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Added examples and references to the docs

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Arthur France-Lanord
2024-12-19 18:06:54 +01:00
parent b4a6be2623
commit 095d33dafb
10 changed files with 21003 additions and 3 deletions
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1
doc/src/Packages_details.rst
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@ -994,6 +994,7 @@ Additional pair styles that are less commonly used.
* ``src/EXTRA-PAIR``: filenames -> commands
* :doc:`pair_style <pair_style>`
* ``examples/PACKAGES/dispersion``
----------

16
doc/src/pair_dispersion_d3.rst
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@ -32,7 +32,9 @@ Style *dispersion/d3* computes the dispersion energy-correction used in
the DFT-D3 method of Grimme :ref:`(Grimme1) <Grimme1>`. It would
typically be used with a machine learning potential that was trained
with results from plain DFT calculations without the dispersion
correction through pair_style hybrid/overlay.
correction through pair_style hybrid/overlay. ML potentials are often
combined *a posteriori* with dispersion energy-correction schemes (see
*e.g.* :ref:`(Qamar) <Qamar>` and :ref:`(Batatia) <Batatia>`).
The energy contribution :math:`E_i` for an atom :math:`i` is given by:
@ -139,10 +141,18 @@ none
**(Grimme1)** S. Grimme, J. Antony, S. Ehrlich, and H. Krieg, J. Chem. Phys. 132, 154104 (2010).
.. _Qamar:
**(Qamar)** M. Qamar, M. Mrovec, T. Lysogorskiy, A. Bochkarev, and R. Drautz, J. Chem. Theory Comput. 19, 5151 (2023).
.. _Batatia:
**(Batatia)** I. Batatia, *et al.*, arXiv:2401.0096 (2023).
.. _Grimme2:
**(Grimme2)** S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem. 32, 1456 (2011); DOI:10.1002/jcc.21759.
**(Grimme2)** S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem. 32, 1456 (2011).
.. _Sherrill:
**(Sherrill)** D. G. A. Smith, L. A. Burns, K. Patkowski, and C. D. Sherrill, J. Phys. Chem. Lett., 7, 2197, (2016); DOI: 10.1021/acs.jpclett.6b00780.
**(Sherrill)** D. G. A. Smith, L. A. Burns, K. Patkowski, and C. D. Sherrill, J. Phys. Chem. Lett., 7, 2197, (2016).

2
doc/utils/sphinx-config/false_positives.txt
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@ -249,6 +249,7 @@ basename
Bashford
bashrc
Baskes
Batatia
Batra
Bayly
bb
@ -3073,6 +3074,7 @@ qE
qeff
qelectron
qeq
Qamar
QeQ
QEq
qfactor

7
examples/PACKAGES/dispersion/README Normal file
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@ -0,0 +1,7 @@
To run these examples, one needs to compile LAMMPS with the ML-PACE (-DPKG_ML-PACE=ON) and the EXTRA-PAIR packages (-DPKG_EXTRA-PAIR=ON).
These examples show how to combine a short-ranged ML potential with a dispersion correction scheme. Here we combine a general-purpose ACE potential for carbon (10.1021/acs.jctc.2c01149), with two different dispersion correction schemes:
- D2 (a pure two-body potential, here tabulated)
- D3 (a many-body potential, implemented in LAMMPS).
We perform an artificially-accelerated melting of a simple cubic carbon crystal.

36
examples/PACKAGES/dispersion/in.d2 Normal file
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@ -0,0 +1,36 @@
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 region box
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace table linear 10000
pair_coeff * * pace potential_files/c_ace.yace C
pair_coeff * * table potential_files/d2.table D2 9.0
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair table
# calculate the e/atom for each pair style individually
variable dUpace equal c_c1/atoms
variable dUd2 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200 8000 0.05
thermo_style custom step time pe press density etotal v_dUpace v_dUd2 temp
thermo 10
run 1000

36
examples/PACKAGES/dispersion/in.d3 Normal file
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@ -0,0 +1,36 @@
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 region box
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace dispersion/d3 bj pbe 16.0 16.0
pair_coeff * * pace potential_files/c_ace.yace C
pair_coeff * * dispersion/d3 C
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair dispersion/d3
# calculate the e/atom for each pair style individually
variable Upace equal c_c1/atoms
variable Ud3 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200 8000 0.05
thermo_style custom step time pe press density etotal v_Upace v_Ud3 temp
thermo 10
run 1000

212
examples/PACKAGES/dispersion/log.19Nov2024.d2.AppleClang Normal file
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@ -0,0 +1,212 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-124-gb4a6be2623)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 1000 atoms
using lattice units in orthogonal box = (0 0 0) to (10 10 10)
create_atoms CPU = 0.000 seconds
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 47.6 remap
Changing box ...
