diff --git a/examples/latte/in.graphene.boxrel b/examples/latte/in.latte.graphene.boxrelax similarity index 68% rename from examples/latte/in.graphene.boxrel rename to examples/latte/in.latte.graphene.boxrelax index 721b7f014f..bd61c358e6 100644 --- a/examples/latte/in.graphene.boxrel +++ b/examples/latte/in.latte.graphene.boxrelax @@ -1,35 +1,35 @@ # Simple water model with LATTE -units metal -atom_style full +units metal +atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.graphene # replicate system if requested -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 variable nrep equal v_x*v_y*v_z if "${nrep} > 1" then "replicate $x $y $z" # initialize system -velocity all create 0.0 87287 loop geom +velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes timestep 0.00025 fix 1 all box/relax iso 0.0 vmax 0.001 -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom etotal diff --git a/examples/latte/in.latte.multiple b/examples/latte/in.latte.multiple index 4888d14ebc..1c5dc3d2d3 100644 --- a/examples/latte/in.latte.multiple +++ b/examples/latte/in.latte.multiple @@ -9,7 +9,7 @@ read_data data.water velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * neighbor 1.0 bin neigh_modify every 1 delay 0 check yes @@ -17,7 +17,7 @@ neigh_modify every 1 delay 0 check yes timestep 0.00025 fix 1 all nve -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom step temp pe etotal press @@ -44,7 +44,7 @@ read_data data.ch4 velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * neighbor 1.0 bin neigh_modify every 1 delay 0 check yes @@ -53,7 +53,7 @@ timestep 0.00025 fix 1 all nve -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom step temp pe etotal press diff --git a/examples/latte/in.latte.sucrose b/examples/latte/in.latte.sucrose deleted file mode 100644 index a10dae5c5e..0000000000 --- a/examples/latte/in.latte.sucrose +++ /dev/null @@ -1,40 +0,0 @@ -# simple sucrose model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.sucrose - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# dynamics - -thermo 10 -run 100 diff --git a/examples/latte/in.latte.sucrose.md b/examples/latte/in.latte.sucrose.md index a10dae5c5e..53eaf80dd7 100644 --- a/examples/latte/in.latte.sucrose.md +++ b/examples/latte/in.latte.sucrose.md @@ -1,35 +1,35 @@ # simple sucrose model with LATTE -units metal -atom_style full +units metal +atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.sucrose # replicate system if requested -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 variable nrep equal v_x*v_y*v_z if "${nrep} > 1" then "replicate $x $y $z" # initialize system -velocity all create 0.0 87287 loop geom +velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes timestep 0.00025 -fix 1 all nve +fix 1 all nve -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom step temp pe etotal press @@ -37,4 +37,4 @@ thermo_style custom step temp pe etotal press # dynamics thermo 10 -run 100 +run 100 diff --git a/examples/latte/in.latte.water b/examples/latte/in.latte.water deleted file mode 100644 index e1185602b4..0000000000 --- a/examples/latte/in.latte.water +++ /dev/null @@ -1,40 +0,0 @@ -# simple water model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.water - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# dynamics - -thermo 10 -run 100 diff --git a/examples/latte/in.latte.water.md b/examples/latte/in.latte.water.md index e1185602b4..7940b7f992 100644 --- a/examples/latte/in.latte.water.md +++ b/examples/latte/in.latte.water.md @@ -1,35 +1,35 @@ # simple water model with LATTE -units metal -atom_style full +units metal +atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.water # replicate system if requested -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 variable nrep equal v_x*v_y*v_z if "${nrep} > 1" then "replicate $x $y $z" # initialize system -velocity all create 0.0 87287 loop geom +velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes timestep 0.00025 -fix 1 all nve +fix 1 all nve -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom step temp pe etotal press @@ -37,4 +37,4 @@ thermo_style custom step temp pe etotal press # dynamics thermo 10 -run 100 +run 100 diff --git a/examples/latte/in.latte.water.min b/examples/latte/in.latte.water.min index 173afee96a..81474a0773 100644 --- a/examples/latte/in.latte.water.min +++ b/examples/latte/in.latte.water.min @@ -1,35 +1,35 @@ # simple water model with LATTE -units metal -atom_style full +units metal +atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates read_data data.water # replicate system if requested -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 variable nrep equal v_x*v_y*v_z if "${nrep} > 1" then "replicate $x $y $z" # initialize system -velocity all create 0.0 87287 loop geom +velocity all create 0.0 87287 loop geom pair_style zero 1.0 -pair_coeff * * +pair_coeff * * -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes timestep 0.00025 -fix 1 all nve +fix 1 all nve -fix 2 all latte NULL +fix 2 all latte fix_modify 2 energy yes thermo_style custom step temp pe etotal press diff --git a/examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1 b/examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1 new file mode 100644 index 0000000000..2350e8ad39 --- /dev/null +++ b/examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1 @@ -0,0 +1,179 @@ +LAMMPS (3 Aug 