diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index a223939d5a..993090baf1 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -133,6 +133,8 @@ Lowercase directories +-------------+------------------------------------------------------------------+ | reax | RDX and TATB models using the ReaxFF | +-------------+------------------------------------------------------------------+ +| rerun | use of rerun and read\_dump commands | ++-------------+------------------------------------------------------------------+ | rigid | rigid bodies modeled as independent or coupled | +-------------+------------------------------------------------------------------+ | shear | sideways shear applied to 2d solid, with and without a void | diff --git a/doc/txt/Examples.txt b/doc/txt/Examples.txt index 86617e13df..04c211cb1d 100644 --- a/doc/txt/Examples.txt +++ b/doc/txt/Examples.txt @@ -94,6 +94,7 @@ python: using embedded Python in a LAMMPS input script qeq: use of the QEQ package for charge equilibration rdf-adf: computing radial and angle distribution functions for water reax: RDX and TATB models using the ReaxFF +rerun: use of rerun and read_dump commands rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void snap: NVE dynamics for BCC tantalum crystal using SNAP potential diff --git a/examples/README b/examples/README index 47463a85d8..0589055e4a 100644 --- a/examples/README +++ b/examples/README @@ -101,6 +101,7 @@ prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script qeq: use of QEQ package for charge equilibration reax: RDX and TATB and several other models using ReaxFF +rerun: use of rerun and read_dump commands rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void snap: examples for using several bundled SNAP potentials diff --git a/examples/rerun/README b/examples/rerun/README new file mode 100644 index 0000000000..66db685d92 --- /dev/null +++ b/examples/rerun/README @@ -0,0 +1,17 @@ +Examples of how to use the rerun and read_dump commands + +in.first - run on any number of procs for any size problem +in.rerun - run on same or different proc count for same size problem +in.read_dump - ditto to in.rerun + +The thermo output on the same timesteps should be identical +to within round-off errors. + +in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma +in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma + +In both bases the time averaged RDF is computed 10x times, every 100 +steps for 1000 total. In the rerun, the pair style cutoff is changed +so the RDF can be computed to a longer distance without re-running the +simulation. The RDF values in the 2 files should be the same (within +round-off) for the first 50 bins. diff --git a/examples/rerun/in.first b/examples/rerun/in.first new file mode 100644 index 0000000000..2aa4c1974c --- /dev/null +++ b/examples/rerun/in.first @@ -0,0 +1,33 @@ +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +dump 1 all custom 100 lj.dump id type x y z vx vy vz + +thermo 100 +run 1000 diff --git a/examples/rerun/in.rdf.first b/examples/rerun/in.rdf.first new file mode 100644 index 0000000000..f9d1ecf55e --- /dev/null +++ b/examples/rerun/in.rdf.first @@ -0,0 +1,36 @@ +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +dump 1 all custom 100 lj.dump id type x y z + +compute myRDF all rdf 50 cutoff 2.5 +fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector + +thermo 100 +run 1000 diff --git a/examples/rerun/in.rdf.rerun b/examples/rerun/in.rdf.rerun new file mode 100644 index 0000000000..5562cac74d --- /dev/null +++ b/examples/rerun/in.rdf.rerun @@ -0,0 +1,31 @@ +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +pair_style lj/cut 5.0 +pair_coeff 1 1 1.0 1.0 + +neighbor 0.3 bin + +compute myRDF all rdf 100 cutoff 5.0 +fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector + +thermo 100 + +rerun lj.dump dump x y z + diff --git a/examples/rerun/in.read_dump b/examples/rerun/in.read_dump new file mode 100644 index 0000000000..3c1310b305 --- /dev/null +++ b/examples/rerun/in.read_dump @@ -0,0 +1,37 @@ +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin + +thermo 100 + +read_dump lj.dump 200 x y z vx vy vz +run 0 post no + +read_dump lj.dump 800 x y z vx vy vz +run 0 post no + +read_dump lj.dump 600 x y z vx vy vz +run 0 post no + +read_dump lj.dump 400 x y z vx vy vz +run 0 post no diff --git a/examples/rerun/in.rerun b/examples/rerun/in.rerun new file mode 100644 index 0000000000..a695006f26 --- /dev/null +++ b/examples/rerun/in.rerun @@ -0,0 +1,29 @@ +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin + +thermo 100 + +rerun lj.dump first 200 last 800 every 200 & + dump x y z vx vy vz + diff --git a/examples/rerun/log.09Jan20.first.g++.4 b/examples/rerun/log.09Jan20.first.g++.4 new file mode 100644 index 0000000000..cabc17c851 --- /dev/null +++ b/examples/rerun/log.09Jan20.first.g++.4 @@ -0,0 +1,97 @@ +LAMMPS (09 Jan 2020) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.00173283 secs +mass 1 1.0 + +velocity all create 1.44 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 delay 0 every 20 check no + +fix 1 all nve + +dump 1 all custom 100 lj.dump id type x y z vx vy vz + +thermo 100 +run 1000 +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 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.869 | 7.869 | 7.869 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 + 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 + 200 0.75953175 -5.7618892 0 -4.6226272 0.20910575 + 300 0.74624286 -5.741962 0 -4.6226327 0.32016436 + 400 0.74155675 -5.7343359 0 -4.6220356 0.3777989 + 500 0.73249345 -5.7206946 0 -4.6219887 0.44253023 + 600 0.72087255 -5.7029314 0 -4.6216563 0.55730354 + 700 0.71489947 -5.693532 0 -4.6212164 0.61322381 + 800 0.70876958 -5.6840594 0 -4.6209382 0.66822293 + 900 0.70799522 -5.6828388 0 -4.6208791 0.66961272 + 1000 0.70325878 -5.6750833 0 -4.6202281 0.7112575 +Loop time of 6.3349 on 4 procs for 1000 steps with 32000 atoms + +Performance: 68193.673 tau/day, 157.856 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.3538 | 4.6712 | 5.0021 | 12.8 | 73.74 +Neigh | 0.59378 | 0.65229 | 0.75202 | 8.0 | 10.30 +Comm | 0.28101 | 0.69839 | 1.0586 | 38.5 | 11.02 +Output | 0.21601 | 0.21682 | 0.21718 | 0.1 | 3.42 +Modify | 0.074002 | 0.074803 | 0.075779 | 0.2 | 1.18 +Other | | 0.0214 | | | 0.34 + +Nlocal: 8000 ave 8049 max 7942 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 8632.5 ave 8685 max 8591 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 299934 ave 303105 max 295137 min +Histogram: 1 0 0 0 0 0 1 1 0 1 + +Total # of neighbors = 1199738 +Ave neighs/atom = 37.4918 +Neighbor list builds = 50 +Dangerous builds not checked +Total wall time: 0:00:06 diff --git a/examples/rerun/log.09Jan20.rdf.first.g++.4 b/examples/rerun/log.09Jan20.rdf.first.g++.4 new file mode 100644 index 0000000000..7d029f23d4 --- /dev/null +++ b/examples/rerun/log.09Jan20.rdf.first.g++.4 @@ -0,0 +1,105 @@ +LAMMPS (09 Jan 2020) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.00100017 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +dump 1 all custom 100 lj.dump id type x y z + +compute myRDF all rdf 50 cutoff 2.5 +fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector + +thermo 100 +run 1000 +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/newton + bin: standard + (2) compute rdf, occasional + attributes: half, newton on, cut 2.8 + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.487 | 8.487 | 8.487 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 + 