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Moved brownian dynamics files to be in USER-BROWNIAN package

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This commit is contained in:
Sam Cameron
2020-12-19 17:42:47 +00:00
parent d9440a582c
commit 4c1f449350
21 changed files with 160 additions and 162 deletions
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2
cmake/CMakeLists.txt
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@ -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-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-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-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) set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU)
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES}) foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF) option(PKG_${PKG} "Build ${PKG} Package" OFF)

4
doc/src/Commands_fix.rst
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@ -39,8 +39,8 @@ OPT.
* :doc:`ave/time <fix_ave_time>` * :doc:`ave/time <fix_ave_time>`
* :doc:`aveforce <fix_aveforce>` * :doc:`aveforce <fix_aveforce>`
* :doc:`balance <fix_balance>` * :doc:`balance <fix_balance>`
* :doc:`bd/sphere <fix_bd_sphere>` * :doc:`brownian/asphere <fix_brownian_asphere>`
* :doc:`bd/asphere <fix_bd_asphere>` * :doc:`brownian/sphere <fix_brownian_sphere>`
* :doc:`bocs <fix_bocs>` * :doc:`bocs <fix_bocs>`
* :doc:`bond/break <fix_bond_break>` * :doc:`bond/break <fix_bond_break>`
* :doc:`bond/create <fix_bond_create>` * :doc:`bond/create <fix_bond_create>`

4
doc/src/fix.rst
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@ -182,8 +182,8 @@ accelerated styles exist.
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities * :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom * :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
* :doc:`balance <fix_balance>` - perform dynamic load-balancing * :doc:`balance <fix_balance>` - perform dynamic load-balancing
* :doc:`bd/asphere <fix_bd_asphere>` - integrate positions and orientations in overdamped motion * :doc:`brownian/asphere <fix_brownian_asphere>` - overdamped translational and rotational brownian for ellipsoids
* :doc:`bd/sphere <fix_bd_sphere>` - overdamped translational and rotational brownian dynamics * :doc:`brownian/sphere <fix_brownian_sphere>` - overdamped translational and rotational brownian for spheres
* :doc:`bocs <fix_bocs>` - NPT style time integration with pressure correction * :doc:`bocs <fix_bocs>` - NPT style time integration with pressure correction
* :doc:`bond/break <fix_bond_break>` - break bonds on the fly * :doc:`bond/break <fix_bond_break>` - break bonds on the fly
* :doc:`bond/create <fix_bond_create>` - create bonds on the fly * :doc:`bond/create <fix_bond_create>` - create bonds on the fly

22
doc/src/fix_bd_asphere.rst → doc/src/fix_brownian_asphere.rst
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@ -1,17 +1,17 @@
.. index:: fix bd/asphere .. index:: fix brownian/asphere
fix bd/asphere command fix brownian/asphere command
====================== ============================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. 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 <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* bd/asphere = style name of this fix command * brownian/asphere = style name of this fix command
* gamma_t = translational friction coefficient * gamma_t = translational friction coefficient
* gamma_r = rotational friction coefficient * gamma_r = rotational friction coefficient
* diff_t = translational diffusion coefficient * diff_t = translational diffusion coefficient
@ -32,10 +32,10 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
fix 1 all bd/asphere 1.0 1.0 1.0 1.0 1294019 fix 1 all brownian/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 brownian/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 brownian/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 19581092 dipole rng gaussian
Description Description
@ -59,7 +59,7 @@ Chapter 4 of :ref:`(Goldstein) <GoldsteinCM1>`), :math:`dW_t` and
The quaternions :math:`q` of the ellipsoid are updated each timestep from The quaternions :math:`q` of the ellipsoid are updated each timestep from
the angular velocity vector. the angular velocity vector.
See :doc:`fix bd/sphere <fix_bd_sphere>` for discussion on the See :doc:`fix brownian/sphere <fix_brownian_sphere>` for discussion on the
values of :math:`\gamma_t`, :math:`\gamma_r`, :math:`D_t`, values of :math:`\gamma_t`, :math:`\gamma_r`, :math:`D_t`,
:math:`D_r`, and temperature when simulating equilibrium systems. :math:`D_r`, and temperature when simulating equilibrium systems.
@ -124,7 +124,7 @@ be point particles.
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`fix bd/sphere <fix_bd_sphere>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix brownian/sphere <fix_brownian_sphere>`, :doc:`fix langevin <fix_langevin>`,
:doc:`fix nve/asphere <fix_nve_asphere>`, :doc:`atom style <atom_style>` :doc:`fix nve/asphere <fix_nve_asphere>`, :doc:`atom style <atom_style>`
Default Default

