Downgrade to Version 2.0

environment.yml

@@ -3,4 +3,5 @@ channels:
 dependencies:
 - python
 - notebook
-- lammps =2023.08.02=*_2
+- lammps
+- mlip =2.0

in.my

@@ -10,7 +10,7 @@ variable        tdamp equal 0.1
 variable        seed index 826626413
 # Potential
 
-pair_style       mlip load_from=pot.almtp extrapolation_control=true extrapolation_control:threshold_break=10 extrapolation_control:threshold_save=2 extrapolation_control:save_extrapolative_to=out/preselected.cfg
+pair_style       mlip mlip.ini
 pair_coeff       * *
 
 group           bottom id 1:540

mlip.ini

@@ -0,0 +1,2 @@
+mtp-filename pot.almtp
+select FALSE

run.ipynb

@@ -1 +1 @@
-{"metadata":{"kernelspec":{"name":"python3","display_name":"Python 3 (ipykernel)","language":"python"},"language_info":{"name":"python","version":"3.11.5","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat_minor":5,"nbformat":4,"cells":[{"id":"c666d019-3478-4b2e-8823-a0c8f113574e","cell_type":"code","source":"!mpirun -n 4 lmp_mpi -in in.my","metadata":{"trusted":true},"outputs":[{"name":"stdout","text":"LAMMPS (2 Aug 2023)\n  using 6 OpenMP thread(s) per MPI task\nReading data file ...\n  orthogonal box = (0 0 0) to (39.571507 38.0777 40.436125)\n  2 by 2 by 1 MPI processor grid\n  reading atoms ...\n  1621 atoms\n  read_data CPU = 0.003 seconds\n540 atoms in group bottom\n540 atoms in group top\n540 atoms in group middle\n1 atoms in group addatom\nWrapper initialization\n\tabinitio = false\n\tcalculate_efs = true\n\tcheck_errors = false\n\textrapolation_control = true\n\tfit = false\n\tlotf = false\n\tmlip = true\n\tselect = false\n\twrite_cfgs = false\n\twrite_cfgs:skip = 0\n\tmlip:load_from = pot.almtp\nMLIP type is non-linear MTP\nSelection: loading state from \"pot.almtp\"\nSelection: loaded the following weights:\n\tenergy_weight = 0.000000\n\tforce_weight = 0.000000\n\tstress_weight = 0.000000\n\tsite_en_weight = 1.000000\n\nSelection: loading state complete.\n\tadd_grade_feature = true\n\tthreshold_break = 10.000000\n\tthreshold_save = 2.000000\n\tsave_extrapolative_to = out/preselected.cfg\nWrapper initialization complete\nNeighbor list info ...\n  update: every = 1 steps, delay = 5 steps, check = yes\n  max neighbors/atom: 2000, page size: 100000\n  master list distance cutoff = 8\n  ghost atom cutoff = 8\n  binsize = 4, bins = 10 10 11\n  1 neighbor lists, perpetual/occasional/extra = 1 0 0\n  (1) pair mlip, perpetual\n      attributes: full, newton on\n      pair build: full/bin/atomonly\n      stencil: full/bin/3d\n      bin: standard\nSetting up Verlet run ...\n  Unit style    : metal\n  Current step  : 0\n  Time step     : 0.001\nPer MPI rank memory allocation (min/avg/max) = 7.501 | 7.501 | 7.501 Mbytes\n   Step          Temp     \n         0   225.57766    \n\nRank 1, Breaking threshold exceeded (MV-grade: 12.188860) on 1 processor\n\n\n","output_type":"stream"}],"execution_count":1},{"id":"aafa21cf-b568-41d3-81b9-8c2d6ffe0e46","cell_type":"code","source":"!cat log.lammps","metadata":{"trusted":true},"outputs":[{"name":"stdout","text":"LAMMPS (2 Aug 2023)\n  using 6 OpenMP thread(s) per MPI task\n# Initialization\nunits           metal\nboundary        p p f\natom_style      atomic\nprocessors      * * 1\nvariable T equal 670.0\n# System and atom definition\nread_data       Cu_1621.data\nReading data file ...\n  orthogonal box = (0 0 0) to (39.571507 38.0777 40.436125)\n  2 by 2 by 1 MPI processor grid\n  reading atoms ...