROR on proc 26: Angle atoms 9137 9135 9136 missing on proc 26 at step 2097861 (../ntopo_angle_all.cpp:64) ********************************************* Entire job completed on Mon 09 October 2023 at 13:21:33 CST after 16827 s (4:40:27) and running 1 tasks.