added the reference log files for example inputs under PACKAGES/eff
This commit is contained in:
Trung Nguyen
@ -0,0 +1,90 @@
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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
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using 1 OpenMP thread(s) per MPI task
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variable sname index Be-solid
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units electron
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newton on
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boundary p p p
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atom_style electron
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read_data data.${sname}
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read_data data.Be-solid
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Reading data file ...
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orthogonal box = (0 0 0) to (64.288 63.628618 63.225)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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20160 atoms
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read_data CPU = 0.060 seconds
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pair_style eff/cut 31.6125
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pair_coeff * *
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comm_modify vel yes
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neigh_modify one 10000 page 100000
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compute effTemp all temp/eff
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thermo 10
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thermo_style custom step etotal pe ke temp press
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thermo_modify temp effTemp
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compute 1 all property/atom spin eradius
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dump 1 all custom 1 ${sname}.spe.lammpstrj id type x y z c_1[1] c_1[2]
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dump 1 all custom 1 Be-solid.spe.lammpstrj id type x y z c_1[1] c_1[2]
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fix 1 all nve/eff
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run 0
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
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|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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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: 10000, page size: 100000
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master list distance cutoff = 33.6125
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ghost atom cutoff = 33.6125
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binsize = 16.80625, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair eff/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) = 152.2 | 157 | 161.7 Mbytes
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Step TotEng PotEng KinEng Temp Press
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0 -49308.807 -49308.807 0 0 1.7906684e+11
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Loop time of 2.49575e-06 on 4 procs for 0 steps with 20160 atoms
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140.2% CPU use with 4 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 | 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 | | 2.496e-06 | | |100.00
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Nlocal: 5040 ave 5040 max 5040 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 97370 ave 97370 max 97370 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 3.11643e+07 ave 3.241e+07 max 2.99372e+07 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Total # of neighbors = 1.2465734e+08
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Ave neighs/atom = 6183.4
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:03
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118
examples/PACKAGES/eff/ECP/SiC/bulk/log.01Feb25.SiC.g++.4
Normal file
118
examples/PACKAGES/eff/ECP/SiC/bulk/log.01Feb25.SiC.g++.4
Normal file
@ -0,0 +1,118 @@
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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
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|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
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using 1 OpenMP thread(s) per MPI task
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variable sname index SiC
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variable nstep equal 100
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units electron
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newton on
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boundary p p p
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atom_style electron
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read_data data.${sname}
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read_data data.SiC
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Reading data file ...
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orthogonal box = (0 0 0) to (41.1 41.1 41.1)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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5000 atoms
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read_data CPU = 0.016 seconds
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pair_style eff/cut 20.0 limit/eradius pressure/evirials ecp 1 Si 2 C
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pair_coeff * *
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pair_coeff 1 s 0.320852 2.283269 0.814857
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pair_coeff 2 p 22.721015 0.728733 1.103199 17.695345 6.693621
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comm_modify vel yes
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neigh_modify one 4000 page 40000
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compute energies all pair eff/cut
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variable eke equal c_energies[1]
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variable epauli equal c_energies[2]
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variable ecoul equal c_energies[3]
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variable erres equal c_energies[4]
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variable etotalnew equal c_energies[1]+c_energies[2]+c_energies[3]+c_energies[4]
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thermo ${nstep}
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thermo 100
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thermo_style custom step etotal pe ke v_etotalnew v_eke v_epauli v_ecoul v_erres
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thermo_modify format float %16.8f
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thermo_modify lost warn norm yes flush yes
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# Minimization
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min_style cg
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dump 1 all xyz ${nstep} ${sname}.min.xyz
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dump 1 all xyz 100 ${sname}.min.xyz
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dump 1 all xyz 100 SiC.min.xyz
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compute 1 all property/atom spin eradius erforce
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dump 2 all custom ${nstep} ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
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dump 2 all custom 100 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
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dump 2 all custom 100 SiC.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
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dump 3 all custom ${nstep} ${sname}.data.restart id type q c_1[1] c_1[2] x y z
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dump 3 all custom 100 ${sname}.data.restart id type q c_1[1] c_1[2] x y z
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dump 3 all custom 100 SiC.data.restart id type q c_1[1] c_1[2] x y z
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min_modify line quadratic
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minimize 0 1e-8 100000 1000000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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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: 4000, page size: 40000
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master list distance cutoff = 22
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ghost atom cutoff = 22
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binsize = 11, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair eff/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) = 20.12 | 20.7 | 21.34 Mbytes
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Step TotEng PotEng KinEng v_etotalnew v_eke v_epauli v_ecoul v_erres
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0 -0.61266585 -0.61266585 0.00000000 -3063.32924433 2666.66666667 2055.59661323 -7785.59252422 0.00000000
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27 -0.87995767 -0.87995767 0.00000000 -4399.78836066 2569.46885777 446.25650389 -7415.51372232 0.00000000
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Loop time of 7.78522 on 4 procs for 27 steps with 5000 atoms
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|
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|
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
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|
Minimization stats:
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|
Stopping criterion = force tolerance
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Energy initial, next-to-last, final =
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|
-0.612665848866385 -0.879957672127075 -0.879957672129693
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Force two-norm initial, final = 254.76567 6.2598998e-09
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Force max component initial, final = 2.9077051 3.4450958e-10
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|