\n  1621 atoms\n  read_data CPU = 0.003 seconds\nvariable        tdamp equal 0.1\nvariable        seed index 826626413\n# Potential\n\npair_style       mlip load_from=pot.almtp extrapolation_control=true extrapolation_control:threshold_break=10 extrapolation_control:threshold_save=2 extrapolation_control:save_extrapolative_to=out/preselected.cfg\npair_coeff       * *\n\ngroup           bottom id 1:540\n540 atoms in group bottom\ngroup           top id 1081:1620\n540 atoms in group top\ngroup           middle id 541:1080\n540 atoms in group middle\ngroup           addatom id 1621\n1 atoms in group addatom\nneighbor        3 bin\nneigh_modify    every 1 delay 5 check yes\ntimestep        0.001\nvelocity        addatom set -0.033 0.05 -13  #Angstroms/picosecond  100m/s\nvelocity        top create ${T} ${seed} dist gaussian\nvelocity        top create 670 ${seed} dist gaussian\nvelocity        top create 670 826626413 dist gaussian\nfix             1 addatom nve\nfix             2 top nve\nfix             freeze bottom setforce 0.0 0.0 0.0\nfix             5 top wall/reflect zhi EDGE#wall reflection\nfix             6 middle nvt temp ${T} ${T} ${tdamp}\nfix             6 middle nvt temp 670 ${T} ${tdamp}\nfix             6 middle nvt temp 670 670 ${tdamp}\nfix             6 middle nvt temp 670 670 0.1\nfix             7 all wall/reflect zlo EDGE#wall reflection\nthermo_style    custom step temp\nthermo_modify   lost error\nthermo          100\ndump            1 all custom 1000 dump.trj id type x y z\nrun             5000\nNeighbor list info ...\n  update: every = 1 steps, delay = 5 steps, check = yes\n  max neighbors/atom: 2000, page size: 100000\n  master list distance cutoff = 8\n  ghost atom cutoff = 8\n  binsize = 4, bins = 10 10 11\n  1 neighbor lists, perpetual/occasional/extra = 1 0 0\n  (1) pair mlip, perpetual\n      attributes: full, newton on\n      pair build: full/bin/atomonly\n      stencil: full/bin/3d\n      bin: standard\nPer MPI rank memory allocation (min/avg/max) = 7.501 | 7.501 | 7.501 Mbytes\n   Step          Temp     \n         0   225.57766    \n","output_type":"stream"}],"execution_count":2},{"id":"cba34562-755a-4595-8683-b0ae22939426","cell_type":"code","source":"","metadata":{"trusted":true},"outputs":[],"execution_count":null}]}
+{"metadata":{"kernelspec":{"name":"python3","display_name":"Python 3 (ipykernel)","language":"python"},"language_info":{"name":"python","version":"3.11.6","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat_minor":5,"nbformat":4,"cells":[{"id":"c666d019-3478-4b2e-8823-a0c8f113574e","cell_type":"code","source":"!mpirun -n 4 lmp_mpi -in in.my","metadata":{"trusted":true},"outputs":[{"name":"stdout","text":"[jupyter-pyiron-2ddev-2dtest-2dlammps-2dmlip-2dokq1zopm:00731] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n[jupyter-pyiron-2ddev-2dtest-2dlammps-2dmlip-2dokq1zopm:00728] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n[jupyter-pyiron-2ddev-2dtest-2dlammps-2dmlip-2dokq1zopm:00730] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n[jupyter-pyiron-2ddev-2dtest-2dlammps-2dmlip-2dokq1zopm:00729] mca_base_component_repository_open: unable to open mca_btl_openib: librdmacm.so.1: cannot open shared object file: No such file or directory (ignored)\n--------------------------------------------------------------------------\nWARNING: Linux kernel CMA support was requested via the\nbtl_vader_single_copy_mechanism MCA variable, but CMA support is\nnot available due to restrictive ptrace settings.\n\nThe vader shared memory BTL will fall back on another single-copy\nmechanism if one is available. This may result in lower performance.