diff --git a/doc/src/bond_bpm_rotational.rst b/doc/src/bond_bpm_rotational.rst index 3ecd1cf9503..e4cfef3d512 100644 --- a/doc/src/bond_bpm_rotational.rst +++ b/doc/src/bond_bpm_rotational.rst @@ -132,8 +132,8 @@ or :doc:`read_restart ` commands: * :math:`k_b` (force*distance/radians units) * :math:`f_{r,c}` (force units) * :math:`f_{s,c}` (force units) -* :math:`\tau_{b,c}` (force*distance units) * :math:`\tau_{t,c}` (force*distance units) +* :math:`\tau_{b,c}` (force*distance units) * :math:`\gamma_n` (force/velocity units) * :math:`\gamma_s` (force/velocity units) * :math:`\gamma_r` (force*distance/velocity units) @@ -154,8 +154,11 @@ page on BPMs. If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break during a simulation run. This will prevent some unnecessary calculation. -However, if a bond reaches a damage criterion greater than one, -it will trigger an error. +The recommended bond communication distance no longer depends on bond failure +coefficients (which are ignored) but instead corresponds to the typical heurestic +maximum strain used by typical non-bpm bond styles. Similar behavior to *break no* +can also be attained by setting arbitrarily high values for all four failure +coefficients. One cannot use *break no* with *smooth yes*. If the *store/local* keyword is used, an internal fix will track bonds that break during the simulation. Whenever a bond breaks, data is processed diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 4bc5cd34631..c868a47a12e 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -117,8 +117,11 @@ page on BPMs. If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break during a simulation run. This will prevent some unnecessary calculation. -However, if a bond reaches a strain greater than :math:`\epsilon_c`, -it will trigger an error. +The recommended bond communication distance no longer depends on the value of +:math:`\epsilon_c` (which is ignored) but instead corresponds to the typical +heurestic maximum strain used by typical non-bpm bond styles. Similar behavior +to *break no* can also be attained by setting an arbitrarily high value of +:math:`\epsilon_c`. One cannot use *break no* with *smooth yes*. .. versionadded:: TBD diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index e0f15ccd622..11a460e9cae 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -235,12 +235,15 @@ given by: .. math:: - \eta_n = \alpha (m_{eff}k_n)^{1/2} + \eta_n = \alpha (m_{eff}k_{nd})^{1/2} -For normal contact models based on material parameters, :math:`k_n = 4/3Ea`. This -damping model is not compatible with cohesive normal models such as *JKR* or *DMT*. -The parameter :math:`\alpha` is related to the restitution coefficient *e* -according to: +where :math:`k_{nd}` is an effective harmonic stiffness equal to the ratio of +the normal force to the overlap. For example, :math:`k_{nd} = 4/3Ea` for a +Hertz contact model based on material parameters with :math:`a` being +the contact radius of :math:`\sqrt{\delta R}`. For Hooke, :math:`k_{nd}` +is simply the spring constant or :math:`k_{n}`. This damping model is not +compatible with cohesive normal models such as *JKR* or *DMT*. The parameter +:math:`\alpha` is related to the restitution coefficient *e* according to: .. math:: @@ -251,25 +254,26 @@ of the normal contact model parameters should be between 0 and 1, but no error check is performed on this. The *coeff_restitution* model is useful when a specific normal coefficient of -restitution :math:`e` is required. In these models, the normal coefficient of -restitution :math:`e` is specified as an input. Following the approach of -:ref:`(Brilliantov et al) `, when using the *hooke* normal model, -*coeff_restitution* calculates the damping coefficient as: +restitution :math:`e` is required. It operates much like the *Tsuji* model +but, the normal coefficient of restitution :math:`e` is specified as an input +in place of the usual :math:`\eta_{n0}` value in the normal model. Following +the approach of :ref:`(Brilliantov et al) `, when using the *hooke* +normal model, *coeff_restitution* then calculates the damping coefficient as: .. math:: - \eta_n = \sqrt{\frac{4m_{eff}k_n}{1+\left( \frac{\pi}{\log(e)}\right)^2}} , + \eta_n = \sqrt{\frac{4m_{eff}k_{nd}}{1+\left( \frac{\pi}{\log(e)}\right)^2}} , +where :math:`k_{nd}` is the same stiffness defined in the above *Tsuji* model. For any other normal model, e.g. the *hertz* and *hertz/material* models, the damping coefficient is: .. math:: - \eta_n = -2\sqrt{\frac{5}{6}}\frac{\log(e)}{\sqrt{\pi^2+(\log(e))^2}}(R_{eff} \delta_{ij})^{\frac{1}{4}}\sqrt{\frac{3}{2}k_n m_{eff}} , + \eta_n = -2\sqrt{\frac{5}{6}}\frac{\log(e)}{\sqrt{\pi^2+(\log(e))^2}}\sqrt{\frac{3}{2}k_{nd} m_{eff}} , -where :math:`k_n = \frac{4}{3} E_{eff}` for the *hertz/material* model. Since -*coeff_restitution* accounts for the effective mass, effective radius, and -pairwise overlaps (except when used with the *hooke* normal model) when calculating +Since *coeff_restitution* accounts for the effective mass, effective radius, +and pairwise overlaps (except when used with the *hooke* normal model) when calculating the damping coefficient, it accurately reproduces the specified coefficient of restitution for both monodisperse and polydisperse particle pairs. This damping model is not compatible with cohesive normal models such as *JKR* or *DMT*. diff --git a/examples/bpm/pour/in.bpm.pour b/examples/bpm/pour/in.bpm.pour index d9bb60674a6..05c6334b665 100644 --- a/examples/bpm/pour/in.bpm.pour +++ b/examples/bpm/pour/in.bpm.pour @@ -13,9 +13,9 @@ region wall_cyl cylinder z 0.0 0.0 10.0 EDGE EDGE side in region dropzone cylinder z 0.0 0.0 10.0 40.0 50.0 side in pair_style gran/hertz/history 1.0 NULL 0.5 NULL 0.1 1 -bond_style bpm/rotational +bond_style bpm/rotational break no smooth no pair_coeff 1 1 -bond_coeff 1 1.0 0.2 0.01 0.01 2.0 0.4 0.02 0.02 0.2 0.04 0.002 0.002 +bond_coeff 1 1.0 0.2 0.01 0.01 0.0 0.0 0.0 0.0 0.2 0.04 0.002 0.002 compute nbond all nbond/atom compute tbond all reduce sum c_nbond diff --git a/examples/bpm/pour/log.29Aug2024.bpm.pour.g++.4 b/examples/bpm/pour/log.29Aug2024.bpm.pour.g++.4 new file mode 100644 index 00000000000..6c7de496995 --- /dev/null +++ b/examples/bpm/pour/log.29Aug2024.bpm.pour.g++.4 @@ -0,0 +1,1117 @@ +LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-1045-gbcd123c882-modified) +units lj +dimension 3 +boundary m m m +atom_style bpm/sphere +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 +newton on off +comm_modify vel yes cutoff 3.3 +region box block -15 15 -15 15 0 60.0 +create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50 +Created orthogonal box = (-15 -15 0) to (15 15 60) + 1 by 1 by 4 MPI processor grid + +molecule my_mol "rect.mol" +Read molecule template my_mol: +#Made with create_mol.py + 1 molecules + 0 fragments + 63 atoms with max type 1 + 297 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region wall_cyl cylinder z 0.0 0.0 10.0 EDGE EDGE side in +region dropzone cylinder z 0.0 0.0 10.0 40.0 50.0 side in + +pair_style gran/hertz/history 1.0 NULL 0.5 NULL 0.1 1 +bond_style bpm/rotational break no smooth no +pair_coeff 1 1 +bond_coeff 1 1.0 0.2 0.01 0.01 0.0 0.0 0.0 0.0 0.2 0.04 0.002 0.002 + +compute nbond all nbond/atom +compute tbond all reduce sum c_nbond +compute bond_ids all property/local batom1 batom2 +compute bond_properties all bond/local dist b1 + +compute_modify thermo_temp dynamic/dof yes + +fix 1 all wall/gran hertz/history 1.0 NULL 0.5 NULL 0.1 1 