diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 42e6d12ffb..26d86e0a06 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -112,7 +112,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY - USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) + USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS USER-BROWNIAN) set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU) foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 8be0908a1a..361ec7e982 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -39,8 +39,8 @@ OPT. * :doc:`ave/time ` * :doc:`aveforce ` * :doc:`balance ` - * :doc:`bd/sphere ` - * :doc:`bd/asphere ` + * :doc:`brownian/asphere ` + * :doc:`brownian/sphere ` * :doc:`bocs ` * :doc:`bond/break ` * :doc:`bond/create ` diff --git a/doc/src/fix.rst b/doc/src/fix.rst index c395489a58..5efe002f31 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -182,8 +182,8 @@ accelerated styles exist. * :doc:`ave/time ` - compute/output global time-averaged quantities * :doc:`aveforce ` - add an averaged force to each atom * :doc:`balance ` - perform dynamic load-balancing -* :doc:`bd/asphere ` - integrate positions and orientations in overdamped motion -* :doc:`bd/sphere ` - overdamped translational and rotational brownian dynamics +* :doc:`brownian/asphere ` - overdamped translational and rotational brownian for ellipsoids +* :doc:`brownian/sphere ` - overdamped translational and rotational brownian for spheres * :doc:`bocs ` - NPT style time integration with pressure correction * :doc:`bond/break ` - break bonds on the fly * :doc:`bond/create ` - create bonds on the fly diff --git a/doc/src/fix_bd_asphere.rst b/doc/src/fix_brownian_asphere.rst similarity index 86% rename from doc/src/fix_bd_asphere.rst rename to doc/src/fix_brownian_asphere.rst index 67d32e2038..58dd453de9 100644 --- a/doc/src/fix_bd_asphere.rst +++ b/doc/src/fix_brownian_asphere.rst @@ -1,17 +1,17 @@ -.. index:: fix bd/asphere +.. index:: fix brownian/asphere -fix bd/asphere command -====================== +fix brownian/asphere command +============================ Syntax """""" .. parsed-literal:: - fix ID group-ID bd/asphere gamma_t gamma_r diff_t diff_r seed keyword args + fix ID group-ID brownian/asphere gamma_t gamma_r diff_t diff_r seed keyword args * ID, group-ID are documented in :doc:`fix ` command -* bd/asphere = style name of this fix command +* brownian/asphere = style name of this fix command * gamma_t = translational friction coefficient * gamma_r = rotational friction coefficient * diff_t = translational diffusion coefficient @@ -32,10 +32,10 @@ Examples .. code-block:: LAMMPS - fix 1 all bd/asphere 1.0 1.0 1.0 1.0 1294019 - fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 rng none dipole - fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 rng uniform - fix 1 all bd/asphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian + fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 1294019 + fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 19581092 rng none dipole + fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 19581092 rng uniform + fix 1 all brownian/asphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian Description @@ -59,7 +59,7 @@ Chapter 4 of :ref:`(Goldstein) `), :math:`dW_t` and The quaternions :math:`q` of the ellipsoid are updated each timestep from the angular velocity vector. -See :doc:`fix bd/sphere ` for discussion on the +See :doc:`fix brownian/sphere ` for discussion on the values of :math:`\gamma_t`, :math:`\gamma_r`, :math:`D_t`, :math:`D_r`, and temperature when simulating equilibrium systems. @@ -124,7 +124,7 @@ be point particles. Related commands """""""""""""""" -:doc:`fix bd/sphere `, :doc:`fix langevin `, +:doc:`fix brownian/sphere `, :doc:`fix langevin `, :doc:`fix nve/asphere `, :doc:`atom style ` Default diff --git a/doc/src/fix_bd_sphere.rst b/doc/src/fix_brownian_sphere.rst similarity index 92% rename from doc/src/fix_bd_sphere.rst rename to doc/src/fix_brownian_sphere.rst index eeaaca470c..231486dee1 100644 --- a/doc/src/fix_bd_sphere.rst +++ b/doc/src/fix_brownian_sphere.rst @@ -1,17 +1,17 @@ -.. index:: fix bd/sphere +.. index:: fix brownian/sphere -fix bd/sphere command -====================== +fix brownian/sphere command +=========================== Syntax """""" .. parsed-literal:: - fix ID group-ID