diff --git a/examples/PACKAGES/pressure/in.cylinder b/examples/PACKAGES/pressure/in.cylinder new file mode 100644 index 0000000000..39c1c2ec99 --- /dev/null +++ b/examples/PACKAGES/pressure/in.cylinder @@ -0,0 +1,40 @@ +# compute pressure/cylinder for a cylindrical liquid-vapor interface + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block -10 10 -10 10 0 10 +region liquid cylinder z 0 0 5 0 10 +create_box 1 box +create_atoms 1 region liquid +mass 1 1.0 + +velocity all create 0.65 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nvt temp 0.65 0.65 0.2 + + +thermo 50 +#dump id all atom 50 dump.cylinder + +#dump 2 all image 25 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 2 all recenter 0 0 NULL units lattice +compute p all pressure/cylinder 0 10 15 0.25 +fix 3 all ave/time 100 1 100 c_p[*] file cylinder.out mode vector + + +run 1000 diff --git a/examples/PACKAGES/pressure/in.flat b/examples/PACKAGES/pressure/in.flat new file mode 100644 index 0000000000..8f7daa6aad --- /dev/null +++ b/examples/PACKAGES/pressure/in.flat @@ -0,0 +1,43 @@ +# compute pressure/cartesian for a flat liquid-vapor interface + +units lj +atom_style atomic +processors * * 1 + +lattice fcc 0.8442 +region box block 0 10 0 10 0 30 +region liquid block 0 10 0 10 10 20 +create_box 1 box +create_atoms 1 region liquid +mass 1 1.0 + +velocity all create 0.65 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nvt temp 0.7 0.7 0.2 + + +thermo 50 +#dump id all atom 50 dump.flat + +#dump 2 all image 25 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 2 all recenter NULL NULL 15 units lattice +compute p1 all pressure/cartesian z 0.5 +fix 3 all ave/time 100 1 100 c_p1[*] file flat.out mode vector +#compute p2 all pressure/cartesian z 0.25 x 1 +#fix 4 all ave/time 100 1 100 c_p2[*] file flat_2d.out mode vector + + +run 1000 diff --git a/examples/PACKAGES/pressure/in.sphere b/examples/PACKAGES/pressure/in.sphere new file mode 100644 index 0000000000..423ee176ec --- /dev/null +++ b/examples/PACKAGES/pressure/in.sphere @@ -0,0 +1,39 @@ +# compute pressure/spherical for a spherical droplet + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block -10 10 -10 10 -10 10 +region liquid sphere 0 0 0 5 +create_box 1 box +create_atoms 1 region liquid +mass 1 1.0 + +velocity all create 0.65 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nvt temp 0.65 0.65 0.2 + +#dump id all atom 50 dump.sphere + +thermo 50 +#dump 2 all image 25 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 2 all recenter 0 0 0 units lattice +compute p all pressure/spherical 0 0 0 0.25 15 +fix 3 all ave/time 100 1 100 c_p[*] file sphere.out mode vector + + +run 1000 diff --git a/examples/PACKAGES/pressure/log.6Mar2022.cylinder.g++.1 b/examples/PACKAGES/pressure/log.6Mar2022.cylinder.g++.1 new file mode 100644 index 0000000000..fedf1470da --- /dev/null +++ b/examples/PACKAGES/pressure/log.6Mar2022.cylinder.g++.1 @@ -0,0 +1,133 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# compute pressure/cylinder for a cylindrical liquid-vapor interface + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block -10 10 -10 10 0 10 +region liquid cylinder z 0 0 5 0 10 +create_box 1 box +Created orthogonal box = (-16.795962 -16.795962 0) to (16.795962 16.795962 16.795962) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region liquid +Created 3170 atoms + using lattice units in orthogonal box = (-16.795962 -16.795962 0) to (16.795962 16.795962 16.795962) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 