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.graphene +Reading data file ... + triclinic box = (0 0 0) to (10 8 20) with tilt (4.8985872e-16 1.2246468e-15 1.2246468e-15) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 32 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all box/relax iso 0.0 vmax 0.001 + +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom etotal + +# minimization + +thermo 1 +fix 3 all print 1 "Total Energy =" +min_style cg +min_modify dmax 0.1 +min_modify line quadratic +minimize 1.0e-4 1.0e-4 10000 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 11 9 20 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.03 | 7.03 | 7.03 Mbytes + TotEng +-247.46002 +-247.67224 +-247.87937 +-248.08148 +-248.27865 +-248.47096 +-248.65851 +-248.84137 +-249.01964 +-249.19342 +-249.36281 +-249.52791 +-249.68883 +-249.8457 +-249.99865 +-250.1478 +-250.29332 +-250.43535 +-250.57409 +-250.70972 +-250.84247 +-250.97258 +-251.10035 +-251.2261 +-251.35021 +-251.47314 +-251.59543 +-251.71776 +-251.84096 +-251.9661 +-252.09459 +-252.22833 +-252.37003 +-252.52371 +-252.69578 +-252.89752 +-253.15197 +-253.52044 +-254.31418 +-255.6175 +-256.8162 +-258.1227 +-259.38401 +-260.74831 +-262.03991 +-263.5463 +-264.70486 +-267.69143 +-267.88682 +-269.0352 +-270.602 +-270.65395 +-270.7429 +-271.55831 +-271.81159 +-271.87447 +-273.03096 +-273.23109 +-273.27869 +-273.34621 +-273.4082 +-273.45599 +-273.53849 +-273.57478 +-273.71381 +-273.74092 +Loop time of 20.5496 on 1 procs for 65 steps with 32 atoms + +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -247.460020562055 -273.713813242259 -273.740918498854 + Force two-norm initial, final = 201.60784 9.4927634 + Force max component initial, final = 188.92406 2.4327308 + Final line search alpha, max atom move = 0.00022885545 0.0005567437 + Iterations, force evaluations = 65 65 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.7869e-05 | 7.7869e-05 | 7.7869e-05 | 0.0 | 0.00 +Bond | 3.531e-06 | 3.531e-06 | 3.531e-06 | 0.0 | 0.00 +Neigh | 1.3988e-05 | 1.3988e-05 | 1.3988e-05 | 0.0 | 0.00 +Comm | 0.00014355 | 0.00014355 | 0.00014355 | 0.0 | 0.00 +Output | 0.00071475 | 0.00071475 | 0.00071475 | 0.0 | 0.00 +Modify | 20.547 | 20.547 | 20.547 | 0.0 | 99.99 +Other | | 0.001683 | | | 0.01 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 48 ave 48 max 48 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 48 +Ave neighs/atom = 1.5 +Ave special neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:20 diff --git a/examples/latte/log.13Sep22.latte.multiple.g++.1 b/examples/latte/log.13Sep22.latte.multiple.g++.1 new file mode 100644 index 0000000000..ca32c96e15 --- /dev/null +++ b/examples/latte/log.13Sep22.latte.multiple.g++.1 @@ -0,0 +1,189 @@ +LAMMPS (3 Aug 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water +Reading data file ... + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes + Step Temp PotEng TotEng Press + 0 0 -104.95596 -104.95596 48235.442 + 10 336.53107 -105.96027 -104.95977 97996.851 +Loop time of 0.334108 on 1 procs for 10 steps with 24 atoms + +Performance: 0.646 ns/day, 37.123 hours/ns, 29.930 timesteps/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.714e-06 | 3.714e-06 | 3.714e-06 | 0.0 | 0.00 +Bond | 5.02e-07 | 5.02e-07 | 5.02e-07 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.1209e-05 | 1.1209e-05 | 1.1209e-05 | 0.0 | 0.00 +Output | 2.3638e-05 | 2.3638e-05 | 2.3638e-05 | 0.0 | 0.01 +Modify | 0.33404 | 0.33404 | 0.33404 | 0.0 | 99.98 +Other | | 2.795e-05 | | | 0.01 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 1.5416667 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# Clear up previus calculation + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task + +# simple CH4 molecule with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.ch4 +Reading data file ... + triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.007 seconds + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 20 13 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.902 | 5.902 | 5.902 Mbytes + Step Temp PotEng TotEng Press + 0 0 -23.980353 -23.980353 348.02716 + 10 19.123149 -23.990297 -23.98041 18.774332 +Loop time of 0.0121573 on 1 procs for 10 steps with 5 atoms + +Performance: 17.767 ns/day, 1.351 hours/ns, 822.549 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.224e-06 | 1.224e-06 | 1.224e-06 | 0.0 | 0.01 +Bond | 2.93e-07 | 2.93e-07 | 2.93e-07 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 3.845e-06 | 3.845e-06 | 3.845e-06 | 0.0 | 0.03 +Output | 8.633e-06 | 8.633e-06 | 8.633e-06 | 0.0 | 0.07 +Modify | 0.012132 | 0.012132 | 0.012132 | 0.0 | 99.80 +Other | | 1.089e-05 | | | 0.09 + +Nlocal: 5 ave 5 max 5 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7 ave 7 max 7 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10 +Ave neighs/atom = 2 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/latte/log.13Sep22.latte.sucrose.md.g++.1 b/examples/latte/log.13Sep22.latte.sucrose.md.g++.1 new file mode 100644 index 0000000000..9d3a98b66b --- /dev/null +++ b/examples/latte/log.13Sep22.latte.sucrose.md.g++.1 @@ -0,0 +1,112 @@ +LAMMPS (3 Aug 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# simple sucrose model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.sucrose +Reading data file ... + orthogonal box = (0 0 0) to (17.203 18.009 21.643) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 