Added example input files for fix pimdb/nvt and fix pimdb/langevin
This commit is contained in:
Ofir Blumer
11
examples/PACKAGES/pimdb/README
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11
examples/PACKAGES/pimdb/README
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@ -0,0 +1,11 @@
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This directory contains example input files for the pimdb/nvt and pimdb/langevin fix commands.
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The demonstrated system is that of 3 non-interacting bosons in an harmonic trap.
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The input files initiate a simulation of 100 steps using 4 beads. The expected output log files are included.
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The input files can be edited to provide a physically meaningfull output, by extending the simulations to a few nanoseconds
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and increasing the number of beads (32 beads should be enough).
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The total energy can be computed by summing the potential energy and either the virial or primitive kinetic energy estimator, and averaging over time.
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Notice that for pimdb/langevin the summed value of either kinetic estimator is printed across all log files.
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It should be taken from a single log file, with all files providing the same output.
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For pimdb/nvt, one has to sum over the output of all log files. For the potentiak energy, summing over log files is required for both fix commands.
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The obtained energy should be compared to the analytical value of 0.00058031 Hartree.
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57
examples/PACKAGES/pimdb/harmonic_trap_langevin/in.lmp
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57
examples/PACKAGES/pimdb/harmonic_trap_langevin/in.lmp
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@ -0,0 +1,57 @@
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# Units and dimensions
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units electron
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dimension 3
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boundary p p p
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atom_style atomic
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atom_modify map yes
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pair_style none
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# Time step (in femtoseconds)
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timestep 0.5
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# Temperature (in Kelvin)
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variable Temp equal 17.4
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# Force constant (in Hartree energies per Bohr radius squared)
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variable k equal 1.2154614120000001e-08
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# Number of beads
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variable Nbeads equal 4
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variable ibead uloop ${Nbeads} pad
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variable seed equal 18889
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# Create box and atoms. All distances are in Bohr
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region box block -1500 1500 -1500 1500 -1500 1500
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create_box 1 box
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variable a loop 3
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label loop
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variable x1 equal -15.0+0.5*v_a
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variable y1 equal 10.0-0.5*v_a
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variable z1 equal 1+0.5*v_a
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create_atoms 1 single ${x1} ${y1} ${z1}
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next a
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jump SELF loop
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# Electron mass (in amu)
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mass 1 0.00054858
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# Initialize velocities
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velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
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# Add harmonic external force
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fix harm all spring/self ${k}
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# Add harmonic potential energy to total energy and potential energy
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fix_modify harm energy yes
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# PIMD command
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fix pimdb all pimdb/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
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# Outputs
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variable prim_kinetic equal f_pimdb[5]
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variable virial equal f_pimdb[6]
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thermo_style custom step pe v_virial v_prim_kinetic
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thermo 1
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run 100
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236
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.0
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236
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.0
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@ -0,0 +1,236 @@
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LAMMPS (4 Feb 2025)
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Processor partition = 0
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# Units and dimensions
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units electron
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dimension 3
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boundary p p p
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atom_style atomic
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atom_modify map yes
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pair_style none
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# Time step (in femtoseconds)
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timestep 0.5
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# Temperature (in Kelvin)
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variable Temp equal 17.4
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# Force constant (in Hartree energies per Bohr radius squared)
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variable k equal 1.2154614120000001e-08
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# Number of beads
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variable Nbeads equal 4
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variable ibead uloop ${Nbeads} pad
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variable ibead uloop 4 pad
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variable seed equal 18889
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# Create box and atoms. All distances are in Bohr
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region box block -1500 1500 -1500 1500 -1500 1500
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create_box 1 box
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Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
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1 by 1 by 1 MPI processor grid
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variable a loop 3
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label loop
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variable x1 equal -15.0+0.5*v_a
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variable y1 equal 10.0-0.5*v_a
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variable z1 equal 1+0.5*v_a
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create_atoms 1 single ${x1} ${y1} ${z1}
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create_atoms 1 single -14.5 ${y1} ${z1}
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create_atoms 1 single -14.5 9.5 ${z1}
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create_atoms 1 single -14.5 9.5 1.5
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Created 1 atoms
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using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
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create_atoms CPU = 0.000 seconds
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next a
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jump SELF loop
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variable x1 equal -15.0+0.5*v_a
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variable y1 equal 10.0-0.5*v_a