bd/sphere gamma_t gamma_r diff_t diff_r seed keyword args + fix ID group-ID brownian/sphere gamma_t gamma_r diff_t diff_r seed keyword args * ID, group-ID are documented in :doc:`fix ` command -* bd/sphere = style name of this fix command +* brownian/sphere = style name of this fix command * gamma_t = translational friction coefficient * gamma_r = rotational friction coefficient * diff_t = translational diffusion coefficient @@ -32,10 +32,10 @@ Examples .. code-block:: LAMMPS - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 1294019 - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng none dipole - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 rng uniform - fix 1 all bd/sphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian + fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 1294019 + fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 19581092 rng none dipole + fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 19581092 rng uniform + fix 1 all brownian/sphere 1.0 1.0 1.0 1.0 19581092 dipole rng gaussian Description diff --git a/examples/USER/misc/bd_asphere/README.txt b/examples/USER/brownian/bd_asphere/README.txt similarity index 100% rename from examples/USER/misc/bd_asphere/README.txt rename to examples/USER/brownian/bd_asphere/README.txt diff --git a/examples/USER/misc/bd_asphere/in3d.bd b/examples/USER/brownian/bd_asphere/in3d.brownian similarity index 93% rename from examples/USER/misc/bd_asphere/in3d.bd rename to examples/USER/brownian/bd_asphere/in3d.brownian index 6163eb0c58..67d95a82b9 100644 --- a/examples/USER/misc/bd_asphere/in3d.bd +++ b/examples/USER/brownian/bd_asphere/in3d.brownian @@ -36,7 +36,7 @@ neigh_modify every 1 delay 1 check yes pair_style none -fix 1 all bd/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole compute press all pressure NULL virial diff --git a/examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log b/examples/USER/brownian/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log similarity index 74% rename from examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log rename to examples/USER/brownian/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log index c6926dbccf..21bd04f7da 100644 --- a/examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log +++ b/examples/USER/brownian/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log @@ -38,13 +38,13 @@ neigh_modify every 1 delay 1 check yes pair_style none -fix 1 all bd/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/asphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/asphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/asphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/asphere 4 1 7 13 ${seed} rng ${rng} dipole -fix 1 all bd/asphere 4 1 7 13 1974019 rng ${rng} dipole -fix 1 all bd/asphere 4 1 7 13 1974019 rng gaussian dipole +fix 1 all brownian/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 4 1 7 13 ${seed} rng ${rng} dipole +fix 1 all brownian/asphere 4 1 7 13 1974019 rng ${rng} dipole +fix 1 all brownian/asphere 4 1 7 13 1974019 rng gaussian dipole compute press all pressure NULL virial @@ -61,9 +61,9 @@ Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.379 | 5.379 Mbytes Step Temp E_pair c_press 0 1 0 0 50000 1.3923773e+11 0 0 -Loop time of 5.68636 on 1 procs for 50000 steps with 512 atoms +Loop time of 5.61345 on 1 procs for 50000 steps with 512 atoms -Performance: 0.076 tau/day, 8792.977 timesteps/s +Performance: 0.077 tau/day, 8907.171 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: @@ -71,10 +71,10 @@ Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.11589 | 0.11589 | 0.11589 | 0.0 | 2.04 -Output | 2.1155e-05 | 2.1155e-05 | 2.1155e-05 | 0.0 | 0.00 -Modify | 5.4911 | 5.4911 | 5.4911 | 0.0 | 96.57 -Other | | 0.07936 | | | 1.40 +Comm | 0.11822 | 0.11822 | 0.11822 | 0.0 | 2.11 +Output | 2.0199e-05 | 2.0199e-05 | 2.0199e-05 | 0.0 | 0.00 +Modify | 5.4135 | 5.4135 | 5.4135 | 0.0 | 96.44 +Other | | 0.0817 | | | 1.46 Nlocal: 512.000 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -100,9 +100,8 @@ thermo_style custom step temp epair c_msd[*] c_press # write trajectory and thermo in a log-scale frequency -dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz -dump 1 all custom 1000 dump_gaussian_4_1_7_13_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz -dump_modify 1 