diff --git a/doc/src/fix_propel_self.rst b/doc/src/fix_propel_self.rst index 582d9e4294..ba8c48cf6b 100644 --- a/doc/src/fix_propel_self.rst +++ b/doc/src/fix_propel_self.rst @@ -8,22 +8,19 @@ Syntax .. parsed-literal:: - fix ID group-ID propel/self magnitude keyword values + fix ID group-ID propel/self mode magnitude keyword values * ID, group-ID are documented in :doc:`fix ` command * propel/self = style name of this fix command +* mode = *dipole* or *velocity* or *quat* * magnitude = magnitude of self-propulsion force -* one (and only one) keyword/value pair must be appended to args -* keyword = *dipole* or *velocity* or *quat* +* zero or one keyword/value pairs may be appended +* keyword = *qvector* .. parsed-literal:: - *dipole* value = none = apply force along dipole direction - *velocity* value = none = apply force along velocity direction - *quat* values = direction vector *sx* and *sy* and *sz* - *sx* = x component of force direction in ellipsoid frame - *sy* = y component of force direction in ellipsoid frame - *sz* = z component of force direction in ellipsoid frame + *qvector* value = direction of force in ellipsoid frame + *sx*, *sy*, *sz* = components of *qvector* Examples @@ -31,9 +28,9 @@ Examples .. code-block:: LAMMPS - fix propel/self all 40.0 dipole - fix propel/self all 10.0 velocity - fix propel/self all 15.7 quat 1.0 0.0 0.0 + fix active all propel/self dipole 40.0 + fix active all propel/self velocity 10.0 + fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0 Description """"""""""" @@ -50,7 +47,7 @@ is the magnitude of the force, and :math:`e_i` is the vector direction of the force. The specification of :math:`e_i` is based on which of the three keywords (*dipole* or *velocity* or *quat*) one selects. -For keyword *dipole*, :math:`e_i` is just equal to +For mode *dipole*, :math:`e_i` is just equal to the dipole vectors of the atoms in the group. Therefore, if the dipoles are not unit vectors, the :math:`e_i` will not be unit vectors. @@ -66,21 +63,31 @@ are not unit vectors, the :math:`e_i` will not be unit vectors. all the dipole magnitudes to 1.0 unless you have a good reason not to (see the :doc:`set ` command on how to do this). -For keyword *velocity*, :math:`e_i` points in the direction +For mode *velocity*, :math:`e_i` points in the direction of the current velocity (a unit-vector). This can be interpreted as a velocity-dependent friction, as proposed by e.g. :ref:`(Erdmann) `. -For keyword *quat*, :math:`e_i` points in the direction of the unit -vector defined by its arguments *sx*, *sy*, and *sz*, which are -themselves defined within the coordinate frame of the atom's +For mode *quat*, :math:`e_i` points in the direction of a unit +vector, oriented in the coordinate frame of the ellipsoidal particles, +which defaults to point along the x-direction. This default behaviour +can be changed by via the *quatvec* keyword. + +The optional *quatvec* keyword specifies the direction of self-propulsion +via a unit vector (sx,sy,sz). The arguments *sx*, *sy*, and *sz*, are +defined within the coordinate frame of the atom's ellipsoid. For instance, for an ellipsoid with long axis along its x-direction, if one wanted the self-propulsion force to also be along this axis, set *sx* equal to 1 and *sy*, *sz* both equal -to zero. For *quat*, :math:`e_i` will always be a unit vector, -so multiplying all three arguments *sx*, *sy*, and *sz* by a -positive scalar will not change the self-propulsion force -(multiplying by a negative scalar will change the sign of the -force). +to zero. This keyword may only be specified