orthogonal box = (0 0 0) to (47.6 10 10)
orthogonal box = (0 0 0) to (47.6 47.6 10)
orthogonal box = (0 0 0) to (47.6 47.6 47.6)
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace table linear 10000
ACE version: 2023.11.25
Recursive evaluator is used
pair_coeff * * pace potential_files/c_ace.yace C
Loading potential_files/c_ace.yace
Total number of basis functions
C: 20 (r=1) 455 (r>1)
Mapping LAMMPS atom type #1(C) -> ACE species type #0
pair_coeff * * table potential_files/d2.table D2 9.0
Reading pair table potential file potential_files/d2.table with DATE: 2021-12-16
WARNING: 8063 of 20000 force values in table D2 are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
WARNING: 2386 of 20000 distance values in table 1e-06 with relative error
WARNING: over D2 to re-computed values (src/pair_table.cpp:474)
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair table
# calculate the e/atom for each pair style individually
variable dUpace equal c_c1/atoms
variable dUd2 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200 8000 0.05
thermo_style custom step time pe press density etotal v_dUpace v_dUd2 temp
thermo 10
run 1000
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 9 9 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pace, perpetual
attributes: full, newton on, cut 7.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.735 | 3.735 | 3.735 Mbytes
Step Time PotEng Press Density TotEng v_dUpace v_dUd2 Temp
0 0 -262.26589 -9971.6713 0.18493 -236.43971 -0.2577066 -0.0045592958 200
10 0.01 -261.95135 -9935.7706 0.18493 -236.30907 -0.2573846 -0.0045667539 198.57595
20 0.02 -261.06474 -9829.6856 0.18493 -235.62735 -0.25647567 -0.0045890732 196.98928
30 0.03 -259.77497 -9666.145 0.18493 -234.61161 -0.25514862 -0.0046263524 194.86706
40 0.04 -258.39801 -9460.0072 0.18493 -233.60912 -0.25371931 -0.0046787005 191.96713
50 0.05 -257.42829 -9211.9223 0.18493 -232.33835 -0.25268005 -0.00474824 194.29852
60 0.06 -257.64576 -8921.8851 0.18493 -230.82671 -0.25280708 -0.0048386744 207.68885
70 0.07 -260.19291 -8670.2037 0.18493 -229.01696 -0.25523515 -0.0049577577 241.42904
80 0.08 -267.07185 -8527.7285 0.18493 -226.69446 -0.26194291 -0.0051289385 312.68573
90 0.09 -283.47858 -8570.817 0.18493 -223.44732 -0.27806974 -0.0054088431 464.88695
100 0.1 -326.68391 -8824.0846 0.18493 -218.48165 -0.32089849 -0.005785424 837.92705
110 0.11 -448.97353 -8252.1979 0.18493 -212.28931 -0.44287582 -0.0060977064 1832.9017
120 0.12 -650.7035 -5534.1655 0.18493 -223.5567 -0.64441185 -0.0062916514 3307.8593
130 0.13 -933.81125 -4704.2854 0.18493 -286.56971 -0.92739847 -0.0064127776 5012.2907
140 0.14 -1171.2517 -2968.8933 0.18493 -385.87385 -1.1646965 -0.0065552112 6082.0294
150 0.15 -1350.8792 -3465.5935 0.18493 -519.52739 -1.3439344 -0.00694486 6438.0557
160 0.16 -1496.2871 -6052.929 0.18493 -663.03127 -1.4888724 -0.0074146152 6452.8001
170 0.17 -1625.3638 -4723.6011 0.18493 -807.89715 -1.6177834 -0.0075803815 6330.5274
180 0.18 -1993.5565 -6304.6744 0.18493 -981.34811 -1.9859788 -0.0075776623 7838.6235
190 0.19 -2364.1774 531.53194 0.18493 -1206.3755 -2.3564318 -0.0077456419 8966.1115