45 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 18 19 22 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.93 | 5.93 | 5.93 Mbytes + Step Temp PotEng TotEng Press + 0 0 -251.26617 -251.26617 16.617233 + 10 0.025263738 -251.26631 -251.26617 8.0576369 + 20 0.034232485 -251.26636 -251.26617 1.6672772 + 30 0.059079585 -251.2665 -251.26617 11.058355 + 40 0.055499785 -251.26648 -251.26617 14.837599 + 50 0.058499496 -251.2665 -251.26617 6.7180488 + 60 0.071094531 -251.26657 -251.26617 6.6131215 + 70 0.084309398 -251.26665 -251.26617 12.372502 + 80 0.1089929 -251.26679 -251.26617 8.8352747 + 90 0.11378255 -251.26681 -251.26617 5.1175071 + 100 0.13003967 -251.26691 -251.26617 8.2429118 +Loop time of 14.4456 on 1 procs for 100 steps with 45 atoms + +Performance: 0.150 ns/day, 160.507 hours/ns, 6.923 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.5758e-05 | 7.5758e-05 | 7.5758e-05 | 0.0 | 0.00 +Bond | 6.748e-06 | 6.748e-06 | 6.748e-06 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 9.0137e-05 | 9.0137e-05 | 9.0137e-05 | 0.0 | 0.00 +Output | 0.00025976 | 0.00025976 | 0.00025976 | 0.0 | 0.00 +Modify | 14.445 | 14.445 | 14.445 | 0.0 | 99.99 +Other | | 0.0005283 | | | 0.00 + +Nlocal: 45 ave 45 max 45 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 59 ave 59 max 59 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 59 +Ave neighs/atom = 1.3111111 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:14 diff --git a/examples/latte/log.13Sep22.latte.water.md.g++.1 b/examples/latte/log.13Sep22.latte.water.md.g++.1 new file mode 100644 index 0000000000..04cc99135c --- /dev/null +++ b/examples/latte/log.13Sep22.latte.water.md.g++.1 @@ -0,0 +1,112 @@ +LAMMPS (3 Aug 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water +Reading data file ... + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes + Step Temp PotEng TotEng Press + 0 0 -104.95596 -104.95596 48235.442 + 10 336.53107 -105.96027 -104.95977 97996.851 + 20 529.06408 -106.53023 -104.95733 131519.85 + 30 753.62603 -107.19952 -104.959 49296.66 + 40 716.65648 -107.08803 -104.95742 28307.121 + 50 824.04392 -107.40823 -104.95836 102167.59 + 60 933.56146 -107.73479 -104.95933 92508.517 + 70 851.18489 -107.48767 -104.95711 13993.262 + 80 999.8028 -107.93147 -104.95907 36700.736 + 90 998.77488 -107.9257 -104.95636 107233.54 + 100 1281.4438 -108.76963 -104.95992 49702.386 +Loop time of 3.14578 on 1 procs for 100 steps with 24 atoms + +Performance: 0.687 ns/day, 34.953 hours/ns, 31.789 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.0818e-05 | 3.0818e-05 | 3.0818e-05 | 0.0 | 0.00 +Bond | 4.704e-06 | 4.704e-06 | 4.704e-06 | 0.0 | 0.00 +Neigh | 1.8668e-05 | 1.8668e-05 | 1.8668e-05 | 0.0 | 0.00 +Comm | 0.00010831 | 0.00010831 | 0.00010831 | 0.0 | 0.00 +Output | 0.00021087 | 0.00021087 | 0.00021087 | 0.0 | 0.01 +Modify | 3.1452 | 3.1452 | 3.1452 | 0.0 | 99.98 +Other | | 0.0002339 | | | 0.01 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 77 ave 77 max 77 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 31 ave 31 max 31 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 31 +Ave neighs/atom = 1.2916667 +Ave special neighs/atom = 0 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/latte/log.13Sep22.latte.water.min.g++.1 b/examples/latte/log.13Sep22.latte.water.min.g++.1 new file mode 100644 index 0000000000..1b1cc59e10 --- /dev/null +++ b/examples/latte/log.13Sep22.latte.water.min.g++.1 @@ -0,0 +1,122 @@ +LAMMPS (3 Aug 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water +Reading data file ... + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# minimization + +thermo 10 + +min_style fire +minimize 1.0e-4 1.0e-4 500 500 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + Parameters for fire: + dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback + 0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes +Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes + Step Temp PotEng TotEng Press + 0 0 -104.95596 -104.95596 48235.442 + 10 853.69689 -106.31143 -103.7734 79191.444 + 20 1112.0893 -107.2723 -103.96607 82675.468 + 30 1897.6249 -108.36769 -102.72608 71447.508 + 40 3068.3491 -110.06452 -100.94237 47627.967 + 50 3.730935 -110.16042 -110.14932 5913.0643 + 60 28.603141 -110.18885 -110.10381 5778.8586 + 66 54.717686 -110.21503 -110.05236 5739.5831 +Loop time of 2.48723 on 1 procs for 66 steps with 24 atoms + +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -104.955957263186 -110.209885831179 -110.215033825672 + Force two-norm initial, final = 19.119006 0.51695213 + Force max component initial, final = 11.775801 0.1663917 + Final line search alpha, max atom move = 0 0 + Iterations, force evaluations = 66 69 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.7159e-05 | 2.7159e-05 | 2.7159e-05 | 0.0 | 0.00 +Bond | 3.124e-06 | 3.124e-06 | 3.124e-06 | 0.0 | 0.00 +Neigh | 1.0201e-05 | 1.0201e-05 | 1.0201e-05 | 0.0 | 0.00 +Comm | 0.000109 | 0.000109 | 0.000109 | 0.0 | 0.00 +Output | 0.00010568 | 0.00010568 | 0.00010568 | 0.0 | 0.00 +Modify | 2.4866 | 2.4866 | 2.4866 | 0.0 | 99.98 +Other | | 0.0003552 | | | 0.01 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 75 ave 75 max 75 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 33 ave 33 max 33 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 33 +Ave neighs/atom = 1.375 +Ave special neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 b/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 deleted file mode 100644 index bc8843ef7f..0000000000 --- a/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 +++ /dev/null @@ -1,406 +0,0 @@ - The log file for latte_lib - - CONTROL{ } - - WARNING: variable JobName= is missing. I will use a default value instead ... - WARNING: variable PARAMPATH= is missing. I will use a default value instead ... - WARNING: variable DEBUGON= is missing. I will use a default value instead ... - WARNING: variable FERMIM= is missing. I will use a default value instead ... - WARNING: variable CGORLIB= is missing. I will use a default value instead ... - WARNING: variable NORECS= is missing. I will use a default value instead ... - WARNING: variable VDWON= is missing. I will use a default value instead ... - WARNING: variable ORDERNMOL= is missing. I will use a default value instead ... - WARNING: variable LCNON= is missing. I will use a default value instead ... - WARNING: variable LCNITER= is missing. I will use a default value instead ... - WARNING: variable MDON= is missing. I will use a default value instead ... - WARNING: variable PBCON= is missing. I will use a default value instead ... - WARNING: variable RESTART= is missing. I will use a default value instead ... - WARNING: variable NGPU= is missing. I will use a default value instead ... - WARNING: variable COMPFORCE= is missing. I will use a default value instead ... - WARNING: variable DOSFIT= is missing. I will use a default value instead ... - WARNING: variable INTS2FIT= is missing. I will use a default value instead ... - WARNING: variable NFITSTEP= is missing. I will use a default value instead ... - WARNING: variable QFIT= is missing. I will use a default value instead ... - WARNING: variable PPFITON= is missing. I will use a default value instead ... - WARNING: variable ALLFITON= is missing. I will use a default value instead ... - WARNING: variable PPSTEP= is missing. I will use a default value instead ... - WARNING: variable BISTEP= is missing. I will use a default value instead ... - WARNING: variable PP2FIT= is missing. I will use a default value instead ... - WARNING: variable BINT2FIT= is missing. I will use a default value instead ... - WARNING: variable PPNMOL= is missing. I will use a default value instead ... - WARNING: variable PPNGEOM= is missing. I will use a default value instead ... - WARNING: variable PARREP= is missing. I will use a default value instead ... - WARNING: variable VERBOSE= is missing. I will use a default value instead ... - WARNING: variable MIXER= is missing. I will use a default value instead ... - WARNING: variable RESTARTLIB= is missing. I will use a default value instead ... - WARNING: variable CGTOL= is missing. I will use a default value instead ... - WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ... - WARNING: variable COULACC= is missing. I will use a default value instead ... - WARNING: variable COULCUT= is missing. I will use a default value instead ... - WARNING: variable COULR1= is missing. I will use a default value instead ... - WARNING: variable CHTOL= is missing. I will use a default value instead ... - WARNING: variable BETA= is missing. I will use a default value instead ... - WARNING: variable MCSIGMA= is missing. I will use a default value instead ... - WARNING: variable PPBETA= is missing. I will use a default value instead ... - WARNING: variable PPSIGMA= is missing. I will use a default value instead ... - WARNING: variable ER= is missing. I will use a default value instead ... - WARNING: variable INITIALIZED= is missing. I will use a default value instead ... - - - ############### Parameters used for this run ################ - CONTROL{ - xControl= 1 - DEBUGON= 0 - FERMIM= 6 - CGORLIB= 1 - NORECS= 1 - ENTROPYKIND= 1 - PPOTON= 1 - VDWON= 0 - SPINON= 0 - ELECTRO= 1 - ELECMETH= 0 - MAXSCF= 450 - MINSP2ITER= 22 - FULLQCONV= 1 - QITER= 3 - ORDERNMOL= 0 - SPARSEON= 1 - THRESHOLDON= 1 - FILLINSTOP= 100 - BLKSZ= 4 - MSPARSE= 1500 - LCNON= 0 - LCNITER= 4 - RELAX= 0 - MAXITER= 100000 - MDON= 1 - PBCON= 1 - RESTART= 0 - CHARGE= 0 - XBO= 1 - XBODISON= 1 - XBODISORDER= 5 - NGPU= 2 - KON= 0 - COMPFORCE= 1 - DOSFIT= 0 - INTS2FIT= 1 - NFITSTEP= 5000 - QFIT= 0 - PPFITON= 0 - ALLFITON= 0 - PPSTEP= 500 - BISTEP= 500 - PP2FIT= 2 - BINT2FIT= 6 - PPNMOL= 10 - PPNGEOM= 200 - PARREP= 0 - VERBOSE= 0 - MIXER= 0 - RESTARTLIB= 0 - CGTOL= 9.9999999747524271E-007 - KBT= 0.0000000000000000 - SPINTOL= 1.0000000000000000E-004 - ELEC_ETOL= 1.0000000474974513E-003 - ELEC_QTOL= 1.0000000000000000E-008 - COULACC= 9.9999999747524271E-007 - COULCUT= -500.00000000000000 - COULR1= 500.00000000000000 - BREAKTOL= 9.9999999999999995E-007 - QMIX= 0.25000000000000000 - SPINMIX= 0.25000000000000000 - MDMIX= 0.25000000000000000 - NUMTHRESH= 9.9999999999999995E-007 - CHTOL= 9.9999997764825821E-003 - SKIN= 1.0000000000000000 - RLXFTOL= 9.9999999999999995E-008 - BETA= 1000.0000000000000 - MCSIGMA= 0.20000000298023224 - PPBETA= 1000.0000000000000 - PPSIGMA= 9.9999997764825821E-003 - ER= 1.0000000000000000 - JobName=MyJob - BASISTYPE=NONORTHO - SP2CONV=REL - RELAXTYPE=SD - PARAMPATH=./TBparam - COORDSFILE=./coords.dat - INITIALIZED= F - } - - ./TBparam/electrons.dat - MDCONTROL{ } - - WARNING: variable RNDIST= is missing. I will use a default value instead ... - WARNING: variable SEEDINIT= is missing. I will use a default value instead ... - WARNING: variable NPTTYPE= is missing. I will use a default value instead ... - WARNING: variable UDNEIGH= is missing. I will use a default value instead ... - WARNING: variable DUMPFREQ= is missing. I will use a default value instead ... - WARNING: variable RSFREQ= is missing. I will use a default value instead ... - WARNING: variable WRTFREQ= is missing. I will use a default value instead ... - WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ... - WARNING: variable THERMPER= is missing. I will use a default value instead ... - WARNING: variable THERMRUN= is missing. I will use a default value instead ... - WARNING: variable NVTON= is missing. I will use a default value instead ... - WARNING: variable NPTON= is missing. I will use a default value instead ... - WARNING: variable AVEPER= is missing. I will use a default value instead ... - WARNING: variable SEED= is missing. I will use a default value instead ... - WARNING: variable SHOCKON= is missing. I will use a default value instead ... - WARNING: variable SHOCKSTART= is missing. I will use a default value instead ... - WARNING: variable SHOCKDIR= is missing. I will use a default value instead ... - WARNING: variable MDADAPT= is missing. I will use a default value instead ... - WARNING: variable GETHUG= is missing. I will use a default value instead ... - WARNING: variable RSLEVEL= is missing. I will use a default value instead ... - WARNING: variable DT= is missing. I will use a default value instead ... - WARNING: variable TEMPERATURE= is missing. I will use a default value instead ... - WARNING: variable FRICTION= is missing. I will use a default value instead ... - WARNING: variable PTARGET= is missing. I will use a default value instead ... - WARNING: variable UPARTICLE= is missing. I will use a default value instead ... - WARNING: variable USHOCK= is missing. I will use a default value instead ... - WARNING: variable C0= is missing. I will use a default value instead ... - WARNING: variable E0= is missing. I will use a default value instead ... - WARNING: variable V0= is missing. I will use a default value instead ... - WARNING: variable P0= is missing. I will use a default value instead ... - WARNING: variable DUMMY= is missing. I will use a default value instead ... - - - ############### Parameters used for this run ################ - MDCONTROL{ - MAXITER= -1 - UDNEIGH= 1 - DUMPFREQ= 250 - RSFREQ= 500 - WRTFREQ= 25 - TOINITTEMP5= 1 - THERMPER= 500 - THERMRUN= 50000 - NVTON= 0 - NPTON= 0 - AVEPER= 1000 - SEED= 54 - SHOCKON= 0 - SHOCKSTART= 100000 - SHOCKDIR= 1 - MDADAPT= 0 - GETHUG= 0 - RSLEVEL= 0 - DT= 0.25000000000000000 - TEMPERATURE= 300.00000000000000 - FRICTION= 1000.0000000000000 - PTARGET= 0.0000000000000000 - UPARTICLE= 500.00000000000000 - USHOCK= -4590.0000000000000 - C0= 1300.0000000000000 - E0= -795.72497558593750 - V0= 896.98486328125000 - P0= 8.3149001002311707E-002 - RNDIST=GAUSSIAN - SEEDINIT=UNIFORM - NPTTYPE=ISO - DUMMY= F - } - - LIBCALLS 0 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15165627147849 13.850829743067372 0.0000000000000000 3.9653384620309846 - LIBCALLS 1 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15142147081917 13.850596160685321 0.0000000000000000 3.9653428217526296 - 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I will use a default value instead ... - WARNING: variable PARAMPATH= is missing. I will use a default value instead ... - WARNING: variable DEBUGON= is missing. I will use a default value instead ... - WARNING: variable FERMIM= is missing. I will use a default value instead ... - WARNING: variable CGORLIB= is missing. I will use a default value instead ... - WARNING: variable NORECS= is missing. I will use a default value instead ... - WARNING: variable VDWON= is missing. I will use a default value instead ... - WARNING: variable ORDERNMOL= is missing. I will use a default value instead ... - WARNING: variable LCNON= is missing. I will use a default value instead ... - WARNING: variable LCNITER= is missing. I will use a default value instead ... - WARNING: variable MDON= is missing. I will use a default value instead ... - WARNING: variable PBCON= is missing. I will use a default value instead ... - WARNING: variable RESTART= is missing. I will use a default value instead ... - WARNING: variable NGPU= is missing. I will use a default value instead ... - WARNING: variable COMPFORCE= is missing. I will use a default value instead ... - WARNING: variable DOSFIT= is missing. I will use a default value instead ... - WARNING: variable INTS2FIT= is missing. I will use a default value instead ... - WARNING: variable NFITSTEP= is missing. I will use a default value instead ... - WARNING: variable QFIT= is missing. I will use a default value instead ... - WARNING: variable PPFITON= is missing. I will use a default value instead ... - WARNING: variable ALLFITON= is missing. I will use a default value instead ... - WARNING: variable PPSTEP= is missing. I will use a default value instead ... - WARNING: variable BISTEP= is missing. I will use a default value instead ... - WARNING: variable PP2FIT= is missing. I will use a default value instead ... - WARNING: variable BINT2FIT= is missing. I will use a default value instead ... - WARNING: variable PPNMOL= is missing. I will