for mode *quat*. + +.. note:: + + In using keyword *quatvec*, the three arguments *sx*, + *sy*, and *sz* will be automatically normalised to components + of a unit vector internally to avoid users having to explicitly + do so themselves. Therefore, in mode *quat*, the vectors :math:`e_i` + will always be of unit length. + Along with adding a force contribution, this fix can also contribute to the virial (pressure) of the system, defined as @@ -89,10 +96,10 @@ contribute to the virial (pressure) of the system, defined as boundary conditions. See :ref:`(Winkler) ` for a discussion of this active pressure contribution. -For keywords *dipole* and *quat*, this fix is by default +For modes *dipole* and *quat*, this fix is by default included in pressure computations. -For keyword *velocity*, this fix is by default not included +For mode *velocity*, this fix is by default not included in pressure computations. diff --git a/examples/USER/brownian/2d_velocity/in.2d_velocity b/examples/USER/brownian/2d_velocity/in.2d_velocity index b731f5f477..cbd7d543cb 100644 --- a/examples/USER/brownian/2d_velocity/in.2d_velocity +++ b/examples/USER/brownian/2d_velocity/in.2d_velocity @@ -31,7 +31,7 @@ neigh_modify every 1 delay 1 check yes pair_style none fix step all brownian ${gamma_t} ${D_t} ${seed} -fix vel all propel/self ${fp} velocity +fix vel all propel/self velocity ${fp} fix 2 all enforce2d fix_modify vel virial yes diff --git a/examples/USER/brownian/spherical_ABP/in.2d_abp b/examples/USER/brownian/spherical_ABP/in.2d_abp index d626445926..9db5a46cf6 100644 --- a/examples/USER/brownian/spherical_ABP/in.2d_abp +++ b/examples/USER/brownian/spherical_ABP/in.2d_abp @@ -41,7 +41,7 @@ pair_modify shift yes # overdamped brownian dynamics time-step fix step all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} dipole # self-propulsion force along the dipole direction -fix activity all propel/self ${fp} dipole +fix activity all propel/self dipole ${fp} fix 2 all enforce2d diff --git a/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp b/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp index e131d07059..4c3d403f20 100644 --- a/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp +++ b/examples/USER/brownian/spherical_ABP/in.3d_ideal_abp @@ -30,7 +30,7 @@ pair_style none # overdamped brownian dynamics time-step fix step all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} dipole # self-propulsion force along the dipole direction -fix activity all propel/self ${fp} dipole +fix activity all propel/self dipole ${fp} compute press all pressure NULL virial diff --git a/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log b/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log index 0c51314cca..8f334c77fb 100644 --- a/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log +++ b/examples/USER/brownian/spherical_ABP/log_WCA_1_1_1_3_4_2d.lammps.log @@ -10,10 +10,10 @@ Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388 region box block -16 16 -16 16 -0.2 0.2 create_box 1 box Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777) - 2 by 2 by 1 MPI processor grid + 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 1024 atoms - create_atoms CPU = 0.001 seconds + create_atoms CPU = 0.002 seconds mass * 1.0 set type * dipole/random ${seed} 1.0 set type * dipole/random 1974019 1.0 @@ -41,8 +41,8 @@ fix step all brownian/sphere 1 1 1 ${D_r} ${seed} dipole fix step all brownian/sphere 1 1 1 3 ${seed} dipole fix step all brownian/sphere 1 1 1 3 1974019 dipole # self-propulsion force along the dipole direction -fix activity all