0.65 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nvt temp 0.65 0.65 0.2 + + +thermo 50 +#dump id all atom 50 dump.cylinder + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 2 all recenter 0 0 NULL units lattice +compute p all pressure/cylinder 0 10 15 0.25 +fix 3 all ave/time 100 1 100 c_p[*] file cylinder.out mode vector + + +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- compute pressure/cylinder: + +@Article{Addington, + author = {C. K. Addington, Y. Long, K. E. Gubbins}, + title = {The pressure in interfaces having cylindrical geometry}, + journal = {J.~Chem.~Phys.}, + year = 2018, + volume = 149, + pages = {084109} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 24 24 12 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute pressure/cylinder, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.878 | 3.878 | 3.878 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.65 -6.2219331 0 -5.2472407 -1.0193897 + 50 0.40121817 -5.7782233 0 -5.1765859 -0.33373915 + 100 0.56963398 -5.8789288 0 -5.0247474 -0.16859926 + 150 0.68424117 -5.9319873 0 -4.9059493 0.062850222 + 200 0.68608162 -5.9987099 0 -4.9699121 0.21439145 + 250 0.63422098 -6.047104 0 -5.0960726 0.30980602 + 300 0.64028254 -6.107331 0 -5.1472102 0.32133372 + 350 0.64906334 -6.1101542 0 -5.1368663 0.22288375 + 400 0.61848053 -6.0090821 0 -5.081654 0.053336092 + 450 0.60600519 -5.8710484 0 -4.9623273 -0.085701075 + 500 0.60383908 -5.7254198 0 -4.8199469 -0.15560848 + 550 0.60342483 -5.582958 0 -4.6781063 -0.18389998 + 600 0.61415824 -5.4571678 0 -4.5362211 -0.18398358 + 650 0.61997958 -5.3337392 0 -4.4040632 -0.13933776 + 700 0.65521411 -5.2724025 0 -4.2898914 -0.13977767 + 750 0.6525752 -5.18782 0 -4.2092659 -0.087418448 + 800 0.6711302 -5.1682283 0 -4.1618506 -0.080863195 + 850 0.64374266 -5.1290236 0 -4.1637142 -0.012480639 + 900 0.64904492 -5.1463816 0 -4.1731214 -0.015999133 + 950 0.64624835 -5.1529515 0 -4.1838847 0.0037696411 + 1000 0.64602274 -5.1525985 0 -4.1838701 0.022248112 +Loop time of 2.54244 on 1 procs for 1000 steps with 3170 atoms + +Performance: 169915.320 tau/day, 393.322 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 | 1.1455 | 1.1455 | 1.1455 | 0.0 | 45.05 +Neigh | 0.17719 | 0.17719 | 0.17719 | 0.0 | 6.97 +Comm | 0.0067252 | 0.0067252 | 0.0067252 | 0.0 | 0.26 +Output | 0.00069549 | 0.00069549 | 0.00069549 | 0.0 | 0.03 +Modify | 1.2081 | 1.2081 | 1.2081 | 0.0 | 47.52 +Other | | 0.00421 | | | 0.17 + +Nlocal: 3170 ave 3170 max 3170 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1074 ave 1074 max 1074 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 101768 ave 101768 max 101768 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 101768 +Ave neighs/atom = 32.10347 +Neighbor list builds = 50 +Dangerous builds not checked +Total wall time: 0:00:02 diff --git a/examples/PACKAGES/pressure/log.6Mar2022.cylinder.g++.4 b/examples/PACKAGES/pressure/log.6Mar2022.cylinder.g++.4 new file mode 100644 index 0000000000..af787b7b58 --- /dev/null +++ b/examples/PACKAGES/pressure/log.6Mar2022.cylinder.g++.4 @@ -0,0 +1,133 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# compute pressure/cylinder for a cylindrical liquid-vapor interface + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block -10 10 -10 10 0 10 +region liquid cylinder z 0 0 5 0 10 +create_box 1 box +Created orthogonal box = (-16.795962 -16.795962 0) to (16.795962 16.795962 16.795962) + 2 by 2 by 1 MPI processor grid +create_atoms 1 region liquid +Created 3170 atoms + using