18
doc/src/fix_bd_sphere.rst → doc/src/fix_brownian_sphere.rst
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@ -1,17 +1,17 @@
.. index:: fix bd/sphere .. index:: fix brownian/sphere
fix bd/sphere command fix brownian/sphere command
====================== ===========================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. 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 <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* bd/sphere = style name of this fix command * brownian/sphere = style name of this fix command
* gamma_t = translational friction coefficient * gamma_t = translational friction coefficient
* gamma_r = rotational friction coefficient * gamma_r = rotational friction coefficient
* diff_t = translational diffusion coefficient * diff_t = translational diffusion coefficient
@ -32,10 +32,10 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
fix 1 all bd/sphere 1.0 1.0 1.0 1.0 1294019 fix 1 all brownian/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 brownian/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 brownian/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 19581092 dipole rng gaussian
Description Description

0
examples/USER/misc/bd_asphere/README.txt → examples/USER/brownian/bd_asphere/README.txt
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2
examples/USER/misc/bd_asphere/in3d.bd → examples/USER/brownian/bd_asphere/in3d.brownian
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@ -36,7 +36,7 @@ neigh_modify every 1 delay 1 check yes
pair_style none 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 compute press all pressure NULL virial

49
examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log → examples/USER/brownian/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log
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@ -38,13 +38,13 @@ neigh_modify every 1 delay 1 check yes
pair_style none 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
fix 1 all bd/asphere 4 ${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 bd/asphere 4 1 ${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 bd/asphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole fix 1 all brownian/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 brownian/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 brownian/asphere 4 1 7 13 1974019 rng ${rng} dipole
fix 1 all bd/asphere 4 1 7 13 1974019 rng gaussian dipole fix 1 all brownian/asphere 4 1 7 13 1974019 rng gaussian dipole
compute press all pressure NULL virial compute press all pressure NULL virial
@ -61,9 +61,9 @@ Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.379 | 5.379 Mbytes
Step Temp E_pair c_press Step Temp E_pair c_press
0 1 0 0 0 1 0 0
50000 1.3923773e+11 0 0 50000 1.3923773e+11 0 0
Loop time of 5.68636 on 1 procs for 50000 steps with 512 atoms Loop time of 5.61345 on 1 procs for 50000 steps with 512 atoms
Performance: 0.076 tau/day, 8792.977 timesteps/s Performance: 0.077 tau/day, 8907.171 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
@ -71,10 +71,10 @@ Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.11589 | 0.11589 | 0.11589 | 0.0 | 2.04 Comm | 0.11822 | 0.11822 | 0.11822 | 0.0 | 2.11
Output | 2.1155e-05 | 2.1155e-05 | 2.1155e-05 | 0.0 | 0.00 Output | 2.0199e-05 | 2.0199e-05 | 2.0199e-05 | 0.0 | 0.00
Modify | 5.4911 | 5.4911 | 5.4911 | 0.0 | 96.57 Modify | 5.4135 | 5.4135 | 5.4135 | 0.0 | 96.44
Other | | 0.07936 | | | 1.40 Other | | 0.0817 | | | 1.46
Nlocal: 512.000 ave 512 max 512 min Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -100,9 +100,8 @@ thermo_style custom step temp epair c_msd[*] c_press
# write trajectory and thermo in a log-scale frequency # write trajectory and thermo in a log-scale frequency
dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz #dump 1 all custom 1000 dump_${params}_3d.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_modify 1 first yes sort id
timestep 0.00001 timestep 0.00001
thermo 10000 thermo 10000
@ -110,7 +109,7 @@ thermo 10000
# main run # main run
run 120000 run 120000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) 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 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 0 1.3923773e+11 0 0 0 0 0 0
10000 1413805.2 0 1.3943053 1.4055827 1.4346505 4.2345385 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 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 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 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 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0.00079148 | 0.00079148 | 0.00079148 | 0.0 | 0.01 Neigh | 0.00075178 | 0.00075178 | 0.00075178 | 0.0 | 0.01
Comm | 0.029132 | 0.029132 | 0.029132 | 0.0 | 0.21 Comm | 0.0282 | 0.0282 | 0.0282 | 0.0 | 0.21
Output | 0.15178 | 0.15178 | 0.15178 | 0.0 | 1.12 Output | 0.00032692 | 0.00032692 | 0.00032692 | 0.0 | 0.00
Modify | 13.222 | 13.222 | 13.222 | 0.0 | 97.25 Modify | 13.017 | 13.017 | 13.017 | 0.0 | 98.29
Other | | 0.1916 | | | 1.41 Other | | 0.1976 | | | 1.49
Nlocal: 512.000 ave 512 max 512 min Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -151,4 +150,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0.0000000 Ave neighs/atom = 0.0000000
Neighbor list builds = 1110 Neighbor list builds = 1110
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:19 Total wall time: 0:00:18