200 0.2 -2628.1941 -2718.7472 0.18493 -1460.8709 -2.6203861 -0.0078079511 9039.8445
210 0.21 -2836.1527 -4022.5749 0.18493 -1707.0994 -2.828074 -0.0080787109 8743.4799
220 0.22 -3100.9732 1624.4001 0.18493 -1965.972 -3.0927333 -0.0082398276 8789.5409
230 0.23 -3370.6913 3070.9084 0.18493 -2243.5466 -3.3625557 -0.0081356056 8728.6996
240 0.24 -3602.4909 -1735.2825 0.18493 -2501.9426 -3.5942404 -0.0082504747 8522.735
250 0.25 -3857.3489 -2511.3956 0.18493 -2742.6866 -3.8489787 -0.0083702484 8632.0352
260 0.26 -4074.8199 -2326.8585 0.18493 -2978.0184 -4.0662712 -0.0085487139 8493.7195
270 0.27 -4215.6482 473.11218 0.18493 -3199.9538 -4.2069996 -0.0086486808 7865.6201
280 0.28 -4377.3473 -1850.0738 0.18493 -3408.2314 -4.368534 -0.0088133589 7504.9123
290 0.29 -4535.6642 -2083.5888 0.18493 -3600.9914 -4.5267884 -0.0088757925 7238.1817
300 0.3 -4718.0729 882.66946 0.18493 -3786.8652 -4.7093025 -0.008770345 7211.3475
310 0.31 -4880.3655 817.82157 0.18493 -3969.3405 -4.8714715 -0.0088940655 7055.0517
320 0.32 -4933.6562 -1094.978 0.18493 -4130.823 -4.9246965 -0.0089596459 6217.2048
330 0.33 -5061.3213 -268.61359 0.18493 -4269.7685 -5.0522618 -0.0090594545 6129.8489
340 0.34 -5176.3513 -1537.5534 0.18493 -4400.3453 -5.1671457 -0.0092056062 6009.4536
350 0.35 -5283.9957 -1339.04 0.18493 -4523.9189 -5.2747842 -0.009211477 5886.0957
360 0.36 -5350.9893 1996.8109 0.18493 -4641.944 -5.341861 -0.0091282094 5490.9034
370 0.37 -5412.3608 57.954227 0.18493 -4750.0619 -5.4032943 -0.0090665534 5128.8963
380 0.38 -5484.5551 2167.9835 0.18493 -4845.7867 -5.4754679 -0.0090872114 4946.6743
390 0.39 -5542.3904 -503.58325 0.18493 -4932.9381 -5.5331485 -0.0092419018 4719.648
400 0.4 -5602.9693 -2030.2886 0.18493 -5009.4029 -5.593625 -0.0093443079 4596.6259
410 0.41 -5677.8083 71.960087 0.18493 -5081.6393 -5.6683398 -0.0094685032 4616.7808
420 0.42 -5738.5801 974.10458 0.18493 -5151.6613 -5.7290267 -0.0095534249 4545.1463
430 0.43 -5769.2898 299.81162 0.18493 -5216.2361 -5.7597547 -0.0095351226 4282.8922
440 0.44 -5809.1708 465.95162 0.18493 -5273.5878 -5.7995775 -0.0095932998 4147.5975
450 0.45 -5852.9472 57.326979 0.18493 -5325.7106 -5.8433004 -0.0096467857 4082.9622
460 0.46 -5907.6597 682.93706 0.18493 -5374.2257 -5.8979408 -0.0097188622 4130.9557
470 0.47 -5941.4434 -618.62936 0.18493 -5418.8665 -5.9317298 -0.0097135671 4046.8778
480 0.48 -5957.9976 -416.5896 0.18493 -5458.6044 -5.9483591 -0.0096384535 3867.3411
490 0.49 -5979.6344 1385.12 0.18493 -5492.2506 -5.9700417 -0.0095926883 3774.3393
500 0.5 -6024.6758 -9.5652415 0.18493 -5522.3748 -6.0151005 -0.0095753122 3889.8595
510 0.51 -6026.0478 -1080.7173 0.18493 -5546.7752 -6.0163511 -0.0096966662 3711.5256
520 0.52 -6068.8034 -643.46776 0.18493 -5567.3984 -6.0591415 -0.0096618327 3882.9204
530 0.53 -6075.992 2010.2618 0.18493 -5583.54 -6.066495 -0.0094969682 3813.5881
540 0.54 -6079.9143 -885.88914 0.18493 -5594.9638 -6.0704021 -0.0095122311 3755.4964
550 0.55 -6097.3067 -1171.8104 0.18493 -5600.7043 -6.0876578 -0.0096488707 3845.7292
560 0.56 -6117.0227 627.88359 0.18493 -5600.3503 -6.1073753 -0.009647382 4001.1525