Final line search alpha, max atom move = 1 3.4450958e-10
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|
Iterations, force evaluations = 27 37
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|
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|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
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||||||
|
---------------------------------------------------------------
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Pair | 6.976 | 7.3573 | 7.6627 | 10.1 | 94.50
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.11037 | 0.41578 | 0.79718 | 42.4 | 5.34
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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 | | 0.0121 | | | 0.16
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|
|
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Nlocal: 1250 ave 1250 max 1250 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 25192 ave 25192 max 25192 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 1.9985e+06 ave 2.14947e+06 max 1.84582e+06 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Total # of neighbors = 7994000
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Ave neighs/atom = 1598.8
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Neighbor list builds = 0
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Dangerous builds = 0
|
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Total wall time: 0:00:08
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11
examples/PACKAGES/eff/ECP/SiH4/log.01Feb25.SiH4.ang.g++.4
Normal file
11
examples/PACKAGES/eff/ECP/SiH4/log.01Feb25.SiH4.ang.g++.4
Normal file
@ -0,0 +1,11 @@
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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
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using 1 OpenMP thread(s) per MPI task
|
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|
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# Created 2011-01-07
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# General parameters
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|
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variable sname index SiH4.ang
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log ${sname}.log
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log SiH4.ang.log
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11
examples/PACKAGES/eff/ECP/SiH4/log.01Feb25.SiH4.g++.4
Normal file
11
examples/PACKAGES/eff/ECP/SiH4/log.01Feb25.SiH4.g++.4
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
# Created 2011-01-07
|
||||||
|
|
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|
# General parameters
|
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|
|
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variable sname index SiH4
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log ${sname}.log
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log SiH4.log
|
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95
examples/PACKAGES/eff/H/log.01Feb25.h_atom.spe.ang.g++.4
Normal file
95
examples/PACKAGES/eff/H/log.01Feb25.h_atom.spe.ang.g++.4
Normal file
@ -0,0 +1,95 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index h_atom.ang
|
||||||
|
|
||||||
|
units real
|
||||||
|
newton on
|
||||||
|
boundary p p p
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|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.h_atom.ang
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4 atoms
|
||||||
|
read_data CPU = 0.000 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 0.529177249
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
timestep 0.0001
|
||||||
|
|
||||||
|
compute energies all pair eff/cut
|
||||||
|
variable eke equal c_energies[1]
|
||||||
|
variable epauli equal c_energies[2]
|
||||||
|
variable estatics equal c_energies[3]
|
||||||
|
variable errestrain equal c_energies[4]
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
thermo_modify temp effTemp press effPress
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.5291772
|
||||||
|
ghost atom cutoff = 2.5291772
|
||||||
|
binsize = 1.2645886, bins = 1 1 1
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.35 | 4.35 | 4.35 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 367.03102 367.03102 0 1882.5288 389.88475 -1905.3825 0 0 29191582 29191582
|
||||||
|
Loop time of 2.124e-06 on 4 procs for 0 steps with 4 atoms
|
||||||
|
|
||||||
|
70.6% CPU use with 4 MPI tasks x 1 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 | | 2.124e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 1 ave 4 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 549 ave 550 max 546 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 121.5 ave 486 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 486
|
||||||
|
Ave neighs/atom = 121.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
94
examples/PACKAGES/eff/H/log.01Feb25.h_atom.spe.bohr.g++.4
Normal file
94
examples/PACKAGES/eff/H/log.01Feb25.h_atom.spe.bohr.g++.4
Normal file
@ -0,0 +1,94 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index h_atom.bohr
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.h_atom.bohr
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-1 -1 -1) to (1 1 1)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2 atoms
|
||||||
|
read_data CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 1.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute energies all pair eff/cut
|
||||||
|
variable eke equal c_energies[1]
|
||||||
|
variable epauli equal c_energies[2]
|
||||||
|
variable estatics equal c_energies[3]
|
||||||
|
variable errestrain equal c_energies[4]
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
thermo_modify temp effTemp press effPress
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3
|
||||||
|
ghost atom cutoff = 3
|
||||||
|
binsize = 1.5, bins = 2 2 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.301 | 4.301 | 4.301 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 -0.095769122 -0.095769122 0 1.5 0 -1.5957691 0 0 0 0
|
||||||
|
Loop time of 2.4135e-06 on 4 procs for 0 steps with 2 atoms
|
||||||
|
|
||||||
|
0.0% CPU use with 4 MPI tasks x 1 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 | | 2.414e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 0.5 ave 2 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 159.5 ave 160 max 158 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 9.25 ave 37 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 37
|
||||||
|
Ave neighs/atom = 18.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
381
examples/PACKAGES/eff/H2/log.01Feb25.h2.g++.4
Normal file
381
examples/PACKAGES/eff/H2/log.01Feb25.h2.g++.4
Normal file
@ -0,0 +1,381 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index h2
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.h2
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (12.895936 12.895936 12.895936)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
128 atoms
|
||||||
|
read_data CPU = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 6.447968 pressure/evirials
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
min_style cg
|
||||||
|
min_modify line quadratic
|
||||||
|
minimize 0 1.0e-6 1000 2000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 8.447968
|
||||||
|
ghost atom cutoff = 8.447968
|
||||||
|
binsize = 4.223984, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.473 | 5.473 | 5.473 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -25.681592 0 -25.681592 4.1596728e+10
|
||||||
|
43 0 -29.402735 0 -29.402735 5.8094784e+10
|
||||||
|
Loop time of 0.00763171 on 4 procs for 43 steps with 128 atoms
|
||||||
|
|
||||||
|
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = force tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-25.6815917951629 -29.4027346945036 -29.4027347455099
|
||||||
|
Force two-norm initial, final = 0.90233034 1.9851971e-07
|
||||||
|
Force max component initial, final = 0.10428109 2.0171202e-08
|
||||||
|
Final line search alpha, max atom move = 1 2.0171202e-08
|
||||||
|
Iterations, force evaluations = 43 49
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0027162 | 0.0036134 | 0.0039713 | 0.9 | 47.35
|
||||||
|
Neigh | 4.3664e-05 | 4.9777e-05 | 5.6567e-05 | 0.0 | 0.65
|
||||||
|
Comm | 0.0030668 | 0.0034209 | 0.004339 | 0.9 | 44.82
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.0005477 | | | 7.18
|
||||||
|
|
||||||
|
Nlocal: 32 ave 32 max 32 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 928 ave 928 max 928 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2416 ave 2579 max 2253 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 9664
|
||||||
|
Ave neighs/atom = 75.5
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
region part block INF 2.0 INF 2.0 INF 5.0 units box
|
||||||
|
group sub id < 32
|
||||||
|
31 atoms in group sub
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
compute regionT sub temp/region/eff part
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
thermo_style custom step etotal pe ke temp press v_press c_regionT
|
||||||
|
thermo_modify temp effTemp press effPress
|
||||||
|
|
||||||
|
#velocity all create 300.0 4928459 rot yes dist gaussian
|
||||||
|
|
||||||
|
fix 3 all temp/rescale/eff 10 0.0 300.0 0.02 1.0
|
||||||
|
fix 1 all nve/eff
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.723 | 4.723 | 4.723 Mbytes
|
||||||
|
Step TotEng PotEng KinEng Temp Press v_press c_regionT
|
||||||
|
43 -29.402735 -29.402735 0 0 5.8094784e+10 5.8094784e+10 0
|
||||||
|
100 -29.402222 -29.402734 0.00051174152 1.71 5.811788e+10 5.8115522e+10 0.84298014
|
||||||
|
200 -29.401297 -29.402706 0.0014095337 4.71 5.8200069e+10 5.8193571e+10 2.2642129
|
||||||
|
300 -29.400299 -29.402606 0.0023073258 7.71 5.8313355e+10 5.8302716e+10 3.5188104
|
||||||
|
400 -29.399185 -29.40239 0.003205118 10.71 5.8450303e+10 5.8435537e+10 4.4975076
|
||||||
|
500 -29.397917 -29.40202 0.0041029101 13.71 5.8606915e+10 5.8588085e+10 5.0938111
|
||||||
|
600 -29.396468 -29.401468 0.0050007023 16.71 5.8780191e+10 5.8757458e+10 5.214099
|
||||||
|
700 -29.394823 -29.400721 0.0058984944 19.71 5.8967293e+10 5.8940983e+10 4.7987742
|
||||||
|
800 -29.392986 -29.399782 0.0067962866 22.71 5.9165038e+10 5.9135736e+10 3.8586623
|
||||||
|
900 -29.390985 -29.398679 0.0076940787 25.71 5.936952e+10 5.9338162e+10 2.5267164