10
examples/USER/misc/bd_sphere/README.txt → examples/USER/brownian/bd_sphere/README.txt
View File

@ -1,11 +1,11 @@
The input file in2ddipole.bd demonstrates how to run a 2d simulation The input file in2ddipole.brownian demonstrates how to run a
of particles undergoing overdamped brownian motion in both 2d simulation of particles undergoing overdamped brownian motion
translational and rotational degrees of freedom. Dipole in both translational and rotational degrees of freedom. Dipole
updating is turned on, so the package DIPOLE must be built updating is turned on, so the package DIPOLE must be built
for this example to work. for this example to work.
The input file in3d_virial_on.bd demonstrates how to run a The input file in3d_virial_on.brownian demonstrates how to run
similar simulation but in 3d. In this case, the virial a similar simulation but in 3d. In this case, the virial
contribution of the brownian dynamics (the sum contribution of the brownian dynamics (the sum
sum_i <r_i dot sqrt{2D_t}W>/(3*volume) where W is sum_i <r_i dot sqrt{2D_t}W>/(3*volume) where W is
a random variable with mean 0 and variance dt) is a random variable with mean 0 and variance dt) is

2
examples/USER/misc/bd_sphere/in2ddipole.bd → examples/USER/brownian/bd_sphere/in2ddipole.brownian
View File

@ -38,7 +38,7 @@ pair_style none
#compute d all property/atom mux muy muz #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 fix 2 all enforce2d
compute press all pressure NULL virial compute press all pressure NULL virial

2
examples/USER/misc/bd_sphere/in3d_virial_on.bd → examples/USER/brownian/bd_sphere/in3d_virial_on.brownian
View File

@ -33,7 +33,7 @@ neigh_modify every 1 delay 1 check yes
pair_style none 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 fix_modify 1 virial yes
compute press all pressure NULL virial compute press all pressure NULL virial

53
examples/USER/misc/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log → examples/USER/brownian/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log
View File

