From 83a91a4fab413f31e032ae537bbc034a6a3a2d3d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 5 Aug 2022 16:53:13 -0600 Subject: [PATCH] more debug tests with LATTE --- examples/QM/LATTE/README | 11 +- examples/QM/LATTE/log.series.mdi.plugin.1 | 166 +++++++++++++++++++++- 2 files changed, 168 insertions(+), 9 deletions(-) diff --git a/examples/QM/LATTE/README b/examples/QM/LATTE/README index b6f0cd7ce5..4bdd176ab3 100644 --- a/examples/QM/LATTE/README +++ b/examples/QM/LATTE/README @@ -58,7 +58,7 @@ Build with regular make: % cd lammps/lib/mdi % python Install.py -m mpi % cd lammps/src -% make yes-mdi +% make yes-mdi yes-molecule % make mpi # creates lmp_mpi Build with CMake: @@ -73,11 +73,10 @@ Copy the LAMMPS executable into this dir as lmp_mpi. Copy the LATTE executable LATTE_DOUBLE into this dir. The run commands below assume you have done this. - -LD_LIBRARY_PATH must include dir where MDI was built in (1) and put -its libmdi.so file, e.g. mdi/build/MDI_Library. Else when -LATTE_DOUBLE runs it won't be able to find it. - +(5) Insure LD_LIBRARY_PATH includes the dir where MDI was built in (1) +with its libmdi.so file, e.g. mdi/build/MDI_Library. This is needed +so when LATTE_DOUBLE runs as an executable it will able to find +libmdi.so. ------------------ Notes on LATTE usage diff --git a/examples/QM/LATTE/log.series.mdi.plugin.1 b/examples/QM/LATTE/log.series.mdi.plugin.1 index 688120b44b..53836b5011 100644 --- a/examples/QM/LATTE/log.series.mdi.plugin.1 +++ b/examples/QM/LATTE/log.series.mdi.plugin.1 @@ -49,9 +49,9 @@ WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms ma Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes Step Temp PotEng TotEng Press 0 0 -50.539035 -50.539035 -120855.2 -Loop time of 1.9199e-05 on 1 procs for 0 steps with 6 atoms +Loop time of 2.018e-05 on 1 procs for 0 steps with 6 atoms -7661.9% CPU use with 1 MPI tasks x no OpenMP threads +7438.1% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -62,7 +62,7 @@ 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 | | 1.92e-05 | | |100.00 +Other | | 2.018e-05 | | |100.00 Nlocal: 6 ave 6 max 6 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -71,6 +71,166 @@ Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id + write_dump all custom dump.series.plugin.2uo2 id type x y z fx fy fz modify sort id + + clear + +next files + +jump SELF LOOP + + units metal + atom_style full + atom_modify sort 0 0.0 + + read_data ${files}.lmp + read_data 3uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 9 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.002 seconds + + neighbor 0.3 bin + neigh_modify every 1 delay 0 check yes + + fix 1 all mdi/qm virial yes elements 92 8 + + thermo_style custom step temp pe etotal press + thermo 1 + + mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0" +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 16.2, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes + Step Temp PotEng TotEng Press + 0 0 -78.155679 -78.155679 -99931.431 +Loop time of 8.472e-06 on 1 procs for 0 steps with 9 atoms + +0.0% CPU use with 1 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 +Bond | 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 | | 8.472e-06 | | |100.00 + +Nlocal: 9 ave 9 max 9 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id + write_dump all custom dump.series.plugin.3uo2 id type x y z fx fy fz modify sort id + + clear + +next files + +jump SELF LOOP + + units metal + atom_style full + atom_modify sort 0 0.0 + + read_data ${files}.lmp + read_data 4uo2.lmp +Reading data file ... + triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 12 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + + neighbor 0.3 bin + neigh_modify every 1 delay 0 check yes + + fix 1 all mdi/qm virial yes elements 92 8 + + thermo_style custom step temp pe etotal press + thermo 1 + + mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0" +run 0 +WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 10.8, bins = 1 1 1 + 0 neighbor lists, perpetual/occasional/extra = 0 0 0 +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210) +Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes + Step Temp PotEng TotEng Press + 0 0 -102.35713 -102.35713 -31036.168 +Loop time of 2.8666e-05 on 1 procs for 0 steps with 12 atoms + +7332.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 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 | | 2.867e-05 | | |100.00 + +Nlocal: 12 ave 12 max 12 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5 ave 5 max 5 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + Total # of neighbors = 0 Ave neighs/atom = 0 Ave special neighs/atom = 0