lattice units in orthogonal box = (-16.795962 -16.795962 0) to (16.795962 16.795962 16.795962) + create_atoms CPU = 0.000 seconds +mass 1 1.0 + +velocity all create 0.65 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nvt temp 0.65 0.65 0.2 + + +thermo 50 +#dump id all atom 50 dump.cylinder + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 2 all recenter 0 0 NULL units lattice +compute p all pressure/cylinder 0 10 15 0.25 +fix 3 all ave/time 100 1 100 c_p[*] file cylinder.out mode vector + + +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- compute pressure/cylinder: + +@Article{Addington, + author = {C. K. Addington, Y. Long, K. E. Gubbins}, + title = {The pressure in interfaces having cylindrical geometry}, + journal = {J.~Chem.~Phys.}, + year = 2018, + volume = 149, + pages = {084109} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 24 24 12 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute pressure/cylinder, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.033 | 3.043 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.65 -6.2219331 0 -5.2472407 -1.0193897 + 50 0.40121817 -5.7782233 0 -5.1765859 -0.33373915 + 100 0.56963398 -5.8789288 0 -5.0247474 -0.16859926 + 150 0.68424117 -5.9319873 0 -4.9059493 0.062850222 + 200 0.68608162 -5.9987099 0 -4.9699121 0.21439145 + 250 0.63422098 -6.047104 0 -5.0960726 0.30980602 + 300 0.64028254 -6.107331 0 -5.1472102 0.32133372 + 350 0.64906334 -6.1101542 0 -5.1368663 0.22288375 + 400 0.61848053 -6.0090821 0 -5.081654 0.053336092 + 450 0.60600519 -5.8710484 0 -4.9623273 -0.085701075 + 500 0.60383908 -5.7254198 0 -4.8199469 -0.15560848 + 550 0.60342483 -5.582958 0 -4.6781063 -0.18389998 + 600 0.61415824 -5.4571678 0 -4.5362211 -0.18398358 + 650 0.61997958 -5.3337392 0 -4.4040632 -0.13933776 + 700 0.65521411 -5.2724025 0 -4.2898914 -0.13977767 + 750 0.6525752 -5.18782 0 -4.2092659 -0.087418448 + 800 0.6711302 -5.1682283 0 -4.1618506 -0.080863195 + 850 0.64374266 -5.1290236 0 -4.1637142 -0.012480639 + 900 0.64904492 -5.1463816 0 -4.1731214 -0.015999133 + 950 0.64624835 -5.1529515 0 -4.1838847 0.0037696411 + 1000 0.64602274 -5.1525985 0 -4.1838701 0.022248112 +Loop time of 0.709732 on 4 procs for 1000 steps with 3170 atoms + +Performance: 608680.564 tau/day, 1408.983 timesteps/s +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.28555 | 0.29497 | 0.30391 | 1.3 | 41.56 +Neigh | 0.046067 | 0.046753 | 0.047531 | 0.3 | 6.59 +Comm | 0.026197 | 0.037315 | 0.049469 | 4.6 | 5.26 +Output | 0.00049542 | 0.0013801 | 0.0016773 | 1.4 | 0.19 +Modify | 0.32518 | 0.32751 | 0.33044 | 0.3 | 46.15 +Other | | 0.001804 | | | 0.25 + +Nlocal: 792.5 ave 794 max 791 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 1292 ave 1302 max 1284 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 25442 ave 26560 max 24446 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 101768 +Ave neighs/atom = 32.10347 +Neighbor list builds = 50 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pressure/log.6Mar2022.flat.g++.1 b/examples/PACKAGES/pressure/log.6Mar2022.flat.g++.1 new file mode 100644 index 0000000000..0141824bcf --- /dev/null +++ b/examples/PACKAGES/pressure/log.6Mar2022.flat.g++.1 @@ -0,0 +1,139 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# compute pressure/cartesian for a flat liquid-vapor interface + +units lj +atom_style atomic +processors * * 1 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 10 0 10 0 30 +region liquid block 0 10 0 10 10 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.795962 