[Sun Oct 29 17:17:15 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/651/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/dir500/651/pcff+.frc) Current system formula: K40Na866Li7Mg151S31Cl1153O2936H5624 (K40Na866Li7Mg151S31Cl1153O2936H5624) 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: NVT integration for 10 ps with a timestep of 1 fs T is 298.2 K Stage 2.5: NVT integration for 10 ps 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 movable nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 subset_jiemian adf 200 6 7 7 0 3.3 0 3.3 fix ad1 subset_jiemian ave/time 1 10000 10000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF2 subset_jiemian adf 200 6 1 1 0 4.4 0 4.4 fix ad2 subset_jiemian ave/time 1 10000 10000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 subset_jiemian adf 200 3 7 7 0 3.8 0 3.8 fix ad3 subset_jiemian ave/time 1 10000 10000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 subset_jiemian adf 200 3 1 1 0 4.1 0 4.1 fix ad4 subset_jiemian ave/time 1 10000 10000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 subset_jiemian adf 200 1 7 7 0 4.1 0 4.1 fix ad5 subset_jiemian ave/time 1 10000 10000 c_myADF5\[*\] file tmp5.adf mode vector timestep 1 run 10000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 #------------------------------------------------------------------------------- # 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 18: Bond atoms 9937 9936 missing on proc 18 at step 11955 (../ntopo_bond_all.cpp:61) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/651/pcff+.frc) Current system formula: K40Na866Li7Mg151S31Cl1153O2936H5624 (K40Na866Li7Mg151S31Cl1153O2936H5624) 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 3000 steps ending because the max iterations Property Value Units ------------------ ---------- ----------- nSteps: 3000 Initial Fmax: 361.1 kJ/mol/Ang Fmax: 1.1 kJ/mol/Ang Initial Frms: 125.9 kJ/mol/Ang Frms: 0.1 kJ/mol/Ang P: -5900.0 atm V: 141184.1 Ang^3 rho: 1.4079 g/mL Sxx: 6036.9 atm Syy: 6190.6 atm Szz: 5472.4 atm Syz: -4.1 atm Sxz: 190.7 atm Sxy: 36.1 atm Initial Epot: -1200276.3 kJ/mol Epot: -1250537.3 kJ/mol a: 36.8271 Ang b: 36.8271 Ang c: 104.1000 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: 6.9 kJ/mol/Ang sum_fy: 2.8 kJ/mol/Ang sum_fz: 40.3 kJ/mol/Ang Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NVT integration for 10 ps with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 10000 fs T: 298.29 +/- 0.26 K 1000 10.0% P: -161 +/- 82 atm 0 0.0% V: 141184 +/- 0 Ang^3 0 0.0% rho: 1.40793 +/- 0 g/mL 0 0.0% Etotal: -1174655 +/- 86 kJ/mol 1000 10.0% Epot: -1203193 +/- 79 kJ/mol 1000 10.0% Ekin: 28538 +/- 24 kJ/mol 1000 10.0% Evdw: 134050 +/- 220 kJ/mol 2000 20.0% Ecoul: -1337840 +/- 330 kJ/mol 1000 10.0% Sxx: -260 +/- 110 atm 0 0.0% Syy: -150 +/- 100 atm 0 0.0% Szz: 890 +/- 130 atm 0 0.0% Syz: 71 +/- 79 atm 0 0.0% Sxz: 20 +/- 61 atm 0 0.0% Sxy: 64 +/- 66 atm 0 0.0% Stage 2.5: NVT integration for 10 ps with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 10000 fs T: 297.99 +/- 0.48 K 0 0.0% P: -171 +/- 63 atm 0 0.0% V: 141184 +/- 0 Ang^3 0 0.0% rho: 1.40793 +/- 0 g/mL 0 0.0% Etotal: -1175030 +/- 160 kJ/mol 0 0.0% Epot: -1203530 +/- 120 kJ/mol 0 0.0% Ekin: 28508 +/- 46 kJ/mol 0 0.0% Evdw: 134130 +/- 190 kJ/mol 0 0.0% Ecoul: -1338180 +/- 210 kJ/mol 0 0.0% Sxx: -267 +/- 73 atm 0 0.0% Syy: -101 +/- 52 atm 1000 10.0% Szz: 900 +/- 110 atm 0 0.0% Syz: -52 +/- 73 atm 0 0.0% Sxz: 51 +/- 65 atm 1000 10.0% Sxy: -18 +/- 58 atm 0 0.0% Group Interactions analysis for groups layer2/Li_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -10.6 kJ/mol largest E_ab = 24.13 kJ/mol mean = 5.141 kJ/mol mean of squares = 81.09 (kJ/mol)^2 standard deviation = 7.393 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups layer2/Na_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -17.11 kJ/mol largest E_ab = 84.15 kJ/mol mean = 25.94 kJ/mol mean of squares = 1100 (kJ/mol)^2 standard deviation = 20.67 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups layer2/Cl_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -517 kJ/mol largest E_ab = -70.76 kJ/mol mean = -301.5 kJ/mol mean of squares = 1.002e+05 (kJ/mol)^2 standard deviation = 96.35 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups layer2/K_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -38.26 kJ/mol largest E_ab = 39.8 kJ/mol mean = 1.688 kJ/mol mean of squares = 286.2 (kJ/mol)^2 standard deviation = 16.83 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups layer2/Mg_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -412.5 kJ/mol largest E_ab = 35.33 kJ/mol mean = -180 kJ/mol mean of squares = 3.897e+04 (kJ/mol)^2 standard deviation = 81.04 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups layer2/SO4_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -115.5 kJ/mol largest E_ab = -30.19 kJ/mol mean = -65.52 kJ/mol mean of squares = 4665 (kJ/mol)^2 standard deviation = 19.28 kJ/mol -------------------------------------------------------------------- Group Interactions analysis for groups layer2/H2O_1 (total interaction energy evaluations = 100) -------------------------------------------------------------------- smallest E_ab = -841.5 kJ/mol largest E_ab = -708.8 kJ/mol mean = -778.8 kJ/mol mean of squares = 6.071e+05 (kJ/mol)^2 standard deviation = 25.09 kJ/mol -------------------------------------------------------------------- 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 movable nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 subset_jiemian adf 200 6 7 7 0 3.3 0 3.3 fix ad1 subset_jiemian ave/time 1 10000 10000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF2 subset_jiemian adf 200 6 1 1 0 4.4 0 4.4 fix ad2 subset_jiemian ave/time 1 10000 10000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 subset_jiemian adf 200 3 7 7 0 3.8 0 3.8 fix ad3 subset_jiemian ave/time 1 10000 10000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 subset_jiemian adf 200 3 1 1 0 4.1 0 4.1 fix ad4 subset_jiemian ave/time 1 10000 10000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 subset_jiemian adf 200 1 7 7 0 4.1 0 4.1 fix ad5 subset_jiemian ave/time 1 10000 10000 c_myADF5\[*\] file tmp5.adf mode vector timestep 1 run 10000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 ********************************************* WARNING: this LAMMPS stage completed on Sun 29 October 2023 at 17:25:11 CST after 469 s (0:07:49) with the following error: ERROR on proc 18: Bond atoms 9937 9936 missing on proc 18 at step 11955 (../ntopo_bond_all.cpp:61) ********************************************* Entire job completed on Sun 29 October 2023 at 17:25:11 CST after 469 s (0:07:49) and running 1 tasks.