@ -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 1 by 1 by 1 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 1024 atoms Created 1024 atoms
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.002 seconds
mass * 1.0 mass * 1.0
set type * dipole/random ${seed} 1.0 set type * dipole/random ${seed} 1.0
set type * dipole/random 1974019 1.0 set type * dipole/random 1974019 1.0
@ -33,13 +33,13 @@ pair_style none
#compute d all property/atom mux muy muz #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 1 all bd/sphere 4 ${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 bd/sphere 4 1 ${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 bd/sphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole fix 1 all brownian/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 brownian/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 brownian/sphere 4 1 7 13 1974019 rng ${rng} dipole
fix 1 all bd/sphere 4 1 7 13 1974019 rng gaussian dipole fix 1 all brownian/sphere 4 1 7 13 1974019 rng gaussian dipole
fix 2 all enforce2d fix 2 all enforce2d
compute press all pressure NULL virial compute press all pressure NULL virial
@ -56,9 +56,9 @@ Per MPI rank memory allocation (min/avg/max) = 4.289 | 4.289 | 4.289 Mbytes
Step Temp E_pair c_press Step Temp E_pair c_press
0 1 0 0 0 1 0 0
50000 7.3671759e+10 0 0 50000 7.3671759e+10 0 0
Loop time of 11.2219 on 1 procs for 50000 steps with 1024 atoms Loop time of 11.2532 on 1 procs for 50000 steps with 1024 atoms
Performance: 0.038 tau/day, 4455.573 timesteps/s Performance: 0.038 tau/day, 4443.198 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
@ -66,10 +66,10 @@ Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.028513 | 0.028513 | 0.028513 | 0.0 | 0.25 Comm | 0.031456 | 0.031456 | 0.031456 | 0.0 | 0.28
Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Output | 2.0958e-05 | 2.0958e-05 | 2.0958e-05 | 0.0 | 0.00
Modify | 11.048 | 11.048 | 11.048 | 0.0 | 98.45 Modify | 11.067 | 11.067 | 11.067 | 0.0 | 98.35
Other | | 0.1458 | | | 1.30 Other | | 0.1546 | | | 1.37
Nlocal: 1024.00 ave 1024 max 1024 min Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -96,8 +96,9 @@ thermo_style custom step temp epair c_msd[*] c_press
# write trajectory and thermo in a log-scale frequency # write trajectory and thermo in a log-scale frequency
# uncomment next three lines for dump output # uncomment next three lines for dump output
#dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type # x y xu yu mux muy muz fx fy fz dump 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_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 timestep 0.00001
thermo 1000 thermo 1000
@ -105,7 +106,7 @@ thermo 1000
# main run # main run
run 120000 run 120000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) 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 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 0 7.3671759e+10 0 0 0 0 0 0
1000 710744.42 0 0.1332856 0.13577642 0 0.26906203 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 118000 745594.37 0 16.838659 17.585392 0 34.424052 0
119000 714487.42 0 17.064214 17.743478 0 34.807692 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 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 Performance: 3683.037 tau/day, 4262.774 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00 Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0.0015633 | 0.0015633 | 0.0015633 | 0.0 | 0.01 Neigh | 0.0016237 | 0.0016237 | 0.0016237 | 0.0 | 0.01
Comm | 0.021682 | 0.021682 | 0.021682 | 0.0 | 0.08 Comm | 0.027064 | 0.027064 | 0.027064 | 0.0 | 0.10
Output | 0.0032539 | 0.0032539 | 0.0032539 | 0.0 | 0.01 Output | 0.1712 | 0.1712 | 0.1712 | 0.0 | 0.61
Modify | 26.802 | 26.802 | 26.802 | 0.0 | 98.51 Modify | 27.545 | 27.545 | 27.545 | 0.0 | 97.85
Other | | 0.3781 | | | 1.39 Other | | 0.4062 | | | 1.44
Nlocal: 1024.00 ave 1024 max 1024 min Nlocal: 1024.00 ave 1024 max 1024 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -256,4 +257,4 @@ Neighbor list builds = 1049
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:38 Total wall time: 0:00:39

0
examples/USER/misc/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log → examples/USER/brownian/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log
View File

46
src/USER-MISC/fix_bd_asphere.cpp → src/USER-BROWNIAN/fix_brownian_asphere.cpp
View File

