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adjust keyword/function names and command line to be simpler to use

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Axel Kohlmeyer 2022-05-11 09:02:13 -04:00
parent ef3b90e838
commit 4cc3bdd35f
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10 changed files with 394 additions and 386 deletions
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53
doc/src/create_atoms.rst
View File

@ -51,10 +51,12 @@ Syntax
name = name of variable to set with x, y, or z atom position
*radscale* value = factor
factor = scale factor for setting atom radius
*radthresh* value = radius (distance units)
radius = threshold value for *mesh* to determine when to split triangles
*quasirandom* value = number density (inverse distance squared units)
number density = minimum number density for particles placed on *mesh* triangles
*meshmode* values = mode arg
mode = *bisect* or *qrand*
*bisect* arg = radthresh
radthresh = threshold value for *mesh* to determine when to split triangles (distance units)
*qrand* arg = density
density = minimum number density for atoms place on *mesh* triangles (inverse distance squared units)
*rotate* values = theta Rx Ry Rz
theta = rotation angle for single molecule (degrees)
Rx,Ry,Rz = rotation vector for single molecule
@ -77,7 +79,8 @@ Examples
create_atoms 3 single 0 0 5
create_atoms 1 box var v set x xpos set y ypos
create_atoms 2 random 50 12345 NULL overlap 2.0 maxtry 50
create_atoms 1 mesh funnel.stl units box radscale 0.9 radthresh 4.0
create_atoms 1 mesh open_box.stl meshmode qrand 0.1 units box
create_atoms 1 mesh funnel.stl meshmode bisect 4.0 units box radscale 0.9
Description
"""""""""""
@ -138,24 +141,28 @@ For the *mesh* style, a file with a triangle mesh in `ASCII STL format
and one or more particles are placed into the area of each triangle.
Binary STL files (e.g. as frequently offered for 3d-printing) can be
converted to ASCII with the :ref:`stl_bin2txt tool <stlconvert>`. The
use of the *units box* option is required. A particle is created at the
center of each triangle unless the average distance of the triangle
vertices from its center is larger than the *radthresh* value. This
value defaults to the lattice spacing in x direction, but can be set as
an optional keyword. In case the triangle size is over the threshold,
it is split into two halves along the its longest side and each of those
two triangles considered for particle insertion. This operation is
repeated recursively until the condition is met. There will be at least
one sphere per triangle. If the atom style in use allows to set a
per-atom radius this radius is set to the average distance of the
triangle vertices from its center times the value of the *radscale*
keyword (default: 1.0).
The *mesh* style also has a *quasirandom* option which uses a quasirandom
sequence to distribute particles on mesh triangles using an approach
by :ref:`(Roberts) <Roberts2019>`. This option takes a minimal number
density as an argument. Particles are added to the triangle until this
number density is met or exceeded such that every triangle will have
at least one particle.
use of the *units box* option is required. There are two algorithms for
placing atoms available: *bisect* and *qrand*. They can be selected via
the *meshmode* option; *bisect* is the default. If the atom style allows
to set a per-atom radius this radius is set to the average
distance of the triangle vertices from its center times the value of the
*radscale* keyword (default: 1.0). If the atom style supports it, the
atoms created from the mesh are assigned a new molecule ID.
In *bisect* mode a particle is created at the center of each triangle
unless the average distance of the triangle vertices from its center is
larger than the *radthresh* value (default is lattice spacing in
x-direction). In case the average distance is over the threshold, the
triangle is recursively split into two halves along the the longest side
until the threshold is reached. There will be at least one sphere per
triangle. The value of *radthresh* is set as argument to *meshmode
bisect*.
In *qrand* mode a quasirandom sequence is used to distribute particles
on mesh triangles using an approach by :ref:`(Roberts) <Roberts2019>`.
Particles are added to the triangle until minimum number density is met
or exceeded such that every triangle will have at least one particle.
The minimum number density is set as argument to the *qrand* option.
.. note::

3
examples/mesh/in.mesh_box
View File

@ -11,7 +11,8 @@ region lid block 100 110 50 250 50 250 units box
group mobile type 1
set type 1 diameter 7.0
create_atoms 2 mesh open_box.stl units box radthresh 4.0
# create_atoms 2 mesh open_box.stl meshmode bisect 4.0 units box
create_atoms 2 mesh open_box.stl meshmode qrand 0.1 units box
group mesh type 2
pair_style lj/cut 8.76

32
examples/mesh/log.8May22.marble_race.g++.1 → examples/mesh/log.11May22.marble_race.g++.1
View File