first yes sort id +#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id timestep 0.00001 thermo 10000 @@ -110,7 +109,7 @@ 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) = 7.103 | 7.103 | 7.103 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.754 | 5.754 | 5.754 Mbytes Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 0 1.3923773e+11 0 0 0 0 0 0 10000 1413805.2 0 1.3943053 1.4055827 1.4346505 4.2345385 0 @@ -125,20 +124,20 @@ Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 100000 1430838.3 0 14.104796 13.817001 13.596538 41.518335 0 110000 1364246.8 0 15.382464 15.09201 15.017312 45.491785 0 120000 1389237.6 0 16.632972 16.343173 16.015748 48.991892 0 -Loop time of 13.595 on 1 procs for 120000 steps with 512 atoms +Loop time of 13.2439 on 1 procs for 120000 steps with 512 atoms -Performance: 7626.329 tau/day, 8826.770 timesteps/s +Performance: 7828.487 tau/day, 9060.749 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 | 0.00079148 | 0.00079148 | 0.00079148 | 0.0 | 0.01 -Comm | 0.029132 | 0.029132 | 0.029132 | 0.0 | 0.21 -Output | 0.15178 | 0.15178 | 0.15178 | 0.0 | 1.12 -Modify | 13.222 | 13.222 | 13.222 | 0.0 | 97.25 -Other | | 0.1916 | | | 1.41 +Neigh | 0.00075178 | 0.00075178 | 0.00075178 | 0.0 | 0.01 +Comm | 0.0282 | 0.0282 | 0.0282 | 0.0 | 0.21 +Output | 0.00032692 | 0.00032692 | 0.00032692 | 0.0 | 0.00 +Modify | 13.017 | 13.017 | 13.017 | 0.0 | 98.29 +Other | | 0.1976 | | | 1.49 Nlocal: 512.000 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -151,4 +150,4 @@ Total # of neighbors = 0 Ave neighs/atom = 0.0000000 Neighbor list builds = 1110 Dangerous builds = 0 -Total wall time: 0:00:19 +Total wall time: 0:00:18 diff --git a/examples/USER/misc/bd_sphere/README.txt b/examples/USER/brownian/bd_sphere/README.txt similarity index 73% rename from examples/USER/misc/bd_sphere/README.txt rename to examples/USER/brownian/bd_sphere/README.txt index 2f66504581..8987a23601 100644 --- a/examples/USER/misc/bd_sphere/README.txt +++ b/examples/USER/brownian/bd_sphere/README.txt @@ -1,11 +1,11 @@ -The input file in2ddipole.bd demonstrates how to run a 2d simulation -of particles undergoing overdamped brownian motion in both -translational and rotational degrees of freedom. Dipole +The input file in2ddipole.brownian demonstrates how to run a +2d simulation of particles undergoing overdamped brownian motion +in both translational and rotational degrees of freedom. Dipole updating is turned on, so the package DIPOLE must be built for this example to work. -The input file in3d_virial_on.bd demonstrates how to run a -similar simulation but in 3d. In this case, the virial +The input file in3d_virial_on.brownian demonstrates how to run +a similar simulation but in 3d. In this case, the virial contribution of the brownian dynamics (the sum sum_i /(3*volume) where W is a random variable with mean 0 and variance dt) is diff --git a/examples/USER/misc/bd_sphere/in2ddipole.bd b/examples/USER/brownian/bd_sphere/in2ddipole.brownian similarity index 93% rename from examples/USER/misc/bd_sphere/in2ddipole.bd rename to examples/USER/brownian/bd_sphere/in2ddipole.brownian index 1f7898207f..73d90e4ebf 100644 --- a/examples/USER/misc/bd_sphere/in2ddipole.bd +++ b/examples/USER/brownian/bd_sphere/in2ddipole.brownian @@ -38,7 +38,7 @@ pair_style none #compute d all property/atom mux muy muz -fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole fix 2 all enforce2d compute press all pressure NULL virial diff --git a/examples/USER/misc/bd_sphere/in3d_virial_on.bd b/examples/USER/brownian/bd_sphere/in3d_virial_on.brownian similarity index 93% rename from examples/USER/misc/bd_sphere/in3d_virial_on.bd rename to examples/USER/brownian/bd_sphere/in3d_virial_on.brownian index 0e2f02beb0..481d9bc1b4 100644 --- a/examples/USER/misc/bd_sphere/in3d_virial_on.bd +++ b/examples/USER/brownian/bd_sphere/in3d_virial_on.brownian @@ -33,7 +33,7 @@ neigh_modify every 1 delay 1 check yes pair_style none -fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} fix_modify 1 virial yes compute press all pressure NULL virial diff --git a/examples/USER/misc/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log b/examples/USER/brownian/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log similarity index 89% rename from examples/USER/misc/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log