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Merge pull request lammps#4756 from Yi-FanLi/pimd_langevin_lj_sp
fix pimd/langevin: clarify the setting of the quantumness parameter `sp` in the documentation
2 parents 532dcf5 + 74ce8fa commit 8656347

15 files changed

+465
-417
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‎doc/src/fix_pimd.rst‎

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‎examples/PACKAGES/pimd/langevin_reduced_units/in.lmp‎

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timestep 0.00044905847
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fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L ${ibead}
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fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 sp 0.1924 thermostat PILE_L ${ibead}
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thermo_style custom step temp f_1[*] vol press
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thermo 100

‎examples/PACKAGES/pimd/langevin_reduced_units/log.10Sep25.langevin.reduced.g++‎

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LAMMPS (10 Sep 2025 - Development - patch_10Sep2025-285-g0b912432e9-modified)
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Running on 2 partitions of processors

‎examples/PACKAGES/pimd/langevin_reduced_units/log.10Sep25.langevin.reduced.g++.0‎

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LAMMPS (10 Sep 2025 - Development - patch_10Sep2025-285-g0b912432e9-modified)
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Processor partition = 0
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
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using 1 OpenMP thread(s) per MPI task
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variable ibead uloop 32 pad
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units lj
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atom_style atomic
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atom_modify map yes
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boundary p p p
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pair_style lj/cut 2.8015
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read_data data.lj${ibead}
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read_data data.lj01
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Reading data file ...
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orthogonal box = (-3.4945131 -3.4945131 -3.4945131) to (3.4945131 3.4945131 3.4945131)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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200 atoms
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read_data CPU = 0.001 seconds
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pair_coeff * * 1.0 1.0
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pair_modify shift yes
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mass 1 1.0
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timestep 0.00044905847
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fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 sp 0.1924 thermostat PILE_L ${ibead}
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fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 sp 0.1924 thermostat PILE_L 01
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thermo_style custom step temp f_1[*] vol press
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thermo 100
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thermo_modify norm no
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#dump dcd all custom 1 ${ibead}.lammpstrj id type x y z vx vy vz ix iy iz fx fy fz
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#dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
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run 1000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Initializing PI Langevin equation thermostat...
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Bead ID | omega | tau | c1 | c2
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0 0.00000000e+00 1.00000000e+00 9.99775496e-01 2.11886210e-02
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1 1.31787526e+02 3.79398579e-03 9.42536810e-01 3.34102322e-01
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PILE_L thermostat successfully initialized!
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.1015
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ghost atom cutoff = 3.1015
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binsize = 1.55075, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.117 | 3.117 | 3.117 Mbytes
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Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press
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0 0 0 0 -875.67022 841988.51 -421279.13 253.30998 382.47517 -1646.5336 -1.9663356 -0.82731217 341.38937 -1.3810467
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100 14.817371 4422.9853 0 -534.92328 5337.0116 98.252811 7794.4231 306.80873 -0.79835015 13.250964 8.3267012 341.38937 12.562252
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200 13.762897 4108.2246 0 -534.95517 4177.5291 334.44025 -8232.4092 308.68322 0.1241056 12.726742 8.0817572 341.38937 12.177521
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300 12.567041 3751.2617 0 -493.05357 3999.6771 286.94793 8675.7287 309.21515 -0.061380815 14.107894 8.6065735 341.38937 12.246489
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400 11.844955 3535.7192 0 -515.1282 3784.41 290.67609 -85.218746 309.0205 -0.046820083 13.638883 8.2475712 341.38937 11.616699
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500 11.101108 3313.6808 0 -521.46928 3556 274.62448 650.39076 309.45886 -0.1095114 12.806143 7.7267347 341.38937 10.99195
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600 9.9620798 2973.6808 0 -462.66349 3219.3472 323.6578 3169.1089 309.48769 0.081993582 13.761585 8.0387709 341.38937 11.072758
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700 9.3387158 2787.6067 0 -501.1952 2901.7138 343.18094 2002.8977 309.02634 0.15824332 12.74807 7.4599969 341.38937 10.131828
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800 8.9074976 2658.888 0 -523.14785 2864.9389 287.94911 2331.5161 308.67674 -0.057470593 11.606039 6.8145291 341.38937 9.3523989
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900 8.5049897 2538.7394 0 -543.6833 2597.7781 328.04213 599.92997 308.62574 0.099117065 10.499473 6.2153451 341.38937 8.6401113
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1000 8.0728921 2409.7583 0 -571.68303 2533.6673 290.94669 -1268.3145 308.58653 -0.045763228 9.4221992 5.5934009 341.38937 7.8382485
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Loop time of 0.188222 on 1 procs for 1000 steps with 200 atoms
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Performance: 206132.768 tau/day, 5312.885 timesteps/s, 1.063 Matom-step/s
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99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.091306 | 0.091306 | 0.091306 | 0.0 | 48.51
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Neigh | 0.01581 | 0.01581 | 0.01581 | 0.0 | 8.40
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Comm | 0.0038515 | 0.0038515 | 0.0038515 | 0.0 | 2.05
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Output | 9.6502e-05 | 9.6502e-05 | 9.6502e-05 | 0.0 | 0.05
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Modify | 0.076181 | 0.076181 | 0.076181 | 0.0 | 40.47
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Other | | 0.0009761 | | | 0.52
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Nlocal: 200 ave 200 max 200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1117 ave 1117 max 1117 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 7491 ave 7491 max 7491 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 7491
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Ave neighs/atom = 37.455
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Neighbor list builds = 55
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Dangerous builds = 0
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Total wall time: 0:00:00