@ -20,7 +20,7 @@ group mobile type 1
create_atoms 2 mesh race_track.stl units box
Reading STL object Georgs Murmelbahn from file race_track.stl
read 9472 triangles with 1.00 atoms per triangle
read 9472 triangles with 1.00 atoms per triangle added in recursive bisection mode
Created 9472 atoms
using box units in orthogonal box = (-110 -30 -90) to (60 220 130)
create_atoms CPU = 0.040 seconds
@ -66,7 +66,7 @@ Per MPI rank memory allocation (min/avg/max) = 4.803 | 4.803 | 4.803 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 737062.81 0 737062.81 21986.781 9350000
67 0 -2063.91 0 -2063.91 -5.0227698 9350000
Loop time of 0.518872 on 1 procs for 67 steps with 13073 atoms
Loop time of 0.517938 on 1 procs for 67 steps with 13073 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
@ -82,12 +82,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38371 | 0.38371 | 0.38371 | 0.0 | 73.95
Neigh | 0.038019 | 0.038019 | 0.038019 | 0.0 | 7.33
Comm | 0.001586 | 0.001586 | 0.001586 | 0.0 | 0.31
Pair | 0.38475 | 0.38475 | 0.38475 | 0.0 | 74.28
Neigh | 0.037593 | 0.037593 | 0.037593 | 0.0 | 7.26
Comm | 0.0015299 | 0.0015299 | 0.0015299 | 0.0 | 0.30
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.033492 | 0.033492 | 0.033492 | 0.0 | 6.45
Other | | 0.06206 | | | 11.96
Modify | 0.032572 | 0.032572 | 0.032572 | 0.0 | 6.29
Other | | 0.0615 | | | 11.87
Nlocal: 13073 ave 13073 max 13073 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -126,20 +126,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.678 | 3.678 | 3.678 Mbytes
8000 404.7304 -2144.8541 0 2198.2739 43.134333 9350000
9000 435.75368 -2180.3183 0 2495.7179 53.466409 9350000
10000 457.96804 -2194.6681 0 2719.7486 64.521177 9350000
Loop time of 12.1468 on 1 procs for 10000 steps with 13073 atoms
Loop time of 12.1711 on 1 procs for 10000 steps with 13073 atoms
Performance: 71.130 ns/day, 0.337 hours/ns, 823.265 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 70.988 ns/day, 0.338 hours/ns, 821.617 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 | 9.4112 | 9.4112 | 9.4112 | 0.0 | 77.48
Neigh | 1.1197 | 1.1197 | 1.1197 | 0.0 | 9.22
Comm | 0.042153 | 0.042153 | 0.042153 | 0.0 | 0.35
Output | 0.00041578 | 0.00041578 | 0.00041578 | 0.0 | 0.00
Modify | 1.2618 | 1.2618 | 1.2618 | 0.0 | 10.39
Other | | 0.3115 | | | 2.56
Pair | 9.4572 | 9.4572 | 9.4572 | 0.0 | 77.70
Neigh | 1.1196 | 1.1196 | 1.1196 | 0.0 | 9.20
Comm | 0.04293 | 0.04293 | 0.04293 | 0.0 | 0.35
Output | 0.00042467 | 0.00042467 | 0.00042467 | 0.0 | 0.00
Modify | 1.241 | 1.241 | 1.241 | 0.0 | 10.20
Other | | 0.31 | | | 2.55
Nlocal: 13073 ave 13073 max 13073 min
Histogram: 1 0 0 0 0 0 0 0 0 0

36
examples/mesh/log.8May22.marble_race.g++.4 → examples/mesh/log.11May22.marble_race.g++.4
View File