propel/self ${fp} dipole -fix activity all propel/self 4 dipole +fix activity all propel/self dipole ${fp} +fix activity all propel/self dipole 4 fix 2 all enforce2d @@ -66,34 +66,34 @@ Neighbor list info ... pair build: half/bin/newtoff stencil: half/bin/2d/newtoff bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes Step Temp E_pair c_press 0 1 0 -0.53979198 - 50000 1.0371295e+10 0 -0.542818 -Loop time of 2.25396 on 4 procs for 50000 steps with 1024 atoms + 50000 1.0902879e+10 0 -0.53710405 +Loop time of 6.3887 on 1 procs for 50000 steps with 1024 atoms -Performance: 0.192 tau/day, 22183.200 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.068 tau/day, 7826.319 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.1034 | 0.10382 | 0.10438 | 0.1 | 4.61 +Pair | 0.34323 | 0.34323 | 0.34323 | 0.0 | 5.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.26698 | 0.26833 | 0.26924 | 0.2 | 11.90 -Output | 2.2284e-05 | 2.4926e-05 | 3.2332e-05 | 0.0 | 0.00 -Modify | 1.7222 | 1.7237 | 1.727 | 0.1 | 76.48 -Other | | 0.1581 | | | 7.01 +Comm | 0.070232 | 0.070232 | 0.070232 | 0.0 | 1.10 +Output | 2.5077e-05 | 2.5077e-05 | 2.5077e-05 | 0.0 | 0.00 +Modify | 5.8232 | 5.8232 | 5.8232 | 0.0 | 91.15 +Other | | 0.152 | | | 2.38 -Nlocal: 256.000 ave 256 max 256 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 105.000 ave 105 max 105 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 544.000 ave 544 max 544 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 201.000 ave 201 max 201 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2112.00 ave 2112 max 2112 min +Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2176 -Ave neighs/atom = 2.1250000 +Total # of neighbors = 2112 +Ave neighs/atom = 2.0625000 Neighbor list builds = 0 Dangerous builds = 0 reset_timestep 0 @@ -111,53 +111,53 @@ thermo 10000 # main run run 200000 -Per MPI rank memory allocation (min/avg/max) = 5.427 | 5.427 | 5.427 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press - 0 1.0371295e+10 0 0 0 0 0 -0.542818 - 10000 107356.09 0.079828495 0.19584264 0.19679822 0 0.39264086 0.00078740793 - 20000 101692.44 0.11317533 0.40847364 0.42097802 0 0.82945167 0.74111888 - 30000 105763.55 0.10261852 0.68303669 0.66125751 0 1.3442942 0.71112533 - 40000 105127.29 0.12371743 0.97990144 0.94005552 0 1.919957 1.0574552 - 50000 101579.58 0.12771813 1.3059069 1.2364468 0 2.5423537 1.059263 - 60000 104914.36 0.12055843 1.6215593 1.525488 0 3.1470473 0.79873537 - 70000 106629.18 0.1278745 1.9639958 1.8682794 0 3.8322752 0.91950208 - 80000 103286.54 0.13927689 2.3201565 2.2373383 0 4.5574948 1.1875034 - 90000 106451.61 0.093479681 2.6287902 2.5753347 0 5.2041249 1.0861163 - 100000 102199.72 0.13269425 2.9127976 2.9369237 0 5.8497214 1.4841998 - 110000 105229.73 0.10594209 3.1798718 3.3495317 0 6.5294035 1.5444784 - 120000 106262.36 0.11902575 3.6267452 3.7188125 0 7.3455578 1.3366518 - 130000 109388.12 0.10562576 3.929973 4.0226942 0 7.9526672 1.324534 - 140000 107697.35 0.13028752 4.231893 4.3780995 0 8.6099925 1.7406167 - 150000 103928.72 0.12278994 4.5826286 4.7578662 0 9.3404948 1.3024003 - 160000 103370.23 0.11391216 4.8767011 5.1181189 0 9.99482 1.4325241 - 170000 103821.53 0.11163256 5.153318 5.3785963 0 10.531914 1.4569115 - 180000 106824.99 0.13225083 5.4080929 5.7399804 0 11.148073 1.334984 - 190000 101794.6 0.10632938 5.7384925 6.080955 0 11.819448 0.81285422 - 200000 102128.67 0.13703498 6.0414673 6.4511058 0 12.492573 0.42904128 -Loop time of 9.60419 on 4 procs for 200000 steps with 1024 atoms + 0 1.0902879e+10 0 0 0 0 0 -0.53710405 + 10000 103498.6 0.087662767 0.18719065 