Merge branch 'develop' into collected-small-fixes
This commit is contained in:
Axel Kohlmeyer
2
.github/CODEOWNERS
vendored
2
.github/CODEOWNERS
vendored
@ -72,6 +72,8 @@ src/EXTRA-COMMAND/ndx_group.* @akohlmey
|
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src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
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src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
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src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
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src/EXTRA-PAIR/pair_dispersion_d3.* @soniasolomoni @arthurfl
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src/EXTRA-PAIR/d3_parameters.h @soniasolomoni @arthurfl
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src/MISC/*_tracker.* @jtclemm
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src/MC/fix_gcmc.* @athomps
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src/MC/fix_sgcmc.* @athomps
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@ -10,7 +10,7 @@ Syntax
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pair_style dispersion/d3 damping functional cutoff cn_cutoff
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* damping = damping function: *zero*, *zerom*, *bj*, or *bjm*
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* damping = damping function: *original*, *zerom*, *bj*, or *bjm*
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* functional = XC functional form: *pbe*, *pbe0*, ... (see list below)
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* cutoff = global cutoff (distance units)
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* cn_cutoff = coordination number cutoff (distance units)
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@ -20,7 +20,7 @@ Examples
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.. code-block:: LAMMPS
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pair_style dispersion/d3 zero pbe 30.0 20.0
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pair_style dispersion/d3 original pbe 30.0 20.0
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pair_coeff * * C
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Description
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@ -55,9 +55,16 @@ factor, and :math:`f_n^{damp}` are damping functions.
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contributions, according to, for example, the Axilrod-Teller-Muto
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model.
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Available damping functions are the original "zero-damping"
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:ref:`(Grimme1) <Grimme1>`, Becke-Johnson damping :ref:`(Grimme2)
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<Grimme2>`, and their revised forms :ref:`(Sherrill) <Sherrill>`.
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.. versionchanged:: TBD
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renamed *zero* keyword to *original* to avoid conflicts with
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:doc:`pair style zero <pair_zero>` when used as :doc:`hybrid
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sub-style <pair_hybrid>`.
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Available damping functions are the original "zero-damping" (*original*)
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:ref:`(Grimme1) <Grimme1>`, Becke-Johnson damping (*bj*) :ref:`(Grimme2)
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<Grimme2>`, and their revised forms (*zerom* and *bjm*, respectively)
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:ref:`(Sherrill) <Sherrill>`.
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Available XC functional scaling factors are listed in the table below,
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and depend on the selected damping function.
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@ -67,7 +74,7 @@ and depend on the selected damping function.
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+==================+================================================================================+
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| | | | slater-dirac-exchange, b-lyp, b-p, b97-d, revpbe, pbe, pbesol, rpw86-pbe, |
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| | | | rpbe, tpss, b3-lyp, pbe0, hse06, revpbe38, pw6b95, tpss0, b2-plyp, pwpb95, |
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| | zero | | b2gp-plyp, ptpss, hf, mpwlyp, bpbe, bh-lyp, tpssh, pwb6k, b1b95, bop, o-lyp, |
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| | original | | b2gp-plyp, ptpss, hf, mpwlyp, bpbe, bh-lyp, tpssh, pwb6k, b1b95, bop, o-lyp, |
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| | | | o-pbe, ssb, revssb, otpss, b3pw91, revpbe0, pbe38, mpw1b95, mpwb1k, bmk, |
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| | | | cam-b3lyp, lc-wpbe, m05, m052x, m06l, m06, m062x, m06hf, hcth120 |
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+------------------+--------------------------------------------------------------------------------+
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@ -122,6 +129,8 @@ Style *dispersion/d3* is part of the EXTRA-PAIR package. It is only
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enabled if LAMMPS was built with that package. See the :doc:`Build
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package <Build_package>` page for more info.
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The compiled in parameters require the use of :doc:`metal units <units>`.
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It is currently *not* possible to calculate three-body dispersion
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contributions according to, for example, the Axilrod-Teller-Muto model.