@ -20,10 +20,10 @@ group mobile type 1
create_atoms 2 mesh race_track.stl units box
Reading STL object Georgs Murmelbahn from file race_track.stl
read 9472 triangles with 1.00 atoms per triangle
read 9472 triangles with 1.00 atoms per triangle added in recursive bisection mode
Created 9472 atoms
using box units in orthogonal box = (-110 -30 -90) to (60 220 130)
create_atoms CPU = 0.069 seconds
create_atoms CPU = 0.036 seconds
group mesh type 2
9472 atoms in group mesh
@ -73,9 +73,9 @@ Per MPI rank memory allocation (min/avg/max) = 4.506 | 4.54 | 4.57 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 737062.81 0 737062.81 21986.781 9350000
67 0 -2063.91 0 -2063.91 -5.0227698 9350000
Loop time of 0.375696 on 4 procs for 67 steps with 13073 atoms
Loop time of 0.373091 on 4 procs for 67 steps with 13073 atoms
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
@ -89,12 +89,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0026793 | 0.10176 | 0.30773 | 39.0 | 27.09
Neigh | 0.0083945 | 0.011206 | 0.01705 | 3.3 | 2.98
Comm | 0.0076602 | 0.21941 | 0.32088 | 27.2 | 58.40
Pair | 0.0023911 | 0.098676 | 0.3067 | 39.6 | 26.45
Neigh | 0.0054604 | 0.0097001 | 0.017713 | 4.9 | 2.60
Comm | 0.0072159 | 0.22319 | 0.32344 | 27.2 | 59.82
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.0035482 | 0.0090038 | 0.018889 | 6.2 | 2.40
Other | | 0.03432 | | | 9.13
Modify | 0.003044 | 0.0084861 | 0.018696 | 6.5 | 2.27
Other | | 0.03304 | | | 8.86
Nlocal: 3268.25 ave 4314 max 2222 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@ -133,20 +133,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.481 | 3.598 | 3.711 Mbytes
8000 404.7304 -2144.8541 0 2198.2739 43.134332 9350000
9000 435.7537 -2180.3187 0 2495.7178 53.466393 9350000
10000 457.96586 -2194.6411 0 2719.7522 64.522003 9350000
Loop time of 4.62401 on 4 procs for 10000 steps with 13073 atoms
Loop time of 4.60636 on 4 procs for 10000 steps with 13073 atoms
Performance: 186.851 ns/day, 0.128 hours/ns, 2162.627 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 187.567 ns/day, 0.128 hours/ns, 2170.909 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.0661 | 2.4819 | 2.9751 | 25.5 | 53.67
Neigh | 0.18188 | 0.2993 | 0.52875 | 25.5 | 6.47
Comm | 0.40938 | 1.17 | 1.736 | 51.7 | 25.30
Output | 0.00028188 | 0.00049757 | 0.0006548 | 0.0 | 0.01
Modify | 0.22514 | 0.32517 | 0.53165 | 21.2 | 7.03
Other | | 0.3472 | | | 7.51
Pair | 2.0632 | 2.4782 | 2.963 | 25.3 | 53.80
Neigh | 0.18255 | 0.30042 | 0.52984 | 25.5 | 6.52
Comm | 0.40668 | 1.1595 | 1.7224 | 51.6 | 25.17
Output | 0.00032705 | 0.00053493 | 0.00067573 | 0.0 | 0.01
Modify | 0.22563 | 0.32471 | 0.53003 | 21.1 | 7.05
Other | | 0.3429 | | | 7.44
Nlocal: 3268.25 ave 6890 max 1643 min
Histogram: 1 2 0 0 0 0 0 0 0 1