@ -17,7 +17,7 @@
Contributing author: Sam Cameron (University of Bristol) Contributing author: Sam Cameron (University of Bristol)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "fix_bd_asphere.h" #include "fix_brownian_asphere.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -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) Fix(lmp, narg, arg)
{ {
virial_flag = 1; virial_flag = 1;
@ -53,34 +53,34 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) :
if (narg > 11 || narg < 8 ) 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) 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); gamma_t = utils::numeric(FLERR,arg[3],false,lmp);
if (gamma_t <= 0.0) 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."); "coefficient must be > 0.");
gamma_r = utils::numeric(FLERR,arg[4],false,lmp); gamma_r = utils::numeric(FLERR,arg[4],false,lmp);
if (gamma_t <= 0.0) 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."); "coefficient must be > 0.");
diff_t = utils::numeric(FLERR,arg[5],false,lmp); diff_t = utils::numeric(FLERR,arg[5],false,lmp);
if (diff_t <= 0.0) 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."); "coefficient must be > 0.");
diff_r = utils::numeric(FLERR,arg[6],false,lmp); diff_r = utils::numeric(FLERR,arg[6],false,lmp);
if (diff_r <= 0.0) 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."); "coefficient must be > 0.");
seed = utils::inumeric(FLERR,arg[7],false,lmp); 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; noise_flag = 1;
gaussian_noise_flag = 0; gaussian_noise_flag = 0;
@ -90,7 +90,7 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"rng") == 0) { if (strcmp(arg[iarg],"rng") == 0) {
if (narg == iarg + 1) { 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) { if (strcmp(arg[iarg + 1],"uniform") == 0) {
noise_flag = 1; noise_flag = 1;
@ -100,19 +100,19 @@ FixBdAsphere::FixBdAsphere(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg + 1],"none") == 0) { } else if (strcmp(arg[iarg + 1],"none") == 0) {
noise_flag = 0; noise_flag = 0;
} else { } else {
error->all(FLERR,"Illegal fix/bd/asphere command."); error->all(FLERR,"Illegal fix/brownian/asphere command.");
} }
iarg = iarg + 2; iarg = iarg + 2;
} else if (strcmp(arg[iarg],"dipole") == 0) { } else if (strcmp(arg[iarg],"dipole") == 0) {
dipole_flag = DIPOLE; dipole_flag = DIPOLE;
iarg = iarg + 1; iarg = iarg + 1;
} else { } else {
error->all(FLERR,"Illegal fix/bd/asphere command."); error->all(FLERR,"Illegal fix/brownian/asphere command.");
} }
} }
if (dipole_flag == DIPOLE && !atom->mu_flag) 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 // initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me); 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; int mask = 0;
mask |= INITIAL_INTEGRATE; mask |= INITIAL_INTEGRATE;
@ -131,7 +131,7 @@ int FixBdAsphere::setmask()
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixBdAsphere::~FixBdAsphere() FixBrownianAsphere::~FixBrownianAsphere()
{ {
delete random; delete random;
} }
@ -140,13 +140,13 @@ FixBdAsphere::~FixBdAsphere()
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixBdAsphere::init() void FixBrownianAsphere::init()
{ {
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec) if (!avec)
error->all(FLERR,"Compute bd/asphere requires " error->all(FLERR,"Compute brownian/asphere requires "
"atom style ellipsoid"); "atom style ellipsoid");
// check that all particles are finite-size ellipsoids // check that all particles are finite-size ellipsoids
@ -159,7 +159,7 @@ void FixBdAsphere::init()
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) if (mask[i] & groupbit)
if (ellipsoid[i] < 0) 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) { if (dipole_flag == DIPOLE) {
@ -208,7 +208,7 @@ void FixBdAsphere::init()
sqrtdt = sqrt(dt); sqrtdt = sqrt(dt);
} }
void FixBdAsphere::setup(int vflag) void FixBrownianAsphere::setup(int vflag)
{ {
post_force(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 **x = atom->x;
double **v = atom->v; double **v = atom->v;
@ -313,7 +313,7 @@ void FixBdAsphere::initial_integrate(int /* vflag */)
return; 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 *f, double *torque, int d3rot)
{ {
double dx, dy, dz; 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 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 **f = atom->f;
double **x = atom->x; 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; dt = update->dt;

30
src/USER-MISC/fix_bd_asphere.h → src/USER-BROWNIAN/fix_brownian_asphere.h
View File

@ -13,21 +13,21 @@
#ifdef FIX_CLASS #ifdef FIX_CLASS
FixStyle(bd/asphere,FixBdAsphere) FixStyle(brownian/asphere,FixBrownianAsphere)
#else #else
#ifndef LMP_FIX_BD_ASPHERE_H #ifndef LMP_FIX_BROWNIAN_ASPHERE_H
#define LMP_FIX_BD_ASPHERE_H #define LMP_FIX_BROWNIAN_ASPHERE_H
#include "fix.h" #include "fix.h"
namespace LAMMPS_NS { namespace LAMMPS_NS {
class FixBdAsphere : public Fix { class FixBrownianAsphere : public Fix {
public: public:
FixBdAsphere(class LAMMPS *, int, char **); FixBrownianAsphere(class LAMMPS *, int, char **);
virtual ~FixBdAsphere(); virtual ~FixBrownianAsphere();
void init(); void init();
void initial_integrate(int); void initial_integrate(int);
void setup(int); void setup(int);
@ -66,38 +66,38 @@ protected:
/* ERROR/WARNING messages: /* ERROR/WARNING messages:
E: Illegal fix bd/asphere command. E: Illegal fix brownian/asphere command.
Wrong number/type of input arguments. Wrong number/type of input arguments.
E: Compute bd/asphere requires atom style sphere E: Compute brownian/asphere requires atom style sphere
Self-explanatory. Self-explanatory.
E: Compute bd/asphere requires atom style ellipsoid E: Compute brownian/asphere requires atom style ellipsoid
Self-explanatory. Self-explanatory.
E: Compute bd/asphere dipole requires atom attribute mu E: Compute brownian/asphere dipole requires atom attribute mu
Self-explanatory. 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. 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. Self-explanatory.
E: Fix bd/asphere translational diffusion coefficient must be > 0. E: Fix brownian/asphere translational diffusion coefficient must be > 0.
Self-explanatory. Self-explanatory.
E: Fix bd/asphere rotational diffusion coefficient must be > 0. E: Fix brownian/asphere rotational diffusion coefficient must be > 0.
Self-explanatory. Self-explanatory.
E: Fix bd/asphere seed must be > 0. E: Fix brownian/asphere seed must be > 0.
*/ */

