******************************************************************************** ______ __ / ____/___ _______________ _____ ____/ /________ _ / / / __ `/ ___/ ___/ __ `/ __ \/ __ / ___/ __ `/ / /___/ /_/ (__ |__ ) /_/ / / / / /_/ / / / /_/ / \____/\__,_/____/____/\__,_/_/ /_/\__,_/_/ \__,_/ ******************************************************************************** Run info ******************************************************************************** version: Cassandra Version 1.2 20160720 inputfile: rst_MeOHCO2.inp name of run: MeOH_CO2_413_90.opt date (mm/dd/yyyy): 07/20/2016 time: 15:41:25 machine: n434 ******************************************************************************** Verbose log ******************************************************************************** Normal output to logfile ******************************************************************************** Simulation type ******************************************************************************** GEMC_NPT ******************************************************************************** Copy input file ******************************************************************************** # Run_Name MeOH_CO2_413_90.opt # Sim_Type GEMC_NPT # Nbr_Species 2 # VDW_Style LJ cut_tail 14.0 LJ cut_tail 14.0 # Charge_Style coul Ewald 17.0 1E-5 coul Ewald 17.0 1E-5 # Intra_Scaling 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 # Mixing_Rule LB # Seed_Info 1219130951 1219130952 # Rcutoff_Low 0.9 # Pair_Energy TRUE # Molecule_Files MeOH.mcf 650 CO2.mcf 350 # Box_Info 2 CUBIC 39.1243 39.1243 39.1243 CUBIC 54.5993 54.5993 54.5993 # Temperature_Info 413.15 413.15 # Pressure_Info 90.0 90.0 # Move_Probability_Info # Prob_Translation 0.4 0.287 0.567 0.675 0.324 # Prob_Rotation 0.4 33.576 0.572 102.552 179.999 # Prob_Swap 0.1 cbmc cbmc # Prob_Volume 0.1 954.495 7710.024 # Done_Probability_Info # Start_Type checkpoint MeOH_CO2_413_90.chk # Run_Type Equilibration 100 100 # Simulation_Length_Info units sweeps prop_freq 1 coord_freq 5000 run 250000 steps_per_sweep 1000 # Done_Simulation_Length_Info # Average_Info 1 # Pair_Energy TRUE # Property_Info 1 Energy_Total Density Nmols Volume Pressure Enthalpy # Property_Info 2 Energy_Total Density Nmols Volume Pressure Enthalpy # Fragment_Files species1/frag1/frag1.dat 1 species2/frag1/frag1.dat 2 # CBMC_Info kappa_ins 12 kappa_rot 12 kappa_dih 0 rcut_cbmc 6.5 6.5 END ******************************************************************************** Number of species ******************************************************************************** 2 ******************************************************************************** Box info ******************************************************************************** Number of simulation boxes 2 Box 1 is CUBIC Each Side Of : 39.1243 Angstrom Cell basis vector lengths in A, 39.1243 39.1243 39.1243 Cosine of angles alpha, beta, gamma 0.0000 0.0000 0.0000 Distance between box faces 39.1243 39.1243 39.1243 Box volume, A^3 59887.9905 Box 2 is CUBIC Each Side Of : 54.5993 Angstrom Cell basis vector lengths in A, 54.5993 54.5993 54.5993 Cosine of angles alpha, beta, gamma 0.0000 0.0000 0.0000 Distance between box faces 54.5993 54.5993 54.5993 Box volume, A^3 162765.0756 ******************************************************************************** Pair style ******************************************************************************** VDW style used is: LJ in box: 1 VDW sum style is: cut_tail in box: 1 rcut = 14.000 Angstrom VDW style used is: LJ in box: 2 VDW sum style is: cut_tail in box: 2 rcut = 14.000 Angstrom Charge style in box 1 is coul Charge sum style is Ewald in box: 1 Ewald real space cutoff is 17.000 Angstroms. Ewald real space parameter is 0.200 inverse Angstroms Ewald reciprocal cutoff is 1.3545 inverse Angstroms Charge style in box 2 is coul Charge sum style is Ewald in box: 2 Ewald real space cutoff is 17.000 Angstroms. Ewald real space parameter is 0.200 inverse Angstroms Ewald reciprocal cutoff is 1.3545 inverse Angstroms Pair interaction energy array storage enabled Lorentz-Berthelot mixing rule specified ******************************************************************************** Molecule info ******************************************************************************** Reading molecular connectivity information Species: 1 Molecular connectivity file: MeOH.mcf 3 atom(s) specified. 