570 0.57 -6116.9782 1022.7137 0.18493 -5595.5349 -6.1072122 -0.0097660226 4038.0989
580 0.58 -6104.8438 586.99369 0.18493 -5585.7283 -6.0950003 -0.0098435498 4020.0726
590 0.59 -6125.598 676.67444 0.18493 -5570.8412 -6.115679 -0.0099189684 4296.0812
600 0.6 -6122.5635 330.50198 0.18493 -5550.8304 -6.1125554 -0.010008085 4427.547
610 0.61 -6090.3944 -1652.5027 0.18493 -5527.5632 -6.080305 -0.010089423 4358.6103
620 0.62 -6098.1907 -786.82351 0.18493 -5500.2705 -6.0880437 -0.010147009 4630.3422
630 0.63 -6075.0467 -1313.1815 0.18493 -5468.0898 -6.0647788 -0.010267888 4700.3236
640 0.64 -6064.9995 956.38812 0.18493 -5433.2543 -6.0546543 -0.010345133 4892.2857
650 0.65 -6088.4791 -742.68529 0.18493 -5397.0203 -6.078031 -0.010448027 5354.7127
660 0.66 -6042.7568 -141.98203 0.18493 -5361.0033 -6.0321205 -0.010636322 5279.5543
670 0.67 -6036.3033 1653.0956 0.18493 -5327.3039 -6.0256081 -0.010695208 5490.5488
680 0.68 -6017.42 -1452.7402 0.18493 -5293.2338 -6.0064175 -0.011002505 5608.1563
690 0.69 -5955.1575 215.6232 0.18493 -5261.3872 -5.9439668 -0.011190758 5372.6134
700 0.7 -5975.0055 -741.27382 0.18493 -5229.1283 -5.963716 -0.011289528 5776.1333
710 0.71 -5987.7863 -562.99679 0.18493 -5198.2353 -5.9763168 -0.011469527 6114.3469
720 0.72 -5940.3632 -1627.0137 0.18493 -5168.682 -5.9286438 -0.011719374 5975.9613
730 0.73 -5934.8989 -1041.7603 0.18493 -5141.626 -5.9231362 -0.011762772 6143.1698
740 0.74 -5950.037 4094.0388 0.18493 -5117.8607 -5.9382783 -0.011758697 6444.4402
750 0.75 -5883.3455 1214.5891 0.18493 -5096.183 -5.871255 -0.012090503 6095.8499
760 0.76 -5888.6229 -1422.3903 0.18493 -5077.5998 -5.8763074 -0.012315554 6280.6283
770 0.77 -5894.7303 1674.6972 0.18493 -5060.2667 -5.8824244 -0.012305977 6462.1534
780 0.78 -5896.6263 -346.74886 0.18493 -5045.5139 -5.8842953 -0.012331074 6591.0834
790 0.79 -5871.3295 1112.0246 0.18493 -5034.9971 -5.8589147 -0.012414823 6476.6256
800 0.8 -5845.8627 678.3318 0.18493 -5025.1002 -5.8333382 -0.012524474 6356.0511
810 0.81 -5828.4266 -548.60001 0.18493 -5015.2039 -5.8158213 -0.012605321 6297.6624
820 0.82 -5853.214 -491.22619 0.18493 -5003.416 -5.8407273 -0.012486608 6580.9039
830 0.83 -5869.0759 439.56721 0.18493 -4990.5625 -5.8564992 -0.012576678 6803.2784
840 0.84 -5865.1166 -99.478523 0.18493 -4978.8202 -5.8523858 -0.012730825 6863.5511
850 0.85 -5855.2419 -732.55874 0.18493 -4967.3792 -5.84249 -0.012751874 6875.6802
860 0.86 -5866.1013 921.65497 0.18493 -4957.1555 -5.8532203 -0.012880963 7038.9492
870 0.87 -5864.0326 1705.8786 0.18493 -4947.683 -5.8510565 -0.012976114 7096.2854
880 0.88 -5815.8591 759.99567 0.18493 -4938.5735 -5.8027576 -0.013101457 6793.77
890 0.89 -5832.8968 -509.98486 0.18493 -4928.2034 -5.819886 -0.013010787 7006.0183
900 0.9 -5840.2215 940.2682 0.18493 -4914.6206 -5.8271597 -0.013061705 7167.9278
910 0.91 -5814.3807 -1222.9944 0.18493 -4899.2274 -5.801348 -0.013032692 7087.0205
920 0.92 -5799.0309 -583.22898 0.18493 -4882.1693 -5.7857635 -0.013267464 7100.2505
930 0.93 -5804.1259 -143.75436 0.18493 -4862.3717 -5.7906866 -0.013439334 7293.0209
