forked from lijiext/lammps
Merge pull request #276 from akohlmey/doc-updates
Small bugfixes and updates
This commit is contained in:
sjplimp
GitHub
commit
073e8a0524
|
|
@ -14,7 +14,7 @@ info args :pre
|
|||
|
||||
args = one or more of the following keywords: {out}, {all}, {system}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {styles}, {time}, or {configuration}
|
||||
{out} values = {screen}, {log}, {append} filename, {overwrite} filename
|
||||
{styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {region} :ul
|
||||
{styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {pair}, {region} :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
|
|
@ -70,8 +70,9 @@ The {variables} category prints a list of all currently defined
|
|||
variables, their names, styles, definition and last computed value, if
|
||||
available.
|
||||
|
||||
The {styles} category prints the list of styles available in LAMMPS. It
|
||||
supports one of the following options to control what is printed out:
|
||||
The {styles} category prints the list of styles available in the
|
||||
current LAMMPS binary. It supports one of the following options
|
||||
to control which category of styles is printed out:
|
||||
|
||||
all
|
||||
angle
|
||||
|
|
@ -86,6 +87,7 @@ improper
|
|||
integrate
|
||||
kspace
|
||||
minimize
|
||||
pair
|
||||
region :ul
|
||||
|
||||
The {time} category prints the accumulated CPU and wall time for the
|
||||
|
|
|
|||
|
|
@ -0,0 +1,64 @@
|
|||
|
||||
units lj
|
||||
lattice fcc 0.8442
|
||||
boundary f f f
|
||||
|
||||
region ball sphere 0.0 0.0 0.0 5.0
|
||||
region box block -10 10 -10 10 -10 10
|
||||
region half block -10 0 -10 10 -10 10
|
||||
|
||||
# add molecule ids so we can use chunk/atom
|
||||
fix 0 all property/atom mol ghost yes
|
||||
|
||||
create_box 2 box
|
||||
create_atoms 1 region ball
|
||||
|
||||
pair_style lj/cut 4.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
mass * 1.0
|
||||
set group all mol 1
|
||||
|
||||
# label half the sphere with a different type for better visualization
|
||||
set region half type 2
|
||||
|
||||
# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
|
||||
group ball dynamic all region ball
|
||||
|
||||
neigh_modify delay 2 every 1 check yes
|
||||
|
||||
minimize 0.0 0.0 1000 10000
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 1.2 12351235
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
|
||||
|
||||
compute 1 all chunk/atom molecule
|
||||
compute 2 ball omega/chunk 1
|
||||
compute 3 ball inertia/chunk 1
|
||||
|
||||
# compute rotational kinetic energy: 1/2 * I * omega**2
|
||||
variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
|
||||
variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
|
||||
variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
|
||||
|
||||
# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
|
||||
|
||||
thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
||||
thermo 500
|
||||
|
||||
# dump 1 all atom 100 dump.lammpstrj
|
||||
|
||||
# dump 2 all movie 10 ball.mp4 type mass
|
||||
|
||||
# equilibration w/o torque added
|
||||
run 1000 post no
|
||||
|
||||
# start spinning the ball. rotation around z should increase and Erot_z should grow
|
||||
fix 4 ball addtorque 0.0 0.0 200.0
|
||||
run 10000 upto post no
|
||||
|
||||
# continue without adding more torque. rotation continues at fixed speed
|
||||
unfix 4
|
||||
run 5000
|
||||
|
|
@ -0,0 +1,202 @@
|
|||
LAMMPS (9 Nov 2016)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
boundary f f f
|
||||
|
||||
region ball sphere 0.0 0.0 0.0 5.0
|
||||
region box block -10 10 -10 10 -10 10
|
||||
region half block -10 0 -10 10 -10 10
|
||||
|
||||
# add molecule ids so we can use chunk/atom
|
||||
fix 0 all property/atom mol ghost yes
|
||||
|
||||
create_box 2 box
|
||||