2 bond(s) specified. 1 angle(s) specified. 0 dihedral(s) specified. 0 improper(s) specified. 1 fragment(s) specified. 0 fragment bond(s) specified. Reading molecular connectivity information Species: 2 Molecular connectivity file: CO2.mcf 3 atom(s) specified. 2 bond(s) specified. 1 angle(s) specified. 0 dihedral(s) specified. 0 improper(s) specified. 1 fragment(s) specified. 0 fragment bond(s) specified. Species Max molecules ------- ------------- 1 650 2 350 Species 1 ------------------------------------------------------------------------------- Atom parameters read Bond parameters read Angle parameters read Dihedral parameters read Improper parameters read Section "# Intra_Scaling" missing from mcf, will look in input file Intra molecule scaling factors for species 1 VDW 1-2 scaling factor 0.000 VDW 1-3 scaling factor 0.000 VDW 1-4 scaling factor 0.000 VDW 1-N scaling factor 1.000 Coulomb 1-2 scaling factor 0.000 Coulomb 1-3 scaling factor 0.000 Coulomb 1-4 scaling factor 0.000 Coulomb 1-N scaling factor 1.000 Total number of atoms in fragment 1 is 3 Fragment info read Fragment file for fragment 1 is species1/frag1/frag1.dat ------------------------------------------------------------------------------- Species 2 ------------------------------------------------------------------------------- Atom parameters read Bond parameters read Angle parameters read Dihedral parameters read Improper parameters read Section "# Intra_Scaling" missing from mcf, will look in input file Intra molecule scaling factors for species 2 VDW 1-2 scaling factor 0.000 VDW 1-3 scaling factor 0.000 VDW 1-4 scaling factor 0.000 VDW 1-N scaling factor 1.000 Coulomb 1-2 scaling factor 0.000 Coulomb 1-3 scaling factor 0.000 Coulomb 1-4 scaling factor 0.000 Coulomb 1-N scaling factor 1.000 Total number of atoms in fragment 1 is 3 Fragment info read Fragment file for fragment 2 is species2/frag1/frag1.dat ------------------------------------------------------------------------------- Fragment coord info ------------------------------------------------------------------------------- library_coords array successfully allocated Finished loading fragment coordinates from species1/frag1/frag1.dat Finished loading fragment coordinates from species2/frag1/frag1.dat ------------------------------------------------------------------------------- ******************************************************************************** Nonbond tables ******************************************************************************** ******************************************************************************** Start type ******************************************************************************** Starting configuration will be read from checkpoint file MeOH_CO2_413_90.chk ******************************************************************************** Seed info ******************************************************************************** Seed will be read from a checkpoint file ******************************************************************************** Temperature ******************************************************************************** Temperature of box 1 is 413.150 K Temperature of box 2 is 413.150 K ******************************************************************************** Pressure ******************************************************************************** Pressure of box 1 is 90.000 bar = 0.541992E+00 amu / (A ps^2) Pressure of box 2 is 