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@ -1,4 +1,5 @@
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LAMMPS (15 Sep 2022)
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LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-106-g5d02e140d4)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
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using 1 OpenMP thread(s) per MPI task
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# flat membrane demo
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variable r0 equal 0.97
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@ -46,7 +47,7 @@ set type 1 mass 1.0
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Setting atom values ...
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1920 settings made for mass
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set type 1 shape 1 1 1
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set type 1 shape 1 0.99 0.99
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Setting atom values ...
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1920 settings made for shape
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@ -99,7 +100,7 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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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 = 10 steps, check = yes
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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 = 3.6
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ghost atom cutoff = 3.6
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@ -113,47 +114,47 @@ Neighbor list info ...
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||||
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
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Step Temp Press Pxx Pyy
|
||||
0 0.23 -0.0073508785 -0.012283389 -0.012234574
|
||||
200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
|
||||
400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
|
||||
600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283
|
||||
800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525
|
||||
1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05
|
||||
1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929
|
||||
1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05
|
||||
1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081
|
||||
1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131
|
||||
2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705
|
||||
2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05
|
||||
2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857
|
||||
2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
|
||||
2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
|
||||
3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
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||||
Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms
|
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200 0.20906916 -0.0010610794 -0.0011895359 -0.00198968
|
||||
400 0.21907691 -0.00068750897 -0.0013175111 -0.00072355516
|
||||
600 0.22648739 -0.00057306694 -0.000831971 -0.00096776143
|
||||
800 0.2368957 -0.00028517767 -0.00050638195 -0.00052670236
|
||||
1000 0.22735705 -0.00032638104 -0.00037959812 -0.00071879257
|
||||
1200 0.22910882 -0.00019457758 -0.00024451315 -0.00027807764
|
||||
1400 0.22754022 -0.00033048317 -0.00010053263 -0.00075173132
|
||||
1600 0.22503496 -7.593954e-05 5.2989168e-05 -0.00022521685
|
||||
1800 0.22673577 -0.00017917699 1.0176667e-05 -0.00047893102
|
||||
2000 0.22480858 9.318318e-05 0.00031024343 1.2738253e-05
|
||||
2200 0.22387294 -6.9083174e-05 -4.6170865e-05 4.6682009e-05
|
||||
2400 0.22686231 0.00022776785 0.00028204391 0.00030116273
|
||||
2600 0.23055637 8.2778175e-05 0.00027137529 4.2254076e-05
|
||||
2800 0.23126717 0.00044863024 0.00071654709 0.00057652233
|
||||
3000 0.22234736 0.00031577792 0.00051797227 0.00039087282
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||||
Loop time of 7.17991 on 1 procs for 3000 steps with 1920 atoms
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||||
Performance: 383058.431 tau/day, 443.355 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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Performance: 361007.348 tau/day, 417.833 timesteps/s, 802.239 katom-step/s
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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||||
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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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||||
Pair | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67
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||||
Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27
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||||
Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51
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Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01
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Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22
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Other | | 0.02181 | | | 0.32
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Pair | 6.2257 | 6.2257 | 6.2257 | 0.0 | 86.71
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Neigh | 0.11392 | 0.11392 | 0.11392 | 0.0 | 1.59
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||||
Comm | 0.036614 | 0.036614 | 0.036614 | 0.0 | 0.51
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||||
Output | 0.00052672 | 0.00052672 | 0.00052672 | 0.0 | 0.01
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Modify | 0.78577 | 0.78577 | 0.78577 | 0.0 | 10.94
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Other | | 0.01743 | | | 0.24
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||||
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Nlocal: 1920 ave 1920 max 1920 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 772 ave 772 max 772 min
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Nghost: 771 ave 771 max 771 min
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||||
Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 46804 ave 46804 max 46804 min
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Neighs: 46750 ave 46750 max 46750 min
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||||
Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 46804
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Ave neighs/atom = 24.377083
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Neighbor list builds = 99
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Total # of neighbors = 46750
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Ave neighs/atom = 24.348958
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Neighbor list builds = 98
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||||
Dangerous builds = 0
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||||
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Total wall time: 0:00:06
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Total wall time: 0:00:07
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@ -1,4 +1,5 @@
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LAMMPS (15 Sep 2022)
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LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-106-g5d02e140d4)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
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using 1 OpenMP thread(s) per MPI task
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# flat membrane demo
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variable r0 equal 0.97
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@ -46,7 +47,7 @@ set type 1 mass 1.0
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Setting atom values ...