147
examples/mesh/log.11May22.mesh_box.g++.1 Normal file
View File

@ -0,0 +1,147 @@
LAMMPS (4 May 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units real
atom_style hybrid sphere bond
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:130)
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 50 250 50 250 50 250 units box
create_box 2 box
Created orthogonal box = (50 50 50) to (250 250 250)
1 by 1 by 1 MPI processor grid
region particles block 110 190 110 190 110 190 units box
create_atoms 1 region particles
Created 4913 atoms
using lattice units in orthogonal box = (50 50 50) to (250 250 250)
create_atoms CPU = 0.001 seconds
region lid block 100 110 50 250 50 250 units box
group mobile type 1
4913 atoms in group mobile
set type 1 diameter 7.0
Setting atom values ...
4913 settings made for diameter
# create_atoms 2 mesh open_box.stl meshmode bisect 4.0 units box
create_atoms 2 mesh open_box.stl meshmode qrand 0.1 units box
Reading STL object Open Box from file open_box.stl
read 10 triangles with 500.00 atoms per triangle added in quasi-random mode
Created 5000 atoms
using box units in orthogonal box = (50 50 50) to (250 250 250)
create_atoms CPU = 0.001 seconds
group mesh type 2
5000 atoms in group mesh
pair_style lj/cut 8.76
pair_coeff 1 1 0.2339 3.504
pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0))
pair_coeff 1 2 0.2339 7.008 7.8662140345520858986
pair_coeff 2 2 0.0 1.0
mass * 39.95
neigh_modify exclude type 2 2
timestep 1.0
run 0 post no
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.76
ghost atom cutoff = 10.76
binsize = 5.38, bins = 38 38 38
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.64 | 5.64 | 5.64 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1778.6527 0 -1778.6527 -27.271044
Loop time of 1.514e-06 on 1 procs for 0 steps with 9913 atoms
fix dir mobile oneway 10 lid x
fix move mobile nve
fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0
fix rot mesh move rotate 150.0 150.0 150.0 1.0 0.0 0.0 500000.0 units box
reset_timestep 0 time 0.0
velocity mobile create 150.0 54634234
compute ptemp mobile temp
thermo_modify temp ptemp
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520)
thermo 200
compute ke all ke/atom
#dump 2 all movie 200 mesh.mkv c_ke radius size 960 1440 zoom 1.5 box no 0.0 view 120 180
#dump_modify 2 bitrate 4000 framerate 12 color orange 1.0 0.5 0.0 amap min max cf 0.0 6 min blue 0.1 fuchsia 0.2 red 0.4 orange 0.6 yellow max white
#dump 1 all custom 500 open_box.lammpstrj id type mol x y z vx vy vz
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.155 | 6.155 | 6.155 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 150 -1778.6527 0 417.60814 -14.721534 8000000
200 179.67539 -2344.2923 0 286.46789 14.546173 8000000
400 181.6261 -2331.1731 0 328.14895 15.522647 8000000
600 183.6116 -2362.5284 0 325.86464 14.828678 8000000
800 187.69451 -2422.3021 0 325.87189 14.99914 8000000
1000 186.32256 -2393.187 0 334.89931 14.49224 8000000
1200 186.57797 -2406.6141 0 325.21184 15.514285 8000000
1400 188.39717 -2403.2075 0 355.25478 14.282381 8000000
1600 185.774 -2391.15 0 328.90446 16.025507 8000000
1800 186.95292 -2423.2897 0 314.02613 15.51055 8000000
2000 186.0637 -2414.6095 0 309.68668 14.894421 8000000
2200 187.03262 -2409.2253 0 329.25754 14.90094 8000000
2400 186.66862 -2409.987 0 323.16626 15.497536 8000000
2600 184.98646 -2386.3118 0 322.21161 14.935837 8000000
2800 185.83051 -2392.5258 0 328.35604 14.863905 8000000
3000 184.68382 -2397.8429 0 306.24943 15.696458 8000000
3200 187.56974 -2409.8941 0 336.45315 14.352166 8000000
3400 187.5721 -2425.0188 0 321.36292 14.7297 8000000
3600 185.97304 -2391.4399 0 331.52886 15.586758 8000000
3800 185.40034 -2401.6336 0 312.94973 15.742308 8000000
4000 187.71377 -2409.3588 0 339.09729 15.102297 8000000
4200 186.4676 -2394.1921 0 336.01789 15.312368 8000000
4400 186.98262 -2396.3842 0 341.36649 14.764489 8000000
4600 185.98808 -2397.7342 0 325.45468 15.379472 8000000
4800 187.6927 -2422.0727 0 326.07474 14.252141 8000000
5000 188.21075 -2428.1325 0 327.60023 14.694135 8000000
Loop time of 9.49245 on 1 procs for 5000 steps with 9913 atoms
Performance: 45.510 ns/day, 0.527 hours/ns, 526.734 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.3698 | 5.3698 | 5.3698 | 0.0 | 56.57
Bond | 0.00036337 | 0.00036337 | 0.00036337 | 0.0 | 0.00
Neigh | 3.0911 | 3.0911 | 3.0911 | 0.0 | 32.56
Comm | 0.039329 | 0.039329 | 0.039329 | 0.0 | 0.41
Output | 0.0010197 | 0.0010197 | 0.0010197 | 0.0 | 0.01
Modify | 0.86293 | 0.86293 | 0.86293 | 0.0 | 9.09
Other | | 0.1279 | | | 1.35
Nlocal: 9913 ave 9913 max 9913 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 97756 ave 97756 max 97756 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 97756
Ave neighs/atom = 9.8613941
Ave special neighs/atom = 0
Neighbor list builds = 375
Dangerous builds = 1
Total wall time: 0:00:09