90.000 bar = 0.541992E+00 amu / (A ps^2) ******************************************************************************** Move probabilities ******************************************************************************** Probability for translation 0.400000 Maximum displacement width for species 1 in box 1 is 0.28700 Maximum displacement width for species 2 in box 1 is 0.56700 Maximum displacement width for species 1 in box 2 is 0.67500 Maximum displacement width for species 2 in box 2 is 0.32400 Probability for rotation 0.400000 The rotational width for the species 1 in box 1 is 0.5860 radians The rotational width for the species 2 in box 1 is 0.0100 radians The rotational width for the species 1 in box 2 is 1.7899 radians The rotational width for the species 2 in box 2 is 3.1416 radians Probability for particle swap 0.100000 Species 1 will be inserted using CBMC Species 2 will be inserted using CBMC Number of insertable species is 2 Probability for volume move 0.100000 Maximum volume displacement for box 1 is 954.495 A^3 Maximum volume displacement for box 2 is 7710.024 A^3 Volume moves will be performed in actual volumes By default, box_out will be selected according to its mole fraction By default, box_in will be selected with uniform probability By default, species will be selected according to its mole fraction in box_out Number of moves is : 4 ******************************************************************************** CBMC info ******************************************************************************** Kappa for first fragment insertion 12 Orientational bias not supported. Kappa set to zero Kappa for dihedral selection 0 Cutoff for CBMC for box 1 is 6.50 Cutoff for CBMC for box 2 is 6.50 ******************************************************************************** Simulation length info ******************************************************************************** Thermodynamic quantities will be computed every 1 Sweeps Coordinates will be written every 5000 Sweeps movie header file for box 1 is MeOH_CO2_413_90.opt.box1.H movie_XYZ file for box 1 is MeOH_CO2_413_90.opt.box1.xyz movie header file for box 2 is MeOH_CO2_413_90.opt.box2.H movie_XYZ file for box 2 is MeOH_CO2_413_90.opt.box2.xyz The simulation will be run for 250000 Sweeps Instantaneous values will be written every 1 Sweeps A sweep is defined as 1000 steps ******************************************************************************** Property info ******************************************************************************** Total number of property files to be written is 1 for box 1 Maximum number of properties per file is 8 Writing the name of the property files and the corresponding property output Property file 1 is MeOH_CO2_413_90.opt.box1.prp Properties output in these files are Energy_Total Density_1 Density_2 Nmols_1 Nmols_2 Volume Pressure Enthalpy Total number of property files to be written is 1 for box 2 Maximum number of properties per file is 8 Writing the name of the property files and the corresponding property output Property file 1 is MeOH_CO2_413_90.opt.box2.prp Properties output in these files are Energy_Total Density_1 Density_2 Nmols_1 Nmols_2 Volume Pressure Enthalpy ******************************************************************************** Minimum distance cutoff ******************************************************************************** MC low cutoff distance is 0.900 Angstrom ******************************************************************************** Run type ******************************************************************************** The input run type is Equilibration Update frequency is 100 Update frequency for adjusting maximum volume displacement is 100 ******************************************************************************** ******************************************************************************** ************************ Begin Cassandra