add unit test for yaml style thermo output and updated logfile class
This commit is contained in:
Axel Kohlmeyer
@ -118,6 +118,7 @@ ttm: two-temeperature model examples
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vashishta: models using the Vashishta potential
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voronoi: Voronoi tesselation via compute voronoi/atom command
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wall: use of reflective walls with different stochastic models
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yaml: demonstrates use of yaml thermo and dump styles
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Here is how you might run and visualize one of the sample problems:
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37
examples/yaml/in.yaml
Normal file
37
examples/yaml/in.yaml
Normal file
@ -0,0 +1,37 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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thermo_style yaml
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thermo 10
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dump 1 all yaml 25 dump.yaml id type x y z ix iy iz vx vy vz
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dump_modify 1 sort id thermo yes units yes time yes format 1 %5d format float "% 12.8e" format int %2d
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run 100
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run 100
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151
examples/yaml/log.7Apr22.yaml.g++.1
Normal file
151
examples/yaml/log.7Apr22.yaml.g++.1
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@ -0,0 +1,151 @@
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LAMMPS (24 Mar 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (33.591924 33.591924 33.591924)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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using lattice units in orthogonal box = (0 0 0) to (33.591924 33.591924 33.591924)
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create_atoms CPU = 0.003 seconds
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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thermo_style yaml
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thermo 10
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dump 1 all yaml 25 dump.yaml id type x y z ix iy iz vx vy vz
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dump_modify 1 sort id thermo yes units yes time yes format 1 %5d format float "% 12.8e" format int %2d
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run 100
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 24 24 24
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 20.56 | 20.56 | 20.56 Mbytes
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---
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keywords: [Step, Temp, KinEng, PotEng, E_bond, E_angle, E_dihed, E_impro, E_vdwl, E_coul, E_long, Press, ]
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data:
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- [0, 1.44000000000001, 2.15993250000001, -6.77336805323422, 0, 0, 0, 0, -6.77336805323422, 0, 0, -5.01970725908556, ]
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- [10, 1.12539487029313, 1.68803955255514, -6.30005271976029, 0, 0, 0, 0, -6.30005271976029, 0, 0, -2.55968522600129, ]
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- [20, 0.625793798302192, 0.938661363368992, -5.55655653922756, 0, 0, 0, 0, -5.55655653922756, 0, 0, 0.973517658007722, ]
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- [30, 0.745927295413064, 1.11885597777762, -5.73951278150759, 0, 0, 0, 0, -5.73951278150759, 0, 0, 0.339284096694852, ]
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- [40, 0.731026217827733, 1.09650505988764, -5.71764564663628, 0, 0, 0, 0, -5.71764564663628, 0, 0, 0.388973418756238, ]
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- [50, 0.740091517740786, 1.11010258482128, -5.73150426762886, 0, 0, 0, 0, -5.73150426762886, 0, 0, 0.335273324523691, ]
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- [60, 0.750500641591031, 1.12571578266897, -5.74713299283555, 0, 0, 0, 0, -5.74713299283555, 0, 0, 0.26343139026926, ]
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- [70, 0.755436366857812, 1.13311913920702, -5.75480059117447, 0, 0, 0, 0, -5.75480059117447, 0, 0, 0.224276619217515, ]
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- [80, 0.759974280364828, 1.13992579675285, -5.76187162670983, 0, 0, 0, 0, -5.76187162670983, 0, 0, 0.191626237124102, ]
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- [90, 0.760464250735042, 1.14066072934081, -5.76280209529731, 0, 0, 0, 0, -5.76280209529731, 0, 0, 0.189478083345243, ]
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- [100, 0.757453103239936, 1.13614414924569, -5.75850548601596, 0, 0, 0, 0, -5.75850548601596, 0, 0, 0.207261053624723, ]
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...