use a default value instead ... - WARNING: variable PPNGEOM= is missing. I will use a default value instead ... - WARNING: variable PARREP= is missing. I will use a default value instead ... - WARNING: variable VERBOSE= is missing. I will use a default value instead ... - WARNING: variable MIXER= is missing. I will use a default value instead ... - WARNING: variable RESTARTLIB= is missing. I will use a default value instead ... - WARNING: variable CGTOL= is missing. I will use a default value instead ... - WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ... - WARNING: variable COULACC= is missing. I will use a default value instead ... - WARNING: variable COULCUT= is missing. I will use a default value instead ... - WARNING: variable COULR1= is missing. I will use a default value instead ... - WARNING: variable CHTOL= is missing. I will use a default value instead ... - WARNING: variable BETA= is missing. I will use a default value instead ... - WARNING: variable MCSIGMA= is missing. I will use a default value instead ... - WARNING: variable PPBETA= is missing. I will use a default value instead ... - WARNING: variable PPSIGMA= is missing. I will use a default value instead ... - WARNING: variable ER= is missing. I will use a default value instead ... - WARNING: variable INITIALIZED= is missing. I will use a default value instead ... - - - ############### Parameters used for this run ################ - CONTROL{ - xControl= 1 - DEBUGON= 0 - FERMIM= 6 - CGORLIB= 1 - NORECS= 1 - ENTROPYKIND= 1 - PPOTON= 1 - VDWON= 0 - SPINON= 0 - ELECTRO= 1 - ELECMETH= 0 - MAXSCF= 450 - MINSP2ITER= 22 - FULLQCONV= 1 - QITER= 3 - ORDERNMOL= 0 - SPARSEON= 1 - THRESHOLDON= 1 - FILLINSTOP= 100 - BLKSZ= 4 - MSPARSE= 1500 - LCNON= 0 - LCNITER= 4 - RELAX= 0 - MAXITER= 100000 - MDON= 1 - PBCON= 1 - RESTART= 0 - CHARGE= 0 - XBO= 1 - XBODISON= 1 - XBODISORDER= 5 - NGPU= 2 - KON= 0 - COMPFORCE= 1 - DOSFIT= 0 - INTS2FIT= 1 - NFITSTEP= 5000 - QFIT= 0 - PPFITON= 0 - ALLFITON= 0 - PPSTEP= 500 - BISTEP= 500 - PP2FIT= 2 - BINT2FIT= 6 - PPNMOL= 10 - PPNGEOM= 200 - PARREP= 0 - VERBOSE= 0 - MIXER= 0 - RESTARTLIB= 0 - CGTOL= 9.9999999747524271E-007 - KBT= 0.0000000000000000 - SPINTOL= 1.0000000000000000E-004 - ELEC_ETOL= 1.0000000474974513E-003 - ELEC_QTOL= 1.0000000000000000E-008 - COULACC= 9.9999999747524271E-007 - COULCUT= -500.00000000000000 - COULR1= 500.00000000000000 - BREAKTOL= 9.9999999999999995E-007 - QMIX= 0.25000000000000000 - SPINMIX= 0.25000000000000000 - MDMIX= 0.25000000000000000 - NUMTHRESH= 9.9999999999999995E-007 - CHTOL= 9.9999997764825821E-003 - SKIN= 1.0000000000000000 - RLXFTOL= 9.9999999999999995E-008 - BETA= 1000.0000000000000 - MCSIGMA= 0.20000000298023224 - PPBETA= 1000.0000000000000 - PPSIGMA= 9.9999997764825821E-003 - ER= 1.0000000000000000 - JobName=MyJob - BASISTYPE=NONORTHO - SP2CONV=REL - RELAXTYPE=SD - PARAMPATH=./TBparam - COORDSFILE=./coords.dat - INITIALIZED= F - } - - ./TBparam/electrons.dat - MDCONTROL{ } - - WARNING: variable RNDIST= is missing. I will use a default value instead ... - WARNING: variable SEEDINIT= is missing. I will use a default value instead ... - WARNING: variable NPTTYPE= is missing. I will use a default value instead ... - WARNING: variable UDNEIGH= is missing. I will use a default value instead ... - WARNING: variable DUMPFREQ= is missing. I will use a default value instead ... - WARNING: variable RSFREQ= is missing. I will use a default value instead ... - WARNING: variable WRTFREQ= is missing. I will use a default value instead ... - WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ... - WARNING: variable THERMPER= is missing. I will use a default value instead ... - WARNING: variable THERMRUN= is missing. I will use a default value instead ... - WARNING: variable NVTON= is missing. I will use a default value instead ... - WARNING: variable NPTON= is missing. I will use a default value instead ... - WARNING: variable AVEPER= is missing. I will use a default value instead ... - WARNING: variable SEED= is missing. I will use a default value instead ... - WARNING: variable SHOCKON= is missing. I will use a default value instead ... - WARNING: variable SHOCKSTART= is missing. I will use a default value instead ... - WARNING: variable SHOCKDIR= is missing. I will use a default value instead ... - WARNING: variable MDADAPT= is missing. I will use a default value instead ... - WARNING: variable GETHUG= is missing. I will use a default value instead ... - WARNING: variable RSLEVEL= is missing. I will use a default value instead ... - WARNING: variable DT= is missing. I will use a default value instead ... - WARNING: variable TEMPERATURE= is missing. I will use a default value instead ... - WARNING: variable FRICTION= is missing. I will use a default value instead ... - WARNING: variable PTARGET= is missing. I will use a default value instead ... - WARNING: variable UPARTICLE= is missing. I will use a default value instead ... - WARNING: variable USHOCK= is missing. I will use a default value instead ... - WARNING: variable C0= is missing. I will use a default value instead ... - WARNING: variable E0= is missing. I will use a default value instead ... - WARNING: variable V0= is missing. I will use a default value instead ... - WARNING: variable P0= is missing. I will use a default value instead ... - WARNING: variable DUMMY= is missing. I will use a default