zplane 0.0 NULL +fix 2 all wall/gran/region hertz/history 1.0 NULL 0.5 NULL 0.1 1 region wall_cyl +fix 3 all gravity 1e-4 vector 0 0 -1 +fix 4 all deposit 40 0 1500 712511343 mol my_mol region dropzone near 2.0 vz -0.05 -0.05 +fix 5 all nve/bpm/sphere + +timestep 0.05 +thermo_style custom step ke pe pxx pyy pzz c_tbond +thermo 100 +#dump 1 all custom 500 atomDump id radius x y z c_nbond mol +#dump 2 all local 500 bondDump c_bond_ids[*] c_bond_properties[*] +#dump_modify 2 colname 1 "id1" colname 2 "id2" colname 3 "r" colname 4 "r0" + +run 100000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- BPM bond style: doi:10.1039/D3SM01373A + +@Article{Clemmer2024, + author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.}, + title = {A soft departure from jamming: the compaction of deformable + granular matter under high pressures}, + journal = {Soft Matter}, + year = 2024, + volume = 20, + number = 8, + pages = {1702--1718} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 3.3 + binsize = 0.65, bins = 47 47 93 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hertz/history, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.515 | 6.515 | 6.515 Mbytes + Step KinEng 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2.2293935e-05 2.7592964e-05 9.4285714 + 97200 3.7951338e-06 0 1.972518e-05 2.2500533e-05 2.7324564e-05 9.4285714 + 97300 3.7915088e-06 0 1.9577123e-05 2.3151642e-05 2.7299762e-05 9.4285714 + 97400 3.7485224e-06 0 1.9324456e-05 2.30806e-05 2.7089915e-05 9.4285714 + 97500 3.7004488e-06 0 1.9219566e-05 2.2917658e-05 2.6888759e-05 9.4285714 + 97600 3.5146189e-06 0 1.9216453e-05 2.3350177e-05 2.6561724e-05 9.4285714 + 97700 3.2092658e-06 0 1.9210005e-05 2.3618954e-05 2.6020575e-05 9.4285714 + 97800 3.0741264e-06 0 1.8785442e-05 2.3901093e-05 2.5609259e-05 9.4285714 + 97900 3.2689032e-06 0 1.8332069e-05 2.3813462e-05 2.5281581e-05 9.4285714 + 98000 3.4879184e-06 0 1.7639391e-05 2.3233496e-05 2.5115654e-05 9.4285714 + 98100 3.0702391e-06 0 1.7345936e-05 2.36305e-05 2.524874e-05 9.4285714 + 98200 2.9214268e-06 0 1.7751691e-05 2.3810696e-05 2.5038638e-05 9.4285714 + 98300 2.9373287e-06 0 1.7414606e-05 2.3325178e-05 2.4758312e-05 9.4285714 + 98400 2.879615e-06 0 1.8218541e-05 2.3403674e-05 2.4845847e-05 9.4285714 + 98500 2.848204e-06 0 1.9008342e-05 2.3138169e-05 2.481977e-05 9.4285714 + 98600 2.7263423e-06 0 1.8559461e-05 2.2912112e-05 2.4778725e-05 9.4285714 + 98700 2.6065427e-06 0 1.8899571e-05 2.2936881e-05 2.4788275e-05 9.4285714 + 98800 2.4965223e-06 0 1.812463e-05 2.2777276e-05 2.4817472e-05 9.4285714 + 98900 2.5312476e-06 0 1.7188063e-05 2.2549286e-05 2.4758508e-05 9.4285714 + 99000 2.6511883e-06 0 1.7634415e-05 2.2369995e-05 2.4688578e-05 9.4285714 + 99100 2.7173422e-06 0 1.7730299e-05 2.1958527e-05 2.4725265e-05 9.4285714 + 99200 2.7416008e-06 0 1.7354475e-05 2.1383708e-05 2.4972238e-05 9.4285714 + 99300 2.7403492e-06 0 1.7710033e-05 2.0999817e-05 2.5194177e-05 9.4285714 + 99400 2.6759704e-06 0 1.7805932e-05 2.0887012e-05 2.5239724e-05 9.4285714 + 99500 2.7350974e-06 0 1.7591419e-05 2.1055636e-05 2.5010401e-05 9.4285714 + 99600 2.8807532e-06 0 1.7598054e-05 2.1135294e-05 2.4759587e-05 9.4285714 + 99700 2.9230897e-06 0 1.7610982e-05 2.1212426e-05 2.4583469e-05 9.4285714 + 99800 2.9159336e-06 0 1.7740095e-05 2.1476279e-05 2.4546909e-05 9.4285714 + 99900 2.8532894e-06 0 1.7977152e-05 2.14971e-05 2.4856973e-05 9.4285714 + 100000 2.7133352e-06 0 1.8003971e-05 2.1327905e-05 2.5243646e-05 9.4285714 +Loop time of 183.342 on 4 procs for 100000 steps with 2520 atoms + +Performance: 2356254.720 tau/day, 545.429 timesteps/s, 1.374 Matom-step/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.025623 | 1.0356 | 3.8189 | 158.0 | 0.56 +Bond | 2.5126 | 46.913 | 155.81 | 920.8 | 25.59 +Neigh | 2.6046 | 2.623 | 2.6318 | 0.7 | 1.43 +Comm | 2.0083 | 41.613 | 149.8 | 970.4 | 22.70 +Output | 0.12287 | 0.90946 | 1.6958 | 80.6 | 0.50 +Modify | 0.52882 | 5.0973 | 16.247 | 286.1 | 2.78 +Other | | 85.15 | | | 46.44 + +Nlocal: 630 ave 2514 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 49.75 ave 193 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Neighs: 2476 ave 9897 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 9904 +Ave neighs/atom = 3.9301587 +Ave special neighs/atom = 36.31746 +Neighbor list builds = 4880 +Dangerous builds = 0 +Total wall time: 0:03:03 diff --git a/examples/bpm/pour/log.4May2022.bpm.pour.g++.4 b/examples/bpm/pour/log.4May2022.bpm.pour.g++.4 deleted file mode 100644 index 5fc31df9766..00000000000 --- a/examples/bpm/pour/log.4May2022.bpm.pour.g++.4 +++ /dev/null @@ -1,1096 +0,0 @@ -LAMMPS (4 May 2022) -units lj -dimension 3 -boundary m m m -atom_style bpm/sphere -special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 -newton on off -comm_modify vel yes cutoff 3.3 -region box block -15 15 -15 15 0 60.0 -create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50 -Created orthogonal box = (-15 -15 0) to (15 15 60) - 1 by 1 by 4 MPI processor grid - -molecule my_mol "rect.mol" -Read molecule template my_mol: - 1 molecules - 0 fragments - 63 atoms with max type 1 - 297 bonds with max type 1 - 0 angles with max type 0 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -region wall_cyl cylinder z 0.0 0.0 10.0 EDGE EDGE side in -region dropzone cylinder z 0.0 0.0 10.0 40.0 50.0 side in - -pair_style gran/hertz/history 1.0 NULL 0.5 NULL 0.1 1 -bond_style bpm/rotational -pair_coeff 1 1 -bond_coeff 1 1.0 0.2 0.01 0.01 2.0 0.4 0.02 0.02 0.2 0.04 0.002 0.002 - -compute nbond all nbond/atom -compute tbond all reduce sum c_nbond -compute bond_ids all property/local batom1 batom2 -compute bond_properties all bond/local dist b1 - -compute_modify thermo_temp dynamic/dof yes - -fix 1 all wall/gran hertz/history 1.0 NULL 0.5 NULL 0.1 1 zplane 0.0 NULL -fix 2 all wall/gran/region hertz/history 1.0 NULL 0.5 NULL 0.1 1 region wall_cyl -fix 3 all gravity 1e-4 vector 0 0 -1 -fix 4 all deposit 40 0 1500 712511343 mol my_mol region dropzone near 2.0 vz -0.05 -0.05 -fix 5 all nve/bpm/sphere - -timestep 0.05 -thermo_style custom step ke pe pxx pyy pzz c_tbond -thermo 100 -#dump 1 all custom 500 atomDump id radius x y z c_nbond mol -#dump 2 all local 500 bondDump c_bond_ids[*] c_bond_properties[*] -#dump_modify 2 colname 1 "id1" colname 2 "id2" colname 3 "r" colname 4 "r0" - -run 100000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.3 - ghost atom cutoff = 3.3 - binsize = 0.65, bins = 47 47 93 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair gran/hertz/history, perpetual - attributes: half, newton on, size, history - pair build: half/size/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.515 | 6.515 | 6.515 Mbytes - Step KinEng PotEng Pxx Pyy Pzz c_tbond - 0 -0 0 0 0 0 0 - 100 0.0018331948 0 1.2795343e-05 1.3162764e-05 6.0889226e-06 9.4285714 - 200 0.0025933558 0 -9.7246963e-07 4.2628093e-07 2.254606e-06 9.4285714 - 300 0.0036964813 0 -5.214277e-06 9.6942542e-06 8.1928448e-07 9.4285714 - 400 0.0060104433 0 2.3353405e-05 1.8273171e-05 1.2647691e-05 9.4285714 - 500 0.0074435972 0 -1.7839575e-05 3.8686256e-06 -5.120219e-06 9.4285714 - 600 0.0077862298 0 3.8676586e-06 1.3499487e-05 4.1914953e-06 9.4285714 - 700 0.0075577591 0 2.995232e-06 1.2051677e-05 4.8789862e-06 9.4285714 - 800 0.0073958844 0 -1.4258432e-05 1.2272397e-05 -6.8630878e-06 9.4285714 - 900 0.007553697 0 9.9219152e-06 1.2918228e-05 8.8713909e-06 9.4285714 - 1000 0.0075815901 0 -6.1095276e-06 1.2607282e-05 -2.1917025e-06 9.4285714 - 1100 0.0075277384 0 -5.4044191e-06 1.0815313e-05 -3.3464998e-06 9.4285714 - 1200 0.0075026507 0 6.9770766e-06 1.3988236e-05 8.5114688e-06 9.4285714 - 1300 0.0075665473 0 -4.6433628e-06 8.6190703e-06 -3.8381153e-06 9.4285714 - 1400 0.0076224701 0 1.1589382e-06 7.9617716e-06 1.1941326e-06 9.4285714 - 1500 0.007603467 0 3.5774148e-06 1.3039063e-05 5.2641947e-06 9.4285714 - 1600 0.0059810407 0 4.8299936e-06 1.5343107e-05 4.8809408e-06 9.4285714 - 1700 0.0080230318 0 7.7953676e-06 2.5215962e-05 1.2492975e-05 9.4285714 - 1800 0.0087482398 0 4.7318071e-06 1.9559769e-05 4.2711986e-07 9.4285714 - 1900 0.0086877574 0 4.8038566e-06 1.8020212e-05 2.1297032e-06 9.4285714 - 2000 0.0086771118 0 6.1316671e-06 2.6348435e-05 8.9167408e-06 9.4285714 - 2100 0.0084670091 0 5.0586292e-06 1.9876458e-05 4.6539619e-06 9.4285714 - 2200 0.0083650907 0 9.4046949e-06 1.9264472e-05 1.0344742e-05 9.4285714 - 2300 0.0083549595 0 6.3002517e-06 2.0954839e-05 3.9631836e-06 9.4285714 - 2400 0.0083151535 0 4.9801292e-06 1.2138211e-05 6.2493867e-06 9.4285714 - 2500 0.0083898757 0 6.8667997e-06 1.9182698e-05 9.8363046e-06 9.4285714 - 2600 0.0084145705 0 4.1851e-06 1.8890376e-05 5.497773e-06 9.4285714 - 2700 0.0082712696 0 4.9701934e-06 1.7886474e-05 8.3184582e-06 9.4285714 - 2800 0.0073688706 0 1.144302e-05 1.3902577e-05 9.8542094e-06 9.4285714 - 2900 0.0072732669 0 8.2228374e-06 1.2550063e-05 8.7486939e-06 9.4285714 - 3000 0.0072225948 0 1.1788696e-05 1.6856873e-05 1.0219519e-05 9.4285714 - 3100 0.0048244969 0 2.6913622e-05 2.6037751e-05 1.5435674e-05 9.4285714 - 3200 0.0045717035 0 2.3464139e-05 2.1215606e-05 1.7659066e-05 9.4285714 - 3300 0.0047679567 0 6.5564192e-06 1.2866169e-05 1.4234937e-05 9.4285714 - 3400 0.0048448212 0 2.6268527e-06 9.1565649e-06 1.2387928e-05 9.4285714 - 3500 0.0048364711 0 2.8817245e-06 1.0066061e-05 1.1158512e-05 9.4285714 - 3600 0.0047125947 0 4.936496e-06 1.4195118e-05 1.5418285e-05 9.4285714 - 3700 0.0045641049 0 5.9769788e-06 9.8945153e-06 2.0158644e-05 9.4285714 - 3800 0.0045540235 0 6.1868269e-06 9.9425305e-06 1.6312008e-05 9.4285714 - 3900 0.0047271202 0 4.6825739e-06 1.3424496e-05 1.3234307e-05 9.4285714 - 4000 0.0049115261 0 5.5722312e-06 9.2060522e-06 1.6284048e-05 9.4285714 - 4100 0.0046819157 0 7.2200038e-06 1.0870694e-05 1.0519325e-05 9.4285714 - 4200 0.0035133816 0 3.6321041e-05 4.1100939e-05 1.8321255e-05 9.4285714 - 4300 0.0031933917 0 2.4951011e-05 2.5521457e-05 2.588421e-05 9.4285714 - 4400 0.0033515272 0 -5.6220845e-06 -2.4430502e-06 1.0942893e-05 9.4285714 - 4500 0.0034928951 0 6.2053481e-06 4.7764245e-06 1.991749e-05 9.4285714 - 4600 0.0029992338 0 2.369557e-06 4.59349e-06 2.0911379e-05 9.4285714 - 4700 0.0030650658 0 -2.7066449e-06 1.83391e-06 6.7096837e-06 9.4285714 - 4800 0.0031180382 0 3.4620044e-06 3.3494935e-06 1.7175961e-05 9.4285714 - 4900 0.0030365003 0 3.6295178e-06 6.2514468e-06 1.3401316e-05 9.4285714 - 5000 0.0030259714 0 5.1566588e-06 1.3494605e-05 9.7456367e-06 9.4285714 - 5100 0.0030499975 0 6.7608769e-06 1.9415863e-05 1.2078691e-05 9.4285714 - 5200 0.003005436 0 6.7275739e-06 2.0656574e-05 5.906659e-06 9.4285714 - 5300 0.0030000941 0 6.9641454e-06 1.54531e-05 1.7021736e-05 9.4285714 - 5400 0.0031465827 0 6.540246e-06 1.0837198e-05 1.0192016e-05 9.4285714 - 5500 0.0031981585 0 4.9292412e-06 4.6915838e-06 3.029257e-06 9.4285714 - 5600 0.0031525115 0 4.3125052e-06 2.8841432e-06 1.9324111e-05 9.4285714 - 5700 0.0032128781 0 5.1973159e-06 4.7261232e-06 1.5155154e-05 9.4285714 - 5800 0.0030092855 0 5.1574375e-06 1.3330205e-06 1.6470501e-05 9.4285714 - 5900 0.0025015767 0 9.468608e-06 6.3045435e-06 3.0961055e-05 9.4285714 - 6000 0.0024438438 0 8.0212466e-06 1.0032087e-05 2.8378471e-05 9.4285714 - 6100 0.0023816456 0 3.7802286e-06 -3.8999559e-06 1.8398107e-05 9.4285714 - 6200 0.0024459343 0 5.9964052e-07 8.2000754e-07 