Created orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region ball
|
||||
Created 2123 atoms
|
||||
|
||||
pair_style lj/cut 4.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
mass * 1.0
|
||||
set group all mol 1
|
||||
2123 settings made for mol
|
||||
|
||||
# label half the sphere with a different type for better visualization
|
||||
set region half type 2
|
||||
1142 settings made for type
|
||||
|
||||
# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
|
||||
group ball dynamic all region ball
|
||||
dynamic group ball defined
|
||||
|
||||
neigh_modify delay 2 every 1 check yes
|
||||
|
||||
minimize 0.0 0.0 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15 -> bins = 16 16 16
|
||||
Memory usage per processor = 3.68322 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.2285099 0 -6.2285099 -0.38871568
|
||||
1000 0 -7.3616908 0 -7.3616908 -9.1828951e-16
|
||||
Loop time of 12.4181 on 1 procs for 1000 steps with 2123 atoms
|
||||
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-6.22850993032 -7.36169083402 -7.36169083402
|
||||
Force two-norm initial, final = 197.762 3.3539e-12
|
||||
Force max component initial, final = 7.88704 1.52475e-13
|
||||
Final line search alpha, max atom move = 1 1.52475e-13
|
||||
Iterations, force evaluations = 1000 1994
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 12.282 | 12.282 | 12.282 | 0.0 | 98.91
|
||||
Neigh | 0.06315 | 0.06315 | 0.06315 | 0.0 | 0.51
|
||||
Comm | 0.000443 | 0.000443 | 0.000443 | 0.0 | 0.00
|
||||
Output | 2.7e-05 | 2.7e-05 | 2.7e-05 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.07231 | | | 0.58
|
||||
|
||||
Nlocal: 2123 ave 2123 max 2123 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: 270799 ave 270799 max 270799 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 270799
|
||||
Ave neighs/atom = 127.555
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 1.2 12351235
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
|
||||
|
||||
compute 1 all chunk/atom molecule
|
||||
compute 2 ball omega/chunk 1
|
||||
compute 3 ball inertia/chunk 1
|
||||
|
||||
# compute rotational kinetic energy: 1/2 * I * omega**2
|
||||
variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
|
||||
variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
|
||||
variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
|
||||
|
||||
# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
|
||||
|
||||
thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
||||
thermo 500
|
||||
|
||||
# dump 1 all atom 100 dump.lammpstrj
|
||||
|
||||
# dump 2 all movie 10 ball.mp4 type mass
|
||||
|
||||
# equilibration w/o torque added
|
||||
run 1000 post no
|
||||
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15 -> bins = 16 16 16
|
||||
Memory usage per processor = 2.68359 Mbytes
|
||||
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
||||
0 1.7991521 -7.3616908 51125.265 51125.265 51125.265 0.0034331372 -0.0045852283 0.0091015032 0.30129221 0.53743693 2.117541
|
||||
500 0.8882476 -6.43927 52585.112 52205.936 52112.109 0.0033058719 -0.0043753253 0.0089502237 0.2873458 0.49970143 2.0872595
|
||||
1000 0.79407357 -6.337372 53754.145 54093.977 53787.624 0.0033214912 -0.0042125031 0.0090171557 0.29651603 0.47995375 2.1867116
|
||||
Loop time of 4.26119 on 1 procs for 1000 steps with 2123 atoms
|
||||
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
# start spinning the ball. rotation around z should increase and Erot_z should grow
|
||||
fix 4 ball addtorque 0.0 0.0 200.0
|
||||
run 10000 upto post no
|
||||
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
|
||||
Memory usage per processor = 2.68359 Mbytes
|
||||
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
||||
1000 0.79407357 -6.337372 53754.145 54093.977 53787.624 0.0033214912 -0.0042125031 0.0090171557 0.29651603 0.47995375 2.1867116
|
||||