147
examples/mesh/log.11May22.mesh_box.g++.4 Normal file
View File

@ -0,0 +1,147 @@
LAMMPS (4 May 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units real
atom_style hybrid sphere bond
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:130)
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 50 250 50 250 50 250 units box
create_box 2 box
Created orthogonal box = (50 50 50) to (250 250 250)
1 by 2 by 2 MPI processor grid
region particles block 110 190 110 190 110 190 units box
create_atoms 1 region particles
Created 4913 atoms
using lattice units in orthogonal box = (50 50 50) to (250 250 250)
create_atoms CPU = 0.001 seconds
region lid block 100 110 50 250 50 250 units box
group mobile type 1
4913 atoms in group mobile
set type 1 diameter 7.0
Setting atom values ...
4913 settings made for diameter
# create_atoms 2 mesh open_box.stl meshmode bisect 4.0 units box
create_atoms 2 mesh open_box.stl meshmode qrand 0.1 units box
Reading STL object Open Box from file open_box.stl
read 10 triangles with 2000.00 atoms per triangle added in quasi-random mode
Created 5000 atoms
using box units in orthogonal box = (50 50 50) to (250 250 250)
create_atoms CPU = 0.001 seconds
group mesh type 2
5000 atoms in group mesh
pair_style lj/cut 8.76
pair_coeff 1 1 0.2339 3.504
pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0))
pair_coeff 1 2 0.2339 7.008 7.8662140345520858986
pair_coeff 2 2 0.0 1.0
mass * 39.95
neigh_modify exclude type 2 2
timestep 1.0
run 0 post no
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.76
ghost atom cutoff = 10.76
binsize = 5.38, bins = 38 38 38
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.455 | 5.474 | 5.491 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1778.6527 0 -1778.6527 -27.271044
Loop time of 2.8725e-06 on 4 procs for 0 steps with 9913 atoms
fix dir mobile oneway 10 lid x
fix move mobile nve
fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0
fix rot mesh move rotate 150.0 150.0 150.0 1.0 0.0 0.0 500000.0 units box
reset_timestep 0 time 0.0
velocity mobile create 150.0 54634234
compute ptemp mobile temp
thermo_modify temp ptemp
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520)
thermo 200
compute ke all ke/atom
#dump 2 all movie 200 mesh.mkv c_ke radius size 960 1440 zoom 1.5 box no 0.0 view 120 180
#dump_modify 2 bitrate 4000 framerate 12 color orange 1.0 0.5 0.0 amap min max cf 0.0 6 min blue 0.1 fuchsia 0.2 red 0.4 orange 0.6 yellow max white
#dump 1 all custom 500 open_box.lammpstrj id type mol x y z vx vy vz
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.011 | 6.046 | 6.072 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 150 -1778.6527 0 417.60814 -14.721534 8000000
200 178.90737 -2298.4303 0 321.08483 15.681113 8000000
400 182.18748 -2339.8994 0 327.64208 13.983929 8000000
600 182.78421 -2363.0316 0 313.24702 15.533691 8000000
800 185.27077 -2397.561 0 315.12532 14.162041 8000000
1000 185.59249 -2394.3379 0 323.05898 14.45888 8000000
1200 184.9041 -2365.2474 0 342.07022 14.281891 8000000
1400 186.59058 -2397.5471 0 334.46342 15.095686 8000000
1600 184.44411 -2386.6701 0 313.91242 16.825132 8000000
1800 188.29985 -2432.366 0 324.6713 15.109591 8000000
2000 187.05565 -2423.8405 0 314.97946 15.67693 8000000
2200 187.02332 -2411.5557 0 326.79085 14.702305 8000000
2400 185.67262 -2386.3932 0 332.17677 15.796702 8000000
2600 185.97931 -2411.0423 0 312.01823 16.15444 8000000
2800 187.2186 -2403.7584 0 337.44748 15.197009 8000000
3000 185.18778 -2388.9601 0 322.51107 16.289848 8000000
3200 186.38078 -2396.9152 0 332.02344 15.860688 8000000
3400 184.95984 -2386.3632 0 321.77041 16.513329 8000000
3600 187.94957 -2408.3205 0 343.58806 13.931044 8000000
3800 187.1454 -2413.0585 0 327.07559 14.801401 8000000
4000 186.12517 -2394.4218 0 330.77436 14.257144 8000000
4200 186.91955 -2407.2113 0 329.61591 14.869086 8000000
4400 184.72142 -2382.9411 0 321.70176 15.898793 8000000
4600 186.8458 -2408.8059 0 326.94154 14.766765 8000000
4800 187.28977 -2397.6811 0 344.56676 15.301534 8000000
5000 185.17839 -2378.709 0 332.62466 16.043707 8000000
Loop time of 3.41925 on 4 procs for 5000 steps with 9913 atoms
Performance: 126.344 ns/day, 0.190 hours/ns, 1462.309 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.011 | 1.4158 | 1.8652 | 31.9 | 41.41
Bond | 0.00026998 | 0.00029559 | 0.00031513 | 0.0 | 0.01
Neigh | 0.60535 | 0.82114 | 1.0415 | 21.6 | 24.02
Comm | 0.19046 | 0.88593 | 1.5316 | 63.7 | 25.91
Output | 0.00067893 | 0.00085803 | 0.001033 | 0.0 | 0.03
Modify | 0.20164 | 0.23804 | 0.27649 | 6.5 | 6.96
Other | | 0.05722 | | | 1.67
Nlocal: 2478.25 ave 2954 max 2037 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 1043.25 ave 1146 max 940 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 24605.8 ave 32065 max 17721 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 98423
Ave neighs/atom = 9.9286795
Ave special neighs/atom = 0
Neighbor list builds = 371
Dangerous builds = 0
Total wall time: 0:00:03