value instead ... - - - ############### Parameters used for this run ################ - MDCONTROL{ - MAXITER= -1 - UDNEIGH= 1 - DUMPFREQ= 250 - RSFREQ= 500 - WRTFREQ= 25 - TOINITTEMP5= 1 - THERMPER= 500 - THERMRUN= 50000 - NVTON= 0 - NPTON= 0 - AVEPER= 1000 - SEED= 54 - SHOCKON= 0 - SHOCKSTART= 100000 - SHOCKDIR= 1 - MDADAPT= 0 - GETHUG= 0 - RSLEVEL= 0 - DT= 0.25000000000000000 - TEMPERATURE= 300.00000000000000 - FRICTION= 1000.0000000000000 - PTARGET= 0.0000000000000000 - UPARTICLE= 500.00000000000000 - USHOCK= -4590.0000000000000 - C0= 1300.0000000000000 - E0= -795.72497558593750 - V0= 896.98486328125000 - P0= 8.3149001002311707E-002 - RNDIST=GAUSSIAN - SEEDINIT=UNIFORM - NPTTYPE=ISO - DUMMY= F - } - - LIBCALLS 0 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -110.94281402417451 9.3197859655447317 0.0000000000000000 3.3331152608769714 - LIBCALLS 1 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -111.00875524736128 9.3653691493930946 0.0000000000000000 3.3307590218500454 - 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LIBCALLS 98 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.09218577985371 14.515310319889227 0.0000000000000000 3.0759929793994090 - LIBCALLS 99 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.30969482099719 13.692843612811791 0.0000000000000000 3.1081426979179545 - LIBCALLS 100 - Energy Components (TRRHOH, EREP, ENTE, ECOUL) -118.51358261827596 12.884492109393644 0.0000000000000000 3.1405428597121636 diff --git a/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 b/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 deleted file mode 100644 index 3a37136fd3..0000000000 --- a/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 +++ /dev/null @@ -1,170 +0,0 @@ -LAMMPS (11 May 2018) -# Simple water model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.graphene.boxrel - triclinic box = (0 0 0) to (10 8 20) with tilt (4.89859e-16 1.22465e-15 1.22465e-15) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 32 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all box/relax iso 0.0 vmax 0.001 - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom etotal - -# minimization - -thermo 1 -fix 3 all print 1 "Total Energy =" -min_style cg -min_modify dmax 0.1 -min_modify line quadratic -minimize 1.0e-4 1.0e-4 10000 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 11 9 20 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/newton/tri - stencil: half/bin/3d/newton/tri - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.779 | 6.779 | 6.779 Mbytes -TotEng - -247.46002 - -247.67224 - -247.87937 - -248.08148 - -248.27865 - -248.47096 - -248.65851 - -248.84137 - -249.01964 - -249.19342 - -249.36281 - -249.52791 - -249.68883 - -249.8457 - -249.99865 - -250.1478 - -250.29332 - -250.43535 - -250.57409 - -250.70972 - -250.84247 - -250.97258 - -251.10035 - -251.2261 - -251.35021 - -251.47314 - -251.59543 - -251.71776 - -251.84096 - -251.9661 - -252.09459 - -252.22833 - -252.37003 - -252.52371 - -252.69578 - -252.89752 - -253.15197 - -253.52044 - -254.31418 - -255.6175 - -256.8162 - -258.1227 - -259.38401 - -260.74831 - -262.03991 - -263.5463 - -264.70486 - -267.69144 - -267.88682 - -269.03519 - -270.60187 - -270.65382 - -270.74279 - -271.55883 - -271.81248 - -271.87529 - -273.01494 - -273.23948 - -273.28719 - -273.35272 - -273.41591 - -273.46274 - -273.54755 - -273.58318 - -273.73111 - -273.75754 -Loop time of 39.4155 on 1 procs for 65 steps with 32 atoms - -1582.4% CPU use with 1 MPI tasks x no OpenMP threads - -Minimization stats: - Stopping criterion = energy tolerance - Energy initial, next-to-last, final = - -247.460020579 -273.731112592 -273.757543461 - Force two-norm initial, final = 201.608 9.43485 - Force max component initial, final = 188.924 2.41297 - Final line search alpha, max atom move = 0.000223273 0.00053875 - Iterations, force evaluations = 65 65 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00012159 | 0.00012159 | 0.00012159 | 0.0 | 0.00 -Bond | 5.1975e-05 | 5.1975e-05 | 5.1975e-05 | 0.0 | 0.00 -Neigh | 4.1962e-05 | 4.1962e-05 | 4.1962e-05 | 0.0 | 0.00 -Comm | 0.00026107 | 0.00026107 | 0.00026107 | 0.0 | 0.00 -Output | 0.0013342 | 0.0013342 | 0.0013342 | 0.0 | 0.00 -Modify | 39.412 | 39.412 | 39.412 | 0.0 | 99.99 -Other | | 0.00127 | | | 0.00 - -Nlocal: 32 ave 32 max 32 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 100 ave 100 max 100 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 48 ave 48 max 48 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 48 -Ave neighs/atom = 1.5 -Ave special neighs/atom = 0 -Neighbor list builds = 1 -Dangerous builds = 0 -Total wall time: 0:00:40 diff --git a/examples/latte/log.21Jun18.latte.sucrose.g++.1 b/examples/latte/log.21Jun18.latte.sucrose.g++.1 deleted file mode 100644 index cb4526587c..0000000000 --- a/examples/latte/log.21Jun18.latte.sucrose.g++.1 +++ /dev/null @@ -1,103 +0,0 @@ -LAMMPS (11 May 2018) -# simple sucrose model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.sucrose - orthogonal box = (0 0 0) to (17.203 18.009 21.643) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 45 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# dynamics - -thermo 10 -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 18 19 22 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 0.5064 | 0.5064 | 0.5064 Mbytes -Step Temp PotEng TotEng Press - 0 