[Mon Oct 30 18:27:26 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/655/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 6 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/655/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: 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: NVT integration for 3 ns with a timestep of 1 fs T is 298.2 K Stage 2.6: 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 10000 10000 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 10000 10000 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 10000 10000 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 10000 10000 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 10000 10000 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 10000 10000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 10000 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 6 stages: ***** LAMMPS error in LAMMPS.out ***** ERROR on proc 9: Angle atoms 6365 6363 6364 missing on proc 9 at step 3000057 (../ntopo_angle_all.cpp:64) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/655/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: 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 45 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 45 Initial Fmax: 43292.3 kJ/mol/Ang Fmax: 47742.1 kJ/mol/Ang Initial Frms: 1776.7 kJ/mol/Ang Frms: 861.2 kJ/mol/Ang P: 5555.1 atm V: 92859.5 Ang^3 rho: 1.3074 g/mL Sxx: -5338.2 atm Syy: -6014.4 atm Szz: -5312.7 atm Syz: -158.6 atm Sxz: 926.7 atm Sxy: 35.5 atm Initial Epot: 464140.8 kJ/mol Epot: -618376.2 kJ/mol a: 36.8271 Ang b: 36.8271 Ang c: 68.4686 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: 298.27 +/- 0.14 K 0 0.0% P: -2 +/- 15 atm 0 0.0% V: 97567 +/- 42 Ang^3 0 0.0% rho: 1.24434 +/- 0.00053 g/mL 0 0.0% Etotal: -651420 +/- 210 kJ/mol 0 0.0% a: 36.8271 +/- 0 Ang 0 0.0% b: 36.8271 +/- 0 Ang 0 0.0% c: 71.94 +/- 0.031 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: -674970 +/- 210 kJ/mol 0 0.0% Ekin: 23555 +/- 11 kJ/mol 0 0.0% Evdw: 88887 +/- 34 kJ/mol 0 0.0% Ecoul: -764440 +/- 190 kJ/mol 0 0.0% Sxx: 15 +/- 24 atm 0 0.0% Syy: 1 +/- 33 atm 0 0.0% Szz: -8.1 +/- 8.5 atm 0 0.0% Syz: -5 +/- 11 atm 0 0.0% Sxz: -3 +/- 13 atm 0 0.0% Sxy: 0 +/- 15 atm 0 0.0% Stage 2.5: NVT integration for 3 ns with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 3000000.0 fs T: 298.196 +/- 0.061 K 0 0.0% P: 137 +/- 21 atm 0 0.0% V: 97258.1 +/- 1.9e-09 Ang^3 0 0.0% rho: 1.24828 +/- 0 g/mL 0 0.0% Etotal: -651769 +/- 40 kJ/mol 1000 10.0% Epot: -675305 +/- 46 kJ/mol 0 0.0% Ekin: 23548.8 +/- 4.8 kJ/mol 0 0.0% Evdw: 89132 +/- 38 kJ/mol 0 0.0% Ecoul: -764942 +/- 55 kJ/mol 0 0.0% Sxx: -131 +/- 23 atm 0 0.0% Syy: -146 +/- 27 atm 0 0.0% Szz: -134 +/- 31 atm 0 0.0% Syz: -4 +/- 13 atm 0 0.0% Sxz: 5 +/- 12 atm 0 0.0% Sxy: 16 +/- 13 atm 0 0.0% Stage 2.6: 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 10000 10000 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 10000 10000 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 10000 10000 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 10000 10000 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 10000 10000 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 10000 10000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 10000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 ********************************************* WARNING: this LAMMPS stage completed on Tue 31 October 2023 at 19:06:06 CST after 88706 s (24:38:26) with the following error: ERROR on proc 9: Angle atoms 6365 6363 6364 missing on proc 9 at step 3000057 (../ntopo_angle_all.cpp:64) ********************************************* Entire job completed on Tue 31 October 2023 at 19:06:06 CST after 88706 s (24:38:26) and running 1 tasks.