146
examples/mesh/log.8May22.mesh_box.g++.1
View File

@ -1,146 +0,0 @@
LAMMPS (4 May 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units real
atom_style hybrid sphere bond
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:130)
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 50 250 50 250 50 250 units box
create_box 2 box
Created orthogonal box = (50 50 50) to (250 250 250)
1 by 1 by 1 MPI processor grid
region particles block 110 190 110 190 110 190 units box
create_atoms 1 region particles
Created 4913 atoms
using lattice units in orthogonal box = (50 50 50) to (250 250 250)
create_atoms CPU = 0.001 seconds
region lid block 100 110 50 250 50 250 units box
group mobile type 1
4913 atoms in group mobile
set type 1 diameter 7.0
Setting atom values ...
4913 settings made for diameter
create_atoms 2 mesh open_box.stl units box radthresh 4.0
Reading STL object Open Box from file open_box.stl
read 10 triangles with 512.00 atoms per triangle
Created 5120 atoms
using box units in orthogonal box = (50 50 50) to (250 250 250)
create_atoms CPU = 0.001 seconds
group mesh type 2
5120 atoms in group mesh
pair_style lj/cut 8.76
pair_coeff 1 1 0.2339 3.504
pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0))
pair_coeff 1 2 0.2339 7.008 7.8662140345520858986
pair_coeff 2 2 0.0 1.0
mass * 39.95
neigh_modify exclude type 2 2
timestep 1.0
run 0 post no
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.76
ghost atom cutoff = 10.76
binsize = 5.38, bins = 38 38 38
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.641 | 5.641 | 5.641 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1778.6527 0 -1778.6527 -27.271044
Loop time of 1.544e-06 on 1 procs for 0 steps with 10033 atoms
fix dir mobile oneway 10 lid x
fix move mobile nve
fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0
fix rot mesh move rotate 150.0 150.0 150.0 1.0 0.0 0.0 500000.0 units box
reset_timestep 0 time 0.0
velocity mobile create 150.0 54634234
compute ptemp mobile temp
thermo_modify temp ptemp
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520)
thermo 200
compute ke all ke/atom
#dump 2 all movie 200 mesh.mkv c_ke radius size 960 1440 zoom 1.5 box no 0.0 view 120 180
#dump_modify 2 bitrate 4000 framerate 12 color orange 1.0 0.5 0.0 amap min max cf 0.0 6 min blue 0.1 fuchsia 0.2 red 0.4 orange 0.6 yellow max white
#dump 1 all custom 500 open_box.lammpstrj id type mol x y z vx vy vz
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.157 | 6.157 | 6.157 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 150 -1778.6527 0 417.60814 -14.721534 8000000
200 179.71663 -2353.7693 0 277.59468 14.591893 8000000
400 181.98778 -2346.3965 0 318.22101 14.694157 8000000
600 183.48983 -2373.9255 0 312.68467 15.032091 8000000
800 183.99836 -2366.1103 0 327.94574 15.154418 8000000
1000 186.19063 -2405.1258 0 321.02886 14.881141 8000000
1200 185.74206 -2396.0437 0 323.54307 15.729931 8000000
1400 188.03786 -2424.6865 0 328.5147 15.077756 8000000
1600 187.4202 -2437.7998 0 306.35792 16.323387 8000000
1800 186.98057 -2417.0238 0 320.69695 14.445045 8000000
2000 185.81788 -2404.4322 0 316.26462 15.382214 8000000
2200 185.60774 -2386.4973 0 331.12284 15.033058 8000000
2400 187.14304 -2409.5005 0 330.5991 15.226519 8000000
2600 186.63304 -2410.3607 0 322.27162 15.010459 8000000
2800 185.96347 -2421.8039 0 301.02465 15.577503 8000000
3000 185.22976 -2387.0491 0 325.03669 16.111731 8000000
3200 186.32095 -2414.4926 0 313.5702 14.41138 8000000
3400 186.75847 -2414.3018 0 320.16692 15.224392 8000000
3600 184.82282 -2391.1485 0 314.97889 15.96507 8000000
3800 185.71262 -2381.6131 0 337.54256 14.870266 8000000
4000 186.58931 -2399.6637 0 332.32827 14.434356 8000000
4200 185.27225 -2400.3577 0 312.35024 15.429373 8000000
4400 183.90694 -2367.1261 0 325.59133 16.558529 8000000
4600 185.84295 -2403.8288 0 317.23517 14.371372 8000000
4800 184.58178 -2359.4293 0 343.16897 15.516075 8000000
5000 186.15467 -2412.7678 0 312.86031 15.366761 8000000
Loop time of 9.53365 on 1 procs for 5000 steps with 10033 atoms
Performance: 45.313 ns/day, 0.530 hours/ns, 524.458 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.3496 | 5.3496 | 5.3496 | 0.0 | 56.11
Bond | 0.00036644 | 0.00036644 | 0.00036644 | 0.0 | 0.00
Neigh | 3.1301 | 3.1301 | 3.1301 | 0.0 | 32.83
Comm | 0.03837 | 0.03837 | 0.03837 | 0.0 | 0.40
Output | 0.0010388 | 0.0010388 | 0.0010388 | 0.0 | 0.01
Modify | 0.88529 | 0.88529 | 0.88529 | 0.0 | 9.29
Other | | 0.1289 | | | 1.35
Nlocal: 10033 ave 10033 max 10033 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 98536 ave 98536 max 98536 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 98536
Ave neighs/atom = 9.8211901
Ave special neighs/atom = 0
Neighbor list builds = 374
Dangerous builds = 0
Total wall time: 0:00:09