1.6404949e-05 9.4285714 - 6300 0.0025205884 0 4.7129599e-06 8.6972388e-06 2.9892106e-05 9.4285714 - 6400 0.0033754198 0 6.5856871e-06 2.3744673e-05 2.4721217e-05 9.4285714 - 6500 0.0037812296 0 1.376462e-07 2.0230253e-05 1.9719688e-05 9.4285714 - 6600 0.0038043567 0 -2.2279638e-06 1.4780176e-05 2.3799652e-05 9.4285714 - 6700 0.0038213959 0 1.1073632e-05 2.2516034e-05 2.5410459e-05 9.4285714 - 6800 0.0036977776 0 -1.0765937e-05 1.3667142e-05 1.7835133e-05 9.4285714 - 6900 0.0034769765 0 6.7509492e-06 2.840882e-05 2.435267e-05 9.4285714 - 7000 0.0031526409 0 1.4168552e-05 4.4965769e-05 4.5646226e-05 9.4285714 - 7100 0.00317737 0 -5.4803238e-06 3.1967885e-05 2.9211214e-05 9.4285714 - 7200 0.0034448361 0 4.8507597e-06 2.1591795e-05 2.3816498e-05 9.4285714 - 7300 0.0036147362 0 -2.791278e-06 2.9367843e-05 2.072129e-05 9.4285714 - 7400 0.0035651675 0 -1.6177129e-06 7.9033092e-06 2.3377855e-05 9.4285714 - 7500 0.0036394064 0 5.7414518e-06 1.246586e-05 2.8461253e-05 9.4285714 - 7600 0.0033086177 0 -3.6547872e-06 1.9730955e-05 2.8892436e-05 9.4285714 - 7700 0.0033410425 0 6.9618203e-06 6.4576188e-06 3.1766455e-05 9.4285714 - 7800 0.0035764747 0 1.2110077e-05 6.3850506e-06 3.5436107e-05 9.4285714 - 7900 0.0039500913 0 1.1250888e-05 5.2728547e-06 3.4972007e-05 9.4285714 - 8000 0.0042963353 0 1.8776503e-05 4.2083124e-06 3.5010281e-05 9.4285714 - 8100 0.0048297614 0 2.5603506e-05 3.3748362e-06 4.0838382e-05 9.4285714 - 8200 0.0052301447 0 2.2727386e-05 4.8879987e-06 3.4821083e-05 9.4285714 - 8300 0.005169511 0 2.5022891e-05 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9.4285714 - 96000 7.7875968e-07 0 2.8643986e-05 2.2987641e-05 2.6323848e-05 9.4285714 - 96100 7.8525813e-07 0 2.8773044e-05 2.3055913e-05 2.6556088e-05 9.4285714 - 96200 7.7518366e-07 0 2.8878871e-05 2.3101151e-05 2.6812081e-05 9.4285714 - 96300 7.6015915e-07 0 2.8820245e-05 2.3136672e-05 2.6915584e-05 9.4285714 - 96400 7.4067407e-07 0 2.8661992e-05 2.3169734e-05 2.6801804e-05 9.4285714 - 96500 7.0061605e-07 0 2.8400346e-05 2.3121121e-05 2.6529198e-05 9.4285714 - 96600 6.6164038e-07 0 2.8306211e-05 2.3011655e-05 2.6142152e-05 9.4285714 - 96700 6.5255615e-07 0 2.8340108e-05 2.2886154e-05 2.5768282e-05 9.4285714 - 96800 6.5992528e-07 0 2.8315654e-05 2.2712955e-05 2.5506907e-05 9.4285714 - 96900 6.618124e-07 0 2.8440952e-05 2.2580367e-05 2.5361502e-05 9.4285714 - 97000 6.7139818e-07 0 2.8508432e-05 2.253211e-05 2.5304698e-05 9.4285714 - 97100 6.8703272e-07 0 2.8403291e-05 2.25734e-05 2.5272649e-05 9.4285714 - 97200 6.9368757e-07 0 2.8254045e-05 2.2793415e-05 2.5257036e-05 9.4285714 - 97300 6.9652913e-07 0 2.8016561e-05 2.3040992e-05 2.5228068e-05 9.4285714 - 97400 6.9671901e-07 0 2.7837036e-05 2.330333e-05 2.5157239e-05 9.4285714 - 97500 6.891306e-07 0 2.7789433e-05 2.3471237e-05 2.5141846e-05 9.4285714 - 97600 6.76426e-07 0 2.7838847e-05 2.3472664e-05 2.518892e-05 9.4285714 - 97700 6.5763751e-07 0 2.794167e-05 2.3370888e-05 2.5139127e-05 9.4285714 - 97800 6.4854556e-07 0 2.7951511e-05 2.3224106e-05 2.5036326e-05 9.4285714 - 97900 6.5336861e-07 0 2.7923239e-05 2.3092342e-05 2.4920514e-05 9.4285714 - 98000 6.6394525e-07 0 2.7871431e-05 2.2947013e-05 2.480383e-05 9.4285714 - 98100 6.8885885e-07 0 2.7765273e-05 2.2790639e-05 2.4801777e-05 9.4285714 - 98200 7.2201864e-07 0 2.7755504e-05 2.2661812e-05 2.4861739e-05 9.4285714 - 98300 7.3816538e-07 0 2.7765573e-05 2.258486e-05 2.4844206e-05 9.4285714 - 98400 7.3631403e-07 0 2.7757701e-05 2.2578908e-05 2.4841191e-05 9.4285714 - 98500 7.2568853e-07 0 2.7848802e-05 2.2595958e-05 2.4892777e-05 9.4285714 - 98600 7.0490905e-07 0 2.7912207e-05 2.2591875e-05 2.4898698e-05 9.4285714 - 98700 6.8484202e-07 0 2.8009272e-05 2.2597685e-05 2.4985899e-05 9.4285714 - 98800 6.6994522e-07 0 2.8202402e-05 