Loading doc/src/Eqs/pair_ilp_gr_hBN.jpgdeleted 100644 → 0 −301 KiB Loading image diff... doc/src/Eqs/pair_ilp_gr_hBN.texdeleted 100644 → 0 +0 −42 Original line number Diff line number Diff line \documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4} \pdfoutput=1 \bibliographystyle{apsrev4} \usepackage{color} \usepackage{dcolumn} %Align table columns on decimal point \usepackage{amssymb} \usepackage{amsmath} \usepackage{amsthm} \usepackage{graphicx} \usepackage[pdftex]{hyperref} \hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue} \usepackage[all]{hypcap} \newcommand{\red}{\color{red}} \newcommand{\blue}{\color{blue}} \definecolor{green}{rgb}{0,0.5,0} \newcommand{\green}{\color{green}} \newcommand{\white}{\color{white}} %\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}} \thickmuskip=0.5\thickmuskip %shorter spaces in math % \begin{document} % \begingroup \Large \begin{eqnarray*} E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt] V_{ij} & = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\[15pt] \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\[15pt] \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\[15pt] f(\rho) & = & C e^{ -( \rho / \delta )^2 }\\[15pt] {\rm Tap}(r_{ij}) & = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 \end{eqnarray*} \endgroup % \end{document} % examples/USER/misc/kolmogorov_crespi_full/CC.KC-full 0 → 120000 +1 −0 Original line number Diff line number Diff line ../../../../potentials/CC.KC-full No newline at end of file examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.1 0 → 100644 +136 −0 Original line number Diff line number Diff line LAMMPS (8 Mar 2018) using 1 OpenMP thread(s) per MPI task # Initialization units metal boundary p p p atom_style full processors * * 1 # domain decomposition over x and y # System and atom definition # we use 2 atom types so that inter- and intra-layer # interactions can be specified separately # read lammps data file read_data Bi_gr_AB_stack_2L_noH_300K.data orthogonal box = (0 0 0) to (42.6 41.8117 100) 1 by 1 by 1 MPI processor grid reading atoms ... 1360 atoms reading velocities ... 1360 velocities 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors mass 1 12.0107 # carbon mass (g/mole) | membrane mass 2 12.0107 # carbon mass (g/mole) | adsorbate # Separate atom groups group membrane type 1 680 atoms in group membrane group adsorbate type 2 680 atoms in group adsorbate ######################## Potential defition ######################## pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 #################################################################### pair_coeff * * rebo CH.airebo NULL C # chemical Reading potential file CH.airebo with DATE: 2011-10-25 pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range #################################################################### # Neighbor update settings neighbor 2.0 bin neigh_modify every 1 neigh_modify delay 0 neigh_modify check yes # calculate the COM variable adsxcom equal xcm(adsorbate,x) variable adsycom equal xcm(adsorbate,y) variable adszcom equal xcm(adsorbate,z) variable adsvxcom equal vcm(adsorbate,x) variable adsvycom equal vcm(adsorbate,y) variable adsvzcom equal vcm(adsorbate,z) #### Simulation settings #### timestep 0.001 fix subf membrane setforce 0.0 0.0 0.0 fix thermostat all nve compute 0 all pair rebo compute 1 all pair kolmogorov/crespi/full variable REBO equal c_0 variable KC equal c_1 ############################ # Output thermo 100 thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom thermo_modify line one format float %.10f thermo_modify flush yes norm no lost warn #ignore #dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu #dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes ###### Run molecular dynamics ###### run 1000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 5 5 12 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair rebo, perpetual, skip from (2) attributes: full, newton on, ghost pair build: skip/ghost stencil: none bin: none (2) pair kolmogorov/crespi/full, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014 200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577 300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295102 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908 400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496 500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989087 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066 600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093 700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564 800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925 900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638 1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737982 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119 Loop time of 156.142 on 1 procs for 1000 steps with 1360 