0.2007338 0 0.38792445 0.16080254 + 20000 104785.56 0.12719481 0.4197551 0.40722743 0 0.82698253 0.5007164 + 30000 103183.73 0.1126518 0.67800477 0.67921667 0 1.3572214 0.36634317 + 40000 102912.87 0.092584777 0.96234448 0.97188884 0 1.9342333 0.46170129 + 50000 103516.68 0.12761757 1.2381642 1.3203398 0 2.558504 0.85712805 + 60000 104999.77 0.14482924 1.5437166 1.6177103 0 3.1614269 1.1403162 + 70000 103925.7 0.11302021 1.886 1.9262949 0 3.8122949 1.1056086 + 80000 105000.14 0.14502228 2.205833 2.2668945 0 4.4727275 1.0757792 + 90000 105980.8 0.12089413 2.515801 2.647111 0 5.162912 1.1160525 + 100000 106557.86 0.10934038 2.7977098 2.8965145 0 5.6942242 0.56901933 + 110000 104241.46 0.12719985 3.1612652 3.2283956 0 6.3896608 0.95100999 + 120000 101910.56 0.12002691 3.5844099 3.5366227 0 7.1210326 1.2526653 + 130000 104435.28 0.10695039 3.8328815 3.8286503 0 7.6615318 1.6198184 + 140000 104864.99 0.11226471 4.1822059 4.285915 0 8.4681209 1.5190757 + 150000 103209.43 0.11229036 4.430069 4.5491143 0 8.9791833 1.1568204 + 160000 106692.61 0.11151476 4.7593714 5.0322819 0 9.7916533 1.2337266 + 170000 105232.19 0.12039818 5.0665907 5.3612901 0 10.427881 1.3881139 + 180000 107126.86 0.10793969 5.4129878 5.6391008 0 11.052089 1.6691607 + 190000 103814.36 0.096916503 5.7355093 5.9557837 0 11.691293 1.3863335 + 200000 103976.84 0.10928015 6.1871603 6.3393786 0 12.526539 1.1687077 +Loop time of 27.4513 on 1 procs for 200000 steps with 1024 atoms -Performance: 17992.140 tau/day, 20824.236 timesteps/s -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 6294.793 tau/day, 7285.640 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.71756 | 0.75121 | 0.79008 | 3.0 | 7.82 -Neigh | 0.018158 | 0.018773 | 0.019357 | 0.3 | 0.20 -Comm | 1.0469 | 1.0597 | 1.0738 | 1.2 | 11.03 -Output | 0.00051435 | 0.00057078 | 0.00070838 | 0.0 | 0.01 -Modify | 6.8012 | 6.9883 | 7.1513 | 4.9 | 72.76 -Other | | 0.7857 | | | 8.18 +Pair | 3.2525 | 3.2525 | 3.2525 | 0.0 | 11.85 +Neigh | 0.054678 | 0.054678 | 0.054678 | 0.0 | 0.20 +Comm | 0.26582 | 0.26582 | 0.26582 | 0.0 | 0.97 +Output | 0.0006103 | 0.0006103 | 0.0006103 | 0.0 | 0.00 +Modify | 23.265 | 23.265 | 23.265 | 0.0 | 84.75 +Other | | 0.6131 | | | 2.23 -Nlocal: 256.000 ave 265 max 240 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 88.5000 ave 91 max 87 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Neighs: 678.500 ave 713 max 597 min -Histogram: 1 0 0 0 0 0 0 0 1 2 +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 166.000 ave 166 max 166 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2634.00 ave 2634 max 2634 min +Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2714 -Ave neighs/atom = 2.6503906 -Neighbor list builds = 241 +Total # of neighbors = 2634 +Ave neighs/atom = 2.5722656 +Neighbor list builds = 238 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:33 diff --git a/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log b/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log index be6c1d5d41..c5cbe4936d 100644 --- a/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log +++ b/examples/USER/brownian/spherical_ABP/log_ideal_1_1_1_3_4_3d.lammps.log @@ -10,10 +10,10 @@ Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 region box block -8 8 -8 8 -8 8 create_box 1 box Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670) - 2 by 1 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4096 atoms - create_atoms CPU = 0.002 seconds + create_atoms CPU = 0.003 seconds mass * 1.0 set type * dipole/random ${seed} 1.0 set type * dipole/random 1974019 1.0 @@ -31,8 +31,8 @@ fix