940 0.94 -5799.4164 121.27216 0.18493 -4840.561 -5.7856352 -0.01378125 7425.4539
950 0.95 -5781.9344 858.96792 0.18493 -4817.8263 -5.7680739 -0.013860503 7466.1309
960 0.96 -5773.5123 -590.79699 0.18493 -4794.2228 -5.7598081 -0.013704216 7583.6967
970 0.97 -5788.1056 1438.5817 0.18493 -4770.2505 -5.7743365 -0.013769191 7882.3525
980 0.98 -5777.3848 1358.3372 0.18493 -4744.4946 -5.7632772 -0.014107597 7998.7847
990 0.99 -5759.8854 659.65953 0.18493 -4721.466 -5.7458533 -0.014032133 8041.6037
1000 1 -5762.1992 1429.2926 0.18493 -4700.3872 -5.7480845 -0.014114688 8222.7581
Loop time of 34.9571 on 1 procs for 1000 steps with 1000 atoms
Performance: 2.472 ns/day, 9.710 hours/ns, 28.606 timesteps/s, 28.606 katom-step/s
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 34.836 | 34.836 | 34.836 | 0.0 | 99.65
Neigh | 0.1006 | 0.1006 | 0.1006 | 0.0 | 0.29
Comm | 0.0068922 | 0.0068922 | 0.0068922 | 0.0 | 0.02
Output | 0.0024738 | 0.0024738 | 0.0024738 | 0.0 | 0.01
Modify | 0.0089558 | 0.0089558 | 0.0089558 | 0.0 | 0.03
Other | | 0.002429 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2119 ave 2119 max 2119 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 24647 ave 24647 max 24647 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 14952 ave 14952 max 14952 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24647
Ave neighs/atom = 24.647
Neighbor list builds = 73
Dangerous builds = 0
Total wall time: 0:00:35

207
examples/PACKAGES/dispersion/log.19Nov2024.d3.AppleClang Normal file
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@ -0,0 +1,207 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-124-gb4a6be2623)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 1000 atoms
using lattice units in orthogonal box = (0 0 0) to (10 10 10)
create_atoms CPU = 0.000 seconds
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 47.6 remap
Changing box ...
orthogonal box = (0 0 0) to (47.6 10 10)
orthogonal box = (0 0 0) to (47.6 47.6 10)
orthogonal box = (0 0 0) to (47.6 47.6 47.6)
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace dispersion/d3 bj pbe 16.0 16.0
ACE version: 2023.11.25
Recursive evaluator is used
pair_coeff * * pace potential_files/c_ace.yace C
Loading potential_files/c_ace.yace
Total number of basis functions
C: 20 (r=1) 455 (r>1)
Mapping LAMMPS atom type #1(C) -> ACE species type #0
pair_coeff * * dispersion/d3 C
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair dispersion/d3
# calculate the e/atom for each pair style individually
variable Upace equal c_c1/atoms
variable Ud3 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200 8000 0.05
thermo_style custom step time pe press density etotal v_Upace v_Ud3 temp
thermo 10
run 1000
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pace, perpetual
attributes: full, newton on, cut 7.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair dispersion/d3, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.225 | 4.225 | 4.225 Mbytes
Step Time PotEng Press Density TotEng v_Upace v_Ud3 Temp
0 0 -269.22784 -10163.81 0.18493 -243.40166 -0.2577066 -0.011521241 200
