more debug tests with LATTE
This commit is contained in:
Steve Plimpton
@ -58,7 +58,7 @@ Build with regular make:
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% cd lammps/lib/mdi
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% python Install.py -m mpi
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% cd lammps/src
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% make yes-mdi
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% make yes-mdi yes-molecule
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% make mpi # creates lmp_mpi
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Build with CMake:
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@ -73,11 +73,10 @@ Copy the LAMMPS executable into this dir as lmp_mpi.
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Copy the LATTE executable LATTE_DOUBLE into this dir.
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The run commands below assume you have done this.
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LD_LIBRARY_PATH must include dir where MDI was built in (1) and put
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its libmdi.so file, e.g. mdi/build/MDI_Library. Else when
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LATTE_DOUBLE runs it won't be able to find it.
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(5) Insure LD_LIBRARY_PATH includes the dir where MDI was built in (1)
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with its libmdi.so file, e.g. mdi/build/MDI_Library. This is needed
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so when LATTE_DOUBLE runs as an executable it will able to find
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libmdi.so.
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------------------
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Notes on LATTE usage
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@ -49,9 +49,9 @@ WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms ma
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Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
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Step Temp PotEng TotEng Press
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0 0 -50.539035 -50.539035 -120855.2
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Loop time of 1.9199e-05 on 1 procs for 0 steps with 6 atoms
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Loop time of 2.018e-05 on 1 procs for 0 steps with 6 atoms
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7661.9% CPU use with 1 MPI tasks x no OpenMP threads
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7438.1% CPU use with 1 MPI tasks x no 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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@ -62,7 +62,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 1.92e-05 | | |100.00
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Other | | 2.018e-05 | | |100.00
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Nlocal: 6 ave 6 max 6 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -71,6 +71,166 @@ Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
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write_dump all custom dump.series.plugin.2uo2 id type x y z fx fy fz modify sort id
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clear
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next files
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jump SELF LOOP
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units metal
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atom_style full
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atom_modify sort 0 0.0
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read_data ${files}.lmp
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read_data 3uo2.lmp
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Reading data file ...
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triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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9 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.002 seconds
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neighbor 0.3 bin
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neigh_modify every 1 delay 0 check yes
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fix 1 all mdi/qm virial yes elements 92 8
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thermo_style custom step temp pe etotal press
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thermo 1
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mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
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run 0
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WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 0
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ghost atom cutoff = 0
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binsize = 16.2, bins = 1 1 1
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0 neighbor lists, perpetual/occasional/extra = 0 0 0
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WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
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Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
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Step Temp PotEng TotEng Press
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0 0 -78.155679 -78.155679 -99931.431
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Loop time of 8.472e-06 on 1 procs for 0 steps with 9 atoms
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0.0% CPU use with 1 MPI tasks x no 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 | 0 | 0 | 0 | 0.0 | 0.00
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Bond | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 8.472e-06 | | |100.00
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Nlocal: 9 ave 9 max 9 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3 ave 3 max 3 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
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write_dump all custom dump.series.plugin.3uo2 id type x y z fx fy fz modify sort id
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clear
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next files
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jump SELF LOOP
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units metal
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atom_style full
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atom_modify sort 0 0.0
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read_data ${files}.lmp
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read_data 4uo2.lmp
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Reading data file ...
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triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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12 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.001 seconds
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neighbor 0.3 bin
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neigh_modify every 1 delay 0 check yes
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fix 1 all mdi/qm virial yes elements 92 8
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thermo_style custom step temp pe etotal press
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thermo 1
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mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
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run 0
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WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 0
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ghost atom cutoff = 0
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binsize = 10.8, bins = 1 1 1
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0 neighbor lists, perpetual/occasional/extra = 0 0 0
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WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
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Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
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Step Temp PotEng TotEng Press
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0 0 -102.35713 -102.35713 -31036.168
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Loop time of 2.8666e-05 on 1 procs for 0 steps with 12 atoms
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7332.7% CPU use with 1 MPI tasks x no 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 | 0 | 0 | 0 | 0.0 | 0.00
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Bond | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 2.867e-05 | | |100.00
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Nlocal: 12 ave 12 max 12 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5 ave 5 max 5 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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Ave special neighs/atom = 0
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