16.795962 50.387886) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region liquid +Created 4200 atoms + using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 50.387886) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 0.65 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nvt temp 0.7 0.7 0.2 + + +thermo 50 +#dump id all atom 50 dump.flat + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 2 all recenter NULL NULL 15 units lattice +compute p1 all pressure/cartesian z 0.5 +Adjusting first bin width for compute pressure/cartesian from 0.500000 to 0.503879 +fix 3 all ave/time 100 1 100 c_p1[*] file flat.out mode vector +#compute p2 all pressure/cartesian z 0.25 x 1 +#fix 4 all ave/time 100 1 100 c_p2[*] file flat_2d.out mode vector + + +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- compute pressure/cartesian: + +@article{galteland2021nanothermodynamic, +title={Nanothermodynamic description and molecular simulation of a single-phase fluid in a slit pore}, +author={Galteland, Olav and Bedeaux, Dick and Kjelstrup, Signe} +,journal={Nanomaterials}, +volume={11}, +number={1}, +pages={165}, +year={2021}, +publisher={Multidisciplinary Digital Publishing Institute} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 36 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute pressure/cartesian, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.943 | 3.943 | 3.943 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.65 -6.5342767 0 -5.5595088 -1.9070205 + 50 0.36842234 -6.0304191 0 -5.4779172 -0.76896135 + 100 0.50896152 -6.0786202 0 -5.3153597 -0.58839893 + 150 0.63567071 -6.0832159 0 -5.1299368 -0.29587266 + 200 0.72324528 -6.0689996 0 -4.98439 -0.020342078 + 250 0.74387008 -6.1188743 0 -5.0033349 0.11337395 + 300 0.69112666 -6.1838992 0 -5.1474561 0.18290797 + 350 0.67772633 -6.2400592 0 -5.2237117 0.27698807 + 400 0.70714238 -6.2783031 0 -5.2178421 0.41150934 + 450 0.71843478 -6.2870874 0 -5.2096918 0.57099811 + 500 0.69813385 -6.3041653 0 -5.2572139 0.53883987 + 550 0.67043069 -6.3035289 0 -5.2981223 0.36370002 + 600 0.68196102 -6.26442 0 -5.241722 0.22122892 + 650 0.69413189 -6.1759937 0 -5.1350438 0.12782621 + 700 0.70034968 -6.1028735 0 -5.0525991 0.029208853 + 750 0.70266272 -6.036839 0 -4.9830959 -0.088703619 + 800 0.68551399 -5.9410263 0 -4.9130002 -0.18134075 + 850 0.6866836 -5.8390431 0 -4.8092629 -0.27593375 + 900 0.67608249 -5.711593 0 -4.6977107 -0.28650991 + 950 0.68080988 -5.6043546 0 -4.5833829 -0.29765481 + 1000 0.68792271 -5.5015077 0 -4.4698694 -0.27955533 +Loop time of 2.13769 on 1 procs for 1000 steps with 4200 atoms + +Performance: 202087.264 tau/day, 467.795 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.6853 | 1.6853 | 1.6853 | 0.0 | 78.84 +Neigh | 0.2494 | 0.2494 | 0.2494 | 0.0 | 11.67 +Comm | 0.020319 | 0.020319 | 0.020319 | 0.0 | 0.95 +Output | 0.0006408 | 0.0006408 | 0.0006408 | 0.0 | 0.03 +Modify | 0.17491 | 0.17491 | 0.17491 | 0.0 | 8.18 +Other | | 0.007093 | | | 0.33 + +Nlocal: 4200 ave 4200 max 4200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3393 ave 3393 max 3393 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 144737 ave 144737 max 144737 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 144737 +Ave neighs/atom = 34.46119 +Neighbor list builds = 50 +Dangerous builds not checked +Total wall time: 0:00:02 diff --git a/examples/PACKAGES/pressure/log.6Mar2022.flat.g++.4 b/examples/PACKAGES/pressure/log.6Mar2022.flat.g++.4 new file mode 100644 index 