step all brownian/sphere 1 1 1 ${D_r} ${seed} dipole fix step all brownian/sphere 1 1 1 3 ${seed} dipole fix step all brownian/sphere 1 1 1 3 1974019 dipole # self-propulsion force along the dipole direction -fix activity all propel/self ${fp} dipole -fix activity all propel/self 4 dipole +fix activity all propel/self dipole ${fp} +fix activity all propel/self dipole 4 compute press all pressure NULL virial @@ -45,31 +45,31 @@ thermo 50001 run 50000 WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) -Per MPI rank memory allocation (min/avg/max) = 4.319 | 4.319 | 4.319 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.362 | 4.362 | 4.362 Mbytes Step Temp E_pair c_press 0 1 0 0.068021726 - 50000 1.046425e+10 0 0.067505633 -Loop time of 7.83903 on 4 procs for 50000 steps with 4096 atoms + 50000 1.0486812e+10 0 0.068203091 +Loop time of 25.3706 on 1 procs for 50000 steps with 4096 atoms -Performance: 0.055 tau/day, 6378.340 timesteps/s -97.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.017 tau/day, 1970.786 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.50238 | 0.51891 | 0.53617 | 1.7 | 6.62 -Output | 2.6343e-05 | 3.6075e-05 | 4.6997e-05 | 0.0 | 0.00 -Modify | 6.9536 | 6.9732 | 7.0105 | 0.8 | 88.95 -Other | | 0.3469 | | | 4.43 +Comm | 0.31005 | 0.31005 | 0.31005 | 0.0 | 1.22 +Output | 3.2633e-05 | 3.2633e-05 | 3.2633e-05 | 0.0 | 0.00 +Modify | 24.471 | 24.471 | 24.471 | 0.0 | 96.45 +Other | | 0.5897 | | | 2.32 -Nlocal: 1024.00 ave 1024 max 1024 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 353.000 ave 353 max 353 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 817.000 ave 817 max 817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0.0000000 @@ -96,46 +96,46 @@ thermo 10000 # main run run 120000 WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) -Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press - 0 1.046425e+10 0 0 0 0 0 0.067505633 - 10000 106340.56 0 0.2469318 0.23662295 0.2441413 0.72769605 0.19939966 - 20000 104620.27 0 0.55429324 0.5231436 0.54976641 1.6272032 0.26601423 - 30000 106130.45 0 0.87562668 0.84813496 0.89321299 2.6169746 0.30836996 - 40000 105773.31 0 1.2262635 1.1899278 1.2626926 3.6788838 0.35392219 - 50000 103804.88 0 1.5851624 1.5645815 1.6434185 4.7931624 0.33326997 - 60000 105746.45 0 1.9928016 1.9347072 1.9837329 5.9112417 0.2550878 - 70000 104500.3 0 2.3269429 2.2774077 2.3368821 6.9412326 0.25218225 - 80000 105381.46 0 2.7114959 2.6937299 2.7171132 8.122339 0.36940892 - 90000 104542.79 0 3.0828648 3.084417 3.0783207 9.2456025 0.36106481 - 100000 104246.75 0 3.4635513 3.5105066 3.4545226 10.42858 0.3712313 - 110000 103099.55 0 3.8471061 3.9389997 3.8220676 11.608173 0.38466185 - 120000 103098.45 0 4.2014598 4.3456831 4.1888659 12.736009 0.36710217 -Loop time of 22.8893 on 4 procs for 120000 steps with 4096 atoms + 0 1.0486812e+10 0 0 0 0 0 0.068203091 + 10000 104209.87 0 0.25428952 0.2512451 0.23617807 0.74171269 0.1910208 + 20000 104433.46 0 0.55611319 0.57499464 0.54362634 1.6747342 0.27977792 + 30000 104615.53 0 0.88377871 0.8933002 0.88683731 2.6639162 0.31709969 + 40000 105930.5 0 1.2301515 1.262995 1.2479624 3.7411089 0.26149988 + 50000 105556.39 0 1.5798848 1.6402779 1.6392277 4.8593905 0.34401188 + 60000 104644.58 0 1.9782384 1.9902061 2.0327974 6.0012419 0.26709167 + 70000 104314.31 0 2.3681872 2.3695505 2.4241916 7.1619294 0.24191407 + 80000 105700 0 2.7109374 2.7434271 2.8309194 8.2852839 0.28355159 + 90000 103411.61 0 3.1023448 3.0881218 3.1599155 9.350382 0.3070844 + 100000 105432.12 0 3.4853878 3.4372177 3.5153198 10.437925 0.28141015 + 110000 