rename to examples/USER/brownian/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log index a735ea6baa..b10f77f0cd 100644 --- a/examples/USER/misc/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log +++ b/examples/USER/brownian/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log @@ -13,7 +13,7 @@ Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.29 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 @@ -33,13 +33,13 @@ pair_style none #compute d all property/atom mux muy muz -fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/sphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/sphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/sphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole -fix 1 all bd/sphere 4 1 7 13 ${seed} rng ${rng} dipole -fix 1 all bd/sphere 4 1 7 13 1974019 rng ${rng} dipole -fix 1 all bd/sphere 4 1 7 13 1974019 rng gaussian dipole +fix 1 all brownian/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole +fix 1 all brownian/sphere 4 1 7 13 ${seed} rng ${rng} dipole +fix 1 all brownian/sphere 4 1 7 13 1974019 rng ${rng} dipole +fix 1 all brownian/sphere 4 1 7 13 1974019 rng gaussian dipole fix 2 all enforce2d compute press all pressure NULL virial @@ -56,9 +56,9 @@ Per MPI rank memory allocation (min/avg/max) = 4.289 | 4.289 | 4.289 Mbytes Step Temp E_pair c_press 0 1 0 0 50000 7.3671759e+10 0 0 -Loop time of 11.2219 on 1 procs for 50000 steps with 1024 atoms +Loop time of 11.2532 on 1 procs for 50000 steps with 1024 atoms -Performance: 0.038 tau/day, 4455.573 timesteps/s +Performance: 0.038 tau/day, 4443.198 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: @@ -66,10 +66,10 @@ Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.028513 | 0.028513 | 0.028513 | 0.0 | 0.25 -Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 -Modify | 11.048 | 11.048 | 11.048 | 0.0 | 98.45 -Other | | 0.1458 | | | 1.30 +Comm | 0.031456 | 0.031456 | 0.031456 | 0.0 | 0.28 +Output | 2.0958e-05 | 2.0958e-05 | 2.0958e-05 | 0.0 | 0.00 +Modify | 11.067 | 11.067 | 11.067 | 0.0 | 98.35 +Other | | 0.1546 | | | 1.37 Nlocal: 1024.00 ave 1024 max 1024 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -96,8 +96,9 @@ thermo_style custom step temp epair c_msd[*] c_press # write trajectory and thermo in a log-scale frequency # uncomment next three lines for dump output -#dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type # x y xu yu mux muy muz fx fy fz -#dump_modify 1 first yes sort id +dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz +dump 1 all custom 2000 dump_gaussian_4_1_7_13_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz +dump_modify 1 first yes sort id timestep 0.00001 thermo 1000 @@ -105,7 +106,7 @@ thermo 1000 # 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) = 4.664 | 4.664 | 4.664 Mbytes +Per MPI rank memory allocation (min/avg/max) = 6.113 | 6.113 | 6.113 Mbytes Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 0 7.3671759e+10 0 0 0 0 0 0 1000 710744.42 0 0.1332856 0.13577642 0 0.26906203 0 @@ -228,20 +229,20 @@ Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 118000 745594.37 0 16.838659 17.585392 0 34.424052 0 119000 714487.42 0 17.064214 17.743478 0 34.807692 0 120000 716557.14 0 17.105558 17.845925 0 34.951483 0 -Loop time of 27.2068 on 1 procs for 120000 steps with 1024 atoms +Loop time of 28.1507 on 1 procs for 120000 steps with 1024 atoms -Performance: 3810.806 tau/day, 4410.656 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 3683.037 tau/day, 4262.774 timesteps/s +99.9% 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 | 0.0015633 | 0.0015633 | 0.0015633 | 0.0 | 0.01 -Comm | 0.021682 | 0.021682 | 0.021682 | 0.0 | 0.08 -Output | 0.0032539 | 0.0032539 | 0.0032539 | 0.0 | 0.01 -Modify | 26.802 | 26.802 | 26.802 | 0.0 | 98.51 -Other | | 0.3781 | | | 1.39 +Neigh | 0.0016237 | 0.0016237 | 0.0016237 | 0.0 | 0.01 +Comm | 0.027064 | 0.027064 | 0.027064 | 0.0 | 0.10 +Output | 0.1712 | 0.1712 | 0.1712 | 0.0 | 0.61 +Modify | 27.545 | 27.545 | 27.545 | 0.0 | 97.85 +Other | | 0.4062 | | | 1.44 Nlocal: 1024.00 ave 1024 max 1024 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -256,4 +257,4 @@ Neighbor list builds = 1049 Dangerous builds = 0 -Total wall time: 0:00:38 +Total wall time: 0:00:39 diff --git a/examples/USER/misc/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log