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 + 200 0.75953175 -5.7618892 0 -4.6226272 0.20910575 + 300 0.74624286 -5.741962 0 -4.6226327 0.32016436 + 400 0.74155675 -5.7343359 0 -4.6220356 0.3777989 + 500 0.73249345 -5.7206946 0 -4.6219887 0.44253023 + 600 0.72087255 -5.7029314 0 -4.6216563 0.55730354 + 700 0.71489947 -5.693532 0 -4.6212164 0.61322381 + 800 0.70876958 -5.6840594 0 -4.6209382 0.66822293 + 900 0.70799522 -5.6828388 0 -4.6208791 0.66961272 + 1000 0.70325878 -5.6750833 0 -4.6202281 0.7112575 +Loop time of 7.44016 on 4 procs for 1000 steps with 32000 atoms + +Performance: 58063.267 tau/day, 134.406 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.3881 | 5.5809 | 5.7111 | 5.4 | 75.01 +Neigh | 0.80101 | 0.82776 | 0.85702 | 2.2 | 11.13 +Comm | 0.31801 | 0.48426 | 0.72201 | 22.5 | 6.51 +Output | 0.17801 | 0.17801 | 0.17801 | 0.0 | 2.39 +Modify | 0.31201 | 0.33076 | 0.33701 | 1.9 | 4.45 +Other | | 0.0385 | | | 0.52 + +Nlocal: 8000 ave 8049 max 7942 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 8632.5 ave 8685 max 8591 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 299934 ave 303105 max 295137 min +Histogram: 1 0 0 0 0 0 1 1 0 1 + +Total # of neighbors = 1199738 +Ave neighs/atom = 37.4918 +Neighbor list builds = 50 +Dangerous builds not checked +Total wall time: 0:00:07 diff --git a/examples/rerun/log.09Jan20.rdf.rerun.g++.4 b/examples/rerun/log.09Jan20.rdf.rerun.g++.4 new file mode 100644 index 0000000000..7c5137bb08 --- /dev/null +++ b/examples/rerun/log.09Jan20.rdf.rerun.g++.4 @@ -0,0 +1,100 @@ +LAMMPS (09 Jan 2020) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.00183487 secs +mass 1 1.0 + +pair_style lj/cut 5.0 +pair_coeff 1 1 1.0 1.0 + +neighbor 0.3 bin + +compute myRDF all rdf 100 cutoff 5.0 +fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector + +thermo 100 + +rerun lj.dump dump x y z +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 13 13 13 + 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/newton + bin: standard + (2) compute rdf, occasional + attributes: half, newton on, cut 5.3 + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.19 | 15.19 | 15.19 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -7.1616928 0 -7.1616928 -6.8899898 + 100 0 -6.1442754 0 -6.1442754 -1.0825318 + 200 0 -6.1472483 0 -6.1472483 -1.0817213 + 300 0 -6.1274033 0 -6.1274033 -0.95961014 + 400 0 -6.1202956 0 -6.1202956 -0.8988851 + 500 0 -6.1067136 0 -6.1067136 -0.82660368 + 600 0 -6.0893179 0 -6.0893179 -0.70264528 + 700 0 -6.0803044 0 -6.0803044 -0.64232743 + 800 0 -6.0710303 0 -6.0710303 -0.5824798 + 900 0 -6.0698963 0 -6.0698963 -0.58057929 + 1000 0 -6.0627642 0 -6.0627642 -0.53599799 +Loop time of 3.07661 on 4 procs for 11 steps with 32000 atoms + +Performance: 1544.558 tau/day, 3.575 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.077 | | |100.00 + +Nlocal: 8000 ave 8049 max 7942 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 20028 ave 20060 max 19988 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 2.10417e+06 ave 2.12604e+06 max 2.07878e+06 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 8416685 +Ave neighs/atom = 263.021 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/rerun/log.09Jan20.read_dump.g++.4 b/examples/rerun/log.09Jan20.read_dump.g++.4 new file mode 100644 index 0000000000..874309aaa3 --- /dev/null +++ b/examples/rerun/log.09Jan20.read_dump.g++.4 @@ -0,0 +1,118 @@ +LAMMPS (09 Jan 2020) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.001724 secs +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin + +thermo 100 + +read_dump lj.dump 200 x y z vx vy vz + orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 32000 atoms before read + 32000 atoms in snapshot + 0 atoms purged + 32000 atoms replaced + 0 atoms trimmed + 0 