146
examples/mesh/log.8May22.mesh_box.g++.4
View File

@ -1,146 +0,0 @@
LAMMPS (4 May 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units real
atom_style hybrid sphere bond
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:130)
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 50 250 50 250 50 250 units box
create_box 2 box
Created orthogonal box = (50 50 50) to (250 250 250)
1 by 2 by 2 MPI processor grid
region particles block 110 190 110 190 110 190 units box
create_atoms 1 region particles
Created 4913 atoms
using lattice units in orthogonal box = (50 50 50) to (250 250 250)
create_atoms CPU = 0.001 seconds
region lid block 100 110 50 250 50 250 units box
group mobile type 1
4913 atoms in group mobile
set type 1 diameter 7.0
Setting atom values ...
4913 settings made for diameter
create_atoms 2 mesh open_box.stl units box radthresh 4.0
Reading STL object Open Box from file open_box.stl
read 10 triangles with 512.00 atoms per triangle
Created 5120 atoms
using box units in orthogonal box = (50 50 50) to (250 250 250)
create_atoms CPU = 0.000 seconds
group mesh type 2
5120 atoms in group mesh
pair_style lj/cut 8.76
pair_coeff 1 1 0.2339 3.504
pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0))
pair_coeff 1 2 0.2339 7.008 7.8662140345520858986
pair_coeff 2 2 0.0 1.0
mass * 39.95
neigh_modify exclude type 2 2
timestep 1.0
run 0 post no
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.76
ghost atom cutoff = 10.76
binsize = 5.38, bins = 38 38 38
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.457 | 5.476 | 5.493 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1778.6527 0 -1778.6527 -27.271044
Loop time of 3.34625e-06 on 4 procs for 0 steps with 10033 atoms
fix dir mobile oneway 10 lid x
fix move mobile nve
fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0
fix rot mesh move rotate 150.0 150.0 150.0 1.0 0.0 0.0 500000.0 units box
reset_timestep 0 time 0.0
velocity mobile create 150.0 54634234
compute ptemp mobile temp
thermo_modify temp ptemp
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520)
thermo 200
compute ke all ke/atom
#dump 2 all movie 200 mesh.mkv c_ke radius size 960 1440 zoom 1.5 box no 0.0 view 120 180
#dump_modify 2 bitrate 4000 framerate 12 color orange 1.0 0.5 0.0 amap min max cf 0.0 6 min blue 0.1 fuchsia 0.2 red 0.4 orange 0.6 yellow max white
#dump 1 all custom 500 open_box.lammpstrj id type mol x y z vx vy vz
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.998 | 6.028 | 6.059 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 150 -1778.6527 0 417.60814 -14.721534 8000000
200 178.85669 -2312.6876 0 306.08541 15.832907 8000000
400 182.01107 -2334.4183 0 330.54024 14.457841 8000000
600 183.04428 -2348.8534 0 331.23317 15.166984 8000000
800 185.68203 -2396.0112 0 322.69659 14.155191 8000000
1000 185.58372 -2376.7148 0 340.55362 14.125122 8000000
1200 184.96212 -2401.9634 0 306.20372 14.791738 8000000
1400 186.67578 -2392.327 0 340.93097 14.859731 8000000
1600 186.98761 -2418.1463 0 319.67739 15.173567 8000000
1800 188.23692 -2431.082 0 325.03382 15.02044 8000000
2000 184.29434 -2378.8865 0 319.50307 16.504785 8000000
2200 187.1493 -2395.48 0 344.71119 14.464979 8000000
2400 186.60933 -2409.0279 0 323.25719 15.165523 8000000
2600 185.29773 -2391.0001 0 322.08084 15.967212 8000000
2800 185.05884 -2376.7398 0 332.84337 14.263097 8000000
3000 185.03409 -2385.6071 0 323.61377 15.053931 8000000
3200 185.37823 -2400.0415 0 314.21823 16.076039 8000000
3400 187.03675 -2424.3537 0 314.18955 14.596162 8000000
3600 185.55628 -2397.9284 0 318.93826 14.036493 8000000
3800 187.10605 -2408.018 0 331.54002 14.527143 8000000
4000 186.2403 -2410.4382 0 316.44375 15.342402 8000000
4200 187.32974 -2389.1104 0 353.72276 13.931896 8000000
4400 189.27742 -2435.0111 0 336.33944 14.316321 8000000
4600 189.26108 -2453.7231 0 317.38821 15.615617 8000000
4800 187.9187 -2429.9397 0 321.51688 15.226135 8000000
5000 186.91414 -2428.2233 0 308.52478 15.780318 8000000
Loop time of 3.39374 on 4 procs for 5000 steps with 10033 atoms
Performance: 127.293 ns/day, 0.189 hours/ns, 1473.303 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0734 | 1.4274 | 1.7321 | 24.7 | 42.06
Bond | 0.00031015 | 0.00032026 | 0.00033017 | 0.0 | 0.01
Neigh | 0.65409 | 0.83138 | 1.0016 | 17.4 | 24.50
Comm | 0.33062 | 0.82642 | 1.379 | 52.2 | 24.35
Output | 0.00070506 | 0.00086089 | 0.0010669 | 0.0 | 0.03
Modify | 0.21589 | 0.24797 | 0.28078 | 5.5 | 7.31
Other | | 0.05935 | | | 1.75
Nlocal: 2508.25 ave 2930 max 2111 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 1038.5 ave 1110 max 985 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 24668.2 ave 32893 max 17327 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 98673
Ave neighs/atom = 9.834845
Ave special neighs/atom = 0
Neighbor list builds = 371
Dangerous builds = 0
Total wall time: 0:00:03