b/examples/USER/brownian/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log similarity index 100% rename from examples/USER/misc/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log rename to examples/USER/brownian/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log diff --git a/src/USER-MISC/fix_bd_asphere.cpp b/src/USER-BROWNIAN/fix_brownian_asphere.cpp similarity index 85% rename from src/USER-MISC/fix_bd_asphere.cpp rename to src/USER-BROWNIAN/fix_brownian_asphere.cpp index 88772b9237..123a7a5f5f 100644 --- a/src/USER-MISC/fix_bd_asphere.cpp +++ b/src/USER-BROWNIAN/fix_brownian_asphere.cpp @@ -17,7 +17,7 @@ Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ -#include "fix_bd_asphere.h" +#include "fix_brownian_asphere.h" #include #include @@ -42,7 +42,7 @@ enum{NODIPOLE,DIPOLE}; /* ---------------------------------------------------------------------- */ -FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : +FixBrownianAsphere::FixBrownianAsphere(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { virial_flag = 1; @@ -53,34 +53,34 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : if (narg > 11 || narg < 8 ) - error->all(FLERR,"Illegal fix bd/asphere command."); + error->all(FLERR,"Illegal fix brownian/asphere command."); if (!atom->sphere_flag) - error->all(FLERR,"Fix bd/asphere requires atom style sphere"); + error->all(FLERR,"Fix brownian/asphere requires atom style sphere"); gamma_t = utils::numeric(FLERR,arg[3],false,lmp); if (gamma_t <= 0.0) - error->all(FLERR,"Fix bd/asphere translational viscous drag " + error->all(FLERR,"Fix brownian/asphere translational viscous drag " "coefficient must be > 0."); gamma_r = utils::numeric(FLERR,arg[4],false,lmp); if (gamma_t <= 0.0) - error->all(FLERR,"Fix bd/asphere rotational viscous drag " + error->all(FLERR,"Fix brownian/asphere rotational viscous drag " "coefficient must be > 0."); diff_t = utils::numeric(FLERR,arg[5],false,lmp); if (diff_t <= 0.0) - error->all(FLERR,"Fix bd/asphere translational diffusion " + error->all(FLERR,"Fix brownian/asphere translational diffusion " "coefficient must be > 0."); diff_r = utils::numeric(FLERR,arg[6],false,lmp); if (diff_r <= 0.0) - error->all(FLERR,"Fix bd/asphere rotational diffusion " + error->all(FLERR,"Fix brownian/asphere rotational diffusion " "coefficient must be > 0."); seed = utils::inumeric(FLERR,arg[7],false,lmp); - if (seed <= 0) error->all(FLERR,"Fix bd/asphere seed must be > 0."); + if (seed <= 0) error->all(FLERR,"Fix brownian/asphere seed must be > 0."); noise_flag = 1; gaussian_noise_flag = 0; @@ -90,7 +90,7 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg) { if (strcmp(arg[iarg],"rng") == 0) { if (narg == iarg + 1) { - error->all(FLERR,"Illegal fix/bd/asphere command."); + error->all(FLERR,"Illegal fix/brownian/asphere command."); } if (strcmp(arg[iarg + 1],"uniform") == 0) { noise_flag = 1; @@ -100,19 +100,19 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg + 1],"none") == 0) { noise_flag = 0; } else { - error->all(FLERR,"Illegal fix/bd/asphere command."); + error->all(FLERR,"Illegal fix/brownian/asphere command."); } iarg = iarg + 2; } else if (strcmp(arg[iarg],"dipole") == 0) { dipole_flag = DIPOLE; iarg = iarg + 1; } else { - error->all(FLERR,"Illegal fix/bd/asphere command."); + error->all(FLERR,"Illegal fix/brownian/asphere command."); } } if (dipole_flag == DIPOLE && !atom->mu_flag) - error->all(FLERR,"Fix bd/asphere dipole requires atom attribute mu"); + error->all(FLERR,"Fix brownian/asphere dipole requires atom attribute mu"); // initialize Marsaglia RNG with processor-unique seed random = new RanMars(lmp,seed + comm->me); @@ -121,7 +121,7 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -int FixBdAsphere::setmask() +int FixBrownianAsphere::setmask() { int mask = 0; mask |= INITIAL_INTEGRATE; @@ -131,7 +131,7 @@ int FixBdAsphere::setmask() /* ---------------------------------------------------------------------- */ -FixBdAsphere::~FixBdAsphere() +FixBrownianAsphere::~FixBrownianAsphere() { delete random; } @@ -140,13 +140,13 @@ FixBdAsphere::~FixBdAsphere() /* ---------------------------------------------------------------------- */ -void FixBdAsphere::init() +void FixBrownianAsphere::init() { avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); if (!avec) - error->all(FLERR,"Compute bd/asphere requires " + error->all(FLERR,"Compute brownian/asphere requires " "atom style ellipsoid"); // check that all particles are finite-size ellipsoids @@ -159,7 +159,7 @@ void FixBdAsphere::init() for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) if (ellipsoid[i] < 0) - error->one(FLERR,"Fix bd/asphere requires extended particles"); + error->one(FLERR,"Fix brownian/asphere requires extended particles"); if (dipole_flag == DIPOLE) { @@ -208,7 +208,7 @@ void FixBdAsphere::init() sqrtdt = sqrt(dt); } -void FixBdAsphere::setup(int vflag) +void FixBrownianAsphere::setup(int vflag) { post_force(vflag); } @@ -216,7 +216,7 @@ void FixBdAsphere::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixBdAsphere::initial_integrate(int /* vflag */) +void FixBrownianAsphere::initial_integrate(int /* vflag */) { double **x = atom->x; double **v = atom->v; @@ -313,7 +313,7 @@ void FixBdAsphere::initial_integrate(int /* vflag */) return; } -void FixBdAsphere::update_x_and_omega(double *x, double *v, double *omega, +void FixBrownianAsphere::update_x_and_omega(double *x, double *v, double *omega, double *f, double *torque, int d3rot) { double dx, dy, dz; @@ -341,7 +341,7 @@ void FixBdAsphere::update_x_and_omega(double *x, double *v, double *omega, apply random force, stolen from MISC/fix_efield.cpp ------------------------------------------------------------------------- */ -void FixBdAsphere::post_force(int vflag) +void FixBrownianAsphere::post_force(int vflag) { double **f = atom->f; double **x = atom->x; @@ -384,7 +384,7 @@ void FixBdAsphere::post_force(int vflag) } } -void FixBdAsphere::reset_dt() +void FixBrownianAsphere::reset_dt() { dt = update->dt; diff --git a/src/USER-MISC/fix_bd_asphere.h b/src/USER-BROWNIAN/fix_brownian_asphere.h similarity index 69% rename from src/USER-MISC/fix_bd_asphere.h rename to src/USER-BROWNIAN/fix_brownian_asphere.h index 696b659729..31ccf4fc8b 100644 --- a/src/USER-MISC/fix_bd_asphere.h +++ b/src/USER-BROWNIAN/fix_brownian_asphere.h @@ -13,21 +13,21 @@ #ifdef FIX_CLASS -FixStyle(bd/asphere,FixBdAsphere) +FixStyle(brownian/asphere,FixBrownianAsphere) #else -#ifndef LMP_FIX_BD_ASPHERE_H -#define LMP_FIX_BD_ASPHERE_H +#ifndef LMP_FIX_BROWNIAN_ASPHERE_H +#define LMP_FIX_BROWNIAN_ASPHERE_H #include "fix.h" namespace LAMMPS_NS { -class FixBdAsphere : public Fix { +class FixBrownianAsphere : public Fix { public: - FixBdAsphere(class LAMMPS *, int, char **); - virtual ~FixBdAsphere(); + FixBrownianAsphere(class LAMMPS *, int, char **); + virtual ~FixBrownianAsphere(); void init(); void initial_integrate(int); void setup(int); @@ -66,38 +66,38 @@ protected: /* ERROR/WARNING messages: -E: Illegal fix bd/asphere command. +E: Illegal fix brownian/asphere command. Wrong number/type of input arguments. -E: Compute bd/asphere requires atom style sphere +E: Compute brownian/asphere requires atom style sphere Self-explanatory. -E: Compute bd/asphere requires atom style ellipsoid +E: Compute brownian/asphere requires atom style ellipsoid Self-explanatory. -E: Compute bd/asphere dipole requires atom attribute mu +E: Compute brownian/asphere dipole requires atom attribute mu Self-explanatory. -E: Fix bd/asphere translational viscous drag coefficient must be > 0. +E: Fix brownian/asphere translational viscous drag coefficient must be > 0. Self-explanatory. -E: Fix bd/asphere rotational viscous drag coefficient must be > 0. +E: Fix brownian/asphere rotational viscous drag coefficient must be > 0. Self-explanatory. -E: Fix bd/asphere translational diffusion coefficient must be > 0. +E: Fix brownian/asphere translational diffusion coefficient must be > 0. Self-explanatory. -E: Fix bd/asphere rotational diffusion coefficient must be > 0. +E: Fix brownian/asphere rotational diffusion coefficient must be > 0. Self-explanatory. -E: Fix bd/asphere seed must be > 0. +E: Fix brownian/asphere seed must be > 0. */ diff --git a/src/USER-MISC/fix_bd_sphere.cpp b/src/USER-BROWNIAN/fix_brownian_sphere.cpp similarity index 85% rename from src/USER-MISC/fix_bd_sphere.cpp rename to src/USER-BROWNIAN/fix_brownian_sphere.cpp index cc3c788349..c3e0cd2457 100644 --- a/src/USER-MISC/fix_bd_sphere.cpp +++ b/src/USER-BROWNIAN/fix_brownian_sphere.cpp @@ -17,7 +17,7 @@ Contributing author: Sam Cameron (University of Bristol) ------------------------------------------------------------------------- */ -#include "fix_bd_sphere.h" +#include "fix_brownian_sphere.h" #include #include @@ -41,7 +41,7 @@ enum{NONE,DIPOLE}; /* ---------------------------------------------------------------------- */ -FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : +FixBrownianSphere::FixBrownianSphere(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { virial_flag = 1; @@ -51,34 +51,34 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : extra = NONE; if (narg > 11 || narg < 8 ) - error->all(FLERR,"Illegal fix bd/sphere command."); + error->all(FLERR,"Illegal fix brownian/sphere command."); if (!atom->sphere_flag) - error->all(FLERR,"Fix bd/sphere requires atom style sphere"); + error->all(FLERR,"Fix brownian/sphere requires atom style sphere"); gamma_t = utils::numeric(FLERR,arg[3],false,lmp); if (gamma_t <= 0.0) - error->all(FLERR,"Fix bd/sphere translational viscous drag " + error->all(FLERR,"Fix brownian/sphere translational viscous drag " "coefficient must be > 0."); gamma_r = utils::numeric(FLERR,arg[4],false,lmp); if (gamma_t <= 0.0) - error->all(FLERR,"Fix bd/sphere rotational viscous drag " + error->all(FLERR,"Fix brownian/sphere rotational viscous drag " "coefficient must be > 0."); diff_t = utils::numeric(FLERR,arg[5],false,lmp); if (diff_t <= 0.0) - error->all(FLERR,"Fix bd/sphere translational diffusion " + error->all(FLERR,"Fix brownian/sphere translational diffusion " "coefficient must be > 0."); diff_r = utils::numeric(FLERR,arg[6],false,lmp); if (diff_r <= 0.0) - error->all(FLERR,"Fix bd/sphere rotational diffusion " + error->all(FLERR,"Fix brownian/sphere rotational diffusion " "coefficient must be > 0."); seed = utils::inumeric(FLERR,arg[7],false,lmp); - if (seed <= 0) error->all(FLERR,"Fix bd/sphere seed must be > 0."); + if (seed <= 0) error->all(FLERR,"Fix brownian/sphere seed must be > 0."); noise_flag = 1; gaussian_noise_flag = 0; @@ -88,7 +88,7 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg) { if (strcmp(arg[iarg],"rng") == 0) { if (narg == iarg + 1) { - error->all(FLERR,"Illegal fix/bd/sphere command."); + error->all(FLERR,"Illegal fix/brownian/sphere command."); } if (strcmp(arg[iarg + 1],"uniform") == 0) { noise_flag = 1; @@ -98,19 +98,19 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg + 1],"none") == 0) { noise_flag = 0; } else { - error->all(FLERR,"Illegal fix/bd/sphere command."); + error->all(FLERR,"Illegal fix/brownian/sphere command."); } iarg = iarg + 2; } else if (strcmp(arg[iarg],"dipole") == 0) { extra = DIPOLE; iarg = iarg + 1; } else { - error->all(FLERR,"Illegal fix/bd/sphere command."); + error->all(FLERR,"Illegal fix/brownian/sphere command."); } } if (extra == DIPOLE && !atom->mu_flag) - error->all(FLERR,"Fix bd/sphere update dipole requires atom attribute mu"); + error->all(FLERR,"Fix brownian/sphere update dipole requires atom attribute mu"); // initialize Marsaglia RNG with processor-unique seed random = new RanMars(lmp,seed + comm->me); @@ -119,7 +119,7 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -int FixBdSphere::setmask() +int FixBrownianSphere::setmask() { int mask = 0; mask |= INITIAL_INTEGRATE; @@ -129,7 +129,7 @@ int FixBdSphere::setmask() /* ---------------------------------------------------------------------- */ -FixBdSphere::~FixBdSphere() +FixBrownianSphere::~FixBrownianSphere() { delete random; } @@ -138,7 +138,7 @@ FixBdSphere::~FixBdSphere() /* ---------------------------------------------------------------------- */ -void FixBdSphere::init() +void FixBrownianSphere::init() { g1 = force->ftm2v/gamma_t; @@ -161,14 +161,14 @@ void FixBdSphere::init() sqrtdt = sqrt(dt); } -void FixBdSphere::setup(int vflag) +void FixBrownianSphere::setup(int vflag) { post_force(vflag); } /* ---------------------------------------------------------------------- */ -void FixBdSphere::initial_integrate(int /* vflag */) +void FixBrownianSphere::initial_integrate(int /* vflag */) { double **x = atom->x; double **v = atom->v; @@ -270,7 +270,7 @@ void FixBdSphere::initial_integrate(int /* vflag */) apply random force, stolen from MISC/fix_efield.cpp ------------------------------------------------------------------------- */ -void FixBdSphere::post_force(int vflag) +void FixBrownianSphere::post_force(int vflag) { double **f = atom->f; double **x = atom->x; @@ -313,7 +313,7 @@ void FixBdSphere::post_force(int