atoms Performance: 0.553 ns/day, 43.373 hours/ns, 6.404 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 155.99 | 155.99 | 155.99 | 0.0 | 99.90 Bond | 0.00075769 | 0.00075769 | 0.00075769 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.084217 | 0.084217 | 0.084217 | 0.0 | 0.05 Output | 0.0016122 | 0.0016122 | 0.0016122 | 0.0 | 0.00 Modify | 0.034797 | 0.034797 | 0.034797 | 0.0 | 0.02 Other | | 0.02838 | | | 0.02 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7964 ave 7964 max 7964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 265206 ave 265206 max 265206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 265206 Ave neighs/atom = 195.004 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:02:36 examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.4 0 → 100644 +136 −0 Original line number Diff line number Diff line LAMMPS (8 Mar 2018) using 1 OpenMP thread(s) per MPI task # Initialization units metal boundary p p p atom_style full processors * * 1 # domain decomposition over x and y # System and atom definition # we use 2 atom types so that inter- and intra-layer # interactions can be specified separately # read lammps data file read_data Bi_gr_AB_stack_2L_noH_300K.data orthogonal box = (0 0 0) to (42.6 41.8117 100) 2 by 2 by 1 MPI processor grid reading atoms ... 1360 atoms reading velocities ... 1360 velocities 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors mass 1 12.0107 # carbon mass (g/mole) | membrane mass 2 12.0107 # carbon mass (g/mole) | adsorbate # Separate atom groups group membrane type 1 680 atoms in group membrane group adsorbate type 2 680 atoms in group adsorbate ######################## Potential defition ######################## pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 #################################################################### pair_coeff * * rebo CH.airebo NULL C # chemical Reading potential file CH.airebo with DATE: 2011-10-25 pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range #################################################################### # Neighbor update settings neighbor 2.0 bin neigh_modify every 1 neigh_modify delay 0 neigh_modify check yes # calculate the COM variable adsxcom equal xcm(adsorbate,x) variable adsycom equal xcm(adsorbate,y) variable adszcom equal xcm(adsorbate,z) variable adsvxcom equal vcm(adsorbate,x) variable adsvycom equal vcm(adsorbate,y) variable adsvzcom equal vcm(adsorbate,z) #### Simulation settings #### timestep 0.001 fix subf membrane setforce 0.0 0.0 0.0 fix thermostat all nve compute 0 all pair rebo compute 1 all pair kolmogorov/crespi/full variable REBO equal c_0 variable KC equal c_1 ############################ # Output thermo 100 thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom thermo_modify line one format float %.10f thermo_modify flush yes norm no lost warn #ignore #dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu #dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes ###### Run molecular dynamics ###### run 1000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 5 5 12 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair rebo, perpetual, skip from (2) attributes: full, newton on, ghost pair build: skip/ghost stencil: none bin: none (2) pair kolmogorov/crespi/full, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014 200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577 300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295103 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908 400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496 500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989088 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066 600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093 700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564 800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925 900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638 1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737983 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119 Loop time of 42.5422 on 4 procs for 1000 steps with 1360 atoms Performance: 2.031 ns/day, 11.817 hours/ns, 23.506 timesteps/s 98.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 39.928 | 40.992 | 42.377 | 15.8 | 96.36 Bond | 0.0003643 | 0.00043392 | 0.00048113 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12253 | 1.5076 | 2.5698 | 82.1 | 3.54 Output | 0.0012577 | 0.0013637 | 0.0016453 | 0.4 | 0.00 Modify | 0.010833 | 0.012247 | 0.013317 | 0.9 | 0.03 Other | | 0.02864 | | | 0.07 Nlocal: 340 ave 344 max 334 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 4628 ave 4634 max 4624 min Histogram: 1 0 1 0 1 0 0 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 66301.5 ave 67860 max 63963 min Histogram: 1 0 0 0 0 0 1 0 1 1 Total # of neighbors = 265206 Ave neighs/atom = 195.004 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:42 Loading