2.2643734e-05 2.5127513e-05 9.4285714 - 98900 6.2867752e-07 0 2.8292405e-05 2.2674349e-05 2.5309578e-05 9.4285714 - 99000 5.6999626e-07 0 2.8348569e-05 2.2698075e-05 2.5569326e-05 9.4285714 - 99100 5.2675078e-07 0 2.838436e-05 2.2796837e-05 2.5828965e-05 9.4285714 - 99200 4.9993032e-07 0 2.8326221e-05 2.2925652e-05 2.6095918e-05 9.4285714 - 99300 4.8034362e-07 0 2.8358043e-05 2.3048697e-05 2.6357518e-05 9.4285714 - 99400 4.633455e-07 0 2.8395008e-05 2.3187019e-05 2.6590148e-05 9.4285714 - 99500 4.423417e-07 0 2.840813e-05 2.3327273e-05 2.679518e-05 9.4285714 - 99600 4.2336865e-07 0 2.8409328e-05 2.3446846e-05 2.6875881e-05 9.4285714 - 99700 4.0950396e-07 0 2.831088e-05 2.347619e-05 2.6867125e-05 9.4285714 - 99800 3.8946719e-07 0 2.8187415e-05 2.3361958e-05 2.6862163e-05 9.4285714 - 99900 3.5789226e-07 0 2.8087326e-05 2.3222723e-05 2.6889683e-05 9.4285714 - 100000 3.23165e-07 0 2.7995448e-05 2.3145322e-05 2.7024051e-05 9.4285714 -Loop time of 205.426 on 4 procs for 100000 steps with 2520 atoms - -Performance: 2102947.143 tau/day, 486.793 timesteps/s -98.8% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.17838 | 1.2371 | 4.1955 | 153.6 | 0.60 -Bond | 3.018 | 52.249 | 174.87 | 982.2 | 25.43 -Neigh | 3.0057 | 3.0272 | 3.0411 | 0.8 | 1.47 -Comm | 2.8631 | 70.899 | 175.73 | 758.8 | 34.51 -Output | 0.1676 | 1.5052 | 3.0742 | 109.6 | 0.73 -Modify | 1.0679 | 5.7589 | 17.359 | 279.9 | 2.80 -Other | | 70.75 | | | 34.44 - -Nlocal: 630 ave 2513 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 39.25 ave 150 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Neighs: 2458 ave 9821 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 9832 -Ave neighs/atom = 3.9015873 -Ave special neighs/atom = 36.31746 -Neighbor list builds = 5178 -Dangerous builds = 314 -Total wall time: 0:03:25 diff --git a/src/BPM/bond_bpm.cpp b/src/BPM/bond_bpm.cpp index 458f00d77d6..24f8be8fd9e 100644 --- a/src/BPM/bond_bpm.cpp +++ b/src/BPM/bond_bpm.cpp @@ -377,8 +377,13 @@ double BondBPM::equilibrium_distance(int /*i*/) r0_max_estimate = temp; } - // Divide out heuristic prefactor added in comm class - return max_stretch * r0_max_estimate / 1.5; + double dist = r0_max_estimate; + + // Add stretch and remove heuristic prefactor (added in comm class) + if (break_flag) + dist *= max_stretch / 1.5; + + return dist; } /* ---------------------------------------------------------------------- diff --git a/src/BPM/bond_bpm_rotational.cpp b/src/BPM/bond_bpm_rotational.cpp index efb84f17092..abee373c5dc 100644 --- a/src/BPM/bond_bpm_rotational.cpp +++ b/src/BPM/bond_bpm_rotational.cpp @@ -523,7 +523,7 @@ void BondBPMRotational::compute(int eflag, int vflag) breaking = elastic_forces(i1, i2, type, r_mag, r0_mag, r_mag_inv, rhat, r, r0, force1on2, torque1on2, torque2on1); - if (breaking >= 1.0) { + if ((breaking >= 1.0) && break_flag) { bondlist[n][2] = 0; process_broken(i1, i2); continue; @@ -684,6 +684,9 @@ void BondBPMRotational::settings(int narg, char **arg) error->all(FLERR, "Illegal bond bpm command, invalid argument {}", arg[iarg]); } } + + if (smooth_flag && !break_flag) + error->all(FLERR, "Illegal bond bpm command, must turn off smoothing with break no option"); } /* ---------------------------------------------------------------------- diff --git a/src/BPM/bond_bpm_spring.cpp b/src/BPM/bond_bpm_spring.cpp index 0c61c20bf66..0de93fea319 100644 --- a/src/BPM/bond_bpm_spring.cpp +++ b/src/BPM/bond_bpm_spring.cpp @@ -245,7 +245,7 @@ void BondBPMSpring::compute(int eflag, int vflag) r = sqrt(rsq); e = (r - r0) / r0; - if (fabs(e) > ecrit[type]) { + if ((fabs(e) > ecrit[type]) && break_flag) { bondlist[n][2] = 0; process_broken(i1, i2); @@ -485,6 +485,9 @@ void BondBPMSpring::settings(int narg, char **arg) error->all(FLERR, "Illegal