‎examples/PACKAGES/pimd/langevin_reduced_units/log.10Sep25.langevin.reduced.g++.1‎

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LAMMPS (10 Sep 2025 - Development - patch_10Sep2025-285-g0b912432e9-modified)
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Processor partition = 1
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
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using 1 OpenMP thread(s) per MPI task
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variable ibead uloop 32 pad
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units lj
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atom_style atomic
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atom_modify map yes
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boundary p p p
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pair_style lj/cut 2.8015
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read_data data.lj${ibead}
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read_data data.lj02
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Reading data file ...
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orthogonal box = (-3.4945131 -3.4945131 -3.4945131) to (3.4945131 3.4945131 3.4945131)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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200 atoms
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read_data CPU = 0.001 seconds
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pair_coeff * * 1.0 1.0
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pair_modify shift yes
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mass 1 1.0
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timestep 0.00044905847
27+
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fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 sp 0.1924 thermostat PILE_L ${ibead}
29+
fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 sp 0.1924 thermostat PILE_L 02
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thermo_style custom step temp f_1[*] vol press
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thermo 100
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thermo_modify norm no
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#dump dcd all custom 1 ${ibead}.lammpstrj id type x y z vx vy vz ix iy iz fx fy fz
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#dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
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run 1000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.1015
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ghost atom cutoff = 3.1015
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binsize = 1.55075, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.117 | 3.117 | 3.117 Mbytes
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Step Temp f_1[1] f_1[2] f_1[3] f_1[4] f_1[5] f_1[6] f_1[7] f_1[8] f_1[9] f_1[10] Volume Press
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0 0 0 843768.92 -904.74343 841988.51 -421279.13 253.30998 382.47517 -1646.5336 -1.9663356 -0.82731217 341.38937 -0.58528882
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100 3.1989795 954.89538 1014.1504 -520.09611 5337.0116 98.252811 7794.4231 306.80873 -0.79835015 13.250964 8.3267012 341.38937 5.939687
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200 2.051821 612.46858 541.7755 -549.98447 4177.5291 334.44025 -8232.4092 308.68322 0.1241056 12.726742 8.0817572 341.38937 5.1585163
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300 2.0005528 597.165 636.76014 -492.45624 3999.6771 286.94793 8675.7287 309.21515 -0.061380815 14.107894 8.6065735 341.38937 6.1072177
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400 2.1301684 635.85527 629.30382 -501.34009 3784.41 290.67609 -85.218746 309.0205 -0.046820083 13.638883 8.2475712 341.38937 6.0953183
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500 2.1090566 629.5534 661.40704 -527.17197 3556 274.62448 650.39076 309.45886 -0.1095114 12.806143 7.7267347 341.38937 5.6643757
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600 2.1073572 629.04613 563.34039 -484.05666 3219.3472 323.6578 3169.1089 309.48769 0.081993582 13.761585 8.0387709 341.38937 6.2065377
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700 1.9719958 588.64076 524.29412 -497.63256 2901.7138 343.18094 2002.8977 309.02634 0.15824332 12.74807 7.4599969 341.38937 5.9128176
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800 2.0469937 611.0276 634.75777 -516.58664 2864.9389 287.94911 2331.5161 308.67674 -0.057470593 11.606039 6.8145291 341.38937 5.4463933
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900 1.9587768 584.69488 554.57173 -536.54463 2597.7781 328.04213 599.92997 308.62574 0.099117065 10.499473 6.2153451 341.38937 4.9090894
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1000 2.0978183 626.19876 628.76262 -559.36931 2533.6673 290.94669 -1268.3145 308.58653 -0.045763228 9.4221992 5.5934009 341.38937 4.5482659
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Loop time of 0.188222 on 1 procs for 1000 steps with 200 atoms
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Performance: 206132.206 tau/day, 5312.870 timesteps/s, 1.063 Matom-step/s
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99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.092279 | 0.092279 | 0.092279 | 0.0 | 49.03
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Neigh | 0.016436 | 0.016436 | 0.016436 | 0.0 | 8.73
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Comm | 0.0037922 | 0.0037922 | 0.0037922 | 0.0 | 2.01
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Output | 9.8e-05 | 9.8e-05 | 9.8e-05 | 0.0 | 0.05
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Modify | 0.074731 | 0.074731 | 0.074731 | 0.0 | 39.70
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Other | | 0.0008862 | | | 0.47
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Nlocal: 200 ave 200 max 200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1113 ave 1113 max 1113 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 7470 ave 7470 max 7470 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 7470
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Ave neighs/atom = 37.35
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Neighbor list builds = 57
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Dangerous builds = 0
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Total wall time: 0:00:00

‎examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++‎

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‎examples/PACKAGES/pimd/langevin_reduced_units/log.14Jun23.langevin.reduced.g++.0‎

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