|
||||||
|
1000 -29.388873 -29.397465 0.0085918709 28.71 5.9575808e+10 5.9543743e+10 1.1129096
|
||||||
|
1100 -29.386732 -29.396221 0.009489663 31.71 5.9777799e+10 5.9746754e+10 0.12904766
|
||||||
|
1200 -29.38466 -29.395047 0.010387455 34.71 5.9968346e+10 5.9940231e+10 0.23254239
|
||||||
|
1300 -29.382761 -29.394047 0.011285247 37.71 6.0139768e+10 6.0116306e+10 2.0555958
|
||||||
|
1400 -29.381123 -29.393306 0.012183039 40.71 6.0284712e+10 6.0267009e+10 5.9623931
|
||||||
|
1500 -29.379789 -29.39287 0.013080832 43.71 6.0397168e+10 6.0385416e+10 11.867131
|
||||||
|
1600 -29.378749 -29.392728 0.013978624 46.71 6.0473266e+10 6.0466731e+10 19.241519
|
||||||
|
1700 -29.377937 -29.392813 0.014876416 49.71 6.051158e+10 6.0508871e+10 27.309028
|
||||||
|
1800 -29.377239 -29.393013 0.015774208 52.71 6.0512895e+10 6.0512343e+10 35.292057
|
||||||
|
1900 -29.376517 -29.393189 0.016672 55.71 6.0479626e+10 6.0479611e+10 42.576307
|
||||||
|
2000 -29.375623 -29.393193 0.017569792 58.71 6.0415141e+10 6.0414287e+10 48.751559
|
||||||
|
2100 -29.374415 -29.392882 0.018467585 61.71 6.0323201e+10 6.0320436e+10 53.567423
|
||||||
|
2200 -29.372763 -29.392128 0.019365377 64.71 6.0207563e+10 6.0202104e+10 56.859803
|
||||||
|
2300 -29.370562 -29.390825 0.020263169 67.71 6.0071772e+10 6.0063077e+10 58.484447
|
||||||
|
2400 -29.367733 -29.388894 0.021160961 70.71 5.9919081e+10 5.9906793e+10 58.272649
|
||||||
|
2500 -29.36423 -29.386289 0.022058753 73.71 5.9752468e+10 5.9736389e+10 56.015194
|
||||||
|
2600 -29.360049 -29.383005 0.022956545 76.71 5.9574736e+10 5.9554816e+10 51.483979
|
||||||
|
2700 -29.355237 -29.379092 0.023854337 79.71 5.9388664e+10 5.9365044e+10 44.512157
|
||||||
|
2800 -29.349911 -29.374664 0.02475213 82.71 5.9197231e+10 5.9170319e+10 35.165882
|
||||||
|
2900 -29.344268 -29.369918 0.025649922 85.71 5.9003898e+10 5.8974484e+10 24.034217
|
||||||
|
3000 -29.338593 -29.365141 0.026547714 88.71 5.8812903e+10 5.8782274e+10 12.596437
|
||||||
|
3100 -29.333256 -29.360702 0.027445506 91.71 5.8629493e+10 5.8599437e+10 3.4545231
|
||||||
|
3200 -29.328661 -29.357004 0.028343298 94.71 5.8459894e+10 5.8432478e+10 0.016534267
|
||||||
|
3300 -29.325167 -29.354408 0.02924109 97.71 5.8310843e+10 5.828792e+10 5.3243002
|
||||||
|
3400 -29.322991 -29.35313 0.030138882 100.71 5.8188646e+10 5.8171288e+10 20.462635
|
||||||
|
3500 -29.322131 -29.353168 0.031036675 103.71 5.8098076e+10 5.8086277e+10 43.783703
|
||||||
|
3600 -29.322365 -29.3543 0.031934467 106.71 5.8041579e+10 5.8034437e+10 71.730426
|
||||||
|
3700 -29.323314 -29.356147 0.032832259 109.71 5.8019147e+10 5.8015336e+10 100.55288
|
||||||
|
3800 -29.32453 -29.35826 0.033730051 112.71 5.8028749e+10 5.8026989e+10 127.58755
|
||||||
|
3900 -29.325571 -29.360199 0.034627843 115.71 5.8067003e+10 5.8066317e+10 151.55747
|
||||||
|
4000 -29.326051 -29.361577 0.035525635 118.71 5.8129753e+10 5.8129529e+10 172.22883
|
||||||
|
4100 -29.325653 -29.362076 0.036423427 121.71 5.8212438e+10 5.8212365e+10 189.92431
|
||||||
|
4200 -29.324129 -29.36145 0.03732122 124.71 5.8310227e+10 5.8310175e+10 205.15122
|
||||||
|
4300 -29.321298 -29.359517 0.038219012 127.71 5.8417974e+10 5.8417851e+10 218.38021
|
||||||
|
4400 -29.317038 -29.356155 0.039116804 130.71 5.853006e+10 5.8529625e+10 229.92521
|
||||||
|
4500 -29.311285 -29.3513 0.040014596 133.71 5.8640135e+10 5.8638756e+10 239.8628
|
||||||
|
4600 -29.304036 -29.344948 0.040912388 136.71 5.8740796e+10 5.8737084e+10 247.94642
|
||||||
|
4700 -29.295358 -29.337168 0.04181018 139.71 5.8823225e+10 5.8814498e+10 253.48762
|
||||||
|
4800 -29.285407 -29.328115 0.042707973 142.71 5.8876834e+10 5.8858342e+10 255.20199
|
||||||
|
4900 -29.274456 -29.318062 0.043605765 145.71 5.8889029e+10 5.8852994e+10 251.07158
|
||||||
|
5000 -29.262921 -29.307424 0.044503557 148.71 5.8845331e+10 5.8780052e+10 238.3896
|
||||||
|
5100 -29.251383 -29.296784 0.045401349 151.71 5.8730207e+10 5.8619991e+10 214.32208
|
||||||
|
5200 -29.240581 -29.286881 0.046299141 154.71 5.8529067e+10 5.8356259e+10 177.37505
|
||||||
|
5300 -29.231338 -29.278535 0.047196933 157.71 5.8231557e+10 5.7981728e+10 129.63824
|
||||||
|
5400 -29.2244 -29.272495 0.048094725 160.71 5.783545e+10 5.7504658e+10 78.320218
|
||||||
|
5500 -29.220236 -29.269228 0.048992518 163.71 5.734924e+10 5.6948969e+10 34.221251
|
||||||
|
5600 -29.218882 -29.268773 0.04989031 166.71 5.6791455e+10 5.6346643e+10 6.9175951
|
||||||
|
5700 -29.219941 -29.270729 0.050788102 169.71 5.6186504e+10 5.5727327e+10 0.29716744
|
||||||
|
5800 -29.222711 -29.274397 0.051685894 172.71 5.5559255e+10 5.5112403e+10 12.070047
|
||||||
|
5900 -29.226384 -29.278968 0.052583686 175.71 5.4930986e+10 5.4515116e+10 36.620819
|
||||||
|
6000 -29.230194 -29.283676 0.053481478 178.71 5.4317798e+10 5.394343e+10 68.124786
|
||||||
|
6100 -29.233502 -29.287881 0.05437927 181.71 5.373093e+10 5.3402599e+10 102.15151
|
||||||
|
6200 -29.235817 -29.291094 0.055277063 184.71 5.317797e+10 5.2896659e+10 135.88236
|
||||||
|
6300 -29.236796 -29.29297 0.056174855 187.71 5.266419e+10 5.2429163e+10 167.68481
|
||||||
|
6400 -29.236229 -29.293302 0.057072647 190.71 5.2193678e+10 5.2003557e+10 196.5624
|
||||||
|
6500 -29.234036 -29.292006 0.057970439 193.71 5.1770207e+10 5.1623395e+10 221.67578
|
||||||
|
6600 -29.230262 -29.28913 0.058868231 196.71 5.1397868e+10 5.1292425e+10 241.95867
|
||||||
|
6700 -29.225101 -29.284867 0.059766023 199.71 5.1081526e+10 5.1014513e+10 255.81687
|
||||||
|
6800 -29.218918 -29.279582 0.060663816 202.71 5.0827088e+10 5.0793357e+10 260.95381
|
||||||
|
6900 -29.212279 -29.27384 0.061561608 205.71 5.0641515e+10 5.0632006e+10 254.493
|
||||||
|
7000 -29.20597 -29.26843 0.0624594 208.71 5.0532428e+10 5.0532428e+10 233.71509
|
||||||
|
7100 -29.200973 -29.264331 0.063357192 211.71 5.0507114e+10 5.0495687e+10 197.6792
|
||||||
|
7200 -29.198346 -29.262601 0.064254984 214.71 5.0570894e+10 5.0523214e+10 149.34022
|
||||||
|
7300 -29.199011 -29.264163 0.065152776 217.71 5.0725246e+10 5.061858e+10 96.508036
|
||||||
|
7400 -29.203489 -29.26954 0.066050568 220.71 5.0966567e+10 5.0787531e+10 49.67303
|
||||||
|
7500 -29.211725 -29.278674 0.066948361 223.71 5.1286493e+10 5.103478e+10 17.246635
|
||||||
|
7600 -29.223104 -29.29095 0.067846153 226.71 5.167383e+10 5.1359868e+10 1.9485991
|
||||||
|
7700 -29.236642 -29.305386 0.068743945 229.71 5.2117092e+10 5.1756034e+10 1.0837556
|
||||||
|
7800 -29.251244 -29.320885 0.069641737 232.71 5.2606457e+10 5.2212741e+10 9.4375813
|
||||||
|
7900 -29.265892 -29.336432 0.070539529 235.71 5.3134616e+10 5.2719209e+10 21.964752
|
||||||
|
8000 -29.279741 -29.351178 0.071437321 238.71 5.3696722e+10 5.3266678e+10 34.999087
|
||||||
|
8100 -29.292137 -29.364472 0.072335113 241.71 5.4289899e+10 5.3849048e+10 46.31642
|
||||||
|
8200 -29.3026 -29.375833 0.073232906 244.71 5.4912636e+10 5.4462542e+10 54.747327
|
||||||
|
8300 -29.310798 -29.384928 0.074130698 247.71 5.5564256e+10 5.510506e+10 59.766256
|
||||||
|
8400 -29.316514 -29.391542 0.07502849 250.71 5.6244467e+10 5.5775533e+10 61.201976
|
||||||
|
8500 -29.319632 -29.395559 0.075926282 253.71 5.6952997e+10 5.6473403e+10 59.079366
|
||||||
|
8600 -29.32013 -29.396954 0.076824074 256.71 5.7689238e+10 5.719821e+10 53.567555
|
||||||
|
8700 -29.318072 -29.395794 0.077721866 259.71 5.845187e+10 5.7949231e+10 45.014327
|
||||||
|
8800 -29.313622 -29.392241 0.078619658 262.71 5.923839e+10 5.8725125e+10 34.059265
|
||||||
|
8900 -29.307054 -29.386572 0.079517451 265.71 6.0044529e+10 5.9523495e+10 21.822776
|
||||||
|
9000 -29.298773 -29.379188 0.080415243 268.71 6.0863509e+10 6.0340317e+10 10.151211
|
||||||
|
9100 -29.289324 -29.370637 0.081313035 271.71 6.1685216e+10 6.1169112e+10 1.8420489
|
||||||
|
9200 -29.279397 -29.361608 0.082210827 274.71 6.2495436e+10 6.1999812e+10 0.66834686
|
||||||
|
9300 -29.269795 -29.352904 0.083108619 277.71 6.3275527e+10 6.2817393e+10 10.912705
|
||||||
|
9400 -29.261351 -29.345358 0.084006411 280.71 6.400305e+10 6.3600785e+10 36.169722
|
||||||
|
9500 -29.254801 -29.339705 0.084904204 283.71 6.4653796e+10 6.4323113e+10 77.605603
|
||||||
|
9600 -29.250616 -29.336418 0.085801996 286.71 6.520517e+10 6.4954574e+10 132.59334
|
||||||
|
9700 -29.248872 -29.335572 0.086699788 289.71 6.5640092e+10 6.5468097e+10 194.91905
|
||||||
|
9800 -29.249212 -29.33681 0.08759758 292.71 6.59499e+10 6.5845645e+10 256.81628
|
||||||
|
9900 -29.250911 -29.339406 0.088495372 295.71 6.6135085e+10 6.6081884e+10 311.59173
|
||||||
|
10000 -29.253024 -29.342417 0.089393164 298.71 6.6203807e+10 6.6183517e+10 355.23319
|
||||||
|
10043 -29.253759 -29.343588 0.089828702 300.16536 6.6201159e+10 6.6189815e+10 370.38327
|
||||||
|
Loop time of 1.04131 on 4 procs for 10000 steps with 128 atoms
|
||||||
|
|
||||||
|
Performance: 829720.937 fs/day, 0.000 hours/fs, 9603.252 timesteps/s, 1.229 Matom-step/s
|
||||||
|
90.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.43097 | 0.51117 | 0.59532 | 10.4 | 49.09
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.40178 | 0.48688 | 0.56619 | 10.6 | 46.76
|
||||||
|
Output | 0.0046624 | 0.0047434 | 0.0049664 | 0.2 | 0.46
|
||||||
|
Modify | 0.0074002 | 0.007613 | 0.0078044 | 0.2 | 0.73
|
||||||
|
Other | | 0.0309 | | | 2.97
|
||||||
|
|
||||||
|
Nlocal: 32 ave 32 max 32 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 928 ave 928 max 928 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2480 ave 2645 max 2315 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 9920
|
||||||
|
Ave neighs/atom = 77.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
unfix 3
|
||||||
|
|
||||||
|
#compute 1 all property/atom spin eradius
|
||||||
|
#fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0 drag 0.5
|
||||||
|
#dump 1 all custom 100 dump.file id type q c_1[1] c_1[2] x y z
|
||||||
|
|
||||||
|
#fix 1 all nve/eff
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.473 | 5.473 | 5.473 Mbytes
|
||||||
|
Step TotEng PotEng KinEng Temp Press v_press c_regionT
|
||||||
|
10043 -29.253759 -29.343588 0.089828702 300.16536 6.6201159e+10 6.6189815e+10 370.38327
|
||||||
|
10100 -29.253759 -29.344838 0.091079452 304.34478 6.6176296e+10 6.6172538e+10 389.80019
|
||||||
|
10200 -29.253759 -29.345711 0.091951632 307.2592 6.6052925e+10 6.6052773e+10 409.04715
|
||||||
|
10300 -29.253759 -29.344222 0.09046268 302.28382 6.5835973e+10 6.5829924e+10 406.94188
|
||||||
|
10400 -29.253759 -29.339884 0.086124587 287.78795 6.5537696e+10 6.5519727e+10 382.65817