40
src/USER-MISC/fix_bd_sphere.cpp → src/USER-BROWNIAN/fix_brownian_sphere.cpp
View File

@ -17,7 +17,7 @@
Contributing author: Sam Cameron (University of Bristol) Contributing author: Sam Cameron (University of Bristol)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "fix_bd_sphere.h" #include "fix_brownian_sphere.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -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) Fix(lmp, narg, arg)
{ {
virial_flag = 1; virial_flag = 1;
@ -51,34 +51,34 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) :
extra = NONE; extra = NONE;
if (narg > 11 || narg < 8 ) 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) 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); gamma_t = utils::numeric(FLERR,arg[3],false,lmp);
if (gamma_t <= 0.0) 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."); "coefficient must be > 0.");
gamma_r = utils::numeric(FLERR,arg[4],false,lmp); gamma_r = utils::numeric(FLERR,arg[4],false,lmp);
if (gamma_t <= 0.0) 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."); "coefficient must be > 0.");
diff_t = utils::numeric(FLERR,arg[5],false,lmp); diff_t = utils::numeric(FLERR,arg[5],false,lmp);
if (diff_t <= 0.0) 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."); "coefficient must be > 0.");
diff_r = utils::numeric(FLERR,arg[6],false,lmp); diff_r = utils::numeric(FLERR,arg[6],false,lmp);
if (diff_r <= 0.0) 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."); "coefficient must be > 0.");
seed = utils::inumeric(FLERR,arg[7],false,lmp); 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; noise_flag = 1;
gaussian_noise_flag = 0; gaussian_noise_flag = 0;
@ -88,7 +88,7 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"rng") == 0) { if (strcmp(arg[iarg],"rng") == 0) {
if (narg == iarg + 1) { 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) { if (strcmp(arg[iarg + 1],"uniform") == 0) {
noise_flag = 1; noise_flag = 1;
@ -98,19 +98,19 @@ FixBdSphere::FixBdSphere(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg + 1],"none") == 0) { } else if (strcmp(arg[iarg + 1],"none") == 0) {
noise_flag = 0; noise_flag = 0;
} else { } else {
error->all(FLERR,"Illegal fix/bd/sphere command."); error->all(FLERR,"Illegal fix/brownian/sphere command.");
} }
iarg = iarg + 2; iarg = iarg + 2;
} else if (strcmp(arg[iarg],"dipole") == 0) { } else if (strcmp(arg[iarg],"dipole") == 0) {
extra = DIPOLE; extra = DIPOLE;
iarg = iarg + 1; iarg = iarg + 1;
} else { } else {
error->all(FLERR,"Illegal fix/bd/sphere command."); error->all(FLERR,"Illegal fix/brownian/sphere command.");
} }
} }
if (extra == DIPOLE && !atom->mu_flag) 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 // initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me); 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; int mask = 0;
mask |= INITIAL_INTEGRATE; mask |= INITIAL_INTEGRATE;
@ -129,7 +129,7 @@ int FixBdSphere::setmask()
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixBdSphere::~FixBdSphere() FixBrownianSphere::~FixBrownianSphere()
{ {
delete random; delete random;
} }
@ -138,7 +138,7 @@ FixBdSphere::~FixBdSphere()
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixBdSphere::init() void FixBrownianSphere::init()
{ {
g1 = force->ftm2v/gamma_t; g1 = force->ftm2v/gamma_t;
@ -161,14 +161,14 @@ void FixBdSphere::init()
sqrtdt = sqrt(dt); sqrtdt = sqrt(dt);
} }
void FixBdSphere::setup(int vflag) void FixBrownianSphere::setup(int vflag)
{ {
post_force(vflag); post_force(vflag);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixBdSphere::initial_integrate(int /* vflag */) void FixBrownianSphere::initial_integrate(int /* vflag */)
{ {
double **x = atom->x; double **x = atom->x;
double **v = atom->v; double **v = atom->v;
@ -270,7 +270,7 @@ void FixBdSphere::initial_integrate(int /* vflag */)
apply random force, stolen from MISC/fix_efield.cpp 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 **f = atom->f;
double **x = atom->x; 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; dt = update->dt;