simulation **************************** ******************************************************************************** Initial configuration ******************************************************************************** Reading move parameters for box 1 Reading move parameters for species 1 max displacement 0.28734 max rotation 0.58602 Reading move parameters for species 2 max displacement 0.56768 max rotation 0.01000 Reading move parameters for box 2 Reading move parameters for species 1 max displacement 0.67558 max rotation 1.78988 Reading move parameters for species 2 max displacement 3.24564 max rotation 3.14159 Species move info read successfully Initial MC step is 200000000 Reading info for box 1 max volume change 954. Reading info for box 2 max volume change 7710. Box info read successfully Seed info read successfully Number of molecules read successfully Configuration read successfully ******************************************************************************** Charge neutrality check ******************************************************************************** Species 1 has charge: 0.00000000 Species 2 has charge: 0.00000000 Box 1 has charge: 0.00000000 Box 2 has charge: 0.00000000 ******************************************************************************** Compute total energy ******************************************************************************** Starting energy components for box 1 Atomic units-Extensive ----------------------------------------------------------- Total system energy is -1506791.206 Intra molecular energy is 101617.948 Bond energy is 0.000 Bond angle energy is 101617.948 Dihedral angle energy is 0.000 Improper angle energy is 0.000 Intra molecule vdw is 0.000 Intra molecule q is 0.000 Inter molecule vdw is -326023.947 Long range correction is -10681.679 Inter molecule q is 6344904.051 Number of vectors is 1368 Reciprocal ewald is 17645.784 Self ewald is -7634253.363 ----------------------------------------------------------- Starting energy components for box 2 Atomic units-Extensive ----------------------------------------------------------- Total system energy is -145870.256 Intra molecular energy is 15336.453 Bond energy is 0.000 Bond angle energy is 15336.453 Dihedral angle energy is 0.000 Improper angle energy is 0.000 Intra molecule vdw is 0.000 Intra molecule q is 0.000 Inter molecule vdw is -45061.368 Long range correction is -842.550 Inter molecule q is 3886456.590 Number of vectors is 3647 Reciprocal ewald is 10182.544 Self ewald is -4011941.925 ----------------------------------------------------------- ******************************************************************************** Run simulation ******************************************************************************** Step Move Mol Spc Box Success MaxWidth 200000036 translate 1 1 0.01000 0.00575 200000062 rotate 1 1 0.08000 0.55672 200000083 translate 2 1 0.01000 0.01135 200000407 translate 1 1 0.98000 0.01126 200000462 volume 1 0.06000 115. 200000479 rotate 1 1 0.51000 0.58455 200000487 translate 2 2 0.29000 1.88247 200000592 rotate 2 2 0.35000 2.98451 200000901 translate 1 1 0.98000 0.02208 200000904 rotate 1 1 0.44000 0.55532 200001058 rotate 2 1 0.11000 0.01000 200001264 translate 1 2 0.30000 0.40535 200001322 rotate 1 1 0.52000 0.58309 200001448 translate 1 1 0.95000 0.04195 200001501 translate 2 2 0.69000 2.59781 200001696 rotate 1 1 0.55000 0.61224 200001766 rotate 2 2 0.76000 3.13374 200001819 volume 2 0.24000 3701. 200001875 translate 1 1 0.95000 0.07970 200001910 rotate 1 2 0.38000 1.70038 200002113 volume 1 0.00000 11. 200002196 rotate 1 1 0.50000 0.64286 200002277 translate 1 1 0.81000 0.12911 200002520 translate 2 2 0.57000 2.96150 200002674 rotate 1 1 0.55000 0.67500 200002710 translate 1 1 0.78000 0.20141 200002801 rotate 2 2 0.68000 3.14159 200003042 translate 2 1 0.93000 0.02112 200003126 translate 1 1 0.65000 0.26183 200003133 rotate 1 1 0.47000 0.64125 200003449 rotate 2 1 0.22000 0.01000 200003479 translate 2 2 0.66000 3.90918 200003581 translate 1 1 0.50000 0.26183 200003602 rotate 1 1 0.51000 0.67331 200003670 rotate 2 2 0.75000 3.14159 200003691 volume 2 0.00000 370. 