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variable z1 equal 1+0.5*v_a
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create_atoms 1 single ${x1} ${y1} ${z1}
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create_atoms 1 single -14 ${y1} ${z1}
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create_atoms 1 single -14 9 ${z1}
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create_atoms 1 single -14 9 2
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Created 1 atoms
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using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
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create_atoms CPU = 0.001 seconds
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next a
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jump SELF loop
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variable x1 equal -15.0+0.5*v_a
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variable y1 equal 10.0-0.5*v_a
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variable z1 equal 1+0.5*v_a
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create_atoms 1 single ${x1} ${y1} ${z1}
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create_atoms 1 single -13.5 ${y1} ${z1}
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create_atoms 1 single -13.5 8.5 ${z1}
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create_atoms 1 single -13.5 8.5 2.5
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Created 1 atoms
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using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
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create_atoms CPU = 0.000 seconds
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next a
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jump SELF loop
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# Electron mass (in amu)
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mass 1 0.00054858
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# Initialize velocities
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velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
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velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
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velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
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velocity all create 17.4 188891 mom yes rot yes dist gaussian
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# Add harmonic external force
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fix harm all spring/self ${k}
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fix harm all spring/self 1.215461412e-08
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# Add harmonic potential energy to total energy and potential energy
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fix_modify harm energy yes
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# PIMD command
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fix pimdb all pimdb/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
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fix pimdb all pimdb/langevin ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
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# Outputs
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variable prim_kinetic equal f_pimdb[5]
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variable virial equal f_pimdb[6]
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thermo_style custom step pe v_virial v_prim_kinetic
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thermo 1
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run 100
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Initializing PI Langevin equation thermostat...
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Bead ID | omega | tau | c1 | c2
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0 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
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1 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
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2 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
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3 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
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PILE_L thermostat successfully initialized!
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WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
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WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
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Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
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Step PotEng v_virial v_prim_kinetic
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0 0 1.3661449e-08 0.0009918329
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1 1.3158398e-09 1.8742641e-09 0.00099182267
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2 5.0818396e-09 7.1801177e-09 0.00099180053
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3 1.2446727e-08 1.4372388e-08 0.00099176038
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4 2.1754941e-08 3.1274072e-08 0.00099170266
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5 3.2927703e-08 5.2470231e-08 0.00099162511
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6 4.7293056e-08 7.2301291e-08 0.00099153
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7 6.526455e-08 9.5440683e-08 0.00099141194
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8 8.6974168e-08 1.1669162e-07 0.00099127168
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9 1.1249595e-07 1.3551097e-07 0.00099109846
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10 1.4190482e-07 1.6050328e-07 0.00099089759
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11 1.7313555e-07 1.8645705e-07 0.0009906735
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12 2.0672874e-07 2.1181418e-07 0.00099042271
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13 2.4042615e-07 2.4218941e-07 0.00099012073
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14 2.7524432e-07 2.7507982e-07 0.00098977876
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15 3.1513375e-07 3.1771012e-07 0.00098940169
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16 3.6161087e-07 3.6075963e-07 0.00098900826
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17 4.0813191e-07 4.0059005e-07 0.00098859985
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18 4.5194598e-07 4.3883585e-07 0.00098817535
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19 4.9898075e-07 4.8036287e-07 0.00098770764
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20 5.5458728e-07 5.2362451e-07 0.00098721266
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21 6.1220768e-07 5.7705077e-07 0.00098670407
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22 6.6573849e-07 6.3271105e-07 0.00098617081
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23 7.2475089e-07 6.9382916e-07 0.00098557406
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24 7.804837e-07 7.5979853e-07 0.0009849612
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25 8.3194987e-07 8.232213e-07 0.00098434971
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26 8.8723792e-07 8.9901705e-07 0.0009836645
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27 9.3837241e-07 9.7033126e-07 0.0009830068
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28 9.897077e-07 1.0444697e-06 0.00098229311
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29 1.043431e-06 1.1208219e-06 0.00098150213
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30 1.0900368e-06 1.1899315e-06 0.00098077686
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31 1.1303314e-06 1.2560026e-06 0.00098003518
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32 1.1725968e-06 1.3287355e-06 0.00097921099
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33 1.2081344e-06 1.399856e-06 0.0009784037
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34 1.2449387e-06 1.4769272e-06 0.00097754491
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35 1.2852285e-06 1.5642459e-06 0.00097667479
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36 1.3234189e-06 1.6571388e-06 0.00097572641
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37 1.3666391e-06 1.7603492e-06 0.00097475881
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38 1.4102743e-06 1.8666516e-06 0.00097373763
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39 1.454172e-06 1.9696572e-06 0.0009727081
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40 1.5031422e-06 2.0910539e-06 0.00097155807
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41 1.5538491e-06 2.2198868e-06 0.00097030871
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42 1.6079193e-06 2.3576614e-06 0.00096896762
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43 1.6637051e-06 2.496284e-06 0.00096760456
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44 1.7189714e-06 2.637657e-06 0.00096619083
