Loading doc/src/Section_commands.txt +2 −1 Original line number Diff line number Diff line Loading @@ -582,7 +582,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "dt/reset"_fix_dt_reset.html, "efield"_fix_efield.html, "ehex"_fix_ehex.html, "enforce2d"_fix_enforce2d.html, "enforce2d (k)"_fix_enforce2d.html, "evaporate"_fix_evaporate.html, "external"_fix_external.html, "freeze"_fix_freeze.html, Loading Loading @@ -929,6 +929,7 @@ KOKKOS, o = USER-OMP, t = OPT. "adp (o)"_pair_adp.html, "airebo (oi)"_pair_airebo.html, "airebo/morse (oi)"_pair_airebo.html, "atm"_pair_atm.html, "beck (go)"_pair_beck.html, "body"_pair_body.html, "bop"_pair_bop.html, Loading doc/src/pair_atm.txt +59 −73 Original line number Diff line number Diff line Loading @@ -16,7 +16,7 @@ cutoff = global cutoff for 3-body interactions (distance units) :ul [Examples:] pair_style 2.5 pair_style atm 2.5 pair_coeff * * * 0.072 :pre pair_style hybrid/overlay lj/cut 6.5 atm 2.5 Loading @@ -33,106 +33,92 @@ potential for the energy E of a system of atoms as :c,image(Eqs/pair_atm.jpg) where nu is the three-body interaction strength, and the distances between pairs of atoms r12, r23 and r31 and the angles gamma1, gamma2 and gamma3 are shown at the diagram: where nu is the three-body interaction strength. The distances between pairs of atoms r12, r23, r31 and the angles gamma1, gamma2, gamma3 are as shown in this diagram: :c,image(JPG/pair_atm_dia.jpg) There is no \"central\" atom, the interaction is symmetric with respect to permutation of atom types. Note that for the interaction between a triplet of atoms I,J,K, there is no "central" atom. The interaction is symmetric with respect to permutation of the three atoms. In fact, it is computed 3 times by the code with each of I,J,K being atom 1. Thus the nu value must be the same for all those permutations of the atom types of I,J,K as discussed below. The {atm} potential is typically used in combination with a two-body potential using the "pair_style hybrid/overlay"_pair_hybrid.html command as in the example above. The potential is calculated if all three atoms are in the "neighbor list"_neighbor.html and the distances between atoms satisfy r12 r23 r31 > cutoff^3. The potential for a triplet of atom is calculated only if all 3 distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff. The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the restart files read by the "read_restart"_read_restart.html commands: K - the type of the third atom nu (energy/distance^9 units) :ul K = atom type of the third atom (1 to Ntypes) nu = prefactor (energy/distance^9 units) :ul For a single-atom type simulation, only a single entry is required, eg K can be specified in one of two ways. An explicit numeric value can be used, as in the 2nd example above. J <= K is required. LAMMPS sets the coefficients for the other 5 symmetric interactions to the same values. E.g. if I = 1, J = 2, K = 3, then these 6 values are set to the specified nu: nu123, nu132, nu213, nu231, nu312, nu321. This enforces the symmetry discussed above. pair_coeff 1 1 1 nu :pre A wildcard asterisk can be used for K to set the coefficients for multiple triplets of atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). Note that only type triplets with J <= K are considered; if asterisks imply type triplets where K < J, they are ignored. where all three atoms are of type 1. For a two-atom type simulation, more pair_coeff commands can be used. ATM interaction is symmetric with respect to permutation of atoms, it is necessary to provide pair_coeff command for one permutation. For example, the command Note that a pair_coeff command can override a previous setting for the same I,J,K triplet. For example, these commands set nu for all I,J.K triplets, then overwrite nu for just the I,J,K = 2,3,4 triplet: pair_coeff 1 1 2 nu :pre pair_coeff * * * 0.25 pair_coeff 2 3 4 0.1 :pre also implies Note that for a simulation with a single atom type, only a single entry is required, e.g. pair_coeff 1 2 1 nu pair_coeff 2 1 1 nu :pre pair_coeff 1 1 1 0.25 :per Thus, to specify all ATM interactions between two atom types (eg 1 and 2) it is sufficient to provide four pair_coeff commands, eg: For a simulation with two atom types, four pair_coeff commands will specify all possible nu values: pair_coeff 1 1 1 nu1 pair_coeff 1 1 2 nu2 pair_coeff 1 2 2 nu3 pair_coeff 2 2 2 nu4 :pre For 3 atom types, 10 pair_coeff commands (eg 111, 112, 113, 122, 123, 133, 222, 223, 233, 333) will describe all possible ATM interactions, etc. It is not necessary to provide the pair_coeff commands