200003919 translate 1 2 0.63000 0.51074 200004013 translate 1 1 0.55000 0.28802 200004045 rotate 1 1 0.44000 0.63965 200004071 volume 1 0.00000 1. 200004402 translate 1 1 0.55000 0.31682 200004453 rotate 1 2 0.54000 1.78540 200004509 rotate 1 1 0.42000 0.60766 200004533 translate 2 2 0.45000 3.51826 200004802 rotate 2 2 0.69000 3.14159 200004888 translate 1 1 0.52000 0.32949 200004971 rotate 1 1 0.49000 0.57728 200005314 translate 2 2 0.50000 3.51826 200005360 rotate 1 1 0.49000 0.54842 200005378 translate 1 1 0.53000 0.34926 200005598 volume 2 0.00000 37. 200005668 translate 2 1 0.96000 0.04055 200005705 volume 1 0.00000 0. 200005824 rotate 2 2 0.63000 3.14159 200005841 rotate 1 1 0.64000 0.57584 200005897 translate 1 1 0.48000 0.33529 200006204 translate 2 2 0.52000 3.65899 200006279 translate 1 2 0.56000 0.57203 200006284 rotate 1 1 0.50000 0.60463 200006371 translate 1 1 0.43000 0.28835 200006728 rotate 1 1 0.52000 0.63486 200006732 rotate 2 1 0.30000 0.01000 200006849 translate 1 1 0.46000 0.26528 200007021 rotate 2 2 0.76000 3.14159 200007072 translate 2 2 0.48000 3.51263 200007188 rotate 1 1 0.48000 0.60312 200007310 translate 1 1 0.55000 0.29181 200007464 volume 2 0.00000 4. 200007647 rotate 1 1 0.57000 0.63327 200007674 volume 1 0.00000 0. 200007683 translate 1 1 0.49000 0.28597 200007747 translate 2 1 0.94000 0.07623 200007815 rotate 1 2 0.53000 1.87467 200007994 translate 2 2 0.53000 3.72339 200008020 rotate 2 2 0.75000 3.14159 200008131 rotate 1 1 0.46000 0.60161 200008175 translate 1 1 0.44000 0.25166 200008548 rotate 1 1 0.49000 0.57153 200008705 translate 1 1 0.57000 0.28689 200008951 translate 2 2 0.55000 4.09573 200008983 rotate 2 2 0.75000 3.14159 200009023 rotate 1 1 0.52000 0.60011 200009068 translate 1 1 0.52000 0.29836 200009221 volume 2 0.00000 0. 200009237 rotate 2 1 0.35000 0.01000 200009432 rotate 1 1 0.48000 0.57010 200009510 translate 1 1 0.52000 0.31030 200009603 translate 1 2 0.49000 0.56059 200009769 volume 1 0.00000 0. 200009853 rotate 1 1 0.46000 0.54160 200009897 translate 2 2 0.48000 3.93190 200009965 translate 1 1 0.40000 0.24824 200010040 rotate 2 2 0.84000 3.14159 200010166 translate 2 1 0.92000 0.14026 200010242 rotate 1 2 0.49000 1.78094 200010315 rotate 1 1 0.48000 0.51452 200010400 translate 1 1 0.45000 0.22342 200010765 rotate 1 1 0.58000 0.54024 200010815 translate 1 1 0.56000 0.25023 200010961 translate 2 2 0.48000 3.77463 200011151 volume 2 0.00000 0. 200011242 translate 1 1 0.57000 0.28526 200011292 rotate 2 2 0.78000 3.14159 200011310 rotate 1 1 0.52000 0.56725 200011512 volume 1 0.00000 0. 200011663 translate 1 1 0.49000 0.27955 200011683 rotate 2 1 0.48000 0.01000 200011735 rotate 1 1 0.46000 0.53889 200011863 translate 2 2 0.56000 4.22758 200012087 translate 1 1 0.50000 0.27955 200012235 rotate 1 1 0.49000 0.51195 200012280 translate 2 1 0.84000 0.23563 200012301 translate 1 2 0.56000 0.62786 200012374 rotate 2 2 0.65000 3.14159 200012531 translate 1 1 0.47000 0.26278 200012674 rotate 1 1 0.49000 0.48635 200012738 volume 2 0.00000 0. 200012766 rotate 1 2 0.49000 1.69189 200012989 translate 2 2 0.57000 4.81944 200013017 translate 1 1 0.55000 0.28906 200013105 rotate 1 1 0.59000 0.51067 200013430 volume 1 0.00000 0. 200013492 translate 1 1 0.52000 0.30062 200013495 rotate 1 1 0.55000 0.53620 200013563 rotate 2 2 0.76000 3.14159 200013939 translate 2 2 0.52000 5.01222 200013944 rotate 1 1 0.61000 0.56301 200013954 rotate 2 1 0.42000 0.01000 200013996 translate 1 1 0.47000 0.28258 200014296 translate 2 1 0.69000 0.32517 200014332 rotate 1 1 0.56000 0.59116 200014376 translate 1 1 0.55000 0.31084 200014664 rotate 2 2 0.75000 3.14159 200014807 rotate 1 1 0.58000 0.62072 200014846 translate 1 1 0.48000 0.29841 200014946 volume 2 0.00000 0. 