1500 0.68685306 -6.2226287 55026.889 54809.958 55224.858 0.0026096779 -0.0039390202 0.01797948 0.18737807 0.42521238 8.9260406
|
||||
2000 0.65370325 -6.1832475 54914.897 55655.542 55405.781 0.0029310978 -0.0040761978 0.025816421 0.23589612 0.46236922 18.463634
|
||||
2500 0.69337585 -6.2170462 54604.66 54800.001 54488.865 0.0028821313 -0.0045216915 0.035781895 0.22679174 0.56021203 34.882245
|
||||
3000 0.76778067 -6.2850756 53423.198 53620.349 53692.133 0.004088872 -0.004451787 0.044703139 0.44658786 0.53133496 53.64839
|
||||
3500 0.79707238 -6.3044974 53055.225 53071.129 52927.537 0.0036751739 -0.0037584362 0.054889715 0.3583059 0.3748372 79.732181
|
||||
4000 0.80746429 -6.3010044 53519.853 53643.284 54058.105 0.003813517 -0.0041637733 0.062983015 0.38916725 0.46500703 107.22047
|
||||
4500 0.81206394 -6.2884719 53371.354 53883.202 53854.559 0.00385001 -0.003643712 0.072544638 0.39555051 0.35769386 141.71085
|
||||
5000 0.81648687 -6.2737414 53776.764 54233.367 53762.425 0.0024484228 -0.0043310965 0.080673643 0.16118978 0.50866551 174.94929
|
||||
5500 0.81888245 -6.2572796 53908.22 53502.342 54717.506 0.0037110524 -0.00327586 0.088836946 0.37120958 0.28707375 215.91536
|
||||
6000 0.86533749 -6.2804248 53687.533 53571.135 53536.171 0.0025223465 -0.0047753224 0.099646475 0.17078626 0.61081016 265.79156
|
||||
6500 0.88029206 -6.2719195 53344.67 53291.068 53298.665 0.003937416 -0.0033910578 0.10778737 0.41350774 0.30640427 309.61504
|
||||
7000 0.9066019 -6.2714707 53928.646 53524.142 54003.175 0.0028500736 -0.0039730774 0.11855069 0.21902903 0.4224485 379.4875
|
||||
7500 0.94601421 -6.2819912 53534.525 53547.598 53851.344 0.0028610722 -0.0049440438 0.12716472 0.21910969 0.6544472 435.41142
|
||||
8000 0.9562253 -6.2626222 53486.577 53033.175 53858.803 0.0025501008 -0.0048075887 0.13526164 0.17391198 0.61287549 492.69254
|
||||
8500 0.99679401 -6.2691139 53566.766 53721.523 53831.283 0.0034137155 -0.0039265 0.14392854 0.3121189 0.41412316 557.56894
|
||||
9000 1.0371056 -6.2761647 53415.879 53605.078 53985.02 0.0029321914 -0.0046362889 0.1518846 0.2296281 0.57612526 622.6884
|
||||
9500 1.0598491 -6.26216 53493.003 53049.859 53699.774 0.0032127038 -0.0050624912 0.16002437 0.27606311 0.67980256 687.56651
|
||||
10000 1.1014855 -6.2654945 53418.49 53251.964 53867.56 0.0037330249 -0.0056278017 0.17103133 0.37220602 0.84330216 787.85924
|
||||
Loop time of 43.025 on 1 procs for 9000 steps with 2123 atoms
|
||||
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
# continue without adding more torque. rotation continues at fixed speed
|
||||
unfix 4
|
||||
run 5000
|
||||
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
|
||||
Memory usage per processor = 2.68359 Mbytes
|
||||
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
||||
10000 1.1014855 -6.2654945 53418.49 53251.964 53867.56 0.0037330249 -0.0056278017 0.17103133 0.37220602 0.84330216 787.85924
|
||||
10500 1.07259 -6.2363698 52825.233 52896.327 55753.551 0.0035928335 -0.0050843805 0.16344484 0.34094601 0.68370948 744.70621
|
||||
11000 1.0644214 -6.2282099 52016.795 51950.497 54922.101 0.0047316668 -0.0050149935 0.16196531 0.58229343 0.65328165 720.37919
|
||||
11500 1.0887339 -6.2525622 52602.789 52903.594 54461.53 0.0044295697 -0.0046710153 0.16698036 0.51606197 0.57713546 759.26022
|
||||
12000 1.0707466 -6.234719 52785.654 52997.192 54943.066 0.0057389353 -0.0030340721 0.16553451 0.86925773 0.2439353 752.76594
|
||||
12500 1.0758302 -6.2397291 52375.734 52783.309 55011.986 0.0047029783 -0.0023526884 0.16493895 0.57922337 0.14608158 748.29657
|
||||
13000 1.0716957 -6.2354221 52711.183 52788.224 55234.737 0.0034033406 -0.00206283 0.16427569 0.30526962 0.11231401 745.29615
|
||||
13500 1.083667 -6.2475953 52698.902 52203.324 55102.881 0.0032012254 -0.0021366488 0.16381832 0.27002507 0.11916109 739.38261
|
||||