vflag) } } -void FixBdSphere::reset_dt() +void FixBrownianSphere::reset_dt() { dt = update->dt; diff --git a/src/USER-MISC/fix_bd_sphere.h b/src/USER-BROWNIAN/fix_brownian_sphere.h similarity index 70% rename from src/USER-MISC/fix_bd_sphere.h rename to src/USER-BROWNIAN/fix_brownian_sphere.h index 8a3df214a6..8d30001fdd 100644 --- a/src/USER-MISC/fix_bd_sphere.h +++ b/src/USER-BROWNIAN/fix_brownian_sphere.h @@ -13,21 +13,21 @@ #ifdef FIX_CLASS -FixStyle(bd/sphere,FixBdSphere) +FixStyle(brownian/sphere,FixBrownianSphere) #else -#ifndef LMP_FIX_BD_SPHERE_H -#define LMP_FIX_BD_SPHERE_H +#ifndef LMP_FIX_BROWNIAN_SPHERE_H +#define LMP_FIX_BROWNIAN_SPHERE_H #include "fix.h" namespace LAMMPS_NS { -class FixBdSphere : public Fix { +class FixBrownianSphere : public Fix { public: - FixBdSphere(class LAMMPS *, int, char **); - virtual ~FixBdSphere(); + FixBrownianSphere(class LAMMPS *, int, char **); + virtual ~FixBrownianSphere(); void init(); void initial_integrate(int); void setup(int); @@ -61,34 +61,34 @@ protected: /* ERROR/WARNING messages: -E: Illegal fix bd/sphere command. +E: Illegal fix brownian/sphere command. Wrong number/type of input arguments. -E: Compute bd/sphere requires atom style sphere +E: Compute brownian/sphere requires atom style sphere Self-explanatory. -E: Compute bd/sphere requires atom attribute mu +E: Compute brownian/sphere requires atom attribute mu Self-explanatory. -E: Fix bd/sphere translational viscous drag coefficient must be > 0. +E: Fix brownian/sphere translational viscous drag coefficient must be > 0. Self-explanatory. -E: Fix bd/sphere rotational viscous drag coefficient must be > 0. +E: Fix brownian/sphere rotational viscous drag coefficient must be > 0. Self-explanatory. -E: Fix bd/sphere translational diffusion coefficient must be > 0. +E: Fix brownian/sphere translational diffusion coefficient must be > 0. Self-explanatory. -E: Fix bd/sphere rotational diffusion coefficient must be > 0. +E: Fix brownian/sphere rotational diffusion coefficient must be > 0. Self-explanatory. -E: Fix bd/sphere seed must be > 0. +E: Fix brownian/sphere seed must be > 0. */ diff --git a/src/USER-MISC/README b/src/USER-MISC/README index ac41d60dfd..538fdb7952 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -53,8 +53,6 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 -fix bd/sphere, Sam Cameron (U of Bristol), samuel.j.m.cameron at gmail.com, 13 Dec 2020 -fix bd/asphere, Sam Cameron (U of Bristol), samuel.j.m.cameron at gmail.com, 13 Dec 2020 fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 diff --git a/unittest/force-styles/tests/data.bdsphere b/unittest/force-styles/tests/data.brownian similarity index 100% rename from unittest/force-styles/tests/data.bdsphere rename to unittest/force-styles/tests/data.brownian diff --git a/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml b/unittest/force-styles/tests/fix-timestep-brownian.yaml similarity index 97% rename from unittest/force-styles/tests/fix-timestep-bd_sphere.yaml rename to unittest/force-styles/tests/fix-timestep-brownian.yaml index b69f37e206..76477d874e 100644 --- a/unittest/force-styles/tests/fix-timestep-bd_sphere.yaml +++ b/unittest/force-styles/tests/fix-timestep-brownian.yaml @@ -4,12 +4,12 @@ date_generated: Tue Dec 08 12:28:40 2020 epsilon: 1e-12 prerequisites: ! | atom hybrid dipole sphere - fix bd_sphere + fix brownian/sphere pre_commands: ! "" post_commands: ! | - fix test solute bd_sphere 1.0 1.0 1.0 1.0 1049270 dipole + fix test solute brownian/sphere 1.0 1.0 1.0 1.0 1049270 dipole fix_modify test virial yes -input_file: in.bdsphere +input_file: in.brownian natoms: 32 run_pos: ! |2 1 0.8198132185477983 -1.5120221815010249 1.069236010215717 diff --git a/unittest/force-styles/tests/in.bdsphere b/unittest/force-styles/tests/in.brownian similarity index 88% rename from unittest/force-styles/tests/in.bdsphere rename to unittest/force-styles/tests/in.brownian index 1fb583f51d..cf85742e59 100644 --- a/unittest/force-styles/tests/in.bdsphere +++ b/unittest/force-styles/tests/in.brownian @@ -2,7 +2,7 @@ variable newton_pair index on variable newton_bond index on variable units index lj variable input_dir index . -variable data_file index ${input_dir}/data.bdsphere +variable data_file index ${input_dir}/data.brownian variable pair_style index 'zero 8.0' atom_style hybrid dipole sphere