\n\n  Local host: jupyter-pyiron-2ddev-2dtest-2dlammps-2dmlip-2dokq1zopm\n--------------------------------------------------------------------------\n[jupyter-pyiron-2ddev-2dtest-2dlammps-2dmlip-2dokq1zopm:00724] [[38808,0],0] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file util/show_help.c at line 501\n[jupyter-pyiron-2ddev-2dtest-2dlammps-2dmlip-2dokq1zopm:00724] [[38808,0],0] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file util/show_help.c at line 501\nLAMMPS (2 Aug 2023)\nOMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)\n  using 1 OpenMP thread(s) per MPI task\nReading data file ...\n  orthogonal box = (0 0 0) to (39.571507 38.0777 40.436125)\n  2 by 2 by 1 MPI processor grid\n  reading atoms ...\n  1621 atoms\n  read_data CPU = 0.177 seconds\n540 atoms in group bottom\n540 atoms in group top\n540 atoms in group middle\n1 atoms in group addatom\nNeighbor list info ...\n  update: every = 1 steps, delay = 5 steps, check = yes\n  max neighbors/atom: 2000, page size: 100000\n  master list distance cutoff = 8\n  ghost atom cutoff = 8\n  binsize = 4, bins = 10 10 11\n  1 neighbor lists, perpetual/occasional/extra = 1 0 0\n  (1) pair mlip, perpetual\n      attributes: full, newton on\n      pair build: full/bin/atomonly\n      stencil: full/bin/3d\n      bin: standard\nSetting up Verlet run ...\n  Unit style    : metal\n  Current step  : 0\n  Time step     : 0.001\nPer MPI rank memory allocation (min/avg/max) = 3.093 | 3.093 | 3.093 Mbytes\n   Step          Temp     \n         0   225.57766    \n[jupyter-pyiron-2ddev-2dtest-2dlammps-2dmlip-2dokq1zopm:00724] 1 more process has sent help message help-btl-vader.txt / cma-permission-denied\n[jupyter-pyiron-2ddev-2dtest-2dlammps-2dmlip-2dokq1zopm:00724] Set MCA parameter \"orte_base_help_aggregate\" to 0 to see all help / error messages\n       100   354.84347    \n       200   1459.2539    \n       300   2824.3611    \n       400   3294.0879    \n       500   3771.8024    \n       600   3790.0089    \n       700   3581.2988    \n       800   3145.8312    \n       900   2848.9314    \n      1000   2333.6073    \n      1100   1978.8378    \n      1200   1556.9616    \n      1300   1310.1331    \n      1400   1017.0994    \n      1500   898.88343    \n      1600   746.90851    \n      1700   644.98714    \n      1800   592.34997    \n      1900   556.44447    \n      2000   498.12865    \n      2100   466.43243    \n      2200   464.71889    \n      2300   462.99979    \n      2400   456.8836     \n      2500   453.23533    \n      2600   453.54766    \n      2700   468.63687    \n      2800   482.69992    \n      2900   480.10367    \n      3000   493.72072    \n      3100   452.47551    \n      3200   431.05951    \n      3300   436.39       \n      3400   436.51397    \n      3500   447.07811    \n      3600   444.0782     \n      3700   457.87751    \n      3800   458.75419    \n      3900   466.9895     \n      4000   456.13476    \n      4100   462.25806    \n      4200   448.37517    \n      4300   453.12526    \n      4400   445.56108    \n      4500   459.07224    \n      4600   469.94604    \n      4700   477.29289    \n      4800   466.16226    \n      4900   465.86151    \n      5000   471.59464    \nLoop time of 532.496 on 4 procs for 5000 steps with 1621 atoms\n\nPerformance: 0.811 ns/day, 29.583 hours/ns, 9.390 timesteps/s, 15.221 katom-step/s\n24.1% CPU use with 4 MPI tasks x 1 OpenMP threads\n\nMPI task timing breakdown:\nSection |  min time  |  avg time  |  max time  |%varavg| %total\n---------------------------------------------------------------\nPair    | 288.14     | 319.75     | 332.47     | 102.5 | 60.05\nNeigh   | 0.20011    | 0.34023    | 0.52387    |  20.5 |  0.06\nComm    | 191.11     | 203.74     | 235.22     | 127.7 | 38.26\nOutput  | 0.18422    | 0.18482    | 0.18595    |   0.2 |  0.03\nModify  | 6.9584     | 7.27       | 7.6549     |  11.6 |  1.37\nOther   |            | 1.213      |            |       |  0.23\n\nNlocal:         405.25 ave         418 max         377 min\nHistogram: 1 0 0 0 0 0 0 0 1 2\nNghost:            948 ave         974 max         937 min\nHistogram: 2 1 0 0 0 0 0 0 0 1\nNeighs:              0 ave           0 max           0 min\nHistogram: 4 0 0 0 0 0 0 0 0 0\nFullNghs:      64718.5 ave       68010 max       59128 min\nHistogram: 1 0 0 0 0 0 0 1 1 1\n\nTotal # of neighbors = 258874\nAve neighs/atom = 159.70019\nNeighbor list builds = 31\nDangerous builds = 0\nERROR: Cannot reset timestep with active dump - must undump first (src/output.cpp:640)\nLast command: reset_timestep  0\n--------------------------------------------------------------------------\nPrimary job  terminated normally, but 1 process returned\na non-zero exit code. Per user-direction, the job has been aborted.\n--------------------------------------------------------------------------\n--------------------------------------------------------------------------\nmpirun detected that one or more processes exited with non-zero status, thus causing\nthe job to be terminated. The first process to do so was:\n\n  Process name: [[38808,1],0]\n  Exit code:    1\n--------------------------------------------------------------------------\n","output_type":"stream"}],"execution_count":1},{"id":"aafa21cf-b568-41d3-81b9-8c2d6ffe0e46","cell_type":"code","source":"!cat log.lammps","metadata":{"trusted":true},"outputs":[{"name":"stdout","text":"LAMMPS (2 Aug 2023)\nOMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)\n  using 1 OpenMP thread(s) per MPI task\n# Initialization\nunits           metal\nboundary        p p f\natom_style      atomic\nprocessors      * * 1\nvariable T equal 670.0\n# System and atom definition\nread_data       Cu_1621.data\nReading data file ...\n  orthogonal box = (0 0 0) to (39.571507 38.0777 40.436125)\n  2 by 2 by 1 MPI processor grid\n  reading atoms ...\n  1621 atoms\n  read_data CPU = 0.177 seconds\nvariable        tdamp equal 0.1\nvariable        seed index 826626413\n# Potential\n\npair_style       mlip mlip.ini\npair_coeff       * *\n\ngroup           bottom id 1:540\n540 atoms in group bottom\ngroup           top id 1081:1620\n540 atoms in group top\ngroup           middle id 541:1080\n540 atoms in group middle\ngroup           addatom id 1621\n1 atoms in group addatom\nneighbor        3 bin\nneigh_modify    every 1 delay 5 check yes\ntimestep        0.001\nvelocity        addatom set -0.033 0.05 -13  #Angstroms/picosecond  100m/s\nvelocity        top create ${T} ${seed} dist gaussian\nvelocity        top create 670 ${seed} dist gaussian\nvelocity        top create 670 826626413 dist gaussian\nfix             1 addatom nve\nfix             2 top nve\nfix             freeze bottom setforce 0.0 0.0 0.0\nfix             5 top wall/reflect zhi EDGE#wall reflection\nfix             6 middle nvt temp ${T} ${T} ${tdamp}\nfix             6 middle nvt temp 670 ${T} ${tdamp}\nfix             6 middle nvt temp 670 670 ${tdamp}\nfix             6 middle nvt temp 670 670 0.1\nfix             7 all wall/reflect zlo EDGE#wall reflection\nthermo_style    custom step temp\nthermo_modify   lost error\nthermo          100\ndump            1 all custom 1000 dump.trj id type x y z\nrun             5000\nNeighbor list info ...