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1920 settings made for mass
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||||
|
||||
set type 1 shape 1 1 1
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set type 1 shape 1 0.99 0.99
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||||
Setting atom values ...
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1920 settings made for shape
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|
||||
@ -99,7 +100,7 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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|
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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 = 10 steps, check = yes
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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 = 3.6
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ghost atom cutoff = 3.6
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@ -113,47 +114,47 @@ Neighbor list info ...
|
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Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes
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Step Temp Press Pxx Pyy
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0 0.23 -0.0073508785 -0.012283389 -0.012234574
|
||||
200 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502
|
||||
400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093
|
||||
600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609
|
||||
800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294
|
||||
1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572
|
||||
1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505
|
||||
1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05
|
||||
1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754
|
||||
1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05
|
||||
2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213
|
||||
2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05
|
||||
2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05
|
||||
2600 0.23085675 0.00014029405 0.00017983536 0.00017895001
|
||||
2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243
|
||||
3000 0.23421357 0.00023505702 0.00020752013 0.00053567111
|
||||
Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms
|
||||
200 0.21866566 -0.0011213114 -0.0017540296 -0.0017008786
|
||||
400 0.22409469 -0.00055137604 -0.00050366017 -0.0012846672
|
||||
600 0.21623646 -0.0004808564 -0.00063496522 -0.00071617302
|
||||
800 0.22248339 -0.00066333806 -0.00093812145 -0.00099410261
|
||||
1000 0.22367907 -0.0003439459 -0.00076259578 -0.00013354375
|
||||
1200 0.23276206 8.5764334e-06 -0.00036165178 0.00038543803
|
||||
1400 0.23129049 -5.1997966e-06 -0.00040514787 0.00017093646
|
||||
1600 0.22074564 -0.0001604642 -0.00053959031 9.0463391e-05
|
||||
1800 0.2276062 -0.00015655254 -0.00042925633 5.4938379e-05
|
||||
2000 0.22469391 -3.6198836e-05 -1.8538296e-06 -0.00010464749
|
||||
2200 0.22737515 -1.8967356e-05 0.0001341006 -0.00022739894
|
||||
2400 0.22607533 0.00014650382 -2.4871789e-05 0.00058296255
|
||||
2600 0.24044743 0.00045066449 0.00049153595 0.00078042437
|
||||
2800 0.23346628 0.00017994019 -5.0897724e-05 0.00046011801
|
||||
3000 0.22427206 0.00040437022 0.00049580531 0.00046259202
|
||||
Loop time of 5.04539 on 4 procs for 3000 steps with 1920 atoms
|
||||
|
||||
Performance: 553164.568 tau/day, 640.237 timesteps/s
|
||||