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45 1.7656688e-06 2.795845e-06 0.00096470693
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46 1.8092153e-06 2.9727162e-06 0.00096303835
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47 1.8415769e-06 3.1451673e-06 0.00096140406
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48 1.8664597e-06 3.3241907e-06 0.00095971129
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49 1.8940033e-06 3.5094834e-06 0.00095790964
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50 1.9211844e-06 3.7049195e-06 0.00095603039
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51 1.9533838e-06 3.9139587e-06 0.0009540918
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52 1.9833776e-06 4.1289537e-06 0.0009520767
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53 2.0106231e-06 4.3481079e-06 0.00095003676
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54 2.0429292e-06 4.5702968e-06 0.00094802906
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55 2.0747842e-06 4.7928135e-06 0.00094600351
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56 2.1043981e-06 5.0253448e-06 0.0009438419
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57 2.1474343e-06 5.2569331e-06 0.00094169256
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58 2.2115003e-06 5.4997767e-06 0.00093948055
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59 2.2773037e-06 5.7547729e-06 0.00093714003
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60 2.3402972e-06 6.0074589e-06 0.00093480857
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61 2.4107157e-06 6.2647899e-06 0.00093244785
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62 2.4953095e-06 6.5384938e-06 0.00092998209
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63 2.58923e-06 6.8124372e-06 0.00092751453
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64 2.682021e-06 7.0913777e-06 0.00092505171
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65 2.7538688e-06 7.3773956e-06 0.00092256944
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66 2.8444661e-06 7.6811232e-06 0.00091984092
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67 2.9532286e-06 7.9951107e-06 0.0009170037
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68 3.0551339e-06 8.3096758e-06 0.00091414977
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69 3.1625164e-06 8.6232285e-06 0.00091137219
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70 3.2717759e-06 8.9388929e-06 0.00090857909
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71 3.3924986e-06 9.2524846e-06 0.00090583473
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72 3.5236727e-06 9.5688611e-06 0.00090308342
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73 3.6440162e-06 9.8873586e-06 0.00090026584
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74 3.7692169e-06 1.0203245e-05 0.00089755256
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75 3.8946044e-06 1.0523755e-05 0.00089485804
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76 4.0498738e-06 1.0848398e-05 0.00089217189
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77 4.2099346e-06 1.1164286e-05 0.00088956967
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78 4.3589564e-06 1.1466652e-05 0.00088700311
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79 4.5069481e-06 1.177381e-05 0.00088439373
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80 4.6635354e-06 1.2059606e-05 0.00088199635
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81 4.8398269e-06 1.233837e-05 0.0008797438
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82 5.0191539e-06 1.261531e-05 0.00087745162
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83 5.205285e-06 1.2899972e-05 0.00087506863
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84 5.3708116e-06 1.3160246e-05 0.00087288444
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85 5.5534416e-06 1.3438712e-05 0.00087052617
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86 5.7613e-06 1.372546e-05 0.00086818634
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87 5.9645662e-06 1.4017631e-05 0.00086572407
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88 6.1830289e-06 1.4328439e-05 0.000862992
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89 6.423646e-06 1.4640964e-05 0.00086017364
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90 6.688219e-06 1.4978644e-05 0.0008570595
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91 6.9305603e-06 1.5307214e-05 0.00085411601
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92 7.1857573e-06 1.5649328e-05 0.00085112325
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93 7.4653538e-06 1.6015833e-05 0.0008479391
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94 7.8132911e-06 1.6393131e-05 0.00084474237
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95 8.1540941e-06 1.674573e-05 0.00084165639
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96 8.4943231e-06 1.7094435e-05 0.00083858996
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97 8.8504733e-06 1.7451741e-05 0.00083536142
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98 9.2042324e-06 1.780703e-05 0.00083221292
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99 9.5058078e-06 1.8141862e-05 0.00082913227
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100 9.8087647e-06 1.8457846e-05 0.00082619877
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Loop time of 0.00831106 on 1 procs for 100 steps with 3 atoms
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Performance: 519789292.822 fs/day, 0.000 hours/fs, 12032.160 timesteps/s, 36.096 katom-step/s
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96.4% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 4.265e-05 | 4.265e-05 | 4.265e-05 | 0.0 | 0.51
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Comm | 0.00031198 | 0.00031198 | 0.00031198 | 0.0 | 3.75
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Output | 0.0010369 | 0.0010369 | 0.0010369 | 0.0 | 12.48
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Modify | 0.0063106 | 0.0063106 | 0.0063106 | 0.0 | 75.93
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Other | | 0.000609 | | | 7.33
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Nlocal: 3 ave 3 max 3 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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Neighbor list builds = 33
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Dangerous builds = 0
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228
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.1
Normal file
228
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.1
Normal file
@ -0,0 +1,228 @@
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LAMMPS (4 Feb 2025)
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Processor partition = 1
|
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# Units and dimensions
|
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units electron
|
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dimension 3
|
||||
boundary p p p
|
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atom_style atomic
|
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atom_modify map yes
|
||||
pair_style none
|
||||
|
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# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
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# Temperature (in Kelvin)
|
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variable Temp equal 17.4
|
||||
|
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# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
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create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188892 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimdb/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
|
||||
fix pimdb all pimdb/langevin ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
|
||||
|
||||
# Outputs
|
||||
variable prim_kinetic equal f_pimdb[5]
|
||||
variable virial equal f_pimdb[6]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 1.3661449e-08 0.0009918329
|
||||
1 7.3810761e-10 1.8742641e-09 0.00099182267
|
||||
2 3.0654593e-09 7.1801177e-09 0.00099180053
|
||||
3 6.4534507e-09 1.4372388e-08 0.00099176038
|
||||
4 1.1681892e-08 3.1274072e-08 0.00099170266
|
||||
5 1.8404818e-08 5.2470231e-08 0.00099162511
|
||||
6 2.6171374e-08 7.2301291e-08 0.00099153
|
||||
7 3.5990441e-08 9.5440683e-08 0.00099141194
|
||||
8 4.9770229e-08 1.1669162e-07 0.00099127168
|
||||
9 6.6159035e-08 1.3551097e-07 0.00099109846
|
||||
10 8.7281867e-08 1.6050328e-07 0.00099089759
|
||||
11 1.1505206e-07 1.8645705e-07 0.0009906735
|
||||
12 1.4564491e-07 2.1181418e-07 0.00099042271
|
||||
13 1.8674942e-07 2.4218941e-07 0.00099012073
|
||||
14 2.3275077e-07 2.7507982e-07 0.00098977876
|
||||
15 2.833552e-07 3.1771012e-07 0.00098940169
|
||||
16 3.3078875e-07 3.6075963e-07 0.00098900826
|
||||
17 3.7783787e-07 4.0059005e-07 0.00098859985
|
||||
18 4.3007763e-07 4.3883585e-07 0.00098817535
|
||||
19 4.8592613e-07 4.8036287e-07 0.00098770764
|
||||
20 5.4429898e-07 5.2362451e-07 0.00098721266
|
||||
21 6.0140068e-07 5.7705077e-07 0.00098670407
|
||||
22 6.6036274e-07 6.3271105e-07 0.00098617081