28
src/USER-MISC/fix_bd_sphere.h → src/USER-BROWNIAN/fix_brownian_sphere.h
View File

@ -13,21 +13,21 @@
#ifdef FIX_CLASS #ifdef FIX_CLASS
FixStyle(bd/sphere,FixBdSphere) FixStyle(brownian/sphere,FixBrownianSphere)
#else #else
#ifndef LMP_FIX_BD_SPHERE_H #ifndef LMP_FIX_BROWNIAN_SPHERE_H
#define LMP_FIX_BD_SPHERE_H #define LMP_FIX_BROWNIAN_SPHERE_H
#include "fix.h" #include "fix.h"
namespace LAMMPS_NS { namespace LAMMPS_NS {
class FixBdSphere : public Fix { class FixBrownianSphere : public Fix {
public: public:
FixBdSphere(class LAMMPS *, int, char **); FixBrownianSphere(class LAMMPS *, int, char **);
virtual ~FixBdSphere(); virtual ~FixBrownianSphere();
void init(); void init();
void initial_integrate(int); void initial_integrate(int);
void setup(int); void setup(int);
@ -61,34 +61,34 @@ protected:
/* ERROR/WARNING messages: /* ERROR/WARNING messages:
E: Illegal fix bd/sphere command. E: Illegal fix brownian/sphere command.
Wrong number/type of input arguments. Wrong number/type of input arguments.
E: Compute bd/sphere requires atom style sphere E: Compute brownian/sphere requires atom style sphere
Self-explanatory. Self-explanatory.
E: Compute bd/sphere requires atom attribute mu E: Compute brownian/sphere requires atom attribute mu
Self-explanatory. 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. 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. Self-explanatory.
E: Fix bd/sphere translational diffusion coefficient must be > 0. E: Fix brownian/sphere translational diffusion coefficient must be > 0.
Self-explanatory. Self-explanatory.
E: Fix bd/sphere rotational diffusion coefficient must be > 0. E: Fix brownian/sphere rotational diffusion coefficient must be > 0.
Self-explanatory. Self-explanatory.
E: Fix bd/sphere seed must be > 0. E: Fix brownian/sphere seed must be > 0.
*/ */

2
src/USER-MISC/README
View File

@ -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 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 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 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/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 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 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018

0
unittest/force-styles/tests/data.bdsphere → unittest/force-styles/tests/data.brownian
View File

6
unittest/force-styles/tests/fix-timestep-bd_sphere.yaml → unittest/force-styles/tests/fix-timestep-brownian.yaml
View File

@ -4,12 +4,12 @@ date_generated: Tue Dec 08 12:28:40 2020
epsilon: 1e-12 epsilon: 1e-12
prerequisites: ! | prerequisites: ! |
atom hybrid dipole sphere atom hybrid dipole sphere
fix bd_sphere fix brownian/sphere
pre_commands: ! "" pre_commands: ! ""
post_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 fix_modify test virial yes
input_file: in.bdsphere input_file: in.brownian
natoms: 32 natoms: 32
run_pos: ! |2 run_pos: ! |2
1 0.8198132185477983 -1.5120221815010249 1.069236010215717 1 0.8198132185477983 -1.5120221815010249 1.069236010215717

2
unittest/force-styles/tests/in.bdsphere → unittest/force-styles/tests/in.brownian
View File

@ -2,7 +2,7 @@ variable newton_pair index on
variable newton_bond index on variable newton_bond index on
variable units index lj variable units index lj
variable input_dir index . 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' variable pair_style index 'zero 8.0'
atom_style hybrid dipole sphere atom_style hybrid dipole sphere