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 513736.789 tau/day, 594.603 timesteps/s, 1.142 Matom-step/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21
|
||||
Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54
|
||||
Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28
|
||||
Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50
|
||||
Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57
|
||||
Other | | 2.338 | | | 49.90
|
||||
Pair | 4.1163 | 4.2634 | 4.4004 | 6.5 | 84.50
|
||||
Neigh | 0.00088605 | 0.032793 | 0.083516 | 19.1 | 0.65
|
||||
Comm | 0.006704 | 0.20003 | 0.40672 | 42.5 | 3.96
|
||||
Output | 0.00033812 | 0.0012192 | 0.0020905 | 2.3 | 0.02
|
||||
Modify | 0.00035967 | 0.20167 | 0.42535 | 45.0 | 4.00
|
||||
Other | | 0.3462 | | | 6.86
|
||||
|
||||
Nlocal: 480 ave 1011 max 0 min
|
||||
Nlocal: 480 ave 1052 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 860 ave 1771 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 11697.8 ave 30095 max 0 min
|
||||
Nghost: 854.5 ave 1801 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 11684.2 ave 31145 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 46791
|
||||
Ave neighs/atom = 24.370313
|
||||
Neighbor list builds = 99
|
||||
Total # of neighbors = 46737
|
||||
Ave neighs/atom = 24.342188
|
||||
Neighbor list builds = 98
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:04
|
||||
Total wall time: 0:00:05
|
||||
@ -32,7 +32,7 @@
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using MathConst::MY_4PI;
|
||||
using MathConst::MY_PI;
|
||||
using MathConst::MY_PI2;
|
||||
using MathConst::MY_TWOBYSIXTH;
|
||||
|
||||
@ -487,7 +487,7 @@ double PairYLZ::ylz_analytic(const int i, const int j, double a1[3][3], double a
|
||||
|
||||
uA = -energy_well * t1 * cos_t;
|
||||
U = uA * phi;
|
||||
dUdr = MY_4PI / (rcut - rmin) * (t1) *sin(t) * phi * energy_well;
|
||||
dUdr = MY_PI * zt / (rcut - rmin) * (t1) *sin(t) * phi * energy_well;
|
||||
dUdphi = uA;
|
||||
}
|
||||
|
||||
|
||||
@ -29,6 +29,7 @@
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <algorithm>
|
||||
#include <cmath>
|
||||
@ -58,6 +59,7 @@ static constexpr double autoang = 0.52917725; // atomic units (Bohr) to Angst
|
||||
static constexpr double autoev = 27.21140795; // atomic units (Hartree) to eV
|
||||
|
||||
#include "d3_parameters.h"
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Constructor (Required)
|
||||
------------------------------------------------------------------------- */
|
||||
@ -75,6 +77,7 @@ PairDispersionD3::PairDispersionD3(LAMMPS *lmp) :
|
||||
one_coeff = 1;
|
||||
single_enable = 0;
|
||||
|
||||
dampingCode = 0;
|
||||
s6 = s8 = s18 = rs6 = rs8 = rs18 = a1 = a2 = alpha = alpha6 = alpha8 = 0.0;
|
||||
}
|
||||
|
||||
@ -130,12 +133,20 @@ void PairDispersionD3::allocate()
|
||||
|
||||
void PairDispersionD3::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all(FLERR, "Pair_style dispersion/d3 needs 4 arguments");
|
||||
if (narg != 4) error->all(FLERR, "Pair style dispersion/d3 needs 4 arguments");
|
||||
if (strcmp("metal", update->unit_style) != 0)
|
||||
error->all(FLERR, Error::NOLASTLINE, "Pair style dispersion/d3 requires metal units");
|
||||
|
||||
damping_type = arg[0];
|
||||
std::string damping_type = arg[0];
|
||||
std::string functional_name = arg[1];
|
||||
|
||||
std::transform(damping_type.begin(), damping_type.end(), damping_type.begin(), ::tolower);
|
||||
std::unordered_map<std::string, int> dampingMap = {
|
||||
{"original", 1}, {"zero", 1}, {"zerom", 2}, {"bj", 3}, {"bjm", 4}};
|
||||