atoms added + 32000 atoms after read +run 0 post no +WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + 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 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.75953173 -5.7618854 0 -4.6226234 0.20912952 +Loop time of 2.26498e-06 on 4 procs for 0 steps with 32000 atoms + + +read_dump lj.dump 800 x y z vx vy vz + orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 32000 atoms before read + 32000 atoms in snapshot + 0 atoms purged + 32000 atoms replaced + 0 atoms trimmed + 0 atoms added + 32000 atoms after read +run 0 post no +WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) +Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes +Step Temp E_pair E_mol TotEng Press + 800 0.70876957 -5.6840545 0 -4.6209334 0.66823926 +Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms + + +read_dump lj.dump 600 x y z vx vy vz + orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 32000 atoms before read + 32000 atoms in snapshot + 0 atoms purged + 32000 atoms replaced + 0 atoms trimmed + 0 atoms added + 32000 atoms after read +run 0 post no +WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) +Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes +Step Temp E_pair E_mol TotEng Press + 600 0.72087256 -5.7029306 0 -4.6216556 0.55729873 +Loop time of 7.7486e-07 on 4 procs for 0 steps with 32000 atoms + + +read_dump lj.dump 400 x y z vx vy vz + orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 32000 atoms before read + 32000 atoms in snapshot + 0 atoms purged + 32000 atoms replaced + 0 atoms trimmed + 0 atoms added + 32000 atoms after read +run 0 post no +WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) +Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes +Step Temp E_pair E_mol TotEng Press + 400 0.74155677 -5.7343336 0 -4.6220332 0.37780193 +Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms + +Total wall time: 0:00:00 diff --git a/examples/rerun/log.09Jan20.rerun.g++.4 b/examples/rerun/log.09Jan20.rerun.g++.4 new file mode 100644 index 0000000000..f654e2c777 --- /dev/null +++ b/examples/rerun/log.09Jan20.rerun.g++.4 @@ -0,0 +1,86 @@ +LAMMPS (09 Jan 2020) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.00100017 secs +mass 1 1.0 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin + +thermo 100 + +rerun lj.dump first 200 last 800 every 200 dump x y z vx vy vz +WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + 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 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.716 | 6.718 | 6.721 Mbytes +Step Temp E_pair E_mol TotEng Press + 200 0.75953173 -5.7618854 0 -4.6226234 0.20912952 + 400 0.74155677 -5.7343336 0 -4.6220332 0.37780193 + 600 0.72087256 -5.7029306 0 -4.6216556 0.55729873 + 800 0.70876957 -5.6840545 0 -4.6209334 0.66823926 +Loop time of 0.375898 on 4 procs for 4 steps with 32000 atoms + +Performance: 4596.990 tau/day, 10.641 timesteps/s +98.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.3759 | | |100.00 + +Nlocal: 8000 ave 8073 max 7933 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 8693.25 ave 8731 max 8658 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Neighs: 299786 ave 302947 max 293888 min +Histogram: 1 0 0 0 0 0 0 1 1 1 + +Total # of neighbors = 1199142 +Ave neighs/atom = 37.4732 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/rerun/rdf.09Jan20.first.g++.4 b/examples/rerun/rdf.09Jan20.first.g++.4 new file mode 100644 index 0000000000..d78e0ce2c1 --- /dev/null +++ b/examples/rerun/rdf.09Jan20.first.g++.4 @@ -0,0 +1,54 @@ +# Time-averaged data for fix 2 +# TimeStep Number-of-rows +# Row c_myRDF[1] c_myRDF[2] c_myRDF[3] +1000 50 +1 0.025 0 0 +2 0.075 0 0 +3 0.125 0 0 +4 0.175 0 0 +5 0.225 0 0 +6 0.275 0 0 +7 0.325 