10 0.01 -268.91964 -10127.847 0.18493 -243.27102 -0.25738458 -0.011535063 198.62494
20 0.02 -268.05119 -10021.494 0.18493 -242.5888 -0.25647533 -0.011575864 197.18284
30 0.03 -266.79002 -9857.2901 0.18493 -241.57047 -0.25514731 -0.011642708 195.30224
40 0.04 -265.45358 -9649.9442 0.18493 -240.56451 -0.25371725 -0.011736332 192.743
50 0.05 -264.54017 -9399.8893 0.18493 -239.28691 -0.25268225 -0.011857921 195.56328
60 0.06 -264.84455 -9107.3451 0.18493 -237.76286 -0.25283226 -0.012012287 209.72282
70 0.07 -267.54089 -8854.1606 0.18493 -235.93446 -0.25532927 -0.012211616 244.7627
80 0.08 -274.69989 -8711.2474 0.18493 -233.58133 -0.26221917 -0.012480714 318.42543
90 0.09 -291.68522 -8756.6345 0.18493 -230.28474 -0.27882098 -0.012864244 475.4903
100 0.1 -336.53367 -9016.4269 0.18493 -225.24755 -0.32311293 -0.013420742 861.80867
110 0.11 -462.90616 -8357.1414 0.18493 -219.19569 -0.44877872 -0.014127434 1887.3136
120 0.12 -664.15468 -5565.4794 0.18493 -231.32848 -0.6492232 -0.014931481 3351.841
130 0.13 -951.27098 -4652.5905 0.18493 -296.51652 -0.93543038 -0.015840607 5070.4715
140 0.14 -1205.6849 -3059.3194 0.18493 -401.34104 -1.1889266 -0.016758343 6228.9038
150 0.15 -1368.2885 -3497.3843 0.18493 -536.7151 -1.3504708 -0.017817669 6439.7716
160 0.16 -1520.501 -6000.4048 0.18493 -684.00631 -1.5015432 -0.018957846 6477.8828
170 0.17 -1677.3308 -5214.7894 0.18493 -832.38224 -1.6573798 -0.019950977 6543.3498
180 0.18 -2036.1717 -6040.7531 0.18493 -1010.1766 -2.0151604 -0.021011265 7945.3889
190 0.19 -2426.025 -487.78008 0.18493 -1241.4345 -2.4041702 -0.021854823 9173.5651
200 0.2 -2649.652 -2086.9328 0.18493 -1497.0738 -2.6266612 -0.022990776 8925.6586
210 0.21 -2905.7206 -4044.8259 0.18493 -1752.1211 -2.8818676 -0.023853045 8933.5677
220 0.22 -3203.3911 288.82854 0.18493 -2015.2741 -3.1789474 -0.024443725 9200.8743
230 0.23 -3447.7955 1829.3253 0.18493 -2294.2011 -3.4229059 -0.024889587 8933.5277
240 0.24 -3649.3383 -844.48619 0.18493 -2554.8833 -3.6239948 -0.025343484 8475.5482
250 0.25 -3922.1756 -1174.8574 0.18493 -2804.68 -3.8967376 -0.025438016 8653.9761
260 0.26 -4102.7824 -939.91049 0.18493 -3042.8292 -4.0770147 -0.02576773 8208.3634
270 0.27 -4256.3052 -1049.3894 0.18493 -3264.1472 -4.2304066 -0.025898538 7683.3516
280 0.28 -4448.3259 413.88293 0.18493 -3468.6691 -4.4219661 -0.026359771 7586.5408
290 0.29 -4598.6994 -1514.3544 0.18493 -3664.9764 -4.5723737 -0.026325728 7230.8268
300 0.3 -4766.7768 -1227.1717 0.18493 -3847.0265 -4.7401544 -0.026622463 7122.6211
310 0.31 -4897.8433 -889.83589 0.18493 -4018.537 -4.8709081 -0.026935247 6809.4191
320 0.32 -5002.8382 -932.43967 0.18493 -4177.0644 -4.9756735 -0.027164737 6394.8594
330 0.33 -5136.2116 634.66692 0.18493 -4326.4989 -5.1090176 -0.027194004 6270.4807
340 0.34 -5275.1001 568.17936 0.18493 -4468.5857 -5.2477786 -0.027321502 6245.7125
350 0.35 -5357.0809 408.84517 0.18493 -4598.2143 -5.3296099 -0.027470942 5876.7239
360 0.36 -5419.0026 1796.4367 0.18493 -4716.1124 -5.3913649 -0.027637632 5443.2379
370 0.37 -5463.3559 -3068.041 0.18493 -4818.7605 -5.4355423 -0.027813594 4991.7992
380 0.38 -5580.6461 -304.67279 0.18493 -4912.0844 -5.5528568 -0.027789339 5177.3962