if (!dampingMap.count(damping_type))
|
||||
error->all(FLERR, Error::NOPOINTER, "Unknown damping type {} for pair style dispersion/d3",
|
||||
damping_type);
|
||||
dampingCode = dampingMap[damping_type];
|
||||
|
||||
rthr = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
cn_thr = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
@ -154,7 +165,7 @@ int PairDispersionD3::find_atomic_number(std::string &key)
|
||||
{
|
||||
std::transform(key.begin(), key.end(), key.begin(), ::tolower);
|
||||
if (key.length() == 1) key += " ";
|
||||
key.resize(2);
|
||||
if (key.length() > 2) return -1;
|
||||
|
||||
std::vector<std::string> element_table = {
|
||||
"h ", "he", "li", "be", "b ", "c ", "n ", "o ", "f ", "ne", "na", "mg", "al", "si",
|
||||
@ -283,6 +294,8 @@ void PairDispersionD3::coeff(int narg, char **arg)
|
||||
for (int i = 0; i < ntypes; i++) {
|
||||
element = arg[i + 2];
|
||||
atomic_numbers[i] = find_atomic_number(element);
|
||||
if (atomic_numbers[i] < 0)
|
||||
error->all(FLERR, Error::NOLASTLINE, "Element {} not supported", element);
|
||||
}
|
||||
|
||||
int count = 0;
|
||||
@ -450,11 +463,6 @@ double *PairDispersionD3::get_dC6(int iat, int jat, double cni, double cnj)
|
||||
|
||||
void PairDispersionD3::compute(int eflag, int vflag)
|
||||
{
|
||||
|
||||
std::unordered_map<std::string, int> dampingMap = {
|
||||
{"zero", 1}, {"zerom", 2}, {"bj", 3}, {"bjm", 4}};
|
||||
int dampingCode = dampingMap[damping_type];
|
||||
|
||||
double evdwl = 0.0;
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
@ -518,7 +526,8 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
t6 = t8 = e6 = e8 = evdwl = fpair = fpair1 = fpair2 = 0.0;
|
||||
|
||||
switch (dampingCode) {
|
||||
case 1: { // zero
|
||||
|
||||
case 1: { // original
|
||||
|
||||
double r0 = r / r0ab[type[i]][type[j]];
|
||||
|
||||
@ -539,6 +548,7 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
fpair = fpair1 + fpair2;
|
||||
fpair *= factor_lj;
|
||||
} break;
|
||||
|
||||
case 2: { // zerom
|
||||
|
||||
double r0 = r0ab[type[i]][type[j]];
|
||||
@ -564,6 +574,7 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
fpair = fpair1 + fpair2;
|
||||
fpair *= factor_lj;
|
||||
} break;
|
||||
|
||||
case 3: { // bj
|
||||
|
||||
double r0 = sqrt(C8 / C6);
|
||||
@ -584,6 +595,7 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
fpair = -(tmp6 + tmp8);
|
||||
fpair *= factor_lj;
|
||||
} break;
|
||||
|
||||
case 4: { // bjm
|
||||
|
||||
double r0 = sqrt(C8 / C6);
|
||||
@ -603,10 +615,15 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
|
||||
fpair = -(tmp6 + tmp8);
|
||||
fpair *= factor_lj;
|
||||
}
|
||||
} break;
|
||||
|
||||
default: {
|
||||
// this should not happen with the error check in the init_style function
|
||||
error->all(FLERR, Error::NOLASTLINE, "Damping code {} unknown", dampingCode);
|
||||
} break;
|
||||
}
|
||||
|
||||
if (eflag) { evdwl = -(s6 * e6 + s8 * e8) * factor_lj; }
|
||||
if (eflag) evdwl = -(s6 * e6 + s8 * e8) * factor_lj;
|
||||
|
||||
double rest = (s6 * e6 + s8 * e8) / C6;
|
||||
|
||||
@ -693,12 +710,6 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
|
||||
void PairDispersionD3::set_funcpar(std::string &functional_name)
|
||||
{
|
||||
|
||||
std::unordered_map<std::string, int> dampingMap = {
|
||||
{"zero", 1}, {"zerom", 2}, {"bj", 3}, {"bjm", 4}};
|
||||
|
||||
int dampingCode = dampingMap[damping_type];
|
||||
|
||||
switch (dampingCode) {
|
||||
|
||||
case 1: { // zero
|
||||
@ -962,14 +973,10 @@ void PairDispersionD3::set_funcpar(std::string &functional_name)