0 0 +8 0.375 0 0 +9 0.425 0 0 +10 0.475 0 0 +11 0.525 0 0 +12 0.575 0 0 +13 0.625 0 0 +14 0.675 0 0 +15 0.725 0 0 +16 0.775 0 0 +17 0.825 0 0 +18 0.875 1.53863e-05 6.25e-06 +19 0.925 0.0217263 0.00986875 +20 0.975 0.506735 0.265431 +21 1.025 1.92083 1.33605 +22 1.075 2.8749 3.09855 +23 1.125 2.7805 4.96541 +24 1.175 2.21879 6.59047 +25 1.225 1.67622 7.92484 +26 1.275 1.25407 9.00629 +27 1.325 0.963413 9.90353 +28 1.375 0.774441 10.6802 +29 1.425 0.656196 11.3871 +30 1.475 0.589364 12.0672 +31 1.525 0.560681 12.7589 +32 1.575 0.560195 13.4961 +33 1.625 0.587995 14.3197 +34 1.675 0.632155 15.2605 +35 1.725 0.706585 16.3758 +36 1.775 0.805303 17.7216 +37 1.825 0.925415 19.3565 +38 1.875 1.05672 21.3271 +39 1.925 1.17634 23.6394 +40 1.975 1.2557 26.2375 +41 2.025 1.30009 29.0653 +42 2.075 1.30889 32.0546 +43 2.125 1.27704 35.1135 +44 2.175 1.21808 38.17 +45 2.225 1.13622 41.1536 +46 2.275 1.05072 44.0382 +47 2.325 0.973786 46.8303 +48 2.375 0.910095 49.5533 +49 2.425 0.866474 52.256 +50 2.475 0.841724 54.991 diff --git a/examples/rerun/rdf.09Jan20.rerun.g++.4 b/examples/rerun/rdf.09Jan20.rerun.g++.4 new file mode 100644 index 0000000000..3fa6acc461 --- /dev/null +++ b/examples/rerun/rdf.09Jan20.rerun.g++.4 @@ -0,0 +1,104 @@ +# Time-averaged data for fix 2 +# TimeStep Number-of-rows +# Row c_myRDF[1] c_myRDF[2] c_myRDF[3] +1000 100 +1 0.025 0 0 +2 0.075 0 0 +3 0.125 0 0 +4 0.175 0 0 +5 0.225 0 0 +6 0.275 0 0 +7 0.325 0 0 +8 0.375 0 0 +9 0.425 0 0 +10 0.475 0 0 +11 0.525 0 0 +12 0.575 0 0 +13 0.625 0 0 +14 0.675 0 0 +15 0.725 0 0 +16 0.775 0 0 +17 0.825 0 0 +18 0.875 1.53863e-05 6.25e-06 +19 0.925 0.021685 0.00985 +20 0.975 0.506834 0.265463 +21 1.025 1.92047 1.33588 +22 1.075 2.87514 3.09853 +23 1.125 2.78062 4.96547 +24 1.175 2.21869 6.59046 +25 1.225 1.67626 7.92486 +26 1.275 1.25409 9.00633 +27 1.325 0.963245 9.90341 +28 1.375 0.774535 10.6802 +29 1.425 0.65626 11.3871 +30 1.475 0.58925 12.0672 +31 1.525 0.560782 12.759 +32 1.575 0.560133 13.496 +33 1.625 0.588008 14.3197 +34 1.675 0.632185 15.2605 +35 1.725 0.706541 16.3757 +36 1.775 0.805341 17.7216 +37 1.825 0.925351 19.3565 +38 1.875 1.05677 21.3271 +39 1.925 1.17639 23.6395 +40 1.975 1.25571 26.2376 +41 2.025 1.30011 29.0655 +42 2.075 1.30883 32.0547 +43 2.125 1.27702 35.1134 +44 2.175 1.21813 38.17 +45 2.225 1.13617 41.1536 +46 2.275 1.05073 44.0382 +47 2.325 0.97376 46.8302 +48 2.375 0.91012 49.5533 +49 2.425 0.866556 52.2563 +50 2.475 0.841651 54.991 +51 2.525 0.839516 57.8301 +52 2.575 0.848795 60.8153 +53 2.625 0.868861 63.991 +54 2.675 0.896335 67.393 +55 2.725 0.925794 71.0395 +56 2.775 0.961909 74.9685 +57 2.825 0.999727 79.2005 +58 2.875 1.03745 83.749 +59 2.925 1.07355 88.6208 +60 2.975 1.10406 93.8039 +61 3.025 1.11993 99.2397 +62 3.075 1.12062 104.86 +63 3.125 1.10531 110.586 +64 3.175 1.07711 116.345 +65 3.225 1.04268 122.097 +66 3.275 1.00838 127.834 +67 3.325 0.974855 133.55 +68 3.375 0.949817 139.289 +69 3.425 0.936519 145.116 +70 3.475 0.92942 151.069 +71 3.525 0.930926 157.205 +72 3.575 0.940561 163.581 +73 3.625 0.94956 170.199 +74 3.675 0.964202 177.107 +75 3.725 0.97905 184.312 +76 3.775 0.991906 191.81 +77 3.825 1.00093 199.577 +78 3.875 1.01248 207.641 +79 3.925 1.02301 216.001 +80 3.975 1.03474 224.673 +81 4.025 1.04171 233.624 +82 4.075 1.04725 242.849 +83 4.125 1.04997 252.325 +84 4.175 1.04758 262.01 +85 4.225 1.03985 271.856 +86 4.275 1.02755 281.817 +87 4.325 1.00883 291.826 +88 4.375 0.99045 301.882 +89 4.425 0.97287 311.986 +90 4.475 0.958469 322.166 +91 4.525 0.952552 332.512 +92 4.575 0.948064 343.037 +93 4.625 0.952592 353.845 +94 4.675 0.958837 364.96 +95 4.725 0.970831 376.457 +96 4.775 0.985248 388.372 +97 4.825 0.998873 400.707 +98 4.875 1.0119 413.462 +99 4.925 1.02446 426.643 +100 4.975 1.03613 440.245