|
||||
23 7.3748601e-07 6.9382916e-07 0.00098557406
|
||||
24 8.1086859e-07 7.5979853e-07 0.0009849612
|
||||
25 8.8638234e-07 8.232213e-07 0.00098434971
|
||||
26 9.8252709e-07 8.9901705e-07 0.0009836645
|
||||
27 1.0768657e-06 9.7033126e-07 0.0009830068
|
||||
28 1.1810654e-06 1.0444697e-06 0.00098229311
|
||||
29 1.2964318e-06 1.1208219e-06 0.00098150213
|
||||
30 1.4097624e-06 1.1899315e-06 0.00098077686
|
||||
31 1.5368367e-06 1.2560026e-06 0.00098003518
|
||||
32 1.6777082e-06 1.3287355e-06 0.00097921099
|
||||
33 1.8186759e-06 1.399856e-06 0.0009784037
|
||||
34 1.9730383e-06 1.4769272e-06 0.00097754491
|
||||
35 2.1285065e-06 1.5642459e-06 0.00097667479
|
||||
36 2.2809575e-06 1.6571388e-06 0.00097572641
|
||||
37 2.4393024e-06 1.7603492e-06 0.00097475881
|
||||
38 2.6212592e-06 1.8666516e-06 0.00097373763
|
||||
39 2.8115312e-06 1.9696572e-06 0.0009727081
|
||||
40 3.0115212e-06 2.0910539e-06 0.00097155807
|
||||
41 3.2325069e-06 2.2198868e-06 0.00097030871
|
||||
42 3.4582526e-06 2.3576614e-06 0.00096896762
|
||||
43 3.6838101e-06 2.496284e-06 0.00096760456
|
||||
44 3.9267475e-06 2.637657e-06 0.00096619083
|
||||
45 4.1942569e-06 2.795845e-06 0.00096470693
|
||||
46 4.4694976e-06 2.9727162e-06 0.00096303835
|
||||
47 4.7570486e-06 3.1451673e-06 0.00096140406
|
||||
48 5.0917213e-06 3.3241907e-06 0.00095971129
|
||||
49 5.4581889e-06 3.5094834e-06 0.00095790964
|
||||
50 5.8607381e-06 3.7049195e-06 0.00095603039
|
||||
51 6.2673583e-06 3.9139587e-06 0.0009540918
|
||||
52 6.6764632e-06 4.1289537e-06 0.0009520767
|
||||
53 7.0828028e-06 4.3481079e-06 0.00095003676
|
||||
54 7.4858144e-06 4.5702968e-06 0.00094802906
|
||||
55 7.8711706e-06 4.7928135e-06 0.00094600351
|
||||
56 8.2756726e-06 5.0253448e-06 0.0009438419
|
||||
57 8.6667628e-06 5.2569331e-06 0.00094169256
|
||||
58 9.0585083e-06 5.4997767e-06 0.00093948055
|
||||
59 9.4634766e-06 5.7547729e-06 0.00093714003
|
||||
60 9.8696653e-06 6.0074589e-06 0.00093480857
|
||||
61 1.0308345e-05 6.2647899e-06 0.00093244785
|
||||
62 1.0757919e-05 6.5384938e-06 0.00092998209
|
||||
63 1.1183568e-05 6.8124372e-06 0.00092751453
|
||||
64 1.1585073e-05 7.0913777e-06 0.00092505171
|
||||
65 1.1993605e-05 7.3773956e-06 0.00092256944
|
||||
66 1.2382612e-05 7.6811232e-06 0.00091984092
|
||||
67 1.2768116e-05 7.9951107e-06 0.0009170037
|
||||
68 1.3181941e-05 8.3096758e-06 0.00091414977
|
||||
69 1.3605472e-05 8.6232285e-06 0.00091137219
|
||||
70 1.4027012e-05 8.9388929e-06 0.00090857909
|
||||
71 1.4471706e-05 9.2524846e-06 0.00090583473
|
||||
72 1.4896833e-05 9.5688611e-06 0.00090308342
|
||||
73 1.5345003e-05 9.8873586e-06 0.00090026584
|
||||
74 1.5779905e-05 1.0203245e-05 0.00089755256
|
||||
75 1.6189898e-05 1.0523755e-05 0.00089485804
|
||||
76 1.6654778e-05 1.0848398e-05 0.00089217189
|
||||
77 1.7131363e-05 1.1164286e-05 0.00088956967
|
||||
78 1.7572176e-05 1.1466652e-05 0.00088700311
|
||||
79 1.8000817e-05 1.177381e-05 0.00088439373
|
||||
80 1.838117e-05 1.2059606e-05 0.00088199635
|
||||
81 1.8762432e-05 1.233837e-05 0.0008797438
|
||||
82 1.9099052e-05 1.261531e-05 0.00087745162
|
||||
83 1.9507863e-05 1.2899972e-05 0.00087506863
|
||||
84 1.9885648e-05 1.3160246e-05 0.00087288444
|
||||
85 2.0266439e-05 1.3438712e-05 0.00087052617
|
||||
86 2.0612316e-05 1.372546e-05 0.00086818634
|
||||
87 2.0959061e-05 1.4017631e-05 0.00086572407
|
||||
88 2.13065e-05 1.4328439e-05 0.000862992
|
||||
89 2.1634898e-05 1.4640964e-05 0.00086017364
|
||||
90 2.2023174e-05 1.4978644e-05 0.0008570595
|
||||
91 2.2431573e-05 1.5307214e-05 0.00085411601
|
||||
92 2.2872283e-05 1.5649328e-05 0.00085112325
|
||||
93 2.338476e-05 1.6015833e-05 0.0008479391
|
||||
94 2.3912199e-05 1.6393131e-05 0.00084474237
|
||||
95 2.437725e-05 1.674573e-05 0.00084165639
|
||||
96 2.4828999e-05 1.7094435e-05 0.00083858996
|
||||
97 2.5286762e-05 1.7451741e-05 0.00083536142
|
||||
98 2.5769956e-05 1.780703e-05 0.00083221292
|
||||
99 2.624134e-05 1.8141862e-05 0.00082913227
|
||||
100 2.6731735e-05 1.8457846e-05 0.00082619877
|
||||
Loop time of 0.00828251 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 521580766.419 fs/day, 0.000 hours/fs, 12073.629 timesteps/s, 36.221 katom-step/s
|
||||
88.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 4.9248e-05 | 4.9248e-05 | 4.9248e-05 | 0.0 | 0.59
|
||||
Comm | 0.00027661 | 0.00027661 | 0.00027661 | 0.0 | 3.34
|
||||
Output | 0.00095948 | 0.00095948 | 0.00095948 | 0.0 | 11.58
|
||||
Modify | 0.0064815 | 0.0064815 | 0.0064815 | 0.0 | 78.26
|
||||
Other | | 0.0005157 | | | 6.23
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 44
|
||||
Dangerous builds = 0
|
||||
228
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.2
Normal file
228
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.2
Normal file
@ -0,0 +1,228 @@
|
||||
LAMMPS (4 Feb 2025)
|
||||
Processor partition = 2
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188893 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimdb/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
|
||||
fix pimdb all pimdb/langevin ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
|
||||
|
||||
# Outputs
|
||||
variable prim_kinetic equal f_pimdb[5]
|
||||
variable virial equal f_pimdb[6]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 1.3661449e-08 0.0009918329
|
||||
1 8.3480048e-10 1.8742641e-09 0.00099182267
|
||||
2 2.8201389e-09 7.1801177e-09 0.00099180053
|
||||
3 7.3605781e-09 1.4372388e-08 0.00099176038
|
||||
4 1.4967393e-08 3.1274072e-08 0.00099170266
|
||||
5 2.4978087e-08 5.2470231e-08 0.00099162511
|
||||
6 3.5908849e-08 7.2301291e-08 0.00099153
|
||||
7 4.8226614e-08 9.5440683e-08 0.00099141194
|
||||
8 6.3621045e-08 1.1669162e-07 0.00099127168
|
||||
9 8.0119736e-08 1.3551097e-07 0.00099109846
|
||||
10 9.7965614e-08 1.6050328e-07 0.00099089759
|
||||
11 1.1538858e-07 1.8645705e-07 0.0009906735
|
||||
12 1.365443e-07 2.1181418e-07 0.00099042271
|
||||
13 1.5920175e-07 2.4218941e-07 0.00099012073
|
||||
14 1.8252589e-07 2.7507982e-07 0.00098977876
|
||||
15 2.0858909e-07 3.1771012e-07 0.00098940169
|
||||
16 2.3676046e-07 3.6075963e-07 0.00098900826
|
||||
17 2.689757e-07 4.0059005e-07 0.00098859985
|
||||
18 3.0022172e-07 4.3883585e-07 0.00098817535
|
||||
19 3.3127637e-07 4.8036287e-07 0.00098770764
|
||||
20 3.6044366e-07 5.2362451e-07 0.00098721266
|
||||
21 3.8484646e-07 5.7705077e-07 0.00098670407
|
||||
22 4.1435067e-07 6.3271105e-07 0.00098617081
|
||||
23 4.4508994e-07 6.9382916e-07 0.00098557406
|
||||
24 4.7879333e-07 7.5979853e-07 0.0009849612
|
||||
25 5.0918223e-07 8.232213e-07 0.00098434971
|
||||
26 5.4733661e-07 8.9901705e-07 0.0009836645
|
||||
27 5.7932115e-07 9.7033126e-07 0.0009830068
|
||||
28 6.1775401e-07 1.0444697e-06 0.00098229311
|
||||
29 6.6883535e-07 1.1208219e-06 0.00098150213
|
||||
30 7.0943445e-07 1.1899315e-06 0.00098077686
|
||||
31 7.4477897e-07 1.2560026e-06 0.00098003518
|
||||
32 7.8183156e-07 1.3287355e-06 0.00097921099
|
||||
33 8.1987667e-07 1.399856e-06 0.0009784037
|
||||
34 8.5514962e-07 1.4769272e-06 0.00097754491
|
||||
35 8.9607784e-07 1.5642459e-06 0.00097667479
|
||||
36 9.4986753e-07 1.6571388e-06 0.00097572641
|
||||
37 1.0024729e-06 1.7603492e-06 0.00097475881
|
||||
38 1.0526731e-06 1.8666516e-06 0.00097373763
|
||||
39 1.103419e-06 1.9696572e-06 0.0009727081
|
||||
40 1.1640352e-06 2.0910539e-06 0.00097155807
|
||||
41 1.2292837e-06 2.2198868e-06 0.00097030871
|
||||
42 1.3024454e-06 2.3576614e-06 0.00096896762
|
||||
43 1.3788736e-06 2.496284e-06 0.00096760456
|
||||
44 1.4503248e-06 2.637657e-06 0.00096619083
|
||||
45 1.5334106e-06 2.795845e-06 0.00096470693
|
||||
46 1.6246777e-06 2.9727162e-06 0.00096303835
|
||||
47 1.715884e-06 3.1451673e-06 0.00096140406
|
||||
48 1.8096683e-06 3.3241907e-06 0.00095971129
|
||||
49 1.916714e-06 3.5094834e-06 0.00095790964
|
||||
50 2.0374848e-06 3.7049195e-06 0.00095603039
|
||||
51 2.1747488e-06 3.9139587e-06 0.0009540918
|
||||
52 2.3236882e-06 4.1289537e-06 0.0009520767
|
||||
53 2.4790586e-06 4.3481079e-06 0.00095003676
|
||||
54 2.6478101e-06 4.5702968e-06 0.00094802906
|
||||
55 2.8275135e-06 4.7928135e-06 0.00094600351
|
||||
56 3.0338638e-06 5.0253448e-06 0.0009438419
|
||||
57 3.2428318e-06 5.2569331e-06 0.00094169256
|
||||
58 3.4414566e-06 5.4997767e-06 0.00093948055
|
||||
59 3.6324968e-06 5.7547729e-06 0.00093714003
|
||||
60 3.8269172e-06 6.0074589e-06 0.00093480857
|
||||
61 4.0183315e-06 6.2647899e-06 0.00093244785
|
||||
62 4.2263009e-06 6.5384938e-06 0.00092998209
|
||||
63 4.4382735e-06 6.8124372e-06 0.00092751453
|
||||
64 4.6488232e-06 7.0913777e-06 0.00092505171
|
||||
65 4.8707403e-06 7.3773956e-06 0.00092256944
|
||||
66 5.1178339e-06 7.6811232e-06 0.00091984092
|
||||
67 5.377713e-06 7.9951107e-06 0.0009170037
|
||||
68 5.63843e-06 8.3096758e-06 0.00091414977
|
||||
69 5.8975743e-06 8.6232285e-06 0.00091137219
|
||||
70 6.168921e-06 8.9388929e-06 0.00090857909
|
||||
71 6.4488238e-06 9.2524846e-06 0.00090583473
|
||||
72 6.7115203e-06 9.5688611e-06 0.00090308342
|
||||
73 6.995134e-06 9.8873586e-06 0.00090026584
|
||||
74 7.284199e-06 1.0203245e-05 0.00089755256
|
||||
75 7.6029528e-06 1.0523755e-05 0.00089485804
|
||||
76 7.9431391e-06 1.0848398e-05 0.00089217189
|
||||
77 8.2768015e-06 1.1164286e-05 0.00088956967
|
||||
78 8.6058917e-06 1.1466652e-05 0.00088700311
|
||||