bond bpm command, invalid argument {}", arg[iarg]); } } + + if (smooth_flag && !break_flag) + error->all(FLERR, "Illegal bond bpm command, must turn off smoothing with break no option"); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-FIX/fix_deform_pressure.cpp b/src/EXTRA-FIX/fix_deform_pressure.cpp index e93def4926d..a5b7b1fcb15 100644 --- a/src/EXTRA-FIX/fix_deform_pressure.cpp +++ b/src/EXTRA-FIX/fix_deform_pressure.cpp @@ -407,6 +407,16 @@ void FixDeformPressure::init() set_box.vol_start = domain->xprd * domain->yprd * domain->zprd; + // reset cumulative counters to match resetting "start" variables in parent + + for (int i = 0; i < 7; i++) { + set_extra[i].cumulative_remap = 0.0; + set_extra[i].cumulative_shift = 0.0; + set_extra[i].cumulative_vshift[0] = 0.0; + set_extra[i].cumulative_vshift[1] = 0.0; + set_extra[i].cumulative_vshift[2] = 0.0; + } + // check optional variables for PRESSURE or PMEAN style for (int i = 0; i < 7; i++) { diff --git a/src/GRANULAR/gran_sub_mod_damping.cpp b/src/GRANULAR/gran_sub_mod_damping.cpp index 9dd68060ac4..3aa888372ce 100644 --- a/src/GRANULAR/gran_sub_mod_damping.cpp +++ b/src/GRANULAR/gran_sub_mod_damping.cpp @@ -152,9 +152,8 @@ double GranSubModDampingTsuji::calculate_forces() ------------------------------------------------------------------------- */ GranSubModDampingCoeffRestitution::GranSubModDampingCoeffRestitution(GranularModel *gm, LAMMPS *lmp) : - GranSubModDamping(gm, lmp) + GranSubModDampingTsuji(gm, lmp) { - allow_cohesion = 0; } /* ---------------------------------------------------------------------- */ @@ -171,17 +170,3 @@ void GranSubModDampingCoeffRestitution::init() damp /= sqrt(MY_PI * MY_PI + logcor * logcor); } } - -/* ---------------------------------------------------------------------- */ - -double GranSubModDampingCoeffRestitution::calculate_forces() -{ - // in case argument <= 0 due to precision issues - double sqrt1; - if (gm->delta > 0.0) - sqrt1 = MAX(0.0, gm->meff * gm->Fnormal / gm->delta); - else - sqrt1 = 0.0; - damp_prefactor = damp * sqrt(sqrt1); - return -damp_prefactor * gm->vnnr; -} diff --git a/src/GRANULAR/gran_sub_mod_damping.h b/src/GRANULAR/gran_sub_mod_damping.h index c931e385cca..98c31d680a3 100644 --- a/src/GRANULAR/gran_sub_mod_damping.h +++ b/src/GRANULAR/gran_sub_mod_damping.h @@ -87,11 +87,10 @@ namespace Granular_NS { /* ---------------------------------------------------------------------- */ - class GranSubModDampingCoeffRestitution : public GranSubModDamping { + class GranSubModDampingCoeffRestitution : public GranSubModDampingTsuji { public: GranSubModDampingCoeffRestitution(class GranularModel *, class LAMMPS *); void init() override; - double calculate_forces() override; }; /* ---------------------------------------------------------------------- */ diff --git a/src/domain.cpp b/src/domain.cpp index 419091775ab..572575ad222 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -1668,7 +1668,7 @@ void Domain::remap(double *x) adjust 3 image flags encoded in image accordingly resulting coord must satisfy lo <= coord < hi MAX is important since coord - prd < lo can happen when coord = hi - for triclinic, point is converted to lamda coords (0-1) before doing remap + for triclinic, point is converted to lamda coords (0-1) within remap() image = 10 bits for each dimension increment/decrement in wrap-around fashion ------------------------------------------------------------------------- */ @@ -1679,9 +1679,7 @@ void Domain::remap_all() imageint *image = atom->image; int nlocal = atom->nlocal; - if (triclinic) x2lamda(nlocal); for (int i = 0; i < nlocal; i++) remap(x[i],image[i]); - if (triclinic) lamda2x(nlocal); } /* ----------------------------------------------------------------------