200015038 translate 2 2 0.43000 4.31051 200015175 translate 1 2 0.62000 0.77855 200015214 rotate 1 1 0.53000 0.65175 200015348 translate 1 1 0.49000 0.29244 200015586 volume 1 0.00000 0. 200015648 rotate 1 1 0.49000 0.61917 200015668 rotate 2 2 0.80000 3.14159 200015791 translate 1 1 0.49000 0.28659 200015948 rotate 2 1 0.53000 0.01050 200016003 rotate 1 2 0.43000 1.60730 200016054 rotate 1 1 0.45000 0.58821 200016163 translate 2 2 0.53000 4.56914 200016252 translate 1 1 0.54000 0.30952 200016271 translate 2 1 0.70000 0.45524 200016514 rotate 1 1 0.52000 0.61762 200016693 rotate 2 2 0.77000 3.14159 200016713 translate 1 1 0.51000 0.31571 200016838 volume 2 0.00000 0. 200016982 rotate 1 1 0.49000 0.58674 200017182 translate 1 1 0.47000 0.29676 200017361 rotate 1 1 0.50000 0.61608 200017433 translate 2 2 0.58000 5.30020 200017576 volume 1 0.00000 0. 200017631 translate 1 1 0.44000 0.26115 200017803 rotate 1 1 0.53000 0.64688 200017843 rotate 2 2 0.77000 3.14159 200018027 translate 1 2 0.40000 0.62284 200018028 rotate 2 1 0.50000 0.01103 200018087 translate 1 1 0.55000 0.28727 200018246 rotate 1 1 0.50000 0.67922 200018364 translate 2 1 0.62000 0.56449 200018420 volume 2 0.00000 0. 200018487 translate 2 2 0.46000 4.87619 200018556 translate 1 1 0.52000 0.29876 200018669 rotate 1 1 0.43000 0.64526 200018706 rotate 1 2 0.53000 1.68766 200018899 rotate 2 2 0.80000 3.14159 200018994 translate 1 1 0.54000 0.32266 200019134 rotate 1 1 0.43000 0.61300 200019385 translate 1 1 0.40000 0.25813 200019491 volume 1 0.00000 0. 200019590 rotate 1 1 0.47000 0.58235 200019648 translate 2 2 0.52000 5.07123 200019772 translate 1 1 0.45000 0.23231 200020015 rotate 2 2 0.75000 3.14159 200020064 rotate 1 1 0.52000 0.61147 200020126 volume 2 0.00000 0. 200020201 translate 1 1 0.51000 0.23696 200020203 rotate 2 1 0.45000 0.01047 200020482 rotate 1 1 0.42000 0.58089 200020594 translate 2 1 0.48000 0.54191 200020727 translate 2 2 0.41000 4.15841 200020728 translate 1 1 0.58000 0.27487 200020825 rotate 1 1 0.47000 0.55185 200020943 translate 1 2 0.52000 0.64775 200021197 translate 1 1 0.49000 0.26938 200021261 rotate 1 1 0.43000 0.52426 200021319 rotate 2 2 0.71000 3.14159 200021428 volume 1 0.00000 0. 200021580 translate 1 1 0.64000 0.34480 200021676 rotate 1 2 0.50000 1.77204 200021740 rotate 1 1 0.61000 0.55047 200021826 translate 2 2 0.57000 4.74059 200022028 translate 1 1 0.41000 0.28274 200022141 volume 2 0.00000 0. 200022202 rotate 1 1 0.52000 0.57799 200022257 rotate 2 1 0.56000 0.01100 200022302 rotate 2 2 0.78000 3.14159 200022427 translate 1 1 0.45000 0.25446 200022650 rotate 1 1 0.41000 0.54909 200022651 translate 2 1 0.46000 0.49856 200022893 translate 1 1 0.49000 0.24938 200022932 translate 2 2 0.53000 5.02502 200023098 rotate 1 1 0.57000 0.57655 200023282 translate 1 1 0.58000 0.28928 200023322 rotate 2 2 0.79000 3.14159 200023501 rotate 1 1 0.46000 0.54772 200023727 translate 1 1 0.49000 0.28349 200023728 volume 1 0.00000 0. 200023764 translate 1 2 0.52000 0.67366 200023927 translate 2 2 0.51000 5.12553 200023992 rotate 1 1 0.50000 0.57511 200024114 translate 1 1 0.44000 0.24947 200024366 rotate 2 1 0.53000 0.01155 200024440 volume 2 0.00000 0. 200024455 rotate 1 1 0.47000 0.54635 200024488 rotate 2 2 0.77000 3.14159 200024528 translate 1 1 0.57000 0.28440 200024629 translate 2 1 0.58000 0.57833 200024636 rotate 1 2 0.41000 1.68344 200024908 translate 1 1 0.51000 0.29008 200024922 rotate 1 1 0.54000 0.57367 200025297 rotate 1 1 0.51000 0.60235 200025312 translate 2 2 0.50000 5.12553 200025406 translate 1 1 0.54000 0.31329 200025580 volume 1 0.00000 0. 200025638 rotate 2 2 0.79000 3.14159 200025756 rotate 1 1 0.49000 0.57223 200025803 translate 1 1 0.36000 0.22557 ************ERROR************ Error: existing configuration of molecule 79 of species 1 in box 1 tripped an overlap error This error occurred in subroutine GEMC_Particle_Transfer on step 200026174. Fatal Error. Stopping program.