0000000000..04bed6e521 --- /dev/null +++ b/examples/PACKAGES/pressure/log.6Mar2022.flat.g++.4 @@ -0,0 +1,139 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# compute pressure/cartesian for a flat liquid-vapor interface + +units lj +atom_style atomic +processors * * 1 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 10 0 10 0 30 +region liquid block 0 10 0 10 10 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.795962 16.795962 50.387886) + 2 by 2 by 1 MPI processor grid +create_atoms 1 region liquid +Created 4200 atoms + using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 50.387886) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 0.65 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nvt temp 0.7 0.7 0.2 + + +thermo 50 +#dump id all atom 50 dump.flat + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 2 all recenter NULL NULL 15 units lattice +compute p1 all pressure/cartesian z 0.5 +Adjusting first bin width for compute pressure/cartesian from 0.500000 to 0.503879 +fix 3 all ave/time 100 1 100 c_p1[*] file flat.out mode vector +#compute p2 all pressure/cartesian z 0.25 x 1 +#fix 4 all ave/time 100 1 100 c_p2[*] file flat_2d.out mode vector + + +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- compute pressure/cartesian: + +@article{galteland2021nanothermodynamic, +title={Nanothermodynamic description and molecular simulation of a single-phase fluid in a slit pore}, +author={Galteland, Olav and Bedeaux, Dick and Kjelstrup, Signe} +,journal={Nanomaterials}, +volume={11}, +number={1}, +pages={165}, +year={2021}, +publisher={Multidisciplinary Digital Publishing Institute} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 36 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute pressure/cartesian, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.083 | 3.083 | 3.083 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.65 -6.5342767 0 -5.5595088 -1.9070205 + 50 0.36842234 -6.0304191 0 -5.4779172 -0.76896135 + 100 0.50896152 -6.0786202 0 -5.3153597 -0.58839893 + 150 0.63567071 -6.0832159 0 -5.1299368 -0.29587266 + 200 0.72324528 -6.0689996 0 -4.98439 -0.020342078 + 250 0.74387008 -6.1188743 0 -5.0033349 0.11337395 + 300 0.69112666 -6.1838992 0 -5.1474561 0.18290797 + 350 0.67772633 -6.2400592 0 -5.2237117 0.27698807 + 400 0.70714238 -6.2783031 0 -5.2178421 0.41150934 + 450 0.71843478 -6.2870874 0 -5.2096918 0.57099811 + 500 0.69813385 -6.3041653 0 -5.2572139 0.53883987 + 550 0.67043069 -6.3035289 0 -5.2981223 0.36370002 + 600 0.68196102 -6.26442 0 -5.241722 0.22122892 + 650 0.69413189 -6.1759937 0 -5.1350438 0.12782621 + 700 0.70034968 -6.1028735 0 -5.0525991 0.029208853 + 750 0.70266272 -6.036839 0 -4.9830959 -0.088703619 + 800 0.68551399 -5.9410263 0 -4.9130002 -0.18134075 + 850 0.6866836 -5.8390431 0 -4.8092629 -0.27593375 + 900 0.67608249 -5.711593 0 -4.6977107 -0.28650991 + 950 0.68080988 -5.6043546 0 -4.5833829 -0.29765481 + 1000 0.68792271 -5.5015077 0 -4.4698694 -0.27955533 +Loop time of 0.675356 on 4 procs for 1000 steps with 4200 atoms + +Performance: 639662.349 tau/day, 1480.700 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.47174 | 0.48429 | 0.49671 | 1.5 | 71.71 +Neigh | 0.069839 | 0.071447 | 0.072509 | 0.4 | 10.58 +Comm | 0.046053 | 0.059527 | 0.073675 | 4.5 | 8.81 +Output | 0.0007041 | 0.0022594 | 0.0027829 | 1.9 | 0.33 +Modify | 0.054631 | 0.055179 | 0.056783 | 0.4 | 8.17 +Other | | 0.002651 | | | 0.39 + +Nlocal: 1050 ave 1071 max 1026 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 1952.75 