79 8.9683477e-06 1.177381e-05 0.00088439373
|
||||
80 9.3324487e-06 1.2059606e-05 0.00088199635
|
||||
81 9.6876036e-06 1.233837e-05 0.0008797438
|
||||
82 1.0061754e-05 1.261531e-05 0.00087745162
|
||||
83 1.0457019e-05 1.2899972e-05 0.00087506863
|
||||
84 1.0866064e-05 1.3160246e-05 0.00087288444
|
||||
85 1.1298832e-05 1.3438712e-05 0.00087052617
|
||||
86 1.1762526e-05 1.372546e-05 0.00086818634
|
||||
87 1.2264941e-05 1.4017631e-05 0.00086572407
|
||||
88 1.2784125e-05 1.4328439e-05 0.000862992
|
||||
89 1.332533e-05 1.4640964e-05 0.00086017364
|
||||
90 1.3897966e-05 1.4978644e-05 0.0008570595
|
||||
91 1.4473024e-05 1.5307214e-05 0.00085411601
|
||||
92 1.5067033e-05 1.5649328e-05 0.00085112325
|
||||
93 1.5677943e-05 1.6015833e-05 0.0008479391
|
||||
94 1.6254294e-05 1.6393131e-05 0.00084474237
|
||||
95 1.6791089e-05 1.674573e-05 0.00084165639
|
||||
96 1.7362795e-05 1.7094435e-05 0.00083858996
|
||||
97 1.7961498e-05 1.7451741e-05 0.00083536142
|
||||
98 1.8568337e-05 1.780703e-05 0.00083221292
|
||||
99 1.9188379e-05 1.8141862e-05 0.00082913227
|
||||
100 1.9789011e-05 1.8457846e-05 0.00082619877
|
||||
Loop time of 0.00829826 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 520591251.874 fs/day, 0.000 hours/fs, 12050.723 timesteps/s, 36.152 katom-step/s
|
||||
79.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 4.6257e-05 | 4.6257e-05 | 4.6257e-05 | 0.0 | 0.56
|
||||
Comm | 0.00029611 | 0.00029611 | 0.00029611 | 0.0 | 3.57
|
||||
Output | 0.00096988 | 0.00096988 | 0.00096988 | 0.0 | 11.69
|
||||
Modify | 0.0064529 | 0.0064529 | 0.0064529 | 0.0 | 77.76
|
||||
Other | | 0.0005331 | | | 6.42
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 41
|
||||
Dangerous builds = 0
|
||||
228
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.3
Normal file
228
examples/PACKAGES/pimdb/harmonic_trap_langevin/log.lammps.3
Normal file
@ -0,0 +1,228 @@
|
||||
LAMMPS (4 Feb 2025)
|
||||
Processor partition = 3
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188894 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimdb/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
|
||||
fix pimdb all pimdb/langevin ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
|
||||
|
||||
# Outputs
|
||||
variable prim_kinetic equal f_pimdb[5]
|
||||
variable virial equal f_pimdb[6]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 1.3661449e-08 0.0009918329
|
||||
1 8.448696e-10 1.8742641e-09 0.00099182267
|
||||
2 3.5286528e-09 7.1801177e-09 0.00099180053
|
||||
3 8.2936659e-09 1.4372388e-08 0.00099176038
|
||||
4 1.4586045e-08 3.1274072e-08 0.00099170266
|
||||
5 2.4161875e-08 5.2470231e-08 0.00099162511
|
||||
6 3.8801085e-08 7.2301291e-08 0.00099153
|
||||
7 5.9758384e-08 9.5440683e-08 0.00099141194
|
||||
8 8.5838823e-08 1.1669162e-07 0.00099127168
|
||||
9 1.1684437e-07 1.3551097e-07 0.00099109846
|
||||
10 1.4954974e-07 1.6050328e-07 0.00099089759
|
||||
11 1.8686687e-07 1.8645705e-07 0.0009906735
|
||||
12 2.2747543e-07 2.1181418e-07 0.00099042271
|
||||
13 2.807392e-07 2.4218941e-07 0.00099012073
|
||||
14 3.3827867e-07 2.7507982e-07 0.00098977876
|
||||
15 3.9918359e-07 3.1771012e-07 0.00098940169
|
||||
16 4.6034561e-07 3.6075963e-07 0.00098900826
|
||||
17 5.2315136e-07 4.0059005e-07 0.00098859985
|
||||
18 5.8457073e-07 4.3883585e-07 0.00098817535
|
||||
19 6.5273892e-07 4.8036287e-07 0.00098770764
|
||||
20 7.2150647e-07 5.2362451e-07 0.00098721266
|
||||
21 8.0596691e-07 5.7705077e-07 0.00098670407
|
||||
22 8.946994e-07 6.3271105e-07 0.00098617081
|
||||
23 9.9120142e-07 6.9382916e-07 0.00098557406
|
||||
24 1.09722e-06 7.5979853e-07 0.0009849612
|
||||
25 1.2053692e-06 8.232213e-07 0.00098434971
|
||||
26 1.3196547e-06 8.9901705e-07 0.0009836645
|
||||
27 1.4380033e-06 9.7033126e-07 0.0009830068
|
||||
28 1.5700587e-06 1.0444697e-06 0.00098229311
|
||||
29 1.7089133e-06 1.1208219e-06 0.00098150213
|
||||
30 1.839944e-06 1.1899315e-06 0.00098077686
|
||||
31 1.9718088e-06 1.2560026e-06 0.00098003518
|
||||
32 2.1244847e-06 1.3287355e-06 0.00097921099
|
||||
33 2.2823018e-06 1.399856e-06 0.0009784037
|
||||
34 2.4607034e-06 1.4769272e-06 0.00097754491
|
||||
35 2.6410061e-06 1.5642459e-06 0.00097667479
|
||||
36 2.8395019e-06 1.6571388e-06 0.00097572641
|
||||
37 3.0476467e-06 1.7603492e-06 0.00097475881
|
||||
38 3.2661567e-06 1.8666516e-06 0.00097373763
|
||||
39 3.4857766e-06 1.9696572e-06 0.0009727081
|
||||
40 3.7310241e-06 2.0910539e-06 0.00097155807
|
||||
41 3.9947356e-06 2.2198868e-06 0.00097030871
|
||||
42 4.2722057e-06 2.3576614e-06 0.00096896762
|
||||
43 4.5444932e-06 2.496284e-06 0.00096760456
|
||||
44 4.8307956e-06 2.637657e-06 0.00096619083
|
||||
45 5.1356773e-06 2.795845e-06 0.00096470693
|
||||
46 5.4835294e-06 2.9727162e-06 0.00096303835
|
||||
47 5.8235502e-06 3.1451673e-06 0.00096140406
|
||||
48 6.1541132e-06 3.3241907e-06 0.00095971129
|
||||
49 6.4796693e-06 3.5094834e-06 0.00095790964
|
||||
50 6.8009213e-06 3.7049195e-06 0.00095603039
|
||||
51 7.1253629e-06 3.9139587e-06 0.0009540918
|
||||
52 7.4712081e-06 4.1289537e-06 0.0009520767
|
||||
53 7.8322309e-06 4.3481079e-06 0.00095003676
|
||||
54 8.1941694e-06 4.5702968e-06 0.00094802906
|
||||
55 8.579188e-06 4.7928135e-06 0.00094600351
|
||||
56 8.9656493e-06 5.0253448e-06 0.0009438419
|
||||
57 9.351102e-06 5.2569331e-06 0.00094169256
|
||||
58 9.7645407e-06 5.4997767e-06 0.00093948055
|
||||
59 1.0230434e-05 5.7547729e-06 0.00093714003
|
||||
60 1.0724041e-05 6.0074589e-06 0.00093480857
|
||||
61 1.1207453e-05 6.2647899e-06 0.00093244785
|
||||
62 1.171285e-05 6.5384938e-06 0.00092998209
|
||||
63 1.221299e-05 6.8124372e-06 0.00092751453
|
||||
64 1.2743686e-05 7.0913777e-06 0.00092505171
|
||||
65 1.3295725e-05 7.3773956e-06 0.00092256944
|
||||
66 1.3906023e-05 7.6811232e-06 0.00091984092
|
||||
67 1.4511348e-05 7.9951107e-06 0.0009170037
|
||||
68 1.5116776e-05 8.3096758e-06 0.00091414977
|
||||
69 1.571005e-05 8.6232285e-06 0.00091137219
|
||||
70 1.6297136e-05 8.9388929e-06 0.00090857909
|
||||
71 1.6849099e-05 9.2524846e-06 0.00090583473
|
||||
72 1.7417168e-05 9.5688611e-06 0.00090308342
|
||||
73 1.7971613e-05 9.8873586e-06 0.00090026584
|
||||
74 1.8509472e-05 1.0203245e-05 0.00089755256
|
||||
75 1.9047825e-05 1.0523755e-05 0.00089485804
|
||||
76 1.9510646e-05 1.0848398e-05 0.00089217189
|
||||
77 1.9903304e-05 1.1164286e-05 0.00088956967
|
||||
78 2.0300948e-05 1.1466652e-05 0.00088700311
|
||||
79 2.0696905e-05 1.177381e-05 0.00088439373
|
||||
80 2.1058218e-05 1.2059606e-05 0.00088199635
|
||||
81 2.139726e-05 1.233837e-05 0.0008797438
|
||||
82 2.1755155e-05 1.261531e-05 0.00087745162
|
||||
83 2.2051018e-05 1.2899972e-05 0.00087506863
|
||||
84 2.2294567e-05 1.3160246e-05 0.00087288444
|
||||
85 2.2559076e-05 1.3438712e-05 0.00087052617
|
||||
86 2.2815918e-05 1.372546e-05 0.00086818634
|
||||
87 2.3062616e-05 1.4017631e-05 0.00086572407
|
||||
88 2.3324206e-05 1.4328439e-05 0.000862992
|
||||
89 2.3559323e-05 1.4640964e-05 0.00086017364
|
||||
90 2.3792776e-05 1.4978644e-05 0.0008570595
|
||||
91 2.3990667e-05 1.5307214e-05 0.00085411601
|
||||
92 2.4198637e-05 1.5649328e-05 0.00085112325
|
||||
93 2.4419398e-05 1.6015833e-05 0.0008479391
|
||||
94 2.4625252e-05 1.6393131e-05 0.00084474237
|
||||
95 2.4816363e-05 1.674573e-05 0.00084165639
|
||||
96 2.4982897e-05 1.7094435e-05 0.00083858996
|
||||
97 2.5153682e-05 1.7451741e-05 0.00083536142
|
||||
98 2.5288512e-05 1.780703e-05 0.00083221292
|
||||
99 2.5384836e-05 1.8141862e-05 0.00082913227
|
||||
100 2.5401412e-05 1.8457846e-05 0.00082619877
|
||||
Loop time of 0.00828746 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 521269232.663 fs/day, 0.000 hours/fs, 12066.417 timesteps/s, 36.199 katom-step/s
|
||||
97.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 5.2767e-05 | 5.2767e-05 | 5.2767e-05 | 0.0 | 0.64
|
||||
Comm | 0.00029534 | 0.00029534 | 0.00029534 | 0.0 | 3.56
|
||||
Output | 0.001037 | 0.001037 | 0.001037 | 0.0 | 12.51
|
||||
Modify | 0.0063429 | 0.0063429 | 0.0063429 | 0.0 | 76.54
|
||||
Other | | 0.0005594 | | | 6.75
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 42
|
||||
Dangerous builds = 0
|
||||
1
examples/PACKAGES/pimdb/harmonic_trap_langevin/run.sh
Normal file
1
examples/PACKAGES/pimdb/harmonic_trap_langevin/run.sh
Normal file
@ -0,0 +1 @@
|
||||
mpirun -np $NBEADS $LMP -in in.lmp -partition ${NBEADS}x1
|
||||
60
examples/PACKAGES/pimdb/harmonic_trap_nvt/in.lmp
Normal file
60
examples/PACKAGES/pimdb/harmonic_trap_nvt/in.lmp
Normal file
@ -0,0 +1,60 @@
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Number of Nose-Hoover chains
|
||||
variable nhc equal 4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc}
|
||||
|
||||
# Outputs
|
||||
variable virial equal f_pimdb[3]
|
||||
variable prim_kinetic equal f_pimdb[4]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
236
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.0
Normal file
236
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.0
Normal file
@ -0,0 +1,236 @@
|
||||
LAMMPS (4 Feb 2025)
|
||||
Processor partition = 0
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Number of Nose-Hoover chains
|
||||
variable nhc equal 4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188891 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc}
|
||||
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc ${nhc}