for interactions of all combinations of atom types: if some combination is not defined then there is no ATM interaction for this combination and all its permutations. For a simulation with three atom types, ten pair_coeff commands will specify all possible nu values: -------------------- [Steve:] I think a better syntax for the pair coeff command might be this: pair_coeff I J v1 v2 ... vN when 1,2,...N are the number of atom types defined. Then there be one pair_coeff command for each type pair, the same syntax as all other potentials in LAMMPS use. [Sergey:] The reason for my original pair_coeff command syntax is that I would like to reserve further arguments for possible extension of ATM potential in LAMMPS to further terms in the multipole expansion of many-body dispersion interaction. For example, the next term would be dipole-dipole-quadrupole, it may be activated if the next argument of pair_coeff is present without breaking backward compatibility. Also, the command you propose (i) will not account that the value of nu for different permutations of atom types is the same, and (ii) will make the numbering of atom types messy since there is no requirement to supply the values of nu for all triplets. -------------------- I think a better syntax for the pair coeff command might be this: pair_coeff I J v1 v2 ... vN when 1,2,...N are the number of atom types defined. Then there be one pair_coeff command for each type pair, the same syntax as all other potentials in LAMMPS use. Note that you refer to "elements", but the pair coeff command knows nothing about elements. Only atom types. There could be 10 atom types that all map to the same chemical element. pair_coeff 1 1 1 nu1 pair_coeff 1 1 2 nu2 pair_coeff 1 1 3 nu3 pair_coeff 1 2 2 nu4 pair_coeff 1 2 3 nu5 pair_coeff 1 3 3 nu6 pair_coeff 2 2 2 nu7 pair_coeff 2 2 3 nu8 pair_coeff 2 3 3 nu9 pair_coeff 3 3 3 nu10 :pre By default the nu value for all triplets is set to 0.0. Thus it is not required to provide pair_coeff commands that enumerate triplet interactions for all K types. If some I,J,K combination is not speficied, then there will be no 3-body ATM interactions for that combination and all its permutations. However, as with all pair styles, it is required to specify a pair_coeff command for all I,J combinations, else an error will result. :line Loading doc/src/pair_style.txt +1 −0 Original line number Diff line number Diff line Loading @@ -103,6 +103,7 @@ in the pair section of "this page"_Section_commands.html#cmd_5. "pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin "pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart "pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ "pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential "pair_style beck"_pair_beck.html - Beck potential "pair_style body"_pair_body.html - interactions between body particles "pair_style bop"_pair_bop.html - BOP potential of Pettifor Loading examples/atm/log.9Jul18.atm.g++.1 +15 −15 Original line number Diff line number Diff line Loading @@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms Time spent = 0.00120211 secs Time spent = 0.00125098 secs pair_style hybrid/overlay lj/cut 4.5 atm 2.5 pair_coeff * * lj/cut 1.0 1.0 Loading Loading @@ -60,26 +60,26 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.033 -4.5929584 0 -3.0438458 -3.6506231 5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817 10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204 15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887 20 1.0350606 -4.595891 0 -3.0436883 -3.4478779 25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695 Loop time of 34.5602 on 1 procs for 25 steps with 4000 atoms 0 1.033 -4.733482 0 -3.1843694 -3.924644 5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065 10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962 15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106 20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572 25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651 Loop time of 27.841 on 1 procs for 25 steps with 4000 atoms Performance: 124.999 tau/day, 0.723 timesteps/s Performance: 155.167 tau/day, 0.898 timesteps/s 100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 34.556 | 34.556 | 34.556 | 0.0 | 99.99 Pair | 27.837 | 27.837 | 27.837 | 0.0 | 99.