14000 1.085106 -6.2490655 52767.613 52353.974 55225.438 0.0025647931 -0.0022235227 0.1636534 0.17355699 0.12942041 739.53587
|
||||
14500 1.0838261 -6.2477856 52292.343 51995.567 54735.836 0.001794954 -0.0029396951 0.16409339 0.084239299 0.22466783 736.92607
|
||||
15000 1.0827419 -6.2468971 51917.584 51388.833 54481.681 0.0017979486 -0.0025793756 0.16196568 0.083914884 0.17094953 714.60575
|
||||
Loop time of 22.7848 on 1 procs for 5000 steps with 2123 atoms
|
||||
|
||||
Performance: 94800.138 tau/day, 219.445 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 | 18.891 | 18.891 | 18.891 | 0.0 | 82.91
|
||||
Neigh | 3.5735 | 3.5735 | 3.5735 | 0.0 | 15.68
|
||||
Comm | 0.005778 | 0.005778 | 0.005778 | 0.0 | 0.03
|
||||
Output | 0.001862 | 0.001862 | 0.001862 | 0.0 | 0.01
|
||||
Modify | 0.27476 | 0.27476 | 0.27476 | 0.0 | 1.21
|
||||
Other | | 0.0379 | | | 0.17
|
||||
|
||||
Nlocal: 2123 ave 2123 max 2123 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: 242472 ave 242472 max 242472 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 242472
|
||||
Ave neighs/atom = 114.212
|
||||
Neighbor list builds = 560
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:22
|
||||
|
|
@ -0,0 +1,202 @@
|
|||
LAMMPS (9 Nov 2016)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
boundary f f f
|
||||
|
||||
region ball sphere 0.0 0.0 0.0 5.0
|
||||
region box block -10 10 -10 10 -10 10
|
||||
region half block -10 0 -10 10 -10 10
|
||||
|
||||
# add molecule ids so we can use chunk/atom
|
||||
fix 0 all property/atom mol ghost yes
|
||||
|
||||
create_box 2 box
|
||||
Created orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region ball
|
||||
Created 2123 atoms
|
||||
|
||||
pair_style lj/cut 4.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
mass * 1.0
|
||||
set group all mol 1
|
||||
2123 settings made for mol
|
||||
|
||||
# label half the sphere with a different type for better visualization
|
||||
set region half type 2
|
||||
1142 settings made for type
|
||||
|
||||
# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
|
||||
group ball dynamic all region ball
|
||||
dynamic group ball defined
|
||||
|
||||
neigh_modify delay 2 every 1 check yes
|
||||
|
||||
minimize 0.0 0.0 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15 -> bins = 16 16 16
|
||||
Memory usage per processor = 3.77014 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.2285099 0 -6.2285099 -0.38871568
|
||||
1000 0 -7.3616908 0 -7.3616908 -9.7399049e-16
|
||||
Loop time of 8.29581 on 4 procs for 1000 steps with 2123 atoms
|
||||
|
||||
89.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-6.22850993032 -7.36169083402 -7.36169083402
|
||||
Force two-norm initial, final = 197.762 3.40861e-12
|
||||
Force max component initial, final = 7.88704 1.60379e-13
|
||||
Final line search alpha, max atom move = 1 1.60379e-13
|
||||
Iterations, force evaluations = 1000 1994
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.8462 | 6.8198 | 8.0872 | 34.0 | 82.21
|
||||
Neigh | 0.021211 | 0.028936 | 0.035891 | 3.8 | 0.35
|
||||
Comm | 0.10672 | 1.3842 | 2.3694 | 76.2 | 16.69
|
||||
Output | 2.8e-05 | 3.35e-05 | 5e-05 | 0.2 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0629 | | | 0.76
|
||||
|
||||
Nlocal: 530.75 ave 543 max 514 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Nghost: 1058.25 ave 1075 max 1046 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Neighs: 67699.8 ave 82013 max 55681 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 270799
|
||||
Ave neighs/atom = 127.555
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 1.2 12351235
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
|
||||
|
||||
compute 1 all chunk/atom molecule
|
||||
compute 2 ball omega/chunk 1
|
||||
compute 3 ball inertia/chunk 1
|
||||
|
||||
# compute rotational kinetic energy: 1/2 * I * omega**2
|
||||
variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
|
||||
variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
|
||||
variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
|
||||
|
||||
# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
|
||||
|
||||
thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
||||
thermo 500
|
||||
|
||||
# dump 1 all atom 100 dump.lammpstrj
|
||||
|
||||
# dump 2 all movie 10 ball.mp4 type mass
|
||||
|
||||
# equilibration w/o torque added
|
||||
run 1000 post no
|
||||
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15 -> bins = 16 16 16
|
||||
Memory usage per processor = 2.77052 Mbytes
|
||||
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
||||
0 1.7991521 -7.3616908 51125.265 51125.265 51125.265 0.0040198435 -0.0024237256 0.0011306245 0.4130702 0.15016629 0.032677011
|
||||
500 0.90968729 -6.4603004 52559.075 52593.598 52370.876 0.0039073429 -0.0023505431 0.0011032256 0.40121833 0.14529121 0.031870471
|
||||
1000 0.80269935 -6.3456699 53966.859 54192.03 54298.931 0.0040875347 -0.0023098179 0.00077010445 0.45083753 0.14456425 0.016101285
|
||||
Loop time of 2.3842 on 4 procs for 1000 steps with 2123 atoms
|
||||
|
||||
89.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
# start spinning the ball. rotation around z should increase and Erot_z should grow
|
||||
fix 4 ball addtorque 0.0 0.0 200.0
|
||||
run 10000 upto post no
|
||||
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
|
||||
Memory usage per processor = 2.77052 Mbytes
|
||||
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
||||
1000 0.80269935 -6.3456699 53966.859 54192.03 54298.931 0.0040875347 -0.0023098179 0.00077010445 0.45083753 0.14456425 0.016101285
|
||||
1500 0.68922642 -6.2266953 54966.109 54681.607 54947.256 0.0038798951 -0.0016325797 0.0099837591 0.41371853 0.072871893 2.7384461
|
||||
2000 0.64105167 -6.1739656 54782.995 54570.486 54910.316 0.0034645832 -0.0027243304 0.017763588 0.32878936 0.20251043 8.6633395
|
||||
2500 0.69929409 -6.2287557 54307.47 53952.925 54538.409 0.0035199565 -0.0022538001 0.028279733 0.33643732 0.13703004 21.808363
|
||||
3000 0.77013056 -6.2945597 53916.743 53801.81 53955.863 0.0039732989 -0.0024543292 0.037182149 0.42559463 0.16204384 37.297319
|
||||
3500 0.80807105 -6.3246605 53451.163 53387.178 53474.789 0.0043137676 -0.0020556348 0.047270147 0.49732542 0.11279735 59.743821
|
||||
4000 0.81007199 -6.3142362 53334.317 53243.089 53685.963 0.0038548696 -0.0031009535 0.055811043 0.3962745 0.25599044 83.612467
|
||||
4500 0.7850954 -6.2735818 53738.002 53682.367 53639.471 0.0033046861 -0.0018472801 0.065975851 0.29343502 0.091594032 116.74129
|
||||
5000 0.77992741 -6.2508277 53864.644 53804.867 53877.025 0.0038258186 -0.0028703189 0.073848203 0.39420539 0.2216419 146.91071
|
||||
5500 0.79428302 -6.2467907 54353.329 53987.578 54234.062 0.0034715133 -0.0030161617 0.082746129 0.32751699 0.24556875 185.66819
|
||||
6000 0.82211943 -6.2549436 54273.545 53195.299 54061.645 0.0030929934 -0.0031282112 0.090458895 0.25960687 0.26027676 221.18813
|
||||
6500 0.87630771 -6.2870988 54042.229 53505.982 54492.239 0.0026486452 -0.0024783378 0.10046947 0.18956181 0.1643211 275.02546
|
||||
7000 0.88614639 -6.2727488 53701.993 52682.206 53948.142 0.0035384498 -0.0035905797 0.11030427 0.33619131 0.33959641 328.19439
|
||||
7500 0.92102182 -6.2787281 53410.068 52577.853 53132.511 0.0033084315 -0.0031776605 0.11973875 0.2923058 0.26545312 380.8902
|
||||
8000 0.94010525 -6.2697758 53732.562 53384.271 53795.933 0.0046460009 -0.0032755993 0.12803006 0.5799174 0.28639462 440.90328
|
||||
8500 0.95359399 -6.252319 53444.305 53558.444 53789.691 0.0037919474 -0.0035729209 0.13616177 0.38423423 0.34185722 498.63117
|
||||
9000 0.98631627 -6.25197 53115.01 54017.327 53955.578 0.0045084495 -0.0034368377 0.14488919 0.53981096 0.31902236 566.34143
|
||||