|
||||
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc 4
|
||||
|
||||
# Outputs
|
||||
variable virial equal f_pimdb[3]
|
||||
variable prim_kinetic equal f_pimdb[4]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Fix pimd/nvt -P/(beta^2 * hbar^2) = -2.2139311e-05 (kcal/mol/A^2)
|
||||
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 0 0.00024794798
|
||||
1 8.5849317e-10 4.5664581e-10 0.00024794215
|
||||
2 3.4338094e-09 1.3424585e-09 0.00024793325
|
||||
3 7.7255501e-09 2.6573351e-09 0.00024792129
|
||||
4 1.3733112e-08 4.4011211e-09 0.00024790626
|
||||
5 2.1455686e-08 6.5736113e-09 0.00024788818
|
||||
6 3.0892259e-08 9.1745487e-09 0.00024786704
|
||||
7 4.2041614e-08 1.2203626e-08 0.00024784285
|
||||
8 5.4902328e-08 1.5660483e-08 0.0002478156
|
||||
9 6.9472776e-08 1.9544712e-08 0.00024778532
|
||||
10 8.5751128e-08 2.385585e-08 0.00024775199
|
||||
11 1.0373535e-07 2.8593386e-08 0.00024771564
|
||||
12 1.234232e-07 3.3756758e-08 0.00024767626
|
||||
13 1.4481225e-07 3.9345352e-08 0.00024763386
|
||||
14 1.6789985e-07 4.5358504e-08 0.00024758844
|
||||
15 1.9268316e-07 5.1795501e-08 0.00024754003
|
||||
16 2.1915914e-07 5.8655576e-08 0.00024748862
|
||||
17 2.4732452e-07 6.5937915e-08 0.00024743423
|
||||
18 2.7717588e-07 7.3641654e-08 0.00024737686
|
||||
19 3.0870956e-07 8.1765876e-08 0.00024731653
|
||||
20 3.4192172e-07 9.0309618e-08 0.00024725324
|
||||
21 3.7680831e-07 9.9271863e-08 0.00024718701
|
||||
22 4.1336509e-07 1.0865155e-07 0.00024711785
|
||||
23 4.5158762e-07 1.1844756e-07 0.00024704578
|
||||
24 4.9147126e-07 1.2865874e-07 0.0002469708
|
||||
25 5.3301119e-07 1.3928387e-07 0.00024689293
|
||||
26 5.7620236e-07 1.5032169e-07 0.00024681218
|
||||
27 6.2103957e-07 1.6177089e-07 0.00024672857
|
||||
28 6.675174e-07 1.7363012e-07 0.00024664212
|
||||
29 7.1563024e-07 1.8589798e-07 0.00024655283
|
||||
30 7.6537229e-07 1.9857299e-07 0.00024646073
|
||||
31 8.1673756e-07 2.1165368e-07 0.00024636584
|
||||
32 8.6971988e-07 2.2513849e-07 0.00024626816
|
||||
33 9.2431288e-07 2.3902582e-07 0.00024616772
|
||||
34 9.8051001e-07 2.5331402e-07 0.00024606453
|
||||
35 1.0383045e-06 2.6800143e-07 0.00024595862
|
||||
36 1.0976895e-06 2.8308629e-07 0.00024585001
|
||||
37 1.1586578e-06 2.9856682e-07 0.0002457387
|
||||
38 1.2212021e-06 3.1444121e-07 0.00024562473
|
||||
39 1.2853151e-06 3.3070757e-07 0.00024550812
|
||||
40 1.350989e-06 3.4736399e-07 0.00024538888
|
||||
41 1.4182159e-06 3.644085e-07 0.00024526703
|
||||
42 1.4869879e-06 3.8183911e-07 0.00024514261
|
||||
43 1.5572969e-06 3.9965375e-07 0.00024501562
|
||||
44 1.6291343e-06 4.1785034e-07 0.0002448861
|
||||
45 1.7024917e-06 4.3642673e-07 0.00024475406
|
||||
46 1.7773604e-06 4.5538075e-07 0.00024461954
|
||||
47 1.8537315e-06 4.7471016e-07 0.00024448255
|
||||
48 1.9315959e-06 4.9441271e-07 0.00024434312
|
||||
49 2.0109445e-06 5.1448608e-07 0.00024420127
|
||||
50 2.0917677e-06 5.3492792e-07 0.00024405703
|
||||
51 2.1740562e-06 5.5573584e-07 0.00024391043
|
||||
52 2.2578001e-06 5.769074e-07 0.00024376149
|
||||
53 2.3429895e-06 5.9844014e-07 0.00024361023
|
||||
54 2.4296146e-06 6.2033154e-07 0.00024345669
|
||||
55 2.5176649e-06 6.4257904e-07 0.00024330088
|
||||
56 2.6071302e-06 6.6518005e-07 0.00024314285
|
||||
57 2.6980001e-06 6.8813194e-07 0.00024298261
|
||||
58 2.7902637e-06 7.1143203e-07 0.0002428202
|
||||
59 2.8839103e-06 7.3507763e-07 0.00024265563
|
||||
60 2.9789289e-06 7.5906598e-07 0.00024248895
|
||||
61 3.0753084e-06 7.833943e-07 0.00024232018
|
||||
62 3.1730376e-06 8.0805977e-07 0.00024214934
|
||||
63 3.2721049e-06 8.3305953e-07 0.00024197647
|
||||
64 3.372499e-06 8.5839069e-07 0.00024180161
|
||||
65 3.474208e-06 8.8405032e-07 0.00024162477
|
||||
66 3.5772201e-06 9.1003545e-07 0.00024144598
|
||||
67 3.6815235e-06 9.3634309e-07 0.00024126529
|
||||
68 3.7871058e-06 9.6297021e-07 0.00024108272
|
||||
69 3.893955e-06 9.8991374e-07 0.0002408983
|
||||
70 4.0020586e-06 1.0171706e-06 0.00024071206
|
||||
71 4.1114041e-06 1.0447376e-06 0.00024052403
|
||||
72 4.2219789e-06 1.0726116e-06 0.00024033425
|
||||
73 4.3337702e-06 1.1007895e-06 0.00024014274
|
||||
74 4.4467651e-06 1.1292679e-06 0.00023994955
|
||||
75 4.5609507e-06 1.1580437e-06 0.0002397547
|
||||
76 4.6763137e-06 1.1871136e-06 0.00023955822
|
||||
77 4.792841e-06 1.2164741e-06 0.00023936014
|
||||
78 4.9105191e-06 1.2461221e-06 0.00023916051
|
||||
79 5.0293346e-06 1.276054e-06 0.00023895935
|
||||
80 5.149274e-06 1.3062666e-06 0.00023875669
|
||||
81 5.2703234e-06 1.3367563e-06 0.00023855257
|
||||
82 5.392469e-06 1.3675198e-06 0.00023834703
|
||||
83 5.515697e-06 1.3985535e-06 0.00023814009
|
||||
84 5.6399934e-06 1.4298539e-06 0.00023793178
|
||||
85 5.7653439e-06 1.4614174e-06 0.00023772215
|
||||
86 5.8917344e-06 1.4932406e-06 0.00023751123
|
||||
87 6.0191505e-06 1.5253199e-06 0.00023729904
|
||||
88 6.1475779e-06 1.5576515e-06 0.00023708563
|
||||
89 6.277002e-06 1.590232e-06 0.00023687102
|
||||
90 6.4074081e-06 1.6230576e-06 0.00023665526
|
||||
91 6.5387817e-06 1.6561246e-06 0.00023643837
|
||||
92 6.6711079e-06 1.6894294e-06 0.00023622039
|
||||
93 6.8043718e-06 1.7229682e-06 0.00023600135
|
||||
94 6.9385585e-06 1.7567372e-06 0.00023578129
|
||||
95 7.0736529e-06 1.7907328e-06 0.00023556024
|
||||
96 7.2096401e-06 1.8249512e-06 0.00023533824
|
||||
97 7.3465046e-06 1.8593885e-06 0.00023511531
|
||||
98 7.4842314e-06 1.8940408e-06 0.0002348915
|
||||
99 7.622805e-06 1.9289045e-06 0.00023466684
|
||||
100 7.76221e-06 1.9639756e-06 0.00023444136
|
||||
Loop time of 0.00502911 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 858998737.550 fs/day, 0.000 hours/fs, 19884.230 timesteps/s, 59.653 katom-step/s
|
||||
80.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 3.3682e-05 | 3.3682e-05 | 3.3682e-05 | 0.0 | 0.67
|
||||
Comm | 0.00029392 | 0.00029392 | 0.00029392 | 0.0 | 5.84
|
||||
Output | 0.00092846 | 0.00092846 | 0.00092846 | 0.0 | 18.46
|
||||
Modify | 0.0031767 | 0.0031767 | 0.0031767 | 0.0 | 63.17
|
||||
Other | | 0.0005963 | | | 11.86
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 24
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
234
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.1
Normal file
234
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.1
Normal file
@ -0,0 +1,234 @@
|
||||
LAMMPS (4 Feb 2025)
|
||||
Processor partition = 1
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Number of Nose-Hoover chains
|
||||
variable nhc equal 4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188892 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc}
|
||||
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc ${nhc}
|
||||
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc 4
|
||||
|
||||
# Outputs
|
||||
variable virial equal f_pimdb[3]
|
||||
variable prim_kinetic equal f_pimdb[4]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 0 0.00024796164
|
||||
1 8.5850843e-10 5.313724e-10 0.00024796083
|
||||
2 3.4339027e-09 1.4919466e-09 0.00024795841
|
||||
3 7.7257901e-09 2.8816048e-09 0.00024795438
|
||||
4 1.3733516e-08 4.7001635e-09 0.00024794873
|
||||
5 2.1456164e-08 6.9473741e-09 0.00024794148
|
||||
6 3.0892555e-08 9.6229225e-09 0.00024793261
|
||||
7 4.2041252e-08 1.2726429e-08 0.00024792214
|
||||
8 5.4900553e-08 1.6257449e-08 0.00024791006
|
||||
9 6.9468499e-08 2.0215473e-08 0.00024789638
|
||||
10 8.5742867e-08 2.4599926e-08 0.0002478811
|
||||
11 1.0372118e-07 2.9410168e-08 0.00024786422
|
||||
12 1.2340069e-07 3.4645495e-08 0.00024784576
|
||||
13 1.447784e-07 4.0305136e-08 0.0002478257
|
||||
14 1.6785106e-07 4.6388259e-08 0.00024780406
|
||||
15 1.9261515e-07 5.2893965e-08 0.00024778084
|
||||
16 2.190669e-07 5.9821291e-08 0.00024775605
|
||||
17 2.4720228e-07 6.7169211e-08 0.00024772969
|
||||
18 2.7701701e-07 7.4936635e-08 0.00024770176
|
||||
19 3.0850655e-07 8.312241e-08 0.00024767228
|
||||
20 3.416661e-07 9.1725317e-08 0.00024764125
|
||||
21 3.7649064e-07 1.0074408e-07 0.00024760868
|
||||
22 4.1297485e-07 1.1017735e-07 0.00024757457
|
||||
23 4.511132e-07 1.2002372e-07 0.00024753893
|
||||
24 4.9089989e-07 1.3028173e-07 0.00024750177
|
||||
25 5.3232887e-07 1.4094984e-07 0.0002474631
|
||||
26 5.7539386e-07 1.5202647e-07 0.00024742293
|
||||
27 6.2008832e-07 1.6350996e-07 0.00024738126
|
||||
28 6.6640547e-07 1.7539859e-07 0.00024733811
|
||||
29 7.1433828e-07 1.876906e-07 0.00024729348
|
||||
30 7.6387949e-07 2.0038414e-07 0.00024724738
|
||||
31 8.150216e-07 2.1347732e-07 0.00024719983
|
||||
32 8.6775685e-07 2.2696818e-07 0.00024715084
|
||||
33 9.2207727e-07 2.4085472e-07 0.0002471004
|
||||
34 9.7797464e-07 2.5513485e-07 0.00024704855
|
||||
35 1.0354405e-06 2.6980645e-07 0.00024699528
|
||||
36 1.0944662e-06 2.8486732e-07 0.00024694061
|
||||
37 1.1550427e-06 3.0031522e-07 0.00024688456
|
||||
38 1.2171611e-06 3.1614785e-07 0.00024682713
|
||||
39 1.2808118e-06 3.3236283e-07 0.00024676833
|
||||
40 1.3459853e-06 3.4895776e-07 0.00024670818
|
||||
41 1.4126717e-06 3.6593016e-07 0.0002466467
|
||||
42 1.4808611e-06 3.832775e-07 0.0002465839
|
||||
43 1.5505431e-06 4.009972e-07 0.00024651978
|
||||
44 1.6217074e-06 4.1908663e-07 0.00024645437
|
||||
45 1.6943431e-06 4.3754308e-07 0.00024638767
|
||||
46 1.7684394e-06 4.5636381e-07 0.00024631971
|
||||
47 1.8439852e-06 4.7554603e-07 0.0002462505