|
||||
s8 = 1.206;
|
||||
break;
|
||||
default:
|
||||
error->all(FLERR, "Functional name unknown");
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Functional {} not supported with original damping function", functional_name);
|
||||
break;
|
||||
}
|
||||
//fprintf(stderr,"s6 : %f\n", s6);
|
||||
//fprintf(stderr,"s8 : %f\n", s8);
|
||||
//fprintf(stderr,"rs6 : %f\n", rs6);
|
||||
//fprintf(stderr,"rs8 : %f\n", rs8);
|
||||
//fprintf(stderr,"alpha : %f\n", alpha);
|
||||
} break;
|
||||
|
||||
case 2: { // zerom
|
||||
@ -1024,14 +1031,10 @@ void PairDispersionD3::set_funcpar(std::string &functional_name)
|
||||
rs8 = 0.003160;
|
||||
break;
|
||||
default:
|
||||
error->all(FLERR, "Functional name unknown");
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Functional {} not supported with zerom damping function", functional_name);
|
||||
break;
|
||||
}
|
||||
//fprintf(stderr,"s6 : %f\n", s6);
|
||||
//fprintf(stderr,"s8 : %f\n", s8);
|
||||
//fprintf(stderr,"rs6 : %f\n", rs6);
|
||||
//fprintf(stderr,"rs8 : %f\n", rs8);
|
||||
//fprintf(stderr,"alpha : %f\n", alpha);
|
||||
|
||||
rs8 = rs8 / autoang;
|
||||
} break;
|
||||
@ -1334,16 +1337,11 @@ void PairDispersionD3::set_funcpar(std::string &functional_name)
|
||||
a2 = 4.5000;
|
||||
break;
|
||||
default:
|
||||
error->all(FLERR, "Functional name unknown");
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Functional {} not supported with bj damping function", functional_name);
|
||||
break;
|
||||
}
|
||||
|
||||
//fprintf(stderr,"s6 : %f\n", s6);
|
||||
//fprintf(stderr,"s8 : %f\n", s8);
|
||||
//fprintf(stderr,"a1 : %f\n", a1);
|
||||
//fprintf(stderr,"a2 : %f\n", a2);
|
||||
//fprintf(stderr,"alpha : %f\n", alpha);
|
||||
|
||||
a2 = a2 * autoang;
|
||||
} break;
|
||||
|
||||
@ -1400,21 +1398,17 @@ void PairDispersionD3::set_funcpar(std::string &functional_name)
|
||||
a2 = 3.593680;
|
||||
break;
|
||||
default:
|
||||
error->all(FLERR, "Functional name unknown");
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Functional {} not supported with bjm damping function", functional_name);
|
||||
break;
|
||||
}
|
||||
|
||||
//fprintf(stderr,"s6 : %f\n", s6);
|
||||
//fprintf(stderr,"s8 : %f\n", s8);
|
||||
//fprintf(stderr,"a1 : %f\n", a1);
|
||||
//fprintf(stderr,"a2 : %f\n", a2);
|
||||
//fprintf(stderr,"alpha : %f\n", alpha);
|
||||
|
||||
a2 = a2 * autoang;
|
||||
|
||||
} break;
|
||||
default:
|
||||
error->all(FLERR, "Damping type unknown");
|
||||
// this should not happen with the error check in the init_style function
|
||||
error->all(FLERR, Error::NOLASTLINE, "Damping code {} unknown", dampingCode);
|
||||
break;
|
||||
}
|
||||
}
|
||||
@ -1436,8 +1430,6 @@ double PairDispersionD3::init_one(int i, int j)
|
||||
void PairDispersionD3::init_style()
|
||||
{
|
||||
if (atom->tag_enable == 0) error->all(FLERR, "Pair style D3 requires atom IDs");
|
||||
//if (force->newton_pair == 0)
|
||||
// error->all(FLERR,"Pair style D3 requires newton pair on");
|
||||
|
||||
// need an half neighbor list
|
||||
neighbor->add_request(this);
|
||||
|
||||
@ -48,7 +48,7 @@ class PairDispersionD3 : public Pair {
|
||||
double rthr; // R^2 distance to cutoff for D3_calculation
|
||||
double cn_thr; // R^2 distance to cutoff for CN_calculation
|
||||
|
||||
std::string damping_type; // damping function type
|
||||
int dampingCode;
|
||||
double s6, s8, s18, rs6, rs8, rs18; // XC parameters
|
||||
double a1, a2, alpha, alpha6, alpha8;
|
||||
|
||||
|
||||
Reference in New Issue
Block a user