9500 1.0328238 -6.2632597 53287.675 53682.978 53769.692 0.0044595175 -0.0025931203 0.15416363 0.5298739 0.1804895 638.95665
|
||||
10000 1.0741755 -6.2667785 53103.657 53319.569 53601.523 0.0059237675 -0.0019561182 0.16445664 0.93173079 0.10201096 724.85302
|
||||
Loop time of 21.8398 on 4 procs for 9000 steps with 2123 atoms
|
||||
|
||||
90.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
# continue without adding more torque. rotation continues at fixed speed
|
||||
unfix 4
|
||||
run 5000
|
||||
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
|
||||
Memory usage per processor = 2.77052 Mbytes
|
||||
Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
|
||||
10000 1.0741755 -6.2667785 53103.657 53319.569 53601.523 0.0059237675 -0.0019561182 0.16445664 0.93173079 0.10201096 724.85302
|
||||
10500 1.0588571 -6.2509381 52374.303 52131.544 55020.367 0.0048843769 -0.0018716797 0.15729531 0.62475047 0.091313217 680.65188
|
||||
11000 1.0554911 -6.2471863 52803.345 52177.891 55200.756 0.0042073234 -0.0024283269 0.15742315 0.46735107 0.15384055 683.99392
|
||||
11500 1.0559499 -6.2469955 54031.351 52919.728 54882.35 0.0046703444 -0.0016225764 0.15994353 0.58926908 0.06966232 701.99832
|
||||
12000 1.0311805 -6.2224471 52812.51 52444.13 55356.101 0.0044986993 -0.0019225732 0.15672327 0.53441759 0.096924293 679.83334
|
||||
12500 1.0423882 -6.2339087 52000.562 52043.013 55003.272 0.0038688875 -0.0022935053 0.1548654 0.38917977 0.13687746 659.57977
|
||||
13000 1.0548857 -6.2465445 52196.499 52869.024 54622.553 0.0036650563 -0.0025542156 0.1590498 0.35056832 0.17245921 690.88895
|
||||
13500 1.0443009 -6.2360149 51921.746 53124.078 54750.325 0.0052756473 -0.0011658069 0.15689119 0.72255483 0.036100621 673.83538
|
||||
14000 1.0505583 -6.241923 51861.696 52153.234 54321.531 0.0037119391 -0.00045576703 0.15738082 0.35728798 0.0054167284 672.73745
|
||||
14500 1.040343 -6.2316147 52035.588 51680.479 54443.305 0.0026177168 -0.0014795729 0.15428968 0.1782854 0.056567797 648.01978
|
||||
15000 1.0404962 -6.2322338 52376.795 51327.453 54677.693 0.0025711787 -0.0021695312 0.15403509 0.17313044 0.12079571 648.66363
|
||||
Loop time of 11.9695 on 4 procs for 5000 steps with 2123 atoms
|
||||
|
||||
Performance: 180458.440 tau/day, 417.728 timesteps/s
|
||||
89.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.0313 | 8.4017 | 9.6932 | 35.5 | 70.19
|
||||
Neigh | 0.97886 | 1.3633 | 1.7406 | 26.8 | 11.39
|
||||
Comm | 0.34002 | 2.0227 | 3.7911 | 94.9 | 16.90
|
||||
Output | 0.001198 | 0.0015522 | 0.002578 | 1.5 | 0.01
|
||||
Modify | 0.12841 | 0.131 | 0.13336 | 0.5 | 1.09
|
||||
Other | | 0.04924 | | | 0.41
|
||||
|
||||
Nlocal: 530.75 ave 534 max 529 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 1038 ave 1048 max 1029 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 60482.5 ave 72547 max 49124 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 241930
|
||||
Ave neighs/atom = 113.957
|
||||
Neighbor list builds = 555
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:44
|
||||
|
|
@ -48,6 +48,7 @@ FixAddTorque::FixAddTorque(LAMMPS *lmp, int narg, char **arg) :
|
|||
global_freq = 1;
|
||||
extscalar = 1;
|
||||
extvector = 1;
|
||||
dynamic_group_allow = 1;
|
||||
respa_level_support = 1;
|
||||
ilevel_respa = 0;
|
||||
|
||||
|
|
|
|||
|
|
@ -89,7 +89,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
|
|||
|
||||
suffix = suffix2 = NULL;
|
||||
suffix_enable = 0;
|
||||
exename = arg[0];
|
||||
if (arg) exename = arg[0];
|
||||
else exename = NULL;
|
||||
packargs = NULL;
|
||||
num_package = 0;
|
||||
char *rfile = NULL;
|
||||
|
|
|
|||
|
|
@ -164,6 +164,8 @@ void Universe::add_world(char *str)
|
|||
char *ptr;
|
||||
|
||||
n = 1;
|
||||
nper = 0;
|
||||
|
||||
if (str != NULL) {
|
||||
|
||||
// check for valid partition argument
|
||||
|
|
|
|||
Loading…
Reference in New Issue