|
||||||
|
10500 -29.253759 -29.33263 0.078870586 263.54848 6.5173326e+10 6.5140691e+10 337.96709
|
||||||
|
10600 -29.253759 -29.32285 0.069091456 230.87122 6.476052e+10 6.4713236e+10 277.25232
|
||||||
|
10700 -29.253759 -29.311365 0.057605907 192.4919 6.4318542e+10 6.4258684e+10 207.17514
|
||||||
|
10800 -29.253759 -29.299325 0.045566125 152.26061 6.3867235e+10 6.379814e+10 136.00177
|
||||||
|
10900 -29.253759 -29.288069 0.034309769 114.64714 6.3425834e+10 6.3351345e+10 72.65992
|
||||||
|
11000 -29.253759 -29.278938 0.025178778 84.135657 6.3011735e+10 6.2935563e+10 25.640652
|
||||||
|
11100 -29.253759 -29.273091 0.01933168 64.597401 6.2639343e+10 6.2564598e+10 1.8969587
|
||||||
|
11200 -29.253759 -29.271337 0.01757805 58.737592 6.2319122e+10 6.224804e+10 5.9017765
|
||||||
|
11300 -29.253759 -29.27402 0.02026083 67.702184 6.2056961e+10 6.1990807e+10 39.010867
|
||||||
|
11400 -29.253759 -29.280964 0.02720461 90.905038 6.1853928e+10 6.1793041e+10 99.231156
|
||||||
|
11500 -29.253759 -29.291496 0.037737065 126.09956 6.1706426e+10 6.1650353e+10 181.43067
|
||||||
|
11600 -29.253759 -29.304538 0.050778773 169.67883 6.1606742e+10 6.1554398e+10 277.95525
|
||||||
|
11700 -29.253759 -29.318745 0.064985916 217.15243 6.1543891e+10 6.1493702e+10 379.55439
|
||||||
|
11800 -29.253759 -29.332682 0.078922995 263.72361 6.1504653e+10 6.1454647e+10 476.47604
|
||||||
|
11900 -29.253759 -29.344999 0.091239641 304.88006 6.1474696e+10 6.1422513e+10 559.5746
|
||||||
|
12000 -29.253759 -29.354586 0.10082711 336.91689 6.1439645e+10 6.1382484e+10 621.28769
|
||||||
|
12100 -29.253759 -29.360694 0.10693515 357.32707 6.1386022e+10 6.1320551e+10 656.36975
|
||||||
|
12200 -29.253759 -29.362996 0.10923714 365.01925 6.1301987e+10 6.1224243e+10 662.31507
|
||||||
|
12300 -29.253759 -29.361599 0.10783979 360.34996 6.1177837e+10 6.1083188e+10 639.45046
|
||||||
|
12400 -29.253759 -29.357 0.10324072 344.98202 6.1006282e+10 6.0889481e+10 590.72007
|
||||||
|
12500 -29.253759 -29.350003 0.096243698 321.60127 6.0782503e+10 6.0637874e+10 521.21754
|
||||||
|
12600 -29.253759 -29.341604 0.087845122 293.53717 6.0504033e+10 6.032581e+10 437.54122
|
||||||
|
12700 -29.253759 -29.332866 0.079107181 264.33907 6.017052e+10 5.995332e+10 347.0566
|
||||||
|
12800 -29.253759 -29.324792 0.071033241 237.35975 5.9783407e+10 5.9522812e+10 257.14865
|
||||||
|
12900 -29.253759 -29.318218 0.064459023 215.3918 5.9345591e+10 5.9038771e+10 174.53724
|
||||||
|
13000 -29.253759 -29.313729 0.059970255 200.39245 5.8861097e+10 5.8507403e+10 104.71393
|
||||||
|
13100 -29.253759 -29.311613 0.057853612 193.31962 5.8334792e+10 5.7936245e+10 51.540581
|
||||||
|
13200 -29.253759 -29.311843 0.05808372 194.08853 5.777218e+10 5.7333762e+10 17.031706
|
||||||
|
13300 -29.253759 -29.314104 0.060345047 201.64482 5.7179263e+10 5.6708972e+10 1.3240561
|
||||||
|
13400 -29.253759 -29.317843 0.064084089 214.13895 5.6562484e+10 5.6071106e+10 2.82093
|
||||||
|
13500 -29.253759 -29.322344 0.068584649 229.17771 5.5928737e+10 5.542933e+10 18.484961
|
||||||
|
13600 -29.253759 -29.326816 0.073057273 244.12312 5.528542e+10 5.4792545e+10 44.242832
|
||||||
|
13700 -29.253759 -29.330492 0.076733214 256.40639 5.4640519e+10 5.4169259e+10 75.458518
|
||||||
|
13800 -29.253759 -29.332712 0.07895342 263.82528 5.4002682e+10 5.3567542e+10 107.42845
|
||||||
|
13900 -29.253759 -29.333003 0.079244028 264.79635 5.3381274e+10 5.2995036e+10 135.85235
|
||||||
|
14000 -29.253759 -29.33113 0.077371384 258.53885 5.2786371e+10 5.2459011e+10 157.23725
|
||||||
|
14100 -29.253759 -29.327131 0.073371666 245.17367 5.2228695e+10 5.196645e+10 169.19917
|
||||||
|
14200 -29.253759 -29.321311 0.06755247 225.72865 5.1719461e+10 5.1524114e+10 170.63669
|
||||||
|
14300 -29.253759 -29.314225 0.060466227 202.04975 5.1270133e+10 5.1138601e+10 161.76275
|
||||||
|
14400 -29.253759 -29.306617 0.052857773 176.62587 5.089211e+10 5.0816349e+10 143.99448
|
||||||
|
14500 -29.253759 -29.29935 0.045590774 152.34297 5.059633e+10 5.0563589e+10 119.71531
|
||||||
|
14600 -29.253759 -29.293319 0.039559773 132.1902 5.0392837e+10 5.0386251e+10 91.93698
|
||||||
|
14700 -29.253759 -29.289355 0.035596197 118.94579 5.029032e+10 5.0289808e+10 63.900552
|
||||||
|
14800 -29.253759 -29.288137 0.034377629 114.8739 5.029568e+10 5.0279104e+10 38.66315
|
||||||
|
14900 -29.253759 -29.290109 0.036349691 121.46361 5.0413636e+10 5.0358148e+10 18.71998
|
||||||
|
15000 -29.253759 -29.295428 0.041669069 139.23847 5.0646422e+10 5.0529927e+10 5.7077538
|
||||||
|
15100 -29.253759 -29.303933 0.050174363 167.65917 5.099359e+10 5.079623e+10 0.22655448
|
||||||
|
15200 -29.253759 -29.315148 0.061388837 205.13268 5.1451944e+10 5.1157502e+10 1.802684
|
||||||
|
15300 -29.253759 -29.328315 0.074555888 249.13079 5.2015605e+10 5.1612742e+10 8.997261
|
||||||
|
15400 -29.253759 -29.342464 0.088704628 296.40923 5.2676201e+10 5.2159429e+10 19.646426
|
||||||
|
15500 -29.253759 -29.356499 0.10273965 343.30769 5.3423173e+10 5.2793473e+10 31.201748
|
||||||
|
15600 -29.253759 -29.369305 0.11554633 386.10162 5.4244166e+10 5.3509204e+10 41.12616
|
||||||
|
15700 -29.253759 -29.37986 0.1261011 421.37071 5.5125447e+10 5.429932e+10 47.293231
|
||||||
|
15800 -29.253759 -29.387334 0.13357524 446.34577 5.6052334e+10 5.5154866e+10 48.336756
|
||||||
|
15900 -29.253759 -29.39118 0.13742108 459.19674 5.7009617e+10 5.6065206e+10 43.903332
|
||||||
|
16000 -29.253759 -29.39119 0.13743084 459.22936 5.798194e+10 5.7018034e+10 34.771959
|
||||||
|
16100 -29.253759 -29.38752 0.13376082 446.96588 5.8954112e+10 5.7999411e+10 22.820321
|
||||||
|
16200 -29.253759 -29.380676 0.12691686 424.09659 5.9911355e+10 5.8993881e+10 10.835339
|
||||||
|
16300 -29.253759 -29.37146 0.11770099 393.30145 6.083948e+10 5.9984681e+10 2.1841693
|
||||||
|
16400 -29.253759 -29.360882 0.10712336 357.956 6.1725019e+10 6.095406e+10 0.37905177
|
||||||
|
16500 -29.253759 -29.350047 0.096287961 321.74918 6.255531e+10 6.1883732e+10 8.5837627
|
||||||
|
16600 -29.253759 -29.340023 0.086263871 288.25337 6.3318582e+10 6.2755451e+10 29.119377
|
||||||
|
16700 -29.253759 -29.331716 0.077957034 260.49582 6.4004055e+10 6.3551677e+10 63.031437
|
||||||
|
16800 -29.253759 -29.325757 0.071998194 240.58417 6.460208e+10 6.4256316e+10 109.77858
|
||||||
|
16900 -29.253759 -29.322421 0.06866219 229.43681 6.5104343e+10 6.4855474e+10 167.09379
|
||||||
|
17000 -29.253759 -29.32159 0.067830842 226.65884 6.5504142e+10 6.5338169e+10 231.05378
|
||||||
|
17100 -29.253759 -29.322766 0.06900694 230.58881 6.5796723e+10 6.5696949e+10 296.37046
|
||||||
|
17200 -29.253759 -29.325139 0.071380489 238.52009 6.5979662e+10 6.5928378e+10 356.89258
|
||||||
|
17300 -29.253759 -29.3277 0.073941262 247.07699 6.6053264e+10 6.6033329e+10 406.27733
|
||||||
|
17400 -29.253759 -29.329384 0.075624794 252.70257 6.6020907e+10 6.6017081e+10 438.765
|
||||||
|
17500 -29.253759 -29.329232 0.075473164 252.19589 6.5889298e+10 6.5889197e+10 449.9672
|
||||||
|
17600 -29.253759 -29.326547 0.072788435 243.22479 6.5668557e+10 6.566317e+10 437.56505
|
||||||
|
17700 -29.253759 -29.321015 0.067255999 224.73798 6.537209e+10 6.5355863e+10 401.81223
|
||||||
|
17800 -29.253759 -29.312777 0.059017856 197.20998 6.5016192e+10 6.4986737e+10 345.75083
|
||||||
|
17900 -29.253759 -29.302441 0.048681923 162.67214 6.461938e+10 6.4576898e+10 275.07707
|
||||||
|
18000 -29.253759 -29.291021 0.037262252 124.51296 6.4201459e+10 6.4148001e+10 197.63846
|
||||||
|
18100 -29.253759 -29.279814 0.026055453 87.065095 6.3782375e+10 6.3721066e+10 122.59764
|
||||||
|
18200 -29.253759 -29.270228 0.016469061 55.031873 6.3380961e+10 6.3315275e+10 59.354773
|
||||||
|
18300 -29.253759 -29.263585 0.009826229 32.834645 6.3013664e+10 6.2946844e+10 16.367993
|
||||||
|
18400 -29.253759 -29.260935 0.0071761426 23.9793 6.2693422e+10 6.2628079e+10 0.04021999
|
||||||
|
18500 -29.253759 -29.262899 0.0091396789 30.540517 6.2428791e+10 6.2366686e+10 13.840884
|
||||||
|
18600 -29.253759 -29.269574 0.01581463 52.84507 6.2223448e+10 6.2165441e+10 57.800802
|
||||||
|
18700 -29.253759 -29.280514 0.026755117 89.403044 6.2076104e+10 6.2022224e+10 128.46082
|
||||||
|
18800 -29.253759 -29.294786 0.041027472 137.09456 6.1980858e+10 6.1930427e+10 219.28144
|
||||||
|
18900 -29.253759 -29.311091 0.057332365 191.57786 6.1927902e+10 6.1879682e+10 321.44654
|
||||||
|
19000 -29.253759 -29.327932 0.074172828 247.85078 6.1904521e+10 6.1856811e+10 424.935
|
||||||
|
19100 -29.253759 -29.343801 0.090041852 300.87761 6.1896231e+10 6.1846902e+10 519.70032
|
||||||
|
19200 -29.253759 -29.357361 0.10360217 346.18982 6.1887942e+10 6.1834406e+10 596.79434
|
||||||
|
19300 -29.253759 -29.367593 0.11383425 380.38063 6.1865031e+10 6.1804149e+10 649.29447
|
||||||
|
19400 -29.253759 -29.373894 0.12013535 401.43594 6.1814231e+10 6.1742208e+10 672.93539
|
||||||
|
19500 -29.253759 -29.37612 0.12236075 408.87221 6.1724294e+10 6.1636603e+10 666.39687
|
||||||
|
19600 -29.253759 -29.374566 0.12080701 403.68034 6.1586396e+10 6.1477781e+10 631.24827
|
||||||
|
19700 -29.253759 -29.369903 0.11614425 388.09956 6.1394308e+10 6.1258917e+10 571.59167
|
||||||
|
19800 -29.253759 -29.363069 0.10931013 365.26317 6.1144351e+10 6.0976023e+10 493.47418
|
||||||
|
19900 -29.253759 -29.35514 0.10138144 338.76918 6.0835203e+10 6.0627905e+10 404.15587
|
||||||
|
20000 -29.253759 -29.347199 0.093439728 312.23172 6.0467587e+10 6.0215993e+10 311.32317
|
||||||
|
20043 -29.253759 -29.344026 0.090267282 301.63089 6.0292085e+10 6.002012e+10 272.18496
|
||||||
|
Loop time of 1.02899 on 4 procs for 10000 steps with 128 atoms
|
||||||
|
|
||||||
|
Performance: 839654.865 fs/day, 0.000 hours/fs, 9718.228 timesteps/s, 1.244 Matom-step/s
|
||||||
|
91.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.42341 | 0.50618 | 0.59534 | 10.4 | 49.19
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.39233 | 0.48231 | 0.56438 | 10.7 | 46.87
|
||||||
|
Output | 0.0047128 | 0.0048033 | 0.0050386 | 0.2 | 0.47
|
||||||
|
Modify | 0.0052563 | 0.0055253 | 0.0058241 | 0.3 | 0.54
|
||||||
|
Other | | 0.03018 | | | 2.93
|
||||||
|
|
||||||
|
Nlocal: 32 ave 32 max 32 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 928 ave 928 max 928 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2416 ave 2582 max 2250 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 9664
|
||||||
|
Ave neighs/atom = 75.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