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Loop time of 1.89046 on 1 procs for 100 steps with 32000 atoms
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Performance: 22851.622 tau/day, 52.897 timesteps/s
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99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 1.2896 | 1.2896 | 1.2896 | 0.0 | 68.22
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Neigh | 0.17687 | 0.17687 | 0.17687 | 0.0 | 9.36
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Comm | 0.014543 | 0.014543 | 0.014543 | 0.0 | 0.77
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Output | 0.37678 | 0.37678 | 0.37678 | 0.0 | 19.93
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Modify | 0.028638 | 0.028638 | 0.028638 | 0.0 | 1.51
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Other | | 0.003975 | | | 0.21
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 19657 ave 19657 max 19657 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1202833
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Ave neighs/atom = 37.588531
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Neighbor list builds = 5
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Dangerous builds not checked
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run 100
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 20.57 | 20.57 | 20.57 Mbytes
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---
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keywords: [Step, Temp, KinEng, PotEng, E_bond, E_angle, E_dihed, E_impro, E_vdwl, E_coul, E_long, Press, ]
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data:
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- [100, 0.757453103239935, 1.13614414924569, -5.7585054860159, 0, 0, 0, 0, -5.7585054860159, 0, 0, 0.207261053624721, ]
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- [110, 0.759322359337036, 1.13894794576996, -5.7614668389562, 0, 0, 0, 0, -5.7614668389562, 0, 0, 0.194314975399602, ]
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- [120, 0.759372342462676, 1.13902291811546, -5.76149365656489, 0, 0, 0, 0, -5.76149365656489, 0, 0, 0.191600048851267, ]
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- [130, 0.756833027516501, 1.13521406472659, -5.75777334823494, 0, 0, 0, 0, -5.75777334823494, 0, 0, 0.208792327853067, ]
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- [140, 0.759725426691298, 1.13955252790757, -5.76208910746081, 0, 0, 0, 0, -5.76208910746081, 0, 0, 0.193895435346637, ]
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- [150, 0.760545839455106, 1.14078310859643, -5.7633284876011, 0, 0, 0, 0, -5.7633284876011, 0, 0, 0.187959630462945, ]
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- [160, 0.758404626168493, 1.13757138903589, -5.76023198892283, 0, 0, 0, 0, -5.76023198892283, 0, 0, 0.19692107984108, ]
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- [170, 0.758880300638885, 1.13828487844424, -5.76103232235402, 0, 0, 0, 0, -5.76103232235402, 0, 0, 0.197653518549842, ]
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- [180, 0.753691827878246, 1.13050241251294, -5.75304767384283, 0, 0, 0, 0, -5.75304767384283, 0, 0, 0.237041776410937, ]
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- [190, 0.757361226563721, 1.13600633853809, -5.75852399133222, 0, 0, 0, 0, -5.75852399133222, 0, 0, 0.219529562657488, ]
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- [200, 0.759531750132731, 1.13926202214831, -5.76188923485725, 0, 0, 0, 0, -5.76188923485725, 0, 0, 0.209105747192796, ]
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...
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Loop time of 1.93916 on 1 procs for 100 steps with 32000 atoms
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Performance: 22277.687 tau/day, 51.569 timesteps/s
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99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 1.3292 | 1.3292 | 1.3292 | 0.0 | 68.55
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Neigh | 0.18317 | 0.18317 | 0.18317 | 0.0 | 9.45
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Comm | 0.013626 | 0.013626 | 0.013626 | 0.0 | 0.70
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Output | 0.38206 | 0.38206 | 0.38206 | 0.0 | 19.70
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Modify | 0.027034 | 0.027034 | 0.027034 | 0.0 | 1.39
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Other | | 0.004028 | | | 0.21
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 19570 ave 19570 max 19570 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.19982e+06 ave 1.19982e+06 max 1.19982e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1199821
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Ave neighs/atom = 37.494406
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Neighbor list builds = 5
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Dangerous builds not checked
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Total wall time: 0:00:04
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@ -14,14 +14,19 @@
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################################################################################
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# LAMMPS output formats
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# Written by Richard Berger <richard.berger@temple.edu>
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# and Axel Kohlmeyer <akohlmey@gmail.com>
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################################################################################
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import re
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import re, yaml
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try:
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from yaml import CSafeLoader as Loader, CSafeDumper as Dumper
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except ImportError:
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from yaml import SafeLoader as Loader, SafeDumper as Dumper
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class LogFile:
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"""Reads LAMMPS log files and extracts the thermo information
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It supports both the default thermo output style (including custom) and multi.
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It supports the line, multi, and yaml thermo output styles.