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001323 | 0.001323 | 0.001323 | 0.0 | 0.00 Output | 0.00018287 | 0.00018287 | 0.00018287 | 0.0 | 0.00 Modify | 0.0016184 | 0.0016184 | 0.0016184 | 0.0 | 0.00 Other | | 0.0006311 | | | 0.00 Comm | 0.0015321 | 0.0015321 | 0.0015321 | 0.0 | 0.01 Output | 0.00016594 | 0.00016594 | 0.00016594 | 0.0 | 0.00 Modify | 0.001785 | 0.001785 | 0.001785 | 0.0 | 0.01 Other | | 0.0006731 | | | 0.00 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -97,4 +97,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:36 Total wall time: 0:00:29 examples/atm/log.9Jul18.atm.g++.4 +15 −15 Original line number Diff line number Diff line Loading @@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms Time spent = 0.000735998 secs Time spent = 0.000769138 secs pair_style hybrid/overlay lj/cut 4.5 atm 2.5 pair_coeff * * lj/cut 1.0 1.0 Loading Loading @@ -60,26 +60,26 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.033 -4.5929584 0 -3.0438458 -3.6506231 5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817 10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204 15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887 20 1.0350606 -4.595891 0 -3.0436883 -3.4478779 25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695 Loop time of 10.061 on 4 procs for 25 steps with 4000 atoms 0 1.033 -4.733482 0 -3.1843694 -3.924644 5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065 10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962 15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106 20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572 25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651 Loop time of 7.22029 on 4 procs for 25 steps with 4000 atoms Performance: 429.382 tau/day, 2.485 timesteps/s Performance: 598.314 tau/day, 3.462 timesteps/s 100.0% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.8393 | 9.9439 | 10.008 | 2.0 | 98.84 Pair | 7.1346 | 7.1684 | 7.1863 | 0.8 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.052154 | 0.11613 | 0.22077 | 18.7 | 1.15 Output | 7.2241e-05 | 8.2552e-05 | 0.00011158 | 0.0 | 0.00 Modify | 0.00053763 | 0.00055265 | 0.00056624 | 0.0 | 0.01 Other | | 0.0002971 | | | 0.00 Comm | 0.032945 | 0.0509 | 0.084664 | 9.1 | 0.70 Output | 0.00010133 | 0.00011051 | 0.00013804 | 0.0 | 0.00 Modify | 0.00059557 | 0.00060683 | 0.00061274 | 0.0 | 0.01 Other | | 0.000318 | | | 0.00 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Loading @@ -97,4 +97,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:10 Total wall time: 0:00:07 Loading
doc/src/Section_commands.txt +2 −1 Original line number Diff line number Diff line Loading @@ -582,7 +582,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "dt/reset"_fix_dt_reset.html, "efield"_fix_efield.html, "ehex"_fix_ehex.html, "enforce2d"_fix_enforce2d.html, "enforce2d (k)"_fix_enforce2d.html, "evaporate"_fix_evaporate.html, "external"_fix_external.html, "freeze"_fix_freeze.html, Loading Loading @@ -929,6 +929,7 @@ KOKKOS, o = USER-OMP, t = OPT. "adp (o)"_pair_adp.html, "airebo (oi)"_pair_airebo.html, "airebo/morse (oi)"_pair_airebo.html, "atm"_pair_atm.html, "beck (go)"_pair_beck.html, "body"_pair_body.html, "bop"_pair_bop.html, Loading
doc/src/pair_atm.txt +59 −73 Original line number Diff line number Diff line Loading @@ -16,7 +16,7 @@ cutoff = global cutoff for 3-body interactions (distance units) :ul [Examples:] pair_style 2.5 pair_style atm 2.5 pair_coeff * * * 0.072 :pre pair_style hybrid/overlay lj/cut 6.5 atm 2.5 Loading @@ -33,106 +33,92 @@ potential for the energy E of a system of atoms as :c,image(Eqs/pair_atm.jpg) where nu is the three-body interaction strength, and the distances between pairs of atoms r12, r23 and r31 and the angles gamma1, gamma2 and gamma3 are shown at the diagram: where nu is the three-body interaction strength. The distances between pairs of atoms r12, r23, r31 and the angles gamma1, gamma2, gamma3 are as shown in this diagram: :c,image(JPG/pair_atm_dia.jpg) There is no \"central\" atom, the interaction is symmetric with respect to permutation of atom types. Note that for the interaction between a triplet of atoms I,J,K, there is no "central" atom. The interaction is symmetric with respect to permutation of the three atoms. In fact, it is computed 3 times by the code with each of I,J,K being atom 1. Thus the nu value must be the same for all those permutations of the atom types of I,J,K as discussed below. The {atm} potential is typically used in combination with a two-body potential using the "pair_style hybrid/overlay"_pair_hybrid.html command as in the example above. The potential is calculated if all three atoms are in the "neighbor list"_neighbor.html and the distances between atoms satisfy r12 r23 r31 > cutoff^3. The potential for a triplet of atom is calculated only if all 3 distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff. The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the restart files read by the "read_restart"_read_restart.html commands: K - the type of the third atom nu (energy/distance^9 units) :ul K = atom type of the third atom (1 to Ntypes) nu = prefactor (energy/distance^9 units) :ul For a single-atom type simulation, only a single entry is required, eg K can be specified in one of two ways. An explicit numeric value can be used, as in the 2nd example above. J <= K is required. LAMMPS sets the coefficients for the other 5 symmetric interactions to the same values. E.g. if I = 1, J = 2, K = 3, then these 6 values are set to the specified nu: nu123, nu132, nu213, nu231, nu312, nu321. This enforces the symmetry discussed above. pair_coeff 1 1 1 nu :pre A wildcard asterisk can be used for K to set the coefficients for multiple triplets of atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). Note that only type triplets with J <= K are considered; if asterisks imply type triplets where K < J, they are ignored. where all three atoms are of type 1. For a two-atom type simulation, more pair_coeff commands can be used. ATM interaction is symmetric with respect to permutation of atoms, it is necessary to provide pair_coeff command for one permutation. For example, the command Note that a pair_coeff command can override a previous setting for the same I,J,K triplet. For example, these commands set nu for all I,J.K triplets, then overwrite nu for just the I,J,K = 2,3,4 triplet: pair_coeff 1 1 2 nu :pre pair_coeff * * * 0.25 pair_coeff 2 3 4 0.1 :pre also implies Note that for a simulation with a single atom type, only a single entry is required, e.g. pair_coeff 1 2 1 nu pair_coeff 2 1 1 nu :pre pair_coeff 1 1 1 0.25 :per Thus, to specify all ATM interactions between two atom types (eg 1 and 2) it is sufficient to provide four pair_coeff commands, eg: For a simulation with two atom types, four pair_coeff commands will specify all possible nu values: pair_coeff 1 1 1 nu1 pair_coeff 1 1 2 nu2 pair_coeff 1 2 2 nu3 pair_coeff 2 2 2 nu4 :pre For 3 atom types, 10 pair_coeff commands (eg 111, 112, 113, 122, 123, 133, 222, 223, 233, 333) will describe all possible ATM interactions, etc. It is not necessary to provide the pair_coeff commands for interactions of all combinations of atom types: if some combination is not defined then there is no ATM interaction for this combination and all its permutations. For a simulation with three atom types, ten pair_coeff commands will specify all possible nu values: -------------------- [Steve:] I think a better syntax for the pair coeff command might be this: pair_coeff I J v1 v2 ... vN when 1,2,...N are the number of atom types defined. Then there be one pair_coeff command for each type pair, the same syntax as all other potentials in LAMMPS use. [Sergey:] The reason for my original pair_coeff command syntax is that I would like to reserve further arguments for possible extension of ATM potential in LAMMPS to further terms in the multipole expansion of many-body dispersion interaction. For example, the next term would be dipole-dipole-quadrupole, it may be activated if the next argument of pair_coeff is present without breaking backward compatibility. Also, the command you propose (i) will not account that the value of nu for different permutations of atom types is the same, and (ii) will make the numbering of atom types messy since there is no requirement to supply the values of nu for all triplets. -------------------- I think a better syntax for the pair coeff command might be this: pair_coeff I J v1 v2 ... vN when 1,2,...N are the number of atom types defined. Then there be one pair_coeff command for each type pair, the same syntax as all other potentials in LAMMPS use. Note that you refer to "elements", but the pair coeff command knows nothing about elements. Only atom types. There could be 10 atom types that all map to the same chemical element. pair_coeff 1 1 1 nu1 pair_coeff 1 1 2 nu2 pair_coeff 1 1 3 nu3 pair_coeff 1 2 2 nu4 pair_coeff 1 2 3 nu5 pair_coeff 1 3 3 nu6 pair_coeff 2 2 2 nu7 pair_coeff 2 2 3 nu8 pair_coeff 2 3 3 nu9 pair_coeff 3 3 3 nu10 :pre By default the nu value for all triplets is set to 0.0. Thus it is not required to provide pair_coeff commands that enumerate triplet interactions for all K types. If some I,J,K combination is not speficied, then there will be no 3-body ATM interactions for that combination and all its permutations. However, as with all pair styles, it is required to specify a pair_coeff command for all I,J combinations, else an error will result. :line Loading