161
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.npt.g++.4
Normal file
161
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.npt.g++.4
Normal file
@ -0,0 +1,161 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index h2bulk
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.h2bulk
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (61.255694 61.255694 61.255694)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
13718 atoms
|
||||||
|
read_data CPU = 0.048 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 30.627847
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neigh_modify one 20000 page 200000
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
thermo_style custom step pe temp press vol
|
||||||
|
thermo_modify temp effTemp
|
||||||
|
|
||||||
|
# structure minimization
|
||||||
|
dump 1 all xyz 1 ${sname}.min.xyz
|
||||||
|
dump 1 all xyz 1 h2bulk.min.xyz
|
||||||
|
min_style cg
|
||||||
|
minimize 0 1.0e-4 1 10000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 20000, page size: 200000
|
||||||
|
master list distance cutoff = 32.627847
|
||||||
|
ghost atom cutoff = 32.627847
|
||||||
|
binsize = 16.313924, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 87.11 | 93.61 | 100.1 Mbytes
|
||||||
|
Step PotEng Temp Press Volume
|
||||||
|
0 -2871.4801 0 2.8596879e+10 229847.29
|
||||||
|
1 -2872.8077 0 2.8046824e+10 229847.29
|
||||||
|
Loop time of 1.02378 on 4 procs for 1 steps with 13718 atoms
|
||||||
|
|
||||||
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = max iterations
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-2871.48013813359 -2871.48013813359 -2872.8076730722
|
||||||
|
Force two-norm initial, final = 5.4264823 5.0563616
|
||||||
|
Force max component initial, final = 0.21424475 0.19518835
|
||||||
|
Final line search alpha, max atom move = 0.046675588 0.0091105311
|
||||||
|
Iterations, force evaluations = 1 1
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.7704 | 0.89228 | 1.0165 | 11.0 | 87.16
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0028288 | 0.12705 | 0.24891 | 29.2 | 12.41
|
||||||
|
Output | 0.0037898 | 0.0038794 | 0.0039584 | 0.1 | 0.38
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.0005774 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 3429.5 ave 3800 max 3078 min
|
||||||
|
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||||
|
Nghost: 65600.5 ave 67122 max 64060 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
Neighs: 1.49352e+07 ave 1.64494e+07 max 1.33918e+07 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 59740807
|
||||||
|
Ave neighs/atom = 4354.9211
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
undump 1
|
||||||
|
|
||||||
|
# create initial velocities according to temp, w/out e radial dof
|
||||||
|
velocity all create 20000.0 4928459 rot yes dist gaussian
|
||||||
|
|
||||||
|
# npt
|
||||||
|
fix 1 all npt/eff temp 20000.0 20000.0 1.0 iso 1e9 1e9 1.0
|
||||||
|
variable density equal 11.2058851*mass(all)
|
||||||
|
thermo_style custom step pe temp press vol v_density
|
||||||
|
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
|
||||||
|
thermo_modify temp effTemp
|
||||||
|
|
||||||
|
dump 2 all xyz 10000 ${sname}.npt.xyz
|
||||||
|
dump 2 all xyz 10000 h2bulk.npt.xyz
|
||||||
|
compute 1 all property/atom spin eradius
|
||||||
|
dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||||
|
dump 3 all custom 10000 h2bulk.npt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
run 10
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 79.61 | 86.11 | 92.6 Mbytes
|
||||||
|
Step PotEng Temp Press Volume v_density
|
||||||
|
1 -2872.8077 40002.916 1.392533e+11 229847.29 154332.61
|
||||||
|
2 -2872.8075 40002.808 1.3925254e+11 229847.72 154332.61
|
||||||
|
3 -2872.8072 40002.493 1.3925022e+11 229849.01 154332.61
|
||||||
|
4 -2872.8068 40001.97 1.3924633e+11 229851.15 154332.61
|
||||||
|
5 -2872.8064 40001.241 1.3924088e+11 229854.15 154332.61
|
||||||
|
6 -2872.8058 40000.304 1.3923386e+11 229858.01 154332.61
|
||||||
|
7 -2872.8052 39999.161 1.3922528e+11 229862.72 154332.61
|
||||||
|
8 -2872.8045 39997.81 1.3921514e+11 229868.29 154332.61
|
||||||
|
9 -2872.8037 39996.253 1.3920343e+11 229874.72 154332.61
|
||||||
|
10 -2872.8028 39994.488 1.3919016e+11 229882.01 154332.61
|
||||||
|
11 -2872.8018 39992.517 1.3917533e+11 229890.15 154332.61
|
||||||
|
Loop time of 10.5538 on 4 procs for 10 steps with 13718 atoms
|
||||||
|
|
||||||
|
Performance: 81.866 fs/day, 0.293 hours/fs, 0.948 timesteps/s, 12.998 katom-step/s
|
||||||
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 8.6596 | 9.2995 | 10.519 | 24.8 | 88.12
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.029706 | 1.2492 | 1.8893 | 67.7 | 11.84
|
||||||
|
Output | 0.00056676 | 0.00059312 | 0.00063847 | 0.0 | 0.01
|
||||||
|
Modify | 0.0017284 | 0.0019179 | 0.0020891 | 0.4 | 0.02
|
||||||
|
Other | | 0.002503 | | | 0.02
|
||||||
|
|
||||||
|
Nlocal: 3429.5 ave 3800 max 3078 min
|
||||||
|
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||||
|
Nghost: 65600.5 ave 67122 max 64060 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
Neighs: 1.49356e+07 ave 1.64691e+07 max 1.33702e+07 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 59742327
|
||||||
|
Ave neighs/atom = 4355.0319
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
unfix 1
|
||||||
|
undump 2
|
||||||
|
undump 3
|
||||||
|
Total wall time: 0:00:14
|
||||||
161
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.nve.ang.g++.4
Normal file
161
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.nve.ang.g++.4
Normal file
@ -0,0 +1,161 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index h2bulk.ang
|
||||||
|
|
||||||
|
units real
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.h2bulk.ang
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (32.41512 32.41512 32.41512)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
13718 atoms
|
||||||
|
read_data CPU = 0.039 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 16.207559818252903 limit/eradius pressure/evirials
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neigh_modify one 10000 page 100000
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
compute energies all pair eff/cut
|
||||||
|
variable eke equal c_energies[1]
|
||||||
|
variable epauli equal c_energies[2]
|
||||||
|
variable ecoul equal c_energies[3]
|
||||||
|
variable erres equal c_energies[4]
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
|
||||||
|
thermo_modify temp effTemp press effPress flush yes
|
||||||
|
|
||||||
|
# structure minimization
|
||||||
|
min_style cg
|
||||||
|
minimize 0 1.0e-4 10 10
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 10000, page size: 100000
|
||||||
|
master list distance cutoff = 18.20756
|
||||||
|
ghost atom cutoff = 18.20756
|
||||||
|
binsize = 9.1037799, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 99.9 | 106.9 | 113.6 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
|
||||||
|
0 -1801882.2 -1801882.2 0 1941449.2 111650.99 -3854982.4 0 169191.44 169191.44 0
|
||||||
|
10 -1812982.2 -1812982.2 0 2023531 93131.746 -3929644.9 0 204251.79 204251.79 0
|
||||||
|
Loop time of 11.8971 on 4 procs for 10 steps with 13718 atoms
|
||||||
|
|
||||||
|
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = max force evaluations
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-1801882.20439777 -1811783.39715666 -1812982.21160594
|
||||||
|
Force two-norm initial, final = 4976.0965 945.50616
|
||||||
|
Force max component initial, final = 134.44103 23.528388
|
||||||
|
Final line search alpha, max atom move = 0.0010624281 0.024997221
|
||||||
|
Iterations, force evaluations = 10 10
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 9.9682 | 10.823 | 11.655 | 22.1 | 90.97
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.23254 | 1.0651 | 1.9201 | 70.3 | 8.95
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.009102 | | | 0.08
|
||||||
|
|
||||||
|
Nlocal: 3429.5 ave 3800 max 3078 min
|
||||||
|
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||||
|
Nghost: 75372.5 ave 75724 max 75002 min
|
||||||
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||||
|
Neighs: 1.74322e+07 ave 1.91106e+07 max 1.57195e+07 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 69728955
|
||||||
|
Ave neighs/atom = 5083.0263
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
|
||||||
|
|
||||||
|
# nve
|
||||||
|
fix 1 all nve/eff
|
||||||
|
#fix 2 all imd 8888 trate 1 unwrap on nowait on
|
||||||
|
|
||||||
|
compute peatom all pe/atom
|
||||||
|
compute keatom all ke/atom/eff
|
||||||
|
|
||||||
|
dump 2 all xyz 1000 ${sname}.nve.xyz
|
||||||
|
dump 2 all xyz 1000 h2bulk.ang.nve.xyz
|
||||||
|
compute 1 all property/atom spin eradius
|
||||||
|
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
|
||||||
|
dump 3 all custom 1000 h2bulk.ang.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 101 | 105.7 | 110.5 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
|
||||||
|
10 -995226.78 -1812982.2 817755.43 2023531 93131.746 -3929644.9 0 1301774.2 1301774.2 40002.916
|
||||||
|
20 -995226.78 -1812951.8 817725.06 2023530.9 93136.224 -3929618.9 0 1301757.1 1301757.1 40001.431
|
||||||
|
Loop time of 9.29954 on 4 procs for 10 steps with 13718 atoms
|
||||||
|
|
||||||
|
Performance: 0.000 ns/day, 258320.521 hours/ns, 1.075 timesteps/s, 14.751 katom-step/s
|
||||||
|
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 8.5126 | 8.8333 | 9.1491 | 9.5 | 94.99
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.14252 | 0.45853 | 0.77938 | 41.7 | 4.93
|
||||||
|
Output | 0.0046943 | 0.0047097 | 0.0047198 | 0.0 | 0.05
|
||||||
|
Modify | 0.00051144 | 0.00055804 | 0.00059726 | 0.0 | 0.01
|
||||||
|
Other | | 0.002462 | | | 0.03
|
||||||
|
|
||||||
|
Nlocal: 3429.5 ave 3610 max 3249 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 75372.5 ave 75553 max 75192 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 1.74471e+07 ave 1.82017e+07 max 1.66315e+07 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 69788395
|
||||||
|
Ave neighs/atom = 5087.3593
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
unfix 1
|
||||||
|
#unfix 2
|
||||||
|
undump 2
|
||||||
|
undump 3
|
||||||
|
Total wall time: 0:00:24
|
||||||
150
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.nve.g++.4
Normal file
150