doc/src/Eqs/pair_ilp_gr_hBN.texdeleted 100644 → 0 +0 −42 Original line number Diff line number Diff line \documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4} \pdfoutput=1 \bibliographystyle{apsrev4} \usepackage{color} \usepackage{dcolumn} %Align table columns on decimal point \usepackage{amssymb} \usepackage{amsmath} \usepackage{amsthm} \usepackage{graphicx} \usepackage[pdftex]{hyperref} \hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue} \usepackage[all]{hypcap} \newcommand{\red}{\color{red}} \newcommand{\blue}{\color{blue}} \definecolor{green}{rgb}{0,0.5,0} \newcommand{\green}{\color{green}} \newcommand{\white}{\color{white}} %\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}} \thickmuskip=0.5\thickmuskip %shorter spaces in math % \begin{document} % \begingroup \Large \begin{eqnarray*} E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt] V_{ij} & = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} \cdot \frac{C_6}{r^6_{ij}} \right \}\\[15pt] \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\[15pt] \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\[15pt] f(\rho) & = & C e^{ -( \rho / \delta )^2 }\\[15pt] {\rm Tap}(r_{ij}) & = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 \end{eqnarray*} \endgroup % \end{document} %
examples/USER/misc/kolmogorov_crespi_full/CC.KC-full 0 → 120000 +1 −0 Original line number Diff line number Diff line ../../../../potentials/CC.KC-full No newline at end of file
examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.1 0 → 100644 +136 −0 Original line number Diff line number Diff line LAMMPS (8 Mar 2018) using 1 OpenMP thread(s) per MPI task # Initialization units metal boundary p p p atom_style full processors * * 1 # domain decomposition over x and y # System and atom definition # we use 2 atom types so that inter- and intra-layer # interactions can be specified separately # read lammps data file read_data Bi_gr_AB_stack_2L_noH_300K.data orthogonal box = (0 0 0) to (42.6 41.8117 100) 1 by 1 by 1 MPI processor grid reading atoms ... 1360 atoms reading velocities ... 1360 velocities 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors mass 1 12.0107 # carbon mass (g/mole) | membrane mass 2 12.0107 # carbon mass (g/mole) | adsorbate # Separate atom groups group membrane type 1 680 atoms in group membrane group adsorbate type 2 680 atoms in group adsorbate ######################## Potential defition ######################## pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 #################################################################### pair_coeff * * rebo CH.airebo NULL C # chemical Reading potential file CH.airebo with DATE: 2011-10-25 pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range #################################################################### # Neighbor update settings neighbor 2.0 bin neigh_modify every 1 neigh_modify delay 0 neigh_modify check yes # calculate the COM variable adsxcom equal xcm(adsorbate,x) variable adsycom equal xcm(adsorbate,y) variable adszcom equal xcm(adsorbate,z) variable adsvxcom equal vcm(adsorbate,x) variable adsvycom equal vcm(adsorbate,y) variable adsvzcom equal vcm(adsorbate,z) #### Simulation settings #### timestep 0.001 fix subf membrane setforce 0.0 0.0 0.0 fix thermostat all nve compute 0 all pair rebo compute 1 all pair kolmogorov/crespi/full variable REBO equal c_0 variable KC equal c_1 ############################ # Output thermo 100 thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom thermo_modify line one format float %.10f thermo_modify flush yes norm no lost warn #ignore #dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu #dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes ###### Run molecular dynamics ###### run 1000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 5 5 12 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair rebo, perpetual, skip from (2) attributes: full, newton on, ghost pair build: skip/ghost stencil: none bin: none (2) pair kolmogorov/crespi/full, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014 200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577 300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295102 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908 400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496 500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989087 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066 600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093 700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564 800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925 900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638 1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737982 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119 Loop time of 156.142 on 1 procs for 1000 steps with 1360 atoms Performance: 0.553 ns/day, 43.373 hours/ns, 6.404 timesteps/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 155.99 | 155.99 | 155.99 | 0.0 | 99.90 Bond | 0.00075769 | 0.00075769 | 0.00075769 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.084217 | 0.084217 | 0.084217 | 0.0 | 0.05 Output | 0.0016122 | 0.0016122 | 0.0016122 | 0.0 | 0.00 Modify | 0.034797 | 0.034797 | 0.034797 | 0.0 | 0.02 Other | | 0.02838 | | | 0.02 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7964 ave 7964 max 7964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 265206 ave 265206 max 265206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 265206 Ave neighs/atom = 195.004 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:02:36
examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.4 0 → 100644 +136 −0 Original line number Diff line number Diff line LAMMPS (8 Mar 2018) using 1 OpenMP thread(s) per MPI task # Initialization units metal boundary p p p atom_style full processors * * 1 # domain decomposition over x and y # System and atom definition # we use 2 atom types so that inter- and intra-layer # interactions can be specified separately # read lammps data file read_data Bi_gr_AB_stack_2L_noH_300K.data orthogonal box = (0 0 0) to (42.6 41.8117 100) 2 by 2 by 1 MPI processor grid reading atoms ... 1360 atoms reading velocities ... 1360 velocities 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors mass 1 12.0107 # carbon mass (g/mole) | membrane mass 2 12.0107 # carbon mass (g/mole) | adsorbate # Separate atom groups group membrane type 1 680 atoms in group membrane group adsorbate type 2 680 atoms in group adsorbate ######################## Potential defition ######################## pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 #################################################################### pair_coeff * * rebo CH.airebo NULL C # chemical Reading potential file CH.airebo with DATE: 2011-10-25 pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range #################################################################### # Neighbor update settings neighbor 2.0 bin neigh_modify every 1 neigh_modify delay 0 neigh_modify check yes # calculate the COM variable adsxcom equal xcm(adsorbate,x) variable adsycom equal xcm(adsorbate,y) variable adszcom equal xcm(adsorbate,z) variable adsvxcom equal vcm(adsorbate,x) variable adsvycom equal vcm(adsorbate,y) variable adsvzcom equal vcm(adsorbate,z) #### Simulation settings #### timestep 0.001 fix subf membrane setforce 0.0 0.0 0.0 fix thermostat all nve compute 0 all pair rebo compute 1 all pair kolmogorov/crespi/full variable REBO equal c_0 variable KC equal c_1 ############################ # Output thermo 100 thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom thermo_modify line one format float %.10f thermo_modify flush yes norm no lost warn #ignore #dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu #dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes ###### Run molecular dynamics ###### run 1000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 5 5 12 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair rebo, perpetual, skip from (2) attributes: full, newton on, ghost pair build: skip/ghost stencil: none bin: none (2) pair kolmogorov/crespi/full, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014 200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577 300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295103 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908 400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496 500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989088 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066 600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093 700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564 800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925 900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638 1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737983 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119 Loop time of 42.5422 on 4 procs for 1000 steps with 1360 atoms Performance: 2.031 ns/day, 11.817 hours/ns, 23.506 timesteps/s 98.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 39.928 | 40.992 | 42.377 | 15.8 | 96.36 Bond | 0.0003643 | 0.00043392 | 0.00048113 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12253 | 1.5076 | 2.5698 | 82.1 | 3.54 Output | 0.0012577 | 0.0013637 | 0.0016453 | 0.4 | 0.00 Modify | 0.010833 | 0.012247 | 0.013317 | 0.9 | 0.03 Other | | 0.02864 | | | 0.07 Nlocal: 340 ave 344 max 334 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 4628 ave 4634 max 4624 min Histogram: 1 0 1 0 1 0 0 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 66301.5 ave 67860 max 63963 min Histogram: 1 0 0 0 0 0 1 0 1 1 Total # of neighbors = 265206 Ave neighs/atom = 195.004 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:42