68
src/create_atoms.cpp
View File

@ -56,8 +56,9 @@ enum { BOX, REGION, SINGLE, RANDOM, MESH };
enum { ATOM, MOLECULE };
enum { COUNT, INSERT, INSERT_SELECTED };
enum { NONE, RATIO, SUBSET };
enum { TRICENTER, QUASIRANDOM };
enum { BISECTION, QUASIRANDOM };
static constexpr const char *mesh_name[] = {"recursive bisection", "quasi-random"};
/* ---------------------------------------------------------------------- */
CreateAtoms::CreateAtoms(LAMMPS *lmp) : Command(lmp), basistype(nullptr) {}
@ -89,7 +90,6 @@ void CreateAtoms::command(int narg, char **arg)
ntype = utils::inumeric(FLERR, arg[0], false, lmp);
const char *meshfile;
radthresh = 1.0;
int iarg;
if (strcmp(arg[1], "box") == 0) {
style = BOX;
@ -138,7 +138,6 @@ void CreateAtoms::command(int narg, char **arg)
int scaleflag = 1;
remapflag = 0;
mesh_style = TRICENTER;
mode = ATOM;
int molseed;
ranmol = nullptr;
@ -152,7 +151,8 @@ void CreateAtoms::command(int narg, char **arg)
maxtry = DEFAULT_MAXTRY;
radscale = 1.0;
radthresh = domain->lattice->xlattice;
mesh_style = BISECTION;
mesh_density = 1.0;
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = ntype;
@ -261,31 +261,27 @@ void CreateAtoms::command(int narg, char **arg)
maxtry = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (maxtry <= 0) error->all(FLERR, "Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg], "meshmode") == 0) {
if (style != MESH)
error->all(FLERR, "Create_atoms meshmode can only be used with mesh style");
if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "create_atoms meshmode", error);
if (strcmp(arg[iarg + 1], "bisect") == 0) {
mesh_style = BISECTION;
radthresh = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
} else if (strcmp(arg[iarg + 1], "qrand") == 0) {
mesh_style = QUASIRANDOM;
mesh_density = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
} else
error->all(FLERR, "Unknown create_atoms meshmode {}", arg[iarg + 2]);
iarg += 3;
} else if (strcmp(arg[iarg], "radscale") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_atoms radscale", error);
if (style != MESH)
error->all(FLERR, "Create_atoms radscale can only be used with mesh style");
if (mesh_style != TRICENTER)
error->all(FLERR, "Create_atoms radscale can only be used with tricenter mesh style");
if ((style != MESH) && (mesh_style != BISECTION))
error->all(FLERR, "Create_atoms radscale can only be used with mesh style in bisect mode");
if (!atom->radius_flag)
error->all(FLERR, "Must have atom attribute radius to set radscale factor");
radscale = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "radthresh") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_atoms radthresh", error);
if (style != MESH)
error->all(FLERR, "Create_atoms radthresh can only be used with mesh style");
if (mesh_style != TRICENTER)
error->all(FLERR, "Create_atoms radthresh can only be used with tricenter mesh style");
radthresh = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "quasirandom") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_atoms quasirandom", error);
if (style != MESH)
error->all(FLERR, "Create_atoms quasirandom can only be used with mesh style");
mesh_style = QUASIRANDOM;
mesh_density = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else
error->all(FLERR, "Illegal create_atoms command option {}", arg[iarg]);
}
@ -864,7 +860,7 @@ void CreateAtoms::add_random()
or split into two halves along the longest side and recurse
------------------------------------------------------------------------- */
int CreateAtoms::add_tricenter(const double vert[3][3], tagint molid)
int CreateAtoms::add_bisection(const double vert[3][3], tagint molid)
{
double center[3], temp[3];
@ -917,8 +913,8 @@ int CreateAtoms::add_tricenter(const double vert[3][3], tagint molid)
}
}
ilocal = add_tricenter(vert1, molid);
ilocal += add_tricenter(vert2, molid);
ilocal = add_bisection(vert1, molid);
ilocal += add_bisection(vert2, molid);
} else {
/*
@ -983,7 +979,7 @@ int CreateAtoms::add_quasirandom(const double vert[3][3], tagint molid)
for (int i = 0; i < nparticles; i++) {
// Define point in unit square
xi = (i + 1) * INV_P_CONST;
yi = (i + 1) * INV_SQ_P_CONST; // Add seed function of vertices
yi = (i + 1) * INV_SQ_P_CONST; // Add seed function of vertices
xi += seed;
yi += seed;
@ -1014,7 +1010,6 @@ int CreateAtoms::add_quasirandom(const double vert[3][3], tagint molid)
int idx = atom->nlocal - 1;
if (atom->molecule_flag) atom->molecule[idx] = molid;
}
}
return nparticles;
@ -1044,11 +1039,11 @@ void CreateAtoms::add_mesh(const char *filename)
FILE *fp = fopen(filename, "r");
if (fp == nullptr) error->one(FLERR, "Cannot open file {}: {}", filename, utils::getsyserror());
TextFileReader reader(fp, "triangles");
TextFileReader reader(fp, "STL mesh");
try {
char *line = reader.next_line();
if (!line || !utils::strmatch(line, "^solid"))
throw TokenizerException("Invalid triangles file format", "");
throw TokenizerException("Invalid STL mesh file format", "");
line += 6;
if (comm->me == 0)
@ -1085,12 +1080,14 @@ void CreateAtoms::add_mesh(const char *filename)
if (!line || !utils::strmatch(line, "^ *endfacet"))
throw TokenizerException("Error reading endfacet", "");
// now we have the three vertices ... proceed with adding atoms
++ntriangle;
if (mesh_style == TRICENTER) {
// now we have three vertices ... proceed with adding atom in center of triangle
// or splitting recursively into halves as needed to get the desired density
atomlocal += add_tricenter(vert, molid);
if (mesh_style == BISECTION) {
// add in center of triangle or bisecting recursively along longest edge
// as needed to get the desired atom density/radii
atomlocal += add_bisection(vert, molid);
} else if (mesh_style == QUASIRANDOM) {
// add quasi-random distribution of atoms
atomlocal += add_quasirandom(vert, molid);
}
}
@ -1102,7 +1099,8 @@ void CreateAtoms::add_mesh(const char *filename)
MPI_Allreduce(&atomlocal, &atomall, 1, MPI_LMP_BIGINT, MPI_SUM, world);
double ratio = (double) atomall / (double) ntriangle;
if (comm->me == 0)
utils::logmesg(lmp, " read {} triangles with {:.2f} atoms per triangle\n", ntriangle, ratio);
utils::logmesg(lmp, " read {} triangles with {:.2f} atoms per triangle added in {} mode\n",
ntriangle, ratio, mesh_name[mesh_style]);
}
}

2
src/create_atoms.h
View File

@ -67,7 +67,7 @@ class CreateAtoms : public Command {
void add_single();
void add_random();
void add_mesh(const char *);
int add_tricenter(const double [3][3], tagint);
int add_bisection(const double [3][3], tagint);
int add_quasirandom(const double [3][3], tagint);
void add_lattice();
void loop_lattice(int);