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.nve.g++.4
Normal file
@ -0,0 +1,150 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index h2bulk
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.h2bulk
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (61.255694 61.255694 61.255694)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
13718 atoms
|
||||||
|
read_data CPU = 0.036 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 30.627847
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neigh_modify one 10000 page 100000
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step pe temp press
|
||||||
|
thermo_modify temp effTemp
|
||||||
|
|
||||||
|
# structure minimization
|
||||||
|
min_style cg
|
||||||
|
minimize 0 1.0e-4 10 10
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 10000, page size: 100000
|
||||||
|
master list distance cutoff = 32.627847
|
||||||
|
ghost atom cutoff = 32.627847
|
||||||
|
binsize = 16.313924, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 86.33 | 92.54 | 98.55 Mbytes
|
||||||
|
Step PotEng Temp Press
|
||||||
|
0 -2871.4801 0 2.8596879e+10
|
||||||
|
10 -2882.3401 0 2.1869586e+10
|
||||||
|
Loop time of 11.6123 on 4 procs for 10 steps with 13718 atoms
|
||||||
|
|
||||||
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = max force evaluations
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-2871.48013813359 -2881.24844591398 -2882.34005034714
|
||||||
|
Force two-norm initial, final = 5.4264823 1.3218657
|
||||||
|
Force max component initial, final = 0.21424475 0.025681865
|
||||||
|
Final line search alpha, max atom move = 0.4402147 0.011305535
|
||||||
|
Iterations, force evaluations = 10 10
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 9.2083 | 10.221 | 11.528 | 31.2 | 88.02
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.07895 | 1.3856 | 2.3982 | 84.8 | 11.93
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.005564 | | | 0.05
|
||||||
|
|
||||||
|
Nlocal: 3429.5 ave 3800 max 3078 min
|
||||||
|
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||||
|
Nghost: 65600.5 ave 67122 max 64060 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
Neighs: 1.49352e+07 ave 1.64494e+07 max 1.33918e+07 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 59740807
|
||||||
|
Ave neighs/atom = 4354.9211
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
|
||||||
|
|
||||||
|
# nve
|
||||||
|
fix 1 all nve/eff
|
||||||
|
#fix 2 all imd 8888 trate 1 unwrap on nowait on
|
||||||
|
|
||||||
|
compute peatom all pe/atom
|
||||||
|
compute keatom all ke/atom/eff
|
||||||
|
|
||||||
|
dump 2 all xyz 1000 ${sname}.nve.xyz
|
||||||
|
dump 2 all xyz 1000 h2bulk.nve.xyz
|
||||||
|
compute 1 all property/atom spin eradius
|
||||||
|
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
|
||||||
|
dump 3 all custom 1000 h2bulk.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 82.52 | 87.21 | 91.69 Mbytes
|
||||||
|
Step PotEng Temp Press
|
||||||
|
10 -2882.3401 40002.916 1.3307606e+11
|
||||||
|
20 -2882.2908 40001.405 1.3306905e+11
|
||||||
|
Loop time of 9.25154 on 4 procs for 10 steps with 13718 atoms
|
||||||
|
|
||||||
|
Performance: 93.390 fs/day, 0.257 hours/fs, 1.081 timesteps/s, 14.828 katom-step/s
|
||||||
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 8.2948 | 8.675 | 8.9946 | 10.1 | 93.77
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.2531 | 0.57292 | 0.9531 | 39.5 | 6.19
|
||||||
|
Output | 3.7757e-05 | 5.7819e-05 | 7.5679e-05 | 0.0 | 0.00
|
||||||
|
Modify | 0.0005098 | 0.0005357 | 0.00055895 | 0.0 | 0.01
|
||||||
|
Other | | 0.002988 | | | 0.03
|
||||||
|
|
||||||
|
Nlocal: 3429.5 ave 3610 max 3249 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 65600.5 ave 66951 max 64250 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 1.49409e+07 ave 1.56765e+07 max 1.41457e+07 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 59763523
|
||||||
|
Ave neighs/atom = 4356.577
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
unfix 1
|
||||||
|
#unfix 2
|
||||||
|
undump 2
|
||||||
|
undump 3
|
||||||
|
Total wall time: 0:00:23
|
||||||
@ -0,0 +1,111 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index Li-dendritic
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.Li-dendritic
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (100.224 100.224 100.224)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
3456 atoms
|
||||||
|
read_data CPU = 0.023 seconds
|
||||||
|
#read_restart ${sname}.min.restart2
|
||||||
|
|
||||||
|
pair_style eff/cut 50.112
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step etotal pe ke temp press
|
||||||
|
thermo_modify temp effTemp
|
||||||
|
|
||||||
|
compute 1 all property/atom spin eradius
|
||||||
|
dump 1 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
dump 1 all custom 10 Li-dendritic.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
dump 2 all xyz 10 ${sname}.min.xyz
|
||||||
|
dump 2 all xyz 10 Li-dendritic.min.xyz
|
||||||
|
|
||||||
|
restart 10 ${sname}.nve.restart1 ${sname}.nve.restart2
|
||||||
|
restart 10 Li-dendritic.nve.restart1 ${sname}.nve.restart2
|
||||||
|
restart 10 Li-dendritic.nve.restart1 Li-dendritic.nve.restart2
|
||||||
|
|
||||||
|
#min_style cg
|
||||||
|
#min_modify line quadratic dmax 2.0
|
||||||
|
#minimize 0.0 1.0e-5 10000 100000
|
||||||
|
|
||||||
|
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||||
|
|
||||||
|
fix 1 all nve/eff
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 52.112
|
||||||
|
ghost atom cutoff = 52.112
|
||||||
|
binsize = 26.056, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 11.4 | 11.59 | 11.78 Mbytes
|
||||||
|
Step TotEng PotEng KinEng Temp Press
|
||||||
|
0 -5167.408 -5172.3316 4.9236061 1201.0429 -1.5761339e+09
|
||||||
|
10 -5167.408 -5172.3292 4.9211748 1200.4498 -1.5762759e+09
|
||||||
|
20 -5167.408 -5172.3219 4.9139105 1198.6778 -1.5767007e+09
|
||||||
|
30 -5167.408 -5172.3099 4.9019017 1195.7484 -1.5774041e+09
|
||||||
|
40 -5167.408 -5172.2933 4.885295 1191.6974 -1.5783794e+09
|
||||||
|
50 -5167.408 -5172.2723 4.8642936 1186.5744 -1.5796171e+09
|
||||||
|
60 -5167.408 -5172.2471 4.839155 1180.4422 -1.5811053e+09
|
||||||
|
70 -5167.408 -5172.2182 4.8101883 1173.3762 -1.5828297e+09
|
||||||
|
80 -5167.408 -5172.1857 4.7777514 1165.4637 -1.5847737e+09
|
||||||
|
90 -5167.408 -5172.1502 4.7422469 1156.8029 -1.5869184e+09
|
||||||
|
100 -5167.408 -5172.1121 4.7041183 1147.502 -1.5892434e+09
|
||||||
|
Loop time of 9.14099 on 4 procs for 100 steps with 3456 atoms
|
||||||
|
|
||||||
|
Performance: 945.193 fs/day, 0.025 hours/fs, 10.940 timesteps/s, 37.808 katom-step/s
|
||||||
|
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 7.0683 | 7.7216 | 8.7585 | 22.7 | 84.47
|
||||||
|
Neigh | 0.24686 | 0.25299 | 0.2618 | 1.2 | 2.77
|
||||||
|
Comm | 0.079533 | 1.1252 | 1.784 | 60.0 | 12.31
|
||||||
|
Output | 0.035036 | 0.03505 | 0.03506 | 0.0 | 0.38
|
||||||
|
Modify | 0.0014139 | 0.0014999 | 0.0015446 | 0.1 | 0.02
|
||||||
|
Other | | 0.004642 | | | 0.05
|
||||||
|
|
||||||
|
Nlocal: 864 ave 888 max 851 min
|
||||||
|
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||||
|
Nghost: 17185 ave 17198 max 17161 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||||
|
Neighs: 890568 ave 965810 max 799750 min
|
||||||
|
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 3562272
|
||||||
|
Ave neighs/atom = 1030.75
|
||||||
|
Neighbor list builds = 10
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:09
|
||||||
@ -0,0 +1,178 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index Li-dendritic
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.Li-dendritic
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (100.224 100.224 100.224)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
3456 atoms
|
||||||
|
read_data CPU = 0.016 seconds
|
||||||
|
#read_restart ${sname}.min.restart
|
||||||
|
|
||||||
|
pair_style eff/cut 50.112
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step pe temp press
|
||||||
|
thermo_modify temp effTemp press effPress
|
||||||
|
|
||||||
|
print "Starting minimizer"
|
||||||
|
Starting minimizer
|
||||||
|
min_style cg
|
||||||
|
|
||||||
|
compute 1 all property/atom spin eradius
|
||||||
|
#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q c_1[1] c_1[2]
|
||||||
|
#dump 2 all xyz 100 ${sname}.min.xyz
|
||||||
|
min_modify line quadratic dmax 0.05
|
||||||
|
minimize 0 1.0e-7 100 100
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 52.112
|
||||||
|
ghost atom cutoff = 52.112
|
||||||
|
binsize = 26.056, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 14.88 | 15.07 | 15.26 Mbytes
|
||||||
|
Step PotEng Temp Press
|
||||||
|
0 -5172.3316 0 -1.6720594e+09
|
||||||
|
10 -5199.5494 0 -1.6721099e+09
|
||||||
|
20 -5220.9343 0 -1.6720299e+09
|
||||||
|
30 -5238.4037 0 -1.6694987e+09
|
||||||
|
40 -5252.5928 0 -1.6515154e+09
|
||||||
|
50 -5263.7845 0 -1.5851579e+09
|
||||||
|
60 -5271.8051 0 -1.4304709e+09
|
||||||
|
70 -5275.1692 0 -1.2764647e+09
|
||||||
|
80 -5276.9804 0 -1.1135845e+09
|
||||||
|
87 -5277.5186 0 -1.0157231e+09
|
||||||
|
Loop time of 9.1237 on 4 procs for 87 steps with 3456 atoms
|
||||||
|
|
||||||
|
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = max force evaluations
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-5172.33158699748 -5277.50851484438 -5277.51857905665
|
||||||
|
Force two-norm initial, final = 10.47944 0.61719987
|
||||||
|
Force max component initial, final = 0.33333431 0.020508985
|
||||||
|
Final line search alpha, max atom move = 0.48148149 0.0098746969
|
||||||
|
Iterations, force evaluations = 87 101
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 7.2296 | 8.0451 | 8.9943 | 23.5 | 88.18
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.11943 | 1.0682 | 1.8834 | 64.3 | 11.71
|
||||||
|
Output | 0.00021247 | 0.00022521 | 0.00026234 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.01011 | | | 0.11
|
||||||
|
|
||||||
|
Nlocal: 864 ave 864 max 864 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 17185 ave 17185 max 17185 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 890568 ave 968400 max 812736 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 3562272
|
||||||
|
Ave neighs/atom = 1030.75
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_restart ${sname}.min.restart
|
||||||
|
write_restart Li-dendritic.min.restart
|
||||||
|
System init for write_restart ...