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:param filename: path to log file
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:type filename: str
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@ -33,11 +38,13 @@ class LogFile:
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STYLE_DEFAULT = 0
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STYLE_MULTI = 1
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STYLE_YAML = 2
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def __init__(self, filename):
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alpha = re.compile(r'[a-df-zA-DF-Z]') # except e or E for floating-point numbers
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kvpairs = re.compile(r'([a-zA-Z_0-9]+)\s+=\s*([0-9\.eE\-]+)')
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style = LogFile.STYLE_DEFAULT
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yamllog = ""
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self.runs = []
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self.errors = []
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with open(filename, 'rt') as f:
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@ -54,6 +61,24 @@ class LogFile:
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current_run = {}
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for k in keys:
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current_run[k] = []
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elif re.match(r'^(keywords:.*$|data:$|---$| - \[.*\]$)', line):
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style = LogFile.STYLE_YAML
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yamllog += line;
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current_run = {}
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elif re.match(r'^\.\.\.$', line):
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thermo = yaml.load(yamllog, Loader=Loader)
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for k in thermo['keywords']:
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current_run[k] = []
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for step in thermo['data']:
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icol = 0
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for k in thermo['keywords']:
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current_run[k].append(step[icol])
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icol += 1
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self.runs.append(current_run)
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yamllog = ""
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elif re.match(r'^------* Step ', line):
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if not in_thermo:
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current_run = {'Step': [], 'CPU': []}
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@ -65,28 +90,29 @@ class LogFile:
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cpu = float(str_cpu.split('=')[1].split()[0])
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current_run["Step"].append(step)
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current_run["CPU"].append(cpu)
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elif line.startswith('Loop time of'):
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in_thermo = False
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self.runs.append(current_run)
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if style != LogFile.STYLE_YAML:
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self.runs.append(current_run)
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elif in_thermo and in_data_section:
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if style == LogFile.STYLE_DEFAULT:
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if alpha.search(line):
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continue
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for k, v in zip(keys, map(float, line.split())):
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current_run[k].append(v)
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elif style == LogFile.STYLE_MULTI:
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if '=' not in line:
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in_data_section = False
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continue
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for k,v in kvpairs.findall(line):
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if k not in current_run:
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current_run[k] = [float(v)]
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else:
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current_run[k].append(float(v))
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class AvgChunkFile:
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"""Reads files generated by fix ave/chunk
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@ -7,6 +7,7 @@ EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples'
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DEFAULT_STYLE_EXAMPLE_LOG="melt/log.8Apr21.melt.g++.1"
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MULTI_STYLE_EXAMPLE_LOG="peptide/log.27Nov18.peptide.g++.1"
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AVG_CHUNK_FILE="VISCOSITY/profile.13Oct16.nemd.2d.g++.1"
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YAML_STYLE_EXAMPLE_LOG="yaml/log.7Apr22.yaml.g++.1"
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class Logfiles(unittest.TestCase):
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def testLogFileNotFound(self):
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@ -58,6 +59,27 @@ class Logfiles(unittest.TestCase):
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self.assertEqual(run0["Step"], list(range(0,350, 50)))
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def testYamlLogFile(self):
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log = LogFile(os.path.join(EXAMPLES_DIR, YAML_STYLE_EXAMPLE_LOG))
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self.assertEqual(len(log.runs), 2)
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run = log.runs[0]
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self.assertEqual(len(run.keys()), 12)
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self.assertIn("Step", run)
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self.assertIn("Temp", run)
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self.assertIn("E_vdwl", run)
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self.assertIn("E_coul", run)
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self.assertIn("E_bond", run)
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self.assertIn("E_angle", run)
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self.assertIn("Press", run)
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self.assertEqual(len(run["Step"]), 11)
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self.assertEqual(len(run["Temp"]), 11)
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self.assertEqual(len(run["E_vdwl"]), 11)
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self.assertEqual(len(run["E_coul"]), 11)
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self.assertEqual(len(run["E_bond"]), 11)
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self.assertEqual(len(run["E_angle"]), 11)
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self.assertEqual(len(run["Press"]), 11)
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self.assertEqual(log.runs[0]["Step"], [0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100])
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class AvgChunkFiles(unittest.TestCase):
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def testAvgChunkFileNotFound(self):
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