390 0.39 -5641.4967 148.18125 0.18493 -4999.847 -5.6136572 -0.027839476 4968.9867
400 0.4 -5665.4653 369.42211 0.18493 -5081.4437 -5.6374901 -0.027975159 4522.7106
410 0.41 -5727.4286 -1574.6321 0.18493 -5154.123 -5.6993182 -0.028110465 4439.7247
420 0.42 -5803.826 610.74413 0.18493 -5221.4478 -5.7756645 -0.028161516 4509.9843
430 0.43 -5850.4029 2172.9548 0.18493 -5286.4767 -5.8222074 -0.028195559 4367.0904
440 0.44 -5869.2916 -679.92811 0.18493 -5343.1567 -5.8411375 -0.028154024 4074.4308
450 0.45 -5912.3342 -577.02779 0.18493 -5394.3218 -5.8841456 -0.028188608 4011.5301
460 0.46 -5967.1367 850.99628 0.18493 -5441.6429 -5.9387568 -0.028379849 4069.466
470 0.47 -5993.0037 -1787.4629 0.18493 -5484.4184 -5.9644216 -0.028582147 3938.526
480 0.48 -6026.5187 -144.22806 0.18493 -5522.0869 -5.9978628 -0.028655951 3906.3609
490 0.49 -6058.3397 -45.646348 0.18493 -5555.5067 -6.0295665 -0.028773239 3893.98
500 0.5 -6094.053 764.47978 0.18493 -5584.5286 -6.0653038 -0.028749181 3945.7985
510 0.51 -6098.8878 906.01959 0.18493 -5610.4273 -6.070001 -0.028886805 3782.6771
520 0.52 -6080.1583 54.99003 0.18493 -5630.1057 -6.0511675 -0.028990843 3485.2438
530 0.53 -6117.0422 -1673.4592 0.18493 -5643.3456 -6.0880145 -0.029027675 3668.3448
540 0.54 -6151.4264 -524.82139 0.18493 -5651.1622 -6.1223536 -0.029072849 3874.0869
550 0.55 -6170.7654 1712.0999 0.18493 -5655.2802 -6.1417382 -0.029027209 3991.9593
560 0.56 -6166.8009 -477.56946 0.18493 -5653.6954 -6.1377583 -0.029042602 3973.5309
570 0.57 -6160.7091 -361.66608 0.18493 -5647.2641 -6.1315307 -0.029178391 3976.1597
580 0.58 -6173.9145 325.00145 0.18493 -5635.2676 -6.1445792 -0.029335346 4171.3251
590 0.59 -6167.1178 -80.037617 0.18493 -5618.4987 -6.1375514 -0.029566418 4248.5508
600 0.6 -6148.2177 916.0679 0.18493 -5596.6135 -6.118551 -0.029666683 4271.6675
610 0.61 -6125.7165 -1139.7588 0.18493 -5569.1718 -6.095964 -0.029752453 4309.927
620 0.62 -6142.796 308.70088 0.18493 -5536.1149 -6.112915 -0.029880966 4698.1874
630 0.63 -6129.9383 -47.803419 0.18493 -5500.3524 -6.1000374 -0.029900918 4875.5639
640 0.64 -6099.3919 -923.16834 0.18493 -5462.9283 -6.0694692 -0.029922646 4928.8258
650 0.65 -6084.579 -244.8304 0.18493 -5424.1831 -6.0544676 -0.03011135 5114.1586
660 0.66 -6066.472 465.56678 0.18493 -5385.1376 -6.0362355 -0.030236485 5276.3088
670 0.67 -6047.6719 2243.8323 0.18493 -5346.1225 -6.0173701 -0.030301802 5432.8556
680 0.68 -6022.6745 -1836.221 0.18493 -5310.102 -5.9922687 -0.030405809 5518.2188
690 0.69 -5978.8342 -1304.3184 0.18493 -5273.8837 -5.9482612 -0.030573058 5459.1937
700 0.7 -5991.2943 323.69703 0.18493 -5238.9272 -5.9606473 -0.030647003 5826.3913
710 0.71 -5986.361 1186.1641 0.18493 -5203.6284 -5.955542 -0.030819088 6061.545
720 0.72 -5954.192 1799.9381 0.18493 -5171.8208 -5.9232663 -0.030925694 6058.7458
730 0.73 -5916.014 -865.73853 0.18493 -5143.0037 -5.8848943 -0.031119775 5986.2542
740 0.74 -5910.7744 -68.556634 0.18493 -5116.9017 -5.8795688 -0.031205553 6147.8139
750 0.75 -5906.9676 1246.8702 0.18493 -5092.9874 -5.8757585 -0.031209094 6303.5288