105723.04 0 3.8405786 3.7967805 3.8738332 11.511192 0.33248553 + 120000 104734.31 0 4.2454301 4.1714561 4.2234474 12.640334 0.3603781 +Loop time of 63.7803 on 1 procs for 120000 steps with 4096 atoms -Performance: 4529.619 tau/day, 5242.615 timesteps/s -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 1625.581 tau/day, 1881.459 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0.0049489 | 0.0050479 | 0.0050978 | 0.1 | 0.02 -Comm | 0.082752 | 0.084491 | 0.085332 | 0.4 | 0.37 -Output | 0.00054352 | 0.0006034 | 0.00064793 | 0.0 | 0.00 -Modify | 21.069 | 21.521 | 21.964 | 7.0 | 94.02 -Other | | 1.278 | | | 5.58 +Neigh | 0.013032 | 0.013032 | 0.013032 | 0.0 | 0.02 +Comm | 0.093045 | 0.093045 | 0.093045 | 0.0 | 0.15 +Output | 0.00069845 | 0.00069845 | 0.00069845 | 0.0 | 0.00 +Modify | 62.279 | 62.279 | 62.279 | 0.0 | 97.65 +Other | | 1.394 | | | 2.19 -Nlocal: 1024.00 ave 1050 max 1010 min -Histogram: 2 0 0 1 0 0 0 0 0 1 +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0.00000 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0.0000000 -Neighbor list builds = 2169 +Neighbor list builds = 2174 Dangerous builds = 0 # if you want to check that rotational diffusion is behaving as expected, @@ -147,4 +147,4 @@ Dangerous builds = 0 #dump_modify 1 first yes sort id #run 120000 -Total wall time: 0:00:30 +Total wall time: 0:01:29 diff --git a/src/USER-BROWNIAN/fix_propel_self.cpp b/src/USER-BROWNIAN/fix_propel_self.cpp index 1755f59840..59bb080cc5 100644 --- a/src/USER-BROWNIAN/fix_propel_self.cpp +++ b/src/USER-BROWNIAN/fix_propel_self.cpp @@ -16,8 +16,7 @@ Thanks to Liesbeth Janssen @ Eindhoven University for useful discussions! - Current maintainer: Sam Cameron @ University of Bristol - + Current maintainer: Sam Cameron @ University of Bristol ----------------------------------------------------------------------- */ #include @@ -49,44 +48,47 @@ FixPropelSelf::FixPropelSelf(LAMMPS *lmp, int narg, char **arg) : virial_flag = 1; - if (narg < 5) + if (narg != 5 && narg != 9) error->all(FLERR,"Illegal fix propel/self command"); - - magnitude = utils::numeric(FLERR,arg[3],false,lmp); - if (strcmp(arg[4],"velocity") == 0) { + if (strcmp(arg[3],"velocity") == 0) { mode = VELOCITY; thermo_virial = 0; - if (narg != 5) { - error->all(FLERR,"Illegal fix propel/self command"); - } - } else if (strcmp(arg[4],"dipole") == 0) { + } else if (strcmp(arg[3],"dipole") == 0) { mode = DIPOLE; thermo_virial = 1; - if (narg != 5) { - error->all(FLERR,"Illegal fix propel/self command"); - } - } else if (strcmp(arg[4],"quat") == 0) { + } else if (strcmp(arg[3],"quat") == 0) { mode = QUAT; thermo_virial = 1; - if (narg != 8) { - error->all(FLERR,"Illegal fix propel/self command"); - } else { - sx = utils::numeric(FLERR,arg[5],false,lmp); - sy = utils::numeric(FLERR,arg[6],false,lmp); - sz = utils::numeric(FLERR,arg[7],false,lmp); - double qnorm = sqrt(sx*sx + sy*sy + sz*sz); - sx = sx/qnorm; - sy = sy/qnorm; - sz = sz/qnorm; - } } else { error->all(FLERR,"Illegal fix propel/self command"); } + magnitude = utils::numeric(FLERR,arg[4],false,lmp); + // check for keyword + if (narg == 9) { + if (mode != QUAT) { + error->all(FLERR,"Illegal fix propel/self command"); + } + if (strcmp(arg[5],"qvector") == 0) { + sx = utils::numeric(FLERR,arg[6],false,lmp); + sy = utils::numeric(FLERR,arg[7],false,lmp); + sz = utils::numeric(FLERR,arg[8],false,lmp); + double snorm = sqrt(sx*sx + sy*sy + sz*sz); + sx = sx/snorm; + sy = sy/snorm; + sz = sz/snorm; + } else { + error->all(FLERR,"Illegal fix propel/self command"); + } + } else { + sx = 1.0; + sy = 0.0; + sz = 0.0; + } }