|
||||
48 1.9209691e-06 4.9508689e-07 0.00024618005
|
||||
49 1.9993796e-06 5.1498348e-07 0.00024610839
|
||||
50 2.079205e-06 5.3523286e-07 0.00024603551
|
||||
51 2.1604333e-06 5.5583202e-07 0.00024596145
|
||||
52 2.2430524e-06 5.7677791e-07 0.00024588621
|
||||
53 2.32705e-06 5.9806742e-07 0.00024580981
|
||||
54 2.4124135e-06 6.1969741e-07 0.00024573228
|
||||
55 2.4991302e-06 6.4166468e-07 0.00024565362
|
||||
56 2.5871872e-06 6.6396597e-07 0.00024557386
|
||||
57 2.6765714e-06 6.8659801e-07 0.00024549301
|
||||
58 2.7672695e-06 7.0955745e-07 0.00024541108
|
||||
59 2.859268e-06 7.328409e-07 0.00024532811
|
||||
60 2.9525533e-06 7.5644494e-07 0.00024524409
|
||||
61 3.0471115e-06 7.8036609e-07 0.00024515907
|
||||
62 3.1429287e-06 8.0460083e-07 0.00024507304
|
||||
63 3.2399907e-06 8.2914562e-07 0.00024498603
|
||||
64 3.3382831e-06 8.5399683e-07 0.00024489807
|
||||
65 3.4377915e-06 8.7915084e-07 0.00024480916
|
||||
66 3.5385011e-06 9.0460395e-07 0.00024471933
|
||||
67 3.6403972e-06 9.3035245e-07 0.0002446286
|
||||
68 3.7434648e-06 9.5639257e-07 0.00024453698
|
||||
69 3.8476886e-06 9.8272051e-07 0.0002444445
|
||||
70 3.9530535e-06 1.0093324e-06 0.00024435118
|
||||
71 4.0595439e-06 1.0362244e-06 0.00024425703
|
||||
72 4.1671443e-06 1.0633926e-06 0.00024416208
|
||||
73 4.275839e-06 1.0908331e-06 0.00024406635
|
||||
74 4.3856121e-06 1.1185418e-06 0.00024396985
|
||||
75 4.4964475e-06 1.1465147e-06 0.00024387262
|
||||
76 4.6083292e-06 1.1747478e-06 0.00024377466
|
||||
77 4.7212408e-06 1.2032371e-06 0.00024367601
|
||||
78 4.835166e-06 1.2319783e-06 0.00024357668
|
||||
79 4.9500883e-06 1.2609674e-06 0.00024347669
|
||||
80 5.0659909e-06 1.2902001e-06 0.00024337607
|
||||
81 5.1828572e-06 1.3196723e-06 0.00024327483
|
||||
82 5.3006702e-06 1.3493797e-06 0.000243173
|
||||
83 5.419413e-06 1.379318e-06 0.0002430706
|
||||
84 5.5390685e-06 1.4094831e-06 0.00024296765
|
||||
85 5.6596194e-06 1.4398705e-06 0.00024286417
|
||||
86 5.7810485e-06 1.4704759e-06 0.00024276019
|
||||
87 5.9033384e-06 1.501295e-06 0.00024265573
|
||||
88 6.0264715e-06 1.5323234e-06 0.00024255081
|
||||
89 6.1504303e-06 1.5635565e-06 0.00024244545
|
||||
90 6.275197e-06 1.5949902e-06 0.00024233967
|
||||
91 6.400754e-06 1.6266197e-06 0.0002422335
|
||||
92 6.5270834e-06 1.6584408e-06 0.00024212696
|
||||
93 6.6541672e-06 1.6904488e-06 0.00024202007
|
||||
94 6.7819875e-06 1.7226394e-06 0.00024191285
|
||||
95 6.9105262e-06 1.7550078e-06 0.00024180534
|
||||
96 7.0397651e-06 1.7875497e-06 0.00024169754
|
||||
97 7.169686e-06 1.8202604e-06 0.00024158948
|
||||
98 7.3002707e-06 1.8531354e-06 0.00024148118
|
||||
99 7.4315008e-06 1.88617e-06 0.00024137268
|
||||
100 7.563358e-06 1.9193596e-06 0.00024126398
|
||||
Loop time of 0.0050955 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 847807054.814 fs/day, 0.000 hours/fs, 19625.163 timesteps/s, 58.875 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 2.3358e-05 | 2.3358e-05 | 2.3358e-05 | 0.0 | 0.46
|
||||
Comm | 0.00022527 | 0.00022527 | 0.00022527 | 0.0 | 4.42
|
||||
Output | 0.00078435 | 0.00078435 | 0.00078435 | 0.0 | 15.39
|
||||
Modify | 0.0036209 | 0.0036209 | 0.0036209 | 0.0 | 71.06
|
||||
Other | | 0.0004416 | | | 8.67
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
234
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.2
Normal file
234
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.2
Normal file
@ -0,0 +1,234 @@
|
||||
LAMMPS (4 Feb 2025)
|
||||
Processor partition = 2
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Number of Nose-Hoover chains
|
||||
variable nhc equal 4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188893 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc}
|
||||
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc ${nhc}
|
||||
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc 4
|
||||
|
||||
# Outputs
|
||||
variable virial equal f_pimdb[3]
|
||||
variable prim_kinetic equal f_pimdb[4]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 0 0.00024796164
|
||||
1 8.5850845e-10 -3.6831179e-10 0.0002479594
|
||||
2 3.4338783e-09 -3.0736303e-10 0.00024795267
|
||||
3 7.7256433e-09 1.8277487e-10 0.00024794145
|
||||
4 1.3733026e-08 1.1019528e-09 0.00024792576
|
||||
5 2.145494e-08 2.449944e-09 0.00024790558
|
||||
6 3.0889985e-08 4.226444e-09 0.00024788093
|
||||
7 4.2036455e-08 6.4310711e-09 0.00024785181
|
||||
8 5.4892332e-08 9.0633658e-09 0.00024781823
|
||||
9 6.9455288e-08 1.2122792e-08 0.00024778019
|
||||
10 8.572269e-08 1.5608734e-08 0.0002477377
|
||||
11 1.0369159e-07 1.9520504e-08 0.00024769077
|
||||
12 1.2335875e-07 2.3857331e-08 0.00024763941
|
||||
13 1.4472059e-07 2.8618373e-08 0.00024758363
|
||||
14 1.6777327e-07 3.3802708e-08 0.00024752344
|
||||
15 1.9251262e-07 3.940934e-08 0.00024745886
|
||||
16 2.1893415e-07 4.5437194e-08 0.00024738989
|
||||
17 2.4703311e-07 5.1885122e-08 0.00024731656
|
||||
18 2.768044e-07 5.8751899e-08 0.00024723887
|
||||
19 3.0824267e-07 6.6036227e-08 0.00024715685
|
||||
20 3.4134222e-07 7.3736729e-08 0.00024707051
|
||||
21 3.7609709e-07 8.1851958e-08 0.00024697986
|
||||
22 4.1250102e-07 9.0380389e-08 0.00024688494
|
||||
23 4.5054742e-07 9.9320426e-08 0.00024678575
|
||||
24 4.9022945e-07 1.086704e-07 0.00024668231
|
||||
25 5.3153996e-07 1.1842856e-07 0.00024657466
|
||||
26 5.744715e-07 1.285931e-07 0.00024646281
|
||||
27 6.1901635e-07 1.3916212e-07 0.00024634678
|
||||
28 6.6516648e-07 1.5013367e-07 0.0002462266
|
||||
29 7.1291361e-07 1.6150571e-07 0.00024610229
|
||||
30 7.6224914e-07 1.7327614e-07 0.00024597388
|
||||
31 8.1316422e-07 1.8544279e-07 0.0002458414
|
||||
32 8.6564969e-07 1.9800342e-07 0.00024570487
|
||||
33 9.1969614e-07 2.109557e-07 0.00024556432
|
||||
34 9.7529388e-07 2.2429727e-07 0.00024541978
|
||||
35 1.0324329e-06 2.3802567e-07 0.00024527128
|
||||
36 1.0911031e-06 2.5213838e-07 0.00024511886
|
||||
37 1.1512938e-06 2.6663282e-07 0.00024496253
|
||||
38 1.2129943e-06 2.8150634e-07 0.00024480234
|
||||
39 1.2761936e-06 2.9675622e-07 0.00024463831
|
||||
40 1.3408803e-06 3.1237968e-07 0.00024447049
|
||||
41 1.407043e-06 3.2837388e-07 0.0002442989
|
||||
42 1.4746698e-06 3.447359e-07 0.00024412359
|
||||
43 1.5437487e-06 3.6146277e-07 0.00024394458
|
||||
44 1.6142674e-06 3.7855146e-07 0.00024376192
|
||||
45 1.6862132e-06 3.9599886e-07 0.00024357564
|
||||
46 1.7595735e-06 4.1380182e-07 0.00024338577
|
||||
47 1.8343351e-06 4.3195711e-07 0.00024319237
|
||||
48 1.9104848e-06 4.5046147e-07 0.00024299547
|
||||
49 1.9880091e-06 4.6931154e-07 0.00024279511
|
||||
50 2.0668943e-06 4.8850394e-07 0.00024259132
|
||||
51 2.1471263e-06 5.0803521e-07 0.00024238416
|
||||
52 2.228691e-06 5.2790184e-07 0.00024217367
|
||||
53 2.311574e-06 5.4810027e-07 0.00024195988
|
||||
54 2.3957606e-06 5.6862687e-07 0.00024174285
|
||||
55 2.481236e-06 5.8947797e-07 0.00024152261
|
||||
56 2.5679851e-06 6.1064984e-07 0.00024129922
|
||||
57 2.6559926e-06 6.3213871e-07 0.00024107271
|
||||
58 2.7452431e-06 6.5394073e-07 0.00024084313
|
||||
59 2.8357209e-06 6.7605203e-07 0.00024061054
|
||||
60 2.9274101e-06 6.9846868e-07 0.00024037498
|
||||
61 3.0202947e-06 7.2118669e-07 0.00024013649
|
||||
62 3.1143583e-06 7.4420204e-07 0.00023989513
|
||||
63 3.2095846e-06 7.6751065e-07 0.00023965094
|
||||
64 3.3059569e-06 7.911084e-07 0.00023940398
|
||||
65 3.4034585e-06 8.1499113e-07 0.00023915429
|
||||
66 3.5020722e-06 8.3915461e-07 0.00023890193
|
||||
67 3.601781e-06 8.6359461e-07 0.00023864694
|
||||
68 3.7025676e-06 8.8830681e-07 0.00023838939
|
||||
69 3.8044144e-06 9.132869e-07 0.00023812931
|
||||
70 3.9073038e-06 9.3853048e-07 0.00023786677
|
||||
71 4.0112181e-06 9.6403314e-07 0.00023760182
|
||||
72 4.1161392e-06 9.8979043e-07 0.00023733451
|
||||
73 4.2220491e-06 1.0157978e-06 0.0002370649
|
||||
74 4.3289295e-06 1.0420509e-06 0.00023679303
|
||||
75 4.4367621e-06 1.068545e-06 0.00023651897
|
||||
76 4.5455283e-06 1.0952755e-06 0.00023624277
|
||||
77 4.6552095e-06 1.1222378e-06 0.00023596449
|
||||
78 4.7657869e-06 1.1494273e-06 0.00023568418
|
||||
79 4.8772416e-06 1.1768393e-06 0.0002354019
|
||||
80 4.9895545e-06 1.2044689e-06 0.00023511771
|
||||
81 5.1027067e-06 1.2323116e-06 0.00023483166
|
||||
82 5.2166788e-06 1.2603625e-06 0.00023454381
|
||||
83 5.3314515e-06 1.2886168e-06 0.00023425422
|
||||
84 5.4470054e-06 1.3170697e-06 0.00023396295
|
||||
85 5.5633208e-06 1.3457162e-06 0.00023367006
|
||||
86 5.6803783e-06 1.3745516e-06 0.0002333756
|
||||
87 5.798158e-06 1.403571e-06 0.00023307963
|
||||
88 5.9166402e-06 1.4327693e-06 0.00023278222
|
||||
89 6.0358049e-06 1.4621418e-06 0.00023248341
|
||||
90 6.1556323e-06 1.4916833e-06 0.00023218329
|
||||
91 6.2761023e-06 1.5213889e-06 0.00023188189
|
||||
92 6.3971948e-06 1.5512537e-06 0.00023157929
|
||||
93 6.5188897e-06 1.5812727e-06 0.00023127554
|
||||
94 6.6411667e-06 1.6114407e-06 0.0002309707
|
||||
95 6.7640056e-06 1.6417527e-06 0.00023066484
|
||||
96 6.8873862e-06 1.6722038e-06 0.00023035801
|
||||
97 7.011288e-06 1.7027888e-06 0.00023005028
|
||||
98 7.1356907e-06 1.7335027e-06 0.0002297417
|
||||
99 7.2605738e-06 1.7643404e-06 0.00022943234
|
||||
100 7.3859169e-06 1.7952968e-06 0.00022912226
|
||||
Loop time of 0.00507947 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 850481762.482 fs/day, 0.000 hours/fs, 19687.078 timesteps/s, 59.061 katom-step/s