760 0.76 -5906.4776 -1405.1682 0.18493 -5071.3811 -5.8751637 -0.031313926 6467.0548
770 0.77 -5905.3464 472.50467 0.18493 -5052.9549 -5.8738552 -0.031491229 6600.9884
780 0.78 -5924.2458 -921.98835 0.18493 -5037.7723 -5.8926544 -0.031591446 6864.9221
790 0.79 -5889.7281 732.94871 0.18493 -5028.07 -5.8578394 -0.031888732 6672.7498
800 0.8 -5867.9863 -1134.0193 0.18493 -5022.002 -5.8359232 -0.032063073 6551.3705
810 0.81 -5871.8994 -497.25772 0.18493 -5017.3082 -5.8399785 -0.031920926 6618.0234
820 0.82 -5856.2899 1604.2619 0.18493 -5013.7387 -5.8242906 -0.031999275 6524.7848
830 0.83 -5888.4995 56.403587 0.18493 -5009.9563 -5.8562217 -0.03227779 6803.5092
840 0.84 -5871.8315 -988.18571 0.18493 -5005.5991 -5.8393187 -0.032512823 6708.1738
850 0.85 -5882.2676 -283.23078 0.18493 -5001.9778 -5.8493059 -0.032961676 6817.0352
860 0.86 -5912.3952 1375.4443 0.18493 -4996.3864 -5.8794797 -0.032915526 7093.6467
870 0.87 -5903.9361 2796.9283 0.18493 -4991.8252 -5.870891 -0.033045076 7063.4607
880 0.88 -5861.8081 -908.29232 0.18493 -4987.1597 -5.8284887 -0.033319488 6773.3479
890 0.89 -5863.4157 -810.75451 0.18493 -4979.9225 -5.8299552 -0.033460475 6841.8425
900 0.9 -5884.9039 1572.2795 0.18493 -4969.4764 -5.8514328 -0.033471119 7089.145
910 0.91 -5833.544 13.186931 0.18493 -4955.7993 -5.799849 -0.033695039 6797.3258
920 0.92 -5817.465 -685.96605 0.18493 -4938.0488 -5.7839051 -0.033559888 6810.2703
930 0.93 -5839.4058 920.09219 0.18493 -4916.1996 -5.80616 -0.033245799 7149.3836
940 0.94 -5832.3164 1320.7198 0.18493 -4890.4343 -5.7993605 -0.032955909 7294.0108
950 0.95 -5810.697 878.78702 0.18493 -4861.7787 -5.7775761 -0.033120875 7348.5002
960 0.96 -5788.1088 -215.7805 0.18493 -4829.6714 -5.7551007 -0.033008172 7422.2166
970 0.97 -5781.4329 -339.90628 0.18493 -4796.3086 -5.7484812 -0.032951633 7628.8817
980 0.98 -5781.351 2087.8844 0.18493 -4761.7049 -5.7486537 -0.032697256 7896.2219
990 0.99 -5762.4416 -238.18485 0.18493 -4725.7458 -5.7296635 -0.032778098 8028.2559
1000 1 -5722.4631 -413.78218 0.18493 -4691.9647 -5.6896424 -0.032820679 7980.2627
Loop time of 49.5358 on 1 procs for 1000 steps with 1000 atoms
Performance: 1.744 ns/day, 13.760 hours/ns, 20.187 timesteps/s, 20.187 katom-step/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 49.328 | 49.328 | 49.328 | 0.0 | 99.58
Neigh | 0.18371 | 0.18371 | 0.18371 | 0.0 | 0.37
Comm | 0.011635 | 0.011635 | 0.011635 | 0.0 | 0.02
Output | 0.0021156 | 0.0021156 | 0.0021156 | 0.0 | 0.00
Modify | 0.0081661 | 0.0081661 | 0.0081661 | 0.0 | 0.02
Other | | 0.002316 | | | 0.00
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4433 ave 4433 max 4433 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 113113 ave 113113 max 113113 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 15148 ave 15148 max 15148 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 113113
Ave neighs/atom = 113.113
Neighbor list builds = 72
Dangerous builds = 0
Total wall time: 0:00:49

484
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examples/PACKAGES/dispersion/potential_files/d2.table Normal file
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