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
|
||||||
|
#undump 1
|
||||||
|
#undump 2
|
||||||
|
|
||||||
|
# NVT
|
||||||
|
reset_timestep 0
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
print "Starting nvt"
|
||||||
|
Starting nvt
|
||||||
|
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||||
|
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||||
|
dump 1 all custom 100 Li-dendritic.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||||
|
dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||||
|
dump 2 all xyz 100 Li-dendritic.nvt.xyz
|
||||||
|
restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
|
||||||
|
restart 100 Li-dendritic.nvt.restart1 ${sname}.nvt.restart2
|
||||||
|
restart 100 Li-dendritic.nvt.restart1 Li-dendritic.nvt.restart2
|
||||||
|
|
||||||
|
run 100
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 11.9 | 12.09 | 12.28 Mbytes
|
||||||
|
Step PotEng Temp Press
|
||||||
|
0 -5277.5186 0 -1.0157231e+09
|
||||||
|
10 -5277.5187 0.028803274 -1.0157155e+09
|
||||||
|
20 -5277.519 0.12372272 -1.0156917e+09
|
||||||
|
30 -5277.5195 0.29618333 -1.0156507e+09
|
||||||
|
40 -5277.5201 0.55263617 -1.0155924e+09
|
||||||
|
50 -5277.5206 0.8932531 -1.0155176e+09
|
||||||
|
60 -5277.521 1.3127021 -1.015428e+09
|
||||||
|
70 -5277.5211 1.8037418 -1.0153251e+09
|
||||||
|
80 -5277.5208 2.3644081 -1.0152094e+09
|
||||||
|
90 -5277.52 3.0093875 -1.0150781e+09
|
||||||
|
100 -5277.5187 3.7858675 -1.0149239e+09
|
||||||
|
Loop time of 8.47644 on 4 procs for 100 steps with 3456 atoms
|
||||||
|
|
||||||
|
Performance: 5096.477 fs/day, 0.005 hours/fs, 11.797 timesteps/s, 40.772 katom-step/s
|
||||||
|
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 6.8234 | 7.537 | 8.2853 | 24.1 | 88.92
|
||||||
|
Neigh | 0.023585 | 0.024246 | 0.024867 | 0.4 | 0.29
|
||||||
|
Comm | 0.15595 | 0.90456 | 1.6184 | 69.6 | 10.67
|
||||||
|
Output | 0.0032476 | 0.0032612 | 0.0032984 | 0.0 | 0.04
|
||||||
|
Modify | 0.0036078 | 0.0037554 | 0.0039448 | 0.2 | 0.04
|
||||||
|
Other | | 0.003634 | | | 0.04
|
||||||
|
|
||||||
|
Nlocal: 864 ave 881 max 834 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||||
|
Nghost: 17185 ave 17215 max 17168 min
|
||||||
|
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||||
|
Neighs: 890568 ave 976912 max 789323 min
|
||||||
|
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 3562272
|
||||||
|
Ave neighs/atom = 1030.75
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
undump 1
|
||||||
|
undump 2
|
||||||
|
|
||||||
|
Total wall time: 0:00:17
|
||||||
155
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.ang.g++.4
Normal file
155
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.ang.g++.4
Normal file
@ -0,0 +1,155 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index Li.ang
|
||||||
|
|
||||||
|
units real
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
dielectric 1.0
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.Li.ang
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (22.098442 22.098442 22.098442)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2000 atoms
|
||||||
|
read_data CPU = 0.014 seconds
|
||||||
|
#read_restart ${sname}.min.restart
|
||||||
|
|
||||||
|
pair_style eff/cut 11.049221 limit/eradius pressure/evirials
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
neigh_modify one 2000 page 20000
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
compute energies all pair eff/cut
|
||||||
|
variable eke equal c_energies[1]
|
||||||
|
variable epauli equal c_energies[2]
|
||||||
|
variable ecoul equal c_energies[3]
|
||||||
|
variable erres equal c_energies[4]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
|
||||||
|
thermo_modify temp effTemp press effPress flush yes
|
||||||
|
|
||||||
|
#min_style cg
|
||||||
|
#minimize 0 1e-6 100 1000
|
||||||
|
#write_restart ${sname}.min.restart
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
velocity all create 10.0 4928459 rot yes mom yes dist gaussian
|
||||||
|
fix 0 all temp/rescale/eff 1 10.0 3000.0 0.05 1.0
|
||||||
|
#fix 0 all langevin/eff 3000.0 3000.0 10.0 699483
|
||||||
|
fix 1 all nve/eff
|
||||||
|
|
||||||
|
run 200
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 20000
|
||||||
|
master list distance cutoff = 13.049221
|
||||||
|
ghost atom cutoff = 13.049221
|
||||||
|
binsize = 6.5246105, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.772 | 6.887 | 7.001 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
|
||||||
|
0 -1934872.7 -1934932.3 59.586393 1973239.1 9338.8528 -3917510.2 0 119790.47 119790.47 40.06012
|
||||||
|
100 -1932300.8 -1934539.4 2238.5734 1864086.1 9857.8379 -3808483.3 0 -100104.15 -105089 1505
|
||||||
|
200 -1929809.8 -1934272.1 4462.2726 1834011.6 10753.334 -3779037 0 -151616.13 -158905.6 3000
|
||||||
|
Loop time of 6.61662 on 4 procs for 200 steps with 2000 atoms
|
||||||
|
|
||||||
|
Performance: 0.013 ns/day, 1837.949 hours/ns, 30.227 timesteps/s, 60.454 katom-step/s
|
||||||
|
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 5.572 | 5.9389 | 6.2372 | 9.8 | 89.76
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.37051 | 0.66886 | 1.0359 | 29.2 | 10.11
|
||||||
|
Output | 0.00076947 | 0.00078111 | 0.00081552 | 0.0 | 0.01
|
||||||
|
Modify | 0.0035517 | 0.0038042 | 0.0040517 | 0.4 | 0.06
|
||||||
|
Other | | 0.004249 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 10252 ave 10252 max 10252 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 424625 ave 448237 max 400021 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 1698500
|
||||||
|
Ave neighs/atom = 849.25
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
unfix 0
|
||||||
|
unfix 1
|
||||||
|
|
||||||
|
fix 1 all nvt/eff temp 3000.0 3000.0 100.0
|
||||||
|
compute 1 all property/atom spin eradius ervel
|
||||||
|
dump 1 all custom 500 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
|
||||||
|
dump 1 all custom 500 Li.ang.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
|
||||||
|
|
||||||
|
run 500
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 7.522 | 7.656 | 7.751 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
|
||||||
|
200 -1929809.8 -1934272.1 4462.2726 1834011.6 10753.334 -3779037 0 -151616.13 -158905.6 3000
|
||||||
|
300 -1929902.8 -1934223.4 4320.5724 2031898.3 11427.685 -3977549.4 0 268725.75 262717.84 2904.7345
|
||||||
|
400 -1929360.3 -1935088.8 5728.4403 1850892.1 13473.172 -3799454 0 -105609.57 -118457.31 3851.2485
|
||||||
|
500 -1929066.1 -1935648.1 6581.9291 1901305.5 14887.365 -3851840.9 0 7045.2102 -9644.887 4425.0518
|
||||||
|
600 -1929593.6 -1934406.5 4812.986 2003446.8 16194.971 -3954048.4 0 221662.39 211620.13 3235.7857
|
||||||
|
700 -1930061.3 -1933572.3 3510.9499 1811788.7 18436.004 -3763797 0 -182749.21 -186750.23 2360.4227
|
||||||
|
Loop time of 16.6082 on 4 procs for 500 steps with 2000 atoms
|
||||||
|
|
||||||
|
Performance: 0.013 ns/day, 1845.351 hours/ns, 30.106 timesteps/s, 60.211 katom-step/s
|
||||||
|
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 12.79 | 14.632 | 16.232 | 32.8 | 88.10
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.35155 | 1.9504 | 3.7924 | 89.8 | 11.74
|
||||||
|
Output | 0.0034195 | 0.0035878 | 0.0038027 | 0.3 | 0.02
|
||||||
|
Modify | 0.01108 | 0.011237 | 0.0114 | 0.1 | 0.07
|
||||||
|
Other | | 0.01046 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 500 ave 520 max 480 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
Nghost: 10252 ave 10272 max 10232 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
Neighs: 426287 ave 457559 max 396571 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 1705148
|
||||||
|
Ave neighs/atom = 852.574
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:23
|
||||||
166
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.bohr.g++.4
Normal file
166
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.bohr.g++.4
Normal file
@ -0,0 +1,166 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
variable sname index Li.bohr
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton off
|
||||||
|
boundary p p p
|
||||||
|
dielectric 1.0
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.Li.bohr
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (41.76 41.76 41.76)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2000 atoms
|
||||||
|
read_data CPU = 0.006 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 20.88 limit/eradius pressure/evirials
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
neigh_modify one 2000 page 20000
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
compute energies all pair eff/cut
|
||||||
|
variable eke equal c_energies[1]
|
||||||
|
variable epauli equal c_energies[2]
|
||||||
|
variable estatics equal c_energies[3]
|
||||||
|
variable errestrain equal c_energies[4]
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain press v_press temp
|
||||||
|
thermo_modify temp effTemp press effPress
|
||||||
|
|
||||||
|
min_style cg
|
||||||
|
minimize 0 1e-6 100 200
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 20000
|
||||||
|
master list distance cutoff = 22.88
|
||||||
|
ghost atom cutoff = 22.88
|
||||||
|
binsize = 11.44, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/atomonly/newtoff
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 9.51 | 9.51 | 9.51 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Press v_press Temp
|
||||||
|
0 -3083.509 -3083.509 0 3144.5578 14.882406 -6242.9492 0 1.2112606e+10 1.2112606e+10 0
|
||||||
|
10 -3085.4657 -3085.4657 0 3062.6201 21.113244 -6169.199 0 1.797769e+09 1.797769e+09 0
|
||||||
|
20 -3085.9152 -3085.9152 0 3063.3218 21.843788 -6171.0808 0 1.9306772e+09 1.9306772e+09 0
|
||||||
|
30 -3086.103 -3086.103 0 3065.4937 21.7953 -6173.392 0 2.1693045e+09 2.1693045e+09 0
|
||||||
|
40 -3086.2065 -3086.2065 0 3062.3955 22.002457 -6170.6045 0 1.7527596e+09 1.7527596e+09 0
|
||||||
|
50 -3086.2558 -3086.2558 0 3059.7162 22.165243 -6168.1372 0 1.4005967e+09 1.4005967e+09 0
|
||||||
|
60 -3086.2823 -3086.2823 0 3061.7509 22.016476 -6170.0497 0 1.6419693e+09 1.6419693e+09 0
|
||||||
|
70 -3086.3068 -3086.3068 0 3063.1496 22.125331 -6171.5817 0 1.8371954e+09 1.8371954e+09 0
|
||||||
|
80 -3086.3286 -3086.3286 0 3063.4058 22.112083 -6171.8465 0 1.8595352e+09 1.8595352e+09 0
|
||||||
|
90 -3086.342 -3086.342 0 3062.6876 22.145517 -6171.1752 0 1.761838e+09 1.761838e+09 0
|
||||||
|
100 -3086.3493 -3086.3493 0 3061.4985 22.1758 -6170.0236 0 1.6034889e+09 1.6034889e+09 0
|
||||||
|
Loop time of 9.51021 on 4 procs for 100 steps with 2000 atoms
|
||||||
|
|
||||||
|
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = max iterations
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-3083.5089570212 -3086.34842671529 -3086.34926128553
|
||||||
|
Force two-norm initial, final = 3.4238461 0.15353209
|
||||||
|
Force max component initial, final = 0.15119069 0.017560878
|
||||||
|
Final line search alpha, max atom move = 0.75419179 0.01324427
|
||||||
|
Iterations, force evaluations = 100 191
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 8.8842 | 9.0722 | 9.2808 | 5.4 | 95.39
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.04463 | 0.04473 | 0.04481 | 0.0 | 0.47
|
||||||
|
Output | 0.00071317 | 0.00073223 | 0.0007793 | 0.0 | 0.01
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.3926 | | | 4.13
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 10252 ave 10252 max 10252 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 648158 ave 648158 max 648158 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2592632
|
||||||
|
Ave neighs/atom = 1296.316
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5
|
||||||
|
|
||||||
|
fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0
|
||||||
|
|
||||||
|
compute 1 all property/atom spin eradius
|
||||||
|
dump 1 all custom 100 ${sname}.spe.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
dump 1 all custom 100 Li.bohr.spe.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||||
|