0 -251.26617 -251.26617 16.617234 - 10 0.025263709 -251.26631 -251.26617 8.0576708 - 20 0.034232467 -251.26636 -251.26617 1.6673442 - 30 0.059079556 -251.2665 -251.26617 11.058458 - 40 0.055499766 -251.26648 -251.26617 14.837775 - 50 0.058499509 -251.2665 -251.26617 6.7183113 - 60 0.071094535 -251.26657 -251.26617 6.6133687 - 70 0.084309439 -251.26665 -251.26617 12.372721 - 80 0.1089929 -251.26679 -251.26617 8.8355516 - 90 0.11378257 -251.26681 -251.26617 5.1177922 - 100 0.13003966 -251.26691 -251.26617 8.2431185 -Loop time of 27.8386 on 1 procs for 100 steps with 45 atoms - -Performance: 0.078 ns/day, 309.318 hours/ns, 3.592 timesteps/s -1799.6% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.00 -Bond | 7.4148e-05 | 7.4148e-05 | 7.4148e-05 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00016689 | 0.00016689 | 0.00016689 | 0.0 | 0.00 -Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00 -Modify | 27.837 | 27.837 | 27.837 | 0.0 |100.00 -Other | | 0.0005403 | | | 0.00 - -Nlocal: 45 ave 45 max 45 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 59 ave 59 max 59 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 59 -Ave neighs/atom = 1.31111 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:28 diff --git a/examples/latte/log.21Jun18.latte.water.g++.1 b/examples/latte/log.21Jun18.latte.water.g++.1 deleted file mode 100644 index 0decce1f98..0000000000 --- a/examples/latte/log.21Jun18.latte.water.g++.1 +++ /dev/null @@ -1,103 +0,0 @@ -LAMMPS (11 May 2018) -# simple water model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.water - orthogonal box = (0 0 0) to (6.267 6.267 6.267) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 24 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# dynamics - -thermo 10 -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes -Step Temp PotEng TotEng Press - 0 0 -104.95594 -104.95594 48236.006 - 10 336.5303 -105.96026 -104.95976 97997.303 - 20 529.06385 -106.53021 -104.95731 131520.49 - 30 753.62616 -107.1995 -104.95898 49297.371 - 40 716.6565 -107.08802 -104.95741 28307.272 - 50 824.04417 -107.40822 -104.95835 102167.48 - 60 933.56056 -107.73478 -104.95932 92508.792 - 70 851.18518 -107.48766 -104.95711 13993.28 - 80 999.80265 -107.93146 -104.95906 36700.417 - 90 998.77707 -107.92569 -104.95634 107233.7 - 100 1281.4446 -108.76961 -104.95989 49703.193 -Loop time of 10.6388 on 1 procs for 100 steps with 24 atoms - -Performance: 0.203 ns/day, 118.209 hours/ns, 9.400 timesteps/s -6459.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 7.6771e-05 | 7.6771e-05 | 7.6771e-05 | 0.0 | 0.00 -Bond | 7.5817e-05 | 7.5817e-05 | 7.5817e-05 | 0.0 | 0.00 -Neigh | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 | 0.0 | 0.00 -Comm | 0.00031829 | 0.00031829 | 0.00031829 | 0.0 | 0.00 -Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00 -Modify | 10.637 | 10.637 | 10.637 | 0.0 | 99.99 -Other | | 0.00052 | | | 0.00 - -Nlocal: 24 ave 24 max 24 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 77 ave 77 max 77 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 31 ave 31 max 31 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 31 -Ave neighs/atom = 1.29167 -Ave special neighs/atom = 0 -Neighbor list builds = 2 -Dangerous builds = 0 -Total wall time: 0:00:10 diff --git a/examples/latte/log.21Jun18.latte.water.min.g++.1 b/examples/latte/log.21Jun18.latte.water.min.g++.1 deleted file mode 100644 index 1c8921fd60..0000000000 --- a/examples/latte/log.21Jun18.latte.water.min.g++.1 +++ /dev/null @@ -1,108 +0,0 @@ -LAMMPS (11 May 2018) -# simple water model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.water - orthogonal box = (0 0 0) to (6.267 6.267 6.267) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 24 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# minimization - -thermo 10 - -min_style fire -minimize 1.0e-4 1.0e-4 500 500 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes -Step Temp PotEng TotEng Press - 0 0 -104.95594 -104.95594 48236.006 - 10 349.4534 -105.50948 -104.47056 62157.729 - 20 1253.6636 -107.00863 -103.28151 116456.71 - 30 134.64051 -107.56155 -107.16127 59864.196 - 40 2.4044989 -108.1527 -108.14556 32695.648 - 47 137.26885 -108.30413 -107.89603 60177.442 -Loop time of 6.42677 on 1 procs for 47 steps with 24 atoms - -6481.9% CPU use with 1 MPI tasks x no OpenMP threads - -Minimization stats: - Stopping criterion = energy tolerance - Energy initial, next-to-last, final = - -104.955944301 -108.302982895 -108.304126127 - Force two-norm initial, final = 19.119 3.44609 - Force max component initial, final = 11.7758 1.3408 - Final line search alpha, max atom move = 0 0 - Iterations, force evaluations = 47 47 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.6253e-05 | 4.6253e-05 | 4.6253e-05 | 0.0 | 0.00 -Bond | 3.1948e-05 | 3.1948e-05 | 3.1948e-05 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00014353 | 0.00014353 | 0.00014353 | 0.0 | 0.00 -Output | 0.00012302 | 0.00012302 | 0.00012302 | 0.0 | 0.00 -Modify | 6.426 | 6.426 | 6.426 | 0.0 | 99.99 -Other | | 0.0004699 | | | 0.01 - -Nlocal: 24 ave 24 max 24 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 71 ave 71 max 71 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 37 ave 37 max 37 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 37 -Ave neighs/atom = 1.54167 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:06