doc/src/pair_style.txt +1 −0 Original line number Diff line number Diff line Loading @@ -103,6 +103,7 @@ in the pair section of "this page"_Section_commands.html#cmd_5. "pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin "pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart "pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ "pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential "pair_style beck"_pair_beck.html - Beck potential "pair_style body"_pair_body.html - interactions between body particles "pair_style bop"_pair_bop.html - BOP potential of Pettifor Loading
examples/atm/log.9Jul18.atm.g++.1 +15 −15 Original line number Diff line number Diff line Loading @@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms Time spent = 0.00120211 secs Time spent = 0.00125098 secs pair_style hybrid/overlay lj/cut 4.5 atm 2.5 pair_coeff * * lj/cut 1.0 1.0 Loading Loading @@ -60,26 +60,26 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.033 -4.5929584 0 -3.0438458 -3.6506231 5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817 10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204 15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887 20 1.0350606 -4.595891 0 -3.0436883 -3.4478779 25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695 Loop time of 34.5602 on 1 procs for 25 steps with 4000 atoms 0 1.033 -4.733482 0 -3.1843694 -3.924644 5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065 10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962 15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106 20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572 25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651 Loop time of 27.841 on 1 procs for 25 steps with 4000 atoms Performance: 124.999 tau/day, 0.723 timesteps/s Performance: 155.167 tau/day, 0.898 timesteps/s 100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 34.556 | 34.556 | 34.556 | 0.0 | 99.99 Pair | 27.837 | 27.837 | 27.837 | 0.0 | 99.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001323 | 0.001323 | 0.001323 | 0.0 | 0.00 Output | 0.00018287 | 0.00018287 | 0.00018287 | 0.0 | 0.00 Modify | 0.0016184 | 0.0016184 | 0.0016184 | 0.0 | 0.00 Other | | 0.0006311 | | | 0.00 Comm | 0.0015321 | 0.0015321 | 0.0015321 | 0.0 | 0.01 Output | 0.00016594 | 0.00016594 | 0.00016594 | 0.0 | 0.00 Modify | 0.001785 | 0.001785 | 0.001785 | 0.0 | 0.01 Other | | 0.0006731 | | | 0.00 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -97,4 +97,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:36 Total wall time: 0:00:29
examples/atm/log.9Jul18.atm.g++.4 +15 −15 Original line number Diff line number Diff line Loading @@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms Time spent = 0.000735998 secs Time spent = 0.000769138 secs pair_style hybrid/overlay lj/cut 4.5 atm 2.5 pair_coeff * * lj/cut 1.0 1.0 Loading Loading @@ -60,26 +60,26 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.033 -4.5929584 0 -3.0438458 -3.6506231 5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817 10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204 15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887 20 1.0350606 -4.595891 0 -3.0436883 -3.4478779 25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695 Loop time of 10.061 on 4 procs for 25 steps with 4000 atoms 0 1.033 -4.733482 0 -3.1843694 -3.924644 5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065 10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962 15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106 20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572 25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651 Loop time of 7.22029 on 4 procs for 25 steps with 4000 atoms Performance: 429.382 tau/day, 2.485 timesteps/s Performance: 598.314 tau/day, 3.462 timesteps/s 100.0% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.8393 | 9.9439 | 10.008 | 2.0 | 98.84 Pair | 7.1346 | 7.1684 | 7.1863 | 0.8 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.052154 | 0.11613 | 0.22077 | 18.7 | 1.15 Output | 7.2241e-05 | 8.2552e-05 | 0.00011158 | 0.0 | 0.00 Modify | 0.00053763 | 0.00055265 | 0.00056624 | 0.0 | 0.01 Other | | 0.0002971 | | | 0.00 Comm | 0.032945 | 0.0509 | 0.084664 | 9.1 | 0.70 Output | 0.00010133 | 0.00011051 | 0.00013804 | 0.0 | 0.00 Modify | 0.00059557 | 0.00060683 | 0.00061274 | 0.0 | 0.01 Other | | 0.000318 | | | 0.00 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Loading @@ -97,4 +97,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:10 Total wall time: 0:00:07