|
||||||
|
run 100
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 8.76 | 8.76 | 8.76 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Press v_press Temp
|
||||||
|
100 -3086.3493 -3086.3493 0 3061.4985 22.1758 -6170.0236 0 1.6034889e+09 1.6034889e+09 0
|
||||||
|
110 -3085.709 -3086.35 0.64098668 3062.5195 22.168933 -6171.0384 0 1.9130428e+09 1.8610249e+09 270.41729
|
||||||
|
120 -3084.995 -3086.3497 1.3546418 3064.69 22.151949 -6173.1916 0 2.3968054e+09 2.2869572e+09 571.49172
|
||||||
|
130 -3084.2774 -3086.3449 2.0675114 3067.5683 22.125927 -6176.0391 0 2.9762332e+09 2.8088108e+09 872.23471
|
||||||
|
140 -3083.5543 -3086.3327 2.7783319 3071.0091 22.090343 -6179.4321 0 3.6318905e+09 3.4073653e+09 1172.1133
|
||||||
|
150 -3082.8209 -3086.3101 3.4891918 3074.9323 22.044189 -6183.2866 0 4.3538347e+09 4.0726292e+09 1472.0085
|
||||||
|
160 -3082.0735 -3086.274 4.2005492 3079.2855 21.986186 -6187.5458 0 5.1353281e+09 4.7979569e+09 1772.1135
|
||||||
|
170 -3081.3099 -3086.2215 4.911672 3084.0302 21.914874 -6192.1667 0 5.9710184e+09 5.5781934e+09 2072.1196
|
||||||
|
180 -3080.5276 -3086.1495 5.6218934 3089.1358 21.828679 -6197.1139 0 6.8564778e+09 6.4091119e+09 2371.7454
|
||||||
|
190 -3079.7237 -3086.0546 6.330928 3094.5768 21.725972 -6202.3574 0 7.787914e+09 7.2871001e+09 2670.8705
|
||||||
|
200 -3078.895 -3085.9337 7.0387107 3100.3318 21.605131 -6207.8707 0 8.7619059e+09 8.2089091e+09 2969.4675
|
||||||
|
Loop time of 5.34836 on 4 procs for 100 steps with 2000 atoms
|
||||||
|
|
||||||
|
Performance: 1615.450 fs/day, 0.015 hours/fs, 18.697 timesteps/s, 37.395 katom-step/s
|
||||||
|
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 4.8621 | 5.065 | 5.2272 | 5.9 | 94.70
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.02486 | 0.025085 | 0.025316 | 0.1 | 0.47
|
||||||
|
Output | 0.0016755 | 0.0018282 | 0.0019368 | 0.2 | 0.03
|
||||||
|
Modify | 0.092978 | 0.25534 | 0.4584 | 26.2 | 4.77
|
||||||
|
Other | | 0.00111 | | | 0.02
|
||||||
|
|
||||||
|
Nlocal: 500 ave 518 max 484 min
|
||||||
|
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||||
|
Nghost: 10252 ave 10268 max 10234 min
|
||||||
|
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||||
|
Neighs: 621113 ave 642857 max 604509 min
|
||||||
|
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 2484453
|
||||||
|
Ave neighs/atom = 1242.2265
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:15
|
||||||
1165
examples/PACKAGES/eff/fixed-core/C2H6/log.01Feb25.C2H6fc.ang.g++.4
Normal file
1165
examples/PACKAGES/eff/fixed-core/C2H6/log.01Feb25.C2H6fc.ang.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,158 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
# Created 2010-12-13
|
||||||
|
|
||||||
|
# General parameters
|
||||||
|
|
||||||
|
variable sname index C2H6fc.bohr
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary f f f
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.C2H6fc.bohr
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
22 atoms
|
||||||
|
read_data CPU = 0.000 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 1000.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
compute energies all pair eff/cut
|
||||||
|
variable eke equal c_energies[1]
|
||||||
|
variable epauli equal c_energies[2]
|
||||||
|
variable estatics equal c_energies[3]
|
||||||
|
variable errestrain equal c_energies[4]
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
thermo_modify temp effTemp press effPress
|
||||||
|
|
||||||
|
# Minimization
|
||||||
|
|
||||||
|
min_style cg
|
||||||
|
dump 1 all xyz 10 ${sname}.min.xyz
|
||||||
|
dump 1 all xyz 10 C2H6fc.bohr.min.xyz
|
||||||
|
compute 1 all property/atom spin eradius erforce
|
||||||
|
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||||
|
dump 2 all custom 10 C2H6fc.bohr.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||||
|
dump 3 all custom 10 data.${sname}.restart id type q c_1[1] c_1[2] x y z
|
||||||
|
dump 3 all custom 10 data.C2H6fc.bohr.restart id type q c_1[1] c_1[2] x y z
|
||||||
|
min_modify line quadratic
|
||||||
|
minimize 0 1e-6 1000 2000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 1002
|
||||||
|
ghost atom cutoff = 1002
|
||||||
|
binsize = 501, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.129 | 6.129 | 6.129 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 -67.202286 -67.202286 0 65.187662 2.0185521 -134.4085 0 0 15.150502 15.150502
|
||||||
|
48 -67.202342 -67.202342 0 65.186464 2.0145106 -134.40332 0 0 -0.00017005462 -0.00017005462
|
||||||
|
Loop time of 0.00261219 on 4 procs for 48 steps with 22 atoms
|
||||||
|
|
||||||
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = force tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-67.202286382145 -67.2023415752272 -67.2023415752273
|
||||||
|
Force two-norm initial, final = 0.0096326869 5.0767445e-07
|
||||||
|
Force max component initial, final = 0.0062811481 1.588169e-07
|
||||||
|
Final line search alpha, max atom move = 1 1.588169e-07
|
||||||
|
Iterations, force evaluations = 48 94
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.00010749 | 0.00066682 | 0.0010722 | 0.0 | 25.53
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0005904 | 0.0010031 | 0.0015945 | 1.2 | 38.40
|
||||||
|
Output | 0.00029404 | 0.00030533 | 0.0003226 | 0.0 | 11.69
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 0.0006369 | | | 24.38
|
||||||
|
|
||||||
|
Nlocal: 5.5 ave 6 max 5 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 16.5 ave 17 max 16 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 57.75 ave 92 max 13 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 231
|
||||||
|
Ave neighs/atom = 10.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
undump 1
|
||||||
|
undump 2
|
||||||
|
undump 3
|
||||||
|
|
||||||
|
fix 1 all nvt/eff temp 1 2000 1.0
|
||||||
|
dump 2 all custom 10 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||||
|
dump 2 all custom 10 C2H6fc.bohr.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||||
|
|
||||||
|
run 10000
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.738 | 5.738 | 5.738 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
48 -67.202342 -67.202342 0 65.186464 2.0145106 -134.40332 0 0 -0.00017005463 -0.00017005463
|
||||||
|
10048 -67.202342 -67.202342 1.2683664e-08 65.186455 2.0144921 -134.40329 0 0.00038144568 -0.070540027 -0.070540735
|
||||||
|
Loop time of 0.194625 on 4 procs for 10000 steps with 22 atoms
|
||||||
|
|
||||||
|
Performance: 4439300.953 fs/day, 0.000 hours/fs, 51380.798 timesteps/s, 1.130 Matom-step/s
|
||||||
|
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0161 | 0.064789 | 0.10999 | 14.0 | 33.29
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.031236 | 0.07675 | 0.12576 | 13.2 | 39.43
|
||||||
|
Output | 0.01923 | 0.021471 | 0.025663 | 1.7 | 11.03
|
||||||
|
Modify | 0.011945 | 0.014438 | 0.017136 | 1.6 | 7.42
|
||||||
|
Other | | 0.01718 | | | 8.83
|
||||||
|
|
||||||
|
Nlocal: 5.5 ave 7 max 4 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
Nghost: 16.5 ave 18 max 15 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
Neighs: 57.75 ave 98 max 16 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 231
|
||||||
|
Ave neighs/atom = 10.5
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
40165
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.ang.g++.4
Normal file
40165
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.ang.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
4166
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.bohr.g++.4
Normal file
4166
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.bohr.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,100 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Created 2010-11-28
|
||||||
|
|
||||||
|
# General parameters
|
||||||
|
|
||||||
|
variable sname index CH4fc.ang
|
||||||
|
|
||||||
|
units real
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.CH4fc.ang
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-529.17725 -529.17725 -529.17725) to (529.17725 529.17725 529.17725)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
13 atoms
|
||||||
|
read_data CPU = 0.000 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 1000.0 limit/eradius pressure/evirials
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
compute energies all pair eff/cut
|
||||||
|
variable eke equal c_energies[1]
|
||||||
|
variable epauli equal c_energies[2]
|
||||||
|
variable estatics equal c_energies[3]
|
||||||
|
variable errestrain equal c_energies[4]
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
timestep 0.0001
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
thermo_modify temp effTemp press effPress
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 1002
|
||||||
|
ghost atom cutoff = 1002
|
||||||
|
binsize = 501, bins = 3 3 3
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.387 | 4.387 | 4.387 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 -17700.537 -17700.537 0 20676.282 6270.6707 -44647.489 0 0 0.21737096 0.21737096
|
||||||
|
Loop time of 2.41775e-06 on 4 procs for 0 steps with 13 atoms
|
||||||
|
|
||||||
|
113.7% CPU use with 4 MPI tasks x 1 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 | | 2.418e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 3.25 ave 4 max 3 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 152.75 ave 153 max 152 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 19.5 ave 33 max 6 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 78
|
||||||
|
Ave neighs/atom = 6
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
@ -0,0 +1,99 @@
|
|||||||
|
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Created 2010-11-28
|
||||||
|
|
||||||
|
# General parameters
|
||||||
|
|
||||||
|
variable sname index CH4fc.bohr
|
||||||
|
|
||||||
|
units electron
|
||||||
|
newton on
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
atom_style electron
|
||||||
|
|
||||||
|
read_data data.${sname}
|
||||||
|
read_data data.CH4fc.bohr
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
13 atoms
|
||||||
|
read_data CPU = 0.000 seconds
|
||||||
|
|
||||||
|
pair_style eff/cut 1000.0 limit/eradius pressure/evirials
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
compute energies all pair eff/cut
|
||||||
|
variable eke equal c_energies[1]
|
||||||
|
variable epauli equal c_energies[2]
|
||||||
|
variable estatics equal c_energies[3]
|
||||||
|
variable errestrain equal c_energies[4]
|
||||||
|
|
||||||
|
comm_modify vel yes
|
||||||
|
|
||||||
|
compute peratom all stress/atom NULL
|
||||||
|
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||||
|
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||||
|
|
||||||
|
compute effTemp all temp/eff
|
||||||
|
compute effPress all pressure effTemp
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||||
|
thermo_modify temp effTemp press effPress
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
- EFF package: doi:10.1002/jcc.21637
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 1002
|
||||||
|
ghost atom cutoff = 1002
|
||||||
|
binsize = 501, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair eff/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.388 | 4.388 | 4.388 Mbytes
|
||||||
|
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||||
|
0 -28.207572 -28.207572 0 32.949786 9.9929585 -71.150317 0 0 22025.158 22025.158
|
||||||
|
Loop time of 2.353e-06 on 4 procs for 0 steps with 13 atoms
|
||||||
|
|
||||||
|
53.1% CPU use with 4 MPI tasks x 1 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 | | 2.353e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 3.25 ave 4 max 3 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 152.75 ave 153 max 152 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 19.5 ave 31 max 10 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 78
|
||||||
|
Ave neighs/atom = 6
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
Reference in New Issue
Block a user