|
||||
98.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 3.1029e-05 | 3.1029e-05 | 3.1029e-05 | 0.0 | 0.61
|
||||
Comm | 0.00027821 | 0.00027821 | 0.00027821 | 0.0 | 5.48
|
||||
Output | 0.001016 | 0.001016 | 0.001016 | 0.0 | 20.00
|
||||
Modify | 0.0032013 | 0.0032013 | 0.0032013 | 0.0 | 63.02
|
||||
Other | | 0.0005529 | | | 10.89
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 24
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
234
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.3
Normal file
234
examples/PACKAGES/pimdb/harmonic_trap_nvt/log.lammps.3
Normal file
@ -0,0 +1,234 @@
|
||||
LAMMPS (4 Feb 2025)
|
||||
Processor partition = 3
|
||||
# Units and dimensions
|
||||
units electron
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
pair_style none
|
||||
|
||||
# Time step (in femtoseconds)
|
||||
timestep 0.5
|
||||
|
||||
# Temperature (in Kelvin)
|
||||
variable Temp equal 17.4
|
||||
|
||||
# Number of Nose-Hoover chains
|
||||
variable nhc equal 4
|
||||
|
||||
# Force constant (in Hartree energies per Bohr radius squared)
|
||||
variable k equal 1.2154614120000001e-08
|
||||
|
||||
# Number of beads
|
||||
variable Nbeads equal 4
|
||||
variable ibead uloop ${Nbeads} pad
|
||||
variable ibead uloop 4 pad
|
||||
variable seed equal 18889
|
||||
|
||||
# Create box and atoms. All distances are in Bohr
|
||||
region box block -1500 1500 -1500 1500 -1500 1500
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
variable a loop 3
|
||||
label loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 ${y1} ${z1}
|
||||
create_atoms 1 single -14.5 9.5 ${z1}
|
||||
create_atoms 1 single -14.5 9.5 1.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -14 ${y1} ${z1}
|
||||
create_atoms 1 single -14 9 ${z1}
|
||||
create_atoms 1 single -14 9 2
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
variable x1 equal -15.0+0.5*v_a
|
||||
variable y1 equal 10.0-0.5*v_a
|
||||
variable z1 equal 1+0.5*v_a
|
||||
create_atoms 1 single ${x1} ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 ${y1} ${z1}
|
||||
create_atoms 1 single -13.5 8.5 ${z1}
|
||||
create_atoms 1 single -13.5 8.5 2.5
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
next a
|
||||
jump SELF loop
|
||||
|
||||
# Electron mass (in amu)
|
||||
mass 1 0.00054858
|
||||
|
||||
# Initialize velocities
|
||||
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
|
||||
velocity all create 17.4 188894 mom yes rot yes dist gaussian
|
||||
|
||||
# Add harmonic external force
|
||||
fix harm all spring/self ${k}
|
||||
fix harm all spring/self 1.215461412e-08
|
||||
|
||||
# Add harmonic potential energy to total energy and potential energy
|
||||
fix_modify harm energy yes
|
||||
|
||||
# PIMD command
|
||||
fix pimdb all pimdb/nvt method pimd temp ${Temp} nhc ${nhc}
|
||||
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc ${nhc}
|
||||
fix pimdb all pimdb/nvt method pimd temp 17.4 nhc 4
|
||||
|
||||
# Outputs
|
||||
variable virial equal f_pimdb[3]
|
||||
variable prim_kinetic equal f_pimdb[4]
|
||||
|
||||
thermo_style custom step pe v_virial v_prim_kinetic
|
||||
thermo 1
|
||||
|
||||
run 100
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
|
||||
Step PotEng v_virial v_prim_kinetic
|
||||
0 0 0 0.00024796164
|
||||
1 8.5847879e-10 4.4463719e-10 0.00024796024
|
||||
2 3.4336684e-09 1.3183829e-09 0.00024795602
|
||||
3 7.7250055e-09 2.6210625e-09 0.000247949
|
||||
4 1.3731669e-08 4.3524371e-09 0.00024793917
|
||||
5 2.1452581e-08 6.5122035e-09 0.00024792653
|
||||
6 3.0886407e-08 9.0999942e-09 0.0002479111
|
||||
7 4.2031554e-08 1.2115377e-08 0.00024789287
|
||||
8 5.4886174e-08 1.5557858e-08 0.00024787185
|
||||
9 6.9448162e-08 1.9426875e-08 0.00024784804
|
||||
10 8.5715159e-08 2.3721806e-08 0.00024782146
|
||||
11 1.0368455e-07 2.8441963e-08 0.0002477921
|
||||
12 1.2335346e-07 3.3586595e-08 0.00024775998
|
||||
13 1.4471878e-07 3.9154888e-08 0.0002477251
|
||||
14 1.6777712e-07 4.5145965e-08 0.00024768748
|
||||
15 1.9252485e-07 5.1558884e-08 0.00024764712
|
||||
16 2.1895809e-07 5.8392642e-08 0.00024760403
|
||||
17 2.4707272e-07 6.5646173e-08 0.00024755823
|
||||
18 2.7686434e-07 7.3318348e-08 0.00024750973
|
||||
19 3.0832834e-07 8.1407976e-08 0.00024745854
|
||||
20 3.4145982e-07 8.9913804e-08 0.00024740467
|
||||
21 3.7625367e-07 9.8834518e-08 0.00024734813
|
||||
22 4.127045e-07 1.0816874e-07 0.00024728895
|
||||
23 4.5080671e-07 1.1791504e-07 0.00024722714
|
||||
24 4.9055443e-07 1.2807191e-07 0.00024716271
|
||||
25 5.3194155e-07 1.3863779e-07 0.00024709568
|
||||
26 5.7496174e-07 1.4961107e-07 0.00024702607
|
||||
27 6.1960841e-07 1.6099007e-07 0.00024695389
|
||||
28 6.6587473e-07 1.7277305e-07 0.00024687917
|
||||
29 7.1375365e-07 1.8495821e-07 0.00024680191
|
||||
30 7.6323786e-07 1.975437e-07 0.00024672216
|
||||
31 8.1431984e-07 2.1052759e-07 0.00024663991
|
||||
32 8.6699183e-07 2.2390793e-07 0.0002465552
|
||||
33 9.2124582e-07 2.3768267e-07 0.00024646805
|
||||
34 9.7707361e-07 2.5184974e-07 0.00024637847
|
||||
35 1.0344667e-06 2.6640698e-07 0.0002462865
|
||||
36 1.0934165e-06 2.813522e-07 0.00024619215
|
||||
37 1.1539141e-06 2.9668313e-07 0.00024609545
|
||||
38 1.2159503e-06 3.1239747e-07 0.00024599643
|
||||
39 1.2795157e-06 3.2849286e-07 0.00024589511
|
||||
40 1.344601e-06 3.4496686e-07 0.00024579151
|
||||
41 1.4111961e-06 3.61817e-07 0.00024568566
|
||||
42 1.4792913e-06 3.7904076e-07 0.0002455776
|
||||
43 1.5488762e-06 3.9663555e-07 0.00024546734
|
||||
44 1.6199404e-06 4.1459874e-07 0.00024535492
|
||||
45 1.6924734e-06 4.3292764e-07 0.00024524035
|
||||
46 1.7664643e-06 4.5161952e-07 0.00024512369
|
||||
47 1.841902e-06 4.7067159e-07 0.00024500494
|
||||
48 1.9187753e-06 4.90081e-07 0.00024488415
|
||||
49 1.9970729e-06 5.0984488e-07 0.00024476135
|
||||
50 2.076783e-06 5.2996028e-07 0.00024463656
|
||||
51 2.1578939e-06 5.5042422e-07 0.00024450981
|
||||
52 2.2403935e-06 5.7123366e-07 0.00024438115
|
||||
53 2.3242696e-06 5.9238553e-07 0.0002442506
|
||||
54 2.4095099e-06 6.138767e-07 0.00024411819
|
||||
55 2.4961017e-06 6.3570399e-07 0.00024398396
|
||||
56 2.5840323e-06 6.5786419e-07 0.00024384795
|
||||
57 2.6732887e-06 6.8035404e-07 0.00024371018
|
||||
58 2.7638579e-06 7.0317021e-07 0.0002435707
|
||||
59 2.8557265e-06 7.2630938e-07 0.00024342953
|
||||
60 2.9488811e-06 7.4976814e-07 0.00024328672
|
||||
61 3.0433081e-06 7.7354305e-07 0.0002431423
|
||||
62 3.1389936e-06 7.9763065e-07 0.00024299631
|
||||
63 3.2359238e-06 8.2202741e-07 0.00024284878
|
||||
64 3.3340844e-06 8.4672977e-07 0.00024269976
|
||||
65 3.4334612e-06 8.7173415e-07 0.00024254927
|
||||
66 3.5340397e-06 8.970369e-07 0.00024239736
|
||||
67 3.6358055e-06 9.2263435e-07 0.00024224406
|
||||
68 3.7387437e-06 9.4852279e-07 0.00024208942
|
||||
69 3.8428394e-06 9.7469849e-07 0.00024193348
|
||||
70 3.9480777e-06 1.0011576e-06 0.00024177626
|
||||
71 4.0544433e-06 1.0278964e-06 0.00024161782
|
||||
72 4.1619211e-06 1.054911e-06 0.0002414582
|
||||
73 4.2704954e-06 1.0821976e-06 0.00024129742
|
||||
74 4.3801508e-06 1.1097521e-06 0.00024113554
|
||||
75 4.4908716e-06 1.1375706e-06 0.0002409726
|
||||
76 4.6026419e-06 1.1656492e-06 0.00024080863
|
||||
77 4.7154459e-06 1.1939839e-06 0.00024064367
|
||||
78 4.8292673e-06 1.2225706e-06 0.00024047778
|
||||
79 4.9440901e-06 1.2514052e-06 0.00024031099
|
||||
80 5.059898e-06 1.2804837e-06 0.00024014333
|
||||
81 5.1766745e-06 1.309802e-06 0.00023997487
|
||||
82 5.2944032e-06 1.3393558e-06 0.00023980562
|
||||
83 5.4130674e-06 1.369141e-06 0.00023963565
|
||||
84 5.5326505e-06 1.3991534e-06 0.00023946499
|
||||
85 5.6531355e-06 1.4293887e-06 0.00023929369
|
||||
86 5.7745057e-06 1.4598429e-06 0.00023912178
|
||||
87 5.8967439e-06 1.4905114e-06 0.00023894931
|
||||
88 6.0198332e-06 1.5213902e-06 0.00023877633
|
||||
89 6.1437564e-06 1.5524748e-06 0.00023860287
|
||||
90 6.2684962e-06 1.5837609e-06 0.00023842898
|
||||
91 6.3940353e-06 1.6152441e-06 0.00023825471
|
||||
92 6.5203562e-06 1.6469202e-06 0.0002380801
|
||||
93 6.6474416e-06 1.6787847e-06 0.00023790518
|
||||
94 6.7752739e-06 1.7108332e-06 0.00023773001
|
||||
95 6.9038354e-06 1.7430613e-06 0.00023755463
|
||||
96 7.0331085e-06 1.7754645e-06 0.00023737908
|
||||
97 7.1630755e-06 1.8080385e-06 0.00023720341
|
||||
98 7.2937187e-06 1.8407787e-06 0.00023702765
|
||||
99 7.4250201e-06 1.8736806e-06 0.00023685186
|
||||
100 7.5569619e-06 1.9067398e-06 0.00023667607
|
||||
Loop time of 0.00510222 on 1 procs for 100 steps with 3 atoms
|
||||
|
||||
Performance: 846690098.292 fs/day, 0.000 hours/fs, 19599.308 timesteps/s, 58.798 katom-step/s
|
||||
79.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.5273e-05 | 1.5273e-05 | 1.5273e-05 | 0.0 | 0.30
|
||||
Comm | 0.00013505 | 0.00013505 | 0.00013505 | 0.0 | 2.65
|
||||
Output | 0.00046743 | 0.00046743 | 0.00046743 | 0.0 | 9.16
|
||||
Modify | 0.0042111 | 0.0042111 | 0.0042111 | 0.0 | 82.53
|
||||
Other | | 0.0002734 | | | 5.36
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 24
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
1
examples/PACKAGES/pimdb/harmonic_trap_nvt/run.sh
Normal file
1
examples/PACKAGES/pimdb/harmonic_trap_nvt/run.sh
Normal file
@ -0,0 +1 @@
|
||||
mpirun -np $NBEADS $LMP -in in.lmp -partition ${NBEADS}x1
|
||||
Reference in New Issue
Block a user