\n  update: every = 1 steps, delay = 5 steps, check = yes\n  max neighbors/atom: 2000, page size: 100000\n  master list distance cutoff = 8\n  ghost atom cutoff = 8\n  binsize = 4, bins = 10 10 11\n  1 neighbor lists, perpetual/occasional/extra = 1 0 0\n  (1) pair mlip, perpetual\n      attributes: full, newton on\n      pair build: full/bin/atomonly\n      stencil: full/bin/3d\n      bin: standard\nPer MPI rank memory allocation (min/avg/max) = 3.093 | 3.093 | 3.093 Mbytes\n   Step          Temp     \n         0   225.57766    \n       100   354.84347    \n       200   1459.2539    \n       300   2824.3611    \n       400   3294.0879    \n       500   3771.8024    \n       600   3790.0089    \n       700   3581.2988    \n       800   3145.8312    \n       900   2848.9314    \n      1000   2333.6073    \n      1100   1978.8378    \n      1200   1556.9616    \n      1300   1310.1331    \n      1400   1017.0994    \n      1500   898.88343    \n      1600   746.90851    \n      1700   644.98714    \n      1800   592.34997    \n      1900   556.44447    \n      2000   498.12865    \n      2100   466.43243    \n      2200   464.71889    \n      2300   462.99979    \n      2400   456.8836     \n      2500   453.23533    \n      2600   453.54766    \n      2700   468.63687    \n      2800   482.69992    \n      2900   480.10367    \n      3000   493.72072    \n      3100   452.47551    \n      3200   431.05951    \n      3300   436.39       \n      3400   436.51397    \n      3500   447.07811    \n      3600   444.0782     \n      3700   457.87751    \n      3800   458.75419    \n      3900   466.9895     \n      4000   456.13476    \n      4100   462.25806    \n      4200   448.37517    \n      4300   453.12526    \n      4400   445.56108    \n      4500   459.07224    \n      4600   469.94604    \n      4700   477.29289    \n      4800   466.16226    \n      4900   465.86151    \n      5000   471.59464    \nLoop time of 532.496 on 4 procs for 5000 steps with 1621 atoms\n\nPerformance: 0.811 ns/day, 29.583 hours/ns, 9.390 timesteps/s, 15.221 katom-step/s\n24.1% CPU use with 4 MPI tasks x 1 OpenMP threads\n\nMPI task timing breakdown:\nSection |  min time  |  avg time  |  max time  |%varavg| %total\n---------------------------------------------------------------\nPair    | 288.14     | 319.75     | 332.47     | 102.5 | 60.05\nNeigh   | 0.20011    | 0.34023    | 0.52387    |  20.5 |  0.06\nComm    | 191.11     | 203.74     | 235.22     | 127.7 | 38.26\nOutput  | 0.18422    | 0.18482    | 0.18595    |   0.2 |  0.03\nModify  | 6.9584     | 7.27       | 7.6549     |  11.6 |  1.37\nOther   |            | 1.213      |            |       |  0.23\n\nNlocal:         405.25 ave         418 max         377 min\nHistogram: 1 0 0 0 0 0 0 0 1 2\nNghost:            948 ave         974 max         937 min\nHistogram: 2 1 0 0 0 0 0 0 0 1\nNeighs:              0 ave           0 max           0 min\nHistogram: 4 0 0 0 0 0 0 0 0 0\nFullNghs:      64718.5 ave       68010 max       59128 min\nHistogram: 1 0 0 0 0 0 0 1 1 1\n\nTotal # of neighbors = 258874\nAve neighs/atom = 159.70019\nNeighbor list builds = 31\nDangerous builds = 0\nreset_timestep  0\nERROR: Cannot reset timestep with active dump - must undump first (src/output.cpp:640)\nLast command: reset_timestep  0\n","output_type":"stream"}],"execution_count":2},{"id":"cba34562-755a-4595-8683-b0ae22939426","cell_type":"code","source":"","metadata":{"trusted":true},"outputs":[],"execution_count":null}]}