ave 1977 max 1936 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 36184.2 ave 37407 max 34670 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 144737 +Ave neighs/atom = 34.46119 +Neighbor list builds = 50 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pressure/log.6Mar2022.sphere.g++.1 b/examples/PACKAGES/pressure/log.6Mar2022.sphere.g++.1 new file mode 100644 index 0000000000..c09f34f294 --- /dev/null +++ b/examples/PACKAGES/pressure/log.6Mar2022.sphere.g++.1 @@ -0,0 +1,131 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# compute pressure/spherical for a spherical droplet + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block -10 10 -10 10 -10 10 +region liquid sphere 0 0 0 5 +create_box 1 box +Created orthogonal box = (-16.795962 -16.795962 -16.795962) to (16.795962 16.795962 16.795962) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region liquid +Created 2123 atoms + using lattice units in orthogonal box = (-16.795962 -16.795962 -16.795962) to (16.795962 16.795962 16.795962) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 0.65 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nvt temp 0.65 0.65 0.2 + +#dump id all atom 50 dump.sphere + +thermo 50 +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 2 all recenter 0 0 0 units lattice +compute p all pressure/spherical 0 0 0 0.25 15 +Adjusting bin width for compute pressure/spherical from 0.250000 to 0.245902 +fix 3 all ave/time 100 1 100 c_p[*] file sphere.out mode vector + + +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- compute pressure/spherical: + +@article{galteland2022defining, +title={Defining the pressures of a fluid in a nanoporous, heterogeneous medium}, +author={Galteland, Olav and Rauter, Michael T and Varughese, Kevin K and Bedeaux, Dick and Kjelstrup, Signe}, +journal={arXiv preprint arXiv:2201.13060}, +year={2022} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 24 24 24 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute pressure/spherical, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.11 | 3.11 | 3.11 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.65 -5.982005 0 -5.0074642 -0.32476388 + 50 0.42414771 -5.5700167 0 -4.9340948 -0.074492286 + 100 0.64021145 -5.7405134 0 -4.7806486 -0.0054535408 + 150 0.72663247 -5.8366691 0 -4.7472338 0.089984367 + 200 0.63460122 -5.8577473 0 -4.9062939 0.14140872 + 250 0.62199115 -5.9027866 0 -4.9702393 0.13328919 + 300 0.62406364 -5.8889104 0 -4.9532559 0.063550326 + 350 0.6028994 -5.7552274 0 -4.8513043 -0.027499706 + 400 0.56811588 -5.5416058 0 -4.6898334 -0.061577561 + 450 0.54946762 -5.3409786 0 -4.5171654 -0.060007836 + 500 0.57962648 -5.2096808 0 -4.3406506 -0.052541306 + 550 0.61149882 -5.0920642 0 -4.175248 -0.03806361 + 600 0.63683327 -4.9975996 0 -4.0427996 -0.016868781 + 650 0.67007543 -4.9684574 0 -3.9638177 -0.00087204466 + 700 0.65648313 -4.9612522 0 -3.9769913 0.012954904 + 750 0.62636818 -4.9944273 0 -4.0553176 0.01206773 + 800 0.64474901 -5.0498682 0 -4.0832003 -0.0022579262 + 850 0.64765539 -5.0405969 0 -4.0695714 0.0061653637 + 900 0.65308258 -5.0187376 0 -4.0395752 0.016798783 + 950 0.65225966 -4.9974305 0 -4.0195019 0.0195366 + 1000 0.6407875 -4.9770134 0 -4.0162849 0.0064419231 +Loop time of 1.12311 on 1 procs for 1000 steps with 2123 atoms + +Performance: 384646.552 tau/day, 890.386 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 | 0.72699 | 0.72699 | 0.72699 | 0.0 | 64.73 +Neigh | 0.11083 | 0.11083 | 0.11083 | 0.0 | 9.87 +Comm | 0.0011647 | 0.0011647 | 0.0011647 | 0.0 | 0.10 +Output | 0.0005541 | 0.0005541 | 0.0005541 | 0.0 | 0.05 +Modify | 0.28132 | 0.28132 | 0.28132 | 0.0 | 25.05 +Other | | 0.002256 | | | 0.20 + +Nlocal: 2123 ave 2123 max 2123 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: 63677 ave 63677 max 63677 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 63677 +Ave neighs/atom = 29.993877 +Neighbor list builds = 50 +Dangerous builds not checked +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pressure/log.6Mar2022.sphere.g++.4 b/examples/PACKAGES/pressure/log.6Mar2022.sphere.g++.4 new file mode 100644 index 0000000000..24267e6cf4 --- /dev/null +++ b/examples/PACKAGES/pressure/log.6Mar2022.sphere.g++.4 @@ -0,0 +1,131 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# compute pressure/spherical for a spherical droplet + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block -10 10 -10 10 -10 10 +region liquid sphere 0 0 0 5 +create_box 1 box +Created orthogonal box = (-16.795962 -16.795962 -16.795962) to (16.795962 16.795962 16.795962) + 1 by 2 by 2 MPI processor grid +create_atoms 1 region liquid +Created 2123 atoms + using lattice units in orthogonal box = (-16.795962 -16.795962 -16.795962) to (16.795962 16.795962 16.795962) + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 0.65 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nvt temp 0.65 0.65 0.2 + +#dump id all atom 50 dump.sphere + +thermo 50 +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 2 all recenter 0 0 0 units lattice +compute p all pressure/spherical 0 0 0 0.25 15 +Adjusting bin width for compute pressure/spherical from 0.250000 to 0.245902 +fix 3 all ave/time 100 1 100 c_p[*] file sphere.out mode vector + + +run 1000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- compute pressure/spherical: + +@article{galteland2022defining, +title={Defining the pressures of a fluid in a nanoporous, heterogeneous medium}, +author={Galteland, Olav and Rauter, Michael T and Varughese, Kevin K and Bedeaux, Dick and Kjelstrup, Signe}, +journal={arXiv preprint arXiv:2201.13060}, +year={2022} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 24 24 24 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute pressure/spherical, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.068 | 3.078 | 3.082 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.65 -5.982005 0 -5.0074642 -0.32476388 + 50 0.42414771 -5.5700167 0 -4.9340948 -0.074492286 + 100 0.64021145 -5.7405134 0 -4.7806486 -0.0054535408 + 150 0.72663247 -5.8366691 0 -4.7472338 0.089984367 + 200 0.63460122 -5.8577473 0 -4.9062939 0.14140872 + 250 0.62199115 -5.9027866 0 -4.9702393 0.13328919 + 300 0.62406364 -5.8889104 0 -4.9532559 0.063550326 + 350 0.6028994 -5.7552274 0 -4.8513043 -0.027499706 + 400 0.56811588 -5.5416058 0 -4.6898334 -0.061577561 + 450 0.54946762 -5.3409786 0 -4.5171654 -0.060007836 + 500 0.57962648 -5.2096808 0 -4.3406506 -0.052541306 + 550 0.61149882 -5.0920642 0 -4.175248 -0.03806361 + 600 0.63683327 -4.9975996 0 -4.0427996 -0.016868781 + 650 0.67007543 -4.9684574 0 -3.9638177 -0.00087204466 + 700 0.65648313 -4.9612522 0 -3.9769913 0.012954904 + 750 0.62636818 -4.9944273 0 -4.0553176 0.01206773 + 800 0.64474901 -5.0498682 0 -4.0832003 -0.0022579262 + 850 0.64765539 -5.0405969 0 -4.0695714 0.0061653637 + 900 0.65308258 -5.0187376 0 -4.0395752 0.016798783 + 950 0.65225966 -4.9974305 0 -4.0195019 0.0195366 + 1000 0.6407875 -4.9770134 0 -4.0162849 0.006441923 +Loop time of 0.35176 on 4 procs for 1000 steps with 2123 atoms + +Performance: 1228110.486 tau/day, 2842.848 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17072 | 0.18863 | 0.20606 | 3.7 | 53.63 +Neigh | 0.027172 | 0.030136 | 0.033131 | 1.7 | 8.57 +Comm | 0.024747 | 0.046514 | 0.067648 | 9.3 | 13.22 +Output | 0.00050033 | 0.0013632 | 0.0016527 | 1.3 | 0.39 +Modify | 0.082033 | 0.083964 | 0.086383 | 0.5 | 23.87 +Other | | 0.001148 | | | 0.33 + +Nlocal: 530.75 ave 542 max 513 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Nghost: 627.75 ave 650 max 612 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 15919.2 ave 17564 max 14498 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 63677 +Ave neighs/atom = 29.993877 +Neighbor list builds = 50 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/pressure/in.cylinder b/examples/pressure/in.cylinder deleted file mode 100644 index 59bcebbbc3..0000000000 --- a/examples/pressure/in.cylinder +++ /dev/null @@ -1,40 +0,0 @@ -# compute pressure/cylinder for a cylindrical liquid-vapor interface - -units lj -atom_style atomic - -lattice fcc 0.8442 -region box block -10 10 -10 10 0 10 -region liquid cylinder z 0 0 5 0 10 -create_box 1 box -create_atoms 1 region liquid -mass 1 1.0 - -velocity all create 0.65 87287 loop geom - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify every 20 delay 0 check no - -fix 1 all nvt temp 0.65 0.65 0.2 - - -thermo 50 -#dump id all atom 50 dump.cylinder - -#dump 2 all image 25 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 2 all recenter 0 0 NULL units lattice -compute p all pressure/cylinder 0 10 15 0.25 -fix 3 all ave/time 100 1 100 c_p[*] file cylinder.out mode vector - - -run 1000 diff --git a/examples/pressure/in.flat b/examples/pressure/in.flat deleted file mode 100644 index 1cbf9d6ff2..0000000000 --- a/examples/pressure/in.flat +++ /dev/null @@ -1,42 +0,0 @@ -# compute pressure/cartesian for a flat liquid-vapor interface - -units lj -atom_style atomic - -lattice fcc 0.8442 -region box block 0 10 0 10 0 30 -region liquid block 0 10 0 10 10 20 -create_box 1 box -create_atoms 1 region liquid -mass 1 1.0 - -velocity all create 0.65 87287 loop geom - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify every 20 delay 0 check no - -fix 1 all nvt temp 0.7 0.7 0.2 - - -thermo 50 -#dump id all atom 50 dump.flat - -#dump 2 all image 25 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 2 all recenter NULL NULL 15 units lattice -compute p1 all pressure/cartesian z 0.5 -fix 3 all ave/time 100 1 100 c_p1[*] file flat.out mode vector -#compute p2 all pressure/cartesian z 0.25 x 1 -#fix 4 all ave/time 100 1 100 c_p2[*] file flat_2d.out mode vector - - -run 1000 diff --git a/examples/pressure/in.sphere b/examples/pressure/in.sphere deleted file mode 100644 index 8715c2d321..0000000000 --- a/examples/pressure/in.sphere +++ /dev/null @@ -1,39 +0,0 @@ -# compute pressure/spherical for a spherical droplet - -units lj -atom_style atomic - -lattice fcc 0.8442 -region box block -10 10 -10 10 -10 10 -region liquid sphere 0 0 0 5 -create_box 1 box -create_atoms 1 region liquid -mass 1 1.0 - -velocity all create 0.65 87287 loop geom - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify every 20 delay 0 check no - -fix 1 all nvt temp 0.65 0.65 0.2 - -#dump id all atom 50 dump.sphere - -thermo 50 -#dump 2 all image 25 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 2 all recenter 0 0 0 units lattice -compute p all pressure/spherical 0 0 0 0.25 15 -fix 3 all ave/time 100 1 100 c_p[*] file sphere.out mode vector - - -run 1000